Dahlia Nielsen

Obesity is a global public health crisis. Complementary strategies such a pharmaceuticals and dietary interventions are needed to combat this epidemic. Green tea (GT) is rich in flavonoids, including (�����������������)-epigallocatechin gallate (EGCG). Questions remain regarding translation of anti-obesity activities of EGCG (and all phytochemicals) to humans. Lack of genetic diversity in preclinical models has been proposed as a source of poor translational success, but little research has been done to test this hypothesis. Genetic diversity models, including Outbred (DO) cohorts, may provide data that will improve translational success of phytochemicals. The overall objective of this proposal is to utilize DO mice to develop preliminary ����������������proof-of-concept��������������� data regarding the impact of background genetics on the anti-obesity activities of EGCG. Our central hypothesis is that DO mice with will exhibit significant variability in the anti-obesity activities of EGCG. In the present study, we aim to estimate the following in a DO cohort1) variability in anti-obesity activities of EGCG across diverse genetic backgrounds and 2) narrow-sense heritability of responsiveness/sensitivity to EGCG. The proposed work is innovative, as few studies have used CC or DO mouse cohorts to inform precision nutrition using phytochemicals. The rationale for the proposed work is that achievement of our aims will significantly enhance our understanding of the translatability of EGCG to combat obesity in humans. Our study has the potential to demonstrate whether EGCG has broadly translatable anti-obesity potential, or requires highly personalized implementation based on genetics. These data will inform larger studies that map QTL to identify genetic loci or genes associated with responsiveness/sensitivity to EGCG, which may reveal previously unknown mechanism and targets for EGCG activities, and suggest strategies for precision implementation in humans. These insights will likely facilitate improved translatability and efficacy of EGCG for mitigation of obesity in humans.

Co-PI Nielsen will be responsible for overseeing all experimental design and computational components of this project. This includes QTL analyses, RNA-Seq data QC and processing, eQTL analyses, cross-species eQTL analyses, and network analysis. Nielsen will mentor the Ph.D. student selected for this project; this student will be selected from students in the NCSU Bioinformatics Graduate program. Under Nielsen������������������s supervision, the student will perform most of the analyses required for this project. Nielsen will also co-mentor the students involved with the summer internship program with St. Augustine������������������s. Dr. Doherty will serve as Co-I for the plant stress response, molecular, and biochemical analysis and validation of candidate regulatory interactions. Specifically, Dr. Doherty will oversee in: Aim 1: The phenotyping of the plant-response traits, monitoring general growth parameters and physiology related sensitivity due to WNT and nematode presence. Aim 2: Extraction of RNA, preparation and sequencing of the libraries for the RNA samples. QC will be performed on all samples prior to sequencing. Dr. Doherty will oversee library construction in her lab and will coordinate getting the samples sequenced. Aim 4: In this objective Dr. Doherty will oversee the validation of the predicted mechanisms. Again, the Doherty lab will be responsible for extracting RNA and preparing libraries from the for RNA-seq or generating constructs and IP-ing for ChIP-Seq. Once prepared and checked for quality, Dr. Doherty will coordinate sequencing of the libraries, will retrieve and store the data and will process the resulting data and evaluate the success of the predictions and the targets identified. The Doherty lab will assist with evaluating the success of the approach and interpreting the candidate targets.

This project will develop modern genomic, genetic, and bioinformatics tools to facilitate crop improvement and improve genetic gains in sweetpotato, an important food security and cash crop with highly recognized potential to alleviate hunger, vitamin A deficiency, and poverty in Sub-Saharan Africa (SSA), and predominantly grown in small plot holdings by poor women farmers.

Since 2006, a disorder has been found in sweetpotatoes that causes internal discoloring and necrosis. Outbreaks of this disorder has occurred in specific businesses in North Carolina where the incidence has exceeded 50% while other growers may have only 2% or less occurrence. Complicating this problem, is that with this disorder no visible symptoms occur on the outside of the roots, making it impossible to detect by evaluating the outside of sweetpotato roots. Thus, roots with the disorder can reach the customer without detection. This has occurred with customers of grocery stores and restaurants after sweetpotatoes are cooked. Already some sweetpotato buyers have refused to buy Covington sweetpotato variety from North Carolina in fear of this disorder. We believe that the approximately $200 million dollar North Carolina sweetpotato industry is threatened by this disorder and an emergency situation currently exits. Continued shipment and not knowing the manner to prevent and/or understand the cause of internal necrosis could very negatively impact the North Carolina sweetpotato industry if not solved. This disorder has been studied since its appearance to find the cause(s) and develop remedies. However, despite much work, the cause of internal necrosis (IN) has not yet been determined. Three hypotheses have been developed after preliminary research was completed in 2012: combination of pre‐harvest and post‐harvest factors, ethylene, and disease. The aim of this proposal is to investigate these hypothesis to help understand the cause and ways to remedy the situation.

This proposal seeks support to develop novel glycan reagents that will significantly enhance limits-of-detection and allow for relative quantification and to disseminate these reagents and protocols as well as biospecimens. Collectively, these new reagents, once developed, will be a major contribution to the field of glycomics allowing for the relative quantification of glycans. Furthermore, these novel reagents will be applied in our proposed studies to elucidate glycan biomarkers for the early detection of epithelial ovarian cancer in the domestic hen model.

In this proposal, we will examine the relationship between a plant (Medicago truncatula) and a root knot nematode pathogen that infects that plant's roots. Our goal is to observe how the genetic code of the pathogen influences the biological responses of the plant, specifically at a gene transcription level. To address this question, we implement a technique known as expression quantitative trait locus (eQTL) mapping, which combines gene expression studies together with genetic linkage mapping. This technique is designed to investigate connections between DNA sequence changes and gene expression levels, in a way that compares each region of the genome to every expressed gene. We are transforming this approach to allow a cross-species investigation, in which each each region of the pathogen genome is compared with each expressed plant gene. We follow up on our results from this analysis with gene network identification, in order to characterize more complex cross-talk between species. The results of this study will be fundamental to furthering our understanding of not just plant defenses and susceptibility, but also the myriad of ways in which the pathogen influences the physiology and development of its plant host.

The overall objective of the research outlined in this proposal is to characterize the interaction of Aspergillus flavus with developing maize kernels. Mutants of the fungus impaired in pathogenicity, laser capture microscopy, and deep-sequencing technology will be employed to study tissue specific interactions within maize seeds. The specific objectives of this proposal are: 1) Characterize infection and colonization of maize kernels by A. flavus; 2) Characterize tissue-specific host responses to wild type and nepA mutants of A. flavus; and 3) Monitor seed and fungal gene expression at the interface between A. flavus and the maize embryo. This proposal addresses category number one listed in the priorities for 2009 projects in Microbial Biology: Microbial Associations with Plants: ?Elucidation of molecular mechanisms of disease and resistance interactions between microbial plant pathogens and their host plants. Infection by Aspergillus flavus and subsequent contamination of seed with aflatoxin remain a serious problem within the US. Concerted efforts to reduce aflatoxin contamination have not been successful. The important components of resistance in maize seeds have not been described, making screening for resistance to the disease difficult. Results from these studies will identify regions of the maize seed important in its interaction with A. flavus, better characterize pathogenicity in A. flavus, and build the foundation for better understanding resistance mechanisms in seeds to fungi.

Atopic dermatitis (AD) is a common, chronic, allergic skin condition that causes severe itching. Indeed, it has been estimated that approximately 8% of all dogs that present to their veterinarian do so because of clinical signs due to AD. Affected dogs scratch and rub their skin, causing damage to the skin and frequently causing bacterial or yeast infections. Treatment focuses on appropriate antibiotic therapy of infections, and controlling the allergic response, but AD cannot be cured and so owners and their pets face a lifelong struggle to control the signs. There is evidence that AD is a hereditary problem, and it is extremely common in the West Highland White Terrier (WHWT) in which it was estimated to affect 15% of all dogs. In preliminary work we have collected DNA on over 200 dogs, including affected and normal WHWT in addition to affected dogs of other breeds. We propose to use this DNA to perform a genome wide association study of AD in WHWT to identify chromosomal regions associated with the disease. The long-term goal is to develop genetic tests that can be used by breeders to decrease the prevalence of this condition.

A central goal of ecological and evolutionary research is to identify the genes underlying adaptive traits and to understand the fitness consequences of naturally occurring variation at these loci. Distinguishing these regions and gaining a fuller mechanistic understanding of how changes at the genetic level generate phenotypic variation is challenging; however, this research promises the keenest insights into some of the most fundamental questions in evolutionary biology. For example, how important are regulatory versus structural changes in the evolution of novel phenotypes? What is the relative importance of standing genetic variation versus new mutations in origins of functional variation? And finally, what is the overall impact of Darwinian evolution on the architecture of genome variation? Answering these questions requires the establishment of new model systems that complement and extend research on traditional genetic model organisms- systems with a rich source of natural variation, an extensive research history documenting the importance of this variation, and that are amenable to both field and laboratory analysis. Our project exploits the natural diversity in the wing patterns of Heliconius butterflies, growing genomic resources, and emerging genomic technologies to explore how adaptive phenotypes evolve and influence the architecture of genomic variation within natural populations. We have now cloned and sequenced genomic intervals spanning two of the three major genes that control mimicry-related color pattern in these butterflies. This project will extend this research by focusing on three major goals: (1) cloning the third major color pattern gene responsible for phenotypic variation within H. erato, (2) using high-throughput resequencing to identify nucleotide polymorphisms across targeted genomic intervals, and (3) assaying, with a microarray-based SNP chip, genetic variation across these intervals in three replicate hybrid zones between differently adapted wing pattern races of H. erato. By addressing these aims, we will gain unprecedented insight into a set of genes that control adaptive variation in nature and a better understanding of how selection on these genes influences genomic architecture across geographic landscapes.

This work is a mentored career development award directed at the study of ovarian cancer in the avian (chicken) model. Ovarian cancer is a devastating disease giving rise to significant mortality and morbidity. The main determinant in survival rates is the stage of diagnosis. Currently, most women are diagnosed in the advanced stage of the disease where survival rates are less than 10 percent. Our goal is to eludicate new biomarkers for the diagnoisis of ovarian cancer in its early stage.