Summer Science Research | 2022 Program

Ahado Ali

Advisor: Tamara Davis

The Maintenance of DNA Methylation at Primary and Secondary DMRs

The overall research topic of our lab is genomic imprinting. Genomic imprinting is the process in which a gene's expression is dependent on its parental origin; for instance, though mammals inherit two copies of a gene, one from each parent, only one copy of that gene, either maternally or paternally inherited, will be expressed while the other remains silenced. DNA methylation helps regulate genomic imprinting by distinguishing the paternally inherited copy from the maternal copy and determining which copy gets expressed. This process is achieved by attaching methyl groups to the cytosines present in cytosine:guanine dinucleotides; this often leads to the silencing of a gene. A DMR refers to a differentially methylated region. Primary DMRs are acquired during gametogenesis and remain methylated throughout development, while secondary DMRs acquire methylation after implantation. The regulation and maintenance of methylation in these regions is crucial to the expression of imprinted genes and the proper growth and development of mammals. The improper maintenance of these regions can result in developmental disorders such as Beckwith-Wiedemann and Angelman syndrome.

A goal of the lab is to determine how methylation in these regions is maintained and whether methylation is maintained differently at primary vs. secondary DMRs. To analyze this, we assessed methylation patterns across various developmental stages. My current project consists of analyzing methylation patterns at both non-imprinted loci and primary and secondary DMRs associated with imprinted loci in 18.5 day-old mouse embryos. I am comparing methylation patterns in wild-type mice to homozygous P allele mice. The P allele mice have a mutation in the Dnmt1 gene responsible for maintaining DNA methylation. This mutation makes it difficult for them to maintain global DNA methylation during embryogenesis and leads to early death. Despite the loss of global methylation and methylation at secondary DMRs, methylation at primary DMRs is well maintained, which leads us to believe that the maintenance of methylation at primary vs. secondary DMRs requires separate mechanisms. By further analyzing DNA methylation patterns in wild-type and homozygous P allele mice, we will better understand the mechanisms responsible for acquiring and maintaining DNA methylation at secondary DMRs. The techniques we use in our analysis are bisulfite mutagenesis, which helps us track methylated sites by converting unmethylated cytosine into uracil; PCR then amplifies primary and secondary DMRs associated with imprinted genes as well as sequences associated with non-imprinted genes; Gel electrophoresis then helps determine if the DNA we amplified is the correct size and whether they're suitable for extraction. Future techniques will consist of submitting the samples for next-generation sequencing so that we may analyze the sequence data and compare the methylation levels at each site to understand better how methylation is regulated at both primary and secondary DMRs.

Adelma Argueta-Roman

Advisor: Thomas Mozdzer

Intraspecific variation in photosynthetic rates of Phragmites australis in a common garden study

Salt marshes are one of the most productive ecosystems worldwide, allowing scientists to determine how global change affects ecosystem productivity. Phragmites australis is an invasive species found globally in marshes, and a newly proposed model organism to investigate the role of heritable traits that are demonstrated to influence ecosystem carbon cycling. There is limited data on how global change is affecting heritability in genetic traits. Working with P. australis will help increase understanding of how global change factors like elevated CO2 and nitrogen, influence the way salt marshes may respond due to the widely spread genetic variability of salt marsh plants, and whether plants can evolutionarily keep up. The study will be focusing on photosynthetic factors like ETR, stomatal conductance (gsw), and water usage from 66 genetically unique P. australis. I hypothesize that within the intraspecific variation there will be genotypes that are consistently performing better in terms of higher photosynthetic rates, independent of changing atmospheric conditions. To investigate the role of heritable trait variation, 66 genetically unique plants from two populations were studied in a common garden located at Arnecliff in �������� in order to standardize the conditions the plants are exposed to. Under standard conditions of light, water, temperature, and nutrients, genetic variation can be attributed to significant finds. Plant traits known to influence carbon cycling in salt marshes, specifically the light-saturated photosynthesis (ASAT), stomatal conductance (gs), and water use efficiency are tracked using a fluorometer, among other conditions. All 66 plants will be tracked in a single day over the course of the summer, and ten plants (five of each population) will be tracked overly to determine dinural photosynthetic responses.

Sachi Bower

Advisor: Thomas Mozdzer

Heritability of functional traits and elemental composition in P. australis

Due to their ability to sequester carbon (C), foundation species in coastal wetlands are vitally important to study to understand the effects of climate change. Little is known about how changing functional traits will influence the ability of these foundation species to store carbon.

An ongoing global change experiment at the Smithsonian Global Change Research Wetland on the common reed, Phragmites australis, has been exposing plant communities to elevated concentrations of carbon dioxide (CO2) and nitrogen (N2) since 2011. Previous research has revealed 64 unique genotypes growing in the field experiment, which have also demonstrated tradeoffs to elevated CO2 and N2 exposure. Our driving question is, are plants traits including elemental content of C, N, P, and/or lignin content genetically inherited.

To test this, we grew genotypes from two populations in a common garden at �������� in 2021 and collected the biomass in fall 2021, which will be used to assess for differences in C, N, P, and lignin between genotypes. First, I separated stems and leaves from each genotype to be analyzed in three distinct procedures. C and N content will be measured on an elemental analyzer, phosphorus will be measured spectrophotometrically after combustion and acid digestion; and lignin will be measured using the acetyl bromide method.

This study will be among the first to evaluation the variation of these traits both within, and among populations. The findings will contribute to a parallel decomposition experiment and inform models of the influence of plant traits on wetland carbon sequestration.

Clementine Chen

Advisor: Bárbara Bitarello

Quantifying the evidence for adaptive evolution of the TAS2R38 bitter receptor gene in primates

Taste is a sense that allows the perception and distinction of different flavors via specialized cells in the tongue. Taste buds are in charge of forming taste perception, and type II taste receptors (TAS2R) are the gene family that codes for bitter taste receptors, which are considered G-protein coupled receptors. Combined, these receptors can bind to a large number of molecules, and each receptor has a specific affinity to different molecules. Since bitter taste is important for animals to avoid swallowing potentially harmful chemicals, we believe that the TAS2R genes that code for bitter taste receptors may have evolutionary significance to humans and other primates. Inside the protein family, there are 25 protein-coding genes and 11 pseudogenes that are found in humans.

Specifically, TASR38 is the gene that codes for taste receptor type 2 number 38, which binds to 23 known ligands. The G-protein coupled receptor is associated with the perception of taste phenylthiocarbamide (PTC), which is tasted differently by different people. The TASR38 gene is the most studied protein-coding bitter receptor gene from an evolutionary perspective. In humans, two divergent TAS2R38 haplotypes exist at intermediate frequencies, which has been interpreted as evidence that they have been maintained by balancing selection. However, a more recent study argues that the recent evolution of this gene can be explained fully by ​​demographic events in human evolution. Does the TAS2R38 gene play a role in the adaptive evolution (positive selection and/or balancing selection) of humans and other primates? We hypothesize that specific binding sites in this gene may have been subjected to adaptive evolution in humans. If the hypothesis is correct, there will be an increased dN/dS value (ratio of nonsynonymous substitution rate to synonymous substitution rate) at certain binding sites of the gene, corresponding to those that determine ligand specificity. Although this gene can be found in most mammals sequenced to date, we will focus on primates, since this is the taxonomic group including humans and our closest relatives. We will also test whether evidence for adaptive evolution is different for different subgroups of primates, such as the great apes (chimps, bonobos, gorillas, orangutans, humans), New World, and Old World Monkeys. Another test will also be done to detect if a specialized diet of humans and other primates affected the evolution of their TAS2R38 gene. If so, feeding habits might be a factor that determines the genetic variations of the TAS2R38 gene.

In the Bitarello lab, we will be focusing on using computational methods to conduct experiments at the level of comparative genomics. The data used will be publicly available. To find out the evolutionary relationship between species, the obtained protein-coding sequences will be aligned to create phylogenetic trees. Codon substitution models will be implemented in software PAML and HyPhy to measure the evidence for natural selection at the protein level for different groups (sites in the gene or branches in the phylogeny). 

The phylogenetic analysis results may bring new insights to other scientific fields. Since taste affects food intake, knowing the ligand-binding mechanism helps drug developers understand how bitter taste forms so that they are able to create drugs with higher acceptance by patients. Also, based on a recent study, homozygous carriers of a certain variant of the TAS2R38 gene may be related to pine nut syndrome which suggests that dietary habits may be a potential factor to determine the evolution of bitter taste genes. Besides that, the evolutionary significance of the TAS2R38 bitter receptor gene promotes people’s understanding of cultural evolution in human history and how dietary preferences shape human evolution.  

Kuankuan Hu

Advisor: Thomas Mozdzer

Identification of heritable trait variation in the common reed, Phragmites australis

Phragmites australis, the common reed is a newly identified model organism for ecological and evolutionary studies given its global distribution, and its relatively conservative genetic variation.  In a long-term field experiment at the Smithsonian Global Change Research Wetland (GCREW) where Phragmites was exposed to elevated CO₂ concentrations, elevated nitrogen, or both for nearly a decade, previous research identified changes in genetic diversity and genotypic tradeoffs in the response to these two global change factors. To evaluate the heritability of plant traits, 63 unique Phragmites genotypes were collected from GCREW and a second population at Parker’s Creek, MD. These genotypes were grown in a common garden at �������� established in 2021. This research aims to identify traits that reflect genetic differences, and future work on the offspring of these genotypes (F1s) will determine the heritability of these traits in the future. Relative growth rate is a known heritable plant trait in previous research and is an excellent candidate to examine trait variation in Phragmites. Each week, I measure the height of five tagged shoots from each unique genotype, and these data will be modelled in R to evaluate differences among genotypes and the two populations.  In addition, I will measure specific leaf area and root functional traits to evaluate the breadth of heritable traits in this species. This study is the first to evaluate heritable trait variation within populations of Phragmites and will challenge results of previous research. Through study of inheritable traits, we also expect to gain more insights in development of Phragmites populations, or even of the ecosystem, under current global change factors.

Lana Hwang

Advisor: Monica Chander

Investigating the function of SoxR and Act in Streptomyces coelicolor         

Chander Lab investigates what mechanisms a soil bacterium Streptomyces coelicolor, a producer of four antibiotics including pigmented Red and Act, employs to protect itself from redox-active compounds it produces. Data from previous experiments done in the lab suggest that different mutants have different pellet morphology. It has been observed that when SoxR, a transcription factor that gets activated by Act for a regulon of genes associated with antibiotic resistance, is deleted, pellets tend to be small. A similar trend was observed for the pellet size when Act is not produced. 

The primary goal of my summer research is to confirm that these data are reproducible. We will first look at SoxR complementation clones under a microscope. If the size of ΔsoxR pellets becomes similar to that of the wildtype when SoxR is reintroduced, it is likely that the small pellet size is due to the absence of SoxR. Furthermore, in regards to the function of SoxR, we would like to investigate if the protective role SoxR plays is specific to Act or not. We will look at M510 and M510ΔsoxR which produce a substantial amount of Act and at M1141 and M1141ΔsoxR in which the entire Act cluster is deleted. If SoxR regulates Act only, strains that are not producing Act should look similar to each other and also smaller since SoxR is supposedly inactive when Act is not produced. This leads us to hypothesize that pellets of M1141, M1141ΔsoxR and 510ΔsoxR would be small whereas M510 is huge.

In addition to the microscopy projects described above, we plan to examine microscopic phenotypes of SoxR-regulated genes: ecaA, ecaB, ecaAB and ecaD. We are particularly interested in ecaB since it is an ortholog of a putative monooxygenase PumA found in Pseudomonas aeruginosa that has been contributed to normal biofilm development and phenazine resistance. Via microscopy, I hope to collect data that can provide clues to answering the question of what the functions of SoxR and Act are in S. coelicolor.

Julia Kesack

Advisor: Tamara Davis

Asymmetric Methylation Patterns in Secondary Differentially Methylated Regions of Imprinted Genes

Our lab studies genomic imprinting, which is the differential expression of genes based on parental origin achieved through epigenetic modifications. Many organisms inherit a set of alleles, one from each parent. At imprinted genes, only the maternal or paternal allele is expressed. Differential expression of these genes is achieved via epigenetic modifications, which are chemical modifications to the chromatin that regulate gene expression. Our lab is focused on DNA methylation, or the addition of a methyl (CH3) group to the DNA. Methylation occurs at cytosines followed immediately by guanine, or a CpG, creating a 5-methylcytosine. Imprinted genes contain differentially methylated regions (DMRs) that influence their expression, with the methylated allele often being silenced.

Since methylation controls gene expression, it needs to be stably maintained and this is usually achieved by DNA methyltransferase. DNA methyltransferase faithfully copies the methylation patterns of genes following replication. Previous research completed in our lab has found a higher occurrence of asymmetric methylation at secondary DMRs, which are acquired during gestation, than at primary DMRs, which are inherited at fertilization. Asymmetric methylation is when one DNA strand is methylated at a certain nucleotide, while the complementary strand lacks complementary methylation. Asymmetry does not promote stability, creating questions regarding the potential cause for this asymmetry.

We hypothesize that asymmetric methylation may be caused by the enrichment of 5-methylcytosine to 5-hydroxymethylcytosine. To test this hypothesis, we will analyze 5-methylcytosine and 5-hydroxymethylcytosine levels at primary and secondary DMRs associated with imprinted genes, as well as non-imprinted genes. In bisulfite mutagenesis, both 5-methylcytosine and 5-hydroxymethylcytosine (5hmC) will remain cytosine while unmethylated cytosine will be converted to uracil, showing up as thymine when sequenced. This mutagenesis allows us to differentiate between methylated and unmethylated cytosines. The oxidative bisulfite mutagenesis will then allow for differentiation of 5-methylcytosine from 5hmC. After performing these reactions, we will amplify and sequence the sites of interest to determine if there is 5hmC enrichment specifically at secondary DMRs.

Gillyoung Koh

Advisor: Bárbara Bitarello

Investigation of Long-Term Diversifying Evolution In TAS2R14, A Promiscuous Bitter Taste Receptor In Primates

T2R or TAS2R are Type II taste receptors that are G protein-coupled receptors. When a bitter agonist binds to the receptor, the organism perceives the bitter taste. Bitter-tasting genes code for the proteins which are the bitter-tasting receptors. It is important to perceive bitterness to protect organisms from eating potentially harmful substances, such as cyanide. The receptor encoded from TAS2R14 is very promiscuous. It can bind to more than 150 known, diverse bitter agonists, roughly two-fold more than the second-highest number of known ligands a receptor encoded from a T2R gene can bind to. Possibly, TAS2R14 could have been subjected to long-term balancing selection. In the Bitarello lab, we are exploring whether there is evidence for long-term diversifying evolution in TAS2R14 in the primate lineage. If we can find evidence supporting this, is the long-term diversifying evolution targeting codons in TAS2R14 corresponding to portions of the receptor interacting with the bitter agonists? We hypothesize that this may be true given that certain vertebrate genes have great diversity and that major histocompatibility (MHC) complex genes show balancing selection in certain codons encoding for the binding of antigens. Finally, we will also test whether different subgroups of primates have experienced different selective pressures. 

To answer the research question, we are exploring whether we can find evidence on a phylogenetic scale. We will use publicly available protein-coding data for humans and other primates. Phylogenetic approaches will be used to study the evolution of TASR14 in primates. A phylogenetic tree will be created after performing a multiple sequence alignment. Then, codon substitution models implemented in HyPhy and PAML will be used. Diversifying selection, or adaptive evolution, includes positive and balancing selection but not purifying selection. We are testing whether there has been adaptive evolution in TAS2R14 and if so, whether certain codons have been the target of selection, i.e, those more linked to binding specificities of the receptor. If this is true, we would observe elevated dN/dS (rate of nonsynonymous mutations to the rate of synonymous mutations) in codons that correspond to amino acids that recognize and/or bind the agonists compared to other codons in the gene. We are also testing whether different taxonomic groups (Great Apes, New World Monkeys, Old World Monkeys) or groupings based on dietary habits (herbivore, carnivore, omnivore) have experienced different selective pressures.

Bitter taste receptors are not just found in taste buds, but they can also be found in some areas of human airways. These receptors bind to bitter compounds generated by bacteria and can lead to narrowing of the airways to avoid inhaling the potentially toxic substances. This suggests that bitter taste receptors may fulfill roles that we have not discovered yet and learning more about these bitter taste receptors may aid the healthcare and pharmaceutical industries. Along with protecting airways from bacterial infection, bitter taste receptors may have influenced primates’ diet to avoid eating certain foods which may have been potentially toxic, affecting primate evolution.

Yeipyeng Kwa

Advisor: Gregory Davis

The Role of JH in Specifying Reproductive Fate in the Pea Aphid

Aphids exhibit reproductive polyphenism, a case of phenotypic plasticity in which different environmental conditions determine the mode of reproduction. Aphids will reproduce either viviparously and parthenogenically (asexual females) or oviparously and sexually (sexual females) depending on environmental cues. During the summer months, when nights are shorter (and days are longer), female asexual aphids will produce offspring that are also asexual and female. However, in the late fall, when nights are longer (and days are shorter), these asexual females will produce asexual females, known as sexuparae, that are different in that they will produce offspring comprising sexual females and males. Evidence suggests that the reproductive fate of embryos is dependent on a maternal signal whose transmission is dependent on the environment the mother is exposed to. Results from tests of sufficiency have implicated Juvenile Hormone as a candidate for this maternal signal: topical application of JH in asexual females who will normally produce sexual offspring (i.e., sexuparae) induces them to instead produce asexual females. While this result indicates the sufficiency of JH to induce asexual fate, evidence indicating that JH is required to specify asexual fate is so far lacking. One approach to test the role played by JH is to establish a means to measure JH signaling in embryos specified as either sexual or asexual.  My goal this summer will be to validate a qPCR assay I have been developing as a measure of JH signaling and then apply this assay to embryos specified as either sexual or asexual. If successful, the resulting data should either support or challenge the role of JH in specifying reproductive fate in the pea aphid.

Sunny Li

Advisor: Gregory Davis

When the environmental condition of the terrestrial ecosystem drastically changed, it forces the insect to develop survival strategies, or they will face the problem of extinction. One of the most influential abiotic factors in the environment is cold temperature. Insects in the terrestrial region need a way to survive the cold temperature of winter. One of the strategy strategies, photoperiodism, brings many advantages for multiple species to adjust their adaptation during different seasons. This mechanism works by detecting variation in daytime length and sending the signal to the inner part of the insect to make changes for a better survival rate. The mechanism of Photoperiodism was developed in pea aphids. During the summer months, there are all-female asexual populations, and sexual females and males in the fall. In asexual populations, the oocytes of females are viviparous, which means they complete embryogenesis within the mother (Imagine embryos were ‘stored’ in the mother). On the other hand, the sexual females with fertilized oocytes will begin embryogenesis after the mother lays the eggs. 
During winter fall, the asexual female will interpret the shorter days and send a signal to the embryos developing inside of her to grow as sexual females (and some males). The mother aphid uses the sexual reproductive mode and produces external eggs (with embryos inside) that are frost resistant. In contrast, when female aphids detect longer days, they will switch to the asexual reproductive mode, which is a faster and more efficient model. It is cool to know that the female aphids can adjust to season changes, but what are the factors capable of receiving the long/short days signal and how does the signal interact with which part of the female aphids? Those questions remained unknown.

Based on the result of preliminary research that has been done, insulin influences the switching of the asexual into the sexual reproductive mode in aphids. However, to state that insulin influences aphids, more controlled experiments are needed because there were some uncertain results from the preliminary research. Therefore, the first part of this summer research aimed for a solid experimental result to confirm the effect of insulin on aphids.  Furthermore, a designed method is being created to test where the signal of switching reproductive mode takes place in the aphid. To do that, we will apply two types of insulin (Juvenile hormone (JH) and wortmannin (WT)) together to the virginoparin mother aphids and then analyze the progenies and the reproductive mode of the mother aphids.

Anna Miller

Advisor: Monica Chander

Role of SoxR In Protecting Streptomyces coelicolor From Foreign Phenazine Antibiotics.  

Streptomyces is a versatile and populous genus of bacteria that grows predominantly in soil and decaying vegetation. Characterized by a specialized metabolism that allows for the creation of spores, Streptomyces also produces secondary metabolites including clinically useful antibiotics and immunosuppressives. Historically, Streptomyces griseus was used to mass produce the antibiotic streptomycin, and other Streptomyces species produce an array of other antibiotics. In the soil, Streptomyces encounters foreign antibiotics produced by other bacteria that share the environment. Among these foreign antibiotics are phenazines, which are used for intracellular signaling and electron transport by the bacteria that produce them. I am studying how the model species Streptomyces coelicolor responds to a variety of phenazine antibiotics produced by neighboring bacteria in their shared soil, and how a particular regulatory protein, SoxR, modulates this response. Previous work in the Chander lab suggests that SoxR regulates the metabolism of endogenous antibiotics produced by Streptomyces coelicolor. In order to investigate this hypothesis, we will expose wild type and SoxR mutant Streptomyces coelicolor strains to various redox drugs. We will then perform a complementation to restore SoxR in the mutant strain, or repeat our original experiment to establish if the observed results are due to SoxR’s influence alone.

Tatiana Perez

Advisor: Sydne Record

Seedlings of Prospect Hill

My name is Tatiana Perez, and I am an Environmental Studies student whose summer research is being mentored by Sydne Record. My project this summer is called "Seedlings of Prospect Hill," in reference to the tract of land on which I am working. Here at Prospect Hill, I am working in the Harvard Forest with a small field team to examine the confounding factors that affect the survial of tree seedlings of different species. Specifically, I am focused on how and if patterns of newer seedling survival are facing a 'decoupling' when it comes to previous land use. That is to say, older tree species here at Harvard forest have trended towards seedling recruitment following a pattern consistent with past land use disturbances - whether that be burning, hurricanes, farming, etc. Now, the pattern is less consistent, and seedling species are beginning to recruit in places whose land use  histories in the past may not have been as favorable towards that type of tree. My goal is to understand why this is happening - non-native insects? pathogens? - as well as what type of seedlings are recruiting where around the forest. Using land use history and bug data provided by Harvard forest, as well as seedling census data and field observations collected by myself and my team, I intend to use r and GIS modeling techniques to map how these seedlings are moving and how this change may continue in the forest. By answering this question, we may be able to scale up my research to apply to larger swaths of New England land, gaining a stronger understanding of how different types of land can affect the tree species which can grow there.

Tillie Ripin

Advisor: Monica Chander

In the Chander lab we are studying the transcription factor SoxR and the genes it regulates in Streptomyces coelicolor. SoxR is activated by the antibiotic actinorhodin (Act) that is produced by S. coelicolor, so we are also looking at the Act biosynthetic gene cluster. Because SoxR is activated by Act, it is hypothesized that SoxR and SoxR regulated genes provide self-resistance mechanisms against Act. This is supported by an increase in Act production in ΔsoxR mutants. However, ΔsoxR mutants are still viable, demonstrating that there are other SoxR-independent self-resistance mechanisms. ActAB, located within the Act biosynthetic cluster, provides one of these self-resistance mechanisms by exporting Act. Even ΔactABΔsoxR mutants are viable, leading us to question if there is yet another self-resistance mechanism. This has been the focus of my project, continued from this past spring semester, which explores the gene ActVA-orf1 that is within the Act biosynthetic gene cluster. ActVA-orf1 is a putative Act exporter, so in order to determine if this is an additional self-resistance mechanism, my project this summer, continued from the spring semester, is to create ΔactVA-orf1 mutants. Once these mutants have been made, the ActVA-orf11 gene will be complemented in order to see if any phenotypic differences compared to wild type ActVA-orf1 are reversed. This should demonstrate what role ActVA-orf1 plays in self-resistance mechanisms of S. coelicolor.

Jacqueline Saulnier

Advisor: Tamara Davis

Defining the cause of asymmetric methylation at genomic imprinting-associated secondary DMRs

Genomic imprinting refers to the differential expression of alleles on a parent of origin-specific basis. Deviating from the simplified view of gene expression whereby each allele is equally receptive to transcription and translation into protein, imprinted genes are imbalanced in the expression of the maternal copy compared to its paternal counterpart. This difference is mediated by the addition of methyl groups to cytosines followed by guanines (CpGs) on one of the two parental alleles. The importance of accurately regulating the expression of maternal versus paternal imprinted genes is demonstrated by the various developmental disorders that can result when imprinting goes awry, such as Beckwith-Wiedemann syndrome.

Despite notable strides in the scientific community’s understanding of imprinting since the 1990’s, much remains unknown about why and how this phenomenon occurs. The research I am doing investigates why secondary differentially methylated regions (DMRs) display distinctive asymmetric methylation. Generally, DMRs result when methylation is present on one of the two parental chromosomes, and are further defined as primary or secondary: Primary DMRs are acquired in gametogenesis, mark the chromosome’s parental origin, and control expression of associated imprinted genes. In contrast, secondary DMRs are established in the implanted embryo and are thought to be involved in maintaining differential gene expression. These two regions are further distinguished by variation in the stability of their methylation patterns. While primary DMRs are 90-100% and symmetrically marked, with both complementary strands displaying methylation, methylation at secondary DMRs ranges from 30-90%, with greater instances of asymmetric methylation.

My search to identify the cause of this asymmetry at secondary DMRs is driven by the hypothesis that asymmetry results from 5-hydroxymethylation (5-hmC) enrichment followed by active and/or passive demethylation. The abnormal structure of 5-hmC, the oxidized form of methylcytosine (5-mC), can provoke its replacement with unmethylated cytosine, eliminating 5-mC entirely. Alternatively, failure to recognize 5-hmC can prevent 5-mC from being incorporated into the replicated daughter DNA strand. While preliminary results offer some support for this hypothesis, I am testing it against a greater number of imprinted and non-imprinted genes, and via a more comprehensive oxidative bisulfite sequencing approach. In this technique, a sample of DNA undergoes bisulfite mutagenesis and oxidation (oxBS), converting unmethylated cytosines and oxidized 5-hmC’s to uracil, while another sample is only bisulfite mutagenized (BS), converting unmethylated cytosines alone to uracil. Polymerase Chain Reaction (PCR) amplifies the DMRs, or a methylated region of a non-imprinted gene. This enables quantification of the region’s remaining CpG cytosines, representing 5-mC in the oxBS sample and 5-mC + 5-hmC in the BS. Subtracting these values gives 5-hmC levels at the DMRs. Ultimately, this approach promises further elucidation of the relationship between asymmetric methylation and 5-hmC levels at secondary DMRs, progressing toward a better understanding of their unique property and role in the wider picture of genomic imprinting.

Chloe Tang

Advisor: Tamara Davis

Methylation Analysis of 9.5 dpc Embryo DNA Cmtm4

In embryonic development, both paternal and maternal gene copies are expressed and

contribute to fetal growth. However, only one of the parental copies will be expressed if the gene is imprinted. Imprinted genes are regulated epigenetically through DNA methylation, where a methyl group (-CH3) is added to the gene and silences one of the copies. Consequently, differential gene expression patterns that are essential for fetal development are obtained through differential methylation of the parental alleles, referred to as differentially methylated regions (DMRs). Methylation at primary DMRs, which are inherited at fertilization, has been shown to be stable across development whereas methylation at secondary DMRs, which are acquired during early embryogenesis, is less stable and is asymmetric. If methylation is not established properly, then imprinted genes are not expressed properly and diseases and disorders can arise.

Previous research done in the lab has indicated that imprinted genes have more variable and more asymmetric methylation at secondary DMRs. The observed asymmetry raised the question of why DNA methyltransferase is working inconsistently resulting in asymmetric methylation when its role is to maintain methylation and promote stability. In order to study what is causing this unusual methylation pattern, it is important to analyze methylation patterns on both imprinted and non-imprinted genes.

The goal of this project is to perform methylation analysis on Cmtm4, a non-imprinted gene, to understand its methylation pattern and compare it with the results of imprinted genes. By covalently attaching the complementary strands of DNA to each other using a hairpin linker, we can analyze both strands in order to quantify symmetric versus asymmetric methylation levels. My goal is to compare the methylation patterns between imprinted and non-imprinted genes to better understand how methylation is regulated and maintained. Methods required for this analysis include bisulfite mutagenesis, Polymerase Chain Reaction (PCR), gel electrophoresis, molecular cloning, and sequencing.

Reece Carew-Lyons

Advisor: Bill Malachowski

Enantioselective Total Synthesis of Cephanolide B via Birch-Heck sequence

The Malachowski group has previously focused on synthesizing phenanthridinone analogs with more chiral centers and sp3 carbons, developing the Birch-Heck reaction sequence as an efficient tool to generate these molecules. Another class of molecules known as cephalotaxus diterpenoids have reported antitumor, antineoplastic, and antiviral bioactivities. The sequence used for generating enantioselective phenanthridinone-like molecules can be applied to the synthesis of cephalotaxus diterpenoids, specifically the one I will be working with known as cephanolide B. Using the Birch-Heck sequence previously studied in the Malachowski lab group, the main goal of my project this summer will be to create a tricyclic core structure via an enantioselective Heck reaction. Multiple different approaches using both palladium (II) and nickel (II) catalysts will be used in order to create this 6-6-6 tricyclic structure. Once this reaction can be achieved, it can be taken through the proposed total synthesis to produce cephanolide B. If successful, this will be the most efficient sequence to cephanolide B (only 12 reactions) while also being enantioselective. This proposed sequence could be useful in drug development as the family of cephalotaxus diterpenoids have potent anti-tumor activity.

Trinity Dillard

Advisor: Yan Kung

Exploration of HsMK and ScMK Structure and Functionality

The mevalonate pathway is an important metabolic pathway that is responsible for the production of isoprenoid building blocks. Isoprenoids are the largest class of natural products and are essential for cell life. This class is especially important as isoprenoids are commonly employed in drug treatments. The fourth step in the mevalonate pathways is catalyzed by the enzyme mevalonate kinase (MK). This is an ATP-dependent phosphorylation of mevalonate and is often the target of feedback inhibition. Focusing on two homologs of MK, Homo sapiens (HsMK) and Saccharomyces cerevisiae (ScMK), I will try to crystalize and determine the structure with both an analog of ATP and the substrate mevalonate bound. In addition, I will research MK inhibition, specifically the structure of a competitive inhibitor, GGPP, bound to each MK homolog to determine orientation. The results of this research will aid in the understanding of MK’s structure and functionality.

Christina Douglas

Advisor: Bill Malachowski

Advancing Cephanolide B Synthesis Using Racemic Material

Cephanolide B is a compound with anticancer activity, and an efficient synthesis for this compound would allow for further research of its properties and medicinal application of the compound. Another member of the Malachowski group has proposed an enantioselective, 12-step synthesis for cephanolide B from relatively simple reagents and will be focusing on successfully conducting the second reaction of the process, the enantioselective step. Thus, my research will explore the subsequent steps of the synthesis with racemic material. The results of these experiments will later be applied to the enantioselective product of the second reaction. By taking the racemic product of the second reaction forward through other steps in the synthesis and working to efficiently generate the product of each step, significant progress can be made toward an efficient synthesis of cephanolide B using the proposed synthesis. Another aspect of my research will be to efficiently conduct the Birch reduction-alkylation and esterification necessary to transform 4-methyl phenylacetic acid into one of the necessary starting reagents for cephanolide synthesis. An efficient synthesis of cephanolide B may also make possible the synthesis of various derivatives that could demonstrate better potency or more advantageous drug properties, such as less susceptibility to metabolic decomposition or improved bioavailability.

Yael Eiben

Advisor: Patrick Melvin

Synthesis of Palladium Precatalysts Supported by Various Bidentate Ligands and Investigations into their Catalytic Abilities

Palladium precatalysts have become central to the improvement of a variety of catalytic transformations, but, in particular, cross-coupling reactions. These precatalysts have simultaneously yielded improved reaction conditions and generated novel reactivity. Therefore, we aim to synthesize and fully characterize a library of palladium precatalyst complexes supported by three different types of bidentate ligand: phosphine (P / P) ligands, analogues of bidentate N-heterocyclic carbene (NHC / NHC) ligands, as well as analogues of bidentate phosphine / N-heterocyclic carbene (P / NHC) ligands.  Following the synthesis of the NHC / NHC and P / NHC ligands, we aim to generate novel indenyl-based palladium precatalysts and to fully characterize these new palladium precatalysts by both NMR and X-ray crystallography. Further, we aim to ascertain the catalytic ability of these palladium complexes through the investigation of their efficiency in cross-coupling reactions

Rubia Fernandes

Advisor: Jonas Goldsmith

Bi-organometallic Complex as a Photosynthesizer and Electron Relay Duo-Compound

Transition metal complexes can serve as catalysts and electron shuttles, for producing hydrogen from water and sunlight so that it can be used as carbon-free source of energy. This catalytic process is based on an electron transfer facilitated by the shuttle between multiple transition metal complexes. The cycle is dependent on the interaction between a photosynthesizers, and an electron relay compounds, by combining them into one complex the catalytic process would become more efficient. Ruthenium and Rhodium will serve as the center of the transition metal complexes and they will be united through a COMU peptide coupling sequence. Ultimately, the goal will be to form [Ru(2,2’-bipyridyl)2(2,2’-bipyridine-5-carboxylic acid)]²⁺ and [Rh(4-amino-2,2’-bipyridine)2(2,2’-bipyridyl)]²⁺. Additionally, to reduce the amount of steric hindrance in such a complex structure, the length of the carbon chain in between the bipyridine and the carboxylic acid and amino groups will be explored to see it’s effect on yield and efficiency.

Sarah Gao

Advisor: Yan Kung

The Effect of Different Oligomeric Shapes on the Cofactor Specificity in BpHMGR

The enzyme HMG-CoA reductase (HMGR) in the mevalonate pathway has specific regions dictating the enzyme’s affinity to NADH or NADPH cofactors and is capable of forming polymers. Previous studies show that when the HMGR monomers assemble into a homodimer, the enzyme is specialized for NADPH. However, when an HMGR hexamer (trimer of three HMGR dimers) is formed, the enzyme is affinitive to NADH. My research will focus on whether changing HMGR’s spatial arrangement from a hexamer to three dimers will turn the enzyme’s preference for NADH to NADPH. I will perform mutagenesis studies on BpHMGR, which prefers NADH, by introducing a mutant that breaks the interfaces between the three HMGR dimers, thus switching HMGR from expressing hexamer to expressing homodimers. After expressing and purifying the mutated enzymes, I will determine their oligomeric states using size-exclusion chromatography. Furthermore, I will conduct kinetic experiments to test the enzyme’s activity and identify their NAD(P)H preferences. The potential results of this research will lead to a better understanding of the relationship between HMGR structure and cofactor specificity.

Madelynn Hicks

Advisor: Jonas Goldsmith

The Synthesis and Polymerization of Photosentizers and Electron Relays in Photocatalytic Light Harvesting Systems

The potential of hydrogen as a clean energy source and the pathway to a better, more green future for our planet is well known. Knowledge of water splitting, particularly water splitting which is green, efficient, and less costly, would provide a basis for new ideas concerning the transition to a hydrogen based economy, a cleaner environment, and a brighter future. Transition metal complexes are highly utilized as electron carriers and catalysts in the process of water splitting. More specifically, for this process to occur, transition metal complexes such as photosensitizers (PSs) and electron relays (ERs) must be employed in this electron transfer so hydrogen can be produced. The interaction between these two categories of transition metal complexes is of particular interest as increased efficiency in this portion of the reaction would lend to increased efficiency of the overall reaction, water splitting and hydrogen creation, as a whole. The long-term goal of my research is to use electropolymerization of vinyl groups which can be attached to the PSs and the ERs to create stacked, thin layers of the two such that electron transfer can occur more efficiently. My current goal is to synthesize the vinyl groups which will be attached to these PS and ER complexes.

Yui Kosukegawa

Advisor: Bill Malachowski

The Enantioselective Synthesis of Phenanthidinone Derivatives with Quaternary Carbon Through the Birch-Heck Sequence

The goal of my summer research is to learn the process of developing a new synthetic chemistry tool that would potentially improve current drug candidates. Studies show that currently, there are many drug candidates that have flat, aromatic structures with a high proportion of sp² carbons. However, in fact, drug candidates with more chiral centers and sp³ carbons are more successful in clinical trials. This is because molecules with more quaternary carbons have higher selectivity and prevent undesirable interactions with other biomolecules. They are also believed to be more soluble and therefore better able to distribute themselves around the human body after administration.

This research focuses on the synthesis of phenanthidinone analogs. Phenanthidinone has a flat, aromatic structure like other drug candidates which can cause unwanted bioactivities in the body. To make phenanthidinone analogs with quaternary carbon, a new enantioselective synthetic tool called the Birch-Heck sequence is used. The sequence includes 1) Birch reduction-alkylation, 2) amid synthesis, 3) MOM protection, and finally 4) Mizoroki-Heck reaction. This summer, I will be focusing on the nickel-catalyzed Mizoroki-Heck reaction and improving the yield, stereoselectivity, and substrate scope of the reaction.

Hannah Kreider

Advisor: Bill Malachowski

Enantioselective synthesis of tricyclic compounds with chiral stereocenters using the Birch-Heck Sequence

Phenanthridinone and carbazole are two molecules that are often found in drug candidates due to their biological interactions. Their bioactivity is partially due to their structure: flat, aromatic molecules. However, these flat structures and their high levels of bioactivity often lead to problems such as adverse side effects. In the Malachowski lab, the goal is to develop a synthetic tool to efficiently create analogs of phenanthridinone and carbazole with chiral centers in order to reduce these side effects. Recent structural studies of drug candidates have shown that molecules with more tetrahedral, sp3 centers, including chiral ones, are more likely to succeed in clinical trials and eventually become successful drugs. The tool that allows the efficient and selective formation of chiral tetrahedral carbons, and that I will study this summer, is called the Birch-Heck sequence and it consists of four or five reactions. The first step in the sequence is the Birch reduction-alkylation reaction and it creates prochiral sp3 carbons with a variety of substituents from inexpensive benzoic acid. The second step is an amide bond formation and the third involves an amide nitrogen protection step. The final and most important step, the Mizoroki-Heck reaction, involves an intramolecular desymmetrizing reaction that enantioselectively creates a tricyclic molecule with two chiral centers. The Heck reaction product is an analog of phenanthridinone, but it contains two chiral sp3 carbon centers. The phenanthridinone analogs created using the Birch-Heck sequence will be tested for bioactivity related to anti-cancer properties.

Jenna Krussman

Advisor: Patrick Melvin

Investigation into the Deoxyflorination of Benzyl Alcohols and Benzaldehydes to Obtain Monofluoro- and Difluoromethyl Products

Recently, pharmaceuticals containing fluorine are becoming more prevalent due to the overwhelmingly positive influence fluorine can have on important metabolic properties.  Therefore, the development of quicker and more effective ways of including fluorine into organic molecules is highly impactful. One key method for installing fluorine into organic molecules is deoxyfluorination, a process that replaces an oxygen-containing functional group with fluorine. This summer, we will synthesize two different sulfonimidoyl fluoride reagents as this class of molecule has been previously shown to execute deoxyfluorination efficiently. Then, we will investigate the use of these reagents for the deoxyfluorination of benzyl alcohols to generate monofluoromethyl groups while also pursuing the transformation of benzaldehydes to difluoromethyl substituents.

Ruofei Li

Advisor: Yan Kung

Studying the role of the individual residues of HMGR cofactor helix in cofactor specificity

The mevalonate pathway includes seven enzymes responsible for synthesizing the precursors to steroids and isoprenoids, many of which are used as drugs, fragrances, and fuels. HMG-CoA reductase (HMGR), the third enzyme in the mevalonate pathway, binds two molecules of the cofactor NAD(P)H to reduce HMG-CoA to mevalonate. The cofactor helix is an alpha helix in the vicinity of NAD(P)H in HMGR, which is suspected of controlling the preference for either NADH or NADPH cofactors. The previous work has switched the entire cofactor helix between NADH-preferring DaHMGR and NADPH-preferring SpHMGR, and it turns out that both enzymes also switched their NAD(P)H preference. My research will focus on the relationship between individual residues of the cofactor helix of HMGR and the HMGR cofactor specificity. To address this, I will use mutagenesis to make mutations to switch single, double, or triple residues between DaHMGR and SpHMGR cofactor helix that were previously implicated in cofactor specificity. After expressing, purifying, and applying kinetics experiments on the modified HMGR protein, I will observe and determine the effect of those individual residues on cofactor specificity. This study is important because it gives us a better understanding of the HMGR structure and mechanism.

Darya Ostapenko

Advisor: Sharon Burgmayer

Increasing the effectiveness of Moco model compounds synthesis and deriving Sulfido- Bis(tetrasulfido)molybdenum(IV) Anions

Molybdenum enzymes are a cornerstone of multiple catalytic reactions involved in oxygen transport that are vital for virtually all living organisms, including humans. A Molybdenum cofactor (Moco) is found at the active site of those enzymes. Burgmayer group focuses on making and analyzing the synthetic model compounds for Moco in order to help the scientific community gain a better sense of mechanisms involved in molybdenum enzymes operations.

Synthesizing Moco-resembling complexes is a multistep process that involves numerous intermediate steps and handling special equipment. During the last SSR program, I learned how to use the Schlenk line, gained proficiency in conducting several inorganic synthesis reactions, and studied the impact of factors such as moisture and oxygen presence on the reaction speed and the yield of the products.

This summer, I plan to further develop my IR and NMR spectroscopy skills to finalize my conclusion on whether heating can negatively affect the purity of synthetic [TEA][Tp*Mo(+4)S(S4)], a precursor for one of our model compounds. Moreover, I intend to study and synthesize other complexes involved in Moco modeling, such as 2-pivaloyl-6-chloropterin and [TEA][Tp*Mo(CO)3], while looking for ways to improve the procedures. Later in the research I will be assigned a project first undertaken by a former lab member, Emma. The project entails synthesis and analysis of bis-dithiolene molybdenum complex found in the cofactors of DMSO reductase family enzymes.

In conclusion, my research goal would be to continue working on the projects the group has started in the past, provide other lab members with necessary compounds by synthesizing them, and deepen my understanding of the Burgmayer research.

Erin Ramsey

Advisor: Yan Kung

Structural Analysis of Mevalonate Kinase

The mevalonate pathway is a metabolic pathway that generates precursors to steroids and isoprenoids, compounds with applications ranging from anticancer drugs to biofuels. Mevalonate kinase (MK) is a key enzyme in this pathway that phosphorylates mevalonate using ATP to generate 5-phosphomevalonate. MK is also a major site of feedback inhibition. Although several crystal structures of MK from various organisms are currently available, the structure of MK while bound by both its ATP and mevalonate substrates remains unknown. The goal of this research is to employ X-ray crystallography to visualize the structure of two mevalonate kinase homologs (ScMK and MjMK) when bound by a non-hydrolyzable ATP analog and mevalonate, which will further our understanding of MK’s reaction mechanism and process of inhibition.

Angelina Rogatch

Advisor: Sharon Burgmayer

Silence in Mo-court: Interrogating the Non-innocent Pterin Ligands in Molybdenum Cofactor

Molybdenum enzymes, implicated as among the earliest bioinorganic catalysts, are vital to nearly all forms of life on Earth. The slightest malfunction in the cohesive mechanism of molybdenum bioinorganic catalysis results in severe neurological damage and death in humans. Therefore, the catalytic site of Mo enzymes known as the molybdenum cofactor (Moco) has become a major focus of the Burgmayer research group. In the Burgmayer research group, synthetic model compounds for Moco are actively being used to study pterin dithiolene ligand functions and their biochemical role.

Model compound synthesis is a multi-step process involving both organic and inorganic branches of synthesis. One of the focuses of my research focus is the synthesis of Tp* ligand, an ancillary ligand that improves solubility and stabilizes the model compound (as recorded in Inorg. Chem. 2001, 40, 7, 1677–1682), and TEA⁺[Tp*Mo(CO)₃^-], an inorganic “skeleton” needed for further stages of model compound synthesis. Another potential direction of my research is pterin ligand synthesis. By mastering various synthetic techniques, such as Schlenk line, and developing fluency in different analysis methods, such as FT-NMR, FT-IR, UV-vis, my goal is to optimize the synthetic procedures used by Burgmayer research group.

Eunjeong (Sal) Shin

Advisor: Sharon Burgmayer

Mononuclear molybdenum (Mo) and tungsten (W) enzymes form different groups of enzymes that are essential to the living organisms. These groups of enzymes specifically play an important role in the metabolic and catabolic process of transferring oxygen atoms. They also have structurally complex cofactors, molybdenum cofactor (Moco), which includes molybdopterin (MPT). The role of MPT is still not completely understood and in order to study this cofactor, the team goes through numerous synthesis steps where I will focus on the beginning steps of this synthesis. The cornerstone material, neutralized chlorinated pterin-HCl, is made with four steps, making pterin (using reflux technique), pterin-8-oxide, chlorinated pterin as a form of HCl salt, then obtaining neutralized chlorinated pterin-HCl for later steps. Furthermore, I will be working on finding possible modifications that could make the synthesis faster with higher yield. I will also gain experience on how to work on a Schlenk line under nitrogen which is used for the fifth step, making piv-Cl-pterin, an air-sensitive material.

Catherine Soto

Advisor: Bill Malachowski

Stereoselective synthesis of non-planar phenanthridinone derivatives via Birch-Heck sequence

Tricyclic phenanthridinone derivatives have shown significant bioactivity and may serve as good lead compounds, but their planar architecture can be a liability in drug development programs. For that reason, enantioselective synthetic transformations that produce sp³ carbons and quaternary stereocenters are being explored in Malachowski research group. Quaternary and sp³ carbons have been shown to be more prevalent structures in successful drugs because they had less random or unwanted binding to protein structures. It is also thought to have enhanced solubility, which is essential for drug distribution in the body. However, prior research on phenanthridinone derivatives that have quaternary all-carbon stereocenters has not been reported. The Malachowski group has discovered and recently reported a new synthetic tool called the Birch-Heck sequence that has generated some new phenanthridinone derivatives, but more are needed. 

​​This process is a four-step synthetic sequence where inexpensive benzoic acid is converted into new phenanthridinone structures. My research goal is to develop phenanthridinone derivatives through new synthetic tools that help expand access to complex molecules that have the potential to be better drug candidates. This summer I will be working to further develop this reaction and generate new phenanthridinone derivatives for biological testing for anti-cancer activity

Ebrar Yilmaz

Advisor: Patrick Melvin

Synthesis of Acid Fluorides, Trifluoromethyl Groups and Aryl Fluorides Via Deoxyfluorination Using Sulfonimidoyl Fluorides

Fluorine is one of the more privileged atoms of the periodic table and has been frequently used in the pharmaceutical industry to increase metabolic stability and lipophilicity of potential drug targets. In recent years, a great deal of attention has been given to developing different approaches to incorporate fluorine into organic molecules, with deoxyfluorination being the most prevalent. Our goal is to design reagents that will increase the efficiency of deoxyfluorination reactions. In particular, we aim to synthesize two sulfonimidoyl fluoride reagents that will be utilized 1) to convert benzoic acid substrates into trifluoromethyl substituted compounds; 2) to transform phenols into aryl fluorides and 3) to see how these reagents participate in conjugate addition reactions.

Ruolin Zhang

Advisor: Jonas Goldsmith

Synthesis of a bi-metallic macromolecule and vinyl bipyridine thin films to optimize the photocatalytic water reduction system

The demand for clean and renewable resources has been increasing in the past few decades. Hydrogen, popular clean energy used to slow down global warming in recent decades, was produced in an environmentally-harm way, so it is essential to find a clean production method, the photocatalytic water reduction system. Three molecules included in the system are photosensitizer(PS), electron relay(ER), and Sacrificial Reductant (Sac). Sac will donate the electron to PS, and with the energy from light, the electron in PS will be excited to a higher energy level. ER is the intermediate molecule that can carry the energy from the excited electron to reduce water. The synthesis and attaching between PS and ER are focused on in this research. Two possible applications for PS and ER attaching are the synthesis of bi-metallic macromolecules and vinyl bipyridine thin-film production. The macromolecules are produced when PS is already attached to ER. The period when PS stays at an excited state is short, so it is hard to find an ER in nanoseconds. The pre-connection achieved by peptide bond formation can work out this problem to make electron transfer happen, which can save light energy and increase hydrogen production. The formation of vinyl bipyridine thin films can also increase the efficiency of hydrogen production. The PS and ER now contain the vinyl groups, and their thin films will be put at a pre-position achieved by the electropolymerization process of the group. This summer research aims to successfully synthesize photosensitizers and electron relays that can be used in macromolecules formation and thin films of PS and ER. Additionally, the time and percent yield will be compared to figure out which functional groups on PS and ER are optimal choices for bi-metallic molecule production.

The mevalonate pathway is an important metabolic pathway that is responsible for the production of isoprenoid building blocks. Isoprenoids are the largest class of natural products and are essential for cell life. This class is especially important as isoprenoids are commonly employed in drug treatments. The fourth step in the mevalonate pathways is catalyzed by the enzyme mevalonate kinase (MK). This is an ATP-dependent phosphorylation of mevalonate and is often the target of feedback inhibition. Focusing on two homologs of MK, Homo sapiens (HsMK) and Saccharomyces cerevisiae (ScMK), I will try to crystalize and determine the structure with both an analog of ATP and the substrate mevalonate bound. In addition, I will research MK inhibition, specifically the structure of a competitive inhibitor, GGPP, bound to each MK homolog to determine orientation. The results of this research will aid in the understanding of MK’s structure and functionality.

Jie Ji

Advisor: Chris Murphy

Understanding the Experiences of CS Students with Mental Health Conditions

A considerable amount of research has been done on providing accommodation for students with physical disabilities, but other hinderances in accessibility such as mental illness are prone to be overlooked. In reviewing the practices adopted in universities concerning accessibility, we realize few of them could be applied to mental health due to the stigmatization and subjective invisibility of this topic. Thus arises the necessity of conducting a research dedicated to the experiences of this often neglected group. The purpose of this research is to better support students in competitive fields such as Computer Science who are living with mental health conditions, by providing a safe space for them to voice their reflections. Considering the responsibility of instructors, this project focuses on practical measures to accommodate for students with mental health conditions, instead of a psychological research on their mental state. We will collect information from undergraduate students who are majoring in CS or a related field in different types of institutes, identify as living with a mental health condition, and volunteer to participate in our study. The survey will ask participants to identify and describe the resources they found useful, and also difficulties they encountered in studying CS, with a focus on office hours, TA sessions and relationships with people in the CS field. The expected outcome of the project is a paper to be submitted to a CS Education conference that would provide a qualitative analysis of our findings describing the experiences of CS students living with health conditions, and best practices that CS instructors can use to support those students.

Isabelle Sanford

Advisor: Geoffrey Towell

Accessible Web-Based Data Visualization

The world of web development has seen an increasing focus over time on accessibility. This includes but is not limited to support for vision issues, lack of fine motor control, dyslexia and other cognitive difficulties, and poor device quality. The Web Accessibility Initiative has compiled a set of standards, the Web Content Accessibility Guidelines (WCAG), which lay out exactly what features are necessary to make a website accessible. This push for accessibility has been slow to reach the world of data visualization. We will evaluate several popular data visualization packages with a rubric based on WCAG 2.1, including both whether a feature is possible and whether it is easy and well-documented. This project aims to create a Javascript library which permits and encourages developers to create fully WCAG-compliant bar charts.

Neha Thumu

Advisor: Aline Normoyle

Understanding how character control and level design affect the player experience in video games  

Game Design itself is a field without a clear set of rules that defines success. There is a multitude of factors that can determine whether a player finds a game enjoyable or not. However, for designers, the most crucial element is to focus on the subjective experience rather than objective reality according to Jesse Schell in The Art of Game Design A Book of Lenses.

The research over the summer will focus on studying the elements of game design. Specifically, we will focus on level design, puzzle design, and issues of control (specifically, the interaction between the game and the player). 

The level and puzzle design aspects of the research will be explored through a Monument Valley-inspired game and a statistics game known as Treatment X. 

Monument Valley is a stylistic puzzle game focused on navigating a player through a level by manipulating various mechanics. In our version of the game, we are running experiments to determine which puzzle mechanics most appeal to players. 

Treatment X tackles how to design a game as a means of teaching a concept, specifically statistics. This leads to a critical problem to solve: how much agency can be given to a player without diminishing the learning aspect of the game.

As a mobile augmented reality game, Q*bird faces the challenge of having a phone act as both a controller, for moving the character, and a monitor, to see the character along with the environment they are in. We plan on implementing various control schemes to find the most optimal in terms of player enjoyment and agency.

Mary Rose Gilliland

Advisor: Pedro Marenco

Exploring the Role of Microbialites During the Early Ordovician Period

Our field team investigated and collected samples from mud mounds and adjacent sediment in the Fillmore Formation near Ibex, Utah. Mud mounds are carbonate fossil reefs with enigmatic origins; however, they have been hypothesized to have been built by microbes. These reefs were built during the early Ordovician period (~480 million years ago), a time of transition for reefs as reef-building animals were beginning to evolve. During this period, reefs were built by sponges and microbialites (rocks formed from microbial activity) and existed prior to the evolution of modern coral reefs. Modern reef environments are currently undergoing a comparative transition period as they are experiencing a negative influence from human activity causing them to be replaced by sponges and algae. It is valuable to study these past reefs from the Ordovician Period in order to understand and predict the future of reef systems and their effect on biodiversity.In order to study and collect data on Ordovician fossil reefs, we are analyzing and comparing known microbial samples from the mud mounds and known fill sections. Through comparing the stable isotopes of carbon present and the elemental composition in the known microbialite sample, we plan to develop a geochemical fingerprint to test for a microbial origin of mud mounds.

Emily Lazo

Advisor: Pedro Marenco

Investigating the geochemistry of microbialites in Lower Ordovician reefs

The Ordovician (about 480 million years ago) was a crucial transition period for reefs, where reefs went from microbial- to animal-dominated. The microbial reefs in question were structures called stromatolites and thrombolites (collectively called microbialites), which are thought to have been built by microbial communities. The rock record shows other types of structures that also seem to have functioned as reefs, however we are not sure how these reefs were built. These structures are known as “mud mounds” because they are made primarily of calcium carbonate mud in a domal shape. This shape could not have been maintained without some sort of binding activity of organisms. It has been hypothesised that these mud mounds were made by microbial activity. Today’s reefs are in crisis, as corals are being replaced by microbes and sponges. Because Ordovician reefs were also built by microbes and sponges, it is useful to look at these past reef systems, in a similar transitional phase, to see what happened, and to help us make predictions about what will happen to modern reef environments.

We are working with rock samples from the Fillmore Formation, from our field work in Utah, which we will use to make thin sections to look for microscopic evidence of microbialites. We are using 1) samples taken from rocks that we know are microbialites, 2) samples that we know don’t have microbialites, and 3) samples that we think might have microbialites (mud mounds). Some modern microbial communities tend to concentrate certain elements. We are hoping to find similar patterns in the microbialites to use as a geochemical fingerprint, and in turn use that to determine whether the mud mounds are microbial. Microbialites are generally assumed to use photosynthesis to form. Since photosynthesis can alter the isotopic composition of carbon, we are hoping to find differences in the carbon isotopes between the microbial and non-microbial rocks.

Mishelley Low

Advisor: Selby Hearth

Investigating pigment production of acid mine drainage in Pennsylvania’s anthracite coal belt

Acid Mine Drainage (AMD) occurs when water and oxygen come into contact with reactive minerals that are exposed due to mining activity. The oxidation of these minerals produces metals and acids, which pollute downstream environments and transform streams into a rusty yellow-orange color. This causes devastating environmental aftermath not only for animals and plants living in the area but for public health as drinking water can easily be contaminated. AMD can have an effect that lasts for thousands of years. It is a worldwide issue but is especially relevant in Pennsylvania as it contains coal mines with AMD more than any other state in the country. In this project, I will work with Selby Hearth to do a combination of fieldwork in the Anthracite Coal Belt in Pottstown as well as laboratory work to investigate the mineral properties of precipitates that are produced in AMD environments. We will investigate if it is possible to transform AMD into pigment that can be used for production. In this method, bodies of water would be actively treated and the profit made from pigment could possibly be used to offset money to remediate AMD. In our research, we try to answer if this process can be done widespread or in just site specific areas.

Leila N'Diaye

Advisor: Katherine Marenco

Investigating The Structure and Composition of Ordovician Reefs in Western Utah: Microbes and Sponges as Reef-Builders

Modern coral reefs are bustling ecosystems supported by coral and algae frameworks that provide shelter for a variety of species. Similar structures are found in rocks from the Ordovician Period, ~480 million years ago, yet no coral fossils are present. In the absence of coral, sponges and communities of microbes constructed several varieties of reef structures, referred to as mounds, that supported populations of other organisms. Microbial structures have variable complexities, ranging from enigmatic “mud mounds” to laminated or branching structures. My work will involve studying the Fillmore, Juab, and Wah-Wah rock formations in western Utah to further understand the relationships among these organisms. Analysis will primarily focus on the spatial relationships among reef components, especially the changes in relative abundance and areal coverage through time. 

My research aims to quantify the percentage of rock that each reef component occupies through analysis of a combination of grid data and rock samples, and to create visualizations that illustrate the spatial relationships present in the reef mounds. In the field, a 25cm x 25cm grid was used to create focus areas in rock surfaces from which we recorded the presence of sponges, other fossils, and reef cavities, noting size and proximity to other reef components. Larger samples were collected to be studied in the lab using acetate peels. Initial field observations suggest that the average size of sponges and other fossils increased from the Early to the Middle Ordovician. This may indicate an increased importance of sponges as reef scaffolders over time. Middle Ordovician mounds also display higher relative abundance and diversity of fossils than earlier mounds in the succession. This work will allow me to better understand the evolutionary history of early reefs, and the ecological role that certain reef components played in the construction and maintenance of these reefs. Microbes continue to play an important role in reef-building today, so learning more about ancient microbe-supported reefs can provide information about how these reefs responded to environmental change that may inform our study of climate change in relation to modern coral reefs.

Amina Ahmed

Advisor: David Schaffner

Magnetics Module for PlasmaPy

Data gathered from plasma physics experiments can be analyzed in a number of ways. The most efficient way to analyze raw plasma data is by running it through code which is equipped with the functionality to perform complex calculations. PlasmaPy is an opensource software ecosystem which provides a collection of the functionality needed by plasma physicists.

My project involves coding a module for the magnetics analysis. It includes adding functionality like computing magnetic fields, applying band pass filters, mean subtraction. The aim is for the magnetics module to be added to the PlasmaPy for others in the community to be able to use.

Maxwell Brenton

Advisor: David Schaffner

The �������� Experiment (BMX) produces a confined plasma plume that can provide us with data on the behavior of plasma. One of the variables that is measured by the �������� Experiment is the magnetic field. Using the cylindrical coordinate data of the magnetic field over time in the experiment, I calculated the change in angle between two magnetic field vectors over a time interval of one unit. I made a histogram of the angles that I collected in order to observe the distribution of those changes in angle. The distribution of the resulting histogram could be used to make further observations about the behavior of the plasma.

Queenie Jiang and Catherine Opsahl

Advisor: Michael Noel

Rubidium 85 atoms in a magneto-optical trap (MOT) can be excited into states with high principal quantum numbers n, or Rydberg states, using laser spectroscopy. Resonant energy exchange among these ultracold Rydberg atoms has been used in quantum computing, quantum simulation, and studies of dynamics in closed quantum systems. Prior studies of dipole-dipole interaction have focused on systems with few initial and final states. We have observed interactions among atoms excited to states within the Stark manifold using an electric field. The harmonic nature and large number of states in the manifold allow for rich dynamics in this energy exchange process.

Julia Moylan

Advisor: David Schaffner

�������� Experiment

In the �������� Experiment (BMX), a plasma plume is sent through a cylindrical chamber with probes arranged along the axial direction. As the plume travels, the magnetic field magnitude of the plasma varies. Looking at the intermittency in the magnitude of the magnetic field can indicate magnetic reconnection in the plasma. This is done using a histogram depicting a probability distribution function (PDF) of the incremental differences in magnetic field magnitude. Large tails on the Gaussian curve fit to this histogram could be an indication of the presence of magnetic reconnection. When paired with an analysis of the intermittency in the direction of the magnetic field, this analysis can provide insight into whether the plasma plumes have magnetic field lines that are connected to the plasma source. This is a question that also exists with the plasma solar wind from stars.

Amelia Stevens

Advisor: David Schaffner

Exponential Spectra of Magnetic Field Fluctuations in BMX

The fluctuating magnetic field within a flowing plasma on the �������� Experiment is measured. The fluctuations in time series are decomposed using a Fast Fourier Transform (FFT) and plotted in semi-log form.” The slope of linear fits of the semi-log spectra map to an exponential function of the form e^(-omega*tau). It turns out that the inverse transform of this exponential function takes the form of a Lorentzian function of the form: tau^2/(t^2 + tau^2). The original fluctuations are compared to these Lorentzian structures to see if they are of similar size. If so, this suggests that the magnetic fluctuations are chaotic in origin.

Elizabeth Tompkins

Advisor: Michael Noel

Exciting Atoms to Rydberg States to Observe Long Range Dipole-Dipole Interaction

We can trap and cool rubidium atoms by manipulating wavelengths and frequencies of lasers as well as by applying electric and magnetic fields to the atoms. When the atoms are trapped, we then excite rubidium atoms to Rydberg state using different wavelength lasers. Once at these Rydberg states the atoms have principal quantum numbers that are very high (n=30) causing them to be weakly bound. This weakly bound state allows the atoms to exhibit exaggerated properties that result in long-range dipole-dipole interaction. This long-range interaction allows atoms to exchange energy and interact with one another even when separated by distances of several microns. We will be building the optical apparatus to produce a system that will conduct the trapping and excitation described above. We then can then observe and measure long-range dipole-dipole interaction between atoms.

Marie Wisz

Advisors: Kathryne Daniel and Karen Masters

The Impact of Spiral Pitch Angle on Radial Migration of Stars

As galaxies evolve over time, the orbits of their constituent stars change in size and shape. These two characteristics can be probed in tracer particle simulations of spiral galaxies via the initial and final measures of stellar populations that track the orbital eccentricity and angular momentum of individual stars over time. We investigate how these two characteristics of orbital patterns are influenced by spiral arm pitch angle with a focus on how stars move near the corotation resonance of a spiral pattern. For all pitch angles we find that there are changes in both orbital eccentricity and size for stars across a wide radial range of the galaxy, on different scales. The theoretical expectation is that only the orbital size will change at corotation. This project is in process and will examine trends in these orbital changes around corotation for several pitch angles. We aim to use MaNGA and Galaxy Zoo data to observationally probe related measures. In observed galaxies we cannot access orbital parameters directly so we will look at how the metallicity gradient of spiral galaxies changes with pitch angle. Since galaxies are expected to form with a significant metallicity gradient, a flattening of this gradient can be a useful probe of radial migration. This research will help to further understand the dynamical evolution of galaxies and the impact of spiral arms on radial migration.

Anjali Bose

Advisor: Cora Mukerji

Neurodevelopmental pathways linking early and prolonged institutionalization to adolescent outcomes

Research has shown that in addition to having their physical needs met, children require supportive, stable, and enriching early caregiving environments in order to promote strong neurological and psychological development. Children raised in institutions, such as orphanages, can experience profound early psychosocial deprivation in these environments due to lack of funds, resources or caregivers. To better understand how institutionalization and childhood environment affect brain development, I will use data from the The Bucharest Early Intervention program (BEIP), a longitudinal randomized controlled trial which aims to research how exposure to prolonged institutionalization in the first years of life affects child development using a variety of neural, cognitive, and behavioral measures. This project follows the development of young children in institutional care who were randomly assigned to leave the institution and be placed in high-quality foster care (foster care group; FCG) and children who were randomly assigned to remain in their current institutional care placements (care as usual group; CAUG). In the current study, I will examine how prolonged institutionalization in early childhood impacts patterns of structural brain development over adolescence (from ages 8 to 16) in CAUG versus FCG. A primary region of interest is the anterior cingulate cortex (ACC), which is implicated in cognitive control processes that regulate thinking, memory, planning, and behavioral adaptation. I hypothesize that children reared in the FCG will have better ACC functioning, and therefore stronger executive functioning than children in the CAUG. Disrupted development of neural regions supporting cognitive control in children exposed to prolonged institutionalization could contribute to later difficulties in broader executive functioning and psychopathology. We will conduct longitudinal analyses to test whether changes in brain structure in specific regions (including the ACC) link early experiences of prolonged deprivation to executive functioning and psychopathology later in adolescence. This research will clarify the neural effects of adverse childhood environments and their implications for children’s mental health and inform public policy to better meet childrens’ developmental needs in the context of childcare systems.  

Catherine Fu

Advisor: Cora Mukerji

Impact of Neighborhood Collective Efficacy on Child Verbal Development

The bioecological model of development recognizes that children’s development is illustrated by multiple systems, including the family, school, neighborhood, and the larger ecosystems they interact with (Bronfenbrenner, Morris, 2006). Prior research has focused on examining the effects of neighborhood structural factors and neighborhood process factors (Pei, 2022). According to Pei (2022), neighborhood process factors include collective efficacy, defined as the neighbors’ willingness to intervene on behalf of the common good. Previous studies have shown that collective efficacy has a direct positive impact on children’s cognitive development (Choi, et al., 2018). Family socioeconomic status (SES) is also a strong predictor of child development (Froiland, 2011).

Since the home environment is not the only factor influencing a child’s development, it’s important to evaluate how the ecosystems that children are connected to might interact with each other. A number of studies have revealed that neighborhood conditions might positively support the parenting practices within the home (Choi, et al., 2018), thus influencing the children’s cognitive development.

However, there is a dearth of research studies regarding associations between neighborhood collective efficacy and important aspects of children’s cognitive development, such as children’s verbal development. We plan to utilize the Fragile Family and Child Wellbeing Studies (FFCWS) dataset to test longitudinal associations between neighborhood collective efficacy and child’s verbal development and among familial factors mentioned above. The FFCWS study focused on the low-income families where some children are born to unmarried parents. Data is collected on over 4700 families in the large cities in the United States. Surveys for mothers, fathers, and primary caregivers take place when the child is 3 years old.  Based on the FFCWS, we hypothesize that collective efficacy impacts children’s verbal development indirectly, through shaping factors such as parenting practices (Dupere, et al. 2010), parenting stress (Choi, et al. 2018), and home literacy environments (Aikens & Barbarin, 2008, Froiland, et al. 2011). The results may have important implications for public policy, providing insight into how neighborhood social organization can support families and support the development of verbal skills that are important to academic growth and identify neighborhood efficacy as a potential target for interventions seeking to promote healthy child development. Breaking down systemic barriers to accessing neighborhood resources may help foster children’s early literacy and flourishing.

Jianan Gu

Advisor: Ariana Orvell

Advice Giving and Promotion of Emotional Regulation

Psychological distance, the ability to move one’s mind beyond the present moment and place (Davis et al., 2011; Kross & Ayduk, 2017), is a key construct for emotion regulation (Davis, Gross, & Ochsner, 2011; Kross & Ayduk, 2017). Previous research in social and personality psychology has examined how people can regulate their negative emotions (Gross & John, 2003; Koole, 2009), indicating various approaches to gain psychological distance. These approaches include adopting a more objective perspective (Shiota & Levenson, 2009), using second or third-person pronouns (Orvell et al., 2019; Kross et al., 2014), or considering how the emotional intensity of the situation will fade with time (Bruehlman-Senecal & Ayduk, 2015). This research will examine whether giving oneself advice is another means to promote emotion regulation by enhancing psychological distance. When giving themselves advice, we expect that people should consider the unpleasant event from a more objective and normative perspective, resulting in a decrease in negative emotions.

Participants will be asked to recall a persistent stressor that makes them anxious. They will then be randomly assigned to immerse themselves in the stressor, offer themselves stressor-related advice, or imagine giving a peer stressor-related advice (all in writing). We will measure negative affect, psychological distance, loneliness, confidence in managing the stressor, normative perceptions, and a shift from immersed to a distanced perspective, measured via pronoun use. We hypothesize that participants who give themselves advice or imagine giving a peer advice will demonstrate a more distanced perspective (indexed via language and self-report) and show lower levels of negative emotion (Orvell, 2021). We also predict that giving advice will be associated with feeling less alone, feeling more confident with managing the stressor, more normative perceptions (Orvell, 2021).

Della Guo

Advisor: Heejung Park

Promoting Parenting Efficacy: Examining Maternal Actions in Multicultural Families From South Korea

Although parents commonly do their best to provide for their children, variability occurs in the extent to which they feel confident in their capability of meeting their children’s needs, known as parenting efficacy (Bloomfield & Kendall, 2012).Parenting efficacy is important as confident parents tend to have better parenting behaviors and produce more positive child outcomes (e.g., Leerkes & Burney, 2007). Unfortunately, parenting efficacy may be more challenging to attain for families with immigrant backgrounds due to limited knowledge about their host society despite the desire and pressure to adapt to society (Boruszak-Kiziukiewicz & Kmita, 2020). In South Korea, a previously ethnically homogeneous country under significant social change, the cultural adaptation pressure typically falls on the shoulders of mothers in multicultural families, a unique group that typically consists of Korean fathers and foreign mothers. Indeed, poor parenting efficacy is a common concern for mothers in multicultural families (Bang & Huh, 2011). Thus, my project investigates the extent to which various maternal actions may promote a sense of parenting efficacy in mothers from multicultural families in South Korea. A total of 67 mothers from multicultural families, who have lived in South Korea for an average of 14 years, participated in the daily diary study. Daily maternal actions (e.g., emotional support such as helping the child) and parenting efficacy (i.e., a sense of role fulfillment as a mother) were reported across seven days. In addition to capturing life as it is lived (Bolger et al., 2003), the daily diary method controls for individual variability. Furthermore, given that the data were collected during the COVID-19 pandemic, perceived change in family climates during the pandemic is included as a control variable. I predict that on days when mothers engage in more supportive maternal actions for their children, they also have a higher sense of role fulfillment. 

Keywords: parenting efficacy, maternal action, multicultural family

References

Bang, K.-S., & Huh, B.-Y. (2011). Foreign Immigrant Mothers’ Experiences of Pregnancy, Childbirth, and Child Rearing. Korean Parent-Child Health Journal, 14(1), 36–44.

Bloomfield, L., & Kendall, S. (2012). Parenting self-efficacy, parenting stress and child behaviour before and after a parenting programme. Primary Health Care Research & Development, 13(4), 364–372. https://doi.org/10.1017/S1463423612000060

Bolger, N., Davis, A., & Rafaeli, E. (2003). Diary Methods: Capturing Life as it is Lived. Annual Review of Psychology, 54, 579–616. https://doi.org/10.1146/annurev.psych.54.101601.145030

Boruszak-Kiziukiewicz, J., & Kmita, G. (2020). Parenting Self-Efficacy in Immigrant Families—A Systematic Review. Frontiers in Psychology, 11. https://www.frontiersin.org/article/10.3389/fpsyg.2020.00985

Leerkes, E. M., & Burney, R. V. (2007). The Development of Parenting Efficacy Among New Mothers and Fathers. Infancy, 12(1), 45–67. https://doi.org/10.1111/j.1532-7078.2007.tb00233.x

Julia Katowitz

Advisor: Ariana Orvell

Persistence and Conventions in Children

Research has demonstrated that rituals—fixed series of actions or behaviors, repeated in a rigid fashion—provide a powerful tool among adults for promoting self-control (Tian et al. 2018, 852). However, studies have yet to demonstrate whether children’s self-control can benefit from the enactment of a ritual. The purpose of this experiment is to determine whether leading children through a movement-based ritual can increase their ability to enact self-control during a tedious task.

Children will be introduced to a tedious job, a “peg-turning task” requiring persistence. While completing this work task, children will have the opportunity to take breaks by playing a more entertaining game. Before beginning the peg-turning task, children randomly assigned to a  ritual condition will be taught a ritual involving a series of repeated hand and body movements, while children randomly assigned to a control condition will be led through a less restricted movement activity. We predict that children who are in the ritual condition will persist longer at the tedious task, and spend less time playing the entertaining game, compared to children in the control condition.

The results of this study will contribute to existing literature by demonstrating whether children’s ability to exert self-control can be enhanced by engaging in rituals. These findings may have implications for educational practices, like providing children with an easy-to-implement strategy (i.e., simple rituals) to help them persevere through difficult tasks, like homework. Understanding the impact of a ritual on self-control would create a means to empower children when they are torn between immediate gratification and achieving a future goal.

Elizabeth Nuth

Advisor: Cora Mukerji

Impact of Child Maltreatment at Varying Ages on Adolescents' Behavioral Outcomes

Even with a growing body of research on adverse childhood experiences (ACEs), the mechanisms at play that lead to the development of internalizing and externalizing behavioral symptoms following ACEs remain unclear.  ACEs, especially child maltreatment, can affect all aspects of a child’s development, from their cognition to their emotion regulation and behavior (Bevilacqua et al., 2021; Hunt et al., 2017; McLaughlin et al., 2019).  Previous research has shown that child maltreatment is significantly associated with behavioral problems through adolescence (Thompson et al., 2016) while other studies have found that child maltreatment experienced in middle childhood led to higher levels of emotion dysregulation in adulthood when compared to adults who experienced trauma during other points in childhood, such as early or late childhood (Dunn et al. 2018).  Further research is needed to determine the role that the timing of maltreatment plays in modulating effects on mental health to inform policy and clinical practice.  Therefore, we will conduct a project testing which adolescent behavior outcomes are more greatly impacted by maltreatment at age 3 compared to age 5.  We will utilize data from the Fragile Families and Child Wellbeing Study to examine how earlier versus later exposure to child maltreatment may impact internalizing and externalizing symptoms in adolescence.  In line with preliminary findings from prior work, we hypothesize that adolescents are more likely to develop internalizing disorders if they experienced higher levels of maltreatment at age 3 versus age 5, more specifically, their score will be greater for internalizing behavioral problems at age 15.  We also hypothesize that adolescents are more likely to develop externalizing disorders if they experience maltreatment at age 5 versus age 3, more specifically, their scores will be greater for externalizing behavioral problems at age 15.  The results can provide meaningful insight into when early interventions may be needed for children who have been maltreated and inform the development of more focused interventions following maltreatment at different ages.

References

Bevilacqua, L., Kelly, Y., Heilmann, A., Priest, N., & Lacey, R. E. (2021). Adverse childhood experiences and trajectories of internalizing, externalizing, and prosocial behaviors from childhood to adolescence. Child Abuse & Neglect, 112, 104890. https://doi.org/10.1016/j.chiabu.2020.104890

Dunn, E. C., Nishimi, K., Gomez, S. H., Powers, A., & Bradley, B. (2018). Developmental timing of trauma exposure and emotion dysregulation in adulthood: Are there sensitive periods when trauma is most harmful? Journal of Affective Disorders, 227, 869–877. https://doi.org/10.1016/j.jad.2017.10.045

Hunt, T. K. A., Slack, K. S., & Berger, L. M. (2017). Adverse childhood experiences and behavioral problems in middle childhood. Child Abuse & Neglect, 67, 391–402. https://doi.org/10.1016/j.chiabu.2016.11.005

McLaughlin, K. A., Weissman, D., & Bitrán, D. (2019). Childhood Adversity and Neural Development: A Systematic Review. Annual Review of Developmental Psychology, 1, 277–312. https://doi.org/10.1146/annurev-devpsych-121318-084950

Thompson, R., English, D. J., & White, C. R. (2016). Maltreatment history as persistent risk: An extension of Li and Godinet (2014). Children and Youth Services Review, 64, 117–121. https://doi.org/10.1016/j.childyouth.2016.03.003

Catherine O'Connor

Advisor: Cora Mukerji

Neurodevelopmental pathways linking early psychosocial deprivation and adolescent outcomes

Orphaned or abandoned children living in institutions face psychosocial deprivation marked by low caregiver availability and limited cognitive inputs (Smyke et al., 2007). Children exposed to early institutionalization can experience difficulties in executive functioning (Wade et al., 2019), brain development (Gee et al., 2013), and language ability (Humphreys et al., 2020). The Bucharest Early Intervention Project (BEIP) is a randomized clinical trial examining whether the harmful effects of early institutionalization can be mitigated by removing children from institutions and placing them into high-quality family based care early in life. This foster care intervention included regular support from social workers to aid parents and children in the challenges of the initial transition and beyond. Comparing developmental outcomes from children randomly assigned to high quality foster placements and those who remained in their current institutions can reveal the effects of removal from a neglectful environment and supportive caregiving on cognition and mental health outcomes later in life. Previous studies in the BEIP sample have followed these children into late childhood and adolescence and found distinct outcomes between groups. Those who received foster care exhibited higher IQ at age 12 (Almas et al., 2016) and a lower rate of psychiatric disorders at age 16 relative to their counterparts who were originally randomized to remain in institutions (Humphreys et al., 2020). Another longitudinal study of previously-institutionalized children identified a link between early deprivation and steeper reductions in cortical gray matter in adults (Mackes et al., 2019). In contrast, studies with neurotypical children and adolescents who were never exposed to institutionalization have shown higher rates of cortical thinning to be associated with psychopathology (Fujisawa et al., 2015; Gogtay & Thompson, 2010) and decreases in IQ (Burgaleta et al., 2014). In the BEIP sample, those who received foster care demonstrated more cortical thinning from ages 8 to 16 than those who remained in institutions (Sheridan et al., (under review)), despite having better cognitive and mental health outcomes. It is critical to understand the functional consequences of the enhanced cortical thinning seen in the intervention group. Using data from the BEIP, we seek to determine the effects of early caregiving environments on gray matter structure and its implications for cognitive development. Specifically, we will examine whether the foster care intervention in early childhood improves general cognition at age 16 through changes in cortical thickness during adolescence. In addition, we seek to determine if general cognition is related to vulnerability to psychopathology during this period. We will conduct a path analysis examining whether change in cortical thickness from ages 8 to 16 in the inferior frontal gyrus mediates the link between the foster care intervention and IQ at age 16. We will then examine whether IQ at age 16 is, in turn, associated with vulnerability to general psychopathology at age 16. We expect that the effect of the foster care intervention on general cognition at age 16 will be mediated by patterns of cortical thinning from ages 8 to 16. This change in general cognition will, in turn, be associated with a lower general vulnerability to psychopathology in the foster care group compared to those originally randomized to remain in institutions. This research may emphasize the value of early intervention to remediate the effects of institutionalization on trajectories of brain development. Further, it may highlight the necessity of developing public policy and interventions to support better developmental outcomes for previously institutionalized children, such as the prioritization of social interaction and cognitive stimulation in group-residence homes.

Marrian Tan

Advisor: Anjali Thapar

Detection of Deception: an ERP study

Although deception has been studied for decades, most theories proposed for lie detection rely on unreliable and indirect behavioral (e.g. increased pitches of voice, less frequent blinks) or physiological parameters (e.g. changes in heart rate and blood pressure). Recently, researchers have found that studies using functional magnetic resonance imaging (fMRI) and electroencephalography (EEG)/event-related potential (ERP) are more reliable in detecting deception. However, given the complicated nature of this cognitive process, valid findings on the neurocognitive basis of deception remain limited and controversial. Therefore, the goal of this study is to explore valid paradigms for discriminating lying from telling the truth. Among the theories (e.g. emotional approach, self-presentation perspective) that attempt to explain cognitive processes of deception, the cognitive load approach gains the most support from fMRI and EEG studies, assuming that deception demands more cognitive control. Thus, we hypothesize that deceptive behavior requires more cognitive control both to inhibit the truth response and to select the deceptive response conflicting with the truth. Ideally, such additional effort will be reflected in both ERP waveforms and behavioral measurement (i.e. response time). Given the high temporal resolution of EEG and ERP, we will use them as measurement tools to record and analyze neural activities during deception. Understanding the neurocognitive mechanism underlying the deception process will both move us forward in making a neurophysiological connection to our complicated cognition and provide essential insights for the credibility-assessing process, especially in criminal settings.

Keywords: ERP; deception detection; cognitive control