FY24 Special GGA Funding Recipients

Jennifer Baltzegar, Postdoctoral Researcher in Genetics, Genetic Engineering & Society Center

Michael Reiskind, Associate Professor, Department of Entomology and Plant Pathology, Global One Health Academy

Zach Brown, Associate Professor, Department of Agricultural and Resource Economics, Genetic Engineering & Society Center

Cole Butler PhD student, Biomathematical Program

Abstract: Mosquitoes are important vectors of human diseases and insecticides remain the most common and effective method of control. However, insecticide resistance threatens the efficacy of control measures, thus limiting the viable tools vector management specialists have during disease outbreaks. We are examining the evolution of insecticide resistance haplotypes in a population of Aedes albopictus from Wake County, North Carolina under a biological and socio-economic framework. We will use a custom-designed probe capture sequencing panel to sequence and fully reconstruct full haplotypes of the entire voltage-gated sodium channel in a strategically selected subset of samples from our repository of Ae. albopictus. With this information, we will aim to 1) characterize all non-synonymous single nucleotide polymorphisms (SNPs) in the voltage-gated sodium channel that are present in the sequenced population, 2) determine if there have been demographic changes in the Ae. albopictus population in response to the introduction of insecticide resistance haplotype frequencies, 3) incorporate these and other genetic data into a socio-economic model that will assess our hypothesis that socio-economic behaviors of Wake County residents contribute to increased frequency of insecticide resistance by correlating patterns of resistance haplotypes with social and economic factors.

Shobhan Gaddameedhi, Associate Professor of the Environmental Health Sciences, Department of Biological Sciences

Cathrine Hoyo, Goodnight Innovation Distinguished Professor, Department
of Biological Sciences

Abstract: Shift work affects millions of people, with approximately 25% of the U.S. workforce. Though day shifts are relatively benign, frequent exposure to more irregular forms—like night, evening, or split schedules—could potentially incur long-lasting health effects. Rotating shifts are particularly notorious for having epidemiological ties to increased risk of cancer, metabolic disorder, cardiovascular, and neurodegenerative disease. Disruption of the biological clock is believed to be a significant contributor to these health risks. However, the full extent of molecular mechanisms and potential biomarkers has not been uncovered. Our proposal aims to determine if real time shift work alters differentially methylated regions (DMRs) and transcriptomics of genomic DNA of cancer hallmarks genes and whether these changes influence DNA damage repair. This research will advance insight into elevated cancer risk caused by circadian clock disruption in shift workers and further facilitate identification of potential biomarkers or therapeutic targets for application in real-world treatment scenarios for individuals with circadian clock/sleep disruption.

Joseph Gage, Assistant Professor, Department of Crop and Soil Sciences

Christine Hawkes, Professor, Department of Plant and Microbial Biology

Rubén Rellán-Álvarez, Assistant Professor, Department of Molecular and Structural Biochemistry

Abstract: Plant microbiomes are increasingly recognized as important mediators of plant phenotypes. They represent an essential avenue for enhancing agricultural sustainability in a future where we need to grow more food under less favorable conditions. Recent evidence suggests that plant microbiomes can increase plant stress tolerance, improve disease resistance, and broaden access to otherwise inaccessible soil organic resources, which will be increasingly important in the face of expected extreme weather, more intense disease pressure, and higher fertilizer costs. Yet crop breeding programs have disrupted plant-microbe relationships, requiring novel solutions to re-engage beneficial taxa. Here, we propose to collect preliminary data on the genetics of maize microbiomes associated with modern maize, wild relatives, and a set of lines derived from crosses between the two. This will allow for paired tests of microbiome differences between each of the six parental lines (B73 and five diverse teosintes), and will also enable us to test for microbiome composition intermediate between the parents in the introgression lines. The proposed work is a step towards robustly integrating the maize microbiome with maize genetics, evolution, and breeding.

Claire Gordy, Associate Teaching Professor, Biological Sciences, College of Sciences 

Melissa Ramirez, Associate Teaching Professor, Biological Sciences, College of Sciences, Director of Undergraduate Programs, Genetics & Genomics Academy

Martha Burford Reiskind, Associate Research Professor, Biological Sciences, College of Sciences, Director of the GG Scholars graduate program, Genetics & Genomics Academy

Co-funded with the Global One Health Academy.

Abstract: The NC State Genetics and Genomics Academy seeks to strengthen graduate training, broaden the reach of undergraduate research opportunities, and build connections among the Research, Graduate Education, Undergraduate Education, and Outreach pillars of the GGA. In Academic Year 2023-24, we created and piloted a training program (Wolfpack Solutions Tiered Mentoring Program, WS-TMP) that integrates rich, structured training experiences at the graduate and undergraduate levels with interdisciplinary research and direct training in equitable and anti-racist teaching, mentoring, and discipline-based education research that prepares the next generation of faculty to transform science education. Using this seed grant funding, we will support current WS-TMP participants in immersive research and continued training in research and mentoring strategies during Summer 2024. We will evaluate the effectiveness of this program, using the data collected to support the expansion of this program as part of a training grant proposal to be submitted to external funding agencies.

Skylar Hopkins, Assistant Professor, Department of Applied Ecology, Expertise: Disease ecology

Alex Nelson, PhD student, CALS Applied Ecology, Expertise: Parasitology

Kenzie Pereira, Postdoctoral Researcher, CALS Applied Ecology, Expertise: Immunology/Physiology

Bradley Allf, Postdoctoral Researcher, CALS Applied Ecology, Expertise: Citizen Science

David Andow, CALS Applied Ecology, Expertise: Genetics-based diet analysis

James Flowers, CVM Pop. Health & Pathobio., Expertise: Parasitology

Ivana Mali, CNR For. & Env. Resources, Expertise: Herpetology

Liz Kierepka, NC Museum of Nat. Sciences Conservation, Expertise: genetics

Mike Cove, NC Museum of Nat. Sciences Mammalogy, Expertise: Citizen Science

Jeffrey Beane, NC Museum of Nat. Sciences, Expertise: Herpetology

Abstract: Snakes are important to ecosystems and human health, but many snake species are experiencing population declines while others are invading new regions and wreaking havoc on native ecosystems. To conserve and control snakes, we need to understand snake ecology, including identifying the prey that snakes consume and the parasites that snakes spread. But existing methods for quantifying diets and parasitism are not broadly accessible and are biased towards detecting some species more often than others. We propose to combine our interdisciplinary expertise in genetics, herpetology, parasitology, disease ecology, mammalogy, and citizen science to (Aim 1) develop genetics-based methods for quantifying snake diets and parasitism in living and roadkill snakes; (Aim 2) quantify the cost and accuracy benefits of the new methods compared to alternatives; and (Aim 3) use the new methods to collect critical preliminary data for a collaborative NSF Division of Environmental Biology proposal. To accomplish this goal, we will necropsy roadkilled snakes from several species with different diets. We will compare the visually observed parasites and prey items in these snakes to those detected by new metabarcoding and metagenomics approaches. This proposal has the potential to develop accurate new genetics-based methods for quantifying diets and parasites not just in snakes, but in any vertebrate hosts, creating new tools that will benefit wildlife management and human health.

Max Scott, Professor, Department of Entomology and Plant Pathology

Alun Lloyd, Drexel Professor, Department of Mathematics, Associate Dean for Academic Affairs

Abstract: Feeding by insect pests causes considerable losses in food production either directly or through disease transmission.  Genetic approaches can be used to control insect pest populations. The most well-known method is the sterile insect technique, where females that mate with released sterile males will not produce offspring. Like most areas of Genetics & Genomics, the development of CRISPR/Cas9 technologies has led to the development of new methods for genetic pest management such as homing gene drive and Y-linked editors or YLE. For the latter, the Cas9 gene is inserted onto the Y chromosome along with single guide RNA (sgRNA) genes that target X-linked haploinsufficient genes. We propose to develop and evaluate YLE strains for spotted wing Drosophila (SWD), a global invasive pest of soft-skinned fruit. We will collect genetic data on the efficacy of established sgRNA strains targeting X-linked genes. These data along with life history trait information will be used to build mathematical models for population suppression using YLE strains. We will use a bacterial recombinase to make strains with a Y-linked Cas9 gene. The modeling will be used to design future cage suppression experiments. An effective YLE strain could provide North Carolina farmers with an efficient pest-specific method for control of SWD. 

Kasie Raymann, Assistant Professor, Department of Plant and Microbial Biology

Louis-Marie Bobay, Assistant Professor, Department of Biological Sciences, Bioinformatics Research Center

Abstract: The recent rise of metagenomic sequencing has revealed a wealth of information regarding natural microbial communities. However, microbial communities are very complex and metagenomic sequencing is typically unable to yield fine scale variants such as strains of a given species. As such, our knowledge of the dynamics and biology of natural microbial populations remains limited. The goal of this project is to develop a new bioinformatic tool to accurately reconstruct strain genotypes from metagenomic sequencing data. Using Markov Chain Monte Carlo sampling, patterns of linkage and Bayesian statistics, the alpha version of our tool can accurately reconstruct the genotype of bacterial strains and outperforms currently available methods. We propose to improve our approach and to apply it to characterize the population dynamics of microbial communities during host-to-host transmissions using the bee gut microbiome as a model system. Thanks to its simplicity and stability, the bee microbiome is an excellent model to study the fine scale dynamics of microbial populations. Overall, results of this project will provide fundamental information regarding the processes driving population dynamics, such as strain colonization, strain warfare, strain competition and population stability.

Xingcheng Lin, Department of Physics and Bioinformatics Program, College of Sciences

Hong Wang, Department of Physics and Toxicology Program, College of Sciences

Yang Zhang, Department of Textile Engineering, Chemistry and Science, Wilson College of Textiles

Abstract: Genome structure is tightly regulated by epigenetic profiles and lays the foundation for numerous DNA-templated processes, yet how the one-dimensional epigenetic information correlates with the heterogeneous three-dimensional genome structure remains elusive. In this study, we will initiate a multiscale approach, integrating multiple computational and experimental techniques to simulate and visualize chromatin organization at the nanoscale resolution. In Aim 1, we will develop a predictive model characterizing transcription factors’ binding specificities towards target DNAs, along with a systematic simulation protocol capturing chromatin structures with distinct epigenetic variations. Aim 2 will leverage the latest developments in functional super-resolution fluorescence microscopy (f-SRFM) and high-speed Atomic Force Microscopy (AFM) to directly visualize chromatin higher-order structures. Correlation between experiment and simulation will validate and fine-tune the modeling parameters. Through quantitative characterization of physicochemical nucleosomal interactions, we aim to establish a systematic framework enabling prediction and direct visualization of higher-order chromatin structures and their modulation by various epigenetic profiles. Knowledge acquired from our synergistic efforts promises to elucidate the structure-epigenetics relationship of chromatin and guide therapeutic efforts to correct aberrant genome function.

Jeff Yoder, Professor of Innate Immunology, College of Veterinary Medicine, Head of GGA Research Committee

Martha Burford Reiskind, Associate Research Professor, Biological Sciences, College of Sciences, Director of the GG Scholars graduate program, Genetics & Genomics Academy

Dahlia Nielsen, Biological Sciences Department, College of Sciences, Head of GGA Seminar Series

Abstract: Invasive species are a major, global threat to biodiversity and ecosystem health. While gaining information on how and when species become invasive is critical, most genetic studies focus on the source of the invasion (introduction) and not on the evolutionary process of invasion (i.e. during establishment and spread). Using the invasive red lionfish (Pterois volitans) as a model, our overall goal is to analyze genomic differences among individuals representing the native population and across the invasive range (introduced, core, and leading-edge regions). With a team including expertise in population genomics, evolutionary ecology and immunology, this project will identify genomic regions under directional selection and regions known to encode rapidly evolving genes related to immune defense (MHC) and predator defense (toxin genes). This GGA Seed Grant will generate preliminary transcriptomic and proteomic data from two red lionfish revealing core immune and toxin gene sequences as well as toxin proteins. These results will provide essential data for a collaborative grant proposal currently being developed by the PI and Co-Is.

Hong Wang, Professor, Physics Department, College of Sciences, Toxicology Program, Center for Human Health and the Environment

Abstract: The Faculty Bridge Fund will support Dr. Wang’s group to collect additional preliminary data to resubmit an NSF proposal. Chromosome organization during interphase is driven by the cohesin complex assisted by its loader protein NIBPL, which carries out progressive enlargement of DNA loops (loop extrusion). Wang’s group discovered that cohesin and PARP1 strongly bind to R-loops. However, how R-loops and cohesin regulate cohesin-mediated DNA loop extrusion is largely unknown. To fill this knowledge gap, Dr. Wang submitted an NSF proposal entitled “Collaborative Research: Mechanisms and Regulation of Cohesin-mediated DNA Binding and Loop Extrusion”, which was reviewed positively by the Genetic Mechanisms Study Section. However, there are two major comments that need to be addressed with additional experimental data: 1) “the organization of the DNA in chromatin is not considered”; 2) “no preliminary data supporting the visualization of R-loops and PARP1 to the cohesin system are provided”. This GGA Faculty Bridge Fund will enable Dr. Wang’s group to collect additional atomic force microscopy (AFM) and high-speed AFM data to show: 1) the additional capacity to study cohesin-DNA binding in the context of chromatin; and 2) the ability to differentiate PARP1 and cohesin on DNA. With the addition of preliminary data mentioned above, Dr. Wang plans to resubmit this proposal to the NSF Genetic Mechanisms Program by the end of June 2024. We will request total NSF funding of $899,999.

Alejandra Huerta, Assistant Professor, Department of Entomology and Plant Pathology, Director of the Kelman Scholars Summer Research Program, College of Agriculture and Life Sciences. Expertise: Mechanisms of bacterial virulence and bacterial competition dynamics.

Ignazio Carbone, Professor, Department of Entomology and Plant Pathology, Director of the Center for Integrated Fungal Research. Expertise: Galaxy portal for phage phylogenies and genomic comparisons

Stephanie Mathews, Assistant Teaching Professor, Microbiology Program, Department of Biological Sciences. Expertise: Phage biology and phage STEM outreach modules lead

Abstract: While many contemporary microbiome studies provide descriptive analyses of the fungal, bacterial, and viral communities in natural and managed ecosystems, bacteriophage (phage), viruses that infect bacteria, are underexplored, especially at the community level. With the support of this GGA grant, data will be generated to demonstrate to grant reviewers that our research team has the expertise to successfully test the hypothesis that biogeography delimits bacterial pathogen and phage population interactions across managed and natural ecosystems. We will collect, isolate, characterize, and sequence 25 bacterial genomes, associated with two economically important bacterial diseases, the bacterial spot of peach and soft rot of potato, in addition to 50 phage genomes associated with the phytobacteria that cause these diseases. Sample collection will include peach and potato farms throughout the Eastern US (Michigan to Alabama). Bacterial and phage genomes will undergo comparative genomic analyses to better understand how geographic origin, climate, and host (species and variety) impact bacterial virulence. The genomic data that will be generated will allow us to develop predictive models on the genetic basis that contribute to phage and bacterial coevolution and ecology.

James R. Duduit, Horticultural Science
Name of advisor: Dr. Wusheng Liu

Abstract: Bacterial wilt (BW), caused by Ralstonia solanacearum (Rs), poses a substantial threat to global agriculture. This soil-borne bacterium infects the xylem, causing rapid wilting in economically vital crops, including tomatoes (Solanum lycopersicum L.). Successful approaches have not been developed to halt plant death once Rs successfully colonizes a plant, making BW management extremely difficult. Acceptable resistance in known tomato genotypes is closely associated with reduced fruit size, impeding the development of large-fruited tomatoes with acceptable Rs resistance. Moreover, BW resistance (R) genes have not been identified in tomato yet, causing the understanding of the molecular mechanisms of BW resistance to remain largely unknown. We identified a candidate BW resistance gene from tomato through genome-wide association analysis. We propose to use genetic engineering and gene editing to functionally characterize the role of this candidate gene in BW resistance in the BW-resistant tomato cultivar Hawaii 7996 and the BW-susceptible tomato cultivar Heinz 1706. We hypotheze that this candidate gene is a tomato BW resistance (R) gene and provides hypersensitive response
(HR) to tomatoes upon BW infection. Our research will reveal the function of this gene in BW resistance as the first BW R gene, offering insights into the molecular genetics mechanism of Rs resistance in tomatoes. The outcomes hold promise for tomato breeding for improved BW resistance and release of BW-resistant tomatoes employing this gene. Unraveling the intricacies of Rs resistance mechanisms at the molecular level is crucial for advancing crop resilience and developing sustainable strategies to mitigate the impact of bacterial wilt on global agriculture.

Nathan Harry, Functional Genomics (Genetics & Genomics)
Name of advisor: Christina Zakas

Abstract: In this dissertation I present an in-depth study of developmental gene regulatory evolution in Streblospio benedicti, a marine annelid with distinct genetically determined developmental morphs. I focus on regulatory modifications to early development, including maternal effects, heterochrony, and the transition from maternal to zygotic genetic control in early development. I dissect how these elements shape developmental processes due to evolutionary adaptations in organisms. My investigation of maternal effects reveals significant insights into the influence of variations in maternal mRNA on early development and life-history traits. By analyzing gene expression in eggs from different developmental morphs, my research highlights the link between maternally provided transcripts and evolutionary developmental shifts. Utilizing eggs from F 1 hybrid crosses, my study effectively differentiates allele-specific
effects from parent-of-origin effects on mRNA expression, underscoring the pivotal role of maternal mRNA in guiding developmental pathways. My research employs a developmental RNAseq time-series dataset generated specifically for this dissertation to explore heterochrony and cis-trans regulatory modifications. This approach uncovers the impact of changes in gene expression timing (heterochrony) on developmental evolution, demonstrating how these temporal shifts influence developmental pathways and morphological changes. Furthermore, the study delves into the evolutionary significance of cis- and trans-acting regulatory elements, revealing how alterations in these elements contribute to evolutionary shifts in gene regulation and organismal development.
Ongoing experiments focus on the timing of zygotic genome activation (ZGA),
employing bioinformatics tools and click chemistry to analyze gene expression patterns related to this critical developmental phase. An independent validation using immunohistochemistry to label TDP-43, a transcription factor essential for the onset of ZGA, also forms part of this investigation. These efforts are expected to enhance the understanding of ZGA’s timing and mechanics in S. benedicti, promising to provide significant contributions to the field of developmental gene regulatory evolution.

Yu-Ming Lin, Forestry and Environmental Resources
Name of advisor: Fikret Isik
Committee: James Holland, Christian Maltecca, Jeffrey Dunne, Dario Grattapaglia

Abstract: The AgriSeq technology (targeted GBS) for loblolly pine (Pinus taeda L.) was designed to be a more cost-effective genotyping solution compared to the Pita50K SNP array platform, catering to the broader breeding community. Chapter one compares the two genotyping platforms for quality control using multivariate methods and genomic relationships. The findings suggested that the low-density platform is a reliable alternative to the Pita50K SNP array. While genomic relationship coefficients aligned well, the inbreeding coefficients from the low-density platform were slightly inflated. Both platforms effectively identified outliers within full-sibs families through multivariate methods. Chapter two compares the efficacy of a low-density genotyping platform and the 50K SNP array for detecting pedigree errors and outliers among full-sibs families.
Genomic relationship coefficients and shared haplotype length were used as metrics. A predictive model will be developed to estimate the probability of an individual being an outlier. Chapter three focuses on genotype imputation, comparing population-based and pedigree-based algorithms to extend genotypes from the low-density AgriSeq scale (1K) to the medium-density scale (10K). Preliminary results indicate promising imputation accuracy, with the pedigree-based algorithm reaching around 84% accuracy, while the population-based algorithm achieves approximately 67% accuracy. Chapter four will explore the impact of different genomic relationship matrices—from low-density, medium-density, and imputed genotypes—on genomic prediction accuracies in a multigenerational population.