Past Summer Scholars

2022 Summer Scholars

Ariana Duval

Major: Agricultural & Environmental Sciences
Mentor: Lindsey Constantini, PhD (NCCU)

Mapping KSHV Viral DNA Replication Proteins Locations

Kaposi Sarcoma Herpesvirus (KSHV) is a virus known to cause various human cancers and diseases such as Kaposi’s Sarcoma (KS), Multicentric Castleman’s disease (MCD), and Primary Effusion Lymphoma (PEL). We study how KSHV viral DNA and KSHV viral DNA replication proteins interact with the goal to determine ways to disrupt the molecular interactions and prevent new virus production and spread. My study focuses on optimizing the lab's electron microscope (EM) analysis methods, specifically mapping the KSHV viral DNA replication protein's DNA binding location(s).

Aria Grizzle

Major: Biology/Pre-Med
Mentor: Alex Marshall, PhD (NCCU)

The influence of arsenic on alcohol-induced microglial activation

We are studying the effects of ethanol on the CNS. My focus is on the impact of ethanol and arsenic exposure on microglial activation in the entorhinal cortex. I am using Iba-1 as a marker of neuroinflammation through the use of microscopy and image analysis.

Delaney Hill

Major: Biology
Mentor: Ornit Chiba-Falek, PhD

Investigating humanized mice with TOMM40 long and short poly-T variants to identify gene expression of APOE-TOMM40 gene cluster

My project is based on the hypothesis that gene dysregulation contributes at least part of the risk for Alzheimer’s, and that noncoding variants and epigenetic changes contribute to pathogenic gene expression changes. My project will utilize humanized TOMM40-APOE mice that were previously generated by targeted replacement. I will analyze human APOE and TOMM40 transcript levels in the brain, liver and spleen collected from 4 age groups (3-18 months) of male and female mice carrying the short and long poly-T alleles. The findings of this project will generate new knowledge about the regional regulation of the TOMM40-APOE gene cluster and provide insights into the mechanistic role of this genetic region in aging and its implications to Alzheimer’s disease.

Paola J. Maldonado

Major: Industrial Microbiology
Mentor: Ashley Chi PhD

Using X-Ray Crystallography to investigate the structure of MESH1-CoA

Metazoan Spot Homolog 1 (MESH1) is the metazoan homolog of bacterial SpoT that regulates the bacterial stringent response by degrading the alarmone guanosine pentaphosphate and tetraphosphate [(p)ppGpp]. MESH1 seems to have a significant role in tumor biology that could be used to develop therapeutics to treat various types of cancer. My project aims to investigate the structure between MESH1 and Coenzyme A, one of the identified MESH1 substrates using methods such as x-ray crystallography to gain a better understanding of the role of MESH1.

Brielle-Anne Michel

Major: Biochemistry and Molecular Biology
Mentor: Hiro Matsunami, PhD

Detecting Cell Surface Expression and Maintaining Native Ligand Selectivity with Olfactory Receptor (OR) Chimera

Olfactory Receptors (ORs) are G-protein coupled receptors (GPCRs) that are an essential component in detecting odorous ligands that enter the nasal cavity. Although ORs are known to have abundant cell surface expression on olfactory sensory neurons (OSNs), due to improper protein folding and divergence of residues, many ORs cannot be expressed on the cell surface of non-olfactory cells, causing technical issues for functional assays and biochemical experiments. This project aims to design ORs that show robust cell surface expression, yet maintain the ligand selectivity of their corresponding native receptors by detecting the cell surface expression of olfactory receptor chimeras. Investigating these engineered ORs will provide more insight on how to overcome experimental difficulties in future research concerning olfactory receptors and the detection of odorants, as well as to understand the mechanism of why certain ORs lack cell surface expression on non-olfactory cells.

Brianna Smith

Major: Biology
Mentor: Anne West, MD, PhD

NPAS4 Effect on Neuronal Activity Dependent Transcription

Learning and memory are crucial to survival and are regulated by neuronal activity dependent gene expression, the products of which affect neuronal plasticity. Changes in gene expression are dependent on regulation via the non-coding region of the genome, which includes enhancers and promoters. While promoters are well studied, the detection and mechanisms of enhancer-mediated regulation are still not completely understood. Given that enhancer dysfunction has been seen to be associated with many brain disorders, this area of research is significant. Enhancer function is primarily mediated by transcription factor binding, and a specific neuronal transcription factor, NPAS4 (Neuronal PAS domain protein 4), is seen to preferentially bind to enhancers and is correlated with increased activity dependent transcription. We are investigating the function of NPAS4 in the regulation of enhancer-mediated, activity dependent transcription. Studying the effects of enhancer-binding transcription factors will give us insight to better understand the role of enhancers in human health.

Lucien Tessier

Major: Biology and Linguistics
Mentor: Charlie Gersbach, PhD and Christian McRoberts Amador

Using CRISPRi to repress TOX expression in T cells

T cells are the centerpiece of the adaptive immune system, molding themselves after pathogens to both quell infection and build long-term immunity against future infections by the same pathogen. Unfortunately, in chronic diseases such as viral infections or cancer where T cells are exposed to repeated stimulation, they are reprogrammed to a dysfunctional “exhausted” state. Our project aims to use CRISPRi to reduce expression of TOX, a transcription factor expressed in T cells that has been implicated in the epigenetic maintenance of T cell exhaustion. Successful repression of TOX carries promise of reversing the exhausted T cell state, hence improving immunotherapy by reinvigorating the immune response.

Sydney Vander

Major: Chemistry
Minor: Biology/Math
Mentor: Paul Magwene, PhD

Analyzing Colony Morphology in Saccharomyces cerevisiae

Wild isolates of Saccharomyces cerevisiae exhibit a diverse array of colony morphologies when grown on solid medium, and the development of this complex trait is controlled by multiple signaling pathways. My project examines over 1,000 isolates of S. cerevisiae by culturing them and scoring their phenotypes, based on a scale assigning value to their colony morphologies. By combining this phenotypic data with existing genotypic data available for each isolate, I will perform a genome-wide association study (GWAS). The analysis of this effort will highlight variations in the genetic network controlling colony morphology.

2021 Summer Scholars

Jaye Bullock

Duke University
Mentor: Doug Marchuk
Major: Biology

Project: Characterization of the molecular effects of a novel Gaq Mutation on MAPK/ERK1/2 Signalling as related to Sturge-Weber’s Syndrome

Sturge-Weber’s Syndrome (SWS) is a rare vascular disease caused by an arginine-glutamine substitution (R183Q) in a G-protein subunit, Gaq. This subunit impacts the regulation of proteins that control processes such as cell proliferation and the cell cycle, and one set of proteins in particular, the MAPK/ERK1/2 pathway, affects the integrity of tissues such as blood vessels. Recently, at least one SWS patient was found to have a glutamine-arginine substitution at a different location in the Gaq subunit (Q209R); therefore, we attempted to characterize the ways in which the novel mutation affected the regulation of the MAPK/ERK1/2 pathway by transfecting HMEC-1 and HEK-293 cells with plasmids containing the causative DNA mutation, and performing western blot assays which allowed for comparison of ERK 1/2 signalling with two other Gaq mutations: R183Q and Q209L, a more common variant linked to benign tumor formation.

Emily Da Cruz

Duke University
Mentor: Raphael Valdivia
Major: Neuroscience

Project: Phage integrases as tools for the genetic manipulation of beneficial gut microbe Akkermansia muciniphila

To genetically manipulate Akkermansia muciniphila, a bacteria present in the human gut microbiota that has been linked to various positive health outcomes, we sought to leverage integrases from Akkermansia bacteriophages to stably express exogenous genes in this bacterium. We identified putative bacteriophage integrases and attachment sites from metagenomic datasets, and these genetic elements were synthesized and inserted into a conjugative plasmid for delivery of a drug resistance marker into defined att sites in the A. muciniphila genome. Our initial experiments seek to define the most effective integrases, their regulatory promoter elements, and flanking inverted repeat sites hence we can design vectors to amplify, silence, or activate various genes within A. muciniphila so as to enhance its health-promoting activities in the human gastrointestinal tract.

London Harper

North Carolina Central University
Mentor: John Rawls
Major: Biomedical Sciences

Project: Isolation of Gut Microbes Associated with Obesity in Adolescents

The gut microbiome plays a yet undefined role in obesity in adolescents, a disease that affects one in three children in the United States. My project focuses on the isolation and identification of gut bacteria from adolescents with obesity. These isolates will be used in future studies to help understand the role of the microbiome in obesity and gut microbial ecology, as well as potentially augment treatment for pediatric obesity.

Adriana Moffat

Tufts University
Mentor: Hiro Matsunami
Major: Biochemistry/Biopsychology

Project: Evaluating Expression and Measuring Activation of Olfactory Receptors Associated with Wilson’s Disease

Wilson’s Disease is a rare genetic disorder that causes copper accumulation and poisoning in the body caused by mutations in the ATPB7B copper transporter gene. Wilson’s disease patients have reported the loss of the sense of smell to sulfur odorants like flatulence, natural gas, and skunk spray; and preliminary studies have shown that there are diminished copper concentrations in the nasal mucosa of Wilson’s disease model mice. The goal of this project is to study a set of olfactory receptors linked to the detection of sulfur molecules to investigate whether copper in the olfactory epithelium is essential for the detection of sulfur compounds.

David Ramirez

Duke University
Mentor: Lingchong You
Major: Biomedical Engineering, Electrical/Computer Engineering

Project: Engineering Ecological Community Dynamics using Spatial Configurations

The competitive and cooperative nature of ecological communities has been linked to their geometric spacing from one another. My project looks at the influence of different spatial configurations on ecological community dynamics, specifically their population density, while maintaining a constant initial community composition. I was able to create computational stimulations of different community shapes and circumstances in order to determine which types of community spacings would yield stable or unstable dynamics.

Brittany Saxon

Agnes Scott College
Mentor: Paul Magwene
Major: Public Health

Project: Uncovering Oxidative Stress Resistance Loci in Cryptococcus neoformans

Background: Oxidative stress resistance is a key factor in the of the pathogenicity of the opportunistic fungal pathogen C. neoformans.

Purpose: To better understand how C. neoformans survive within its host, my research focused on discovering loci that control a key virulence factor, oxidative stress resistance.

Methods: Using an assay that measures oxidative stress resistance, I gathered phenotypic data that was later combined with genotypic data through quantitative trait loci (QTL) mapping to discover loci that control variation in oxidative stress resistance.

Makala Sobers

Winston Salem State University
Mentor: Tim Reddy
Major: Biology

Project: New Technologies Used To Identify Gene Regulation of Common Diseases

Throughout the program, I've had the opportunity to rotate through several projects that look at the different techniques used to identify gene regulation in a number of common diseases. First, I participated in a project to study the use of STARR-seq, a reporter gene assay that can identify transcription enhancers in entire genomes. I then participated in two more projects that took a look at the use of siRNA's and ATAC-seq to analyze the expression of RPS26, a gene that appears to possibly be manipulated by the variant rs2271194, which is a variant that has been identified to be associated with polycystic ovary syndrome. Last but not least, I participated in a project that looked at the use of DCAS9 P300 to activate genes that are essential for the Th17 immune system.

2019 Summer Scholars

Tatyana Dunn

North Carolina Central University
Mentor: Ju-ahng Lee
Major: Biology/Pre Med

Project: Hands-on training of modern genetic engineering technologies: Transposon-Mediated transgenesis and targeted genome editing by CRISPR/Cas9

I’m working to understand modern engineering technologies and the use of targeted genome editing by CRISPR/Cas9 to knock out zebrafish tyrosinase (tyr) and knock in lgals3bpb. I have been conducting hands-on experiments to knock in the lgals3bpb gene into the zebrafish genome. I have recently learned to do restriction enzyme mapping, mini and midi kits to extract plasmid DNA, Gel electrophoresis, and injections to run trials to see if the knock in is becoming more efficient through different techniques. Thus far, I have found through various readings and trial runs that CRISPR/Cas9 is efficient at knocking out genes, but knock in efficiency is very low. Out of 300 fish injected, only 3 - 6 survived from each sample injected, but this may have been due to toxicity in the injection mixes. Recently, after extracting plasmid DNA and making new injection mixes, we have had most of our new injected fish survive and will soon be able to tell if the knock in expression is shown. My next step is to identify other methods that can be used to raise the knock-in efficiency of CRISPR/Cas9 in zebrafish.

Natalie Ezem

Duke University
Mentor: Gregory Cole
Major: Sociology/Global Health

Project: Expression pattern of cannabinoid receptors 1 and 2 in zebrafish embryos

I am investigating how 4% Paraformaldehyde (PFA) in Phosphate-Buffered Saline (PBS) impacts cannabinoid receptor genes, also known as cnr1 and cnr2, in zebrafish embryos at one to three days post fertilization. I will be determining the correct cnr1 and cnr2 constructs, synthesizing a cnr1 and cnr2 anti-sense DIG-labelled RNA probe, and performing whole-mount in-situ hybridization on the receptors. Thus far, I have found the cnr2 construct and I am currently redesigning new primers to detect cnr1. Afterwards, I will synthesize probes for these sequences and perform the whole-mount in-situ hybridization.

Dezmond Garrett

University of North Carolina - Greensboro
Mentor: Hiro Matsunami
Major: Kinesiology

Project: Testing olfactory receptors

The goal of my project is to continue to find new agonist ligands of OR1A1 and OR2W1 by exposing them to various odorants. I am testing linkage of odorants predicted by a computational study of results of the project’s Australian collaborators. I will be using the odorants of their predicted study. The activity and linkage will be monitored by the use of luciferase assay. By using human embryonic kidney cells, we will transfect plasmid of the ORs, luciferase to provide luminescence, M3, the transporter protein RTP1S, SV40, and CRE (which act as promoters of Luciferase) into the cells. Once the cells are transfected with the plasmids, we will inject the odorants into the cells and monitor the luminescence to determine the activation of the receptors by the odorants.

Jonathan Harpe

North Carolina Central University
Mentor: Tim Veldman
Major: Biology Pre Med/Psychology

Project: Confirming peripheral miRNA biomarkers by RT-qPCR in epilepsy patients

The purpose of this pilot study is to evaluate peripheral blood of epilepsy patients for expression profiles that distinguish epilepsy from healthy individuals and patients with neurological disorders other than epilepsy (e.g., migraines). We hypothesize that molecular signals known as microRNAs are detectable in blood and are associated with epilepsy along with standard clinical assessments. These type of RNA are small noncoding molecules that are ~22 nucleotides in length and function as post-transcriptional inhibitors for protein synthesis. Past studies show that because of the nature of these molecules, they could potentially indicate signs of being biomarkers for diseases that have very poor prognosis and prevention. I am inducting managing patients into the study and collecting blood samples to ultimately answer the question of whether these miRNAs collected from plasma samples are linked to epilepsy. After sample collection, we are expecting to find statistically significant up or down regulated miRNAs from the epilepsy subgroup to be analyze by their properties and structure to find which miRNAs may become potential biomarkers for their disorder.

Hana Lee

North Carolina Central University
Mentor: Ashley Chi
Major: Biology/Pre Med

Project: The role of MESH1 in an in vivo model of ferroptosis

To test the role of MESH1 in the in vivo ferroptosis models, we knock down the expression of enzyme MESH1 by the tail vein injections of siRNAs that target MESH1 (siMESH1) or non-targeting control (siNT: negative control). As a positive control, we injected liproxstatin that is expected to inhibit ferroptosis, or programmed cell death. We fed these mice with the MCDE diet that has been discovered to induce ferroptosis in the liver. We expected to see a decrease in ferroptosis but an increase in fibrosis markers in the liproxstatin and the siMESH1 groups, compared to the siNT group. Now we are validating the presence of other markers for fibrosis using western blot, qPCR and IF staining. We are testing for markers of ferroptosis and fibrosis using the same method.

Kennedy Lofton

North Carolina Central University
Mentor: Ornit Chiba-Falek
Major: Pharmaceutical Sciences

Project: Using the methylation of DNA to explain a track for gene therapy of AD patients

APOE is correlated with a person having a higher risk of developing Alzheimer’s disease (AD). Therefore, we are investigating if the methylation of AD patients’ DNA changes how their APOE gene is expressed. We are using FANS (Fluorescence-Activated Nuclei Sorting) methodology to sort the cells between neuronal and non-neuronal (glial cells). Next, we are using three different downstream analytical methods to pull different information from the different cell types. For methylation, a MethylEPIC microarray looks at the methylation levels on the cytosine-phosphate-guanine (CpG )islands of the gene. We are also using pyrosequencing to analyze parts of the APOE gene that may lie outside of the CpG islands and their cytosine methylation levels. Finally, we compare data across the different cell types (neuronal and glial), between normal and AD patients, as well as between male and female patients.

Ednan Ochieng

North Carolina Agricultural and Technical State University
Mentor: Raluca Gordân
Major: Mechanical Engineering

Project: Modeling transcription factor specificity

Using experimental assays to measure the DNA binding specificity of transcription factors (TFs) across the human genome is a long and expensive process. To solve this problem, we are training machine-learning models to predict TF binding specificity. We do this by using a Support-Vector Regression (SVR) algorithm that takes as input TF binding measurements for ~30,000 genomic sites, looks for patterns in the sequences, and returns a function that best predicts the TF specificities from sequence. Longer-term, being able to accurately predict TF binding will allows us to examine gene expression regulation in human cells.

Alexandria Scott

North Carolina Central University
Mentor: Paul Magwene
Major: Biomedical Science

Project: Analyzing capsule size variation in Cryptococcus

Cryptococcus is a pathogenic fungus that primarily infects immune compromised people. To investigate what loci controls the capsule size variation, I will be using natural variation within the C. denoeoformans species to understand the genotype to phenotype relationship regarding virulence factors. Specifically, I will be studying the capsule, which surrounds the cell and protects the fungus from various host specific conditions. A cross was made between two genetically diverse strains, one isolated from pigeon excrement and the other laboratory constructed, and I will use the progeny to study capsule size variation. We will focus on what genes control the capsule size. Due to recombination from the cross, the segregate will have genes from both parents which will be examined further using Quantitative Trait Locus (QTL) analysis of the capsule size variation. The results of QTL analysis will ultimately quantify the genetic differences, some of which are responsible for capsule size.

2018 Summer Scholars

Brianna Bowman

University of Illinois at Urbana-Champaign
Mentor: Jenny Tung
Major: Molecular and Cellular Biology

Project: Trade-offs in bone growth and reproduction in mole rats of the Kalahari Desert, South Africa
Damaraland mole rats are eusocial animals that live in colonies, and only one female member of the group reproduces. Any female has the potential to become a “queen” when introduced to an unrelated male, and grows to be larger than the other mole rat “helpers” in her colony. My project entails analysis of mole rat bones to understand better about the mechanism that allows queen mole rats to trigger bone growth, which can occur even after adult maturation. Specifically, I am analyzing the shape of the bone using 3D data from microCT scans and analyzing genome-wide gene expression data from bone cells derived from queens and helpers. I will combine the bone growth data with functional genomic data on bone cell gene expression to investigate how changes in gene regulation contribute to social plasticity in mole rats. Our findings show that in a small sample size, there is no statistically significant difference in relative volume of trabecular bone in femurs between queen and helper mole rats.

Layne Clements

North Carolina Central University
Mentor: Doug Marchuk
Majors: Biology and Pre-Med

Project: Decoding the pathogenesis hereditary hemorrhagic telangiectasia
Hereditary Hemorrhagic Telangiectasia (HHT) is an inherited, vascular malformation disorder which causes focal lesions on organs and membranes throughout the body. This project aims to test Knudson's hypothesis (also known as the two-hit model) for vascular malformations by identifying paired somatic and germline variants on genes commonly associated with CCM and HHT. For inherited cancers, Alfred Knudson (1971) hypothesized that if an individual inherited one mutated allele, it would necessitate a somatic mutation in the corresponding allele to cause disease; hence the coining of the "two-hit model." To execute this project, we are using computational tools such as MuTech2 to identify mutations in targeted next generation sequencing data. This involves testing several specific genomic amplification methods such as Polymerase Chain Reaction (PCR) to enable sequencing from Formalin-fixed, Paraffin-embedded (FFPE) samples. SureSelect and SNaPshot assays are the methods currently used to verify the amplification of the particular HHT-related gene mutations of interested. We have results that demonstrate a two base pair deletion and a twelve base pair deletion. We are now attempting to verify the deletions' existences through the methods previously mentioned. If these deletions are verified, it could identify that HHT’s pathogenesis follows the two-hit model. Future steps will be taken to identify more variants to support our hypothesis.

George Crawley, IV

Duke University
Mentor: Ornit Chiba-Falek
Majors: Biology, Chemistry, African American Studies

Project: Phenotypic characterization of the APOE gene variants
Late Onset Alzheimer’s disease (LOAD) is an irreversible, progressive brain disorder that damages memory, mental skills, and ultimately the ability to carry out simple tasks. Studies strongly suggest that genetic factors play a role in the onset of LOAD. The apolipoprotein E (APOE) gene is a known to potentially influence one’s risk for LOAD onset. There are three alleles of the APOE gene; ApoE₂(E2), ApoE₃(E3), and ApoE₄(E4). These three variants are defined by two single nucleotide polymorphisms (SNPs). The E2allele is the rarest form of APOE and has been shown to display some protective effects. The E3 variant is the most common allele, and is believed to play a more neutral role in the disease. The E4variant increases the risk of developing Alzheimer’s. The E4gene variant is the largest genetic risk factor for the onset of AD. The lifetime risk estimate of developing AD by age eight-five is approximately 65 percent in people that have two copies of the E4 allele, but only about ten percent in people with two copies of the E3 allele. Based on previous studies, E4 has been found to be associated with increases in some toxic effects that are associated with AD pathology.

The complete function of APOE is still unknown, therefore the objective is to characterize the age-related phenotypes associated with nuclear architectures by measuring markers for heterochromatin organization, and changes in the nuclear envelope structure.

Kayla Hammond

North Carolina Central University
Mentor: Tim Reddy
Major: Biology

Project: Optimizing endometrial cells for large scale genomic assays
Preterm Birth (PTB) affects hundreds of thousands of women every year. Babies that are born before 37 weeks of gestation can be plagued with various issues such as pneumonia , hearing, vision loss and many others. With PTB being the leading cause of neonatal morbidity and mortality this issue must be investigated further.

There are very few therapeutic options that prevent PTB. 17 Alpha-Hydroxyprogesterone Caproate (17P) , is a synthetic form of progesterone that has been shown to reduce the recurrence of pre-term birth in some women. 17P acts by changing gene regulation in endometrial cells, which are affected in PTB. Unfortunately, 17P’s mechanisms are unknown, understanding 17P will create new opportunities to end the development of pre-term birth; this can be done with a high-throughput reporter assay.

A reporter assay is an assay that allows enhancer activity to be seen within a sample. A high-throughput reporter assay will make it possible to see enhancer activity within multiple samples, this is pivotal as it will allow me to see what enhancers are active within 17P when gene regulation is underway. It is because of this that I will optimize a high throughput reporter assay called STARR-seq and transfect reporter plasmids into endometrial cells without triggering a cell stress response, in order to further understand 17P and its effects on preterm birth.

Naeema Hopkins-Kotb

Duke Unversity
Mentor: Beth Sullivan
Majors: Biology, Global Health, and Chemistry

Project: Investigating Human Dicentric X Chromosome Stability Using a Mouse-Human Hybrid Model

Dicentric X chromosomes (iso(X)) – X chromosomes with two centromeres – are associated with diseases like Turner syndrome and reproductive abnormalities but can also be stable in humans. The mechanism by which this stability occurs is unclear due to the lack of in vitro assays able to track the chromosomes over time. In order to examine dicentric X chromosome stability, this study molecularly and cytogenetically characterizes dicentric X chromosomes created by a push-pull assay to model patient dicentric structures. By visualizing the dicentric X chromosome centromeres by fluorescence in situ hybridization (FISH) and using PCR interrogation sites across the long arm of the X chromosome, we determine the intercentromere distance, breakage points and overall dicentric structure of induced dicentric X chromosomes with the goal of tracking the different stability outcomes after their formation. Our preliminary results have shown that the push-pull assay creates dicentric chromosomes at a high frequency, with differences in dicentric structure and variable long-term stability. This data will be useful in future analyses of centromere function correlated to chromosome structure. Our results have implications for understanding the molecular basis of genome instability and aneuploidy and provide a powerful model to enhance our clinical understanding of dicentric-related disease.

Savoya Joyner

North Carolina Central University
Mentor: David MacAlpine
Major: Biology

Project: Investigating the role of MCM10 during initiation of DNA replication
All eukaryotic organisms undergo DNA replication, and DNA synthesis is initiated at different origins of replications. MCM10 is a conserved protein across eukaryotes and is essential for genome copying to occur. MCM10 has been shown to activate MCM2-7 helicase, which unwinds the DNA. During DNA replication, chromatin structure must change, but it is unclear what changes occur around the origin of replication during early S phase. The phenotypes of MCM10 conditional mutants (plus axin/doxycycline) in Saccharomyces cerevisiae were investigated with a long-term goal of examining how chromatin structure changes at origins of DNA replication. The restrictive conditions delayed cell cycle progression and also decreased cell growth. These results sugges that conditional mutants of MCM10 are good candidates to study chromatin structure immediately before initiation of replication. This also shows the significance of the MCM10 protein during DNA replication. Studying replication is importants because mistakes in replication can lead to genomic instability.

David Mangum

University of North Carolina at Greensboro
Mentor: Paul Magwene
Major: Computer Science

Project: The Benefits of Sex: Aneuploidy, Mitochondrial Recombination, and De Novo Mutations
Cryptococcus species are opportunistic pathogenic yeasts that are the cause of death in nearly 180,000 individuals, annually. During sexual reproduction, partial or complete duplication of chromosomes and genetic mutations may arise de novo. Also, mitochondrial inheritance patterns are thought to differ between a-α bisexual and α-α unisexual mating. While all of the aforementioned factors have reported links to virulence, genome-wide estimates of aneuploidy generation, mutation rate, and mitochondrial inheritance during sexual reproduction are still lacking. Here we investigate these factors in Cryptococcus deneoformans using whole genome sequencing data from 124 progeny generated via a-α bisexual and α-α unisexual reproduction. Within these progeny, aneuploidy of chromosomes 1, 7, and 10 was observed. Progeny generated from bisexual reprodcution exhibited uniparental mitochondrial genome inheritance from the MATa parental strain; by contrast progeny generated via unisexual reproduction exhibited both uniparental and biparental inheritance of mitochondrial genomes as well as mitochondrial recombination. We estimate a mutation rate of 0.021 mutations per Mb and observe a slightly higher average rate of mutation in unisexualy produced progeny versus bisexualy produced progeny. This high-density, genome-wide study of aneuploidy, mutation rate, and mitochondrial inheritance advances our understanding of virulence factors in Cryptococcus.

Christina Magana-Ramirez

California State University Monterey Bay
Mentor: Raluca Gordân
Majors: Mathematics and Computer Science

Project: UV Damage in Transcription Factor Binding Sites
Ultraviolet radiation damages DNA through the formation of covalent bonds between adjacent pyrimidines, which can affect the binding of transcription factors (TFs) and expression of genes. In this project, we explore the sensitivity of TF binding sites to UV radiation. For predicted binding sites corresponding to TFs Myc, E2f1 and Ets1 obtained from Integrative Modeling and Analysis of Differential Specificity (iMADS), we compared the expected versus observed DNA damage using publicly available UV-damage database. At certain positions within TF binding sites, we observed a trend of increased or decreased UV damage in the cell compared to the damage expected from sequence alone. We hypothesize that protein binding could potentially prevent or promote damage due to the DNA structural changes induced by TF binding. Future studies could explore the impact of TF binding on UV damage. Our results provide new insights into DNA recognition by TFs and contribute to research in carcinogenesis caused by UV-induced damage.

Eliud Rivas-Hernandez

University of Puerto Rico
Mentor: Raphael Valdivia
Majors: Microbiology and Computer Science

Project: Identifying mucin-degrading genes in Akkermansia muciniphila
The microbiome plays a significant role in human health Akkermansia muciniphila is a gram-negative bacterium and represents up to 3-5 percent of the gut microbiome. Clinical studies have shown a positive correlation between an abundance of A. muciniphila and human health. In the Valdivia lab, we are building a collection of A. muciniphila transposon mutants to elucidate what genes are required for mucin degradation, which means it can use mucin as its sole source for carbon and nitrogen. Understanding the genetics of A. muciniphila and its intriguing ability to consume mucin will help identify regulatory factors. Knowing the regulatory factors in charge of mucin consumption will lead to addressing the mechanisms that can improve human health. We have already found some genes, such as Amuc_0394, Amuc_0543, and Amuc_1246, that are part of mucin degradation by A. muciniphila. We also recently isolated a novel Akkermansia, as well as novel and potential bacterial competitors that could influence gut microbiome A. muciniphila abundance. This project will contribute to our understanding of A. muciniphila colonization and interactions within the gut, in addition to building the necessary bacterial collections for future studies.

2017 Summer Scholars

Jai Eun (Jennifer) Huh

Class of 2020
Mentor: Ashley Chi
Major: Biology

The Chi lab seeks to understand special components linked with cysteine-deprived death in tumor cells. My project focuses on ferroptosis (an iron-dependent form of regulated necrosis) and DDR2 gene that is believed to activate this cellular pathway in tumor cells. The Chi lab previously found that overexpression of DDR2 is linked to ferroptosis in secondary tumor cells, suggesting the possibility of bypassing the tumor-resistant pathway. This summer, I’ll use genetic techniques such as site-directed mutagenesis, gateway cloning, q-PCR etc. to upregulate DDR2 in primary breast cancer cell and to observe the effect in hopes of elucidating the mechanism behind DDR2 and ferroptosis.

Ashish Vankara

Class of 2019
Mentor: Charlie Gersbach
Major: Biomedical Engineering

Developing a method to efficiently derive satellite cells and myocytes from human iPSCs can be very useful in a laboratory context. For my project this summer, I’m working on reviewing different differentiation protocols to find an optimal method to induce the paraxial mesoderm lineage and eventually derive dorsal somites and skeletal muscle cells via CRIPSR/Cas9 based transcriptional activators. These activators will be delivered to the cells via adenovirus that I will generate in lab.

Ammara Aqeel

Class of 2019
Mentor: Deepak Voora
Major: Biology

Platelet malfunctions can lead to problems such as thrombosis and consequent blockages in blood flow. Antiplatelet therapy employed against such conditions shows variation in efficacy across individuals. Our project lies in the field of precision medicine and aims to develop a prognostic test for whole blood that can predict patient response likelihood to antiplatelet therapy. This will involve translating RNA transcripts suspected to be associated with platelet function to whole blood by measuring their expression using PCR assays. This will remove reliance on platelet RNA which is both expensive and hard to obtain in large quantities and thus, allow for a feasible testing mechanism that can be incorporated into routine practice.

Jeffrey Gu

Class of 2020
Mentor: Ornit Chiba-Falek
Major: Neuroscience

The Chiba-Falek lab studies the mechanisms and structural variants of the SNCA gene, which has been associated with synucleinopathies such as Parkinson’s Disease and dementia with Lewy Bodies. My project centers around using CRISPR/Cas9 genome editing technology to alter a single nucleotide polymorphism (SNP) that is highly associated with Parkinson’s Disease. The risk allele alters the binding sites of one miRNA. By changing the SNP from a mutant (pathogenic) to a normal genotype, we hope to see increased levels of binding of miRNA to SNCA mRNA and therefore decreased levels of SNCA gene expression. Another facet of my project involves profiling the DNA methylation patterns of both the normal wild-type SNCA gene and the pathogenic triplicated-SNCA gene, with a focus on Intron 1 and Exon 1 of the gene. Both approaches will use induced pluripotent stem cells (iPSC) and iPSC-derived neurons as the model system. Through the work done in the Chiba-Falek lab, we hope to gain a greater understanding of the SNCA gene regulation and possibly develop strategies to safely regulate SNCA gene expression.

Christopher Lin

Class of 2019
Mentor: Xiling Shen
Major: Computational Sciences

Cancer models are essential in developing and evaluating treatments. However, there are many ways to create a model cancer system, which may or may not accurately reflect actual tumor behavior. To address this, my project will involve analysis of single-cell RNA-seq data from xenograft and organoid models as well as patient tissue samples to evaluate the efficacy of these models. Using various computational techniques, the goal of my project is to identify subpopulations of cells based on gene expression, and use their composition to compare these cancer models.

Austin Zhang

Class of 2020
Mentor: Ashley Chi
Major: Biology and Computational Sciences

Identifying proteins requires running collected mass spectrometry data through databases. Different search tools yield different results due to the differences in each tool's search algorithm/process. We aim to evaluate search efficacy by evaluating different search tools.

2016 Summer Scholars

Jadesola Akinwutan

Class of 2018
Mentor: Ashley Chi
Project: Analyzing the Effects of HDDC3 Knockout Using the CRISPR/Cas9 within Kidney Cancer Cells
Major: Biology and Global Health

The Chi lab uses DNA various genetic tools such as DNA microarrays to further understand the architecture of human body cells and how they physiologically and pathologically change in human diseases.MESH1 is an enzyme that has the potential to hydrolyze nucleotide derivatives and modulate cellular stress response. However, ppGpp, the substrate of MESH1 is only found within bacteria, not in humans. Chi lab revealed that knocking out MESH1 from cells has the potential to alter the cancer cell response to chemotherapy by redirecting the production of stress-relieving antioxidants. My summer project at the Chi lab focuses on using the CRISPR/Cas9 system and four guiding RNAs in targeting MESH1(HDDC3) gene to make complete knock-out of MESH1 within cancer cells and analyzing the effects/phenotypes of these knock-out cells. I am a rising sophomore looking to double major in Biology and Global Health.

Andrew Grover

Class of 2018
Mentor: Lawrence David
Project: Enumeration of Cells in Gut Model Bioreactor
Major: Chemistry

Othmane Jadi

Class of 2019
Mentor: Sandeep Dave
Project: Investigating Gene Mutations to Identify Involvement in Oncogenesis
Major: Chemistry; Minor: Computational Biology and Bioinformatics

Ariel Kantor

Class of 2019
Mentor: Charlie Gersbach
Project: Engineered CRISPR/Cas9 Complex for Control of Endogenous Gene Regulation
Major: Biology with a concentration in Biomechanics and Pharmacology; Innovation and Entrepreneurship; Markets and Management Studies

Madison Zamora

Class of 2018
Mentor: Ornit Chiba-Falek
Project: Using iPSC-Derived Neurons to Functionally Evaluate the Role of SNPA Triplication in the Context of Synucleinopathies
Major: Biology; Minor: Chemistry; Certificate: Science and Society

2015 Summer Scholars