2018 Summer Scholars

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group photo of summer scholars outside Duke


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

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 E2 allele 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 E4 variant increases the risk of developing Alzheimer’s. The E4 gene 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

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.


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.

Savoya Joyner

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.


Christina Magana-Ramirez

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

Eliud Rives-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.