37th Annual Graduate Student Symposium February 11, 2013 Stanley G. Stephens Room 3503 Thomas Hall The Genetics Graduate Students Association welcomes you to their 37th Annual Graduate Student Symposium 9:45 a.m. Opening Remarks Dr. Stephanie E. Curtis Director of Graduate Program Session I 10:00 a.m. 10:15 a.m. 10:30 a.m. 10:45 a.m. Moderator: Lauren Dembeck Jessica Nye Bill Barrington Emily Moore Steven Vensko 11:00 a.m. Coffee Break Session II 11:15 a.m. 11:30 a.m. 11:45 a.m. Moderator: Becky Edman Tiffany Garbutt Bhupinder Sehra Megan Garlapow 12:00 p.m. Lunch Continued on Next Page 1 Session III 1:00 p.m. 1:15 p.m. 1:30 p.m. 1:45 p.m. 2:00 p.m. Moderator: April Wynn John Shorter Richard Gell Lauren Dembeck Chad Hunter Hayley Crockett 2:15 p.m. Break Session IV 2:30 p.m. 2:45 p.m. 3:00 p.m. 3:15 p.m. 3:30 p.m. Moderator: Randi Wheatley Matt Robinson Kate Coyle Shante Bryant Katherine Knudsen Sarah Cash 4:30 p.m. Presentation of Department of Genetics Awards East Village, Hillsborough Street Outstanding Teaching Apprentice Awards Dr. Stephanie Curtis Dr. Ted Emigh Presentation of the Department of Genetics Outstanding Presentation Speaker Awards Dr. David Threadgill 2 Genetic Variation of Heart Rate in Drosophila Jessica Nye Advisor: Trudy Mackay Cardiovascular disease is the leading cause of death in the world and claims a life every thirtynine seconds in the United States. The heritability of cardiovascular disease in humans is currently estimated between 38% and 66%. While this disease has a high genetic component, other factors are known to impact its prevalence such as environment, diet, exercise, and personality characteristics. All these confounding factors make determining the genetic basis of variation in susceptibility to cardiovascular disease difficult in humans. Drosophila is the only invertebrate model organism with a pumping heart developmentally homologous to that of a vertebrate. By combining the advantages of the invertebrate model system with evolutionary conservation of basic biological processes between Drosophila and humans, Drosophila can be used to identify genes homologous to those affecting vertebrate heart rate. The Drosophila Genetic Reference Panel (DGRP) is a newly created collection of inbred lines derived from a wild population, and poses a promising model for identifying genes affecting natural variation in heart rate. I have screened DGRP lines for heart rate variation. Larval heart rate has significant genetic and phenotypic variation. I have identified 78 candidate genes from a genome-wide association study to identify the molecular variants associated with heart rate and their human orthologs. Societal Influences on Disease Susceptibility as Reflected by Diet Bill Barrington Advisor: David Threadgill Colorectal cancer is the second leading cause of cancer-related deaths in the United States. Mouse models provide a valuable research tool for investigating cancer susceptibility, and have been used to show that diet plays an important role in the development of colorectal cancer. However, little is know about how diets interact with genetic background to alter cancer susceptibility. In my research, I use mouse models on different genetic backgrounds to compare the impact of six different diets, mimicking popular diets consumed by many individuals today, on susceptibility to developing colorectal cancer. I am using gene expression analysis from mice on different diets to investigate the relationship between diet, gene expression, and genetic background on development of colorectal cancer. Additionally, I am examining the impact these diets have on the mouse gut microbiome, which is emerging as an important mediator of health and disease. Lastly, I am comparing the effect of diets on a variety of phenotypes such as activity level, inflammation, and health biomarkers. Ultimately, this research will determine relationships between diet and cancer susceptibility, identify genes involved in cancer susceptibility, and investigate interactions between diet, gut microbiome, and genetic background on cancer susceptibility. 3 Impact of a Novel Sex Determination Locus on Regulatory Gene Networks and Reproductive Fitness in African Cichlid Fish Emily Moore Advisor: Reade Roberts African cichlid fish are an excellent evolutionary model for studying diversity within many phenotypically divergent but closely related species in a natural context. Adaptive radiations within the African Great Lakes led not only to a variety of morphological and habitat specializations, but also instances of novel sex determination loci (SDL) which (when present) interact with ancestral sex determiners to create a polygenic sex determination system. Laboratory families of Metriaclima pyrsonotus with female (W) and male (Y) SDL will be used to examine gene expression and fitness differences between individuals of four genotypic sexes (XX/ZZ, XX/WZ, and XY/WZ females; XY/ZZ males). RNA-seq from key time-points in developing gonads will allow investigation into the gene modules that regulate sex differentiation, and may lead to identification of novel sex determination mechanisms and insight into control of the core vertebrate sex determination network. Studies of animals with recently evolved, polygenic SDL suggest higher reproductive fitness in individuals with the newest locus, so relative reproductive fitness between genotypic classes of M. pyrsonotus will be assessed through gonad histology, egg production, and conspecific, intrasex aggression levels. Preliminary data suggest that females with the W sex determiner have differential gene expression and produce more eggs; ongoing research in the Roberts lab is currently addressing behavioral dominance between W and non-W females. 4 Understanding the Spread of the Selfish Genetic Element Medea in Populations of Red Flour Beetles Sarah Cash Advisors: Fred Gould and Marcé Lorenzen Selfish genetic elements spread by causing their own inheritance in more than the fifty percent of a heterozygous individual’s offspring expected under Mendelian inheritance. One such element, called Medea, is found in some populations of the red flour beetle (Tribolium castaneum), and it increases in frequency by killing off any offspring of a Medea-carrying mother that do not inherit Medea. While models make predictions about how the element should spread in natural populations, no prior empirical studies had been performed to test these models in the lab or field. We have addressed an assumption of these models by demonstrating that a single copy of a Medea allele inherited by heterozygous offspring is sufficient to compensate for any potential increase in egg toxicity produced by a homozygous Medea mother. Further, we have examined how Medea allele frequency changes over time within a single lab population. To assess the field-level dynamics of Medea, red flour beetles were collected from populations across the United States, and Medea-1 genotyping is revealing the current distribution of this element. Future research will focus on examining what factors are responsible for the contemporary Medea distributions by testing whether Medea distribution and Tribolium castaneum population structure are reflective of one another, and whether the genetic backgrounds of wild Tribolium populations influence the spread of Medea elements. Uncovering how selfish genetic elements like Medea spread and maintain themselves within populations—and ultimately, species—is critical for expanding our overall understanding of evolutionary biology. 17 Identification and Characterization of Seminal Fluid Proteins in Monogamous and Promiscuous Vole Species Katherine Knudsen Advisor: Lisa McGraw A long-standing question in evolutionary biology lies in how mating systems evolve. Prairie voles (Microtus ochrogaster) are unique among mammals in that they are socially monogamous and sexual partners often form long-term pair bonds. To the contrary, the closely related meadow vole (Microtus pennsylvanicus) is promiscuous. Studies in a variety of taxa suggest that seminal fluid proteins (SFPs) may play an important role in the evolution of mating systems. For example, in Drosophila, SFPs have been shown to have numerous effects on female mating behavior including increasing ovulation rate and egg-laying and decreasing female receptivity to mating with other males. Some SFPs have been shown to have toxic effects in the female, including decreasing her lifespan. While several studies have identified SFPs in mouse (Mus musculus) and rat (Rattus norvegicus), the contribution of SFPs to mating system evolution and how they might influence the female’s behavior has been largely unexplored. I plan to utilize the vole models to identify and characterize SFPs in a monogamous and promiscuous species to begin to understand the contribution of these proteins to mammalian mating system evolution. By identifying and characterizing the SFP profiles in the prairie vole and meadow vole, I will be able to exploit these model organisms for study of reproductive behavior physiology and begin to understand how the evolution of reproductive traits relates to mating system evolution. Given that most SFP studies have been performed in insects, this research will provide a deeper understanding of the effects of SFPs on female mating behavior in mammals. 16 Reassessment of the Contributions by Dosage Compensation to the Demasculinization of the Drosophila melanogaster X Chromosome Steven Vensko Advisor: Eric Stone The forces believed to shape the Drosophila melanogaster X chromosome, including dosage compensation, meiotic sex chromosome inactivation and sexual antagonism, are not well understood and remain a controversial subject. Improved models of these forces allow for a better understanding of Drosophila sex chromosome evolution. Recent research suggests the mechanism which equalizes X-linked gene expression between the heterogametic Drosophila males and homogametic Drosophila females through two-fold upregulation of expression in males, X-linked dosage compensation, creates a disadvantageous environment for male-biased expressed genes. It has been proposed that this unfavorable environment has contributed to an enrichment of X chromosome -> Autosome retrotransposition events, a deficit of X-linked male-biased expressed genes near dosage compensated regions of the X chromosome, and a significant positive correlation between the degree of male-bias and distance from dosage compensated regions on the X chromosome. Other research provides conflicting yet indirect evidence of dosage compensation having neutral or beneficial effects on X-linked male-biased expressed genes. We utilized publicly available datasets to reconsider the effects of dosage compensation on X-linked male-biased expressed genes. Our results do not corroborate previous claims of detrimental effects by dosage compensation on male-biased expressed genes and instead provide examples directly contradicting current theory. We find no evidence that dosage compensation has detrimental effects on male-biased expressed genes, suggesting it has neither played a role in the enrichment of X chromosome -> Autosome retrotransposition events nor shaped the distribution of male-biased expressed genes on the X chromosome. 5 Identifying the Genetic Cause of the NOD and WSB iPSC Phenotype Tiffany Garbutt Advisor: David Threadgill Mouse embryonic stem cells (mESCs) are a useful molecular research tool due to their undifferentiated, proliferative state. Induced pluripotent stem cells (iPSCs) are artificially derived stem cells generated through somatic reprogramming and are an attractive alternative to mESCs. However, non-permissive mouse strains cannot form mESCs or iPSCs under standard conditions for unknown genetic reasons. We have generated fibroblast-derived iPSCs from six of the eight parental strains of the Collaborative Cross Mouse Genetic Reference Population. The two remaining strains, NOD and WSB fail to produce stable iPSCs and form developmentally primed epiblast stem cell (EpiSC)-like colonies in response to somatic fibroblast reprogramming. We are investigating the genetic mechanism and inheritance pattern governing the EpiSC-like iPSC phenotype and will identify candidate gene(s) through genetic mapping. Candidate gene(s) will be functionally tested using a targeting vector with a docking site for overexpression and knockdown experiments. This research will provide insights into the genetic networks controlling pluripotency identity and successful iPSC generation. 6 Genetic Analysis of a Post-infectious Model of Irritable Bowel Syndrome Shante Bryant Advisor: David Threadgill Irritable bowel syndrome (IBS) is one of the most predominant functional bowel disorders affecting approximately 20% of the population in the developed world and 7-10% of people worldwide. Quality of life for patients suffering from IBS can be greatly reduced by symptoms such as changes in bowel habits, abdominal pain and bloating, cramping, flatulence, and passage of mucus. The etiology of IBS is likely to be multi-factorial; environmental factors, genetics, variation in gut flora, nervous system alterations, dysfunction of the brain-gut axis, and psychosocial stressors have all been examined and are thought to contribute to the development of the disorder. Treatment options vary tremendously and are generally aimed at treating symptoms individually and not at addressing IBS as a physiopathological entity. A major limitation to understanding the development of IBS and creating more effective treatment options is the absence of a valid animal model. Existing animal models can be categorized as either post-inflammatory or post-infectious. We plan to develop an appropriate mouse model in which symptoms of human IBS can be replicated and examined collectively by comparing three post-infectious models for their ability to induce two major problematic symptoms that IBS patients experience, intestinal motility dysfunction and visceral hypersensitivity. The infectious agents to be examined include Trichnella spiralis (pathogenic worm), Cryptosporidium parvum (infectious protozoan species), and Citrobacter rodentium (gram-negative bacterium). Once a model is selected, we will identify casual genetic links that contribute to the development of IBS symptoms using the Collaborative Cross genetic reference panel. 15 Evolution of Sex-determining Loci and Associated Traits in African Cichlid Fishes Kate Coyle Advisor: Reade Roberts Several species of East African cichlid fishes display sexually dimorphic “blotched” pigmentation patterns that confer an adaptive advantage to females by making them less conspicuous to predators, but males with a similar pattern suffer in their ability to attract a mate. Selection has caused linkage of the pigmentation allele to a sex-determining locus, ensuring that only females inherit this trait. Previous research has mapped Lake Malawi blotched morphs to the paired-box transcription factor gene Pax7, located on chromosome 5 at a W female-determining locus. Another nearby lake, Lake Victoria, contains cichlids displaying similar female-specific blotched morphs that appear to have evolved in parallel. An association study has indicated two candidate genes for similar blotched morphs on chromosome 14 in Lake Victoria cichlids; Pax3, from the same family as Pax7, and Epha4, an ephrin receptor gene that may play a part in migration of dark-colored melanophores during development. We will use a q-RTPCR expression assay to determine if there is a significant change in transcribed levels of Pax3 or Epha4 between fin tissue from blotched and plain individuals. Additionally, we will use nextgeneration sequencing of several species carrying these blotch/sex loci to look for hallmarks of sex chromosome evolution such as lack of recombination and proliferation of tandem repeats. The assembled sequences will also serve as powerful tools for elucidating the evolutionary history of sex chromosomes by showing signatures of selective sweeps, inversions, and other genetic rearrangements that have caused Pax7 to remain tightly connected to this sex locus. 14 Identifying cis-regulatory Elements Involved in Ovule Formation in Arabidopsis thaliana Bhupinder Sehra Advisor: Bob Franks In Arabidopsis thaliana the gynoecium (seed pod) contains the Carpel Margin Meristem (CMM), which gives rise to the ovules and is essential for plant reproduction. Mutations in the transcriptional regulators SEUSS (SEU) and AINTEGUMENTA (ANT) display a synergistic phenotypic enhancement within the gynoecium. The seu ant double mutants show loss of ovules and disruption of other CMM derived structures, while single mutants display only mild phenotypes. Transcriptomics and qRT-PCR revealed candidate genes thought to be downstream targets of SEU and ANT. In-situ hybridization showed several transcripts to be preferentially expressed in the developing CMM, including members of the REPRODUCTIVE MERISTEMS (REM) family, PERIANTHA, PHABULOSA, LEAFY and GROWTH REGULATING FACTOR 5, which are transcription regulators. In addition, TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS 1 (TAA1) and SHATTERPROOF2 (SHP2) have been also been identified as genes that are likely important for ovule development. Promoter analysis of these genes using computational and experimental approaches identified cis-regulatory elements that contribute to gene expression in the CMM. A REM15:GUS reporter construct revealed a region of putative elements spanning 1.1kb upstream of the transcription start site, thought to be required for expression during late ovule development. Conserved sequences and putative motifs were discovered in this region, by aligning orthologs in several Brassicacaeae species and via de novo motif finding. Computational approaches in analyzing the promoter, intronic and downstream regions of PAN, TAA1, SHP2 and REM15 have identified several areas of putative regulatory elements that may be responsible for gene expression and these regions will be tested in-planta. Identifying cis-regulatory elements important for gene expression during ovule development will allow us to understand the regulatory mechanisms of CMM development and the transcriptional hierarchy controlled by SEU and ANT. 7 Comparative Genetics of Food Consumption Megan Garlapow Advisors: Trudy Mackay and David Threadgill Consumption of excessive calories associates with an increased incidence of type 2 diabetes, obesity, cardiovascular disease, and other disorders and diseases. To examine genetic variation and evolutionary conservation of food consumption, we will use a comparative approach consisting of the 192 sequenced lines of the Drosophila Genetic Reference Panel (DGRP) and available data on Mus musculus. Food consumption ad lib in 164 lines of the DGRP has shown significant differences among the lines, between the sexes, and in line-by-sex interactions. Preliminary analyses of predicted significant genes from correlating phenotype with single nucleotide polymorphisms analyzed via DavID indicate an Epidermal Growth Factor (EGF) signaling pathway enrichment of 43%. The role of EGF signaling in control of invertebrate food consumption remains largely unexplored. Correlatively, perturbed M. musculus EGF signaling associates with differences in volume of food consumed, supporting the evolutionary hypothesis that the primary controls of volume of food consumed are conserved across divergent species. Our two model organisms are likely to reveal ways in which food consumption is controlled by EGF signaling and genetics that would not be known using just one of the systems and will reveal ways in which overall food consumption is conserved between divergent species. Conserved genetic elements in both D. melanogaster and M. musculus are more likely to be conserved in humans. Validation experiments in both organisms will improve understanding of the components of the EGF signaling cascade that function to affect food consumption. 8 Maintaining Flexibility: Recombination Rate in a Fluctuating Environment Matthew Robinson Advisor: Nadia Singh Meiotic recombination is a critical factor in the generation and maintenance of genetic variation. Genetic variation is the substrate of the evolutionary process, and it has been suggested that the more genetic variation that exists in a natural population, the greater the potential for adaptation. It has therefore been hypothesized that fluctuating environments should favor increased recombination rate, as the increased adaptive potential provided by increased recombination rate has a greater fitness benefit in the context of a dynamic adaptive landscape. Here we test this hypothesis directly using D. melanogaster as an experimental model system. For this experiment, we exploited laboratory populations of D. melanogaster that had been maintained for three years in one of three thermal environments: 16 oC, 25 oC, or fluctuating temperature (alternating 16 and 25oC every generation). We used a two-step crossing scheme using the visible markers ebony and rough to measure the recombination rate of chromosome 3 as a proxy for genomic recombination rate. We measured recombination rate at 16o, 25o and at 20.5o, the midpoint between the two extremes of the laboratory selection process. The results obtained from this experiment will help shed light on the evolution of recombination rate in general, and in particular will allow us to test whether increased recombination rate is favored within fluctuating environments. Given that we are measuring recombination rate at a variety of temperatures, our results will also illuminate the degree to which recombination rates are plastic as a function of temperature. Particularly exciting is our ability to glean insight into the evolution of phenotypic plasticity in recombination rate, as one might predict that fluctuating environments should also favor increased phenotypic plasticity. 13 Do Males Matter? Exploring Male-mediated Effects on Female Meiotic Recombination Chad Hunter Advisor: Nadia Singh Meiotic recombination is a critical genetic process as well as a driving evolutionary force. Rates of crossing-over are highly variable within and between species due to both genetic and environmental factors. Early studies in Drosophila implicated female genetic background as a major determinant of recombination rate and recent work has highlighted male genetic background as a possible mediator as well. This latter result is puzzling since Drosophila males do not undergo meiotic recombination. We used classical genetics to address the question of how maternal and paternal genetic background affect crossover rate. We devised a two-step crossing scheme exploiting visible markers to measure rates of crossing over in a 33 cM region of the D. melanogaster X chromosome. In total, we measured crossover rates daily in females from ten inbred lines crossed to males from each of the same ten inbred lines over a period of 10 days. Our experimental design facilitates measuring the contributions of maternal age, female genetic background, male genetic background, and male by female interaction effects on rates of crossing-over in females. Our results indicate both maternal and paternal genotypes, their interaction as well as maternal age significantly affect female meiotic crossover rates in Drosophila. This study confirms a previous effect of male genetic background and also is the first implicating the interaction of male and female genotypes to mediate recombination rate. Our results have implications for deciphering the molecular and genetic basis of recombination rate variation in Drosophila. Creation of a Model to Genetically Engineer Peromyscus maniculatus Hayley Crockett Advisor: David Threadgill Peromyscus maniculatus (Deer mouse) is the most common species of native mice in North America and a known carrier of Hantavirus and Lyme disease. The aim of the study is to create a method to genetically engineer P. maniculatus to generate resistance to the species acting as a disease vector. To achieve this goal, we require stem cells that can be used for genetic engineering and subsequent re-introduction into the germline. To achieve this we have derived P. maniculatus induced pluripotent stem (iPS) cells from mouse embryo-derived fibroblasts via lentiviral induction of four genes coding for transcription factors; Sox2, Oct4, Myc, and Klf4. The quality of the cells is being examined by karyotype analysis and analysis of endogenous transcription factor expression. Future research with the iPS cells will involve the induction of a GFP reporter gene and injection of the engineered cells into blastcysts to create a chimeric mouse. Once the ability to engineer P. maniculatus is established, mice will be engineered to be resistant to carrying the disease vectors for Hantavirus and Lyme disease. 12 The Genetic Architecture of Aggression in Drosophila melanogaster John Shorter Advisor: Trudy Mackay Most animals display aggressive behavior to secure food resources, protect against predators and facilitate access to mating partners. Among social animals, appropriately balanced aggressive behavior gives rise to a stable social organization by creating and maintaining dominance hierarchies. Inappropriate or excessive aggression has detrimental consequences for the individual and a society. Aggressive behavior is genetically complex, influenced by many genes as well as interactions with the environment. However, the genetic pathways affecting variation in aggressive behavior are evolutionarily conserved, enabling general inferences to be drawn from genetic analysis using a model system. We investigated the natural genetic variation of aggression using the Drosophila melanogaster Genetic Reference Panel (DGRP), a collection of 192 inbred lines with fully sequenced genomes. We performed a genome wide association study (GWAS) and identified 244 SNPs associated with variation in aggression. Additionally, we performed an independent experiment to replicate causal candidate SNPs by creating an outbred population from lines representing the extremes of the DGRP. We measured aggressive behavior of 3,000 individuals across 7 generations from this outbred population and will perform QTL mapping to identify loci associated with aggression. We will then compare results between the outbred population and the DGRP to identify overlap between genes and gene networks that influence aggression. We will confirm candidates by using RNAi knockdown to reduce gene expression and quantify its effect on aggression. These experiments will provide insight into the genetic architecture of aggression and identify novel genetic variants responsible for naturally occurring variation in this complex trait. 9 Classical and Next-Generation Mapping of a Novel Mutant in Arabidopsis thaliana Richard Gell Advisors: José Alonso and Anna Stepanova Using molecular genetic approaches, we are investigating the function of plant hormones ethylene and auxin in the model species Arabidopsis thaliana. One of the mutants we are studying, rus1, was isolated as a genetic suppressor of an auxin overproducing mutant sur2. rus1 shows a characteristic pale reticulated leaf phenotype due to a dramatic reduction in the density of mesophyll cells. RUS1 gene encodes a plastidic protein of unknown function. To shed light on the molecular function of RUS1, we performed a suppressor mutagenesis in the rus1 mutant background and identified a second-site mutation, R6-11F, that reverts the cell density of rus1 to wild-type levels and suppresses leaf paleness. In order to to clone the suppressor gene, we performed a mapping cross between the rus1 R6-11F double mutant in Columbia background and rus1 single mutant in the Landsberg erecta background, allowed the F1 plants to self, and in the F2 generation selected plants with the suppressed (i.e. non-pale) phenotype. PCR-based in/del markers spanning the five Arabidopsis chromosomes were used to map the mutant to a 700kb region on the bottom of chromosome 3. In order to identify the mutant locus and the causal mutation within the mapped interval, we pooled the DNA of 50 F2s and are now deepsequencing the library with the Illumina HiSeq. We will then use next-generation mapping to call all non-Columbia and non-Ler polymorphisms in the region and to test T-DNA mutants in the candidate polymorphic loci to identify the causal gene. 10 Natural Variation in Cuticular Hydrocarbons in the Drosophila melanogaster Genetic Reference Panel Lauren Dembeck Advisor: Trudy Mackay Drosophila melanogaster mate choice is strongly influenced by the presence of contact pheromones, which consist of cuticular hydrocarbons (CHCs), on the insect’s cuticle. Hence, variation in CHCs can potentially alter mate choice leading to assortative mating and incipient speciation. We studied natural variation in CHCs using the Drosophila melanogaster Genetic Reference Panel (DGRP). The DGRP is a panel of inbred lines of D. melanogaster derived from a Raleigh, NC, natural population. Complete genome sequences are available for the lines, which enable genome-wide association (GWA) analyses to uncover the genetic basis of natural variation in CHCs. We collected gas chromatography spectra of female DGRP flies and quantified relative abundance of CHC components. We identified 60 CHCs in 170 DGRP lines, including 16 dienes and methyl alkanes that were not previously described. A majority of the CHCs show significant variation, including 7,11-heptacosadiene and 7,11-nonacosadiene, the predominant female pheromones. All CHCs show significant among-line variance with univariate analysis of variance except for two x-C25 monoenes and 9,13-C29. Heritabilities ranged from H2 = 0.98 for 5-C25 to H2 = 0.22 for 7-C29. Future analyses will provide associated loci and correlations with other phenotypes measured in the DGRP. These results may offer insight into the link between variation in pheromone composition with mating behavior and incipient speciation. 11