First NameLast NameYear of GraduationSURF AdvisorSecondary SURF AdvisorAdvisor DepartmentSURF Field of StudyPlease list co-authors of your abstractUpload image(s) in .png format; 1,100 MB max size eachTitle of Abstract/ResearchPlease type your abstract below.
SophiaChertock2022Steven Williams, Biological Sciences - BiochemistryNeglected Tropical DiseasesMcKayla Ford - Detection of a Putative Brugia malayi POU-homeodomain Transcription Factor Binding to its Cognate Promoter ?Neglected tropical diseases are endemic to developing countries andare understudied despite their impact. One such disease, Lymphatic Filariasis, also known as elephantiasis, causes inflammation of the lymphatic system and may lead to swelling of body parts, disability, and pain. It threatens more than 886 million people in 52 countries, and is economically and medically devastating (1). Mosquito-borne parasitic helminths, specifically Brugia malayi, Brugia pahangi, and Wuchereria bancrofti, are transmitted into the bloodstream during blood meals and disrupt lymphatic system functionality, causing the disease.. While mass drug administration in the affected countries has slowed, and in some cases stopped, the spread of the disease, it brings drawbacks such as increased drug resistance and does not treat already existing infections, only prevent new ones. Therefore alternate therapies are needed.
Previously, the SAW lab determined through comparative genomics that UNC-86, a neuronal POU-domain transcription factor, would be a suitable protein to study as a drug target for Brugia malayi. We successfully produced the protein in the pMAL expression system and amplified the DNA sequence where it binds, the mec-3 promoter. However, we were unable to conclusively prove UNC-86/mec-3 binding due to difficulties with the traditional chemiluminescent electrophoretic mobility shift assay (EMSA) protocol.
We redesigned primers essential to producing the Unc-86 binding sites, and optimized said primers. During this process, we discovered contamination in our reagents and refined our workflow to minimize the chance of repeating the mistake. With the DNA produced by those primers, we performed protein/DNA binding assays, using a new optimized variant EMSA. With this new EMSA protocol, we successfully proved the binding of UNC-86 to the mec-3 promoter at multiple binding sites. Additionally, we further purified our UNC-86 protein using an anion exchange chromatography protocol, which will allow more accurate downstream studies using our protein.
One of those downstream studies we plan to perform in the fall is chromatin immunoprecipitation sequencing, or ChIP-Seq. This is a genome-wide protein DNA binding assay that will allow exploration of the UNC-86/mec-3 neuronal interactome, by determining the exact locations of UNC-86 binding. This will give our group experience in bioinformatics and genomics, and will indicate how essential of a role UNC-86 plays in the neuronal interactome, which is essential to understand if UNC-86 is further developed as a drug target.
RezwanaUddin2019Laura Katz, Biological Sciences - Biological SciencesSingle Cell "Omics" - - Analyses of Giant Viruses in Microbial EukaryotesAnalyses of Giant Viruses in Microbial Eukaryotes

Nucleocytoplasmic large DNA viruses (NCLDVs) are a group of complex and understudied ancient viruses that have capabilities unlike other known viruses including: semi autonomous glycosylation, containing promoters to augment transcription, almost complete systems of translation, and more. However, some NCLDVs are very divergent, and have no known related taxa, even among other viruses, making their evolutionary history difficult to understand.
This summer, I researched and analyzed the presence of viral DNA from NCLDV in ciliates and testate amoeba. We first searched for viral capsid proteins in whole genome amplifications (WGAs) of ciliates: Loxodes, Spirostomum, Halteria and two testate amoebae species: Hyalosphenia elegans, and Hyalosphenia papilio by comparing viral sequences and sequences from the WGAs. To do so, we created a reference database containing 500+ NCLDV capsid proteins, and compared our long sequences from WGAs, the query, to this reference database using a BLASTx tool. Once these sequences were BLASTed against each other, we organized the results of these hits through Excel. Only results with low e-values close to 0.00 and high percent identities above 30%, which indicate high similarity and confidence of the match, were then used for further analyses. The threshold for percent identities was lowered to 30% because viruses are constantly evolving, so there may be many reasons for a lower percent identity if this is not accounted for in the reference or BLAST database.
Next, the long sequences containing NCLDV proteins were run through DFAST, a bacterial database pipeline that helps with further identification of potential viral protein/species from BLAST results. Although DFAST does not focus on analyzing viral proteins, this tool helped characterize protein function for those identified as “hypothetical proteins” using BLAST’s protein structure searches. Lastly, we mapped each WGA’s long sequences on SeqBuilder Pro with annotations of where viral proteins might be located on a genomic map. Out of the five WGAs we blasted for viral proteins, only Loxodes showed very strong hits. Popular viral hits included: Yellowstone lake mimivirus, Chrysochromulina ericina virus, Marseillevirus, Tuapnavirus, and Iridovirus.
My partner and I created a protocol for BLASTing the viral DNA database against other eukaryotic sequences, which will be useful for future analyses in the lab. We are fascinated by the unique capabilities and newly discovered autonomous features in NCLDVs, and hope the results from these pilot analyses can contribute to a better understanding of the evolutionary history of NCLDVs and relationship between NCLDVs and microbial eukaryotes.
MadelineRyan2020Michael Baressi, Biological Sciences - Biological SciencesDevelopmental Biology - MRyan_Figure1.png
MRyan_Figure2.png
Modeling effects of loss of meteorin gene functions during zebrafish brain development Meteorin is a putative glial cell differentiation factor, expressed in the vertebrate nervous system by neuroglial progenitor cells and cells of the astrocyte lineage. However, its precise role during normal brain development is not clear. We spent this summer using zebrafish to model whether loss and gain of Meteorin functions could perturb neural development and induce degenerative or behavioral changes in the mutants. Due to genome duplication, METEORIN gene has two paralogs in zebrafish: meteorin (metrn) and meteorin-like (metrnl). We had previously determined that both show restricted but partially overlapping patterns of expression in the central nervous system during early development of zebrafish embryos. Thus, we used zebrafish mutants of both genes, created earlier in the lab using CRISPR-Cas9 knockout method, as a way to model loss of function of these genes. Throughout my research experience this summer I sought to characterize: 1) expression patterns of metrn and metrnl paralogs in wildtype zebrafish, their single and double mutants, and 2) the effects of these mutations on proliferation and differentiation of radial glia, and 3) the effects of overexpression of these genes on proliferation and differentiation of radial glia. We were able to confirm gene expression of mtern within the developing zebrafish brain using in situ hybridization. However, the mutants produced did not show reduced levels of expression (Figure 1). In addition, we noticed a distinct and consistent phenotype known as cyclopia in embryos that were injected and made to overexpress metrn mRNA at the one cell stage. These same embryos that were injected also show a slight reduction in radial glia, based on the reduced expression of GFP (Figure 2). This phenotype indicates that Meteorin may be acting on pathways involved in axis development and patterning. I was able to present my work this past July at the Annual Meeting of the Society for Developmental Biology in Boston, MA.
YihuiJiang2020Denise McKahn, Engineering - EngineeringEngineering - - dynamic model of coaxial ground-source geothermal systemsGlobal warming is an urgent and comprehensive problem. As one of the effective ways to mitigate global warming, reducing CO2 emissions requires large-scale transformations in electricity production, transportation, industry, and land use. “Decarbonizing” is becoming a challenge for every institution, including Smith College. In 2007, Smith joined the Climate Leadership Network by signing the Carbon Commitment and set a target date, 2030, for achieving carbon neutrality. To meet this goal, Smith College is considering the conversion of the central heating system to a geothermal heat exchanger (GHX) system, in which the central heating plant is converted from one that burns fossil fuel to one that extracts heat from the ground and uses wind or solar electricity to power the system.
Although the purchase and installation cost of a GHX system is often higher than that of other heating and cooling systems, properly sized and installed GHXs consume 25% to 50% less energy than conventional heating or cooling systems. GHX can reduce emissions up to 44% compared with air-source heat pumps and up to 72% compared with electric resistance heating with standard air-conditioning equipment.
The Field House Geothermal Pilot Project is aimed to build a coaxial GHX for the smith college Field House, where a test borehole will be drilled before installing GHX in large scale on campus. Compared to U-tubes, the more widely used pipes in geothermal applications, coaxial pipes show higher thermal performance characteristics, for instance, lower pressure loss and higher heat flux at equivalent inlet flow rates1, than U-tube pipes, and therefore coaxial was chosen to be the pipe type. In order to optimize the heat pump and decrease the energy consumption, Distributed Temperature Sensing(DTS) system will be applied to monitor the spatial temperature variation underground and to quantify the behavior of groundwater flow and in situ GHX thermal performance. DTS is a technique that employs the interaction of laser light with the core of a fiber optic cable to calculate the temperatures of the cable at different sections of the fiber. My research designed and selected an appropriate fiber optic cable for the field house application, in conjunction with the …..interegator and splicing.
I developed and one dimensional, control-oriented model of the temperature distribution in the coaxial bore hole. This dynamic model of temperature variation will be calibrated and experimentally validated following drilling, expected to take place in august.
Recently, many studies (Luo et al., 20152; Montagud et al., 20133; Puttagunta et al., 20104) have done performance analysis of GHX based on control-oriented models. Most of the analyses were done in regard to U-tube system (Bouhacina et al.,20125; Patterson et al.,20176) using line source model or cylindrical source model. The model I developed over the course of the spring semester and surf fellowship will be calibrated and validated as a part of my honor’s thesis in the coming academic year.
So far, DTS has been done research on over the summer and the company of DTS interrogator (Silixa XT-DTS), fiber optic cable (Brugg 3.2 mm nylon-jacketed stainless loose tube), and jacket material are roughly decided.


Citation:
1. Raghavan, Niranjan, "Numerical and Experimental Design of Coaxial Shallow Geothermal Energy Systems" (2016). All Theses. 2443.
2. Luo, J., Rohn, J., Bayer, M., Priess, A., Wilkmann, L., Xiang, W., 2015. Heating and
cooling performance analysis of a ground source heat pump system in Southern Germany. Geothermics 53, 57–66. https://doi.org/10.1016/j.geothermics.2014.04.0. (2015).
3. Montagud, C., Corberán, J., Ruiz-Calvo, F., 2013. Experimrntal and modeling analysis of a ground source heat pump system. Appl. Energy 109, 328–336.
4. Puttagunta, S., Aldrich, R.A., Owens, D., Mantha, P., 2010. Residential ground-source heat pumps: in-field system performance and energy modeling. GRC Trans. 34 (2010), 941–948. Retrieved from: http://www.carb-swa.com/Collateral/ Documents/CARB-SWA/Research/Ground_Source_Heat_Pumps.pdf.
5. “Analysis of Thermal and Dynamic Comportment of a Geothermal Vertical U-Tube Heat Exchanger.” Energy and Buildings, Elsevier, 20 Dec. 2012, www.sciencedirect.com/science/article/pii/S0378778812006512.
6. “Geothermal Reservoir Characterization Using Distributed Temperature Sensing at Brady Geothermal Field, Nevada.” The Leading Edge, library.seg.org/doi/10.1190/tle36121024a1.1.


EmmalineLongnecker2020Andrew Berke, Chemistry - ChemistryAtmospheric Chemistry - - Infrared Spectroscopy of the Solvation Environment with in SOA Mimicking SolutionsWhile the reaction of organic aerosols (OA) to secondary organic aerosols (SOA) has been established, details regarding the reaction environment are lacking in the literature. Previous research in the Berke group has shown certain short chain alcohols to act as an accelerant for the development SOA, but a lack of information about the solvation matrix of the solute/solvent system presented complications in understand the overall system. The current study aimed to further investigate this system.
The development of a method to visualize phase and concentration changes in the system without contamination was both a novel and key endeavor. The novel procedure is executed by placing 2 mL of solution into the articulated section of a straw, flash freezing, and slicing the straw at the articulation points. Each slice is then placed into its own vial and the thawed sample is tested with FTIR-ATR allowing for a vertical image to be created from the spectra.
The articulation layer analysis method, as described above, was used with several ammonium sulfate, water, and short chain alcohol systems. A pattern developed in which some short chain alcohols separated from the ammonium sulfate solution while others were entirely miscible. This was observed in the development of alcohol peaks and the disappearance of ammonium sulfate peaks in the top slices of the straw where the solution appeared to separate, or rather the steady presence of both alcohol and ammonium sulfate peaks throughout the straw in miscible solutions. Preliminary analysis suggests if the ratio of polar to non-polar bonds in the short chain alcohol is above 0.3 the alcohol will be miscible in the salt solution and if it is below it will separate. Such information, in combination with further research about where OA sit in solution will be useful in the development of more accurate climate models.
MordredYuan2021Kevin Shea, Chemistry - ChemistryChemistry - - The synthesis of the derivatives of neurolenin D from Neurolaena lobateOne of the ongoing projects in Shea Lab is about the modification of neurolenin D to turn it into a more bio-interactive molecule that can potentially treat lymphatic filariasis, a tropical disease that infected millions of people and can have serious effects, in most cases elephantiasis[1]. While the drugs already available commercially are only capable of killing microfilariae, they are not really helpful in the treatment of lymphatic filariasis with adult worms present. Therefore, a novel drug that can deal with this specific problem is required.

In the summer research, neurolenin D was first extracted from commercially available Neurolaena lobate through the process of Soxhlet extraction, charcoal filtration, column chromatography, and recrystallization. The specific procedures were found in the honor thesis written by Catherine McGeough. The presence of pure neurolenin D was proved by the analysis of the proton and carbon NMR spectroscopy (Figure 1) of the product. The peaks and the integration number were in accordance with the data provided by Catherine.

The newly synthesized neurolenin D was then treated with Dess-Martin
Periodinane. The reaction went as predicted. But after a set of workup procedures were done, there were still remnants of neurolenin D shown in the NMR spectrum. In order for the reaction to go to completion, the reactants were added again, and the reaction was allowed to run for a second time. The peaks showing the transformation of the reactant to the product in the proton NMR spectra were monitored to make sure the reaction was going to the correct direction. Column chromatography was then conducted to obtain a purer oxidation product of neurolenin d with a percent yield that is relatively high. Through this reaction, the secondary alcohol in neurolenin D was successfully transformed into a ketone, allowing the molecule to further participate in more complicated reactions and form new derivatives.

Future experiments should be conducted on the reductive amination on the newly synthesized ketone. The procedures are adapted from a similar experiment to Richard F. Borch [2].

LinneaSchultz2022Kate Queeney, Chemistry - ChemistrySurface ChemistryElizabeth Apiche - Altering Silicon Surfaces with Thin Hydrophilic Polymer FilmsThe main goal of this study was to generate thin hydrophilic silicon surfaces that are neutrally charged and to further investigate whether the surfaces obtained can be further functionalized post fabrication to alter their features. Previous studies in the Queeney Lab focused on altering the chemistry of the surfaces independent of topography by comparing oxidized hydrophilic surfaces to hydrophobic alkyl monolayers. In this study, we were concerned with generating thin hydrophilic surfaces that are neutrally charged in order to isolate the effects of surfaces wettability from those of surface charge. We used reactive layer-by-layer (LbL) deposition approach to adsorb thin polymer films on the silicon surfaces. This method generated reactive covalently crosslinked thin films using a polyamine and a polymer containing the reactive azlactone functionality. The polyamine used was poly allylamine Hydrochloride (PAH) followed by the chemically reactive polymer poly(2-vinyl-4,4-dimethylazlactone) (PVDMA). Afterwards, we confirmed our results using ellipsometry and contact angle to make sure that the surfaces we generated were both thin and hydrophilic and that the results obtained were fairly reproducible. We used Infra-Red (IR) spectroscopy to ensure that the polymers were successfully adsorbed on the surfaces as we claimed. In the case of functionalization experiments, we functionalized the surfaces post-fabrication using polymers containing primary amine groups and confirmed the results using ellipsometry, contact angle measurements as well IR spectroscopy to make sure that the primary amines reacted with any residual azlactone functionality.
Successful adsorption of PAH was indicated by extremely thin films on silicon surfaces with film growth between 1Åand 5Å. These results were expected for PAH as it lies ‘flat’ on the silicon surfaces resulting in tiny growth in film thicknesses. PAH generated hydrophilic surfaces as indicated by the low contact angle measurements from the goniometer. Similarly, PVDMA yielded hydrophilic silicon surfaces with film growth between 4Åand 6Å to some degree of reproducibility. IR spectra generated for PAH-adsorbed surfaces did not yield the N-H bending modes attributed to the NH3+in the PAH structure. This, we thought, was due to the fact that the PAH adsorbed was below the detection limit of the FT-IR. However, spectra for the PVDMA-adsorbed after PAH indicated amide peak at approx. 1670cm-1suggesting that the adsorbed PAH reacted with the azlactone ring producing the amide groups. The amide peak was also observed with functionalization. Future work on this project include the investigation of the effects of post-fabrication functionalization on silicon surfaces.
GracieWessels2020Steven Williams, Biological Sciences - Biological SciencesSAW lab (Experimental biology)Rachael Newhallunnamed copy.pngNeuromuscular Responses to Anti-Parasitic drugs: The Effect of Neurolenin B. on C. elegans Lifecycle and BehaviorC. elegans is a common soil nematode that is regularly used in a variety of different lab environments due to its easily-maintained lifecycle and its ability to be observed under a normal light microscope. This course of research aimed to test the viability of Neurolenin B and other Neurolenin derivatives on C. elegans, for the purpose of examining the scope of Neruolenin effectiveness on non-target parasite species. Previous research surrounding the effect of Neurolenin on Lymphatic filariasis (LF), the initial target of the drug, have proven effective to a certain extent. LF individuals displayed a variety of different neuromuscular responses to the drug, including spasms, slowed motion, and death. Thus, Neurolenin effectiveness in C. elegans can offer promising information about the scope of the drug's anti-parasitic potential.
To properly perform drug-testing on C. elegans, a viable culture of individuals was grown and maintained over several generations. To begin this process, a single C. elegans culture was pipetted onto several nematode-growth agar plates, and seeded with OP50 E. coli. The lifecycle of C. elegans, from larval to adult stages, was closely monitored over the course of several weeks, including the inclusion of a nematode-specific liquid medium. After sufficient numbers of C. elegans were acquired (in both solid and liquid environments), liquid cultures were seeded with Neurolenin B as to observe the subsequent response of C. elegans. Although C. elegans did not appear to have a particularly strong response to the drug, most individuals exhibited mild curling behavior in the liquid environment, as opposed to the normal thrashing and slithering motions displayed by untreated C. elegans.
The responsiveness of C. elegans to Neurolenin derivatives can offer crucial insight into the scope of Neurolenin effectiveness as it pertains to species specificity. In other words, Neurolenin can be assumed to be effective across a wide scope of parasite species if it effects two different species in the same way. Although C. elegans and LF parasites did not respond in the same way to the drug, other Neurolenin derivatives may effect the nematodes differently and thus offer more insight about the biochemical targets of the drug.
ElizabethApiche2020Kate Queeney, ChemistryMaren BuckChemistryChemistryLinnea Schultz - Altering Silicon Surfaces with Thin Hydrophilic Polymer FilmsThe main goal of this study was to generate thin hydrophilic silicon surfaces that are neutrally charged and to further investigate whether the surfaces obtained can be further functionalized post fabrication to alter their features. Previous studies in the Queeney Lab focused on altering the chemistry of the surfaces independent of topography by comparing oxidized hydrophilic surfaces to hydrophobic alkyl monolayers. In this study, we were concerned with generating thin hydrophilic surfaces that are neutrally charged in order to isolate the effects of surfaces wettability from those of surface charge. We used reactive layer-by-layer (LbL) deposition approach to adsorb thin polymer films on the silicon surfaces. This method generated reactive covalently crosslinked thin films using a polyamine and a polymer containing the reactive azlactone functionality. The polyamine used was poly allylamine Hydrochloride (PAH) followed by the chemically reactive polymer poly(2-vinyl-4,4-dimethylazlactone) (PVDMA). Afterwards, we confirmed our results using ellipsometry and contact angle to make sure that the surfaces we generated were both thin and hydrophilic and that the results obtained were fairly reproducible. We used Infra-Red (IR) spectroscopy to ensure that the polymers were successfully adsorbed on the surfaces as we claimed. In the case of functionalization experiments, we functionalized the surfaces post-fabrication using polymers containing primary amine groups and confirmed the results using ellipsometry, contact angle measurements as well IR spectroscopy to make sure that the primary amines reacted with any residual azlactone functionality.
Successful adsorption of PAH was indicated by extremely thin films on silicon surfaces with film growth between 1Åand 5Å. These results were expected for PAH as it lies ‘flat’ on the silicon surfaces resulting in tiny growth in film thicknesses. PAH generated hydrophilic surfaces as indicated by the low contact angle measurements from the goniometer. Similarly, PVDMA yielded hydrophilic silicon surfaces with film growth between 4Åand 6Å to some degree of reproducibility. IR spectra generated for PAH-adsorbed surfaces did not yield the N-H bending modes attributed to the NH3+in the PAH structure. This, we thought, was due to the fact that the PAH adsorbed was below the detection limit of the FT-IR. However, spectra for the PVDMA-adsorbed after PAH indicated amide peak at approx. 1670cm-1suggesting that the adsorbed PAH reacted with the azlactone ring producing the amide groups. The amide peak was also observed with functionalization. Future work on this project include the investigation of the effects of post-fabrication functionalization on silicon surfaces.
YanxuanLi2020Sarah Moore, EngineeringMaren BuckEngineeringBiomedical Engineering - Screen Shot 2019-09-05 at 11.27.55 PM.pngSite Specific Protein Polymer Conjugation for Cancer Drug Delivery According to the American Cancer Society, in 2019, an estimated 1,762,450 cancers will be diagnosed. Cancer is a collection of disease that causes by mutated genes and lead to the unchecked growth of cells. The characteristic of cancer included uncontrolled proliferate, immortality, angiogenesis, invasion and metastasis. It is difficult for the immune system to distinguish between healthy cells and mutated cells. Therefore, traditional chemotherapy can only targets cells that grow rapidly and result in severe side effects. One of the solutions will be targeted cancer therapy. Our research aims to develop a protein polymer conjugation to target a biomarker called integrins, which are heterodimeric cell-surface adhesion molecules that related to cancer cells adhesion, migration and invasion. Integrins bind their ligands through recognition of short amino-acid sequences—arginine-glycine-aspartic acid (RGD), which is a frequent recognition motif. Research shows that integrins promote pathogenic process, including cancer, marked them as potential cancer therapeutic target. The proteins we previously engineered has RGD motif and can interact with integrins.

This summer, we focused on characterizing and synthesizing the polymer to conjugate with engineered protein. Polymers are macromolecules composed of many repeating units termed monomers. The repeating monomer can react with different chemical groups to serve various purposes. The polymer we used is Poly(2-vinyl-4,4-dimethylazlactone) (PVDMA). PVDMA can be synthesized using free radical polymerization, including a controlled method called reversible-addition fragmentation chain-transfer(RAFT) polymerization, of the corresponding vinyl monomer 2-vinl-4,4-dimethylazlactone(VDMA). RAFT polymerization allows for control over the molecular weight and size-distribution(polydispersity) of the polymer in the presence of chain-transfer reagent(CTA). In our experiment, highly active azlactone side chains of PVDMA undergoing a ring opening reaction with maleimide group first and then triethylene glycol monomethyl ether(mTEG). Maleimide will have a high efficiency, high yield and specific couple reaction with the only thiol in cysteine that located at the N terminal of RGD protein. The efficiency of treatment can be improved by using maleimide groups. Then, PVDMA can be functionalized with the hydrophilic methoxy terminated mTEG, which allows the polymer to be soluble in water. We also functionalized the PVDMA with only mTEG. The primary amine in the engineered protein can react with the azlactone ring too. The gel electrophoresis result shows that shorter polymer with about 25% mTEG conjugated with protein better. Different ratio of maleimide and mTEG had been tried in our experiment but more troubleshooting was needed to yield a final soluble product with no byproduct.
According to the American Cancer Society, in 2019, an estimated 1,762,450 cancers will be diagnosed. Cancer is a collection of diseases caused by mutated genes that lead to the unchecked growth of cells. It is difficult for the immune system to distinguish between healthy cells and mutated cells. Traditional chemotherapy targets all cells that grow rapidly and results in severe side effects. There is great need for better, less toxic treatments. One promising solution is targeted therapy. Our research aims to develop a protein-polymer conjugate to target a tumor biomarker called integrins, to enable targeted drug delivery to cancers cells with integrins. Integrins are heterodimeric cell-surface adhesion molecules that relate to cancer cells migration and invasion. Integrins bind their ligands through recognition of short amino-acid sequences—arginine-glycine-aspartic acid (RGD), which is a frequent integrin recognition motif. We are working with engineered proteins that contain the RGD motif and interact with integrins.

This summer, we focused on characterizing and synthesizing the polymer to conjugate to the integrin-binding protein. Polymers are macromolecules composed of many repeating units termed monomers. The monomer can react with different chemical groups to serve various purposes. The polymer we used is poly(2-vinyl-4,4-dimethylazlactone) (PVDMA). PVDMA can be synthesized using free radical polymerization, including a controlled method called reversible-addition fragmentation chain-transfer (RAFT) polymerization, of the corresponding vinyl monomer 2-vinl-4,4-dimethylazlactone (VDMA). RAFT polymerization allows for control over the molecular weight and size-distribution (polydispersity) of the polymer. In our experiments, a fraction of the highly reactive azlactone side chains of PVDMA underwent a ring opening reaction with maleimide groups, for later conjugation to a unique thiol in the targeting protein. Alternatively, primary amines in the targeting protein can react directly with the azlactone ring. Then, PVDMA was functionalized with the hydrophilic methoxy terminated triethylene glycol monomethyl ether (mTEG), which allows the polymer to be soluble in water. As a control, we functionalized the PVDMA with only mTEG. We reacted targeting protein to different polymer constructs, and used gel electrophoresis to determine extent of conjugation of polymer to protein. The protein gel in figure 2 shows that, when using primary amines in the protein to conjugate to polymer, shorter polymer where 25% of the polymer was functionalized with mTEG conjugated to protein better compared to when longer polymers were used or when a greater fraction of the polymer was functionalized with mTEG. We are continuing to explore conjugation of protein to polymer using the maleimide group.
TamaraThomas2021Steven Williams, Biological SciencesSteven WIlliamsBiological SciencesMolecular Biology - - Development of a New Molecular Diagnostic Assay to Detect M. perstans in Human Blood Here we describe a novel, species-specific, quantitative, real-time PCR assay for the detection of the parasite Mansonella perstans. M. perstans is closely related to Wuchereria bancrofti, the causative agent of lymphatic filariasis in Africa, and has the potential to cause false-positive results when using antigen detection-based tests. To combat this problem, we capitalized on the sensitivity and specificity of PCR-based assays to develop a new quantitative PCR (qPCR)assay for M. perstans based on the detection of species-specific repetitive DNA sequences using our previously published genomics/bioinformatics-based platform. M. perstans was sequenced using Illumina next-generation sequencing and the raw sequence reads were ported to the bioinformatic tool RepeatExplorer to screen for the most highly repeated DNA sequences. These sequences were used to design qPCR primer and probe sets to optimize the sensitivity and specificity of the qPCR assay. The primer and probe set that produced the best sensitivity and specificity was selected for further study and tested using M. perstans DNA, human DNA and the DNA of several related filarial parasites. Results from the real-time amplification plots showed that only the M. perstans DNA was amplified and that attogram levels of DNA could be
detected.

Following these laboratory-based studies, field samples collected in several countries
in Africa were tested and results were compared to the standard antigen detection-based method for lymphatic filariasis (FTS strip test). Results from our experiments showed that our assay consistently outperformed the gold standard by showing earlier detection at a lower Ct- value. Our assay due to its targeting of highly repetitive sequences in the M.perstans DNA instead of the interspaced repeats of the ribosomal DNA (the method of M.perstans DNA targeting use by the gold standard) was able to detect at a ten-fold lower threshold of DNA amplification due to the abundance of targeted DNA repeats. Nevertheless, some samples that were not detected by the gold standard showed inconsistent detection between the sample replicates by our assay. These samples will be further tested and results will be analyzed and submitted for journal review. One goal is to determine the proportion of positive tests that are due, in fact, to the presence of M. perstans.

Erika Melara2020Andrew Guswa, Engineering - EngineeringEngineering - Environmental - - Assessment of Water Yield Balance for the Cocheco Watershed Using QSWATAs the environment experiences changes in its landscape, science uses valid tools to measure these accurately and draw conclusions that contribute to sustainable decision-making. This data may act as a base-line to help preserve the quantity and quality of resources including water. The objective of this research was to implement QSWAT, a QGIS interface (Quantum Geographic Information System) of SWAT (Soil Water Assessment Tool), to quantify the annual water balance components of the Cocheco Watershed for the year 2010 and to compare these values with data provided from Harvard Forest. Additionally, this scaled modeling program was used to evaluate the amount of nitrogen and explore the effects of future land use scenarios (2060) on the quality of water. These future scenarios, designed by Harvard Forest, were tailored to vary from a high to low planning and innovation, from a globalized to a localized economy, from a stable population to an increasing immigration rate, and from a high to a low value of ecosystem services, among other factors. The outputs were obtained from the main channel file, specifically for the routing reach 25. For the current land use of the Cocheco Watershed (2010), the QSWAT model was able to match the precipitation, PET, ET, latitude flow, groundwater flow, and water yield with a difference of 15% or less of the original values. Components, such as, surface runoff and percolation differed by more than 15%, which can be attributed to discrepancies in the calibration of the input parameters. A future land use (2060) featuring a low innovation, a globalized economy, an increasing immigration rate, and a high value of natural resources showed the greatest amount of annual nitrogen loading with approximately 189,000 kg. Meanwhile, the current land use of the Cocheco Watershed (2010) presented the lowest average nitrogen loading with 34,000 kg. These results are not conclusive yet since there is no data that could provide a contrast. Thus, suggesting a need for further research of the region and the performance of the nitrogen model to distinguish clear relationships between nitrogen and land use.
Lizette Carpenter2020Katherine Kinnaird, Statistical and Data Sciences - Computer ScienceComputer Science - Aligned Hierarchies Our goal was to create a python package that creates the aligned hierarchies for music-based data streams. The aligned hierarchies for a given music-based data stream is the collection of all possible hierarchical structure decompositions aligned on a common axis. Our python package, ah, offers all possible structure decompositions in one cohesive object. The output of our package comes from Katherine Kinnaird's thesis Aligned Hierarchies for Sequential Data and MATLAB code. We translated Kinnaird’s MATLAB code into python to create a python package that may be used to build aligned hierarchies by others. Our package are organized into five modules: example.py, utilities.py, search.py, transform.py and assemble.py. Each module contains the functions that collectively outputs aligned hierarchies.
WinnieMbugua2021Judith Cardell, Engineering - EngineeringElectrical Engineering - - Transactive Energy and Blockchain; the move to sustainable electricity production.Over the past few years, there has been a massive shift to sustainability options in all the major industries, food, clothing, automotive and even accessories, with the deadline to change our ways only being moved closer. While these have been huge milestones, the move to sustainable energy options is the most necessary but the longest overdue. The main problem is that our power systems are not up to date with current trends in sustainability. Generation and distribution of sustainable forms of power on the grid and on a retail scale is the best solution for sustainability in electricity production. This system can be implemented using Transactive Energy (TE).

Transactive energy is defined by the National Institute of Standards and Technology as a system of economic and control mechanisms that allows the dynamic balance of supply and demand across the entire electrical infrastructure using value as a key operational parameter. It is a set of techniques that incorporates dynamic pricing, allowing distributed energy resources (small scale producers of electricity like generators and solar panels) to sell their power at the market price. It also allows people to buy or sell electricity when it is most convenient for them to. Under transactive energy, people become prosumers; producers and consumers of electricity. With transactive energy, prosumers are able to adjust their prices at different times of the day based on demand (a concept known as dynamic pricing). This requires the use of Advanced Metering Infrastructure (AMI) to track consumption trends. This would mean that a lot of energy consumption data is required to make transactive energy work. Not surprisingly, one of the main concerns with switching to transactive energy is data privacy. The employment of blockchain to implement transactive energy is a solution to this and many other concerns.

Blockchain is a distributed ledger that facilitates the process of recording transactions and tracking assets. It eliminates the need for a centralized body due to the transparency of all the transactions with the parties involved. It ensures safety in that no transaction can be deleted but can only be reversed using another recorded transaction visible to all parties. Also, the data is inaccessible to people outside the involved parties as it requires a unique key. With the employment of blockchain technology in transactive energy, electricity production could largely shift to sustainable sources like wind and solar mitigating the climate change crisis.
VeronicaPickard2021Benita Jackson, Psychology - PsychologyPsychologyXinyu Chu, Clio Dinan, Virginia Cafferky - Division of Domestic Housework and LaborSmith College
Summer Undergraduate Research Fellowship (SURF) Abstract
Summer 2019

Literature Review of Division of Domestic Labor Among Married Wife-Husband Couples: Implications for Well-Being
Veronica Pickard ’21, Virginia Cafferky ’21 (U Rochestor), Clio Dinan ’20, Xinyu Chu ’20, & Benita Jackson
Married couples must negotiate the division of domestic work, the perceived fairness of which shapes individual and relational wellbeing. Examining how couples collaborate on housework, or fail to, provides important insight into gender roles, interpersonal power and status, and overall happiness both within and outside marriages. A systematic review of 48 empirical studies on married individuals and couples suggests that when this division is perceived as unequal, relationships and individual psychological outcomes suffer. Overall, we found that wives compared to husbands generally complete more household chores. Gender roles and ideologies appears to mediate how fair actors perceive the division of domestic work. For example, wives with traditional homemaking roles perceive the division of labor as fair even if they perform the majority of domestic work. Conversely, wives with egalitarian gender ideologies engage in less housework regardless of their husbands’ ideologies. Status, such as socioeconomic status, education level, and power within the marriage appear to be key determinants of perceived fairness. Most findings suggested that when wives earn or work less than their male counterparts, they are more likely to perceive the division of labor as unfair. Increases in education level and income for wives were minimally associated with changes in the actual amount of time spent on housework, with varying implications for perceived fairness. Even if the wife has a higher status, gender role ideology prevails when it comes to the division of household labor. Relationship satisfaction also influences the perception of fairness in the division of domestic work. Despite gender and status, when a marriage partner is happier with their relationship, that person is more likely to perceive the division of housework as fair regardless of how equal it is by more objective measures. Conversely, individuals who report unequal support, psychological distress, or relationship dissatisfaction are more likely to perceive the division of domestic labor as unfair. Overall, this review revealed consistency in findings across a variety of populations, methods, and measuresstudies. Still, these findings warrant qualification. Many of the studies in this review used secondary data. Therefore, researchers did not have control over method. Most studies reviewed relied on participant self-reporting, which creates concerns of response bias and potential misunderstandings of the questions being asked. As with any qualitative review, we cannot quantify the consistency of findings, which can be for future research. Additionally, most participants were American, White, and middle-class; this homogeneity raises concerns about the generalizability of this work.
TaylorMcCain2020Annaliese Beery, Psychology - NeuroscienceNeuroscience - Partner-preference test 2019-09-05 at 7.50.39 PM.pngThe Effects of Gestational Folic Acid on Adult BehaviorFolic acid (FA), a B vitamin and a methylating agent important for neural tube development, may have effects on adult social behavior and epigenetics1. Because of its necessary role in neural tube development, starting in 1998 the FDA began fortifying grains with FA in the US to decrease miscarriage rates2. Although this was effective, minimal information is known of the effects of high gestational FA on offspring behavior. As miscarriage rates in the US have continued to decrease since the mandated fortification of FA in grains, Autism Spectrum Disorder (ASD) rates have been increasing3, and human epidemiological studies have provided correlative evidence that FA exposure may alter the rate of ASD4,5. Since this mandated fortification, doctors have continued to prescribe the equivalent amount of FA (400mcg daily) to pregnant women as was prescribed prior to the fortification of FA in grains6. It is possible that these increasing rates could partially be due to the increased amount of FA consumed by pregnant mothers7. In order to study the effects of dietary gestational FA on adult behavior, an initial experiment was completed. Rat mothers were placed on three FA diets and the behavior of their offspring was examined through play/fighting behavior tests, anxiety tests, and sociability tests. Partner-preference tests in prairie voles were completed to test for changes in bond formation. The results of this initial study found that high and low levels of gestational FA significantly increased aggressive behaviors in Long-Evans rats and had near significant effects on same-sex partner-preference formation in prairie voles.

In order to further investigate the results gathered from the initial experiment, a second study began over the summer as my SURF project (which will be used for my senior thesis). Prairie vole dams were placed on either a low FA diet (.4 mg/kg) or a control FA diet (2 mg/kg) and continued on the diets throughout pregnancy and weaning. Pups were placed on a control AIN-93G FA diet following weaning. Behavioral tests were completed on the pups to measure aggression (play/fighting tests) and changes in social bond formation (partner-preference tests)(see figure). Prairie voles were specifically chosen for this experiment due to their unique ability to form selective social bonds (partner preferences) for opposite-sex mates and same-sex cagemates. These tests continued throughout the summer and will be ongoing throughout the fall semester.


1 Barua S, Kuizon S, Junaid MA (2014) Folic acid supplementation in pregnancy and implications in health and disease. J Biomed Sci 21:77.

2 CDC. Updated Estimates of Neural Tube Defects Prevented by Mandatory Folic Acid Fortification — United States, 1995–2011. MMWR Morb Mort Wkly Rep. 2015: 64(01); 1-5.

3 Baio J, Wiggins L, Christensen DL, et al. Prevalence of Autism Spectrum Disorder Among Children Aged 8 Years — Autism and Developmental Disabilities Monitoring Network, 11 Sites, United States, 2014. MMWR Surveill Summ 2018;67(No. SS-6):1–23. DOI: http://dx.doi.org/10.15585/mmwr.ss6706a1

4 Engel, SM, Daniels, JL (2011). On the complex relationship between genes and environment in the etiology of autism. Epidemiology. 2011. 22: 486-488. DOI: 10.1097/EDE.0b013e31821daf1c.

5 LaSalle, JM (2013). Epigenomic strategies at the interface of genetic and environmental risk factors for autism. Journal of Human Genetics. 58, 396-401(2013).

6 CDC. Updated Estimates of Neural Tube Defects Prevented by Mandatory Folic Acid Fortification — United States, 1995–2011. MMWR Morb Mort Wkly Rep. 2015: 64(01); 1-5.

7 Surén, Pål et al. ASSOCIATION BETWEEN MATERNAL USE OF FOLIC ACID SUPPLEMENTS AND RISK OF AUTISM IN CHILDREN. JAMA : the journal of the American Medical Association 309.6 (2013): 570–577. PMC. Web. 10 Sept. 2018.
OliviaDel Guercio2020Patricia Cahn,Mathematics and Statistics - Mathematics and StatisticsKnot TheoryHana Sambora and Jack KendrickAn Invariant of 3-Colored KnotsIn this work we present a method for computing a type of knot invariant called the dihedral linking number for all 3-colorable knots on the database Knotinfo. An invariant is a value associated with a knot that does not change when the knot is deformed. The (ordinary) linking number of a pair of knots measures how many times one knot wraps around another, and can be computed from a diagram of the link. The dihedral linking number is a property derived from a single 3-colored knot (rather than a link), and is equal to the linking number of a pair of knots obtained from the 3-colored knot; these two knots sit in another three-dimensional space called a branched cover. The dihedral linking number can be used not only to gauge whether two knots are the same, but also provide information on the ampichirality and invertibility of a given knot.
To calculate the dihedral linking number three pieces of information are necessary: the overstrand list, coloring list, and sign list. We leverage a piece of readily available information known as the gauss code to find all of these values. The overstrand list tells us which strands come together at a crossing. We can construct a matrix where each row corresponds to a crossing, making the coefficient of each strand present at the crossing 1. If the crossing has three strands of the same color or of all different colors, adding the colors together will be equivalent to 0 modulo 3. So, each row can be set equal to 0 in order to solve for an appropriate 3 coloring. In order to convert the matrix to reduced row echelon form, we made use of an existing Python row reduction algorithm and adapted it work modulo any prime number. After determining which variables are free in the reduced row echelon form of the matrix, we can determine how many colorings exist for the knot. We can then make a list of valid colorings to use, since each coloring can yield a different dihedral linking number. Using the process outlined by Kauffman in Virtual Knot Theory (1999), a knot can be reconstructed from its Gauss code. By reconstructing the knot and using the original gauss code, the sign of each crossing can be found.
After collecting these three pieces of information, we have two programs that can compute the dihedral linking number. To start, our advisor gave us an existing program called colorings.py which calculates the dihedral linking number and other related information in two different ways. We mainly used this to test our own code. Much of our later time was spent double checking our advisor’s code and writing out each of the cases it computes. Combined with our previously explained programs, colorings.py accurately computes the dihedral linking number for all knots listed in a knot database called KnotInfo. Thus, our main accomplishment for the summer was automating this calculation and tabulating the results. We also began to extend this work to 5-colored knots.
AbigailEdwards2020Sarah Witkowski, Exercise and Sports Studies - Biological SciencesCardiovascular Disease - thesis conceptual model .pngThe effects of stress on vascular function in healthy, premenopausal, Black womenCardiovascular diseases (CVDs) remain the leading cause of morbidity and mortality in women in developed societies worldwide. Black women are at greater risk for CVDs compared with white women. Risk for CVD may develop earlier in life for Black women due to adverse health behaviors, socioeconomic factors, social environment, and access to care.
One theory regarding the increased CVD risk of Black women investigates the role of psychological stress as a potential nontraditional CVD risk factor. Racial and ethnic discrimination has been postulated as a multidimensional environmental stressor at the societal and individual levels. Chronic exposure to stress is associated with altered physiological functioning, which may increase risks for a broader range of health conditions (McEwen, B. et. al. 1998). Racism or even the perception of racism materializes into poor physical health and increased CVD risk for Black women. The overall goal of this research is to evaluate the relationships between arterial stiffness, a subclinical CVD risk factor, and experiences of racial discrimination and stress in young, healthy, Black women (Figure 1).
Central arterial stiffness is an independent predictor of CVD risk and mortality. It is assessed by carotid-femoral pulse wave velocity (cfPWV) and augmentation index (AIx). Pulse wave velocity measures the speed with which a pulse of blood travels down the aorta. Higher pulse wave velocity indicates a stiffer, less compliant vessel. Augmentation index (AIx) is a measure of the amplitude of the reflected arterial wave that amplifies the forward wave. Stiffer, less compliant vessels produce greater reflected waves. Some studies show differences in PWV and AIx by race/ethnicity and sex. However, there is a gap in knowledge about arterial stiffness in young, Black women. I hypothesize that PWV and AIx at rest will be positively correlated with measures of stress and discrimination in young, Black women.
Participants are healthy, non-smoking, premenopausal, Black women ages 18-24. PWV and AIx are measured at rest, on days 2-5 of the participant’s menstrual cycle. Perceived stress scores, everyday discrimination scores, and heightened vigilance scores are evaluated via questionnaire. Semi-structured interviews on experiences with racial discrimination are conducted.
Data collection is ongoing. Understanding relationships between experiences of stress and discrimination and blood vessel function may uncover novel mechanisms underlying differences in CVD risk in Black women. In the future, this work may inform public health and medical care.

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Figure 1. Conceptual model proposing potential mechanism for subclinical CVD risk in Black women.
BillieCullison2019Laura Katz, Biological Sciences - Biological SciencesBiology/BioinformaticsRobin Sleith, Agnes KM Weiner, Laura A KatzBillieCullisonFigure.pngPilferer or Pal: The relationship between Hyalosphenia papilio and its algal "symbiont”Several species of Arcellinida (Amoebozoa) harbor algae of the genus Chlorella within their tests. Previous work assumed that the amoebae harbor the entire green alga, leading to the prediction that both nuclear and plastid Chlorella genomes should be present within the amoeba (Gomaa et al, 2014). We have carried out single-cell genomics and transcriptomics on 35 Hyalosphenia papilio, all of which contain green symbionts. The presence of algal nuclear DNA within the majority of H. papilio samples would indicate a symbiotic relationship; whereas its absence may indicate kleptoplasty, with the amoeba having digested the algae and only retaining the chloroplasts for photosynthesis. Surprisingly, we find very little Chlorella nuclear signal within the transcriptomes and genomes generated in our lab. This suggests that the relationship between the algae and the amoeba is actually one of kleptoplasty instead of a symbiosis. We are now using the genome/transcriptome data and microscopy techniques to further explore this relationship. In addition, we are comparing transcriptome data of H. papilio and Hyalosphenia elegans (no symbionts) to study differential gene expression in response to oxidative stress in the species containing a photosynthetic plastid. Together, these data yield insights into the microbiomes of microbes.
MadeleineLerner2020Annaliese Beery, Psychology - PsychologyNeuroscience/Neuroendocrinology - MLerner_Voles Huddling.pngDopamine and the role of reward in prairie vole peer relationshipsPrairie voles (Microtus ochrogaster) are one of the few mammals that are socially monogamous and demonstrate biparental care (Carter et al., 1995). These bonds can be measured quantitatively through recognizable behaviors such as huddling (see attached photo), grooming, and mate guarding. In addition to their selective reproductive relationships, prairie voles also develop selective same-sex relationships, showing many of these same affiliative behaviors towards their same-sex peers (Lee et al., 2019). As such, this species is commonly used to study relationships, both reproductive (opposite-sex “pair” bonds) and non-reproductive (same-sex “peer” bonds).
Prior research has revealed that dopamine is essential for the formation and maintenance of prairie vole mate bonds (Aragona et al., 2003). However, dopamine is not necessary for the formation of female peer bonds in a closely related species, the meadow vole (Microtus pennsylvanicus) (Beery & Zucker, 2010). In addition, endogenous opioids mediate the formation and maintenance of prairie vole pair bonds (Burkett et al., 2011). Our research aims to determine the role of dopamine signaling in peer preference formation of female prairie voles. We administered haloperidol, a dopamine antagonist, and apomorphine, a dopamine agonist, to examine how altering dopamine reward signaling would affect peer bond formation. We ran behavioral tests including the partner preference test (PPT) and the socially conditioned place preference test (SCPP), measuring behaviors such as huddling, aggression, and time spent on bedding that is associated with the partner vole to assess formation of peer bonds (or lack thereof). We also began the process of using receptor autoradiography to analyze structural changes in the dopamine and opioid reward systems related to different social (isolated vs. paired) conditions.
We found that dopamine is sufficient, but not necessary, for the formation of peer partner preference in prairie voles. These results suggest that same-sex partner preference does not rely on the dopamine reward system. This corroborates what we know about female meadow vole relationships, and further suggests different mechanisms for the regulation of reproductive vs. non-reproductive relationships. In the context of evolution, it makes sense that opposite-sex relationships may be more strongly reinforced by reward system activation to encourage reproduction. Future research in this area will be focused on the role of the opioid reward system in peer bond formation, specific dopamine and opioid receptors that may be involved in peer bond maintenance, and changes in receptor density resulting from different social housing conditions.



References

Aragona, B. J., Liu, Y., Curtis, J. T., Stephan, F. K., & Wang, Z. (2003). A Critical Role for
Nucleus Accumbens Dopamine in Partner-Preference Formation in Male Prairie Voles. J Neurosci, 23(8), 3483–3490. doi: 10.1523/jneurosci.23-08-03483.2003

Beery, A. K., & Zucker, I. (2010). Oxytocin and same-sex social behavior in female meadow voles. Neuroscience, 169(2), 665–673. doi: 10.1016/j.neuroscience.2010.05.023

Burkett, J. P., Spiegel, L. L., Inoue, K., Murphy, A. Z., & Young, L. J. (2011). Activation of μ-Opioid Receptors in the Dorsal Striatum is Necessary for Adult Social Attachment in Monogamous Prairie Voles. Neuropsychopharmacology, 36(11), 2200–2210. doi: 10.1038/npp.2011.117

Carter, C. S., Devries, A. C., & Getz, L. L. (1995). Physiological substrates of mammalian monogamy: The prairie vole model. Neurosci Biobehav Rev, 19(2), 303–314. doi: 10.1016/0149-7634(94)00070-h

Lee, N. S., Goodwin, N. L., Freitas, K. E., & Beery, A. K. (2019). Affiliation, Aggression, and Selectivity of Peer Relationships in Meadow and Prairie Voles. Front Behav Neurosci, 13. doi: 10.3389/fnbeh.2019.00052
AmyHagen2021Sara Pruss, Geosciences - GeosciencesGeosciences - - Evaluating Mercury as a Proxy for Redox Conditions in Newfoundland SPICE Strata This summer, my SURF research project with Professor Sara Pruss focused on rocks containing the Steptoean Positive Isotopic Carbon Excursion, or SPICE event, from western Newfoundland. The SPICE event is a global carbon isotopic excursion that corresponds to a mass extinction of trilobites in the Late Cambrian (Saltzman et al. 1998). Because SPICE also involves a mercury excursion, it has been hypothesized that large igneous provinces (LIPs) may have been the cause. The goal of our research was to examine the relationship between mercury and organic carbon in samples from Newfoundland, Canada to test the idea that mercury might serve as a proxy for changing marine oxygen conditions rather than LIP volcanism (Pruss et al. 2019).
We began this process by traveling to western Newfoundland for a week to collect samples. Once back at Smith, I constructed a mercury curve for the section by drilling powder from each rock and analyzing it with the Hydra-C in the Center for Aqueous Biogeochemical Research. I drilled additional powder for carbon isotopes, which were sent off-site and are still processing. To analyze samples for total organic carbon, I crushed rocks using a shatterbox and dissolved the inorganic carbon from powders using HCl. This data is waiting to be processed at Amherst College. To help connect chemical data to the environments in which the rocks were formed, I created thin sections of about 20 rocks that contained the SPICE peaks or exhibited remarkable facies. This semester I will be continuing to analyze thin sections, constructing a stratigraphic column, and considering new data as it becomes available.


Refs:
Saltzman, M. R., Runnegar, B., & Lohmann, K. C. (1998). Carbon isotope stratigraphy of Upper Cambrian (Steptoean Stage) sequences of the eastern Great Basin: Record of a global oceanographic event. GSA Bulletin, 110(3), 285–297.
Pruss, S. B., Jones, D. S., Fike, D. A., Tosca, N. J., & Wignall, P. B. (2019). Marine anoxia and sedimentary mercury enrichments during the Late Cambrian SPICE event in northern Scotland. Geology, 47(5), 475–478.
AshleyFishbein2020Jesse Bellemare, Biological Sciences - Biological SciencesEcology - Effects of Recent Climate Change on Clintonia borealis in Western MassachusettsOver the summer, I studied the effects of recent climate change on local populations of Clintonia borealis, also known as the blue-bead lily. To do this, I resurveyed nine sites that were previously surveyed in 2010-2011 with my SURF advisor, Jesse Bellemare. We were able to relocate the exact research plot sites used in the previous surveys of this species. These study sites were located along a ~1000 m elevational gradient from the Connecticut River Valley to the top of Mt. Greylock, allowing us to compare populations living in different climates without traveling very far from campus. The sites also varied in canopy cover, slope aspect, and water status which provided clues as to the ideal habitat for the blue-bead lily.

Our results showed that all the sites were shrinking in population size, or leaf size, or both. The attached image shows these trends (not all sites have been added yet). Plants at lower elevation (warmer) sites also produced opposing leaves that were more asymmetrical, indicating that they might be more physiologically or developmentally stressed by their warmer environments. There was also a shift toward plants with fewer leaves and much less sexual reproduction. Considering that the years between the two surveys were some of the most extreme on record, we believe the changing climate is likely the primary cause of stress and recent changes in these populations. Our results were significant, and we hope to publish them in an academic journal next year.
YilinWang2020Alicia Grubb, Computer Science - Computer ScienceComputer Science Omema Ibrahim屏幕快照 2019-09-06 00.57.13.pngTowards Merging Models over Different Time Intervals BloomingLeaf is an analysis and modeling tool that allows stakeholders to model goals and intentions. The tool helps users understand model evolution and tradeoffs by evaluating how intentions change over time. Prior work looked at creating models piecemeal, by constructing models of individual actors over different time periods and then merging them together. Grubb proposed an algorithm for merging goal models and showed a potential application; but, did not implement the proposed semi-automated algorithm. In this project, we explored the problem domain of this merge algorithm and developed underlying tooling.

To fully implement the algorithm, we needed to merge both the visual syntax and underlying semantics of both un-timed and evolving goal models. We worked on the merging of timed functions. In this project, all functions are step-wise atomic functions over disjoint neighboring intervals, where the atomic functions are constant, increase, decrease, and stochastic. Consider the functions in Figure 1, Model A is an increasing function over the interval [tA1, tA2) and Model B is a constant function over the interval [tB1, tB2). The purpose of our algorithm is to specify Model AB.

Specifying the resulting Model AB depends on the underlying timeline over which each model is defined. For example, in Figure 1, if tA2 < tB1 then there exists an unspecified gap in the function. If tA2 > tB1 then there exists an overlap in the function which may result in a conflict.
Finally, if tA2 = tB1 then the two functions align. In Figure 1, Model AB assumes the case where tA2 = tB1 with the new interval [tA1, tB2). We focused on the tA2 = tB1 case in this research project.

With this timeline, we investigated how the two functions should be merged. We found that Model A and Model B can be merged into either an increase function followed by a constant function, or an increase function with a single time point specified. We proved (by contradiction) the soundness of our assertion. We implemented the first case of the merge algorithm (tA2 = tB1). Future work will finish the implementation for the two other cases and create a web interface for the merge algorithm.
MackenzieLitz2020Michael Baressi, Biological Sciences - Biological SciencesBiologyJake Schnabl, Morgan Schwartz, Michael BarresiScreen Shot 2019-09-05 at 7.46.15 PM.pngCharacterizing the migration of cranial neural crest cells in the developing zebrafish forebrainThe complex zebrafish forebrain requires the coordination of many cell types during development in order to function. We have discovered a novel population of cranial neural crest cells (CNCCs) that migrate into the diencephalon around 16 hours post fertilization (hpf). Cranial neural crest cells have previously been shown to contribute to early craniofacial bone, cartilage, among other structures, but have never been found to re-enter the central nervous system (CNS). This summer I worked to quantitatively describe the new forebrain-contributing CNCCs’ migratory paths.
First, we collected a timelapse from 16hpf to 24hpf using confocal microscopy and a photoconvertible sox10 reporter line (sox10:NLS-eos) which fluorescently labels CNCCs. We then processed images using FIJI and MAMUT cell tracking software to manually trace migrating cells through time and 3D space. I then used Python to analyze the physical characteristics of the migrating CNCC tracks.
Through visual inspection, we noticed the presence of four path groupings: dorsal, ventral, posterior, and middle. I manually sorted cell tracks into each path, as shown in four colors imposed on a maximum intensity projection of a brightfield and sox10:NLS-eos (CNCCs in green) image of the final time point collected, figure 1A. Within these path groups, I set out to analyze characteristics of the migratory paths that could be unique from one-another, including speed throughout migration, persistence, and cell division rates of migrating cells.
I first plotted the speed of the CNCCs over time by path along with the smoothed average, figure 1B. Cells generally move faster at the beginning timepoints (1-60), and slow down once they have moved more anterior. In comparison, the middle and ventral path CNCCs move faster than the posterior and dorsal paths at timepoints 1-60 (avg speed dorsal: 3.42um/s, middle: 4.22um/s, ventral: 4.68um/s, posterior: 3.35um/s), and all cells slow to 1.5-2um/s average for timepoints 61-180. Additionally, I measured cell persistence as displacement/distance-traveled and compared between paths, figure 1C. A one-way ANOVA showed a significant difference in persistence between the posterior path, and the three more anterior paths. Finally, CNCCs in the dorsal path were only observed to divide once, while cells in the middle and ventral paths that divided, divided two or three times, figure 1D. Further analysis is needed to explore whether these quantitative descriptions are substantial and to understand the biological significance of the four migratory paths.
GiovannaNoe-Wilson2020Laura Katz, Biological Sciences - Biological SciencesBiology - surfme.pngCommunity diversity of Foraminifera over time and space and in response to temperature.Foraminifera are eukaryotic organisms that can be found in almost all aquatic environments, however, they are most abundant in marine conditions. They contain hard shells which have left behind an extensive fossil record. Thanks to these unique attributes of high abundance, wide distributions and extensive fossil record, foraminifera are great bioindicators of world ocean conditions (Franzo et al., 2019, Schratzberger & Ingels, 2018). Past studies of these eukaryotes and their distribution patterns were done using morphological features and characteristics, which can lead to inconsistencies and errors in taxonomy identification (Roberts et al., 2016 Pawlowski & Holzman 2007). The importance and use of GPS allows for more accurate data collection. Having an accurate location of where species are distributed and can be found helps create a baseline, so that future studies can be accurately done.

This summer my goal was to use molecular techniques based on DNA and RNA sequences to help identify foraminiferal species and their distribution patterns. I then processed samples collected from a salt marsh along the Connecticut coast. Collections were done with repetition of previously sampled sites using Fulcrum and ArcGIS. The samples collected were epi-benthic, meaning ~2 centimeters below the marsh surface. Sorting of the samples was done on site, using a fractionated filters that ranged in size from 2 um – 80 um. Sieving allows for sorting of the foraminiferal species according to their life stages (gametic to adult) and between the different species. Samples were then processed back in the lab using foraminifera specific primers to characterize a portion of rRNA and DNA from foraminifera so that they could be used for high-throughput sequencing. Analyses and mapping of the resulting data will be done this coming fall using bioinformatic tools and mapping software.

References:
Franzo, A., Asioli, A., Roscioli, C., Patrolecco, L., Bazzaro., M., Del Negro, P., Cibic, T. (2019). Influence of natural and anthropogenic disturbances on foraminifera and free-living nematodes in four lagoons of the Po delta system. Esturine, Coastal and Shelf Science (220)99-110.
Pawlowski, Jan, Holzmann, Maria., (2007). Diversity and geographic distribution of benthic foraminifera: a molecular perspective. Biodivers Conserv, 17:317-328.
Roberts, Angela., Austin, Williams., Evans, Katharine., Bird, Clare., Schweizer, Magali., Darling, Kate. (2016). PloS one, 11(7), e0158754.
Schratzberger, M., and Ingels, J. (2017). Meiofauna matters: the roles of meiofauna in benthic ecosystems. J. Exp. Mar. Biol. Ecol. 502, 12–25. doi: 10.1016/j.jembe.2017.01.007
MercedesWoolley2020Randy Frost, Psychology - PsychologyPsychologyMolly Eldevik '19, Becky Braverman '20-J - The Proust Phenomenon and Hoarding: The relationship between Autobiographical Memory and PossessionsThe Proust Phenomenon, named for the French writer Marcel Proust, is the sudden experience of a powerful memory. Intense memory flashbacks can be triggered by certain sensory experience (e.g. taste, odor, and sight) Many people with Hoarding problems describe a similar experience of memory recall and nostalgia at the sight of a cherished possession. This study examined the relationship between saving and acquiring behaviors and the frequency and intensity of memories associated with sensory experiences. It was found that those with more significant hoarding symptoms reported more Proust-like experience in regard to emotion and memory vividness when asked about their possession. This research was presented at the International OCD Foundation Conference in summer 2019. Projects like this inform my work in Exposure and Response Prevention Therapy (ERP) with patients who have hoarding disorder, as well as OCD, whom I saw while also doing this research. In addition to working on this project, we began preparing two studies for fall 2019, one on the role of an online course meant to increase willingness to engage in ERP and the other is a case study involving a trial of Deep Transcranial Magnetic Stimulation (TMS) for a patient with treatment resistant co-morbid OCD and Hoarding Disorder.
LucyGrant2022Jan Vriezen, Biological Sciences - Biological SciencesMicrobiology - CVAP3wMitC_80kv_40m_closeuppyocins (1) (2).pngThe Effect of Mitomycin on Production of Pyocins in BacteriaThe overarching goal of this experiment is to test if Mitomycin C has a significant effect on the production of bacteriocin-like products, particularly pyocins, in various bacteria. The twenty bacterial samples were grown on agar plates in 25 degrees Celsius for two days, and separated into two groups of liquid cultures, one inoculated with Mitomycin C and one without any presence of Mitomycin C. After seven days of incubation at 25 degrees Celsius with agitation, both samples were transferred to copper grids and observed under a transmission electron microscope for the presence of bacteriocin-like products. The positive control, CVAP #3, was overwhelmingly positive, as expected. The negative controls, E. coli, and S. epi were both negative. However, S. epi without Mitomycin C showed bacteriocin-like products under the microscope, while they showed none after introduction to Mitomycin C. It is likely that this has to do with the dosage, but it is unknown whether to increase or decrease the amount of Mitomycin C present in order to increase production. Of the twenty samples tested, six of the bacteria inoculated with Mitomycin C showed positive production of bacteriocin-like products. Four showed overwhelmingly increased production, while two showed only moderately increased production of bacteriocin-like products. Based on these results, we are able to ascertain that there is a correlation between Mitomycin C and the increased production of bacteriocin-like products in gram-negative bacteria. Further experimentation is needed to discern the novelty of this reaction.
JuliaRiccardi2020Nnmadi Pole, Psychology - PsychologyPsychologyLauren ForandoLab.png
Screen Shot 2019-09-05 at 7.34.16 PM.png
Evaluating Stress in Social Justice ConversationsConversations concerning social justice issues can be activators of stress. Such conversations have been associated with episodes of unrest on many campuses throughout the United States, including Smith College. The hypothalamus-pituitary-adrenal (HPA) axis modulates the mammalian endocrine stress response. The hormone cortisol is an often used measure of stress in both laboratory and field research. Salivary cortisol is a widely accepted choice for field research where more invasive measures such as blood and urine are not appropriate (Hellhammer, Wüst, & Kudielka, 2009; Dedovic, Duchesne, Andrews, Engert, & Pruessner, 2009). Heart rate variability (HRV) is the change of a heart’s interbeat interval over time. HRV is another marker of stress and stress regulation used in psychological research. Reduced HRV has been observed in psychiatric conditions such as posttraumatic stress disorder (PTSD) and anxiety disorders (Rajendra Acharya, Paul, Kannathal, Lim, & Suri, 2006; Verkuil, Brosschot, Tollenaar, Lane, Thayer, 2016).

The present study analyzes data from an ongoing study conducted by faculty at the Smith College School for Social Work. One aim of the study is to evaluate stress as an outcome of conversations regarding gender, politics, class, and race following varied group or individual training sessions. The study uses the Critical Conversations Model, a framework for change-inducing social justice dialogue where systems of oppression are evaluated through verbal reflection and analysis (Kang & O’Neill, 2018). In this study, heart rate variability and salivary cortisol were selected as the most appropriate, noninvasive, and effective measurement of stress. Heart rate data was collected utilizing a Polar V800 watch and corresponding H10 chest strap sensor. Heart rate was collected continuously throughout the social justice conversations. Saliva samples were obtained by synthetic swab before and after the social justice conversations.

Salivary cortisol was assayed using Salimetrics Elisa kits from the same lot for two semesters of participants. We are currently in the process of refining our collection method as the current collection container size slows assay procedure speed significantly. We are focusing efforts on elucidating whether or not the time samples are thawed before assay is affecting our results. Future work will include completing cortisol assays, analyzing HRV from the raw heart rate data, and evaluating differences in HRV and cortisol for participants in session and across sessions.

References
Dedovic, K., Duchesne, A., Andrews, J., Engert, V., & Pruessner, J. C. (2009). The brain and the stress axis: The neural correlates of cortisol regulation in response to stress. NeuroImage, 47(3), 864–871. doi: 10.1016/j.neuroimage.2009.05.074

Hellhammer, D. H., Wüst, S., & Kudielka, B. M. (2009). Salivary cortisol as a biomarker in stress research. Psychoneuroendocrinology, 34(2), 163–171. doi: 10.1016/j.psyneuen.2008.10.026

Kang, H.-K., & O’Neill, P. (2018). Teaching Note—Constructing Critical Conversations: A Model for Facilitating Classroom Dialogue for Critical Learning. Journal of Social Work Education, 54(1), 187–193. doi: 10.1080/10437797.2017.1341857

Rajendra Acharya, U., Paul Joseph, K., Kannathal, N., Lim, C. M., & Suri, J. S. (2006). Heart rate variability: a review. Medical & Biological Engineering & Computing, 44(12), 1031–1051. https://doi.org/10.1007/s11517-006-0119-0

Verkuil, B., Brosschot, J. F., Tollenaar, M. S., Lane, R. D., & Thayer, J. F. (2016). Prolonged Non-metabolic Heart Rate Variability Reduction as a Physiological Marker of Psychological Stress in Daily Life. Annals of Behavioral Medicine, 50(5), 704–714. doi: 10.1007/s12160-016-9795-7



Berry Williams2020Laura Katz, Biological SciencesRobin SleithBiological SciencesPlant microbiome - - Driving force behind the wide variation in SAR communities of the carnivorous pitcher plantPitcher plants are carnivorous plants, which typically grow in low nutrient environments such a fens and bogs. These herbaceous plants acquire nitrogen, phosphorus and other micronutrients from prey captured in the passive pitfall traps of their cone shaped leaves (2). The liquid that naturally collects in these leaves hosts diverse and complex inqiline ecosystems, consisting partially of microorganisms. The primary objective of this research study was to test if the highly diverse SAR communities within the locally isolated individual pitchers is driven by chance or outside factors.
I hypothesized that, as is true within isolated island communities, physical properties, degree of isolation and genetic drift may be the dominant influences shaping these microbial community compositions (1). Possible causes of heterogeneity we explored in this study were pitcher fluid pH and volume, pitcher size and sample site location. Our samples were collected from several New England sites: Hawley Bog, Harvard Forest, Orono Bog and Acadia National Park. Samples from these sites were collected from purple pitcher plants, Sarracenia purpurea. Additionally, we analyzed samples from several species of tropical pitcher plants growing in the Smith College greenhouses.
Each pitcher was sampled following the same set of steps and carefully documented throughout the process. Pitchers were measured, the biofilm within was swabbed and the fluid was collected. Samples were filtered of large debris and observed under a light microscope. The DNA and RNA was extracted, then PCRs and gel electrophoresis were run before sending samples for high throughput sequencing.
The majority of my summer SURF hours were spent collecting and preparing samples for genetic analysis. I plan to use this data in the coming semester to compare the individual communities within these ecological units to assess possible trends of similarities and differences of species richness and abundance. Preliminary results indicate that although species richness is fairly consistent across samples, the relative abundance varies widely. Further analysis will allow us to explore potential influences on individual SAR community compositions.

References
1. C. C. Witt. Why are diversity and endemism linked on islands? Museum of Vertebrate Zoology, 3101 Valley Life Sciences Bldg, Univ. of California, Berkeley, CA 94720-3160, USA (present address: Dept of Biology and Museum of Southwestern Biology, Univ. of New Mexico, Albuquerque, NM 87131, USA). ? S. Maliakal-Witt, Archbold Biological Station, 123 Main Drive, Venus, FL 33960, USA.19 February 2007.

2. Adlassnig, W., Peroutka, M., & Lendl, T. (2011). Traps of carnivorous pitcher plants as a habitat: composition of the fluid, biodiversity and mutualistic activities. Annals of botany, 107(2), 181–194. doi:10.1093/aob/mcq238
LaurenForando2021Non-Smith Advisor - PsychologyPsychologyJulia RiccardiLab.png
Screen Shot 2019-09-05 at 7.34.16 PM.png
Evaluating Stress in Social Justice ConversationsConversations concerning social justice issues can be activators of stress. Such conversations have been associated with episodes of unrest on many campuses throughout the United States, including Smith College. The hypothalamus-pituitary-adrenal (HPA) axis modulates the mammalian endocrine stress response. The hormone cortisol is an often used measure of stress in both laboratory and field research. Salivary cortisol is a widely accepted choice for field research where more invasive measures such as blood and urine are not appropriate (Hellhammer, Wüst, & Kudielka, 2009; Dedovic, Duchesne, Andrews, Engert, & Pruessner, 2009). Heart rate variability (HRV) is the change of a heart’s interbeat interval over time. HRV is another marker of stress and stress regulation used in psychological research. Reduced HRV has been observed in psychiatric conditions such as posttraumatic stress disorder (PTSD) and anxiety disorders (Rajendra Acharya, Paul, Kannathal, Lim, & Suri, 2006; Verkuil, Brosschot, Tollenaar, Lane, Thayer, 2016).
The present study analyzes data from an ongoing study conducted by faculty at the Smith College School for Social Work. One aim of the study is to evaluate stress as an outcome of conversations regarding gender, politics, class, and race following varied group or individual training sessions. The study uses the Critical Conversations Model, a framework for change-inducing social justice dialogue where systems of oppression are evaluated through verbal reflection and analysis (Kang & O’Neill, 2018). In this study, heart rate variability and salivary cortisol were selected as the most appropriate, noninvasive, and effective measurement of stress. Heart rate data was collected utilizing a Polar V800 watch and corresponding H10 chest strap sensor. Heart rate was collected continuously throughout the social justice conversations. Saliva samples were obtained by synthetic swab before and after the social justice conversations.
Salivary cortisol was assayed using Salimetrics Elisa kits from the same lot for two semesters of participants. We are currently in the process of refining our collection method as the current collection container size slows assay procedure speed significantly. We are focusing efforts on elucidating whether or not the time samples are thawed before assay is affecting our results. Future work will include completing cortisol assays, analyzing HRV from the raw heart rate data, and evaluating differences in HRV and cortisol for participants in session and across sessions.

References
Dedovic, K., Duchesne, A., Andrews, J., Engert, V., & Pruessner, J. C. (2009). The brain and the stress axis: The neural correlates of cortisol regulation in response to stress. NeuroImage, 47(3), 864–871. doi: 10.1016/j.neuroimage.2009.05.074
Hellhammer, D. H., Wüst, S., & Kudielka, B. M. (2009). Salivary cortisol as a biomarker in stress research. Psychoneuroendocrinology, 34(2), 163–171. doi: 10.1016/j.psyneuen.2008.10.026
Kang, H.-K., & O’Neill, P. (2018). Teaching Note—Constructing Critical Conversations: A Model for Facilitating Classroom Dialogue for Critical Learning. Journal of Social Work Education, 54(1), 187–193. doi: 10.1080/10437797.2017.1341857
Rajendra Acharya, U., Paul Joseph, K., Kannathal, N., Lim, C. M., & Suri, J. S. (2006). Heart rate variability: a review. Medical & Biological Engineering & Computing, 44(12), 1031–1051. https://doi.org/10.1007/s11517-006-0119-0
Verkuil, B., Brosschot, J. F., Tollenaar, M. S., Lane, R. D., & Thayer, J. F. (2016). Prolonged Non-metabolic Heart Rate Variability Reduction as a Physiological Marker of Psychological Stress in Daily Life. Annals of Behavioral Medicine, 50(5), 704–714. doi: 10.1007/s12160-016-9795-7
RanaGahwagy2022Kinuyo Kanamaru, Geosciences - GeosciencesGeoscience - Rana_gahwagy_1.png
Rana_gahwagy_2.png
Trees as Archives for Climatic and Anthropogenic Suppressants in Western MassachusettsTrees form annual growth bands as they grow, but can they tell us more than the tree’s age? We hypothesized that trees act as a living archive of past climate and can help us to monitor present environmental conditions. We wanted to understand how different trees respond to various environmental suppressants by comparing the growth pattern against chemical elements intensities, local weather station data, mercury (Hg) concentration, and power plant generated electricity. A sample of each of Acer rubrum (Red Maple), Quercus rubra (Red Oak), and Pinus ponderosa (Ponderosa Pine) was taken near Mount Tom Power Plant in Massachusetts. I-trax core scanner was used to acquire the elemental composition of each year and we looked mostly at heavy metal and other pollutants. Hydra C was also used on the Red Oak and Ponderosa Pine samples to quantify Hg concentration year by year. Interestingly, The pine tree retained a much higher concentration peaked around 8 ng/g in 1972 and declined thereafter, while the oak sample peaked around 3 ng/g in 1965 and decreased afterward. However, in 2010, the red oak Hg levels increased and almost matched the pine tree concentration up until 2017. The sudden increase in the red oak located less than a kilometer away from the power plant coincides with its high demand in 2009. This suggests that trees do respond to chemical suppressants. More analysis is needed on Red Oaks and Ponderosa Pines of varying distances to the power plant to understand the relationship between tree response in relation to locality and species with pollutants and other suppressants as well as the season of growth.
ChrissharaRobinson2020Laura Katz, Biological SciencesRobin SleithBiological SciencesBiology - - Temporal changes in pitcher plant protist communityNepenthes is a family of carnivorous plants that grow pitcher-shaped leaves that fill with water and serve as pitfall traps for various insects and small organisms. Common belief is that the fluid inside of closed pitchers is “sterile” and has antimicrobial properties. For this project I am monitoring changes in microbial community structure and diversity over time, with a focus on protists within the SAR clade. If closed pitcher fluid is inhospitable to microbial life, then older, open pitchers should have a more diverse SAR community than younger, newly opened pitchers. Samples were collected from the same two pitchers, one initially closed and one open, from each of three species of tropical pitcher plant (N. maxima, N. truncata, N. x balfouriana hybrid) in the Smith College Greenhouse (Northampton, MA). DNA and RNA were extracted from filters. The gels for newly opened pitchers had medium bands suggesting that they have at least a small SAR community.
CaitlinTimmons2022Laura Katz, Biological Sciences - Biological SciencesEvolution + Genetics - CTimmons_Fig1.png
CTimmons_Fig2.png
Exploring 'aging' nuclei in the uncultivable ciliate LoxodesLoxodes is an uncultivable ciliate and a member of the understudied class Karyorelictea. Like all ciliates, it is characterized by nuclear dimorphism—the separation of germline and somatic DNA within a single cell. Each Loxodes cell has two macronuclei, which house its somatic DNA, and two micronuclei, which house its germline DNA. A feature unique to the class Karyorelictea is that their macronuclei do not divide when the cell undergoes division. During asexual division in Loxodes, both macronuclei from the parent cell are inherited by two daughter cells, and a new macronucleus develops in each daughter cell from a micronucleus. As a result, each daughter cell possesses one ‘old’ macronucleus and one ‘new’ macronucleus. Based on these age differences, we hypothesize that there is a difference in DNA content between the macronuclei of a single Loxodes cell. To investigate this question, Loxodes cells were hand-picked out of water samples from Hawley Bog and their nuclei were stained with DAPI, a blue fluorescent stain that binds to DNA. Developing a nuclear staining protocol for Loxodes was non-trivial, as the cells are uncultivable, fragile, and difficult to permeabilize. After a successful protocol was implemented, fluorescent microscopy was performed on the ciliates using a laser-scanning confocal microscope. Z-stacks of each cell were processed with the image quantification software ImageJ to measure the amount of fluorescence from each macronucleus, and the difference in fluorescence between the macronuclei in each cell. Thus far the macronuclei of every cell display a difference in fluorescence. Eventually we will be able to use the amount of fluorescence in a nucleus to calculate the amount of DNA it possesses. Our next steps are to perform nuclear stains on cells with known genome sizes to provide points of comparison for our measurements, and continue gathering data on Loxodes nuclei.

Carla Schwartz2020Laura Katz, Biological Sciences - Biological SciencesBiologyN/AC.Schwartz Abstract Picture .pngExamining animal associated foraminifera across space and time Foraminifera are unicellular eukaryotes with network-like pseudopods and amoeba-like tests (Pawlowski, 2003). They are found in a variety of environments, including freshwater and saltwater, and are important because they can be used as bioindicators of environmental changes and pollution. There has been evidence that foraminifera can act as parasites, living on the shells of other aquatic organisms and using the calcium carbonate to build up their own shells. This intriguing hypothesis was built upon this summer. Two trips were made to Madison, Connecticut, a coastal town, to collect foraminifera. To successfully collect foraminifera, the outsides of shells were swabbed with a sterile q-tip approximately 20 times (shells could range from clams and oysters to crab shells). The q-tips were then placed in a test tube with buffer to help with preservation, and taken back to the lab. A separate experiment at Smith College also focused on testing the hypothesis that foraminifera are living on the shells of other organisms. Sterile clam and snail shells were purchased, placed in mesh bags, and put in the two fishtanks in Burton Hall. One snail shell and one clam shell were swabbed once a week, in addition to the sides of the tanks. This experiment was meant to compare free living foraminifera to animal associated foraminifera. Another aspect of this project was to explore the difference in foraminiferal abundance and diversity in each of the two tanks. One tank is filtered regularly, meaning that the community composition of foraminifera in that tank may vary from the community composition in the other tank. Finally, the foraminifera on the ‘fake’ or purchased shells could be compared with the foraminifera on real shells found at the bottom of the tank. In the lab, the DNA and RNA were extracted from the samples and PCR (Polymerase Chain Reaction) was performed on the extracted genetic material using specific foraminiferal primers.
Preliminary results show that foraminifera are both present (DNA) and active (RNA) on the shells swabbed in Madison, Connecticut, and on the shells in the two fish tanks in Burton Hall. Further analysis needs to be done to determine how community compositions vary across environments. Bioinformatics work in the future will be vital in gaining more information about the foraminifera present on the shells.
RubyWu2020Elizabeth Jamieson, Chemistry and Biochemistry - ChemistryChemistryMilagros De Pasquale ‘20, Laurie Brutus ‘20RW MD LB Join Surf abstract 2019.pngInvestigation of the Spiroiminodihydantoin Lesion’s Structural and Dynamic Effects on an 11-mer Deoxyribonucleotide DuplexGuanine, which has the lowest redox potential of nucleobases, is easily oxidized by reactive oxygen species (ROS) produced exo- and endogenously through environmental pollutants or cellular metabolic processes. Hyper-oxidation of this base produces the spiroiminodihydantoin (Sp) lesion which leads to cell death and cancer if left unrepaired (Wenke et al., 2013) (Fig. 1, 2). Nuclear Magnetic Resonance Spectroscopy (NMR) is a technique that examines the way the Sp lesion may potentially change the structure of DNA. It can also be used to measure the rate of exchange of nucleobase imino protons with water, which can provide information on the dynamic properties of the DNA helix. Differences in the base-pair breathing of the control versus lesioned helix can help determine how base excision repair (BER) glycosylases function to recognize the lesion for insertion of the proper base (Crenshaw et al., 2011).
This summer, base pair opening kinetics were investigated by titrating ammonium chloride base into an 11-mer control DNA in order to ensure exchange during base pair opening. The exchange rates (kex) of the imino protons were measured through magnetization transfer with surrounding water, and the rate constants obtained were graphed against increasing base concentration (Fig. 3, 4). From this linear relationship, we hope to extract the rate of base pair opening (kop) for each imino proton and compare it with values obtained from titration experiments on DNA with both stereoisomers of the Sp lesion. Differences in base pair kinetics between the control and Sp duplexes can provide insight into the dynamic effect the lesion may have on DNA. In the future, we plan to perform kinetic titration studies on both stereoisomers of the Sp lesion to evaluate any possible differences in the damage done to the helical structure.


Wenke, B.B.; Huiting, L.N.; Frankel, E.B.; Lane, B.F.; Nunez, M.E. Base Pair Opening in a Deoxynucleotide Duplex Containing a cis-syn Thymine Cyclobutane Dimer Lesion. Biochemistry 2013, 52, 9275−9285

Crenshaw, C. M.; Wade, J. E.; Arthanari, H.; Frueh, D.; Lane, B. F.; Núñez, M. E. Hidden in Plain Sight: Subtle Effects of the 8-Oxoguanine Lesion on the Structure, Dynamics, and Thermodynamics of a 15-Base-Pair Oligodeoxynucleotide Duplex. Biochemistry 2011, 50 (39), 8463–8477.
McKaylaFord2020Steven Williams, Biological Sciences - Biological Sciencesbiological sciencesSophie Chertock - Characterization of the Binding of a Putative Brugia Malayi POU-homeodomain Transcription Factor and its Cognate PromoterNeglected tropical diseases are endemic to developing countries andare understudied despite their impact. One such disease, Lymphatic Filariasis, also known as elephantiasis, causes inflammation of the lymphatic system and may lead to swelling of body parts, disability, and pain. It threatens more than 886 million people in 52 countries, and is economically and medically devastating (1). Mosquito-borne parasitic helminths, specifically Brugia malayi, Brugia pahangi, and Wuchereria bancrofti, are transmitted into the bloodstream during blood meals and disrupt lymphatic system functionality, causing the disease.. While mass drug administration in the affected countries has slowed, and in some cases stopped, the spread of the disease, it brings drawbacks such as increased drug resistance and does not treat already existing infections, only prevent new ones. Therefore alternate therapies are needed.

Previously, the SAW lab determined through comparative genomics that UNC-86, a neuronal POU-domain transcription factor, would be a suitable protein to study as a drug target for Brugia malayi. We successfully produced the protein in the pMAL expression system and amplified the DNA sequence where it binds, the mec-3 promoter. However, we were unable to conclusively prove UNC-86/mec-3 binding due to difficulties with the traditional chemiluminescent electrophoretic mobility shift assay (EMSA) protocol.

We redesigned primers essential to producing the Unc-86 binding sites, and optimized said primers. During this process, we discovered contamination in our reagents and refined our workflow to minimize the chance of repeating the mistake. With the DNA produced by those primers, we performed protein/DNA binding assays, using a new optimized variant EMSA. With this new EMSA protocol, we successfully proved the binding of UNC-86 to the mec-3 promoter at multiple binding sites. Additionally, we further purified our UNC-86 protein using an anion exchange chromatography protocol, which will allow more accurate downstream studies using our protein.

One of the downstream studies we plan to perform in the fall is chromatin immunoprecipitation sequencing, or ChIP-Seq. This is a genome-wide protein DNA binding assay that will allow exploration of the UNC-86/mec-3 neuronal interactome, by determining the exact locations of UNC-86 binding. This will give our group experience in bioinformatics and genomics, and will indicate how essential of a role UNC-86 plays in the neuronal interactome, which is essential to understand if UNC-86 is further developed as a drug target.

1. WHO: Lymphatic filariasis. 2019. https://www.who.int/news-room/fact-sheets/detail/lymphatic-filariasis (Accessed August 27, 2019)
LizzettePerez Perez2019Steven Williams, Biological Sciences - Biological SciencesSTEMJessica R grant, Susan Haynes, Kevin M Shea, Steven A Williams - Anti-filarial Activity of Natural Neurolenin D and Synthetic Neurolenin DerivativesLymphatic filariasis (LF) is a common vector-borne disease in many regions of the tropics and is one of the leading cause of permanent and long-term disability worldwide. Current drugs used to treat LF are given annually for about five to ten years due to poor activity in killing adult nematodes. However, because of the prolonged administration, therapeutic resistance to current antihelminthics has become increasingly important. Therefore, there is a need to develop novel, safe and short course micro- and macrofilaricide treatments that can help accelerate the elimination and eradication of LF. Our work has focused on studying the bioactivity of natural sesquiterpene lactones, isolated from the plant Neurolaena lobata, and synthetic analogs, against the lymphatic filarial parasite B. pahangi. These analogs were created by modification of the neurolenin scaffold including esterification at the reactive secondary alcohol position. The bioactivity of natural neurolenin and the synthetic analogs was measured in vitro against male and female adult parasites by adding one dose (3 µg/mL) of the respective drug and then monitoring parasites' loss of motility as the read-out over a period of 100 hours. Interestingly, the activity of the sesquiterpene lactones varies between male and female parasites, indicating the presence of some mechanism resulting in gender selectivity. The basis of the bioactivity of neurolenin B, one of the germacranolide sesquiterpene lactones from N. lobata to exhibit a strong activity against the motility of adult worms, was studied using RNA-Seq analysis. In this study, we analyzed the global gene expression profile of B. pahangi by comparing drug-treated and untreated female adult nematodes in a time series transcriptome analysis. Studying the effect of neurolenin B on the transcriptome will provide us with insight into the molecular target and mechanism of action of the compound in killing adult worms. These results will provide further useful information on the impact of sesquiterpene lactones as promising alternatives for the treatment of LF and perhaps other diseases caused by parasitic nematodes.
StormLewis2021Camille Washington-Ombre, Environmental Science and Policy - Environmental Science and PolicyES&P (Environmental Justice) - Environmental Justice in Morocco Based on the increasing threat of climate change, communities across the Middle-East and North Africa are faced with extreme challenges related to agricultural production. In response, researchers and policy makers are implementing community-based initiatives to increase North Africa’s adaptive capacity to changing climates. This study investigated the potential for community-based adaptation in Morocco. In particular, this research focused on the role of women-led local rural organizations (LROs) within the Middle Atlas of Morocco in the development of sustainable responses to drought. By working with women-led LROs, we can empower stakeholders to carry out resilient initiatives that prepare their communities for the threat of changing climates. Using a participatory action-based approach, Professor Washington Ottombre collaborated with women-led cooperatives and farmers to explore climate related issues affecting local communities. Through a combination of interviews and tours of irrigation systems, we evaluated the strengths and weaknesses of both cooperatives and irrigation systems throughout the Middle Atlas. In an effort to give back to our partner organizations, we taught English courses at the community center in Azrou. This project not only sheds light on the administrative and environmental challenges faced when operating a cooperative, but also documented conflicts for farmers related to common pool resource management. This preliminary research serves as a foundation for future work with the Fulbright Program and/or the American Institute for Maghrib Studies. In turn, this research will inform the country’s necessity for community-based efforts to increase Morocco’s adaptive capacity to climate change.
ChaseRyan-Embry2022Virginia Hayssen, Biological Sciences - Biological SciencesBiology - crocuta plate.pngOrganization and Identification of Smith College’s Vertebrate Holdings, Assistance on Research on the Spotted Hyena, Crocuta crocuta, and Data Organization for The American Society of MammalogistsThe Department of Biological Sciences at Smith College possesses a large collection of preserved vertebrates. This collection is intended for use as a teaching collection, allowing students to have a close-up or hands on experience with vertebrates that may not be commonly seen in the area. Some of the specimens in the collection were collected as early as the late 1800’s. Due to the extensive and long-standing nature of this collection, in recent years both the labeling, as well as the organization, had fallen into disarray.

I used my knowledge of morphology, and online databases of various species, in order to identify unknown specimens, or verify previously existing labels. I worked to create a labelling system for the collection. Each specimen was identified, to the most detail possible, and a label stating this taxonomic information was attached to the jar. These jars were then organized taxonomically in the shelves, and a database of the specimens in this collection, to allow for ease of use for teachers and students, was created. The rest of the vertebrate biology laboratory was also organized and cleaned. I was assisted on this project by another Smith student, Andie Rawson.

I also worked with Professor Hayssen to assist in her research on the spotted hyena, Crocuta crocuta. Specifically, this was to assist with her writing a Mammalian Species Account on the spotted hyena. I worked to find and order various sources, edit bibliographies, and organize morphological data, and create, and edit figures (see figure attached). In addition, I organized data on committee members in the American Society of Mammalogists to assist with choosing a member to be honored with the Jackson Award for their years of service.
YuhuiDu2020Kate Queeney, Chemistry - ChemistryChemistry - - Tuning Hydrophobicity and Wettability of Si(100) Surfaces via Hydrosilylation of AlkenesBiofilms are organized bacterial communities that are held together by their own extracellular matrix.1 They have been playing important roles in both beneficial and deleterious interactions such as symbiosis and bacterial infections.2 Because biofilms may affect the way that macroscopic organisms attach to the surfaces differently,3 it is important to understand the intricacies of the interactions between surfaces, biofilms and macroscopic organisms. Although there has been a lot of dedication to studying the characteristics of biofilms, the early stages of the attachment of bacteria to surfaces are not well understood. Silicon, a commonly used material due to its abundance, has many applications such as electronics, sensors, and biological devices because of their versatility and compatibility.4 It is also commonly used as a substrate for studies of biological species because of its stability.

The Queeney Lab has paid special attention to bacterial interactions with silicon surfaces with different surface nanotopography and surface chemistry. They were able to systematically and independently change these two variables in order to differentiate their effects on biofilm nucleation.5 However, on a smaller scale, they were not able to distinguish the effects of surface charge and hydrophobicity due to their use of negatively charged hydroxyl groups as their hydrophilic surfaces in contrast to the neutrally charged alkyl groups as their hydrophobic surfaces.5 Expansion of the surface chemistry library could allow us to isolate these effects and to eventually better understand the mechanisms for complex bacterial interactions.

The goals of this project are to generate reproducible hydrophilic, neutrally charged surfaces on silicon substrates, and to potentially tune their functionality to fit specific applications. The major approach is hydrosilylation of alkenes on Si(100), which forms very stable and densely packed alkyl monolayers by forming stable Si-C covalent bonds. This approach could produce sophisticated surface chemistry with defined structures that are resistant to side reactions in a biological environment.4 More specifically, there has been an increasing interest in hydrosilylation of molecules that have carboxylic acid end groups on Si(100) surfaces because they can be easily modified with other chemicals in order to control their hydrophobicity and surface charge. Therefore, we aim to expand the silicon surface monolayer chemistry through hydrosilylation carboxy-terminated alkenes on Si(100) and eventually to be able to tailor the monolayers.

Bibliography:
Gennari, O.; Marchesano, V.; Rega, R.; Mecozzi, L.; Nazzaro, F.; Fratianni, F.; Coppola, R.; Masucci, L.; Mazzon, E.; Bramanti, A.; et al. Pyroelectric Effect Enables Simple and Rapid Evaluation of Biofilm Formation. ACS Applied Materials & Interfaces2018, 10(18), 15467–15476. https://doi.org/10.1021/acsami.8b02815.
Hobley, L.; Harkins, C.; MacPhee, C. E.; Stanley-Wall, N. R. Giving Structure to the Biofilm Matrix: An Overview of Individual Strategies and Emerging Common Themes. FEMS Microbiology Reviews2015, 39(5), 649–669. https://doi.org/10.1093/femsre/fuv015.
Zobell, C. E.; Allen, E. C. The Significance of Marine Bacteria in the Fouling of Submerged Surfaces. J. Bacteriol.1935, 29(3), 239–251.
Dietrich, P.; Michalik, F.; Schmidt, R.; Gahl, C.; Mao, G.; Breusing, M.; Raschke, M. B.; Priewisch, B.; Elsässer, T.; Mendelsohn, R.; et al. An Anchoring Strategy for Photoswitchable Biosensor Technology: Azobenzene-Modified SAMs on Si(111). Applied Physics A2008, 93(2), 285–292. https://doi.org/10.1007/s00339-008-4828-0.
Zhang, J.; Huang, J.; Say, C.; Dorit, R. L.; Queeney, K. T. Deconvoluting the Effects of Surface Chemistry and Nanoscale Topography: Pseudomonas Aeruginosa Biofilm Nucleation on Si-Based Substrates. Journal of Colloid and Interface Science 2018, 519, 203–213. https://doi.org/10.1016/j.jcis.2018.02.068.
XinyuChu2020Benita Jackson, Psychology - Psychologyhealth psychology Veronica Pickard, Virginia Cafferky, Clio Dinan & Benita Jackson - Literature Review of Division of Domestic Labor Among Married Wife-Husband Couples: Implications for Well-BeingMarried couples must negotiate the division of domestic work, the perceived fairness of which shapes individual and relational wellbeing. Examining how couples collaborate on housework, or fail to, provides important insight into gender roles, interpersonal power and status, and overall happiness both within and outside marriages. A systematic review of 48 empirical studies on married individuals and couples suggests that when this division is perceived as unequal, relationships and individual psychological outcomes suffer. Overall, we found that wives compared to husbands generally complete more household chores. Gender roles and ideologies appears to mediate how fair actors perceive the division of domestic work. For example, wives with traditional homemaking roles perceive the division of labor as fair even if they perform the majority of domestic work. Conversely, wives with egalitarian gender ideologies engage in less housework regardless of their husbands’ ideologies. Status, such as socioeconomic status,
education level, and power within the marriage appear to be key determinants of perceived fairness. Most findings suggested that when wives earn or work less than their male counterparts, they are more likely to perceive the division of labor as unfair. Increases in education level and income for wives were minimally associated with changes in the actual amount of time spent on housework, with varying implications for perceived fairness. Even if the wife has a higher status, gender role ideology prevails when it comes to the division of household labor. Relationship satisfaction also influences the perception of fairness in the division of domestic work. Despite gender and status, when a marriage partner is happier with their relationship, that person is more likely to perceive the division of housework as fair regardless of how equal it is by more objective measures. Conversely, individuals who report unequal support, psychological distress,
or relationship dissatisfaction are more likely to perceive the division of domestic labor as unfair.Overall, this review revealed consistency in findings across a variety of populations, methods, and measuresstudies. Still, these findings warrant qualification. Many of the studies in this review used secondary data. Therefore, researchers did not have control over method. Most studies reviewed relied on participant self-reporting, which creates concerns of response bias and potential misunderstandings of the questions being asked. As with any qualitative review, we cannot quantify the consistency of findings, which can be for future research. Additionally, most participants were American, White, and middle-class; this homogeneity raises concerns about the generalizability of this work.
SydneyAbraham2021Camille Washington-Ombre, Environmental Science and Policy - Environmental Science and PolicyEnvironmental Science and Policy - IMG_20190624_123316.pngEnvironmental Justice in Morocco Morocco, like many agriculture-dependent economies in North Africa and the Middle East, is considered highly vulnerable to the effects of climate change. Water scarcity in particular is projected to highly impact the livelihood of farmers, food accessibility, and the economies of rural regions.

This research aims to identify how communities come together, organize, and distribute resources in the face of a hardship such as water scarcity caused by climate change. This research also seeks to examine what adaptations, if any, would be beneficial to address hardships caused by climate change, how these adaptations should be implemented, and what support would be necessary for them to be successful. All of this is being examined with a specific focus on gender and women’s cooperatives in rural regions in Morocco.

The research conducted over the course of this summer did not yield any conclusive results, as this is part of an ongoing study. However, the participatory research conducted did help to shape the trajectory of this project and will prove a solid foundation. Research methods utilized included interviews with stakeholders, participatory activities with community members, introduction to technology such as irrigation schemes, mapping, and reviewing scholarly sources prior to the trip.




Image caption: An irrigation scheme near Azrou, Morocco. Farmers who utilize these canals commit to only using a certain amount of water as to ensure that all farmers have access to water.
Nadia PenkoffLidbeck2021Michael Baressi, Biological Sciences - NeuroscienceNeuroscienceJake Schnabl, Mackenzie Litz, Michael Barresi - Cranial neural crest contributes to larval CNS develop,net We challenge the canonical model of zebrafish forebrain development and propose that cranial neural crest cells (NCCs) break convention by re-entering the central nervous system (CNS) where we demonstrate they are a required cell type for normal forebrain development. We exploit the conserved process of vertebrate forebrain development in the zebrafish model system to uncover the presence of neural crest cells developing in concert with the forebrain commissures. Emerging from midbrain near the dorsal neural tube, we propose that these cells not only exhibit the proliferative and migratory qualities typically attributed to NCC, but that many branching paths of migrating NCC indicate multiple cell divisions, supporting that this is an active population of neural stem cells even during migration. Using lineage tracing techniques and live cell tracking with a sox10:nls-eos line to distinguish possible NCC from myelinating glial cells, we show NCCs break convention by re-entering the CNS, showing an exciting broad range of potential cell fates, much like other hox negative NCC described in other parts of the peripheral nervous system (PNS). The deficiency of NCC in a tfap2a/2c LOF mutant contributes to significant deformation of forebrain development, highlighting their importance: these same NCCs then contribute to forebrain neuronal populations and are required to position and maintain separation between the forebrain commissures. We show that these cells are positive for the neuronal marker HuC/D and olig2, as well as the broader sox10 label from the sox10:nls-eos line revealing these cells to be sox10 positive in proximity to the dorsal neural tube, consistent with the canonical definition of cranial NCCs. Ultimately, by unraveling the coordinated efforts of migrating neural crest, neural progenitors, and glial cells that construct the relatively simple zebrafish forebrain, we can provide insight into potentially conserved mechanisms underlying brain development. Funded by the NSF.
EleanorDonaher2020Katherine Kinnaird, Statistical and Data Sciences - Computer ScienceAligned Heirarchies - Aligned Hierarchies Python PackageThe goal of this research was to take existing MATLAB code and reprogram it to Python to be more compatible with other Google research. The code itself underwent multiple steps analyzing musical data to isolate repeated patterns found within, furthering the goal of reproducing "original" music. Main challenges involved restructuring the code to better suit the strengths of the language, and redesigning the overall format of the program to better represent its eventual utility as a library.
AnnaFreund2020Alexandra Strom, Chemistry - ChemistryOrganometallic Ligand Design - AF Synthesizing Functional Ligands.pngSynthesizing Functional LigandsThe scope of this project is to create a functional ligand that aids in the catalyst turnover and reduces product inhibition, two problems that occur when catalytically functionalizing arenes. Pharmaceuticals and agrochemicals are interesting in the products produced by functional arenes because of the products common structure.

Literature conditions to create the desired ligand were used as inspiration for the attempted reaction. By opening the strained cyclohexene oxide with reactive sodium cyclopentadienide, the product would have produced a desired charged compound that would be neutralized with methyl iodide in a second step (Figure 1). After a number of trial reactions, it was discovered that the reaction never took place. It is hypothesized that the reaction was too dilute with solvent for the reactants to react with each other. To increase the likelihood of the reactant reacting, cyclopentadienyllithium was used instead sodium cyclopentadienide.

Eventually the addition of the methyl was done without quenching in between in an attempt to understand what was occurring in the reaction. Through GCMS it was discovered that in both the lithium and sodium cyclopentatdiene reactions, the cyclohexene oxide would attack other oxides, polymerizing 3-4 times before the cyclopentadiene would add, along with other side products (Figure 2). The ratio of cyclopentadiene to oxide, the length of time of which the oxide was added to the reaction, and the temperature of the reaction were all changing in order to observe any differences. Regardless of the changes the oxide would polymerize.

Since the desired cyclohexene ligand could not be created, a pyridine ligand was identified as an alternative target (Figure 3). The pyridine ligand required that the chloromethyl pyridine hydrochloride become a free base for the cyclopentatdienyllithium to react and form the desired ligand. Literature conditions were followed and adapted in order to obtain the desired ligand. It was shown that heating the reaction helped the synthesis of product. Column chromatography was used to purify and isolate the product. 1H NMR confirmed the synthesis of the pyridine product.
XufenLiu2020Jesse Bellemare, Biological Sciences - Biological SciencesEcology - SURF.pngBiogeography and phylogeography of Jeffersonia diphylla populations in the eastern United StatesThe Last Glacial Maximum (~18,000 years ago) profoundly influenced the geographical distribution of plant and animal species, as well as the genetic diversity within species. Despite many 1000s of years of migration and range expansion, some of these patterns might persist down to the present. In particular, it is expected that higher levels of species diversity and genetic diversity, including unique or rare genotypes, will be concentrated in southern areas (former glacial refugia), while northern areas are less diverse. For this study, I worked on Twinleaf (Jeffersonia diphylla), a forest understory species distributed across the eastern U.S. Because the species’ seeds are normally dispersed only short disances via ants, it is possible that the effects of past range contractions due to glaciation still influence the geographic distribution of its genetic diversity. I hypothesized that there would be higher genetic diversity and more phylogenetically-distinct lineages in the southern parts of its native range in Georgia, Alabama, and Tennessee, compared to northern areas, like Minnesota, Michigan, and New York. By assessing the genetic diversity of and reconstructing the phylogenetic relationship among the populations of Jeffersonia diphylla across the country, I tested this hypothesis to better understand the historical processes that might have shaped the modern distribution pattern and genetic diversity of this species.

Sequences of the trnL gene and trnL-trnF intergenic spacer, which is a chloroplast DNA marker, were developed from leaf samples collected from populations across the species’ distribution range in the eastern US. With an expanded sample size from the last year’s work, I detected several distinct chloroplast DNA haplotypes. As predicted, most of the haplotype diversity was present in extreme southern populations near the species range edge in Georgia and Alabama, while the mid-range and northern populations were all genetically identical at the cpDNA marker tested. This suggests that populations in parts of Georgia and Alabama have been distinct and isolated from populations in the remainder of the species’ geographic range since at least the late Pleistocene, and possibly longer given the relatively low rate of mutation expected in these cpDNA sequence regions. The pattern also suggests that these distinctive populations might be of significant conservation value in terms of overall genetic diversity in the species, given their long-term independent evolution. In the light of impending climate change, which is likely to negatively affect these southern populations first, efforts should be made to better understand diversity in these southern areas. Meanwhile, Sanger sequencing was found not to be applicable for the psbA gene and psbA-trnH intergenic spacer for this species, as the sequence contains long repetitive units of a single nucleotide which produce signals that disturb the machine’s ability to read other signals afterwards.
DeniseNava2021Katherine Kinnaird, Statistical and Data Sciences - Computer ScienceComputer ScienceNo co-authors. Please note the image I attached is Kinnaird's Aligned Hierarchies work we were using and referencing when creating the python package.dnava.pngAligned HierarchiesDuring this summer, we created a Python package that reinvented existing Matlab code for Aligned Hierarchies, a representation of musical scores. The Aligned Hierarchies for a given music-based data stream is the collection of all possible hierarchical structure decompositions, aligned on a common time axis. Our goal was to write Python programs that achieved the same goal as in Matlab, however, we had to do this in a cautious manner in order to avoid direct translation between these two different programming languages. During this process we also discovered it would be more effective to use modules to divide the various functions based on their similarities. These are the duties of following modules: transforming, assembling, searching, and utilities for converting music-based data streams into the final product – Aligned Hierarchies.

Throughout the entire project, we created various examples to not only test our programs, but also test our understanding of the Aligned Hierarchies. These examples typically involved converting a small song pattern to numbers (in order for the computer to process it) and depending on the task, as determined by the module they were placed into, the inputs of these functions varied. For example, for a function in the transform module, one of the responsibilities would be to identify and rearrange the numbers accordingly to where the patterns occur in the song. This rearrangement of numbers occurs inside the function, and each function produces and contributes a distinct output that in end is used to create the final product.

In conclusion, one of the most challenging aspects of this project was to combine all the scripts written by different people, and it was here where we realized we must take a step back to develop the plan to effectively debug everything to ensure that all function calls are properly working.
UmaGaffney2020David Gorin, Chemistry - ChemistryOrganic Chemistry - - Oxidative Cross-Coupling Methylation of N-containing Heterocyclic PhenolsThe O-methylation of phenols creates methoxy group that is useful in many syntheses. This motif is found in a number of natural products, including the flavor compound vanillin and several important chemotherapy drugs. However, the process typically used to methylate phenols uses potentially toxic electrophilic reagents such as diazomethane or iodomethane. Because the alcohol of a phenol is nucleophilic, traditionally an electrophilic reagent must be used to create a reaction. However, the Gorin lab has experimented with a method of oxidative cross-coupling that uses two a nucleophilic source of methyl, a copper catalyst, and an oxidizer instead of the dangerous electrophilic methyl sources. This methodology was first successfully attempted with carboxylic acids, then applied to phenols. The Gorin lab has had substantial success using methylboronic acid as a source of methyl when methylating a variety of phenols, and has achieved some very high yields. However, only one phenol previously tried contained nitrogen. Due to the importance of several nitrogen-containing phenols, a project was undertaken to attempt to methylate a number of N-containing heterocyclic phenols. The methodology for each substrate was to use the optimized reaction conditions with a 0.300 catalyst equivalency at 50 degrees Celsius. If thin-layer chromatography and 1H NMR showed that no significant amount of product had formed, the reaction was retried with a 1.00 catalyst equivalency at 75 degrees Celsius. If TLC and NMR showed significant product had formed, the product was isolated using column chromatography and massed to determine yield. Unfortunately, of the nine substrates attempted, product was only successfully isolated for one. The methylation of 7-hydroxy-3,4-dihydro-2(1H)-quinolinone produced a 54% product yield that was confirmed with 13C and 1H NMR. For the other substrates, in several cases no product at all was found, while in other cases four or more products were formed which made it impossible to isolate the desired product. These results suggest that this methylation method is not necessarily ideal for N-containing heterocyclic phenols. The next stage to this project is to consider the methylation of other alcoholic compounds using oxidative cross-coupling.
DinahNahid2019Steven Williams, Biological Sciences - Biological SciencesParasitology - - Assessing the effect of Neurolenin B on Brugia pahangi after short-term exposure and what this could mean for the treatment of Lymphatic filariasisLymphatic filariasis is a tropical disease caused by parasitic nematodes that infect hundreds of millions of people worldwide. Improved drugs are needed that can effectively kill these parasites in the human host. In collaboration with the Shea lab, the Williams lab has tested various sesquiterpene lactones derived from a compound called Neurolenin D on a filarial nematode called Brugia pahangi. Although this nematode does not infect humans, it is biologically similar to one that does: Brugia malayi. The most promising of these compounds is called Neurolenin B, which has undergone further testing of its toxicity and mutagenicity. A next step in studying this compound was to determine whether exposure to the compound for a shorter period of time had an effect on the mortality of the parasites. If the drug is effective against the parasites in a short timeframe, it is likely that a continuous dose of the drug would not be required.
This summer, my focus was on assessing the effect of Neurolenin B on the mortality and motility of Brugia pahangi worms after 24- and 48-hours of exposure. This study had a total of four trials, two of which involved incubating the parasites with Neurolenin B for 24 hours and two for 48 hours before removal of drugged media for drugless media. For each culture, we received approximately 30 male and 30 female worms. They were washed to remove any impurities from shipping and plated in a culture media fluid made in lab. Each male and female set of worms was sorted into its own six-well plate so that there were approximately five worms per well. After plating, four wells of worms in each plate were given Neurolenin B, one was given Levamisole as a positive control, and one well was given 70% ethanol as a negative control.
The Neurolenin B containing wells in the first and second cultures incubated with the drug for 24 hours exhibited a significant effect on the parasites, but none reached 100% mortality. Their motility, however, was significantly affected and is suggestive of a trajectory approaching 100%, hence the increase of the drug incubation time to 48 hours. The two cultures done with a 48-hour drug incubation exhibited 100% mortality in the wells containing Neurolenin B at approximately 60 hours post-drug removal. Based on these results, it is probable that Neurolenin B would not have to be administered continuously for treatment.

YutongLiu2022Gary Felder, Physics - PhysicsPhysics - 3)7[QJ5@NPN8]JCC_}MFX_1.pngA programming work on locating oscillons in the modeling universeThis project aimed at modeling the inflation period of the early universe using a simplified model: two fields with energy and a slight initial fluctuation oscillating and interacting with one another. This project is based on C programming and the data are produced and visualized by Mathematica. For the first few weeks of this summer, I concentrated on learning C language and understanding the existed codes from professor Felder and other researchers before me.

It was noticed through previous trials that abnormal phenomena, one or more energy bumps are observed in some of the trials, which are called oscillons. The energy bumps locate on one field, and at that point, the other field has nearly zero energy. Our goal at this stage is to understand its behavior. This summer, my work concentrated on locating oscillons. On the energy graph drew with Mathematica, an energy bump is pretty easy to locate for human eyes: it is just a bump, except it disappears sometimes during oscillation. But writing code to automatically find it will save time and may give a more precise conclusion than our naked eye. So I tried to figure out an algorithm that can look for a bump in a noisy background. Variance is a measurement of how far apart a set of data spread out, so the variance around the bump should be very high. But as mentioned earlier, those bumps appear on an oscillating field, so they had peaks and troughs, and sometimes they are as flat and noisy as everywhere else. So I looked at the other field, which gives almost all of its energy to the first field when a bump appears. If the codes could find a region of field where the variance is low and the actual value (mean) also approaches zero. I finished the code and professor Felder helped me with debugging. Then to find how small is small enough, I tested the limit by using data from other’s (Chitose and Meghadeepa) work, then I found that the variance that is 0.03 times of the variance of the entire field is a perfect diameter for locating all points on an oscillon.
AnnaTenerowicz2021Laura Katz, Biological Sciences - Biological SciencesEvolutionary Microbiology - - Preliminary exploration of viruses in protists Viruses are difficult to define for many reasons. Viral genomes evolve very quickly and there is no one sequence that is present in all viral genomes, making their evolutionary history difficult to determine. Since their origin is debated, whether or not they came before or after LUCA is also up for debate. For these reasons their presence in genome sequences can be used to elucidate the evolutionary history of protists.
This summer I looked for NCLDV (NucleoCytoplasmic Large DNA Virus) capsid protein sequences in the genome sequences of protists, mostly ciliates and amoeba. To create the genome sequences that were analyzed, protists were isolated from various water samples and PCR (Polymerase Chain Reaction), WGAs (Whole Transcriptome Amplification), and Sanger sequencing were carried out.
To search for viral sequences within the protist genomes we aligned NCLDV capsid protein sequences (524) against one ciliate or amoeba genome using BLAST (Basic Local Alignment Search Tool). Viral genomes have many novel ORFs (Open Reading Frames) making them difficult to compare to available sequence databases, such as BLAST. The protist genome sequences that best aligned to the NCLDV capsid protein sequences were further analyzed using DFast and BLASTx.
This preliminary analysis revealed that there are many potential viral sequences within the protist genome data that we produced. Even when found at a low percent identity, this could be significant due to the rate at which viruses evolve.
MarissaMeadows-McDonnell2022Danielle Ignace, Biological Sciences - Biological SciencesBiology - ecological imperialism.pngRethinking InvasivesIn my high school environmental science class, my teacher instructed us to create ‘Most Wanted’ posters for particularly notorious invasive species prevalent in the area. Words such as ‘dangerous,’ ‘beware,’ and ‘wanted dead or alive’ decorated my and many others’ posters. Although I wasn’t aware of it at the time, looking back at this experience is what sparked my interest in the subject of invasive species--specifically how invaded societies perceive them. Thus, this summer I completed a research project that dealt as much with sociology and history as biology;I focused on the terminology and debate surrounding the eradication of invasive species and its larger parallels with science communication. Invasive species, as it turns out, are key players in the debate on climate change through the acceptance or fight against ‘novel ecosystems,’ and the tenets of environmentalism, biology, and conservation. Some invasion biologists (Simberloff and Vitule, 2014) charge invasive species as serious threats to ecosystem health and adopt an attitude that invasives are guilty until proven innocent. Simberloff and Vitule (2014) also assert that relying on an invasive species’ impact (as opposed to origin) to dictate management policies will only result in unforeseen degradation of natural environments. Thus, terms such as ‘invasional meltdown,’ and ‘alien’ are apt when referring to invasive species--as they correctly embody the real dangers they pose to the environment. Other academic however, maintain that such terminology reeks of xenophobia and only heightens the policing of national borders -- however ecologically arbitrary such borders might be (Pollan, 1994, Comaroff et. al, 2001). From a historical lens, the debate does not become any less complex. While some environmental historians detail the United States’ storied history with invasive species in the early 20th century and reveal the parallels of ecological nativism and [regular] nativism (Pauly, 1996), others declare that invasive species are not immigrants, but remnants of colonialism (Crosby, 1986, Mastnak et. al, 2014) and thus should be eradicated.

In order to understand the nuances of the debate, I consulted experts in different fields--including plant ecologists, an anthropologist, and the director of the Lyman Botanic Gardens. My work included meeting weekly with Professor Ignace, recording podcasts, and constructing a broad literature review that mapped the key ideological turning points in the debate over the past thirty years. I constructed a timeline mapping when and how the debate surrounding invasion biology evolved in the literature. Additionally, I am consulting with Michelle Jackson, a PhD student at UMass Amherst, about writing a publishable manuscript that would join both historical and biological perspectives to create a new set of terminology and acknowledge the history of xenophobia and colonialism within the discipline. Ultimately, I’ve discovered that invasive species embody important questions that transcend the field of invasion biology; questions about nativeness, belonging, and the enforcement of ecological borders in an increasingly globalized yet nativist world.




Works Cited:

Comaroff, J., Comaroff, J.L., (2001). Naturing the nation: aliens, apocalypse, and the
postcolonial state. Social Identities, 7:2, pp. 233-265. Retrieved from:
10.1080/13504630120065301

Crosby, A.W. 2004. Ecological Imperialism: The Biological Expansion of Europe, 900-1900.2nd edition. Cambridge ; New York: Cambridge University Press.

Mastnak, T., et. al., (2014). Botanical decolonization: rethinking native plants.
Environment and Planning D: Society and Space 2014, Volume 32, pp. 363 – 380.
Retrieved from: https://journals.sagepub.com/doi/pdf/10.1068/d13006p

Pauly, P., (1996). The beauty and menace of the Japanese cherry trees: conflicting visions of American ecological independence. Isis, Vol. 87, No. 1, pp. 51-73. Retrieved from: https://www.jstor.org/stable/235734

Pollan, M. (1994). Against Nativism. The New York Times, May 15, 1994, Section 6, pp. 52. Retrieved from: https://www.nytimes.com/1994/05/15/magazine/against-nativism.html?auth=login-email&login=email

Simberloff, D., Vitule, J., (2014). “A Call for an End to Calls for the End of Invasion Biology.” Oikos 123 (4):pp. 408–13. Retrieved from: https://doi.org/10.1111/j.1600-0706.2013.01228.x.

ZoeyZagoria2020David Bickar, Chemistry - ChemistryNeurochemistry - Z. Zagoria Dansyl Dopamine Scheme.pngDetermination of Salivary Dopamine Levels as a Potential Biomarker for Parkinson's DiseaseParkinson’s disease, or PD, is a neurodegenerative disorder affecting a significant part of the American population over 65. Presently, over 1 million people in the US suffer from PD, and millions more worldwide.[1] Because the symptoms of PD mimic those of other diseases and there is no definitive diagnostic test, making a PD diagnosis before the final clinical phase is difficult. Presently, the best diagnostic method is to screen for several potential biomarkers. By the time PD has progressed to its clinical phase and is unambiguously diagnosable, 30-50% of dopaminergic neurons, the neurons that produce dopamine in the central nervous system, have been lost.[3] Finding reliable biomarkers for early PD would permit a confident diagnosis before the disease progresses into its clinical phase, thereby allowing disease-modifying treatments to be developed.[1] In this study, saliva samples, obtained from participants over the age of 65 both with and without PD, were examined to determine if their dopamine concentration, quantified by mass spectrometry, could be used as a potential biomarker for PD. Several problems needed to be addressed to make this approach viable. To determine the full measure of dopamine production, it is necessary to measure both the concentration of dopamine and its metabolites. Additionally, several of these molecules are unstable; this combined with their relatively small size and polarity makes them difficult to separate and identify by mass spectrometry. To address these issues we developed a procedure, based on existing studies, to chemically modify these compounds using dansyl chloride (DNS). Dansyl chloride binds to dopamine and its metabolites (Figure 1) to produce compounds that are larger, more stable, and much more amenable to separation and identification by mass spectrometry. The study is still ongoing.
EsezaKironde2020Lisa Mangiamele, Biological Sciences - Biological SciencesAndrogenic modulation of multimodal display structure in the Bornean rock frog - Eseza figure1.png
Eseza figure2.png
Androgens modulate dynamic changes in multimodal display structure in the Bornean rock frogSignaling is an important way by which animals send a message across to another individual of their own species. In the natural environment, it plays a role in processes such as reproductive isolation, speciation, and character displacement (1-7).
The Mangiamele lab studies the role of a recently-evolved signaling behavior, called “foot-flagging,” in the Bornean rock frog, Staurois parvus. Foot flagging is a gesture that males perform by extending their hind limb and rotating it backwards in an arc (8-9). We know that foot-flagging has emerged because vocalization is not an effective communication signal in the noisy habitat in which these frogs live (10-11). The lab hypothesizes that foot-flagging is androgen-dependent and has coevolved with increased androgen sensitivity in the thigh muscles that control extension, rotation, and retraction of the hind-limb (12,13). This idea is rooted in work demonstrating that androgens mediate sexual signaling in frogs (14-16). But, what is not clear is how a new signal is incorporated into an existing signaling repertoire and whether recently-evolved signals are mediated by similar hormones as ancestral signals
This summer, I worked on a project that investigated these questions. I watched videos of social interactions between two male S. parvus and one female and recorded the behavior of a focal male during aggressive bouts. A bout was defined as a period of short intense activity that was initiated by either a foot-flag or a call. The treatment groups were 1) saline, 2) testosterone, and 3) testosterone + flutamide, an androgen-receptor blocker.
In each group, I observed four main behaviors surrounding foot-flags and calls: upright postures, contact, vocal-sac inflation and foot-flashing. I then used R Studio (17) to create kinematic diagram that mapped the frequency of each behavior (circle diameter) as well as significant transitions between two behaviors (arrows) (Fig. 1). I found that flutamide influences display dynamics in S. parvus by decreasing the occurrences of specific behaviors, as well as the complexity of the entire kinematic diagram. I also discovered that there were more incidences of behavioral repetition with the flutamide group.





Fig 1. Significant transitions between behaviors produced by frogs in the vehicle group (left) and Flutamide-treated group (right) are represented in this kinematic diagram. The circumference of each vertex corresponds to the number of times this behavior was observed. Each arrow width and color represents a transitional probability and the probabilities are grouped into 5 categories. The significance of the behaviors were determined by a permutation test.

In addition, to test whether the frequency of individual behaviors differed between between the testosterone and flutamide-treated frogs, I created box-plots and performed t-tests and zero-inflation tests. Our results showed that there was a statistically significant difference between the number of bouts, in both treatment groups. Additionally, the p-values of all behaviors were significant, apart from “contact”. Overall, this indicates that when flutamide is introduced as an androgen receptor blocker, it decreases the number of bouts occurring. It also decreases the number of upright postures and vocal sac inflations, whilst decreasing the number of calls that occur.




Fig 2. Number of upright postures, contacts, foot-flags, foot-flashes, calls and vocal sac inflations, as well as distributions for the number of bouts, number of behavioral displays and bout lengths by treatment group. Box-and-whiskers show the minimum, maximum, interquartile range and the median number of times each behavior happened.


References

1. Wells, K. D. 1977a. The courtship of frogs. pp. 233-262. In D. H. Taylor, and S. I. Guttman (eds.), The Reproductive Biology of Amphibians. Plenum Publishing.

2. Wells, K. D. 1977b. The sodal behaviour of anuran amphibians. Animal Behaviour 25:666-693.

3. Wells, K. D. 1988. The effect of social interactions on anuran vocal behavior. Pp. 433-454. In B. Fritzsch, M.]. Ryan, W. Wilczynski, T. E. Hetherington, and w. Walkowiak (eds), The Evolution of the Amphibian Auditory System. John Wiley and Sons, New York.

4. Rand, A. S. 1988. An overview of anuran acoustic communication. Pp. 415-431. In B. FritZsch, M.J. Ryan, W. Wilczynski, T. E. Hetherington, and W. Walkowiak (eds), The Evolution of the Amphibian Auditory System. John Wiley and Sons, New York.

5. Gerhardt, H. c., and J.J. Schwartz. 1995. Interspecific interactions and species recognition. pp. 603-632. In H. Heatwole, and B. K. Sullivan (eds.), Amphibian Biology. Vol. 2. Social Behaviour. Surrey Beatty and Sons, Chipping Norton, Australia.

6. Halliday, T. Rand M. Tejedo. 1995. Intrasexual selection and alternative mating behaviour. pp. 419-468. In H. Heatwole, and B. K. Sullivan (eds.), Amphibian Biology. Vol. 2. Social behaviour. Surrey Beatty and Sons, Chipping Norton, Australia.

7. Sullivan, B. K., M.J. Ryan, and P. A. Verrell. 1995. Female choice and mating system structure. pp. 469-517. In H. Heatwole, and B. K. Sullivan (eds.), Amphibian Biology. Vol. 2. Social Behaviour. Surrey Beatty and Sons, Chipping Norton, Australia.

8. Grafe TU, et al. (2012) Multimodal communication in a noisy environment: A case study of the Bornean rock frog Staurois parvus. PLoS One 7(5):e37965.

9. Hödl W, Amézquita A (2001) Visual signaling in anuran amphibians. Anuran Communication, ed Ryan MJ (Smithsonian, Washington, DC).

10. Endler, J. A. 1992. Signals, signal conditions, atid the direction of evolution. American Naturalist 139: S125-S153.

11. Alcock, J. 1998. Animal Behavior. Sinauer Associates, Sunderland, MA.

12. Prikryl T, Aerts P, Havelková P, Herrel A, Rocek Z (2009) Pelvic and thigh musculature ˇ
in frogs (Anura) and origin of anuran jumping locomotion. J Anat 214(1):100–139.

13. Mangiamele, L.A., Fuxjager, M. J., Schuppe, E.R., Taylor, R.S., Hödl, W., Preininger (2016) Increased androgenic sensitivity in the hind limb muscular system marks the evolution of a derived gestural display. PNAS 113 (20): 5664-5669.

14. Kelley DB (2002) Hormonal regulation of motor output in amphibians: Xenopus laevis
vocalizations as a model system. Hormones, Brain, and Behavior, eds Pfaff DW,
Arnold AP, Etgen AM, Fahrbach SE (Academic, Amsterdam), Vol 2, pp 445–468.

15. Wada M, Wingfield JC, Gorbman A (1976) Correlation between blood level of an-
drogens and sexual behavior in male leopard frogs, Rana pipiens. Gen Comp Endocrinol 29(1):72–77.

16. Wetzel DM, Kelley DB (1983) Androgen and gonadotropin effects on male mate calls
in South African clawed frogs, Xenopus laevis. Horm Behav 17(4):388–404.

17. Fuxjager MJ, Barske J, Du S, Day LB, Schlinger BA (2012) Androgens regulate gene expression in avian skeletal muscles. PLoS One 7(12):e51482.
JaweriaShah2022Michael Baressi, Biological Sciences - Biological SciencesZebrafish Embryonic Development - - Cranial Neural Crest Cell Migration is Necessary for the Formation of the ForebrainEarly nervous development is one of the first systems to begin in embryonic development. Yet, it has such a large role in how we behave and grow even after we are born. In zebrafish, we seek to understand how each component of this process can affect their development, specifically neural crest cells in the forebrain.
Neural crest cells migrate from the dorsal neural tube, and function as multipotent stem cells that differentiate into a variety of peripheral cell types; such as cartilage in the head and pigment sensory neurons throughout the body. Specifically in early embryonic development, before hemispheres of the brain are formed, neural crest cells aid in the formation of commissures. The post optic commissure (POC) and the anterior commissure (AC) are areas where crossover of neural cells happen before hemispheres are created. We tend to see the cell types that arise from neural crest cells aid in the creation of these commissures which then allow for the guidance and growth of axons in order for communication to occur on both sides of the nervous system. The long standing theory of neural crest migration has been that they emigrate from the central nervous system into the peripheral body never to return to the brain or spinal cord again. However, we propose that a small subset of the anterior most cranial neural crest cells may serve to support forebrain commissure development in the brain. We purport that these CNCC immigrate back into the brain at the location of presumptive commissure locations. We show that they differentiate into neurons as verified by immunocytochemistry (ICC) with HuC/D labeling among others. We also imaged embryos on the Leica Confocal Microscope in order to collect time lapses of these cells, and afterwards, processed those images in Fiji, a version of ImageJ, to analyze the migration of these cells in order to see if there was any pattern in their movement. We concluded that this population of cells that re-enter the CNS are necessary for proper forebrain development. The loss of CNCCs led to disruptions in the forebrain including reductions in neurons, and disruptions in the formation of commissures. Our work suggests that CNCCs may play more direct roles on brain development than ever thought before.
AlexandraDomeshek2021David Gorin, Chemistry - ChemistryChemistry - - Stabilization of the Cholic Acid-Umbelliferone EsterThe Gorin lab works to synthesize DNA small molecule catalysts (DCats) in order to selectively catalyze common reactions in complex systems. Up to this point the lab has shown that a DNA aptamer— which is to a say single stranded piece of DNA that folds on itself such that it is binds a target substrate with high affinity—when loaded with a small molecule catalyst, is able to hydrolyze a model substrate at 100 times the rate of free floating catalyst. In order to continue with this line of research and eventually introduce this method of catalysis into more complex, and ultimatley biological, systems, it is necessary to stabilize our model cholic acid-umbelliferone substrate. The molecule, upon which the we have been testing the DCat, is inherently unstable due to the resonance stabilization of the negative charge that results from the first step of hydrolysis. Stabilizing the molecule would not only allow us to demonstrate that the DCat is responsible for all measurable hydrolysis, but it is also imperative as we move into biological systems that we are using a model substrate that is stable in buffer conditions.
My work this summer, then, was to synthesize a stabilized form of the cholic acid-umbelliferone ester and measure its background hydrolysis in standard buffer conditions, as well as its catalyzed hydrolysis in the presence of the lab’s most effective DCat to determine the reactivity and viability of this new substrate. The goal molecule was an acyloxymethyl ester which would eliminate the resonance stabilization of the original molecule. After several weeks of syntheses a three step synthesis was successful in producing the desired molecule as confirmed via hydrogen NMR. I then ran a set of hydrolysis assays to determine the stability of this new molecule. I determined that this new molecule was more stable than the original model substrate and exhibited almost no background hydrolysis, but it also demonstrated little catalyzed hydrolysis under standard reaction conditions. At increased concentrations of catalyst, however, significant hydrolysis was noted which indicates that this new molecule could potentially still be useful. The next steps for this line of research involve testing the new substrate more thoroughly against the lab’s DCats, experimenting with attaching different nucleophiles to the DNA aptamer, as well as looking into other methods of stabilizing the original ester such that catalyzed hydrolysis is less difficult to induce.
RiyaoYan2020Maren Buck, Chemistry - ChemistryPolymer Chemistry - EY-I-28.pngSynthesis of pH-dependent photocaged PVDMA hydrogelsIn this study, the shape deformation upon induced swelling of poly(2-vinyl-4,4’-dimethylazlactone) (PVDMA) hydrogels were studied for the application of creating pH-responsive hydrogel actuators. PVDMA hydrogels crosslinked and functionalized with primary diamines were synthesized via photo-initiated ring opening reactions, and characterized by Infrared Spectroscopy and their swelling ratio.

10 % to 25 % Jeffamine-600 crosslinked PVDMA hydrogels were synthesized and then further hydrolyzed or functionalized with dimethyltheylenediamine (DMEDA) to introduce charged carboxylate or amine functional groups into the polymeric network, which causes different swelling behaviors in acidic or basic solutions because of the change in the hydrophobicity of the gels. IR showed complete hydrolysis and functionalization by ~40 min when the gels were immersed in 5 M H2O in DMSO solution (0.1 equiv DBU) and 0.1 M DMEDA in DMSO solution. Hydrolyzed and functionalized gels had opposite trends in swelling ratio in response to pH 3 to 10 solutions because of the opposite charges in the gel. The time required for the gel to reach swollen equilibrium in 0.1 M HCl or NaOH solutions varied from 15 min to 45 min. The reversibility of the pH-responsive swelling behaviors were examined and proved by switching the solvent pH from acidic to basic for a few times.

10 % to 25 % Jeffamine-600 crosslinked PVDMA hydrogels embedded with 65 % to 50 % photocaged hexamethylenediamine crosslinker were synthesized to study the factors (such as crosslinking percentage, gel thickness, functional group, irradiation time and irradiation power) that are related to the shape deformation of hydrogels. The gels were irradiated under the UV lamp at 365 nm wavelength and at 500 mW/cm2 power, which created a crosslinking density gradient through the hydrogel. IR showed that the top surface was more crosslinked than the bottom surface. After hydrolysis or functionalization, flat hydrogels rolled into tubes due to the difference in swelling ratio in the gel. Tube diameters and rolling behaviors were related to irradiation time.

25 % Jeffamine-600 crosslinked PVDMA hydrogels embedded with 50 % photocaged hexamethylenediamine crosslinker and 50 % (1 equiv excess) photocaged DEMEA functionalization groups were synthesized to create rolled gel tubes. The irradiation creates both a crosslinking and functionalization gradient through the gel, and the gels were further hydrolyzed to create opposite charge on the gel surfaces. The tubes were more stable and had more uniform diameter because of both the swelling gradient and the electrostatic attraction between the two surfaces.
YuhanShangguan2022Nicholas Howe, Computer Science - Computer ScienceComputer Science - - Handwritten Syriac Text RecognitionOff-line handwritten text recognition (HTR) systems convert images of handwriting into digital texts. While most of researches in this field deal with Latin and Chinese, studies involve HTR on Syriac context are comparatively rare and less advanced. We used methods based upon deep learning and applied Harald Scheidl’s HTR system to Syriac. The implementation depends on Numpy, CV2, and TensorFlow imports. It consists of five CNN layers, two RNN layers, and the CTC loss and decoding layer. We trained the neural network with approximately two thousand word images from Ceriani Veteris Genesis document. Then we employed data augmentation to improve recognition accuracy. Our results showed that 99% of the words from the Syriac Genesis dataset are correctly recognized by the neural networks; the character error rate for a hold-out test set is 0.173177%. The recognizer can produce transcript predictions for RGB images, gray-scale images, and binary images. We applied it to some other raw manuscripts, which have different handwriting styles, and manually corrected errors to get more training data. The current HTR implementation helps create an initial transcript for us to examine by hand and then we can use the corrected transcript to improve the system further, which will make it progressively easier to generate Syriac transcripts.
SakinaAli2021Sahar Ali Seesi, Computer Sciences - Computer ScienceComputer Science and Bioinformatics - Building a Revised and Updated U12 Spliceosomal Intron Database The project I worked on this summer is one to help create an updated and updatable U12-intron (coding sequences that are spliced by the minor U12-dependent spliceosome) database, which is tied to newer versions of genomes and transcriptomes [1]. Furthermore, this database should be more user-friendly to biologists with data that is downloadable in BED, GTF formats (along with others that are to be determined). Some other features of this database are to be maintainable (with admin access), having prediction tools, the functionality of creating manual entries, and allowing the database to be compatible/used in concurrence with Galaxy, an open source, web-based platform for data intensive biomedical research.

My research this summer consisted of first familiarizing myself with the biological and bioinformatic concepts involved in computationally analyzing U12 introns, investigating the pre-existing database, extracting its data, and starting the planning stages of building a new database. As this project was still in it's extremely early stages during the beginning of the summer, it was extremely important for the whole team to spend time understanding the complex biological mechanism of U12 introns [1]. We also examined the previous work done by the last group and completed a thorough interface analysis of the old database (U12DB) to determine points of weakness that we want to address in our research [2,3].

The next component of my work this summer comprised of extracting and then updating the data out of the old database, which housed outdated intron coordinates. This data will be used for the next phase of the project for training and testing our minor intron prediction algorithm. This task required multiple steps. First, the data was downloaded using mySQL tables as comma-delimited files [3]. The U12 intron coordinates and gene coordinates were converted to the most recent genome versions using UCSC Genome Browser’s LiftOver tool [4]. I am currently using these updated coordinates to annotate which exons in the file have boundaries with minor introns.

The next steps of this project are to finish this task, build a front-end of the database (in collaboration with a group at Quinnipiac University), populate the database, and design and implement PWM and grammar-based prediction algorithms.


Turunen, J.J., Niemela, E., Verma, B., Frilander, M. (2013). The significant other: splicing by the minor spliceosome. Wiley Interdisciplinary Reviews RNA, 4, 61-76. doi: 10.1002/wrna.1141.

Alioto, T.S. U12DB: a database of orthologous U12-type spliceosomal introns. Nucleic Acids Research 2006, doi: 10.1093/nar/gkl796

http://genome.crg.es/cgi-bin/u12db/u12db.cgi

https://genome.ucsc.edu/cgi-bin/hgLiftOver
EleanorMcCartney2020Mary Harrington, Neuroscience - NeuroscienceCircadian Biology, Neuroscience - - Comparing luciferin delivery methods and substrates in DBP:LUC liver expressing mice using in vivo bioluminescence The field of circadian biology has undergone significant technical advancements in the last two decades with the development of transgenic mice and in vivo imaging technology. However, there is still a need for developing less invasive methods that allow for the detection of circadian gene expression in animals operating on thier natural behavioral patterns. This project focuses on developing the least invasive, least expensive, and most robust method of measuring circadian gene expression in genetically modified mice.
DBP:LUC liver mice have had the gene that results in luciferase production inserted just after the DBP gene, a long-known, strongly circadian gene only in the liver. Using this animal model, the circadian expression of DBP can be observed using real-time, in vivo recording of bioluminescence from non-tethered, non-sedated animals. Freely moving mice are kept in light-tight boxes with photomultipliers (PMTs) that can detect the bioluminescence of the liver through the animal's skin. However, challenges remain to optimize the delivery of the substrate, luciferin, that reacts with luciferase to emit bioluminescence.
This summer, work was done to assess two different substrate delivery methods: the mini-osmotic pump and drinking water. While pumps offer the advantage of knowing the precise dose of luciferin mice get, pump implantation surgery is invasive and requires anesthesia which can alter overall circadian rhythms which may serve as a confounding factor. Drinking water offers the advantage of being less invasive but dosing is less precise and drinking patterns may drive the concentration of circulating luciferin and affect the detection of peak DBP expression.
Building off previous work that determined what concentration of luciferin mice can tolerate in their drinking water, a cross-over protocol was designed to compare drinking vs. pump delivery in a within and between subjects study. Additionally, synthetic luciferin, Cycluc, as compared to naturally derived firefly luciferin in pumps. Preliminary results suggest that both pump and drinking are effective ways of administering luciferase substrates. Data collection and analysis will continue into the fall to characterize each substrate delivery mode and substrate. The analysis will continue to focus on whether there is a significant shift in the phase of circadian gene expression driven by drinking patterns or not.
KettyMunyenyembe2020Laura Katz, Biological Sciences - Biological SciencesBiology - K.Munyenyembe_1.png
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Analyses of genome structures in testate amoebae (Arcellinida) using single-cell ‘omicsDespite all the incredible biodiversity that is dominated by microbial communities, much of it has not been explored. This is the case for eukaryotic microbes called testate amoebae (Arcellinida). Testate amoebae are eukaryotic microbes that build shells and are very sensitive to environmental changes (Mieczan 2008). Because of their sensitivity, these microbes can be used as potential bioindicators of environmental changes. Traditionally testate amoebae have been identified using morphology, but recently scientists have begun using molecular tools to explore their genetic diversity and phylogenetic relationships using the SSU and COI genes (Blandenier et al. 2017). Despite this, much remains unknown about the Arcellinida, including their genome structure, ploidy levels and life cycles. This summer my goal was to understand Arcellinda genomes and how specific genes are distributed in their genomes and use DAPI, a fluorescent dye that stains DNA and allows for nuclear visualization. To achieve this goal, genomic and transcriptomic data were used in a number of softwares. First, I used DFAST software that annotates sequences to identify the bacterial candidates that were present in our data. Secondly, I used Vizbin software, which groups similar sequences together and shows phylogenetic relationships based on sequence similarities, as well as centrifuge, a software that classifies short read sequences. Lastly, I did DAPI experiments to stain the Arcellinida nucleus, which has never been successfully done in previous studies. DAPI was very challenging and many experiments failed, but using novel methods, we believe our results show the stained nuclear structure of Arcellinida.
NaomiOstriker2021Laura Katz, Biological Sciences - Biological SciencesBiological Sciences (Evo mol bio) - Hyalosphenia.pngCharacterizing evolutionary relationships and mechanisms of shell-building in arcellinid testate amoebaeDespite their global distribution across multiple continents and important status as bioindicators, very little is known about the evolution and life cycle of the Arcellinida, an order of testate amoebae. These single-celled freshwater protists are characterized by their tests (shells) and lobose pseudopodia, and can range from as small as 10 μm to over 400 μm in length. Because the cellular machinery of testate amoebae is poorly understood, I aim to use transcriptomics to further probe the mechanism of shell-building in Arcellinida. To investigate this, prior literature was used to compile a library of candidate genes with the potential for expression during shell formation, especially genes related to adhesion. As many species of Arcellinida are uncultivable, fresh samples were obtained from local wetlands and examined by light microscopy to identify cells building new tests. These cells were picked and their transcriptomes were amplified and sequenced via high-throughput sequencing. Going forward, we will use bioinformatics and our library of candidate genes to identify arcellinid genes involved in test formation. Over the summer I also aimed to characterize species delineation and the evolutionary relationship between the amoebae Hyalosphenia elegans and Hyalosphenia papilio. To achieve this, individual H. elegans and H. papilio cells were picked, and their genomes were amplified. Custom Arcellinida-specific primers were used to amplify regions of SSU rDNA. These regions were then sequenced and hand-aligned to characterize visible differences in the population, including the presence of single nucleotide polymorphisms and other forms of genetic variation.
MatildaLaBranche2021Adam Hall, Biological Sciences - Biological SciencesNeuroscience - SURFML.pngAnesthetic Pharmacology General anesthetics were discovered over 170 years ago, however the precise mechanisms behind their function is still unknown. Studies have shown that many general anesthetics target GABAA receptors in the central nervous system. Using the CRISPR/cas9 system, the Hall Lab has generated a zebrafish line with KO mutations on the δ subunit of GABAA-R. The anesthetic sensitivity of these fish has been tested using a novel assay that quantifies sensitivity by measuring movement. Thus, it will be determined whether mutating a potential anesthetic target will alter anesthesia in vivo.
Cellular analysis of these mutant fish, however, has not yet been performed. This summer a spinal cord and cell culture procedure was developed to isolate neurons and glial cells. Although only Wildtype fish were used this summer, this procedure will eventually be used on the δ KO zebrafish to isolate cells that can be analyzed through electrophysiology. These experiments will further determine whether the δ subunit of GABAA-R is an important target for general anesthetic agents.

MaggiePrentice2021Christine White-Ziegler, Biological Sciences - Biological SciencesBiological SciencesGrace MooreGMoore_MPrentice_SURF.pngEnvironmental regulation of gene expression in pathogenic and commensal Escherichia coliEscherichia coli can sense a variety of cues found in the environments through which they transit and reside, like changes in pH, oxygen availability, and temperature. By studying how gene expression in E. coli changes in response to these signals, we can learn more about how bacteria adapt to changing environments, such as entry into a human host, and how this contributes to the bacteria’s pathogenicity. Previous work in the White-Ziegler lab has shown that temperature and pH cause genome-wide changes in expression and has identified certain pathways as being thermo- or pH-regulated. Pathways involving small regulatory RNAs’ (sRNAs) are influenced by many factors and determines the expression of certain genes post-transcriptionally. By overexpressing these sRNAs, we hoped to see corresponding genes over or under-expressed, reflecting the signaling pathways that these sRNAs impact.

To explore the effects of sRNAs on enteropathogenic E. coli (EPEC) gene expression, strains of EPEC containing plasmids with a sRNA under the control of an IPTG-inducible promoter were used. This methodology enabled investigation of the molecular and phenotypic response of the pathogen with the overexpression of select sRNAs. EPEC strains containing the sRNA RyhB and DsrA were grown at 23 ̊C and 37 ̊C. QRT-PCR analysis of extracted RNA revealed that while the sRNAs were being produced, there was not the expected overexpression between those grown with and without IPTG. To examine a phenotypic response to sRNA overexpression, cells containing the sRNAs ArcZ and DsrA were grown on swarm plates with and without IPTG at 23 ̊C and 37 ̊C to test the sRNA’s impact on motility. While there were significant differences, there was not the expected difference between cells with overexpressed sRNAs, as the cells with and without IPTG moved the same amount (Figure 1). We concluded that the IPTG induction was not working as expected but due to time constraints could not test possible theories such as incorrect concentrations of IPTG.

The project also included extracting and transferring plasmids containing sRNAs from the EPEC strains into a commensal K-12 strain. Using a boiling lysis protocol, all of the plasmids were successfully extracted and through electroporation, put into a non-pathogenic K-12 background, creating K-12 strains containing DsrA and RyhB. In the future, the remaining sRNA plasmids will be transformed into K-12 and uropathogenic E. coli (UPEC) and their effects tested.

Figure 1. Swarm plates created during the phenotypic experiment using IPTG induction of sRNAs, DsrA and ArcZ grown at 37˚C.
AvaGoga2020David Gorin, Chemistry - ChemistryBiochemistry - DCAT abstract.pngExpanding the Substrate Scope of DNA Catalysts The complexity of biological systems poses a challenge for site-selective chemistry. Using DNA as a molecular recognition domain, site-selective hydrolysis of a cholic acid-derived ester has been demonstrated. DNA-conjugated small molecule catalysts (DCats) have been shown to increase the rate hydrolysis of a target ester by >100-fold compared to equimolar untethered catalyst. To demonstrate that this construct can be tailored to a variety of substrates, a DCat construct targeting an adenosine ester has been developed. My work this summer sought to increase the rate of hydrolysis of the adenosine ester through increasing the nucleophilicity of the small molecule catalyst, attaching multiple catalytic domains, and altering the location of catalyst attachment on the DNA.
MoiraPitrat2020Alexandra Strom, Chemistry - ChemistryChemistry - Figure1.mpitrat.pngRuthenium Catalyst SynthesisAryl alkenes are difficult to functionalize and are commonly used in the agrochemical and pharmaceutical industry. By coordinating a cationic metal complex to an arene starting material, C – H bonds are able to become reactive which then allows the formation of C – C bonds. Ruthenium complexes have been shown to be effective as part of the metal ligand that is used in these types of reactions.

This project focuses on using Ruthenium to make and modify catalysts to be used in the catalytic cycle. Additionally, catalysts were deployed in the full reaction several times. The ruthenium catalyst was synthesized, as characterized by NMR spectroscopy. However, the full catalytic cycle was unsuccessful, as evidenced by a lack of desired product in the GCMS and NMR spectra. After repeating the reaction several times, and trying to vary the temperature, a different route was used and some electrophile screens were run in hopes of being able to make the desired product in a slightly different way which mainly meant by using the Ruthenium ligand as it came instead of trying to modify it first incase the modifications had caused the issues. The first set of screens showed that an impurity existed in the KHMDS which was in a solution of toluene. This impurity caused an unexpected side product to form. The second set of screens made using solid KHMDS were more promising.

Due to the high cost of Ruthenium reagents and the small scale that had been used, one of the starting materials for the catalyst reaction was also synthesized. This took pentamethylcyclopentadiene and Ruthenium(III)chloride which were then refluxed in methanol to give pentamethylcyclopentadiene Ruthenium(II)chloride (Figure 1).

Next steps would be to re-run the latest screen and try to run the catalytic cycle exactly as Takemoto et al. (1) to see if these results can be reproduced.

1. Takemoto, S.; Shibata, E.; Nakajima, M.; Yumoto, Y.; Shimamoto, M.; Matsuzaka, H. Journal of the American Chemical Society 2016, 138, 14836–14839.
Shengqi (Iris)Zhong2021Jill de Villiers, Psychology - PsychologyLanguage acquisition - szhong_pic.pngRefining Romani Language Assessment Test with Rasch AnalysisLanguage assessment is a critical tool to detect kids who fall behind in learning languages so that they can receive further intervention. The tests in English and other dominant European languages have been developed thoroughly, but assessments in other languages are still in progress. This summer, I was involved in revising a Romani language assessment test.

Roma families spread out in Eastern European countries where Romani is not the first language. The linguistic environment of Roma children often consists of at least two languages: a variation of Romani and the official language of the country they live in. However, school placement tests are in non-Romani languages, which Roma children might have not fully mastered at their age. Typically developing Roma children may be diagnosed with cognitive deficits and misplaced in special schools with poor education practices. It is necessary to identify only those children with actual language disorder, namely those who show delay in Romani.

The test consists of 9 blocks with 90 questions. Preliminary data were collected from 250 Romani-speaking children aged from 3 to 10 years old from 7 European countries. Our task was to remove the items that did not fit into a Rasch model. First, one block of the test was removed because the items were either too easy or too hard and therefore failed to differentiate kids with poor language abilities. A DIF analysis on gender was conducted to make sure no gender bias is introduced into the test. Three items that displayed significantly large differences between boys and girls were taken out. A person-item map, which allows comparing person ability and item difficulty on the same scale, was made in Winsteps. According to the map, the test was relatively easy since the person measure mean was higher than item measure mean. However, the test was discriminating, according to the overall statistics. The person map demonstrated a bell-shaped curve, with a majority of children around the mean and a few children on the high and low ends. We also created tentative norms to mark kids with potential language delays using z-scores split by age.

The test is the first Romani language assessment to our knowledge. As a result, the generalizability and validity of our test are unknown. We expect more samples in the future from more countries to test its applicability. Hopefully the assessment could help Roma children receive adequate education and better respect in their countries.
AmeliaOlsen2021Sara Pruss, Geosciences - GeosciencesEnvironmental Geosciences - Geochemical Profile of Orr Formation, House Range Section, Utah (A. E. Olsen)-1.png
Key for Geochemical Profile figure (A. E. Olsen)-1.png
Mercury Enrichments through the S.P.I.C.E. Event in the Orr FormationThe Steptoean Positive Isotopic Carbon Excursion (SPICE) occurred around 500,000,000 years ago. It marked the end of the Cambrian period, and the excursion of carbon isotopes has been explained as the effect of a mass extinction of marine fauna (Saltzman et al., 2000). The SPICE event is present and accepted in different formations around the world; from the Western United States to Scotland to Newfoundland. The global occurrence of this event implies that the extinction was a worldwide mass extinction, rather than a localized extinction event. In some sections the S.P.I.C.E. has been found to mark a period of unusually high mercury. Historically, the accepted understanding of high mercury excursions has been attributed to global volcanic activity. However, in the case of the S.P.I.C.E, no such event exists in the rock record. The presence of this mercury excursion could mean that the current understanding of mercury is incomplete and doesn't take into effect all possible causes, or, that there was major volcanic activity at the end of the Cambrian period that has not yet been recorded.

Initial fieldwork plans for Summer 2019 had focused on formations in Shingle Pass, Nevada. However, an invaluable lesson was taught when we arrived in Nevada to find our desired formations covered by snow; strong backup plans are just as important as the initial. Our fieldwork focused on the Orr formation in Utah, both in the House Range and the Lawson Cove Reservoir. Measurements and samples were taken at meter-scale for both sites. My analyses focused on the House Range section. Specific aim was made to collect samples through the John Wash and Candland at a high density so as to visualize the overlapping behavior of carbon isotopes and mercury during the S.P.I.C.E. found in this section by Saltzman et al. (1998).
Once returned to campus, samples were selected from five-meter scale for thin sectioning, to display specific facies as well as to ascertain species diversity throughout the formation. Every sample was cut and drilled for mercury and carbon isotopes, to avoid including diagenetic cements that could corrupt measurements. Carbon Isotope powders were sent to David Fike at Washington University for analysis. Mercury was measured on the Hydra IIC at Smith. Whole-rock samples were cut and powdered and then dissolved in HCl. These dissolutions will be used to measure TOC, as this research will continue in Spring 2020.

References:

Saltzman, M. R., Runnegar, B., & Lohmann, K. C. (1998). Carbon isotope stratigraphy
of Upper Cambrian (Steptoean Stage) sequences of the eastern Great Basin:
Record of a global oceanographic event. Geological Society of America Bulletin, v.
110, no. 3, p. 285–297.

Saltzman, M. R., Ripperdan, R. L., Brasier, M.D., Lohmann, Kyger C., Robison, R. A.,
Chang, W.T., Peng, S., Ergaliev, E.K., and Runnegar, B., 2000. A global carbon
isotope excursion (SPICE) during the Late Cambrian: relation to trilobite
extinctions, organic-matter burial and sea level. Palaeogeography,
Palaeoclimatology, Palaeoecology, v. 162, no. 321, p. 211–223.

YanwanZhu2021Jill de Villiers, Psychology - PsychologyLinguistics, Psychology - yzhu pic 1.png
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Child language and parental speech: A structural equation modeling approachMuch research has been done on the relationship between a child’s word development and parental speech, such as the famous “30 million word gap” (Hart & Risley 1995). However, it is still in dispute how parental utterances impact children’s language development. In the present study, structural equation models are built to investigate the relationship between a child’s early vocabulary, performance on shared attention tasks, and vocabulary diversity of mother utterance over time.

The present study is based on data from a longitudinal project on children’s language and literacy development, and 141 children are involved. Each child was tested twice on selected tasks, and the second testing was usually several months after the first testing. Each time, the child’s age, vocabulary score (measured by EOWPVT-R) and performance on shared attention tasks were recorded. The vocabulary diversity of maternal speech is measured by vocd. There was a play session for each child and their mother, and the mother’s utterances were transcribed and converted into a CHAT file. Then, the CLAN program was used to obtain the vocd measure of each transcript.

Three structural equation models were examined. Model 1 and Model 2 correspond to testings at Time 1 and Time 2, and Model 3 represents the change in measures over time. Several regression analyses were also conducted to help build the best model. At both Time 1 and Time 2, children’s performance on shared attention tasks and vocd measure of maternal speech are significant predictors of children’s vocabulary score, after accounting for children’s age. As shown by Model 3, the impact of vocabulary diversity of mother utterances on children’s word development persists in the long run.

The models confirm that the quality of parental speech has an effect on children’s vocabulary development. In the future, variables reflecting children’s grammar competence or other language-related abilities can be included in the model to achieve more comprehensive understandings of the relationship between child language and parental speech.

Reference:
Hart, B., & Risley, T. R. (1995). Meaningful differences in the everyday experience of young American children. Baltimore: Brookes.
GraceMoore2020Christine White-Ziegler, Biological Sciences - Biological SciencesMolecular/MicrobiologyMaggie PrenticeGMoore_SURF.pngEnvironmental regulation of gene expression in pathogenic and commensal Escherichia coliEscherichia coli can sense a variety of cues found in the environments through which they transit and reside, like changes in pH, oxygen availability, and temperature. By studying how gene expression in E. coli changes in response to these signals, we can learn more about how bacteria adapt to changing environments, such as entry into a human host, and how this contributes to the bacteria’s pathogenicity. Previous work in the White-Ziegler lab has shown that temperature and pH cause genome-wide changes in expression and has identified certain pathways as being thermo- or pH-regulated. Pathways involving small regulatory RNAs’ (sRNAs) are influenced by many factors and determines the expression of certain genes post-transcriptionally. By overexpressing these sRNAs, we hoped to see corresponding genes over or under-expressed, reflecting the signaling pathways that these sRNAs impact.
To explore the effects of sRNAs on enteropathogenic E. coli (EPEC) gene expression, strains of EPEC containing plasmids with a sRNA under the control of an IPTG-inducible promoter were used. This methodology enabled investigation of the molecular and phenotypic response of the pathogen with the overexpression of select sRNAs. EPEC strains containing the sRNA RyhB and DsrA were grown at 23 ̊C and 37 ̊C. QRT-PCR analysis of extracted RNA revealed that while the sRNAs were being produced, there was not the expected overexpression between those grown with and without IPTG. To examine a phenotypic response to sRNA overexpression, cells containing the sRNAs ArcZ and DsrA were grown on swarm plates with and without IPTG at 23 ̊C and 37 ̊C to test the sRNA’s impact on motility. While there were significant differences, there was not the expected difference between cells with overexpressed sRNAs, as the cells with and without IPTG moved the same amount (Figure 1). We concluded that the IPTG induction was not working as expected but due to time constraints could not test possible theories such as incorrect concentrations of IPTG.
The project also included extracting and transferring plasmids containing sRNAs from the EPEC strains into a commensal K-12 strain. Using a boiling lysis protocol, all of the plasmids were successfully extracted and through electroporation, put into a non-pathogenic K-12 background, creating K-12 strains containing DsrA and RyhB. In the future, the remaining sRNA plasmids will be transformed into K-12 and uropathogenic E. coli (UPEC) and their effects tested.

Figure 1. Swarm plates of phenotypic experiment using IPTG induction of sRNAs.
AdenaCollens2021Laura Katz, Biological Sciences - Biological SciencesGenetics, Microscopy - Screenshot (113).pngSearching for bacterial symbionts in uncultivable ciliatesSymbiotic relationships between eukaryotes and bacteria are found in almost every ecosystem on Earth. Most studies of these systems focus on animal or plant hosts, while there are only limited studied cases of symbiotic relationships between bacteria and microbial eukaryotes (i.e. protists). My research this summer has been developing methods to better understand the bacterial symbionts of ciliates, a diverse group of protists, through bioinformatics and fluorescence microscopy.

I performed bioinformatic analyses on Whole Transcriptome Amplifications from 8 individual Loxodes cells to identify potential bacterial candidates living in, on, or with the ciliate host. To identify the strongest candidates for symbiosis across multiple host cells I compared our host sequences to databases of published sequences using BLAST and PhyloFlash. I also took non-Loxodes sequences binned by protein-coding density in DFAST and identified bacteria from the more densely protein-coding regions to back-up the identified bacterial candidates.

From previous work my team members completed in the spring semester, these bacterial candidates had been identified in cultivable ciliate Chilodonella uncinata. We then ordered a fluorescent probe to match our most likely candidate Caulobacter, and a general probe that would fluoresce most background (non-target) bacteria. Because of the scarcity of data on fluorescent microscopy in ciliates, I needed to develop new protocol to preserve the ciliate for staining and analysis on the Laser Scanning Confocal Microscope (LSCM). After developing a successful protocol for Chilodonella uncinata, I was able to fluoresce Caulobacter bacteria inside the cell using fluorescent in-situ hybridization(FISH) and DAPI nuclear probe.

Although I successfully imaged the target potential symbiotic bacteria, It still might not be a true symbiont of Chilodonella uncinata. I was only able to find Caulobacter inside two cells, while it also fluoresced in the environment around the host cells. More trials must be done to understand the complete picture of the relationship between Chilodonella uncinata and Caulobacter.

This summer, I stained a target bacteria found from genetic analysis in a group of cultivable ciliates known as Chilodonella uncinata. In the fall, I hope to continue method development and investigating the bacterial symbionts of Chilodonella uncinata and begin investigating symbionts in an uncultivable group of ciliates, Loxodes in a further study. Given that protists represent the majority of diversity in eukaryotes, understanding their associations with bacteria will expand our knowledge of adaptation and genome evolution, and ecology.
GelseyTorres2020Maren Buck, Chemistry - ChemistryPolymer Chemistry - Gtorres_SURF19.pngSite Specific Protein Polymer Conjugation for Targeted Drug DeliveryTargeted therapy treatments prevent cancer cells from growing, dividing, and spreading [1]. There are two types often studied: small-molecule drug and monoclonal antibodies [1]. This research focuses on small-molecule drug targeted therapy through synthesizing a protein-polymer conjugate that can enter cancer cells through use of protein marker, mesothelin (MSLN). The protein used for conjugation was engineered by the Sarah Moore Lab. It has one cysteine residue and is based on a fibronectin type III (Fn3) scaffold, which enables binding to MSLN.

To create the protein-polymer conjugate, 2-vinyl-4,4-dimethylazlactone (VDMA) underwent reversible addition-fragmentation chain transfer polymerization (RAFT) to yield poly(2-vinyl-4,4-dimethylazlactone) (PVDMA) (Figure 1). PVDMA was then functionalized with protected N-(2-hydroxyethyl) maleimide and triethylene glycol monomethyl (mTEG) (Figure 2-3). The degree of functionalization of protected maleimide ranged from 0.25 to 0.5 molar equivalence to PVDMA with excess molar ratios of mTEG. The functionalized polymer was characterized using nuclear magnetic resonance (NMR) Spectroscopy and attenuated total reflectance infrared (ATR-IR) Spectroscopy. Future steps would involve removing the protecting group from the maleimide and conjugating functionalized polymer to engineered protein. The conjugation would be accomplished through a thiol bond between the alkene of the maleimide and the cysteine residue of the protein. The resulting conjugate would be characterized using SDS-PAGE and undergo cell internalization studies.

Another route being explored is non-site specific protein-polymer conjugation using an engineered protein with lysine residues. PVDMA will be functionalized with mTEG to increase water solubility (Figure 4). Once functionalized, PVDMA will undergo ring-opening through a click-like reaction by the lysine residues of the protein. This allows for protein-polymer conjugation without side products. Future work would involve functionalizing polymers with varying molar equivalence ratios of mTEG and conjugating them to engineered protein. These will be characterized by NMR Spectroscopy, ATR-IR Spectroscopy, and SDS-PAGE.

1. Targeted Therapy for Cancer https://www.cancer.gov/about-cancer/treatment/types/targeted-therapies.
AliciaWilliams2020Steven Williams, Biological Sciences - Biological SciencesBiological Sciences - A. Williams.pngDeveloping a Sensitive Diagnostic for the Elimination of Onchocerciasis Onchocerciasis is one of many neglected tropical diseases that infect populations in Africa and in the Americas (1). In the Americas, the move towards the elimination of onchocerciasis is substantial, however, in Africa many are still suffering from this disease (2). Onchocerciasis is caused by the filarial nematode, Onchocerca volvulus, which is transmitted through Simulium black flies (1). Upon taking a blood meal from a human host, the black fly introduces stage three filarial larvae into the bite wound where these will develop into adult filariae that can produce microfilaria (mf) which can be detected in the skin and in the lymphatics of connective tissue (1).
On a few occasions, these microfilaria can be detected in blood if they are in high concentrations (3). To investigate this, we used blood spot samples taken in 2016 from Gabon, a country located in Central Africa where onchocerciasis is still active, and extracted DNA from these samples to test for the presence of these microfilaria. We performed DNA extractions and qPCR amplification on 12 of the samples that contained the highest inferred concentration of 176.7 to 96.42. After performing on these 12 samples, no amplification was found from the DNA extracted from these blood spot samples (Lanes A-F) with only the positive control (Lane G) shown to be amplified (Figure 1). This suggests that the DNA extracted from these blood spot samples taken from Gabon were not able to detect O. volvulus mf. The primers used in this project are the o-150 primers that have been used to detect for the presence of mf in skin snips. To further investigate an improved method for detecting O. volvulus mf, we wanted to see if we can improve on existing primers.
The latter half of this summer research was used to realign all O. volvulus sequences containing the o-150 region and design primers at specific locations that would only detect for Onchocerca volvulus and not Onchocerca ochengi, a closely related species that infects cattle. Four primers were designed (1 forward, 3 reverse), from a 75% consensus sequence, that appear to be potential primers that may be able to amplify specifically to O. volvulus. Using DNA samples that contain O. volvulus mf, further testing needs to be done to test the efficiency of these newly designed primers for specificity and efficiency.


1. Choi YJ, Tyagi R, McNulty SN, et. al. (2016), “Genomic Diversity in Onchocerca volvulus and its Wolbachia endosymbiont.”, Nat. Microbiol., 2:16207.
2. Unnasch TR, Golden A, Cama V, Cantey PT, (2018), “Diagnostics for onchocerciasis in the era of elimination.”, International Health, 10, Pages i20–i26.
3. Tritten L, Burkman E, Moorhead A, Satti M, Geary J, et al. (2014), “Detection of Circulating Parasite-Derived MicroRNAs in Filarial Infections.”, PLOS Neglected Tropical Diseases, 8(7): e2971.
ClaraSlesar2021Laura Katz, Biological Sciences - Biological SciencesBiological Sciences - Figure1.PNGIdentification and documentation of testate amoebae: ArcellinidaIdentification and documentation of testate amoebae: Arcellinida

Testate amoebae are unicellular organisms which build shells (tests) either with secreted matter or by using external aggregated particles. The largest, most diverse group of these fall into the category of Arcellinida, an order with 687 described species, characterized by lobose pseudopodia (Kosakyan et al., 2016). There are numerous current studies that focus on these amoebae, but there is still relatively little known about them. The shells (tests) of testate amoebae have long been used as the primary method to describe and differentiate species (Mitchell et al., 2008). With genetic analyses becoming increasingly prevalent in this field, new information on the identification and taxonomic relationships of amoebae are coming to light (Kosakyan et al., 2016). Katz lab genetic studies have identified testate amoebae in samples from Hawley Bog in Massachusetts, which have not been confidently identified through morphological observation. Additionally, many described species in literature lack GenBank reference sequences, so Katz lab phylogenetic analyses show unidentified clades of testate amoebae. To better understand this unidentified genetic data from previous studies in the Katz lab, cells were picked, photo documented, and prepared for genetic analyses using whole genome and whole transcriptome amplifications. The molecular data generated from these cells will be used together with morphological data as references for future testate amoebae community analyses.




References:

Kosakyan, A., Gomaa, F., Lara, E., and Lahr, D.J.G., (2016). Current and future perspectives on
the systematics, taxonomy and nomenclature of testate amoebae. European Journal of Protistology, 55, 105–117. https://doi.org/10.1016/j.ejop.2016.02.001.

Mitchell, E.A.D., Charman, D.J. & Warner, B.G., (2008). Biodiversity and Conservation, 17(9),
2115–2137. https://doi.org/10.1007/s10531-007-9221-3.


StephanieKonas2020Michael Baressi, Biological Sciences - Biological SciencesBiologicals Sciences and Education & Child Study - S. Konas.pngThe Student Scientists Outreach Program Summer 2019The purpose of the “Student Scientists” Outreach Program (SSOP) is “to encourage the development of life-long scientific learners through engaging, student-centered investigative, problem solving curriculum.” The program is centered around the zebrafish model system, utilizing their fast embryonic development, significant response to environmental manipulation, and genetic diversity to not only meet state mandated curriculum requirements, but also work to make this material more engaging and inquiry-based by providing teachers with the latest equipment and training. This summer, the SSOP was able to successfully hold three separate, two-day professional development workshops working with seven different secondary school instructors throughout the Pioneer Valley. The purpose of these workshops was to educate teachers on the unique characteristics of zebrafish, their potential as a learning tool in their classrooms, and the general care of the organisms. In addition, I used the summer to organize the SSOP fish rack and grow up essential lines of zebrafish to be used in the 2019-20 school year. Finally, I was able to continue developing the Barresi Lab’s Student Scientists Outreach website. This website is essential in making the unique materials created by the SSOP easily accessible to educators involved in the program. The website will continue to be the biggest project throughout 2019-20 academic year with a significant amount of work still to be completed.
AshleyRivas2022Sara Pruss, Geosciences - GeosciencesGeosciences - Ashley_Catoche_strat.ai.pngCarbonate Rocks from the Catoche Formation in Newfoundland consist mostly of limestone and preserved fossils from the Lower Ordovician. Before any tests were run for these rocks, a strat column based on the field notes taken was created in order to specify which areas were most viable. All sections taken from Barbace Cove were drilled for Carbon isotope analysis in order to find any variability in the data which could explain the diversity of fossils. The carbon isotope data acquired has not been analyzed, but any discoveries will be made clear during the fall semester. The carbonates were abundant in cephalopods, brachiopods, and other dolomitized and silicified fossils; thin sections of 47 meters of carbonate rock were made to identify these fossils and their preservation. No definite conclusions have been made, but more results are expected to come this upcoming school year that explore what the diversity of fossils is credited to, how the preservation of these fossils was affected by the environment, including the overall geochemistry of these carbonate rocks. In the upcoming year, more thin sections will be made for most of the meters in the Barbace Cove and will be examined under a microscope to view the diversity of the fossils inside these rocks. In addition to the data collected from the carbon isotope drilling, drilling for mercury is also a possibility for a different analysis.Carbonate Rocks from the Catoche Formation in Newfoundland consist mostly of limestone and preserved fossils from the Lower Ordovician. Before any tests were run for these rocks, a strat column based on the field notes taken was created in order to specify which areas were most viable. All sections taken from Barbace Cove were drilled for Carbon isotope analysis in order to find any variability in the data which could explain the diversity of fossils. The carbon isotope data acquired has not been analyzed, but any discoveries will be made clear during the fall semester. The carbonates were abundant in cephalopods, brachiopods, and other dolomitized and silicified fossils; thin sections of 47 meters of carbonate rock were made to identify these fossils and their preservation. No definite conclusions have been made, but more results are expected to come this upcoming school year that explore what the diversity of fossils is credited to, how the preservation of these fossils was affected by the environment, including the overall geochemistry of these carbonate rocks. In the upcoming year, more thin sections will be made for most of the meters in the Barbace Cove and will be examined under a microscope to view the diversity of the fossils inside these rocks. In addition to the data collected from the carbon isotope drilling, drilling for mercury is also a possibility for a different analysis.

KaiaCormier2022Glenn Ellis, Engineering - EngineeringImaginative Education in Engineering Glenn EllisScreen Shot 2019-09-03 at 4.28.23 PM.pngSURF Transforming Engineering Education in Middle SchoolsThis research is based on the theory of IE developed by Kieran Egan (Judson and Egan, 2015; Judson, 2010; IE Research Group, 2010; Egan, 2005; Egan, 1997). Egan has developed an approach that builds on learners’ characteristic ways of thinking to structure their engagement with ideas and knowledge. His intent is to engage learners’ imaginations in their pursuit of understanding and thus engender the kind of caring about learning necessary for developing learners’ capacities to engage in deep learning. Several of Egan’s cognitive tools including: narrative, metaphor, and binary opposites, shape the NGSS standards to present holistic and cohesive engineering curricula for middle school students (Judson and Egan, 2015; Judson, 2010; IE Research Group, 2010; Egan, 2005; Egan, 1997) .
Several units and mini-units were completed over a ten week period of SURF, including the Engineering Design Unit. To accompany these NGSS-aligned transmedia engineering curricula, assessment and support materials for use in Springfield Public Schools (SPS) were created. In addition, preparations to collect data on Catalina’s Revenge, a module focused on the importance and cognition of ethics in the classroom, were completed. The data will likely be presented in the ASEE 2020. Although results have not yet been collected, both curricula will be implemented in the fall of 2019 and data will be collected through teacher and student surveys, observations, and assessments.
GabrielleJoslin2020Jan Vriezen, Biological Sciences - Biological Sciences Antibiotic production by bacteria in soilOdrine HabarugiraGJoslin OHabarugira soil bacteria Acridine Orange red filter.png
GJoslin OHabarugira soil bacteria DAPI blue filter.png
GJoslin OHabarugira soil bacteria DAPI green filter.png
Fluorescent Counting of Soil Bacteria and the Interactions of CVAP #3 and E.coliOur first goal of the summer was to develop a direct counting protocol using fluorescence microscopy to check if plate counts of MacLeish soil samples are representative of actual soil bacteria numbers. We took samples from forest (F) and grassland (G) surface (S) and subsurface (SS). In the literature plate counts are usually 0.1-4% of direct counts. We worked with both DAPI and acridine orange (AO) in developing our protocol and obtained better results with AO. With AO we were also able to distinguish autofluorescence artefacts from bacteria unlike with DAPI. We found our plate counts to be 0.1-2.6% of direct counts using acridine orange as the fluorescent dye. Plate counts also correlated with direct counts in that both increased proportionally to one another. We could also see that colony forming units were in the order GS>GSS>FS which P. Vriezen has seen in his work repeatedly. FSS was way off though.

For our second project, we mixed the bacterial isolates CVAP #3 and E.coli together in a ratio of 1:70.4 and we wanted to see if we got this ratio back from plate counts. We also wanted to see if % inhibition of S. epidermidis by our CVAP #3: E.coli culture correlated with dilution of the CVAP #3: E.coli culture. The conditions at which the CVAP #3 and E.coli cultures were grown meant that CVAP #3 did not kill E.coli. We were able to distinguish CVAP #3 colonies from E.coli colonies on the plates due to morphological differences. When seeded on S.epidermidis CVAP #3 always produced a zone of inhibition whilst E.coli did not, although E.coli was able to grow still. We found that dilution of the culture does not correlate with % inhibition. From our plate counts we found that CVAP #3 and E.coli colonies grew in the ratio they were present in the original culture; plate dilutions of the original CVAP #3: E.coli culture had 1.3% CVAP #3 colonies. We found that the % inhibition of S. epidermidis by our CVAP #3: E.coli culture did not correlate with the dilution of the CVAP #3: E.coli culture.

KerryLeCure2020Lisa Mangiamele, Biological Sciences - Biological SciencesBiological Sciences - Screen Shot 2019-08-01 at 9.42.02 AM.pngAndrogen receptor density in the frog species Staurois parvus, Rana pipiens, and Xenopus laevisHow do new behaviors evolve? This summer I addressed this question by studying the Bornean rock frog (Staurois parvus), a species that has evolved a new communication signal called “foot -flagging.” Foot-flagging is a visual signal, where the hind limb is kicked out and the white webbed foot is more visible. This is a particularly useful behavior due to the noisy environment in the frogs’ native habitat, as a visual signal helps communicate important information that would otherwise be lost due to background noise [1]. This behavior is modulated by androgenic hormones, such as testosterone (T), acting upon androgen receptors (ARs).

Previous studies have shown that AR expression levels are higher in the leg muscle of S. parvus compared to the non-foot-flagging frogs Xenopus laevis and Rana pipiens [2]. There is also a significant difference between S. parvus and X. laevis AR expression in the spinal cord, with S. parvus having a higher amount of AR expressed [2]. These results suggest that a high amount of AR in the hind limb neuromuscular system is associated with the evolution of foot-flagging, however whether or not there is a difference between species in AR expression in the lumbar spinal cord remains unclear. This summer, I began to collect data in preparation for my honors thesis. My goal was to measure the density of silver grains, which reflect AR mRNA abundance as revealed by in situ hybridization,, in the spinal cords of S. parvus, R. pipiens, and X. laevis frogs. By taking images of motoneurons in spinal motor nuclei 8, 9, and 10, which make up the lumbar spinal cord, I was able to quantify the density of AR in this tissue. This was done by taking three images: (A) one brightfield image of the appropriate spinal motor nucleus (SMN) in the lumbar spinal cord, (B) the exact same image using blue filters and adjusting the color gain settings so the background is fully blue, and (C) a background image taken from a nearby site without any tissue with the same blue filters and color gain settings as (B) (Figure 1). Images were taken using a Leica DM4000B microscope, and images were analyzed in ImageJ. Preliminary data has been collected, but not yet analyzed, and this work will continue into the coming academic year for my honors thesis.

1. Grafe, T.U., Preininger, D., Sztatecsny, M., Kasah, R., Dehling, J.M., Proksch, S., Hödl, W., 2012. Multimodal Communication in a Noisy Environment: A Case Study of the Bornean Rock Frog Staurois parvus. PLOS ONE 7, e37965.
2. Mangiamele, L.A., Fuxjager, M.J., Schuppe, E.R., Taylor, R.S., Hödl, W., Preininger, D., 2016. Increased androgenic sensitivity in the hind limb muscular system marks the evolution of a derived gestural display. PNAS 113, 5664–5669.
RebeccaMiller2020Andrew Berke, Chemistry - ChemistryAtmospheric Chemistry - - The Effect of Atmospheric Alcohol Addition Sequence on the Thermodynamics of Aerosol Mimicking SolutionsRebecca Miller/2020
Organic aerosols (OA) and secondary organic aerosols (SOA) are an interesting and inevitable component of Earth’s atmosphere and ecosystems resulting from the partitioning of volatile organic materials. SOAs are formed when a primary pollutant, also know as an OA, reacts with hydroxide, sulfates, nitrates, and/or free radicals in the atmosphere. The product of such reactions is, henceforth, referred to as SOA because it is a secondary environmental pollutant that is formed from a primary pollutant. Aerosols are microscopic particles suspended in the atmosphere that provide a surface for the condensation of water as well as the absorption and scattering of light. The formation of OA and SOA is a topic worth studying because these pollutants can be harmful; therefore, they have an enormous influence on human life and air quality (Yi et al.). Little research has been done to understand the effects of specific alcohols on the reactions of glyoxal with nitrogen-containing compounds. Alcohols are available to these aerosols in the atmosphere, so it is important to observe how different concentrations of alcohols and temperatures affect these reactions.
This research focuses on the effect of alcoholic solvent systems (methanol, ethyl alcohol, tert-butanol, 3-methyl-2-butanol, etc.) on the reaction between ammonium sulfate and glyoxal at changing alcohol concentration and temperature. In previous experiments the alcoholic solvent had been added to the ammonium sulfate and ultra-pure water mixture before the addition of glyoxal. This led us to the question: does the order of alcoholic solvent addition have an effect on product formation?
To address this a new experimental protocol was created. The new set of experiments required a modification of the volumetric flasks used in the creation of solutions. Volumetric flasks were filled to the line with ultra-pure water and then the amount of alcohol needed for each solution was removed. The water line post-removal was marked on the flask to create a secondary demarcation, afterwards the remaining ultra-pure water was drained and the glassware was dried. New experimental solutions were then created using the new glassware where the glyoxal and ammonium sulfate mixture filled the volumetric flask up to the secondary demarcation and left for a predetermined amount of time. At the end of this time the alcohol was added up to the main line of the volumetric flask. A second set of experiments tested the inverse idea; these experiments called for the glyoxal and alcohol to be added together into an empty volumetric flask and sit for a predetermined amount of time until an ammonium sulfate mixture could be added.
Although these experiments are ongoing, preliminary observations suggest the final results of altering the alcohol addition sequence will be varied from the results of the original addition sequence. For the experiments where glyoxal and ammonium sulfate sat together before alcohol addition the solutions were noticeably darker in color. Experiments where the glyoxal and alcohol were mixed together before ammonium sulfate was added yielded in a solution with distinct phase separation. Further experimentation as well as comparison of results from UV-Vis spectroscopy and viscosity measurements should give interesting results that will inform further research in the coming year.





References:
Yi, Y., Cao, Z., Zhou, X., Xue, L., & Wang, W. (2018). Formation of aqueous-phase secondary organic aerosols from glycolaldehyde and ammonium sulfate/amines: A kinetic and mechanistic study. Atmospheric Environment, 181, 117-125.

Advisor: Andrew Berke, Chemistry
AnnieDobroth2021Annaliese Beery, Psychology - NeuroscienceNeuroscience - - Social Conditioning and Maternal Folic Acid in Prairie VolesPrairie voles (Microtus ochrogaster) are unusual rodents because they form strong monogamous bonds with their mates, as well as preferences for familiar same-sex social peers. As a result, prairie voles are useful models in the study of social neuroscience. During SURF, I participated in two different projects that studied prairie vole social behavior in the lab of Professor Annaliese Beery.
Previous work in the Beery lab showed that prairie voles will choose substandard bedding over better bedding in a preference test if they have been conditioned to associate the substandard bedding with their mates. However, this study was inconclusive when looking at same-sex vole pairs. My first project explores female-female social bonds by assessing whether a female vole will prefer substandard bedding associated with social interaction with a cagemate female. We compare the time that each animal spends on high quality and lower quality bedding while allowed to freely roam between the two beddings before and after the vole has been conditioned to associate lower quality bedding with a familiar female. We hypothesize that the voles will initially prefer the high quality bedding, but that their preferences will change once they associate the lower quality bedding with their cagemate. This study is ongoing, but early results suggest that they do show social conditioning toward the bedding associated with a same-sex cagemate.
The second project studied maternal folic acid levels and social interaction. Prior research has shown that deficiencies in folic acid during pregnancy can cause neural tube defects. Pregnant women are advised to take folic acid to lower the incidence of these defects, and most wheat products are supplemented with the vitamin for the same reasons. However, we do not know whether adverse effects can occur from taking too much folic acid, which is one of the main dietary sources of methyl groups for DNA methylation. Rodent studies have shown that folic acid supplementation alters widespread DNA methylation in supplemented young. This project examines whether maternal folic acid levels are linked to behavioral changes in prairie vole social behavior by feeding breeding pairs of voles diets with different quantities of folic acid, and studying the behavior of their pups. This study is ongoing, and results are not yet available.

Bowler, C. M., Cushing, B. S., & Carter, C. S. (2002). Social factors regulate female–female aggression and affiliation in prairie voles. Physiology & Behavior,76(4-5), 559-566.
Goodwin, N. L., Lopez, S. A., Lee, N. S., & Beery, A. K. (2019). Comparative role of reward in long-term peer and mate relationships in voles. Hormones and Behavior,111, 70-77.
Crider, K. S., Bailey, L. B., & Berry, R. J. (2011). Folic Acid Food Fortification—Its History, Effect, Concerns, and Future Directions. Nutrients,3(3), 370-384.
RanYan2021Peter de Villiers, Psychology - PsychologyTheory of Mind; Statistical Analysis - 屏幕快照 2019-08-21 16.01.08.pngThe effect of Language on Children's Development of Theory of MindIt is widely known that false belief understanding serves as an important milestone in children’s development theory of mind. Many theories were proposed in an attempt to explain underlying factors that contribute to such development. The current study examines the linguistic Determinism Theory proposed by J. de Villiers (2005) and Inhibitory Control Theory proposed by Carlson, Mosese and Hix (1998). The Determinism Theory argues that complement understandings facilitates children’s ability to represent other people’s mental states, critical in the development of false belief understanding.The Inhibitory Control theory suggests that ability to inhibit reporting on one’s own reality when asked to consider other people’s state of mind is required in explicit false-belief reasoning. Previous studies have yielded mixed results. Current research investigated the effects of general vocabulary, complement comprehension and inhibitory control of 258 children on their false-belief understanding. Data collection was made possible through the School Readiness Research Consortium. All children were tested at the beginning (Time1) and end (Time 3) during their pre-school year. Hierarchical multiple regression and structural equation models were used in the analyses of the data. The concurrent and longitudinal models suggested that both inhibitory control and complements play roles in children's false-belief development, with complements having a much stronger effect, when children’s ages were controlled. Inhibitory control measures and complement understanding also have indirect effects through children’s false-belief understanding at time 1 on children’s false-belief understanding at time 3. Current model adds to the previous structural equation model proposed in Meng Chen’s thesis (2013) by incorporating the mediation effect of false belief understanding at time 1 in the longitudinal relationship predicting false belief understanding at Time 3. In conclusion, the results appear to be consistent with previous literature and Meng Chen thesis (2013), that both language and inhibitory control play roles in advancing children’s false belief reasoning.

CynthiaLan2021Doreen Weinberger, Physics - PhysicsOptics - CLan_Figure 1.pngMake precision measurements of the refractive index of various media using a Michelson interferometer.Given that light is a form of electromagnetic wave, the fundamental property of wave superposition applies to monochromatic light, meaning constructive and destructive interference patterns can be observed as a result of phase differences between two overlapping coherent beams. Such patterns can be created and observed by the use of a Michelson Interferometer, consisting of a light source, two beam splitters, a fixed mirror, and a movable mirror. Once the monochromatic light source is properly positioned, the beam splitter creates two separate beams traveling at right angles, with one beam striking the fixed mirror and the other the movable mirror. The two beams thus travel along different pathways and are brought back together by the second beamsplitter, producing a circular pattern of interference fringes on an observation screen.

The travel distance of the light beam going through the movable mirror path can be modified using a micrometer to adjust the mirror position. When rotating the micrometer dial to translate the mirror, one observes the outermost circular fringe to appear or disappear depending on the direction of micrometer rotation, while the innermost fringe (circular spot at the center) varies between light and dark. The wavelength of a monochromatic light source can therefore be determined by counting the change in number of light fringes while moving the mirror through a known measured distance, as read by the micrometer.

One important application of the Michelson Interferometer is the determination of the index of refraction of a material, as any transparent medium with a certain refractive index can be inserted between the beam splitter and the movable mirror, perpendicular to the optical path. This changes the effective travel distance of that beam, again measured by the micrometer, and causes the motion of a fixed number of interference fringes. This information can then be used to determine the index of refraction for the given medium, ranging from gases to liquids to crystalline geological samples, using an appropriate mathematical analysis.

To overcome the limitations of precision obtainable from the standard commercial Michelson Interferometer, we hand-built in the laboratory a Michelson Interferometer with all components obtained from ThorLabs. In particular, the micrometer is replaced by a motorized actuator controlled by computer programming, which significantly enhances the precision of our index measurements. Further studies on the limitations of the accuracy and precision of the refractive index measurements for solid samples will be carried out with this set-up, by considering other factors affecting the laboratory operation like precision of the optical alignment.

Figure 1. Standard set-up of the Michelson Interferometer.
( http://hyperphysics.phy-astr.gsu.edu/hbase/phyopt/michel.html)

Figure 2. Interference fringe pattern produced from recombined light beams shown on the observing screen using a He-Ne laser pointer as the light source.
( https://drive.google.com/file/d/1YWEz7BwIk7eUjK4SeUnyEbvDF3h_Ms3t/view?usp=sharing)

Figure 3. Set-up of the hand-built Michelson Interferometer on the optical table, with a computer-controlled motorized actuator visible on the mirror mount near the center of the table. The red laser emerges at the far end of the table and the fringes can be seen on the observation screen taped to the wall.
( https://drive.google.com/file/d/1dbPGjLwxx79PrFBRy2dTygCPwrfIUUFJ/view?usp=sharing)
EmilyAkey2020Aaron Rubin - EngineeringGeotechnical EngineeringMariel Jones, Aaron RubinICTG Abstract LWD on Ballast.pngMeasuring Railroad Ballast Modulus of Elasticity Using Light Weight Deflectometer Light Weight Deflectometers (LWDs) are used to rapidly determine the modulus of elasticity and spring constant of granular materials and pavements. The LWD can be operated by one person making it incredibly efficient to collect this important data. It is primarily used in the field to determine the properties of soils or paving materials, but also has the potential to be used on railroad ballast. However, to date, there have been minimal studies using LWDs on railroad ballast. The goal of this current study was to investigate the repeatability of LWD testing on prepared cylindrical ballast specimens. To use the LWD on ballast we conducted minimum and maximum density tests in accordance with ASTM D4254 on 12-inch interior diameter by 12-inch interior height cylinder specimens at different percentages of fouling ranging from 0 to 60%. Then the LWD measurements were taken on the top of the specimen using a 12-inch diameter plate. In total, 100 measurements were made on minimum density mixtures and 50 maximum density mixtures. The effect of density and fouling on test repeatability and procedural best practices for LWD testing on cylindrical ballast specimens is discussed.
RachelEstrera2021Adam Hall, Biological Sciences - NeuroscienceNeuroscience - - Comparison of DEET and Novel Insect RepellantsMosquitoes are viewed as menaces to humans, acting as blood-borne carriers of diseases like West Nile virus, malaria, and Dengue fever. Accordingly, it’s of interest to humans to identify what attracts mosquitoes and how we might intervene to prevent disease-spreading bites.

Previous research reveals that mosquito antennae house odorant receptors that bind odorants like 1-oct-3-enol and 2-methyl phenol. When activated, the receptors open to allow cation flux, or a current, resulting in excitatory action of the corresponding neurons. N,N-Diethyl-meta-toluamide i.e. DEET acts to block the receptor, dampening the signal induced by the odorants. DEET is the current golden standard of insect repellants, yet it isn’t perfect. With goals of finding an insect repellant that lasts longer, acts against a greater range of bugs (e.g. arthropods like tics), and isn’t toxic to humans, 17 novel insect repellants were assessed for efficacy of inhibition of the odorant-induced signal in comparison to DEET. These novel repellants fall into two chemical categories: carboxamides and acylpiperidines. This summer, I spent most of my time assisting the talented and dedicated Gariel Grant to finish screening the repellants.

Using a two-voltage electrode clamp with Xenopus laevis oocytes expressing GRPOR2/GRPOR7 and GRPOR7/GRPOR8 receptors, DEET and the novel repellents were applied. DEET and one of each of the most potent carboxamides and acylpiperidines were applied in a dose-dependent manner, and there indeed was dose dependency of inhibition of odorant currents by the repellants. Experiments confirmed that the effects of DMSO alone on odorant currents were negligible and that the odorant-induced cation currents could be blocked by NMDG. Interestingly, all the novel repellants inhibited the odorant currents more than DEET, particularly the acylpiperidines. The potential for DEET alternatives is therefore promising. However, there could still be other ways insect repellants function for which DEET is still superior, and the safety of the novel repellents for humans could still be a concern.
Ginny (Virginia)Svec2020Sara Pruss, Geosciences - GeosciencesGeosciences - Gsvec.pngSPICE and Changing Redox Environments at the Lawson Cove locality, Western Utah, USAThe Steptoean Positive Isotopic Carbon Excursion (SPICE) describes a large, positive carbon isotopic excursion related to a global extinction event at the end of the Cambrian Period (Saltzman et al. 1998). Measurements from south China and Kazakhstan suggest that the SPICE event is one of the largest carbon isotopic excursions in the Phanerozoic era. This coincides with a worldwide mass extinction of trilobites, with nearly 80 percent of species becoming extinct (Saltzman et al. 2000). The SPICE event has been largely studied in Utah (Saltzman et al. 2004, Saltzman et al. 2000, Saltzman et al. 1998). Large changes in sedimentation at the beginning of the SPICE excursion have been recorded in many areas including the Lawson Cove locality in Utah, my area of study (Saltzman et al. 1998). It was thought that large igneous province (LIP) volcanism may be the cause of this excursion, owing to the large presence of mercury (Hg) in the sediment of these localities, since LIPs are closely associated with Hg anomalies. The Late Cambrian Spice event, however, is a time with no known LIP. The Hg anomalies instead are thought to be linked to a changing redox environment, which is supported by the abundance of glauconite, a redox-sensitive mineral, found only in the SPICE section and not the surrounding area (Pruss et al. 2019). We want to create a basis similar to previous SPICE research from these localities to ensure our accuracy, then build on that in support of redox changes in the environment being the cause of the Hg anomalies and increasing amounts of C13 isotopes.
We traveled to Utah to the House Range and Lawson Cove locality to collect samples from the Late Cambrian SPICE event. I drilled approximately 0.1 g rock powder from each rock for carbon isotope data, and 1 gram for mercury data. The carbon isotope data is still being processed. The mercury powder was processed on a Hydra-C and the data were collected. It seems that these data were accurate, with one rock having a much higher amount of mercury that I will look into further. I created thin sections of many rocks, and powdered all rocks using a rock crusher and shatterbox. I also began creating a stratigraphic column of Lawson Cove. This semester I will be analyzing the data and thin sections from the summer and continuing my research further.


Works Cited

Pruss, S. B., Jones, D. S., Fike, D. A., Tosca, N. J., & Wignall, P. B. (2019). Marine anoxia and sedimentary mercury enrichments during the Late Cambrian SPICE event in northern Scotland. Geology, 47(5), 475–478.
Saltzman, M. R., Cowan, C. A., Runkel, A. C., Runnegar, B., Stewart, M. C., & Palmer, A. R. (2004). The Late Cambrian Spice (δ13C) Event and the Sauk II-SAUK III Regression: New Evidence from Laurentian Basins in Utah, Iowa, and Newfoundland. Journal of Sedimentary Research, 74(3), 366–377.
Saltzman, M. R., Ripperdan, R. L., Brasier, M. D., Lohmann, K. C., Robison, R. A., Chang, W. T., … Runnegar, B. (2000). A global carbon isotope excursion (SPICE) during the Late Cambrian: relation to trilobite extinctions, organic-matter burial and sea level. Palaeogeography, Palaeoclimatology, Palaeoecology, 162(3), 211–223.
Saltzman, M. R., Runnegar, B., & Lohmann, K. C. (1998). Carbon isotope stratigraphy of Upper Cambrian (Steptoean Stage) sequences of the eastern Great Basin: Record of a global oceanographic event. GSA Bulletin, 110(3), 285–297.
SamikshyaDhami2022Marney Pratt, Biological Sciences - Biological SciencesEcology and diversity Amy Turgeon, Samikshya DhamiS. Dhami.pngParadise Pond Project: Freshwater Mussels as Bio-indicators of Mill River HealthParadise Pond is an impoundment created by a dam on the Mill River (Sinton 2002). The dam disrupts the movement of sediment causing sediment to gradually build up over time. In order to prevent Paradise Pond from completely filling with sediment Smith College moves it by flushing it downriver. To make sure the surrounding ecosystem is not affected, The Paradise Pond Sediment Management Project assesses the impact of sediment redistribution on the health of the ecosystem downriver.
In this study, we are using freshwater mussels as a bio-indicator on the health of the Mill River. An increase of sediment can negatively affect the river mussels because it obstructs their ability to feed and respire (Nedeau 2008). In order to see if the sediment redistribution in 2016 had an impact on the Mill River the Before-After-Control-Impact design was used to compare freshwater mussel shell length in the Manhan river (control) and in the Mill River (Impact) in 2016 (Before) and 2019 (after) (Strayer & Smith 2003). Comparing the different distributions of shell length will help us understand the water quality of the Mill River. This is because the more distributed the shell lengths are the better the mussel population is doing.

In order to assess whether the influx of sediment had any impact on the range of mussel sizes in the rivers in 2016 and 2019, we conducted a two-way Anova test with location and year as the two factors using type III sum of squares. A significant interaction between the location and the year could suggest that the sediment redistribution had an impact on the mussels. There was a significant interaction between the location and the year (F1,482 = 10.8, P = 0.001). In 2016, the mussels in the Mill River were larger in size than the mussels in the Manhan. This was not the case in 2019. This could suggest that there has been better recruitment of mussels in the Mill river compared to the Manhan. The greater variety of mussel sizes in the Mill compared to the Manhan after the sediment redistribution in 2016 suggests that though sediment redistribution had an impact on the mussels, it did not have a negative impact.

Literature Cited:
Nedeau, E. J., 2008. Fresh water mussels and the Connecticut river watershed. Connecticut River Watershed Council, Greengield, Massachusetts.
Sinton, J. 2002, April. A short history of the Mill river watershed 1650-1940.
Strayer, D. L., and D. R. Smith. 2003. A guide to sampling freshwater mussel populations. American Fisheries Society, Monograph 8, Bethesda, Maryland.

AndreaRawson2022Virginia Hayssen, Biological Sciences - Biological SciencesBiological Sciences - SurfAbstractAR.pngMorphological Features and Range of Crocuta crocuta, and the Organization of the Vertebrate Biology LabCrocuta crocuta, the spotted hyena, is a widespread species in Africa that has attracted a large amount of study due to the unique reproductive structure of the female. The goals of this investigation were to generate summary statistics for various morphological features of C. crocuta and to generate a map of the range of C. crocuta in order to support the writing of a Mammalian Species Account for the American Society of Mammalogists.
I reviewed published literature on C. crocuta to obtain data on their morphological features, gender, and location. Morphological features included: external body measurements and skull measurements. The data were then grouped by location and gender, and ranges and averages of morphological measurements for these groups were calculated using Rstudio. A section of the Mammalian Species Account was then written using these calculations. The range map was adapted from an IUCN map for the range of C. crocuta using information of the habitat limits for C. crocuta and publicly available data on the elevation and land cover of Africa. The IUCN map and data on elevation and land cover were imported into ArcMap, and areas where C. crocuta cannot habituate according to the literature on the species (such as lakes) were excluded from the IUCN map.
In addition to this investigation, I worked with another Smith student, Chase Ryan-Embry, to organize and update the collection of specimens in the vertebrate biology lab at Smith College. This included identifying unknown specimens, labeling all specimens in the lab, and creating a database that includes the taxonomic information of the specimens and where they are located in the lab to assist students and instructors in using this resource.
GretaMundt2021Tim Johnson, Botanic GardenTim JohnsonEnvironmental Science and PolicyLandscape Studies - Learning Landscapes: How the new Landscape Master Plan can enhance informal experiential learning at Smith CollegeSmith College is currently creating a new landscape master plan (LMP), which will inform decisions about the management, maintenance, and design of the campus landscape. One of the goals established by the LMP Committee in the LMP Request for Qualifications is to “promote the use of the landscape in teaching, learning, and scholarship.'' This SURF project originally focused on the methodology of landscape-based education. Formal experiential education in the landscape includes interactions such as events, classes, or research experiences, which are guided by educational outcomes derived by educators and their learning objectives. Planning is unlikely to systematically address the needs of these varied experiences. Therefore the project focus shifted towards informal experiential education opportunities based on the lived experiences of individuals experiencing the landscape without the guidance of an educator.
Informal experiential education at Smith is an untapped resource for most students. While there is potential for a heightened educational experience through everyday interactions with the landscape, these interactions are not shaped by formal learning objectives. Therefore, informal experiential education in the landscape is unstructured, unguided, unpredictable, and unassessed.
Research methods included assessing Smith’s current landscape education offerings, interviewing landscape stakeholders at Smith, comparing Smith’s offerings to other institutions, reading literature surrounding landscape, education, and interpretation, and compiling a literature review of institutional guiding documents pertinent to landscapes at Smith. Documents reviewed included the LMP Request for Qualifications, the 2017 Smith College Self Study Narrative, the 2016 Report of the Smith College Study Group on Climate Change, the 2016 Smith College Strategic Plan, and the 2019 Botanic Garden Strategic Plan.
From this research came the conclusion that outdoor informal experiential learning should include learning goals. Potential learning goals were drafted guided by institutional values. These goals aim to guide land management and operations’ approach to future projects and provide an assessment metric for the educational potential of space. Incorporating educational intentions into the LMP and land management will result in increased informal educational outcomes in students, and directly impact course participation and research surrounding the landscape as students engage with their campus. This research experience also included researching accessibility in the landscape, which working with the Office of Disability Services and assessing the Smith landscape based on the principles of Universal Design. These projects will be presented to the Landscape Master Plan Committee in the fall with the hopes of starting the conversation on learning in the landscape and accessibility.
EleanorTarno2021Stylianos Scordillis, Biochemistry - BiochemistryProteomics - E. Tarno Figure for SURF Abstract.pngComparative Proteomes of Fast and Slow Twitch Rat Skeletal MusclesSkeletal muscles govern locomotion in mammals and constitute a large portion of
the body mass. They create contractile forces by harnessing protein molecular motors, myosins, and tension transducers, actins, and are controlled by the regulatory proteins, troponins and tropomyosins, that alter cytoplasmic Ca2+ concentrations. Mammalian skeletal muscles consist of two main cell (fiber) types, type I (slow twitch) and type II (fast twitch). Type II fibers are used for quick and explosive movements such as jumping or sprinting, whereas type I fibers are designed for endurance such as long runs and posture maintenance. Nearly all mammalian muscles are comprised of differing percentages of these two fiber types but have a dominant fiber type. This study used quantitative proteomics to ascertain the relative presence of protein isoforms found in rat soleus (slow, SOL) and medial gastrocnemius (fast, MG) muscles. High pressure liquid chromatography-coupled mass spectrometry was used to determine all the proteins (proteome) in a sample and tandem mass tagging documented their relative abundances.
Muscles excised from adult rats (n=5, 6 mo) were extracted in a buffer that
separates the sarcoplasmic (cytoplasmic) and sarcomeric (contractile apparatus) proteins. These fractions were then digested with trypsin and the resulting peptides were reacted with isobaric mass tags for relative abundance measurements. Nano-liquid chromatography-coupled mass spectrometry yielded 323 protein IDs for the MG and 1023 for the SOL.
Initial data analysis indicates proteins involved in glycolysis are found in a higher
abundance in the MG whereas oxidative phosphorylation proteins were greater in the SOL. Additionally, the myosin fast and slow twitch isoforms, were found in higher abundances in the MG and SOL, respectively. This was also true of the troponins where the MG contained exclusively fast isoforms and the SOL only slow isoforms. Parvalbumin, a calcium binding protein that is found in high abundances in fast twitch muscles, had a 4-fold higher abundance in the MG. Furthermore, the sarcoplasmic/endoplasmic reticulum calcium ATPases (SERCA) which have fast and slow twitch isoforms, were found in the MG, fast, and SOL, slow.


Figure 1: Volcano plots of proteins identified in supernate (A) and pellet (B) fractions. The X axis sorts the proteins by relative abundances between the SOL and MG; proteins to the left of the Y axis are more abundant in the MG and proteins to the right of the Y axis are more abundant in the SOL. The Y axis is the negative log of the p value such that protein closer to the X axis have higher p values. The proteins that differed significantly (± 2-fold and p
YujiaZhou2020Albert Kim, Statistical and Data Sciences - Statistical and Data SciencesStatistical and Data Sciences - ModernDive and FiveThirtyEight: Open Source Data Science Projects This summer, I have worked with my SURF advisor, Prof. Albert Y. Kim, to assist his with two major open-source projects that he is a co-author for: ModernDive and the fivethirtyeight package.

First, I have worked on ModernDive, an online textbook for learning statistics using data science tools, which will be published in print by CRC Press in Fall 2019. This textbook is currently being used by him in both SDS/MTH 220 Introduction to Probability and Statistics and SDS 192 Introduction to Data Science. I have edited, tested and proofread code, improved explanations and examples of theory, worked on the selection, polished the images in the book, as well as improving the data visualization examples in R code. The book is currently being proof-read by CRC Press, and the updated version is available online at http://moderndive.com.

Second, I have contributed to the fivethirtyeight package, an R package providing easy access to the code and data sets published by the data journalism website FiveThirtyEight.com. I have conducted data wrangling, evaluated data quality, conducted background research for dataset documentation purposes for package users to reproduce the analysis in FiveThirtyEight’s original articles. In addition, I initiated a “How to add data to R packages” quickstart guide ( https://github.com/rudeboybert/fivethirtyeight/wiki/Instructions-on-how-to-add-a-new-dataset) for open-source projects with systematic instructions. This will allow future R package contributors to quickly navigate the necessary developer tools and be able contribute to open-source projects on GitHub. At the end of my project, with the help of Prof. Kim I ran a focus group to have SDS students test the starter guide and go through the process once themselves. I incorporated focus group participant feedback and delivered a viable guide for future students who will contribute to this project.
Xian (Elaine)Ye2021Shannon Audley, Psychology - PsychologyPsychology - - Personality and Cognitive Factors in a Transdiagnostic Approach for Eating DisordersCompared to the categorical approach of eating disorders used in DSM-5 that classifies individuals into subtypes of ED based on presence or absence of disordered eating behaviors, the transdiagnostic approach refrains from categorizations and instead studies the underlying mechanism of eating pathologies, such as the personality traits and the cognitive processes. The purpose of our project was to develop a study procedure and to finalize measurements for personality and neurocognitive factors for a pilot study to be conducted in Fall 2019. My research partner and I firstly read the existing literature that investigated the personality and cognitive factors related to the development and the maintenance of eating pathologies. Based on the research, personality traits including obsessionality, perfectionism, experiential avoidance, and impulsivity were identified as our research interests; and the cognitive factors we planned to study were decision making, set-shifting, central coherence, and inhibitory control (Martinez & Craighead, 2015; Smith et al., 2018). Previous empirical studies mostly utilized self-report questionnaires to operationalize personality factors and psychiatric symptoms and conducted the neurocognitive tasks to examine the elements of cognitive processes. We collected different self-report and behavioral measurements of those factors and selected the appropriate instruments by comparing their psychometric properties, accessibility, and feasibility of administration. Considering eating disorders may share common underlying mechanism with other associated disorders, questionnaires that measure symptoms of distress, ADHD, bipolar disorder, personality disorders, substance use, and obsessive-compulsive disorder were also included in the study.
To avoid participants’ cognitive fatigue, the study will consist of two separate sessions. Participants will be required to finish the self-report questionnaires during the first session and need to return to the lab on a different day to complete the neurocognitive tasks. After the procedures were preliminarily decided, my research partner and I wrote an IRB protocol for the study. The work that we did this summer will lend itself to a lab manual for research assistants to conduct the study in the coming semester with Professor Shepherd

References
Martinez, M. A., & Craighead, L. W. (2015). Toward person (ality)‐centered treatment: How consideration of personality and individual differences in anorexia nervosa may improve treatment outcome. Clinical Psychology: Science and Practice,22(3), 296-314.

Smith, K. E., Mason, T. B., Johnson, J. S., Lavender, J. M., & Wonderlich, S. A. (2018). A systematic review of reviews of neurocognitive functioning in eating disorders: The state‐of‐the‐literature and future directions. International Journal of Eating Disorders, 51(8), 798-821.
RebeccaMiller2020Non-Smith Advisor - ChemistryOrganometallic Catalysis - R_Miller Abstract Image.pngIron Catalyzed Cross-Dehydrogenative CouplingTransition metal catalysts have been developed as useful methods for carbon-carbon bond formation. One application of these catalysts is the alpha-arylation of carbonyl compounds, products of which are commonly found with pharmaceutical and agricultural applications. However, this method of cross coupling requires pre-activation of an otherwise unreactive arene, and the presence of base which limits the scope of reactivity. In this study, iron-mediated cross-dehydrogenative coupling of keto ester compounds will be explored without base or pre-activation of the arene. Synthesis of the ethyl keto ester substrate was confirmed by NMR, but purification of the unstable desired compound was unsuccessful due to its chemical similarity to the side products formed in formation and addition of the Grignard reagent and the starting keto ester. Cross-coupling experiments were performed using the crude substrate, however significant impurities hindered analysis and the keto ester decomposed under the high temperature of the reaction conditions. The stable t-butyl keto ester substrate was targeted because it could withstand purification and high temperatures of the cross-coupling. Purification from side products and residual starting material was still unsuccessful again due to chemical similarity. This method of cross-coupling will be studied using commercially available hydroxy ketone derivatives instead of the keto ester. Alternative routes for synthesis of the keto esters will be also pursued to further optimize the reaction and simplify purification.
WillSandke2020Samantha Torquato, Biological Sciences - Biological SciencesMolecular Biology - Perfecting Diagnostic Assays for Marine Mammal Parasites: Parafilaroides decorus and Otostrongylus circumlitisParasites are found all over the globe and in all kinds of species. Several can be harmful for example marine mammals can be infected with heartworms, lungworms, and other nematodes. Identifying these worms is difficult because morphologically they all appear very similar. To counteract this difficulty our lab employs a genetic method of detection. This summer our goal was to perfect an existing diagnostic assay for Parafilaroides decorus and prepare for Next Generation Sequencing on Otostrongylus circumlitis. Our samples came from harbor seals, elephant seals, and California sea lions. In order to perfect the P. decorus assay we isolated DNA from feces and sputum and analyzed varying DNA concentration levels using Quantitative Real-time PCR (qRT-PCR). We found that P. decorus DNA was detected in sputum dilutions at 0.5 ng/µl and in feces dilutions at the same concentration. This means our diagnostic assay can be used on faces and sputum samples (non-invasive) and detect P. decorus DNA (infection) with a concentration as low as 0.5 ng/µl of DNA. For O. circumlitis, our lab had previously created a diagnostic assay to distinguish between Pacific and Atlantic populations. We decided to create a more sensitive assay with no regard to the population area. At the end of the summer, we began to prepare for the new assay by isolating DNA from 14 potential O. circumlitis worms and then running them through 3 primer sets in PCR. We used COX1 primers, SSU primers, and ITS2 primers. We then took the sequences made in the PCRs and got the full DNA sequences back. Through alignments and BLASTing, we were able to successfully identify 11 worms as O. circumlitis. These worms will now be run through Next Generation Sequencing for further confirmation.

Reference:
Keroack, Caroline Dana. "Nematode parasites of marine mammals: phylogenetic and statistical analysis of coevolution" (2014). Theses, Dissertations, and Projects. 71. https://scholarworks.smith.edu/theses/71
Williams, Kalani. “Different Coasts and Different Hosts: Investigating Speciation in the Seal Lungworm Otostrongylus circumlitis” (2018). Theses, Dissertations, and Projects. https://drive.google.com/drive/folders/1p7Nuc3jW3NNj8AvhxySp17hWggFnzFa9
Torquato, S. D. (2018) Seal Distributions and their Parasites [PowerPoint slides]. Retrieved from https://drive.google.com/drive/folders/13LJ0E-asGF78-HRVul_psj7hBYe-93CK
UrsulaMiguel2020Bosiljka Glumac, GeosciencesH. Allen CurranGeosciencesGeosciences - UMiguel_SURF2.pngMovement of large rock boulders by storm waves on San Salvador Island, BahamasStorm waves can drastically impact coastal areas. In the Bahamas, the formation and transport of large rock boulders is one of the consequences of such wave action. Studying the movement of boulders can provide insights into intensity and effects of storms that impact Bahamian islands. In this study, two different coastal settings on San Salvador Island were surveyed: Singer Bar Point, along the low-energy north coast, and The Gulf, along the high-energy south coast. While abroad, I also attended a conference on the geology of the Bahamas and presented a poster on the use of Google Earth historical images for documenting hurricane impact.
My SURF project involved testing the use of RFID (radio frequency identification) technology for tagging and locating boulders (Figure). I spent one week in the field tagging about 100 boulders and cobbles by drilling into the rocks, placing a PIT tag inside, and sealing the hole. The boulders were described and photographed in detail, and their GPS locations were recorded. The use of RFID technology in this kind of research is in its early stages, and this project served as a way of testing its usefulness. This new technology allowed smaller cobbles to be tagged, which was not possible in the past when only GPS location and visual recognition were used and many boulders were not able to be relocated after major storm events. The movement of cobbles is especially interesting for the low-energy north coast of San Salvador, and it could provide powerful insights into the coastal dynamics of a lagoon-protected area.
I plan to continue this research as part of my special studies in 2019/20, and I also plan to return to the study sites in January 2020, after the 2019 hurricane season, to locate the tagged boulders and smaller sediment particles and document any movement caused by waves. This project will serve as a way of testing the use of new technology that can provide a much needed and improved method for boulder relocation after a storm. With this new technology, the impact of storms on these coastal systems can be better documented and communicated with all interested stakeholders - citizens, developers, and the government - in the Bahamas and elsewhere.

Figure: Ursula Miguel ‘20 and Abigail Beckham’19 testing the use of RFID technology in studying the movement of rock boulders by storm waves on San Salvador Island in the Bahamas.
ChelseaPerez2021Will Williams, Physics - PhysicsAtomic Physics - cperez back.png
cperez front.png
Ionization Spectroscopy on Neutral Beryllium-9 My summer project was to help the Williams’ lab prepare for ionization spectroscopy on neutral beryllium-9. To do this, we did three projects. The first was designing and building a circuit to monitor the humidity inside one of the lasers. After we designed the circuit, I spent time in the electronics classroom learning how to solder before building and debugging the circuit. This project was completed and successfully implemented into the lab. I plan to add a digital display to the circuit as part of the electronics course I am taking in the fall.

The second project was to test the wavelength tuning range of two 930 nm laser diodes in an external cavity diode laser (ECDL). The ECDL was built by a senior thesis student last year. To measure the wavelength tuning range, we first install a diode into the laser and aligned all of the internal optics in order to get the laser to lase in a controlled manner. The output light was then sent to an optical fiber that was connected to a spectrometer. The spectrometer allowed us to, in real time, monitor what wavelength the laser was lasing. The range of the first diode we tested was found to be 914 nm to 934.8 nm. Unfortunately we could not get the laser to tune to our goal wavelength of 935 nm. We then tested a second diode and found the wavelength tuning range to be 917 nm to 935 nm, which will work for the ionization spectroscopy project. This project was successful and completed.

Finally, we redesigned a mirror mount inside the ECDL to better improve the performance of the laser. The mirror mount was designed in AutoCAD, 3D printed, and then built out of aluminum in the Center for Design and Fabrication. While the mirror mount is built, the new ECDL design has not yet been tested.
UmeymaIbrahim2022Alicia Grubb, Computer Science - Computer ScienceWeb ToolLucy Wang Uibrahim Model.pngTowards Merging Models over Different Time Intervals BloomingLeaf is an analysis and modeling tool that allows stakeholders to model goals and intentions. The tool helps users understand model evolution and tradeoffs by evaluating how intentions change over time. Prior work looked at creating models piecemeal, by constructing models of individual actors over different time periods and then merging them together. Grubb proposed an algorithm for merging goal models and showed a potential application; but, did not implement the proposed semi-automated algorithm. In this project, we explored the problem domain of this merge algorithm and developed underlying tooling.

To fully implement the algorithm, we needed to merge both the visual syntax and underlying semantics of both un-timed and evolving goal models. We worked on the merging of timed functions. In this project, all functions are step-wise atomic functions over disjoint neighboring intervals, where the atomic functions are constant, increase, decrease, and stochastic. Consider the functions in Figure 1, Model A is an increasing function over the interval [tA1, tA2) and Model B is a constant function over the interval [tB1, tB2). The purpose of our algorithm is to specify Model AB.

Specifying the resulting Model AB depends on the underlying timeline over which each model is defined. For example, in Figure 1, if tA2 < tB1 then there exists an unspecified gap in the function. If tA2 > tB1 then there exists an overlap in the function which may result in a conflict.
Finally, if tA2 = tB1 then the two functions align. In Figure 1, Model AB assumes the case where tA2 = tB1 with the new interval [tA1, tB2). We focused on the tA2 = tB1 case in this research project.

With this timeline, we investigated how the two functions should be merged. We found that Model A and Model B can be merged into either an increase function followed by a constant function, or an increase function with a single time point specified. We proved (by contradiction) the soundness of our assertion. We implemented the first case of the merge algorithm (tA2 = tB1). Future work will finish the implementation for the two other cases and create a web interface for the merge algorithm.
JulietJarrell2021Byron Zamboanga, Psychology - PsychologyPsychology - Double Whammy: Playing Drinking Games as a Form of Prepartying in a Sample of Young Adults Young adults age 18-25 are more at risk for heavy alcohol consumption than other age groups, because they participate in a number of hazardous drinking practices such as pregaming and playing drinking games. There are many types of drinking games, and different kinds of games can affect participants in distinct ways. The present study set out to examine how playing drinking games as a form of pregaming compares to other pregaming styles, and if certain types of drinking games are riskier than others. 482 participants ages 18-25 completed a survey about their pregaming and drinking game behaviors, and the results from this data indicate that those who played drinking games as a form of pregaming consumed approximately one more drink than those who engaged in alternative pregaming styles. Furthermore, those who played Card Games consumed significantly more drinks than participants who played other types of games, and more women than men played Verbal Games. The results of this study can help to improve alcohol intervention efforts by providing more information about types of drinking games and the people who play them.
JiwooSeo2021Denise McKahn, Engineering - EngineeringEngineering - Screen Shot 2019-09-01 at 2.46.14 PM.pngInvestigating the Feasibility of Wastewater Heat Recovery on Smith CampusWastewater heat recovery (WWHR) recycles unused heat from wastewater and uses it to pre-heat clean water that will go through the building pipes. The sewage line and the clean water line (or the refrigerant line) goes through a heat exchanger. The sewage line of the city is a sink, which is a large body of mass that can absorb heat without experiencing any change in temperature. From it, high-temperature sewage is removed and is used to provide heat to clean water which is distributed throughout the buildings in a pipeline. After use, the low-temperature sewage is dumped back into the sewage line. This cycle repeats itself, and with this system, energy will not easily go to waste. Although this system is helpful for Smith’s plan for carbon neutralization by 2030, it is rather unclear if the heat the system provides is actually useful compared to the total heating load. This research was conducted to determine if the wastewater heat recovery system is feasible for Smith, using values found in various case studies.
Using the averages of monthly gas consumption values from the steam plant of Smith College over the past 4 years, the energy provided by sewage was calculated to be rather constant throughout, which means that the WWHR system can be depended on as a constant heat source throughout the year. In the months of June, July, August, and September, the percentage of the heat load from sewage was over the initial rough assumption of 20%, going up to 42%.
Other than the WWHR system, there has been recent discussion about using Paradise Pond as a heat source. Values such as water flow and average temperature of the pond were measured for calculations. It was assumed that 25% of the pond water will be used to generate electricity. From the graph provided, the heat load from the pond is significantly larger than the heat load from the WWHR system, which gives hope that the pond could be a reliable heat source for the College.
DianeAlvarez Benitez2022Glenn Ellis, Engineering - Engineeringengineering - apollo (2).png
apollo13 (2).png
Transforming Engineering Education for Middle Schools (TEEMS)Over the course of the summer I have been involved in a variety of tasks all in order to incorporate Imaginative Education (IE) to the Next Generation Science Standard (NGSS)-aligned curriculum used in middle school classrooms. Imaginative Education includes storylines such as mystery, fantasy, extremes of reality or association with heroes and heroines. Using such storylines creates an environment where students are encouraged to actively engage in classroom activities. Examples of classroom activities could include inquiries, hands-on activities, design thinking, experimentation, discourse and knowledge building. The first part of the summer, we worked on finding creative ways to teach two science units. One of the units was to teach about the different gravitational pull on Earth and on the Moon. By using a storyline of a real life hero and a task at the end of the lesson for students to use what they have learned is an approach for IE. Having prior experience with Photoshop, I was able to help create diagrams and models important for students to visualize the challenge. Aside from providing visuals, I also assisted in finding any resources needed to create the lesson plans. I would help organize the materials needed to build kits for science projects and find online resources to gather more information on the topic. I also attended meetings on the future steps of the research group and how we can ensure that students are able to think critically. This research gave me the opportunity to learn about the efforts to increase engineering learning in secondary education.
ChristinaHung2022Annaliese Beery, Psychology - NeuroscienceNeuroscience - c_hung_surf_abstract_diagram.pngVolcanic Heart: The effects of nervous system autonomic blockade on the formation and expression of same-sex partner preference in female meadow volesMeadow voles (Microtus pennsylvanicus) exhibit seasonally-based social behaviors, forming same-sex partner bonds with other meadow voles in the winter and becoming territorial in the summer. These social interactions may be impacted by cardiac parameters. For example, peripheral oxytocin decreases the heart rate (1), and there is a positive correlation between peripheral oxytocin levels and positive social interactions (2). On the other hand, cortisol is associated with the opposite effect, with salivary cortisol levels and heart rate both increasing during stressful social interactions (3).

In this project, female meadow voles housed in winter conditions were used to test how pharmacological agents that affected their heart rates would affect the voles’ partner preference. The pharmacological agents were Saline (used as the control), ATR (increases heart rate), and ATN (decreases heart rate). Partner preference tests (PPTs) were run to evaluate the effect of these pharmacological agents on female meadow vole social behavior, as they showed whether a free focal vole preferred to spend time huddling with a tethered partner vole or a tethered stranger vole.

The study has two phases: the formation phase and the expression phase. In the formation phase, pharmacological agents were injected before the voles were paired to cohabitate for twenty-four hours, after which PPTs were run. This tested how pharmacological agents affected the formation of the partner preference bond. In the expression phase, the voles were first paired to cohabitate for twenty-four hours, then injected with pharmacological agents immediately before running PPTs. This tested how pharmacological agents affected the expression of the pre-existing partner preference bond.

In the expression phase, three PPTs have been run. In the formation phase, eighteen PPTs have been run, though four will be excluded due to the voles being too stressed to express preferences. Testing is ongoing.


References

1. Gutkowska, J., Jankowski, M., & Antunes-Rodrigues, J. (2014). The role of oxytocin in cardiovascular regulation. Brazilian journal of medical and biological research = Revista brasileira de pesquisas medicas e biologicas, 47(3), 206–214.
doi:10.1590/1414-431X20133309
2. Barraza, J. A. and Zak, P. J. (2009), Empathy toward Strangers Triggers Oxytocin Release and Subsequent Generosity. Annals of the New York Academy of Sciences, 1167: 182-189. doi:10.1111/j.1749-6632.2009.04504.x
3. Kelly, J. , Mangos, G. , Williamson, P. and Whitworth, J. (1998), CORTISOL AND
HYPERTENSION. Clinical and Experimental Pharmacology and Physiology, 25:
S51-S56. doi:10.1111/j.1440-1681.1998.tb02301.x
WayneNdlovu2022Amy Rhodes, Geosciences - GeosciencesAqueous geochemistry - - Effects of road salt on water and soil geochemistry of wetlands in Western MassachusettsDuring winter, large volumes of road salt (NaCl) are added to major routes to melt and prevent the formation of ice on these roads. Road salt can lead to Na and Cl contamination of nearby soils and water bodies through surface runoff and groundwater. Peatlands and wetlands adjacent to roadways may experience varying levels of road salt contamination depending on differences in salt application to roadways and hydrologic flow paths from road to wetland. Organic-rich soils may retain dissolved salt in pore water and by absorption on soil surfaces, which can result in the build up of Na and Cl concentrations in wetlands over time.

We studied the effects of road salt on the surface water, mud, peat, and shallow pore water chemistry of seven wetlands in Western Massachusetts. Three types of wetlands (bogs, fens, and marshes) were identified in relationship to different road ways using a Geographic Information System (GIS). We used an inventory of non-forested peatlands in Massachusetts provided by the Massachusetts Natural Heritage and Endangered Species Program (MA NHESP) and aerial photography. Water, peat and mud samples were collected from Arcadia Bog, Mill Valley Road Bog (MVRB), East Templeton Pond (ETP), Fitzgerald Lake (FL), Quag Bog (QB) and Trout Brook Wetland (TBW).

The inventory of Massachusetts peatlands performed by the Massachusetts Natural Heritage Endangered Species Program (MA NHESP) classifies TBW, MVRB, Arcadia Bog and QB as bogs, which are rainfed peatlands with little to no groundwater input. As would be expected for bogs, our results show that these bogs all have pH values less than 5.5 and low ANC values ranging approximately from 56 to 55 ueq/L. Wetlands with slightly positive ANC values, TBT and QB, potentially could receive some input from groundwater. All bogs are far from major routes, but QB has high chloride concentration of ~4600 μmol/L. By comparison, TBW, MVRB and Arcadia bogs have chloride concentrations ranging approximately from 40-800 μmol/L and further studies will investigate the sources and hydrologic flow paths that may be delivering chloride to different regions of each wetland. Nitrate and sulfate have the lowest anion concentrations which range approximately from 1-45 μmol/L and 1-40 μmol/L respectively. Additionally, the bogs measured in this study had the higher total exchangeable acidity compared to the other wetlands, where results ranged approximately from 3-25 meq/100g. Exchangeable H+ values ranged approximately from 1-41 meq/100g.

ETP is identified in the MA NHESP inventory as a fen; our sampling revealed it as wetland with silty organic mud without thick peat. Although FL, another muddy wetland, is not identified as a fen in the inventory of Massachusetts peatlands, its water and soil geochemistry is similar to that of ETP. Both have high air equilibrated pH values of 7.0 and 7.5 and ANC values range from approximately 250-700 μeq/L. The high ANC values suggest groundwater is seeping into the wetlands. ETP is next to a highway, Rt 2A, therefore has the highest chloride concentration of ~11400 μmol/L whilst FL, which is next to a small road but receives stream runoff from a rural watershed, has a concentration of 1000 μmol/L. Both wetlands have equal concentrations of sulfate ~60 μmol/L and nitrate ~9 μmol/L. Unlike the peatlands, these wetlands have lower total exchangeable acidity, which may be due to greater groundwater input and the absence of peat soil. The presence of groundwater lowers the total acidity in both wetlands, typically
LydiaQuevedo2021Jill de Villiers, PsychologyPeter de Villiers, PsychologyPsychologyPsycholiguistics - Neg Raising Graph Summer 2019.pngSyntactic Complexity and Complement Structures: How Language Helps Children SucceedThe study of psycholinguistics asks, to what extent does language frame and facilitate thought? For child language acquisition, the question becomes: what is necessary for children to accurately learn a language, and what linguistic factors can predict their later success in school? During the summer, my work in the de Villiers’ lab approached this question mainly through two different projects.
The first, conducted under Peter de Villiers, asked whether the degree of Hispanic mothers’ English-Spanish mixing impacted their children’s linguistic skill at the start of school. This was an extension of previous work in the lab, which focused on African American mothers. To be free of linguistic bias, we created a new system to measure the complexity of the mothers’ language, based on the Index of Productive Syntax (Scarborough 1990). We then scored 61 transcripts of Hispanic mothers’ speech (27 English, 12 Spanish, and 22 mixing English and Spanish to varying degrees). Currently, the data is being reformatted for statistical analysis, but we anticipate that a linear regression analysis will show that the syntactic complexity of the mothers’ speech best predicts their children’s future linguistic success, not the degree of mixing or number of utterances. The next step to complete the study is to finish transcribing Spanish-only tapes and the last Mixed tapes so there is a more even number of each; this work will continue in the fall.
The second project, involving all members of the lab, was with Jill de Villiers. We asked how children’s understanding of two- and three-clause complement structures are related to the development of Theory of Mind, an important psychological concept. We believe the mastery of these structures, used to express belief and presuppositions, to lay critical groundwork for Theory of Mind. As a team, our lab developed methodology to evaluate children’s understanding of all three linguistic structures and Theory of Mind. By the end of the summer, we had tested 17 children ages 3;0 to 5;0 and 65 adults. While our results are tentative, the current data clearly shows that children are not treating Neg-Raised statements the same as adults are (see graph). This suggests that the current syntactic model of Neg-Raising is not a complete account of the phenomenon. Depending on whether the results show a relationship between mastery of these linguistic structures and Theory of Mind, our study may also inform future language intervention protocol.
LilyBerlstein2020Jill de Villiers, Psychology - PsychologyPsychology - - Children’s Theory of Mind Ability, Complement Knowledge, and Parental Mind-MindednessBuilding on previous work by de Villiers, this study aimed to examine the relationship between children (aged three to five)’s knowledge of sentences containing tensed complement clauses and their ability to succeed on false belief tasks.
Eleven children from the Smith College Center for Early Childhood Education at Fort Hill, and four children from Nonotuck Community School were tested in this study. Each child completed a total of four tasks. They answered two-clause questions and three-clause questions, completed a task designed to examine how children understand potentially ambiguous negated sentences, and completed false belief tasks. The two-clause stories and the false belief tasks were taken or adapted from previous studies. The three-clause stories and the negation stories along with their corresponding pictures were created by the researchers specifically for this study. The negation stories were partially based on a study by Lewis et al. (2012) that argued children’s misinterpretations of negated sentences using the word “think” were because they incorrectly interpreted the relevance of belief in the sentence instead of the concept itself. Like in Lewis’s study, in the current study children performed truth-value judgments. The researchers have not found evidence that corroborates Lewis et al.’s claim at this point in the study.
There was also a project examining correlations between mind-mindedness in parental speech and childrens’ performance on theory of mind tasks. The parental speech was taken from interviews from a large longitudinal study conducted by the School Readiness Research Consortium. There were two interviews for each parent, one in which the parent was asked to describe their child, and the second in which the parent was shown a video of their child completing a task in the study and then prompted to describe their child. These interviews were transcribed and their statements about their children were qualitatively coded based on Meins et al. (2003)’s mind-mindedness coding system. The system was adapted to include seven categories: cognitive, behavioral, desire, emotion, intention, physical, and general. It was also noted when the speech contained a sentence with a tensed complement. Fifty-three children were added to the existing data set this summer, yielding a total of 101 children for whom we have theory of mind scores and coded parental speech. Preliminary statistical analysis shows a correlation between the parental speech in the desire category and the child’s theory of mind desire scores, as well as between the parental speech categorized as emotion and the theory of mind desire scores.

Citations:
Lewis, S., Hacquard, V., & Lidz, J. ( 2012). The semantics and pragmatics of belief reports in preschoolers. In Proceedings of SALT, 22, 247– 267.
Meins, E., Fernyhough, C., Wainwright, R., Clark-Carter, C., Gupta, M. D., Fradley, E. et al. (2003). Pathways to understanding mind: Construct validity and predictive validity of maternal mind-mindedness. Child Development, 74, 1194–1211.
JordanMoody2020Katherine Kinnaird, Statistical and Data Sciences - Computer ScienceComputer Science - figure4.PNGAligned HierarchiesAligned Hierarchies (ah) is a Python package for finding and encoding repeated structures within musical data. The methods used were originally created by Katherine M Kinnaird in MATLAB before the creation of the Python implementation. Aligned hierarchies takes digitized musical scores or song recordings and finds repeated structures within the chosen song. Then, through segmentation and comparison, the structural components of the song are organized in a hierarchy and combined into a single ‘aligned hierarchies’ composition. Thus, all possible repeated structures are sorted hierarchically and aligned along a common axis denoting time. As seen in the accompanying figure, smaller repeats are towards the top and longer repeats are towards the bottom (Figure from Aligned Hierarchies: A Multi-Scale Structure-Based Representation for Music-Based Data Streams by Katherine M Kinnaird). The current ah package contains four modules: utilities functions, search functions, transformation functions, and assembly functions. An example module is also found within the package, and this example utilizes functions from all four modules to create a full aligned hierarchies implementation.
AylaSay2021Robin Sleith, Biological Sciences - Biological SciencesPitcher plant microbiomes - ayla say fake pitcher.png
ayla say hawley bog sample.png
The source of SAR communities in pitcher plantsI spent my summer studying stramenopile, alveolate, and rhizaria (SAR communities) in pitcher plants. Pitcher plants are carnivorous plants with a tube-like pitcher area filled with water and enzymes used to digest prey (Jaffe et al., 1992). The pitchers digest insects in order to obtain nutrients such as nitrogen, which they cannot get from the nutrient-poor soil where they grow (Gaume & Forterre, 2007; Schulze et al., 1997; Ellison & Gotelli, 2002; Gaume et al., 2002). It is known that SAR communities exist in these plants; however, little is known about how exactly the SAR communities get inside the pitchers in the first place, and where they originate from (Xin-Yue Chan et al., 2016; Ellison & Gotelli, 2002). To test this, I designed an experiment in which I created fake pitcher plants (Falcon tubes) filled with different types of water in order to determine which condition produced the SAR community most similar to those of the greenhouse pitchers (Nepenthes maxima, Nepenthes reinwardtiana, Nepenthes truncata). I also sampled from pitcher plants in the field (at Hawley Bog and Harvard Forest) with the rest of the pitcher plant team so that I had a lot of different real pitcher communities to compare with my fake ones. In order to sample, I swabbed the inside of the pitcher (real or fake) and then pipetted the liquid into a Falcon tube. Back in the lab, I then filtered this liquid and carried out both DNA and RNA extractions. After doing the extractions, I would then do polymerase chain reaction, with the intention of eventually sending off a plate for sequencing. Due to time constraints, I was not able to prepare my samples to send off in time, but I will continue preparations this coming semester. I also found that I will likely need to leave the experiment running for a longer period of time, as the samples from my fake pitchers did not appear to run positive at all (so it is possible that there was not enough time for a SAR community to be established). In the fall, I would like to build on this experiment by analysing the possible factors that could differ between real pitcher and fake pitchers, leading to differences in SAR communities (eg. pH).
JessieChen2020Annaliese Beery, Psychology - PsychologyPsychology - SingleChoice_Social.pngRole of Dopamine in Mediating Social Motivation in Prairie Voles in a Lever-Pressing ParadigmPrairie voles (Microtus ochrogaster), a species of socially monogamous rodents, share a pair bond between mates that is not found in various traditional animal models including lab rats and mice. The existing behavioral test to evaluate pair bond, the classic partner preference test (PPT), involves a three-chamber apparatus, where the focal animal released into the central chamber is allowed to explore a stranger animal and the partner animal each tethered to a side chamber. However, because in a PPT, the focal animal can freely approach either subject, the motivational component of social behavior cannot be clearly distinguished from the reward element.

To better clarify social motivation, my SURF project adopted an operant conditioning paradigm. Specifically, in a two-box experimental apparatus, the focal vole in one chamber is allowed to lever press in order to gain access to its mate, tethered in the other chamber. During a standard 30-minute single-choice social test, the focal vole lever pressed at a progressive ratio (SCPR-1) and the door to the social chamber remained open for one minute for each reward. The single-choice social test is valuable for yielding two measures for quantifying social behavior. First, the number of lever presses and the number of door-opening rewards were recorded during session. Second, each testing session was video-taped, allowing interactions in the social chamber to be behaviorally coded.

Past research indicated that an interaction of oxytocin and dopaminergic signaling pathways plays a critical role in mediating pair bond in prairie voles. The research goal of my SURF project was to further investigate such a neurobiological mechanism using pharmacological manipulations in a lever-pressing paradigm. The focal animals used for this study had been previously trained to lever press (n=7, 5 females, 2 males, age 111-138 days), and all seven pairs of prairie voles were co-housed in long-day lighting cycle throughout the study. Following one habituation day for establishing baseline, the focal subject was intraperitoneally injected with either the dopamine-receptor blockade haloperidol on experimental days or the vehicle solution tartaric acid on control days (dosage 20μl/40g). The single-choice social tests were started 30-60 minutes post-injection, and lasted 30 minutes on SCPR-1 protocol. For preliminary result analysis, the number of lever presses for each subject were compared across time and conditions. As a part of my on-going senior thesis, behavioral data, particularly the length of a characteristic prosocial behavior called huddling, will be later analyzed.
AllisonShoebottom2021Tim Johnson, Botanic Garden - Biological SciencesBiological Sciences - Carex Penn Graph.pngDormancy Exploration on Four Massachusetts Native SpeciesCarex pensylvanica, Arctostaphylos uva-ursi, Trillium, and Comptonia peregrina are four Massachusetts native species, which have high horticultural or ornamental potential and complex dormancy requirements. These dormancy requirements make it difficult for these plants to be propagated by seed, leading to slow output and high cost to the consumer by plant producers. This study aimed to review previous research done on the dormancy requirements of these species, which informed further protocols of solving those dormancies. The first species tested in this study was Carex pensylvanica, a sedge with a high capacity as a lawn alternative. The first step was to gather information from previous studies concerning germination protocols and dormancy experiments. The next step was to do tetrazolium testing on the seeds to determine the viability of the seed populations. Tetrazolium is a chemical that reacts with respiring tissue, where the embryo stains red in viable seeds. This allows the germination protocols to be completed with the overall viability of the seed sets in mind. In Carex pensylvanica, the seeds were bisected through the embryo before the tetrazolium treatment began, due to the hard seed coat of this species. After the bisection, the seeds were left in treatments of 0 hours, 24 hours, and 48 hours of the tetrazolium staining. Each time duration had five groups of thirty seeds. The results of this experiment showed that the control seeds, stained for 0 hours, read as 0% viable. The seed set treated for 24 hours read as 30% viable and the seed set treated for 48 hours read as 51% viable. This implies that the Carex pensylvanica seeds may respire slowly, which could have caused a higher readable viability with sustained exposure to the tetrazolium. Further research and experimentation are necessary to determine the exact cause of this effect. Due to time constraints, the viability testing of the Carex pensylvanica seeds was the only experiment that was completed. Going forward, the viability will be determined for the other three species, and germination tests will be done on all four species with that viability data.
JulietteSaux2020John Loveless, Geosciences - GeosciencesGeosciences - J_SAUX_Fig2.png
J_Saux_Fig1.png
Role of slow slip events on vertical deformation in the Cascadia forearcSlow slip events (SSEs), characterized by aseismic slip spanning several weeks, have been detected on the Cascadia subduction zone. Understanding SSE processes is important to understanding stress accumulation along the subduction interface and the seismic threat it poses for the Pacific Northwest. Occurrence of SSEs at depth implies the presence of accumulated stress below the seismogenic zone. However, it is not fully understood if SSEs fully release the stress imposed on the subduction interface downdip of the seismogenic zone, and what effect they have on landscape evolution of the overlying forearc.
We calculate inter-SSE velocities from Pacific Northwest Geodetic Array GPS position time series after removing the offsets from 31 SSEs between 1996 and 2017, by using a MIDAS robust trend estimator that adjusts for seasonal variation. Using inter-SSE velocities separates the effect of the slow slip events from the interseismic strain accumulation process and permits models to extend slip deficit on the deep portion of the plate interface.
Our results show two distinct zones of coupling: one that is likely coincident with the seismogenic zone and deeper region hosting periodic events of slow slip. These zones of high coupling are separated by a band of low coupling around 30 km depth that could potentially define the lower limit of a future rupture event. Studies simulating coseismic slip show a maximum downdip rupture limit that coincides with our modeled band of low coupling and a range of coseismic slip consistent with our cumulative modeled slip deficit.
Our models predict a vertical deformation signature from SSEs that, spatially, resembles the long-term geologic uplift observed on the Olympic peninsula. While inter-SSE interseismic slip deficit predicts subsidence across the Olympic Peninsula and uplift further inland, adding the SSEs’ uplift signature effectively shifts westward the boundary between uplift and subsidence. The resultant uplift pattern is more consistent with observed interseismic coastal uplift but contains a secondary uplift maximum from SSEs that is not seen in tide and leveling data. This inconsistency could be explained by time-variable coupling throughout the interseismic period.
SamanthaNunziata2020Paulette Peckol, Biological Sciences - Biological Sciencesmarine ecologyChaia Yodaiken2019-08-26.pngIntriguing Introductions: Littorina littorea Grazing Preferences for Native vs. Introduced MacroalgaeThe introduced European gastropod, Littorina littorea, is a dominant, generalist grazer along the northwestern Atlantic coastline. L. littorea has a strong preference for native Ulva spp. in New England; however, when Ulva spp. abundances decline, L. littorea grazes on other macroalgae. When Ulva spp. is unavailable, we found L. littorea grazes on annual macroalgae Leathesia marina, Polysiphonia subtilissima, Cladophora ruchinegeri and Chorda filum in similar amounts, showing no strong preference. This suggests L. littorea contributes to the decline of annual macroalgae as summer progresses. We then investigated grazing preferences of L. littorea for introduced vs. native macroalgae from a non-eutrophic site (Jamestown, RI) and a eutrophic site (East Greenwich, RI). All introduced macroalgae in our study originated from Asia. We asked whether L. littorea’s grazing preferences may affect abundance patterns of these macroalgae.

We measured L. littorea’s herbivory on invasives, Bryopsis maxima and Grateloupia turuturu, and natives, Gymnogongrus griffithsiae, Chondrus crispus, Champia parvula and Fucus vesiculosus, from the non-eutrophic site. L. littorea didn’t consume B. maxima in a preference experiment (Table 1). Natives (e.g. C. crispus) were strongly (t-test, P = 0.002) preferred over B. maxima, suggesting this algal species’ abundance won’t be controlled by L. littorea. Becerro et al. (2001) states B. maxima produces a defensive compound that deters grazers. Similarly, L. littorea didn’t consume invasive G. turuturu in our experiments, and Jones & Thornber (2010) found G. turuturu produces herbivore deterrent compounds. We observed tidepools filled with G. turuturu, suggesting a release from herbivory that could result in it outcompeting other macroalgae.

At the eutrophic site, L. littorea preferred natives, Ulva rigida and Agardhiella subulata, over invasive Gracilaria vermiculophylla (Table 2). When offered introduced species, G. vermiculophylla and Codium fragile, L. littorea strongly preferred C. fragile. C. fragile produces the same chemical compound (dimethylsulfoniopropionate) as Ulva spp. (Lyons et al. 2007), which deters some herbivores; however, dimethylsulfoniopropionate doesn’t deter L. littorea (Peckol & Putnam 2017). G. vermiculophylla produces herbivore deterrents (Nylund et al. 2011; Rempt et al. 2012) that may release this species from herbivory. We observed thick mats of G. vermiculophylla at the eutrophic site.

Introduced macroalgal species have become a dominant feature along coastlines. At our study sites L. littorea consistently preferred native over introduced macroalgae. The lack of grazers has led invasive red macroalgae, G. turuturu and G. vermiculophylla, to flourish. Without future herbivory or intervention, these invasives may outcompete natives, disrupting local ecosystems.
MilagrosDe Pasquale2020Cristina Suarez, ChemistryElizabeth JamiesonChemistryChemistry/BiochemistryLaurie Brutus, Ruby WuRW MD LB Join Surf abstract 2019.pngInvestigation of the Spiroiminodihydantoin Lesion’s Structural and Dynamic Effects on an 11-mer Deoxyribonucleotide DuplexGuanine, which has the lowest redox potential of nucleobases, is easily oxidized by reactive oxygen species (ROS) produced exo- and endogenously through environmental pollutants or cellular metabolic processes. Hyper-oxidation of this base produces the spiroiminodihydantoin (Sp) lesion which leads to cell death and cancer if left unrepaired (Wenke et al., 2013) (Fig. 1, 2). Nuclear Magnetic Resonance Spectroscopy (NMR) is a technique that examines the way the Sp lesion may potentially change the structure of DNA. It can be used to measure the rate of exchange of nucleobase imino protons with water, which can provide information on the dynamic properties of the DNA helix. Differences in the breathing of the control versus lesioned helix can help determine how base excision repair (BER) glycosylases function to recognize the lesion for insertion of the proper base (Crenshaw et al., 2011).
This summer, base pair opening kinetics were investigated by titrating ammonium chloride base into an 11-mer control DNA in order to ensure exchange during base pair opening. The exchange rates (kex) of the imino protons were measured through magnetization transfer with surrounding water, and the rate constants obtained were graphed against increasing base concentration (Fig. 3, 4). From this linear relationship, we hope to extract the rate of base pair opening (kop) for each imino proton and compare it with values obtained from titration experiments on DNA with both stereoisomers of the Sp lesion. Differences in base pair kinetics between the control and Sp duplexes can provide insight into the dynamic effect the lesion may have on DNA. In the future, we plan to perform kinetic titration studies on both stereoisomers of the Sp lesion to evaluate any possible differences in the damage done to the helical structure.

References

Wenke, B.B.; Huiting, L.N.; Frankel, E.B.; Lane, B.F.; Nunez, M.E. Base Pair Opening in a Deoxynucleotide Duplex Containing a cis-syn Thymine Cyclobutane Dimer Lesion. Biochemistry 2013, 52, 9275−9285

Crenshaw, C. M.; Wade, J. E.; Arthanari, H.; Frueh, D.; Lane, B. F.; Núñez, M. E. Hidden in Plain Sight: Subtle Effects of the 8-Oxoguanine Lesion on the Structure, Dynamics, and Thermodynamics of a 15-Base-Pair Oligodeoxynucleotide Duplex. Biochemistry 2011, 50 (39), 8463–8477.
ChaiaYodaiken2021Paulette Peckol, Biological Sciences - Biological SciencesMarine Ecology Samantha NunziataC.Yodaiken1.png
CYodaiken2.png
Intriguing Introductions: Littorina littorea Grazing Preferences for Native vs. Introduced MacroalgaeThe introduced European gastropod, Littorina littorea, is a dominant, generalist grazer along the northwestern Atlantic coastline. L. littorea has a strong preference for native Ulva spp. in New England; however, when Ulva spp. abundances decline, L. littorea grazes on other macroalgae. When Ulva spp. is unavailable, we found L. littorea grazes on annual macroalgae Leathesia marina, Polysiphonia subtilissima, Cladophora ruchinegeri and Chorda filum in similar amounts, showing no strong preference. This suggests L. littorea contributes to the decline of annual macroalgae as summer progresses. We then investigated grazing preferences of L. littorea for introduced vs. native macroalgae from a non-eutrophic site (Jamestown, RI) and a eutrophic site (East Greenwich, RI). All introduced macroalgae in our study originated from Asia. We asked whether L. littorea’s grazing preferences may affect abundance patterns of these macroalgae.
We measured L. littorea’s herbivory on invasives, Bryopsis maxima and Grateloupia turuturu, and natives, Gymnogongrus griffithsiae, Chondrus crispus, Champia parvula and Fucus vesiculosus, from the non-eutrophic site. L. littorea didn’t consume B. maxima in a preference experiment (Table 1). Natives (e.g. C. crispus) were strongly (t-test, P = 0.002) preferred over B. maxima, suggesting this algal species’ abundance won’t be controlled by L. littorea. Becerro et al. (2001) states B. maxima produces a defensive compound that deters grazers. Similarly, L. littorea didn’t consume invasive G. turuturu in our experiments, and Jones & Thornber (2010) found G. turuturu produces herbivore deterrent compounds. We observed tidepools filled with G. turuturu, suggesting a release from herbivory that could result in it outcompeting other macroalgae.
At the eutrophic site, L. littorea preferred natives, Ulva rigida and Agardhiella subulata, over invasive Gracilaria vermiculophylla (Table 2). When offered introduced species, G. vermiculophylla and Codium fragile, L. littorea strongly preferred C. fragile. C. fragile produces the same chemical compound (dimethylsulfoniopropionate) as Ulva spp. (Lyons et al. 2007), which deters some herbivores; however, dimethylsulfoniopropionate doesn’t deter L. littorea (Peckol & Putnam 2017). G. vermiculophylla produces herbivore deterrents (Nylund et al. 2011; Rempt et al. 2012) that may release this species from herbivory. We observed thick mats of G. vermiculophylla at the eutrophic site.
Introduced macroalgal species have become a dominant feature along coastlines. At our study sites L. littorea consistently preferred native over introduced macroalgae. The lack of grazers has led invasive red macroalgae, G. turuturu and G. vermiculophylla, to flourish. Without future herbivory or intervention, these invasives may outcompete natives, disrupting local ecosystems.

(Supported by the Elizabeth B. Horner Fund, Choate Endowed Fund)
(Paulette Peckol, Biological Sciences)
GraceNevil2020Michael Baressi, Biological Sciences - Biological SciencesBiology/Biochemistry - Grace_Nevil_Figure_1.png
Grace_Nevil_Figure_2.png
Defining the role of Reelin signaling during zebrafish brain development Defects in Reelin signaling are associated with the neurodevelopment of Autism Spectrum Disorders (ASD) in humans. Reelin acts through the Very Low Density Lipoprotein receptor (Vldlr) and Apolipoprotein E receptor-2 (ApoER2), which then transduce downstream signals via the cytoplasmic adaptor protein Disabled1 (Dab1). Reelin signaling has been shown to influence neuronal migration via its modulation of the cytoskeleton. However, how Reelin signaling regulates the patterns of neuronal migration through the central nervous system during development, and how these patterns influence later stage behaviors lacks clarity. Previous members of the Barresi Lab have generated loss of function mutations in each of the key Reelin pathway members. I am currently working to define both the individual and combinatorial roles these genes play during neuronal differentiation and positioning from the spinal cord to forebrain (my Honors Thesis). Firstly, we found through in situ hybridization that reelin expression is significantly reduced in subsets of neurons in both our reelin and vldlr mutants (Figure 1). I will continue to work on characterizing the number and positions of distinct progenitor and differentiated cell types – oligodendroglia progenitor cells and glutaminergic neurons, specifically – throughout the CNS. Interestingly, I found that reelin expression is both increased and expanded in our apoER2 mutants (Figure 1). The expression of apoER2 is decreased in our reelin and vldlr mutants; however, expression appears normal in the apoER2 mutants (Figure 2). These data suggest that feedback regulation is involved in the expression of the key players of the Reelin signaling pathway. I hypothesize that reelin upregulates vldlr and downregulates apoER2 while apoER2 upregulates both reelin and vldlr. In addition, I believe apoER2 may act as a repressor of its own expression. I am also interested in quantifying these expression patterns. As such, I designed gene-specific primers for reelin, vldlr, and apoER2 to conduct qRT-PCR on each of our mutants (experiments this fall). I believe that establishing a full assembly of Reelin signaling pathway mutants and understanding their expression patterns will provide a power system to dissect their role during development and later stage behaviors and to investigate how the pathway may contribute to the development of ASD. I was fortunate to present this work at the annual meeting for the Society of Developmental Biology this past July. Stay tuned for more information as my Honors Thesis develops!
AmeliaTurgeon2021Marney Pratt, Biological Sciences - Biological SciencesBiological SciencesSamikshya DhamiAbstract2.pngParadise Pond Project: Freshwater Mussels as Bio-indicators of Mill River Health Paradise Pond is an impoundment created by a dam on the Mill River (Sinton 2002). The dam disrupts the movement of sediment causing sediment to gradually build up over time. In order to prevent Paradise Pond from completely filling with sediment Smith College moves it by flushing it downriver. To make sure the surrounding ecosystem is not affected, The Paradise Pond Sediment Management Project assesses the impact of sediment redistribution on the health of the ecosystem downriver.

In this study, we are using freshwater mussels as a bio-indicator on the health of the
Mill River. An increase of sediment can negatively affect the river mussels because it
obstructs their ability to feed and respire (Nedeau 2008). In order to see if the sediment redistribution in 2016 had an impact on the Mill River the Before-After-Control-Impact design was used to compare freshwater mussel shell length in the Manhan river (control) and in the Mill River (Impact) in 2016 (Before) and 2019 (after) (Strayer & Smith 2003). Comparing the different distributions of shell length will help us understand the water quality of the Mill River. This is because the more distributed the shell lengths are the better the mussel population is doing.

In order to assess whether the influx of sediment had any impact on the range of mussel sizes in the rivers in 2016 and 2019, we conducted a two-way Anova test with location and year as the two factors using type III sum of squares. A significant interaction between the location and the year could suggest that the sediment redistribution had an impact on the mussels. There was a significant interaction between the location and the year (F1,482 = 10.8, P = 0.001). In 2016, the mussels in the Mill River were larger in size than the mussels in the Manhan. This was not the case in 2019. This could suggest that there has been better recruitment of mussels in the Mill river compared to the Manhan. The greater variety of mussel sizes in the Mill compared to the Manhan after the sediment redistribution in 2016 suggests that though sediment redistribution had an impact on the mussels, it did not have a negative impact.

Literature Cited:
Nedeau, E. J., 2008. Fresh water mussels and the Connecticut river watershed. Connecticut River Watershed Council, Greengield, Massachusetts.
Sinton, J. 2002, April. A short history of the Mill river watershed 1650-1940.
Strayer, D. L., and D. R. Smith. 2003. A guide to sampling freshwater mussel populations. American Fisheries Society, Monograph 8, Bethesda, Maryland.
ChristianMadrigal2021Nessy Tania, Mathematics and StatisticsNessy TaniaMathematics and StatisticsComputing Change with PDEVictoria Camarena, Sasha Shrouder - STABILITY OF STRIP FOR 2D INCOMPRESSIBLE FLUIDVortices in 2-Dimensional incompressible fluids modeled by Euler equations with simple shapes such as circles and ellipses are typically stable. Similarly, Beichman and Denisov (2017) showed that a rectangular strip is stable in the periodic domain 0 to $2 \pi$. We will alter the boundary of the strip in the periodic domain, and we will share observations as to how the stability of the vortex changes. We will also observe whether alterations to the strip return to the steady-state strip.
AlinaSiminiouk2020Andrew Guswa, Engineering - EngineeringEngineering - - The Thermosphere Test ProbeCubesats are small satellites that offer a unique platform for scientific investigation in space. The TechEdSat series of cubesats, based at the NASA Ames Research Center, focuses on rapidly developing technologies such as the Exo-Brake drag sail, a passive “space parachute” which rapidly de-orbits the cubesat. This technology has applications in sample return from the International Space Station (ISS). The Thermosphere Test Probe (TTP) is a drag sphere, or “space balloon”, that can allow for the density of the upper thermosphere to be deduced, for automation of the Exo-Brake. It will be integrated within TechEdSat-11 for a late 2020 launch.

For my SURF project in the summer of 2019, I led a team of five other Smith College students to further develop the TTP as a continuation of our work throughout the school year. Our preliminary questions were what material will the balloon consist of, how will we assemble it into a sphere, how will the sphere inflate, and how exactly are we going to deduce density.

We initially expected that the balloon would be made of Mylar, given the flight heritage of other drag spheres. After vacuum testing, we determined that Mylar would not be an option due to leaks. We are currently investigating Teflon FEP film and Kapton film as possible alternatives.

Additionally, an assembly method was developed and optimized for Mylar to develop a sphere. We could not fully test the method’s viability, however we are also working with Thin Red Line Aerospace to explore commercial solutions.

Regarding inflation, the TechEdSat team has flight heritage using water vapor for inflatables in space. After we completed H-generator cell testing, we determined that our best approach would be to use vapor as the primary source of inflation and H-generator cells as a secondary supplement.

We will track the TTP using a COTS GPS from jettison at 400km above the earth’s surface until re-entry at 100km above the earth’s surface to determine density. A plot of altitude over time will be generated using GPS data and will be compared to a predicted plot generated using an orbit propagating tool. The orbit propagator’s atmospheric inputs would be iteratively modified per data point until the trajectories of both match, allowing density to be known at each altitude.

At the end of the summer, students represented Smith College and NASA at the 33rd Annual Conference on Small Satellites in Logan, Utah.
GarielGrant2019Adam Hall, Biological Sciences - Biological SciencesBiological Sciences - GGrant SURF 2019.pngActions of N-N-Diethyl-meta-toluamide (DEET) and Novel Repellents on Human and Mosquito ReceptorsThe carboxamide, DEET is the most effective and widely used insect repellent today. However, drawbacks concerning the efficacy and the safety of the repellent have led to efforts to design new classes of insect repellents. Through quantitative structure-activity relationships, chemists have discovered two chemical groups of novel repellents: the acylpiperidines and the carboxamides, (Fig. 1) with the acylpiperidines generally more potent in biological assays. Although the exact mechanism of action of DEET and other repellents has not yet been thoroughly elucidated, previous research shows that the activity of insect odorant receptors are inhibited in the presence of repellents. Firstly, the present electrophysiological study employed two-electrode voltage clamp with Xenopus laevis oocytes expressing GPROR2/GPROR7 and GPROR8/GPROR7 receptors to assess the effects of the novel repellents on Anopheles gambiae mosquito odorant receptors. Regarding the safety of DEET, reports have linked DEET-containing products to the initiation of seizure activity in users, particularly young children. Despite these claims, there is a lack of evidence of potential mechanisms by which DEET can cause convulsions. Therefore, we employed two-electrode voltage clamp with Xenopus laevis oocytes expressing mammalian GABAA and glycine receptors to explore the actions of DEET at two inhibitory neurotransmitter receptors, both frequent targets of convulsant drugs. Additionally, the actions of the novel repellents (acylpiperidines and carboxamides) were explored relative to that of DEET.

From our investigation of the action of the repellents on mosquito odorant receptors, we found that DEET and all the novel repellents inhibited GPROR2/GPROR7 and GPROR8/GPROR7 receptor currents. Furthermore, we found a strong correlation between the percentage inhibition of GPROR2/GPROR7 receptor currents and the protection time of the repellents, indicating that repellency is linked to the ability to disrupt the insect olfactory system. From our investigation of the action of the repellents on human GABAA and glycine receptors, we found that DEET directly activated GABAA receptor currents and inhibited glycine receptor currents, similarly to the actions of the convulsant strychnine (albeit less potently). With regard to the novel repellents, we found stark differences between the actions of the novel acylpiperidines and the carboxamides (including DEET). The carboxamides, which were generally weaker repellents, showed greater relative toxicity by way of GABAA and glycine receptors while the acylpiperidines with their enhanced repellent activity and possibly lesser relative toxicity by way of GABAA and glycine receptors present an interesting lead in the development of novel insect repellents.



CairaAnderson2020Nessy Tania, Mathematics and StatisticsJennifer BeichmanMathematics and StatisticsMathematicsIssa SusaCAnderson.pngModeling Population Distributions of Animal Groups with Producer-Scrounger BehaviorAmong many animal species, groups form for protection, hunting, and foraging. Patterns emerge from social interactions between the different animals within these groups. In animal groups, some individuals, known as “producers”, search for food (prey) on their own, while others, known as “scroungers”, exploit the producers. This “producer-scrounger” behavior is common in patchy environments where resources are limited. This interaction results in scroungers not receiving as much food as the producers. We built a mathematical model consisting of ordinary differential equations that tracks the population sizes of the producers, scroungers, and their prey. We study the long-term population distributions due to birth, death, and competition.
MarielJones2020Aaron Rubin, Engineering - EngineeringGeotechnical and Transportation EngineeringEmily Katherine AkeyBoxTestsFeaturingE.Akey_TakenbyM.Jones.pngRepeatability of Minimum and Maximum Density Testing on Clean and Fouled BallastBallast material is a critical part of the safety of railways, padding tracks to prevent dynamic vibrations from causing trains to derail. The effectiveness of this material is closely tied to the percentage of fouling that is intermixed with the material. Generally, ballast is placed as compact as practical, but overtime, fouling of the ballast changes the composition of the placed material. Relative density could provide insight into the relative compactness and strength of the material. Unfortunately, the results of minimum or maximum density tests are not well documented in the existing literature. Further, ASTM D4254 and D4253 do provide guidelines for minimum and maximum density testing of large particle diameters, there is minimal discussion in the literature regarding the anticipated error when testing with ballast and fouling. Tests to attempt to characterize this behavior, minimum and maximum density tests were run using Connecticut Granite with granite stone dust used as a fouling material. The samples contained fouling at intervals of 0, 15, 30, 45, and 60% and were placed in a 12-inch interior diameter cylinder mold in accordance with the ASTM standards. For each fouling condition, two operators each conducted 10 minimum density and 5 maximum density tests for a total of 200 minimum density tests and 50 maximum density tests. The effect of fouling, density, and operator, on the repeatability of the tests on ballast is discussed.
KatherineFairbank2021Susan Voss, Engineering - EngineeringEngineering and Audiology - SURF_2019.pngMathematically Describing Ear Canal Cross-Sectional to Improve Absorbance MeasurementsWideband acoustic immittance (WAI) measures are a noninvasive auditory diagnostic tool currently under development to aid in the detection and identification of middle ear hearing problems.The two most widely used WAI measures, reflectance and absorbance, require an estimate of the ear canal's cross-sectional area at the measurement location. Previous work I had done in the lab determined that ear-canal area assumptions made by FDA approved devices, HearID and Titan, does not represent a large range of ears measured, leading to significant effects on actual reflectance and absorbance measurements.

This summer, I aimed to quantify the behavior of cross-sectional area in order to minimize error in acoustic measures. Area was examined as a function of age, sex, height, weight, and depth into the canal. Silicone ear molds were examined from 165 subjects, including 31 subjects from Montclair State University, with ages ranging from 18 to 75 years and roughly equal male and females. The molds were digitized and measured for cross-sectional area 12mm into the canal using two universal markers: the intertragic notch, an indentation separating the tragus and antitragus near the entrance of the canal, and the indentation from the tragus, the external cartilage partially covering the canal’s entrance. After locating the 12mm insertion point, area was measured in increments of 0.6mm along the canal, ranging from 4.8 to 13.2mm in depth. Our lab collaborated with Nick Horton, a statistician at Amherst College, to mathematically analyze the relationship between area and the factors mentioned prior.

Statistical analysis of the data led to the creation of polynomial function with five degrees of freedom, using the 12mm area measures in each decade of life, that allows for estimation of cross-sectional area at a given age. Based on this function, an increase in estimated cross-sectional can be seen across each decade. It was also found that, when accounting for age, other factors such as weight, height, and sex had no significant impact on canal area.

During the Fall 2019 semester, the writing of the paper for this project will be underway. In addition, I will be starting two new projects: describing ear canal length as a function of age as well as developing a probe to measure cross-sectional area of the middle ear in a clinical setting.
ClaraMalekshahi2021Samantha Torquato, Biological Sciences - Biological SciencesGenetics, Parasitology, Marine Biology - californiasealion-001.pngDeveloping and Perfecting Diagnostic Assays for Parasites that Infect Pinnipeds For the vast array of marine mammal species that populate the Atlantic and Pacific Oceans, there is an equally vast collection of marine mammal parasites. This collection of parasites includes lungworms, heartworms, and other kinds of nematodes. Lungworms, especially, can be fatal if in another organ (the heart, for example), if the infection is in an accidental host, or if the parasite is present in juveniles. Identifying different lungworms can be extremely complicated, and is therefore best accomplished through genetic methods such as a diagnostic assay. This summer, the objective was to develop and perfect diagnostic assays for Parafilaroides decorus and Otostrongylus circumlitis, two lungworms regularly found in the California sea lion and the harbor seal, respectively.

The diagnostic assay for P. decorus had already been developed. However, to ensure that the assay was sensitive, varying concentrations of P. decorus DNA isolated from noninvasive samples (feces and sputum) were analyzed by Quantitative Real-time PCR (qRT-PCR). The DNA from P. decorus was regularly picked up in sputum dilutions at 0.5 ng/µl. The same DNA was also regularly picked up in feces dilutions at 0.5 ng/µl. This diagnostic assay can therefore be used on samples obtained through noninvasive methods and is sensitive enough to detect a P. decorus infection in as little as 0.5 ng/µl of DNA.

A diagnostic assay had previously been developed for O. circumlitis that aimed to distinguish between Pacific and Atlantic populations of the parasite. However, as the original assay was not sensitive enough, we were interested in developing a new assay that detected infection. In order to unequivocally identify O. circumlitis worms for use in assay development, potential parasite DNA needed to be sequenced with three primer sets used in phylogenetic analyses. Thus, DNA was isolated from 14 potential O. circumlitis worms. This DNA was then run through PCR, purified or gel isolated, and submitted for Sanger sequencing for each of the three primer sets (COX1, SSU, and ITS2). A total of 11 worms were identified as O. circumlitis (five Atlantic worms and six Pacific worms). The next steps for this project include: next-generation sequencing (NGS) these 11 worms and analyzing the NGS data for cluster repeats.


Reference:
Keroack, Caroline Dana. "Nematode parasites of marine mammals: phylogenetic and statistical analysis of coevolution" (2014). Theses, Dissertations, and Projects. 71. https://scholarworks.smith.edu/theses/71
Williams, Kalani. “Different Coasts and Different Hosts: Investigating Speciation in the Seal Lungworm Otostrongylus circumlitis” (2018). Theses, Dissertations, and Projects. https://drive.google.com/drive/folders/1p7Nuc3jW3NNj8AvhxySp17hWggFnzFa9

LéoYoung2021David Gorin, Chemistry - ChemistryChemistry - - Synthesis of DNA-Catalyst Conjugates for Site Selective Chemistry in Biological SystemsPerforming chemistry in biological systems has posed many issues for scientists. Although chemists are able to perform transformations on one type of functional group relatively easily, it is much harder to perform a transformation on one instance of the functional group. In order to overcome this, our group has engineered DNA-Catalyst conjugates (DCats), which perform in a similar way to enzymes. By using a DNA aptamer that specifically binds to the target molecule with high affinity and attaching it to a small molecule catalyst that performs the desired reaction on the target. Both the aptamer and catalyst are interchangeable in order to perform a wide scope of target specific reactions in biological mixtures. We hypothesize that the DNA aptamer binds the target, holding the catalyst in close proximity and increasing the effective concentration, which also increases the rate of catalysis. While we have previous data that confirms our hypothesis, we have only been assessing our DCats on esters that have some amount of background hydrolysis.
This summer I worked on synthesizing new, more nucleophilic DCats with the hope that they would have the ability to hydrolyze stronger esters, that do not hydrolyze on their own. My work specifically focused on using a cholic acid DNA aptamer and attaching thiol and thiophenol catalysts. Thiols were chosen because of their relevance in biology, specifically in the amino acid cysteine which is found in many catalytic proteins. Besides this I performed some work towards adding multiple catalysts to one DNA aptamer, as there has been evidence previously that the addition of more than one catalyst to an aptamer can have significant rate enhancement. Once DCats were synthesized, I did work on purifying them and testing them for hydrolysis rates in comparison to free catalyst. I found that the thiolated DCats formed disulfide bonds with one another, inhibiting their ability to perform any reaction.
This coming semester, I hope to find an effective solution to reducing the disulfide bonds between catalysts. Besides this I hope to synthesize new DCats with stronger nucleophiles such as DMAP to be tested on stronger esters, which are more resistant to spontaneous hydrolysis.
SashaClapp2019Marney Pratt, Biological Sciences - Biological SciencesBiology/ Ecology - Graph for 2019 abstract mill river Clapp,S.pngItsy Bitsy Teenie Weenie Macroinvertebrates Are Feeding: Assessing the Ecological Impact of Sediment Redistribution in Paradise PondParadise Pond, a precious landmark and an important educational resource Smith College, is an impoundment created by a dam on the Mill River (Sinton 2002). Because dams fundamentally disrupt the movement of both water and sediment, state regulations require that Smith College implement a sediment management protocol to minimize and monitor the ecological impact on the Mill River, while simultaneously preventing Paradise Pond from completely filling with the inevitably accumulating deposition (Wells et al. 2007).The Paradise Pond Sediment Management Project can therefore best be described as a continual assessment of the balance between preserving the iconic Paradise Pond and ensuring the ecological health of the Mill River while doing so. To assess Smith College’s impact on the Mill River, the Before-After-Control-Impact (BACI) design was utilized to compare diversity indices of macroinvertebrates upriver (control) and downriver (impact) of Paradise Pond before and after the July 2016 sediment redistribution (Strayer & Smith 2003). The relative ease with which freshwater invertebrates can be surveyed makes them ideal for determining how sediment management in Paradise Pond might influence the river. Additionally, macroinvertebrates function as an indication of stream health because many are intolerant of environmental variability, and their functional feeding groups provide insight into the ecological roles of taxonomic groups. Comparisons of macroinvertebrate communities in upriver and downriver sites illuminate whether or not sediment redistribution in July 2016 had any impact on the river. Using kicknet sampling, macroinvertebrates were collected each June between 2016 and 2019 at upriver and downriver riffle sites, and were identified to the lowest taxonomic level possible (usually to genus). Relative abundance of functional feeding groups was then calculated. Results show that sediment redistribution had some initial impact on some functional feeding groups in the Mill River. The most significant impact was the decrease in the relative abundance of scrapers downstream and the corresponding increase in collector-gatherers. However, the river recovered fairly quickly once river discharge increased enough to wash away the excess sediment. This suggests that the current sediment management protocol for Paradise Pond does not have long-lasting ecological consequences. However, continued ecological monitoring will be essential as we continue to contend with ever-accumulating sediment and attempt to minimize the human impacts on local aquatic ecosystems.

Literature Cited:
Sinton, J. 2002, April. A Short History of the Mill River Watershed 1650-1940.
Strayer, D. L., and D. R. Smith. 2003. A guide to sampling freshwater mussel populations. American Fisheries Society, Monograph 8, Bethesda, Maryland.
Wells, R. R., E. J. Langendoen, and A. Simon. 2007. Modeling Pre- and Post-Dam Removal Sediment Dynamics: The Kalamazoo River, Michigan1. JAWRA Journal of the American Water Resources Association 43:773–785.
Ruth Penberthy2021Gaby Immerman, Biological SciencesReid Bertone-Johnson EngineeringLandscape Studies, Spacial Analysis - RPenberthy_surf.pngMapping Capen Garden: A Digital Mapping Experiment for the Botanic Garden of Smith CollegeCreating maps that are easy to adjust, update, or used to redesign a space are crucial for the changing landscape around us. At Smith, the landscape design of the campus and various gardens plays a large part in the aesthetic and beauty of the college. For years now, the Botanic Garden has wanted to further develop their online maps. While comprehensive data mapping individual plants existed, there was little data of the surrounding garden’s landscape. There was a general satellite image, but it only offered a vague idea of campus locations. Trees and buildings often hide important landscape features.

It was proposed in early January of 2019 to create a digital 2D map using AutoCAD drafting software for Capen Garden with the hopes that it would speed up the process of redesigning the space. When the project started in the summer, parts of the garden had already been mapped in CAD with the help of previously obtained GIS data. It was then decided that even if a CAD map were to be created for the Botanic Garden, it would also have to be compatible and implemented within the online ArcMap system currently used.

To create the CAD map, some data was able to be taken from a previously existing GIS map and most of the garden was measured and sketched by hand and then drafted electronically. The map is composed of several layers each representing a component of the garden. It allows for the map’s user to customize the map to their personal needs. Once the map was finished in CAD, it was exported into ArcGIS.

The map was edited in ArcGIS desktop to reorganize the currently existing CAD layers to ensure the user could continue to view the map in any way they desire. It was then published online to the Botanic Garden’s Online ArcGIS server.

The map is now accessible to all members of the Botanic Garden and can be edited as Capen Garden will continue to change and grow.
ZihanDiao2022Alicia Grubb, Computer Science - Computer ScienceComputer ScienceNaomi Cebula, Alicia Grubbmodel.png A Preliminary Study of the Utility of Goal Model ConstructionGoal-oriented requirements engineering (GORE) is a subset of requirements engineering, which focuses on the elicitation and analysis of stakeholders' intentions [1]. Grubb proposed several studies aimed at investigating what utility stakeholders derive from constructing and analyzing goal models [2]. In this project, we designed and conducted an empirical study that explored the construction stage of goal modeling, asking whether stakeholders benefit from manually drawing their model (on paper or in a tool) for the purpose of understanding and generating project scenarios. Specifically, we compared reviewing auto-generated models with manually created ones for the purpose of helping students answer their own self-directed questions, the results of which have implications for goal model adoption and automation.

In order to compare subjects’ self-created models with auto-generated models, we asked subjects to discuss a decision they were considering through an online pre-study questionnaire. We manually constructed a goal model from the pre-study. In a one-hour in-person session, participants first answered questions about a training video to measure their understanding. Participants then constructed a model of their decision while talking out loud. Half of the participants in this study used BloomingLeaf (a web-based goal modeling tool), while the remaining participants drew goal models by hand. We prompted participants with a list of prepared questions to help them add new elements and links. After the participants finished their model, we asked them to compare their model to the one we created from their pre-study questionnaire. We then asked them to extend their preferred model with new insights generated. Finally, we asked participants questions to explicate what utility (if any) they experienced in making their decision.

We recruited eight qualified participants at Smith College in the summer of 2019. Each participant was randomly assigned to either the Paper group or the Tool group. They completed an in-person training session and were asked to construct a goal model either on paper or with Bloomingleaf. We used open coding to find themes and categories for qualitative responses. Early analysis showed participants preferred their own model to the researcher generated one. The analysis is ongoing, and we hope to present results later this year.

References:
[1] J. Horkoff, et al.. Goal-oriented Requirements Engineering: An Extended Systematic Mapping Study. Requir. Eng., 24(2):133–160, 2019.
[2] A.M. Grubb. Reflection on Evolutionary Decision Making with Goal Modeling Via Empirical Studies. In Proc. of RE’18, pages 376–381, 2018.
NaomiCebula2022Alicia Grubb, Computer Science - Computer ScienceComputer ScienceLily Diao, Alicia M. Grubbncebula_surf2.pngA Preliminary Study of the Utility of Goal Model ConstructionGoal-oriented requirements engineering (GORE) is a subset of requirements engineering, which focuses on the elicitation and analysis of stakeholders' intentions [1]. Grubb proposed several studies aimed at investigating what utility stakeholders derive from constructing and analyzing goal models [2]. In this project, we designed and conducted an empirical study that explored the construction stage of goal modeling, asking whether stakeholders benefit from manually drawing their model (on paper or in a tool) for the purpose of understanding and generating project scenarios. Specifically, we compared reviewing auto-generated models with manually created ones for the purpose of helping students answer their own self-directed questions, the results of which have implications for goal model adoption and automation.

In order to compare subjects’ self-created models with auto-generated models, we asked subjects to discuss a decision they were considering through an online pre-study questionnaire. We manually constructed a goal model from the pre-study. In a one-hour in-person session, participants first answered questions about a training video to measure their understanding. Participants then constructed a model of their decision while talking out loud. Half of the participants in this study used BloomingLeaf (a web-based goal modeling tool), while the remaining participants drew goal models by hand. We prompted participants with a list of prepared questions to help them add new elements and links. After the participants finished their model, we asked them to compare their model to the one we created from their pre-study questionnaire. We then asked them to extend their preferred model with new insights generated. Finally, we asked participants questions to explicate what utility (if any) they experienced in making their decision.

We recruited eight qualified participants at Smith College in the summer of 2019. Each participant was randomly assigned to either the Paper group or the Tool group. They completed an in-person training session and were asked to construct a goal model either on paper or with Bloomingleaf. We used open coding to find themes and categories for qualitative responses. Early analysis showed participants preferred their own model to the researcher generated one. The analysis is ongoing, and we hope to present results later this year.

References:
[1] J. Horkoff, et al.. Goal-oriented Requirements Engineering: An Extended Systematic Mapping Study. Requir. Eng., 24(2):133–160, 2019.
[2] A.M. Grubb. Reflection on Evolutionary Decision Making with Goal Modeling Via Empirical Studies. In Proc. of RE’18, pages 376–381, 2018.
KathieLi2020Caitlin Shepherd, Psychology - PsychologyClinical Psychology - A Literature Review of Food and Alcohol DisturbanceA recent field of psychological research examines the interplay between eating disorders and alcohol use, beyond the comorbidity and co-occurrence of the two, rather focusing on the motivations of disordered eating behaviors and their relation to alcohol use. The media has used the term “drunkorexia” to colloquially refer to the phenomenon where compensatory behaviors—such as restricting caloric intake, engaging in physical activity of various levels, and using stimulants, laxatives, or diuretics, and purging—are used for either 1) weight control and offsetting the calories gained from alcohol consumption or 2) for increasing the effects of alcohol intoxication, as metabolically caloric restriction leads to alcohol entering the body at a faster rate causing greater blood alcohol levels (Burke, Cremeens, Vail-Smith and Woolsey, 2010). Researchers have attempted to define and operationalize “drunkorexia” in both theoretical and empirical papers and have used the terms alcoholimia, weight-conscious drinking, and food and alcohol disturbance (FAD).

This summer my research partner and I conducted a literature search in the existing drunkorexia and food and alcohol disturbance studies ranging from 2002 to 2019, and we drafted the methods section for a narrative literature review paper. We used the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (“PRISMA”) Statement guidelines to structure our review and began by searching for articles through the electronic databases, PsycINFO, Web of Science, and PubMed. Our initial database search included 177 articles. Then, we removed the duplicate articles and reviewed the remaining 91 articles. In addition to the 91 articles, we conducted another literature search using a snowballing method with the cited reference lists from our retrieved database articles and found 11 articles. In total we reviewed 102 articles for their full-text eligibility. The future directions for this project are that my research partner and I hope to co-author this narrative literature review with Professor Shepherd and submit it for publication to a targeted academic, peer-reviewed journal.

References
Burke, S. C., Cremeens, J., Vail-Smith, K., & Woolsey, C. (2010). Drunkorexia: calorie restriction prior to alcohol consumption among college freshman. Journal of alcohol and drug education, 54(2), 17-34.

Choquette, E. M., Rancourt, D., & Kevin Thompson, J. (2018). From fad to FAD: A theoretical formulation and proposed name change for “drunkorexia” to food and alcohol disturbance (FAD). International Journal of Eating Disorders, 51(8), 831-834.

Thompson-Memmer, C., Glassman, T., & Diehr, A. (2018). Drunkorexia: a new term and diagnostic criteria. Journal of American College Health, 1-7.
QuintonCeluzza2021Michael Baressi, Biological Sciences - Biological SciencesDevelopmental Biology - Bioelectrics - - Testing Bioelectrics: The Role of Bioelectric Patterning on Axis FormationIn order to go from a single celled zygote to an entire organism, the cells must divide. As they do so, they develop different functions and properties. This process, known as cell differentiation, begins early in embryonic development, as the embryo moves through gastrulation and into segmentation. It’s currently believed that cell differentiation is controlled by exposure to morphogens (chemical signals), which regulate gene expression to ultimately determine phenotype - but what if there was something else, working alongside morphogen signaling?

Bioelectrics is the study of the patterns and effects of ion distribution (membrane potential) across an organism. While the exact role of bioelectrics is not well understood, it appears to play a role in controlling regular development across entire organisms. In this context, we are exploring the role bioelectrics plays in early embryonic development, using zebrafish (Danio rerio) as a model organism (specifically the connection between patterns of cell membrane resting potential and normal organism axis formation).

Research this summer has focused on the development of two transgenic reporter lines, prerequisite literature research on morphogen-signaling pathways with known roles in axis formation, and the creation of introductory documentation summarizing research aims and basic protocols. Completion of these smaller projects will guide further research as we look into connections between bioelectric state and organism patterning.
KayleighBoos2021Stylianos Scordillis, Biochemistry - BiochemistryProteomics - Screen Shot 2019-07-31 at 10.59.22 AM.pngCreatine Kinase: Regulation and Post-Translational ModificationThe goal of this project was to determine how creatine kinase (CK) is regulated by phosphorylation, the covalent addition of a phosphate to an amino acid side chain, during skeletal muscle myogenesis in C2C12 cells, that is the development of skeletal muscle from mono-nucleate proliferating cells to multinucleate quiescent cells that spontaneously contract in cell culture. The Scordilis lab has shown the presence of CK proteoforms in immunoblots of whole cell extracts electrophoresced on SDS-PAGE gels. There has not been much research on the phosphorylation state of these proteoforms during myogenesis. Protocols are being established to allow for the separation of these proteoforms by two-dimensional gel electrophoresis as well as by their level of phosphorylation.

The CKs have multiple possible phosphorylation sites, however there are few papers focused on identifying them in the three CK proteoforms: CK-M (43,045 Da), the most prevalent skeletal muscle proteoform, CK-B (42,714 Da), the non-muscle cytoplasmic one, and CK-Mt2 (47,474 Da), the mitochondrial one. The three most common phosphorylation sites for each proteoform were found through compiling those papers that identified potential phosphorylation sites; in Table 1 below are the potential phosphorylation sites narrowed down based on the abundance of papers referencing those sites.


In addition to identifying and comparing potential phosphorylation sites of the three CK proteoforms, ProteinBlast runs were used to compare the amino acid sequences to determine unique peptide differences for future mass spectrometry identifications where the proteoforms differ: CK-M and CK-B share 79.00% sequence identity and the same regions of ATP binding, positions 128-132 and 320-325; CK-M and CK-Mt2 share 67.59% sequence identity but no ATP binding identities; and, similarly, CK-B and CK-Mt2 share 67.31% sequence identity but no regions of ATP binding identity.

During this coming year I plan on continuing this research in the Scordilis lab with the hope to add to the available literature of energy homeostasis sources for exercise in skeletal muscle, especially in terms of myogenesis and repair of muscle following moderate injury.

AhlenneAbreu2022Stylianos Scordillis, Biochemistry - BiochemistryProteomics - AAbreu Immunoblots.pngCreatine Kinase Isoforms: An Immunoblotting StudyCreatine kinase (CK) is an enzyme that is involved in energy homeostasis. It has three common isoforms that are found in different cell types and organelles. The most common cytoplasmic isoform in adult skeletal muscle is CK-M (43,045 Da); in non-skeletal and cardiac muscle the CK-B isoform (42,726 Da) is expressed; and CK-MT2 (47,386 Da) is expressed in the matrix of mitochondria. Using extracts from the soleus and medial gastrocnemius in rats, the distribution of all three isoforms was determined by quantitative immunoblotting.

The extraction technique for the muscles produced sarcomeric (extract pellet, primarily containing the contractile proteins and their regulatory proteins) and sarcoplasmic fractions (extract supernate, primarily the more general housekeeping proteins). Protein extract concentrations were carried out by the Lowry assay. To determine the relative concentrations of the three CK isoforms in the fractions of the two muscles single dimension SDS gel electrophoresis was employed. This technique separates all the proteins in a sample (extract) according to their apparent molecular weight and visualizes the protein bands by use of Coomassie Brilliant Blue R250 dye. An identical gel was also run but not stained; this gel was transferred to a matrix called PVDF which binds all of the proteins (called a blot) and allows for detection of specific proteins by using a specific antibody to a protein. Using such specific antibodies to CK-M, CK-B and CK-MT2 all three proteins were detected in the extracts (Figure 1). These blots demonstrate that all three isoforms are found in the two adult skeletal muscles and that they are differentially distributed in the sarcomeric versus the sarcoplasmic compartments.

I plan on continuing this work during the coming year as a Posse student in the Scordilis lab.
KatelynSmalley2021Paulette Peckol, Biological Sciences - Biological SciencesMarine BiologyVictoria BajtayScreen Shot 2019-07-27 at 4.42.32 PM.png
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Clashing Crabs: Interactions Between Invasive Species, Hemigrapsus sanguineus and Carcinus maenas Both competitive and trophic level interactions shape the behavior and activities of marine organisms occurring in intertidal habitats. Hemigrapsus sanguineus, Asian Shore Crab, and Carcinus maenas, European Green Crab, are invasive species along western Atlantic shorelines. Green Crabs have been present in New England habitats for over 100 years, while the Asian Shore Crab is a more recent introduction. These species have similar food and habitat preferences, and scientists have suggested that the Asian Shore Crab has largely replaced Green Crabs in southern New England. In this study, we investigated whether competition between H. sanguineus and C. maenas might impact their habitat choice and food acquisition, thus affecting their abundance patterns in southern New England.

For our experimental set up (n = 3 for all treatment conditions), we used rectangular (25 cm L x 18 cm W x 17 cm H) aquaria and created suitable habitat with a layer of sand, small pebbles and shells (~3 cm thick). For some treatments we added small rocks as barriers and hiding places. Most experiments were conducted under submerged conditions, with the crabs covered with 5 cm of seawater. Prior to each experiment, we acclimated the crabs for 10 min in opaque containers that allowed for aeration. We then lifted the containers, freeing the crabs to interact during the 30 min experimental period. Most observations were made in a dimly lit room. We first determined that Mytilus edulis, an abundant intertidal mussel species, was the preferred food of both crab species. Both H. sanguineus and C. maenas preferred foraging while submerged (simulating high tide), and were inactive, burrowing during daytime (lighted), intertidal (low tide) conditions. Thus, they displayed no intra- or interspecific interactions during daytime “low tides”. Notably, burrowing techniques differed between species, and were indicative of their habitat preferences. H. sanguineus would tuck its carapace beneath a rock while using circular pushing motions with its claws to wedge itself beneath the rock and deeper into the sediment. In contrast, C. maenas used a movement generated with its hind legs, which propelled the crab vertically downward into the substrata, where it could move laterally while still being buried. These tactics of burrowing reflect their locations in their natural environment: H. sanguineus is usually found tucked underneath rocks while C. maenas can be located patrolling the sediment flats.

We studied intra- and interspecific interactions in the presence and absence of food and complex habitat structure (rocky barriers). In the absence of food and rocky habitat, we observed fights only between conspecific H. sanguineus (a mean of ~4 fights per 30 min). Under conditions of a rocky barrier (without food), we recorded numerous fights between conspecific H. sanguineus (ASC-ASC), as well as interspecific fights with C. maenas (Fig. 1). C. maenas showed no intraspecific interactions under this treatment condition. However, when food present, there were fights in all three treatments (Fig. 2). C. maenas became aggressive, sometimes stealing food from H. sanguineus. Thus, although they have unique approaches, both species have found a strategy that allows them to effectively feed and survive along rocky coastlines. We conclude that the more aggressive behaviors of H. sanguineus has resulted in a habitat shift by C. maenas to shallow subtidal habitats.

(Supported by the Elizabeth B. Horner Fund, Choate Endowed Fund, CFCD)
(Paulette Peckol, Biological Sciences)
AudenBalouch2021Susan Voss, Engineering - EngineeringEngineeringSylvie Rosenstein - Analysis of Wideband Acoustic Immittance from Artificial and Real EarsThe Mimosa Acoustics HearID and the Interacoustics Titan are two FDA approved noninvasive auditory diagnostic tools. The data taken with these instruments have the potential to diagnose factors of conductive hearing loss in young children and adults. The two instruments are used to collect Wideband Acoustic Immittance (WAI) measurements including acoustic impedance, reflectance, and absorbance. The measurements from these devices should be comparable when recorded on the same subject in the same environment, yet yield notably different results. The Titan and HearID instruments have different probe insertion depths in the ear canal. The HearID system is able to be inserted further into the ear canal since the probe tip is foam whereas the Titan probe tip is rubber. The different probe insertion depths is hypothesized to be a significant cause of variation in WAI measurements between the systems.

WAI measurements were made using both the Mimosa Acoustics HearID and Interacoustics Titan inserted into a Larson Davis artificial ear. An artificial ear was used to mimic the behavior of a normal human ear. To investigate the effect of insertion depth on WAI measurements, data was taken at different predetermined locations in the artificial ear canal. Methods were developed to assure that the probes of the two instruments were at the same locations during their measurements. With data collected at various locations, the canal length can be determined based on where the probe sits in the ear canal. These measurements are actively being used in the Voss lab to further study the relative insertion depth in the ear canal between HearID and Titan probes on human subjects. We will continue to contribute to this work in the fall of 2019.

This summer we had the opportunity to visit Massachusetts Eye and Ear as well as Boystown National Research Hospital to discuss research with colleagues of the Voss lab. It was valuable being able to experience the applications and contributions of others in the auditory research field outside of Smith.
SylvieRosenstein 2021Susan Voss, Engineering - EngineeringEngineering Auden Balouch - Analysis of Wideband Acoustic Immittance from Artificial and Real EarsThe Mimosa Acoustics HearID and the Interacoustics Titan are two FDA approved noninvasive auditory diagnostic tools. The data taken with these instruments have the potential to diagnose factors of conductive hearing loss in young children and adults. The two instruments are used to collect Wideband Acoustic Immittance (WAI) measurements including acoustic impedance, reflectance, and absorbance. The measurements from these devices should be comparable when recorded on the same subject in the same environment, yet yield notably different results. The Titan and HearID instruments have different probe insertion depths in the ear canal. The HearID system is able to be inserted further into the ear canal since the probe tip is foam whereas the Titan probe tip is rubber. The different probe insertion depths is hypothesized to be a significant cause of variation in WAI measurements between the systems.

WAI measurements were made using both the Mimosa Acoustics HearID and Interacoustics Titan inserted into a Larson Davis artificial ear. An artificial ear was used to mimic the behavior of a normal human ear. To investigate the effect of insertion depth on WAI measurements, data was taken at different predetermined locations in the artificial ear canal. Methods were developed to assure that the probes of the two instruments were at the same locations during their measurements. With data collected at various locations, the canal length can be determined based on where the probe sits in the ear canal. These measurements are actively being used in the Voss lab to further study the relative insertion depth in the ear canal between HearID and Titan probes on human subjects. We will continue to contribute to this work in the fall of 2019.

This summer we had the opportunity to visit Massachusetts Eye and Ear as well as Boystown National Research Hospital to discuss research with colleagues of the Voss lab. It was valuable being able to experience the applications and contributions of others in the auditory research field outside of Smith.
IsabelAhlstrom2021Robert Newton, Geosciences - GeosciencesGeoscienceClara Brill-CarlatCBrillCarlat_IAhlstrom_Figure1.PNG
CBrillCarlat_IAhlstrom_Figure2.PNG
Bathymetry and Sediment Deposition in Paradise PondParadise Pond is a small, man-made feature along the Mill River on the Smith College campus. Sediment build-up has been a maintenance issue in the pond; sediment is deposited when the water velocity of the Mill River decreases as it enters the pond. Instead of dredging the pond and depositing the sediment in a local landfill, the college has proposed to remove sediment by flushing it downstream through a sluice gate in the dam during high discharge events. To determine how much flushing is necessary, the amount of sediment entering the pond was evaluated using bathymetry mapping.

This summer, bathymetry data was collected using a RiverRay Acoustic Doppler Current Profiler (ADCP) device in deeper water, as well as an Arrow Gold RTK GPS unit and a Leica Total Station in shallower areas. The bathymetric map was constructed in ArcMap (figure 1). The amount of sediment accumulation in the past year, 4,900 cubic meters, was determined by subtracting a summer 2018 bathymetric map from the more recent 2019 map.

A significant portion of the recent sediment accumulation occurred during a December 21, 2018 storm that deposited 2.45 inches of rain. The peak discharge values from the storm are among the top 15 recorded along the Mill River since the 1930s. Using turbidity data, the quantities of suspended sediment entering and exiting the pond during the storm were calculated. The difference between the two quantities, 80 metric tons (560 cubic meters), is the amount of suspended sediment deposited in the pond on December 21 and 22, 2018. The storm also moved heavier bedload sand into the sandbars in the northwestern region of the pond, where the river first enters the pond (figure 2).

Bathymetry maps helped to determine the amount of sediment in Paradise Pond. This evaluation will help the college qualify for the permits necessary to flush the sediment through the dam and downriver.


ClaraBrill-Carlat2021Robert Newton, Geosciences - GeosciencesGeosciencesIsabel AhlstromCBrillCarlat_IAhlstrom_Figure1.PNG
CBrillCarlat_IAhlstrom_Figure2.PNG
Bathymetry and Sediment Deposition in Paradise PondParadise Pond is a small, man-made feature along the Mill River on the Smith College campus. Sediment build-up has been a maintenance issue in the pond; sediment is deposited when the water velocity of the Mill River decreases as it enters the pond. Instead of dredging the pond and depositing the sediment in a local landfill, the college has proposed to remove sediment by flushing it downstream through a sluice gate in the dam during high discharge events. To determine how much flushing is necessary, the amount of sediment entering the pond was evaluated using bathymetry mapping.

This summer, bathymetry data was collected using a RiverRay Acoustic Doppler Current Profiler (ADCP) device in deeper water, as well as an Arrow Gold RTK GPS unit and a Leica Total Station in shallower areas. The bathymetric map was constructed in ArcMap (figure 1). The amount of sediment accumulation in the past year, 4,900 cubic meters, was determined by subtracting a summer 2018 bathymetric map from the more recent 2019 map.

A significant portion of the recent sediment accumulation occurred during a December 21, 2018 storm that deposited 2.45 inches of rain. The peak discharge values from the storm are among the top 15 recorded along the Mill River since the 1930s. Using turbidity data, the quantities of suspended sediment entering and exiting the pond during the storm were calculated. The difference between the two quantities, 80 metric tons (560 cubic meters), is the amount of suspended sediment deposited in the pond on December 21 and 22, 2018. The storm also moved heavier bedload sand into the sandbars in the northwestern region of the pond, where the river first enters the pond (figure 2).

Bathymetry maps helped to determine the amount of sediment in Paradise Pond. This evaluation will help the college qualify for the permits necessary to flush the sediment through the dam and downriver.
Cody (Rebecca)Bloomfield2021Samantha Torquato, Biological Sciences - Biological SciencesMarine Mammal Parasitology - SURF.PNGDevelopment of quantitative real-time PCR-based diagnostic assays for marine mammal lungworms Otostrongylus circumlitis and Parafilaroides decorusParasitic infections exacerbate the challenges of marine mammal conservation (Harvell 2002). As climate change progresses, the prevalence and severity of zoological parasitic infections is projected to increase (Harvell 2002). Thus, identifying and mitigating parasitic infections is an important component of conservation for threatened marine mammal populations (Dailey 2005). Sea lion lungworm (Parafilaroides decorus) and harbor seal lungworm (Otostronglyus circumlitis) are two parasitic nematodes identified as pathogens of concern by partner marine mammal rescue facilities. Previous diagnosis relied on morphological identification, which requires years of experience and often overlooks low-level infections (van Lieshout & Roestenberg 2015). We aim to develop quantitative real-time (qRT)-PCR-based diagnostic assays that are species-specific and sensitive. Previous research identified and sequenced Parafilaroides spp. and O. circumlitis field samples. Over the summer, we sought to optimize and verify the assays. First, we optimized primer annealing temperatures and template DNA concentrations. We tested the assays against a variety of species to confirm specificity. We performed dilution series to estimate the limit of detection. To ensure that our tests would be useful to marine mammal rescue facilities, we tested the assay on noninvasively collected sputum and fecal samples. Our data indicate the Parafilaroides assay can be used on several types of noninvasively collected samples. We tentatively established that Parafilaroides DNA can be detected in sputum field samples. This provides confirmatory evidence for the hypothesized pulmonary-gastrointestinal migration of Parafilaroides within pinnipeds (Dailey, 2005). Originally, the O. circumlitis assays were designed for separate oceans, but we found that one assay performed better on samples from both oceans. We attempted to optimize the O. circumlitis assay but found we may need to redesign the assay. Future work will involve a field trial for the Parafilaroides assay and a redesign of the O. circumlitis assay. We hope that development of these diagnostic assays facilitates conservation efforts of marine mammal populations.
MelRegan2021Adam Hall, Biological Sciences - Biological SciencesBiological Sciences/NeuroscienceN/ADirectActivatioOR2-7---MR.pngCharacterization and Comparison of Natural Insect Repellents on Mosquito Odorant ReceptorsMosquitos (anopheles) are carriers of deadly insect borne diseases such as Yellow Fever, West Nile virus, and Zika virus (Deletre et al, 2015). Plant based repellents have been used for thousands of years to ward off the disease carrying insects (Maia et al, 2011). The molecular mechanisms for repellency have not been explored until recently [1]. This study aims to screen 11 plant based compounds using electrophysiological methods to measure the mosquito odorant receptor current inhibitions caused by the application of natural repellents. The odorant receptors are heterodimers composed of an essential OR7 subunit and a different subunit. This study uses the OR2/ OR7 combination. Odorant ligands naturally emitted by humans allow for the flow of cations through the receptor with the OR2/ OR7 combination activated by 2-methyl phenol. mRNA of the odorant receptors were injected into Xenopus Laevis oocytes and their currents recorded using the two-electrode voltage clamp method. The screening was conducted by co-applying 10uM of the odorant, 2- methyl phenol and 300uM of the natural repellent and measuring the resulting currents. Citronellal, geraniol, limonene and cuminaldehyde have inhibitions that are 20% or greater (see Figure 1) of the odorant current. These natural repellents will be studied further by using other subunit combinations for future characterization of receptor inhibition that might underlie their repellent activity.



Figure 1: Screening of the 11 natural repellents (300 uM) on the OR2/ OR7 receptor combination for their percent inhibition of the receptor current when co-applied with odorant, 2-methyl phenol (10 uM).



References:
Deletre, E., Chandre, F., Williams, L., Duménil, C., Menut, C., & Martin, T. (2015) Electrophysiological and behavioral characterization of bioactive compounds of the Thymus vulgaris, Cymbopogon winterianus, Cuminum cyminum and Cinnamomum zeylanicum essential oils against Anopheles gambiae and prospects for their use as bednet treatments. Parasites & Vectors, vol 8, Article number: 316.
Maia, M. F., & Moore, S. J. (2011). Plant-based insect repellents: a review of their
efficacy, development and testing. Malaria journal, 10 Suppl 1, S11. doi:10.1186/1475-2875-10-S1-S11
AnnaPearson2021John Loveless, Geosciences - GeosciencesGeosciences - Figure for A. Pearson.png
Figure for A. Pearson_1753.png
Understanding the Physical Mechanisms Behind Faulting Styles in IcelandKarson et al.’s 2018 paper, “Rift-parallel strike-slip faulting near the Iceland plate boundary zone”, analyzed an unexpected preponderance of strike-slip faulting in Iceland, suggesting rift propagation away from the Icelandic hotspot as the primary cause. This project tested whether the observed faulting styles in Iceland found in the paper could be explained by a model only considering the primary faults and stress imposed by relative tectonic plate motion and the Icelandic hotspot.
The model was developed by combining a geologic map of Iceland and areas of strike-slip faulting identified in the original paper with a sphere representing the hotspot. The impact of the plate motion between the North American and European Plates in Iceland was modeled using a remote stress tensor, calculated in two different ways: (1) using the angle of relative plate motion and (2) using the spatial gradient of a GPS velocity field. All faults were run through an elastic boundary element program to calculate the slip required to relieve the stress imposed on them. To characterize the modeled faulting styles, P- and T-axes were calculated. The average of the angular difference between the P-axes and T-axes for the model and a set of field data was used for evaluation.
A series of models were first run using the remote stress tensor calculated from GPS velocities and varying an additional impact from the hotspot. Models with 0 to 30 mm of inflation of the hotspot resulted in an average angular misfit of less than 50°. Using the remote stress tensor calculated as uniaxial stress along an azimuth of relative plate motion and the hotspot with 10 mm of inflation, a series of models was also run varying that azimuth in 5° increments from 5° to 180°. Models run at an azimuth of 110° and 120-140° had an average angular difference of less than 50°.
These findings suggest a strong consistency between models using stress based on the GPS velocity field, which should inherently include some impact from the hotspot along with plate motion, and models using stress along a single azimuth as well as the hotspot. Although some areas in northwest Iceland failed to produce results consistent with field data, as a whole these models suggest that very simple boundary conditions, which include the impact of tectonic plate motion and the Icelandic hotspot, agree well with what has been observed in the field.
JasminePacheco-Ramos2019Denise Lello, Biological Sciences - Biological SciencesBiological SciencesJasmine Pacheco-Ramos' 19, Emily Hitchcock ’19, Yeiny Moreno ’20, Giovanna Sabini-Leite ’21, Glenda Perez ‘21, Renee Revolorio Keith ’21 - Coral Reef Ed-Ventures Summer 2019Summer 2019 was the twentieth year of the Smith College collaboration with Hol Chan Marine Reserve on Ambergris Caye, Belize. The goals of Coral Reef Ed-Ventures are to conduct research on coastal ecosystems and communities and to offer an environmental education and conservation experience for the children of San Pedro Town on Ambergris Caye. The research focused on coral mounds at Mexico Rocks, mangroves propagules located in lagoons near the Grand Belizean Estates development, and interviews assessing the eco-cultural identity of local people who work with the natural environment or who have completed a Coral Reef Ed-Ventures camp in the past. We later incorporated many of these research techniques into our teaching activities in two free Coral Ed camps for the island schoolchildren.
Smith students conducted three research projects with professors David Smith (BIO), Denise Lello (BIO), Allen Curran (GSC), and Shannon Audley (EDC). The first project was part of a long-term survey of the health of coral mounds inside the barrier reef at the large Mexico Rocks site that was recently accorded protection as the newest part of Hol Chan Marine Reserve. These surveys assessed the percentages of live coral cover and soft coral abundance, plus diversity, in order to track significant changes over time. Previously, several mounds towards the center of Mexico Rocks and several towards the south end had been sampled with quadrat and transect methods using SCUBA, snorkel, and underwater cameras. These mounds were resampled this year, and two new mounds from a different area were also surveyed.
The second project tracked mangrove survival in the lagoons in the interior of the island in the vicinity of disturbed areas associated with development. Previous research has indicated that several biotic and abiotic factors can impact the persistence of mangrove propagules. We collected data for each propagule (previously mapped), including taking underwater images of organisms associated with the propagules and visual assessment of damage and herbivory. For the third project, students interviewed people who live in San Pedro and work in eco-tourism and/or attended a Coral Reef Ed-Ventures camp as a child. The goal was to elicit stories that reveal ecocultural identity. We interviewed dive masters and scuba instructors, staff from Hol Chan Marine Reserve, and some alums from the Coral Reef Ed-Ventures program. The questions probed how the person viewed interconnections between themselves and nature; experiences that changed their perspectives about the natural environment; and their thoughts on the future of the natural environment, with a focus on how their relationship with nature and life will be affected.
This year’s theme for youth camp was ‘My Roots in the Sea.’ Our student-teacher team created activities focused on seven topics: eco-cultural identity, mangroves, coral reefs, relationships, challenges/threats to the ecosystem, health of humans and ecosystems, and advocacy. Interactive activities (e.g., a beach clean-up, an edible coral polyp activity) were paired with short lectures and videos. This variety of topics allowed campers to make connections between the ocean ecosystems and inhabitants and land-based human activities, as well as gain more awareness about how they can best protect their local environments.
Older children attended an upper level R.E.E.F (Research in Ecology and the Environment is Fun) Program. This year’s theme for the R.E.E.F. program was ‘Human Relationships with the Reef, Research, and Advocacy.’ Campers were introduced to various research methods, including how to calculate percent live coral cover on coral mounds. They also learned about advocacy and threats to the environment. For example, the campers were presented with information about how macro and micro-plastics affect the entire food chain. Two guests from the community were asked to come in and talk about their particular work in the environment in order to give the kids a firm idea of environmental efforts occurring in their community. Chris Summers from ACES (American Crocodile Education Sanctuary) taught about the cultural and ecological importance of mangroves and biological aspects of the crocodiles that live in Ambergris Caye. Mariela Archer, the environmental educator from Hol Chan Marine Reserve, spoke about overfishing and the importance of marine protected areas. We took REEF camp participants on a snorkeling trip to Hol Chan and Shark and Ray Alley so that they could observe the marine protected area and the underwater life that they were learning about. With a greater understanding of the local environment and how research is conducted, campers were able to make meaningful connections between coastal ecosystems and their home on Ambergris Caye.
In summary, our research advanced understanding of changes in coral and mangrove habitats and the education program exposed children on the island to specific environmental changes that impact their everyday lives. This summer of Coral Reef Ed-Ventures was full of new experiences and learning opportunities that we hope to expand upon in coming years.


Supported by the Environmental Science and Policy Program (ES&P) and Agnes Shedd Andreae Fund and Schultz Foundation; Biological Sciences’ B. Elizabeth Horner Fund and Mary E. Schlesinger Botany Fund and a gift from Linda Salisbury, Smith College Trustee Emerita and Class of ’78.

Advisors: L. David Smith and Denise Lello, Biological Sciences, Al Curran, Geosciences, Shannon Audley, Education and Child Studies, and Javier Paredez, Hol Chan Marine Reserve, with help from Joanne Benkley (ES&P and CEEDS).
AthenaZhang2020Elizabeth Jamieson, Chemistry and Biochemistry - ChemistryChemistry and Biochemistry - Presentation1.pngNucleosomal DNA Repair SURF AbstractDNA base lesions, such as 8-oxoguanine (8-oxoG) and spiroiminodihydantoin (Sp), can be formed when DNA is oxidized, causing mutations that result in human disease. The Base Excision Repair (BER) pathway, initiated by DNA glycosylases, can mitigate this damage, but is challenged by the packaging of genomic DNA into chromatin. The effect of this packaging on the repair of the Sp DNA lesion has not yet been examined. Following the procedures of Burrows et al.1and Delaney et al.2, the ability of the DNA glycosylase, Fpg, to repair the 8-oxoG lesion in DNA was investigated during this summer work. Eventually, this project will expand to provide the first experimental data that examines the impact of genomic DNA packaging on the repair of Sp lesions.

DNA repair assays were successfully conducted with 30-mer Cy5-labeled oligonucleotides and Fpg to examine the ability of Fpg to repair 8oxoG:C lesions versus a G:C control. Analysis of substrate and product band intensities on polyacrylamide gels generated an average reaction rate constant (k2) of approximately 3 min-1 which was comparable to the published results.1 A sample repair assay gel was attached to this report.

With the success of the 30-mer assays, similar experiments were carried out with 146-mer Cy5-labeled oligonucleotides and Fpg to demonstrate the ability of this enzyme to repair the 8-oxoG lesion in longer DNA duplexes that are able to be made into nucleosome core particles. Sample preparation and gel running conditions were modified somewhat with these longer DNA duplexes. As with the 30-mer, Fpg was able to successfully excise the 8-oxoG lesion in the 146-mer duplexes.

Moving forward, repair assays will be conducted to examine the ability of Fpg to excise the 8-oxoG lesion in nucleosome particles formed by the 146-mer wrapped around a histone octamer core. Repair assays with nucleosomes containing the Sp lesion and Fpg will also be conducted. These experiments will ultimately allow us to examine the ability of a variety of different DNA glycosylases to excise the Sp lesion from nucleosomes, providing important information about how this kind of DNA damage is repaired in cells.

References:
1. Olmon, D.E.; Delaney, S. ACS Chemical Biology 2017 12 (3), 692-701
2. Krishnamurthy, N.; Muller, G.J.; Burrows, J.C.; David, S.S. Biochemistry 2007 46 (33), 9355-9365
GlendalisPerez2019L.David Smith, Biological SciencesDenise LelloEnvironmental Science and PolicyEnvironmental Science and PolicyGlenda Perez ‘21, Emily Hitchcock ’19, Jasmine Pacheco-Ramos ’19, Yeiny Moreno ’20, Giovanna Sabini-Leite ’21, Renee Revolorio Keith ’21 - Coral Reef Ed-Ventures Summer 2019Summer 2019 was the twentieth year of the Smith College collaboration with Hol Chan Marine Reserve on Ambergris Caye, Belize. The goals of Coral Reef Ed-Ventures are to conduct research on coastal ecosystems and communities and to offer an environmental education and conservation experience for the children of San Pedro Town on Ambergris Caye. The research focused on coral mounds at Mexico Rocks, mangroves propagules located in lagoons near the Grand Belizean Estates development, and interviews assessing the eco-cultural identity of local people who work with the natural environment or who had completed a Coral Reef Ed-Ventures camp in the past. We later incorporated many of these research techniques into our teaching activities in two free camps for the island schoolchildren.

Smith students conducted three research projects with professors David Smith (BIO), Denise Lello (BIO), Allen Curran (GSC), and Shannon Audley (EDC). The first project was part of a long-term survey of the health of coral mounds inside the barrier reef at a site called Mexico Rocks that was recently accorded protection as part of the Hol Chan Marine Reserve. These surveys assess the amount of live coral cover and soft coral abundance and diversity, and track significant changes over time. Previously, several mounds towards the center of Mexico Rocks and several towards the south end had been sampled with quadrat and transect methods using SCUBA, snorkel, and underwater cameras. These were resampled this year and two new mounds from a different area were also surveyed. The second project tracked mangrove survival in the mangrove lagoons in the interior of the island in the vicinity of fill associated with development. Previous research has indicated that several biotic and abiotic factors can impact the persistence of mangrove propagules. Students collected data for each propagule (previously mapped) using underwater images of organisms associated with the propagules and visual assessment of damage and herbivory. For the third project, students interviewed people who live in San Pedro and work in eco-tourism and/or have attended Coral Reef Ed-Ventures camp as a child. The goal was to elicit stories that reveal ecocultural identity. We interviewed dive masters and scuba instructors, staff from Hol Chan Marine Reserve, and some alums from the Coral Reef Ed-Ventures program. The questions probed how the person viewed interconnections between themselves and nature; experiences that changed their perspectives about the natural environment; and their thoughts on the future of the natural environment with a focus on how their relationship with nature and life will be affected.

This year’s theme for youth camp was ‘My Roots in the Sea’. The Smith students created activities focused on seven topics: eco-cultural identity, mangroves, coral reefs, relationships, challenges/threats to the ecosystem, health of humans and ecosystems, and advocacy. Interactive activities (e.g., a beach clean-up, an edible coral polyp activity) were paired with short lectures and videos. This variety of topics allowed campers to make connections between the ocean ecosystems and inhabitants and land-based human activities, as well as gain more awareness about how they can best protect the ocean.

Older children attended an upper level R.E.E.F (Research in Ecology and the Environment is Fun) Program. This year’s theme for the R.E.E.F. program was ‘Human Relationships with the Reef, Research, and Advocacy’. Campers were introduced to various research methods, including how to calculate percent live coral cover on coral mounds. They also learned about advocacy and threats to the environment. For example, the campers were presented with information about how macro and micro-plastics affect the entire food chain. Two guests from the community were asked to come in and talk about their particular work in the environment in order to give the kids a firm idea of environmental efforts occurring in their own community. Chris Summers from ACES (American Crocodile Education Sanctuary) taught about the cultural and ecological importance of mangroves and biological aspects of the crocodiles that live in Ambergris Caye. Mariela Archer, the environmental educator from Hol Chan Marine Reserve, spoke about overfishing and the importance of marine protected areas. We took REEF camp participants on a snorkeling trip to Hol Chan and Shark and Ray Alley so that they could observe the marine protected area and the underwater life that they were learning about. With a greater understanding of the local environment and how research is conducted, campers were able to make meaningful connections between coastal ecosystems and their home on Ambergris Caye.

In summary, our research advanced understanding of changes in coral and mangrove habitats and the education program exposed children on the island to specific environmental changes that impact their everyday lives. This summer of Coral Reef Ed-Ventures was full of new experiences and learning opportunities that we hope to expand upon in coming years.

Supported by the Environmental Science and Policy Program (ES&P) and Agnes Shedd Andreae Fund and Schultz Foundation; Biological Sciences’ B. Elizabeth Horner Fund and Mary E. Schlesinger Botany Fund and a gift from Linda Salisbury ’78. Advisors: L. David Smith and Denise Lello, Biological Sciences, Al Curran, Geosciences, Shannon Audley, Education and Child Studies, and Javier Paredez, Hol Chan Marine Reserve, with help from Joanne Benkley (ES&P and CEEDS).).
GiovannaSabini-Leite2021L.David Smith, Biological Sciences - Biological SciencesEnvironmental ScienceGlenda Perez ‘21, Emily Hitchcock ’19, Jasmine Pacheco-Ramos ’19, Yeiny Moreno ’20, Giovanna Sabini-Leite ’21, Renee Revolorio Keith ’21 - Coral Reef Ed-Ventures Summer 2019Summer 2019 was the twentieth year of the Smith College collaboration with Hol Chan Marine Reserve on Ambergris Caye, Belize. The goals of Coral Reef Ed-Ventures are to conduct research on coastal ecosystems and communities and to offer an environmental education and conservation experience for the children of San Pedro Town on Ambergris Caye. The research focused on coral mounds at Mexico Rocks, mangroves propagules located in lagoons near the Grand Belizean Estates development, and interviews assessing the eco-cultural identity of local people who work with the natural environment or who had completed a Coral Reef Ed-Ventures camp in the past. We later incorporated many of these research techniques into our teaching activities in two free camps for the island schoolchildren.

Smith students conducted three research projects with professors David Smith (BIO), Denise Lello (BIO), Allen Curran (GSC), and Shannon Audley (EDC). The first project was part of a long-term survey of the health of coral mounds inside the barrier reef at a site called Mexico Rocks that was recently accorded protection as part of the Hol Chan Marine Reserve. These surveys assess the amount of live coral cover and soft coral abundance and diversity, and track significant changes over time. Previously, several mounds towards the center of Mexico Rocks and several towards the south end had been sampled with quadrat and transect methods using SCUBA, snorkel, and underwater cameras. These were resampled this year and two new mounds from a different area were also surveyed. The second project tracked mangrove survival in the mangrove lagoons in the interior of the island in the vicinity of fill associated with development. Previous research has indicated that several biotic and abiotic factors can impact the persistence of mangrove propagules. Students collected data for each propagule (previously mapped) using underwater images of organisms associated with the propagules and visual assessment of damage and herbivory. For the third project, students interviewed people who live in San Pedro and work in eco-tourism and/or have attended Coral Reef Ed-Ventures camp as a child. The goal was to elicit stories that reveal ecocultural identity. We interviewed dive masters and scuba instructors, staff from Hol Chan Marine Reserve, and some alums from the Coral Reef Ed-Ventures program. The questions probed how the person viewed interconnections between themselves and nature; experiences that changed their perspectives about the natural environment; and their thoughts on the future of the natural environment with a focus on how their relationship with nature and life will be affected.

This year’s theme for youth camp was ‘My Roots in the Sea’. The Smith students created activities focused on seven topics: eco-cultural identity, mangroves, coral reefs, relationships, challenges/threats to the ecosystem, health of humans and ecosystems, and advocacy. Interactive activities (e.g., a beach clean-up, an edible coral polyp activity) were paired with short lectures and videos. This variety of topics allowed campers to make connections between the ocean ecosystems and inhabitants and land-based human activities, as well as gain more awareness about how they can best protect the ocean.

Older children attended an upper level R.E.E.F (Research in Ecology and the Environment is Fun) Program. This year’s theme for the R.E.E.F. program was ‘Human Relationships with the Reef, Research, and Advocacy’. Campers were introduced to various research methods, including how to calculate percent live coral cover on coral mounds. They also learned about advocacy and threats to the environment. For example, the campers were presented with information about how macro and micro-plastics affect the entire food chain. Two guests from the community were asked to come in and talk about their particular work in the environment in order to give the kids a firm idea of environmental efforts occurring in their own community. Chris Summers from ACES (American Crocodile Education Sanctuary) taught about the cultural and ecological importance of mangroves and biological aspects of the crocodiles that live in Ambergris Caye. Mariela Archer, the environmental educator from Hol Chan Marine Reserve, spoke about overfishing and the importance of marine protected areas. We took REEF camp participants on a snorkeling trip to Hol Chan and Shark and Ray Alley so that they could observe the marine protected area and the underwater life that they were learning about. With a greater understanding of the local environment and how research is conducted, campers were able to make meaningful connections between coastal ecosystems and their home on Ambergris Caye.

In summary, our research advanced understanding of changes in coral and mangrove habitats and the education program exposed children on the island to specific environmental changes that impact their everyday lives. This summer of Coral Reef Ed-Ventures was full of new experiences and learning opportunities that we hope to expand upon in coming years.


Supported by the Environmental Science and Policy Program (ES&P) and Agnes Shedd Andreae Fund and Schultz Foundation; Biological Sciences’ B. Elizabeth Horner Fund and Mary E. Schlesinger Botany Fund and a gift from Linda Salisbury ’78.

Advisors: L. David Smith and Denise Lello, Biological Sciences, Al Curran, Geosciences, Shannon Audley, Education and Child Studies, and Javier Paredez, Hol Chan Marine Reserve, with help from Joanne Benkley (ES&P and CEEDS).