Genetics and Genomics Commons^™

Mapping A New Disease Resistance Locus In An F1 Progeny Derived From Two Grape Wild Relatives, Gaurab Bhattarai

Graduate Theses/Dissertations

Linkage maps and quantitative trait loci (QTL) analysis have become essential tools for the positional cloning of agronomically important genes and for marker-assisted breeding. In this study, two North American grape species, Vitis rupestris and Vitis riparia, and their 294 F₁ progeny were used to construct parental linkage maps and to perform QTL analysis for downy mildew resistance. Single nucleotide polymorphism (SNP) discovery was accomplished using genotyping-by-sequencing (GBS) and resulted in 348,888 SNPs. Of these, 11,063 informative SNP markers (3.17% of the original SNP dataset) were derived after filtering for various quality parameters and missing data. A two-way …

Fungi In A Hot, Dry, Changing World, Miriam I. Hutchinson

Biology ETDs

My doctoral work focused on understanding the reciprocal relationship between fungi and their environment, namely how fungi respond to environmental flux, as well as how fungi can modify and structure their habitats, especially in the context of climate change. As such, I aimed my research on fungi with distinct adaptations to their environmental niches: endophytic fungi that inhabit plant tissue and thermophilic fungi that are capable of growing at the upper temperature limit for eukaryotic life. My research consisted of three studies. First, I investigated the thermophilic species Myceliophthora heterothallica to demonstrate its use as a model organism for efficient …

Warming Up: Climate Change Related Shifts Of Mycorrhizal Fungal Communities In High Latitude Ecosystems, Megan Rae Devan

Biology ETDs

This dissertation examines how climate change affects mycorrhizal fungal communities in boreal and arctic ecosystems. In chapter one, I revealed that increases in fire severity and related increases in deciduous tree dominance result in greater Ascomycota relative abundance (RA) and subsequent declines in Basidiomycota RA. In chapter two I analyzed the effects of post-fire mycorrhizal fungal communites on host growth. There were trends at the fungal genus level that were largely reflected at the guild level across all hosts; however, there were some fungal genera that had the opposite effect on different host species. In chapter three, I found host …

Rising Rural Body-Mass Index Is The Main Driver Of The Global Obesity Epidemic In Adults, Con Burns, Tara Coppinger, Janette Walton, Et Al

Publications

Body-mass index (BMI) has increased steadily in most countries in parallel with a rise in the proportion of the population who live in cities1,2. This has led to a widely reported view that urbanization is one of the most important drivers of the global rise in obesity3,4,5,6. Here we use 2,009 population-based studies, with measurements of height and weight in more than 112 million adults, to report national, regional and global trends in mean BMI segregated by place of residence (a rural or urban area) from 1985 to …

Detecting The Cold: Do Innexins Function In Cold Nociception?, Rachel Barborek

Senior Honors Projects, 2010-2019

Nociception is the perception of and response to harmful stimuli. Nociception is essential for minimizing tissue damage, but aberrant nociceptive pathways can result in chronic pain. Chronic pain in the U.S. is commonly managed with wide-acting opioids, and precisely defining the components of nociceptive pathways could uncover novel targets for pain therapies. I hypothesize that the vitally quick process of nociception would utilize electrical synapses because they transmit signals between neurons more quickly than chemical synapses do. This study, therefore, aims to uncover the potential role of the eight Drosophila melanogaster gap junction proteins, the Innexins, in cold nociception. Wild …

Surveying Apicomplexan Diversity And Dynamics In Narragansett Bay, Evelyn Spencer

Senior Honors Projects

Parasites play an important role in marine ecosystems and their diversity is generally understudied. Apicomplexans, a group of parasitic protists in the phylum Alveolata, infect a wide variety of animal hosts and are abundant in ecosystems spanning from Polar Regions to Neotropical rainforests. Previous data generated from marine sediments in Antarctica, Naples Bay, and off the coast of Oslo, exhibit high diversity and numbers of apicomplexans. Abundance and diversity of these protists are unknown for Narragansett Bay, despite the fact that they infect many commercially important species. The aim of my study was to obtain abundance data and understand genetic …

The Role And Regulation Of Alternative Polyadenylation In The Dna Damage Response, Michael R. Murphy

Dissertations, Theses, and Capstone Projects

Cellular homeostasis is achieved by the dynamic flux in gene expression. Post-transcriptional regulation of coding and non-coding RNA offers a fast method of adapting to a changing cellular environment, including deadenylation, microRNA (miRNA) pathway, and alternative polyadenylation (APA). In this dissertation, I explored some of the mechanisms involved in the post-transcriptional regulation of gene expression. The main hypothesis in these studies is that a single APA event after DNA damage is governed by specific conditions and factors outside of current known regulators of APA, and that the resultant transcript has a role in the DNA damage response (DDR). My aims …

Thiol-Based Misfolding: Linking Redox Balance To Cytosolic Proteostasis, Ford Amy

Dissertations and Theses (Open Access)

The eukaryotic cytosolic proteome is vulnerable to changes in proteostatic and redox balance caused by temperature, pH, oxidants and xenobiotics. Cysteine-containing proteins are especially at risk as the thiol side chain is subject to oxidation, adduction and chelation by thiol-reactive compounds. All of these thiol-modifiers have been demonstrated to induce the heat shock response and recruit protein chaperones to sites of presumed protein aggregation in the budding yeast Saccharomyces cerevisiae. However, endogenous targets of thiol stress toxicity responsible for these outcomes are largely unknown. Furthermore, I hypothesize proteins identified as redox-active are prone to misfolding and aggregation by thiol-specific …

Higher Order Chromosome Organization And Recombination Dynamics Of Meiotic Prophase I In Mouse Spermatocytes, Rhea Kang

Dissertations and Theses (Open Access)

Meiotic recombination is required for parental chromosomes to find each other (pairing/synapsis) and to exchange genetic information thus allowing faithful segregation of chromosomes and the production of haploid gametes. At the start of meiotic prophase I, meiotic chromosomes organize into loop arrays that extrude out of the chromosome axis. Then, a large number of programmed double-strand breaks (DSBs) are formed at specific chromosomal locations or “hotspots” on parental chromosomes, which are repaired by homologous recombination (HR). HR produces either crossovers, which result in the exchange of flanking markers between homologs, or noncrossovers, which are short regions ofgene conversion to the …

Cellular Localization Of Rad51d Mutant Proteins And The Application Of Art To Increase Scientific Literacy In America, Claire L. Chabot

Senior Theses

Ovarian cancers are the leading cause of death from cancer of the female reproductive system. Approximately 50% of ovarian cancers have defects in the homologous recombination (HR) DNA repair pathway that is required for the repair of DNA double-stranded breaks. The status of HR genes, such as BRCA1, BRCA2, and the RAD51 family, contributes to ovarian cancer development as well as treatment decisions regarding chemotherapy, radiation, and immunotherapy. The overarching goal of this project is to identify new insights into HR that can integrate with Precision Medicine Initiatives and align with the goals of the Cancer Moonshot 2020 Program. I …

Fusarium Euwallacea: A Serious Threat To The Native And Ornamental Trees And Shrubs In Southern California, Greg Tyler, Yixing Zheng, Michael Kulinich, Hagop Atamian

Student Scholar Symposium Abstracts and Posters

Fusarium Euwallacea is a fungus that has established symbiotic relationship with the beetle Euwallacea aff. fornicata. The beetle bores through the tree bark and into the sapwood making long tunnels inside the trees. The beetle carries the F. Euwallacea in a specialized structure on its body called mandibular mycangia and cultivates the fungus in the tunnels on which the beetle feeds to grow and reproduce. The growth of the fungus obstructs water and mineral transport in the plant xylem tissue, resulting in dieback, wilt and mortality of the host tree. Fungi are known to secrete proteins called effectors in …

Methylation-Specific Differentiation Of Vaginal Epithelial Cells For Forensic Tissue Typing By Bisulfite Conversion And Pyrosequencing, Elise Pood

Master's Theses

The identification of bodily fluids and tissues is often applied to criminal investigations to clarify events that may or may not have taken place. Current forensic techniques can identify blood, saliva, seminal fluid, and spermatozoa, but there is a clear absence of reliable testing to identify vaginal epithelial tissue. Though there are serological tests available for this purpose, tissue-specific methylation markers have recently been investigated as a candidate for the identification of blood, saliva, and spermatozoa.

In this study, tissue-specific methylation markers were analyzed to identify a set of markers for the differentiation of vaginal fluid from blood, saliva, and …

Characterization Of Developmental Genes In Streptomyces, Erin Orr

Undergraduate Distinction Papers

Characterization of two developmental genes in Streptomyces was carried out by different genetic manipulation techniques in two different species. The construction of an overexpression mutant for a gene encoding a putative c-di-GMP binding protein in Streptomyces scabies was started. This gene was found to be a homologue of a protein that was found to bind to c-di-GMP in a protein binding assay that consisted of streptavidin coated beads and biotinylated c-di-GMP. Attempts at cloning the gene encoding this protein into an overexpression construct were made. Another developmental gene was also investigated. Gene disruption by PCR targeting was used to isolate …

Phylogeny Of The Australian Solanum Dioicum Group Using Seven Nuclear Genes: Testing Symon’S Fruit And Seed Dispersal Hypotheses., Christopher T. Martine, Ingrid E. Jordon-Thaden, Angela J. Mcdonnell, Jason T. Cantley, Daniel S. Hayes, Morgan D. Roche, Emma S. Frawley, Ian S. Gilman, David C. Tank

Faculty Journal Articles

The dioecious and andromonoecious Solanum taxa (the “S. dioicum group”) of the Australian Monsoon Tropics have been the subject of phylogenetic and taxonomic study for decades, yet much of their basic biology is still unknown. This is especially true for plant-animal interactions, including the influence of fruit form and calyx morphology on seed dispersal. We combine field/greenhouse observations and specimen-based study with phylogenetic analysis of seven nuclear regions obtained via a microfluidic PCR-based enrichment strategy and high-throughput sequencing, and present the first species-tree hypothesis for the S. dioicum group. Our results suggest that epizoochorous trample burr seed …

Co-Occurrence Of Manganese Oxidase Genes Indicates Lateral Transfer Between Classes Of Proteobacteria, Jacob Olichney

Student Scholar Showcase

Pseudomonas putida GB-1 is a model organism for the study of manganese oxidation in bacteria, however, the frequency of co-localization of multiple known and suspected manganese oxidizing proteins, as well as their occurrence between species, is unknown. Eight different genes isolated from known manganese oxidizing bacteria (MnxG, MopA, McoA, PputGB1_2552, PputGB1_2553, MoxA, MofA, and Bacillus MnxG) were tested individually using BioPython and BLAST (Basic Local Alignment Search Tool) on multiple genomic databases. BLAST searches had an expect value cutoff of 1e-50, limiting gene homologs to those with high sequence similarity. The abundance of homologous genes across classes of proteobacteria point …

The Sucking Louse Fauna Of Mongolian Rodents: Host Associations, Molecular Phylogenetics And Description Of Two New Species, Chase N. Robinson

Honors College Theses

This study aimed to screen Mongolian rodents for sucking lice (Insecta: Phthiraptera: Anoplura) to better understand host-parasite associations for this understudied region. Nine species, including 3 previously undescribed, from 4 genera were identified. A molecular phylogeny based on 2 mitochondrial genes of collected louse specimens is included.

Molecular Evolutionary Trends And Feeding Ecology Diversification In The Hemiptera, Anchored By The Milkweed Bug Genome, Kristen A. Panfilio, Iris M. Vargas Jentzsch, Joshua B. Benoit, Deniz Erezyilmaz, Yuichiro Suzuki, Stefano Colella, Hugh M. Robertson, Monica F. Poelchau, Robert M. Waterhouse, Panagiotis Ioannidis, Matthew T. Weirauch, Daniel S. T. Hughes, Shwetha C. Murali, John H. Werren, Chris G. C. Jacobs, Elizabeth J. Duncan, David Armisén, Barbara M. I. Vreede, Patrice Baa-Puyoulet, Chloé S. Berger, Chun-Che Chang, Hsu Chao, Mei-Ju M. Chen, Yen-Ta Chen, Christopher P. Childers, Ariel D. Chipman, Andrew G. Cridge, Antonin J. J. Crumière, Peter K. Dearden, Elise M. Didion, Subba Reddy Palli, Jayendra Nath Shukla

Entomology Faculty Publications

Background: The Hemiptera (aphids, cicadas, and true bugs) are a key insect order, with high diversity for feeding ecology and excellent experimental tractability for molecular genetics. Building upon recent sequencing of hemipteran pests such as phloem-feeding aphids and blood-feeding bed bugs, we present the genome sequence and comparative analyses centered on the milkweed bug Oncopeltus fasciatus, a seed feeder of the family Lygaeidae.

Results: The 926-Mb Oncopeltus genome is well represented by the current assembly and official gene set. We use our genomic and RNA-seq data not only to characterize the protein-coding gene repertoire and perform isoform-specific RNAi, but …

X-Inactivation And Epigenetics, Serena Weston

Thinking Matters Symposium Archive

To prevent abnormal development caused by expressing both X chromosomes, female mammals inactivate one of their X chromosomes using an epigenetic process called dosage compensation. This literature review examines how X chromosome inactivation (XCI) occurs during the formation and development of an embryo. This condensation of DNA is marked by histone tail modifications, DNA methylation, and the arrival of structural proteins resulting in extraordinarily stable heterochromatin. X-inactivation is regulated in cis by the X-inactivation center (Xic) that contains the Xist gene and its antisense gene, Tsix. On one X chromosome, Xist RNA is expressed and coats the center of the …

Male Determining Gene Nix May Bring An End To Transmission Of Diseases Through Mosquitoes, Mohammed Mahdi

Thinking Matters Symposium Archive

Female mosquitoes take blood from humans to gain protein needed to produce eggs, and in the process they can transmit viruses, such as Zika, Dengue, and chikungunya, or parasites, such as malaria. Male mosquitoes do not transmit diseases. This literature review will examine what is known about how sex is determined in mosquitoes and how this can be used to manipulate the females that spread diseases to humans. Using CRISPR Cas9, the lab of Zhijian Tu removed the Nix gene from mosquito embryos; all of these were feminized. Ectopic overexpression of Nix gene product in mosquito embryos caused even genetically …

Identification And Functional Testing Of Novel Interacting Protein Partners For The Stress Sensors Wsc1p And Mid2p Of Saccharomyces Cerevisiae, Ednalise Santiago-Cartagena, Sahily González-Crespo, Vladimir Vélez, Nelson Martínez, Jamie Snider, Matthew Jessulat, Hiroyuki Aoki, Zoran Minic, Pearl Akamine, Inoushka Mejías, Luis M. Pérez, Brian C. Rymond, Mohan Babu, Igor Stagljar, José R. Rodríguez-Medina

Biology Faculty Publications

Wsc1p and Mid2p are transmembrane signaling proteins of cell wall stress in the budding yeast Saccharomyces cerevisiae. When an environmental stress compromises cell wall integrity, they activate a cell response through the Cell Wall Integrity (CWI) pathway. Studies have shown that the cytoplasmic domain of Wsc1p initiates the CWI signaling cascade by interacting with Rom2p, a Rho1-GDP-GTP exchange factor. Binding of Rom2p to the cytoplasmic tail of Wsc1p requires dephosphorylation of specific serine residues but the mechanism by which the sensor is dephosphorylated and how it subsequently interacts with Rom2p remains unclear. We hypothesize that Wsc1p and Mid2p must …

Streptococcus Agalactiae Strains With Chromosomal Deletions Evade Detection With Molecular Methods, Isabella A. Tickler, Fred C. Tenover, Scott Dewell, Victoria M. Le, Rachel N. Blackman, Richard V. Goering, Amy E. Rogers, Heather Piwonka, Brittney D. Jung-Hynes, Derrick J. Chen, Michael J. Loeffelholz, Devasena Gnanashanmugam, Ellen Jo Baron

Biology Faculty Publications

Surveillance of circulating microbial populations is critical for monitoring the performance of a molecular diagnostic test. In this study, we characterized 31 isolates of Streptococcus agalactiae (group B Streptococcus [GBS]) from several geographic locations in the United States and Ireland that contain deletions in or adjacent to the region of the chromosome that encodes the hemolysin gene cfb, the region targeted by the Xpert GBS and GBS LB assays. PCR-negative, culture-positive isolates were recognized during verification studies of the Xpert GBS assay in 12 laboratories between 2012 and 2018. Whole-genome sequencing of 15 GBS isolates from 11 laboratories revealed …

Plant Mitochondrial Genome Evolution And Structure Has Been Shaped By Double-Strand Break Repair And Recombination, Emily Wynn

School of Biological Sciences: Dissertations, Theses, and Student Research

Plant mitochondrial genomes are large but contain a small number of genes. These genes have very low mutation rates, but genomes rearrange and expand at significant rates. We propose that much of the apparent complexity of plant mitochondrial genomes can be explained by the interactions of double-strand break repair, recombination, and selection. One possible explanation for the disparity between the low mutation rates of genes and the high divergence of non-genes is that synonymous mutations in genes are not truly neutral. In some species, rps14 has been duplicated in the nucleus, allowing the mitochondrial copy to become a pseudogene. By …

Genomics Based Approaches To Fungal Evolution, Aaron J. Robinson, Donald O. Natvig

Biology ETDs

Advances in DNA sequencing and data analysis make it possible to address questions in population genetics and evolution at the genomic level. Fungi are excellent subjects for such studies, because they are found in diverse environments, have short generation times, can be maintained in culture and have relatively small genomes. My research employed genetic approaches using a variety of sequencing technologies and methods of analysis to explore questions in fungal evolution.

In one study, I explored the genetics behind differences in thermotolerance between isolates of Neurospora discreta from Alaska and New Mexico. Isolates from the two states exhibited differences in …

Cryptic Lineages And A Population Damned To Incipient Extinction? Insights Into The Genetic Structure Of A Mekong River Catfish, Amanda S. Ackiss, Binh T. Dang, Christopher E. Bird, Ellen E. Biesack, Phen Chheng, Latsamy Phounvisouk, Quyen H.D. Vu, Sophorn Uy, Kent E. Carpenter

Biological Sciences Faculty Publications

An understanding of the genetic composition of populations across management boundaries is vital to developing successful strategies for sustaining biodiversity and food resources. This is especially important in ecosystems where habitat fragmentation has altered baseline patterns of gene flow, dividing natural populations into smaller sub-populations and increasing potential loss of genetic variation through genetic drift. River systems can be highly fragmented by dams built for flow regulation and hydropower. We used reduced-representation sequencing to examine genomic patterns in an exploited catfish, Hemibagrus spilopterus, in a hotspot of biodiversity and hydropower development- the Mekong River basin. Our results revealed the …

Unified Methods For Feature Selection In Large-Scale Genomic Studies With Censored Survival Outcomes, Lauren Spirko-Burns, Karthik Devarajan

COBRA Preprint Series

One of the major goals in large-scale genomic studies is to identify genes with a prognostic impact on time-to-event outcomes which provide insight into the disease's process. With rapid developments in high-throughput genomic technologies in the past two decades, the scientific community is able to monitor the expression levels of tens of thousands of genes and proteins resulting in enormous data sets where the number of genomic features is far greater than the number of subjects. Methods based on univariate Cox regression are often used to select genomic features related to survival outcome; however, the Cox model assumes proportional hazards …

Supervised Dimension Reduction For Large-Scale "Omics" Data With Censored Survival Outcomes Under Possible Non-Proportional Hazards, Lauren Spirko-Burns, Karthik Devarajan

COBRA Preprint Series

The past two decades have witnessed significant advances in high-throughput ``omics" technologies such as genomics, proteomics, metabolomics, transcriptomics and radiomics. These technologies have enabled simultaneous measurement of the expression levels of tens of thousands of features from individual patient samples and have generated enormous amounts of data that require analysis and interpretation. One specific area of interest has been in studying the relationship between these features and patient outcomes, such as overall and recurrence-free survival, with the goal of developing a predictive ``omics" profile. Large-scale studies often suffer from the presence of a large fraction of censored observations and potential …

White Shark Genome Reveals Ancient Elasmobranch Adaptations Associated With Wound Healing And The Maintenance Of Genome Stability, Nicholas J. Marra, Michael J. Stanhope, Nathaniel K. Jue, Minghui Wang, Qi Sun, Paulina D. Pavinski Bitar, Vincent P. Richards, Aleksey S. Komissarov, Mike Rayko, Sergey Kliver, Bryce J. Stanhope, Chuck Winkler, Stephen James O'Brien, Agostinho Antunes, Salvador Jorgensen, Mahmood S. Shivji

Biology Faculty Articles

The white shark (Carcharodon carcharias; Chondrichthyes, Elasmobranchii) is one of the most publicly recognized marine animals. Here we report the genome sequence of the white shark and comparative evolutionary genomic analyses to the chondrichthyans, whale shark (Elasmobranchii) and elephant shark (Holocephali), as well as various vertebrates. The 4.63-Gbp white shark genome contains 24,520 predicted genes, and has a repeat content of 58.5%. We provide evidence for a history of positive selection and gene-content enrichments regarding important genome stability-related genes and functional categories, particularly so for the two elasmobranchs. We hypothesize that the molecular adaptive emphasis on genome stability …

Diversity Of Resistance Mechanisms In Carbapenem-Resistant Enterobacteriaceae At A Health Care System In Northern California, From 2013 To 2016, Fiona Senchyna, Rajiv L. Gaur, Johanna Sandlund, Cynthia Truong, Guillaume Tremintin, Dietmar Kültz, Carlos A. Gomez, Fiona B. Tamburini, Tessa Andermann, Ami Bhatt, Isabella A. Tickler, Nancy Watz, Indre Budvytiene, Gongyi Shi, Fred C. Tenover, Niaz Banaei

Biology Faculty Publications

The mechanism of resistance in carbapenem-resistant Enterobacteriaceae (CRE) has therapeutic implications. We comprehensively characterized emerging mechanisms of resistance in CRE between 2013 and 2016 at a health system in Northern California. A total of 38.7% (24/62) of CRE isolates were carbapenemase gene-positive, comprising 25.0% (6/24) blaOXA-48 like, 20.8% (5/24) bla_KPC, 20.8% (5/24) bla_NDM, 20.8% (5/24) bla_SME, 8.3% (2/24) bla_IMP, and 4.2% (1/24) bla_VIM. Between carbapenemases and porin loss, the resistance mechanism was identified in 95.2% (59/62) of CRE isolates. Isolates expressing bla_KPC were 100% susceptible to ceftazidime–avibactam, meropenem–vaborbactam, …

Mrub_3019 Casa Gene Is An Ortholog To E. Coli B2760, Kelsey Heiland, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

This research is part of the Meiothermus ruber genome annotation project which aims to predict gene function with various bioinformatics tools. We investigated the function of Mrub_3019, which encodes the CasA protein involved in the multi-subunit effector complex for the CRISPR-Cas immunity system and predicted it to be an ortholog of E. coli K12 MG1655 b2760 (casA). We predicted that Mrub_3019 encodes the protein CasA, which is involved in PAM recognition of CRISPR interference pathway. Foreign DNA will bind to CasA, which signals Cas3 for helicase-mediated DNA degradation. Our hypothesis is supported by low E-values for pairwise alignment in NCBI …

Mrub_3015 Is Orthologous To The B2757 Gene Found In Escherichia Coli Coding For Casd, Ramona Collins, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

This project is part of the Meiothermus ruber genome analysis project, which uses a collection of online bioinformatics tools to predict gene function. We investigated the biological function of the gene Mrub_3015, which we hypothesize is a component of the CRISPR-Cas prokaryotic defense system. We predict that Mrub_3015 (DNA coordinates 3055550...3056245) encodes the the CRISPR-associated protein cas5, which is integral in maintaining the crRNA-DNA structure, keeping the complex from base pairing with the target phage DNA. Our hypothesis is supported by identical hits for Mrub_3015 and b2527 to the KEGG, Pfam, TIGRfam, CDD and PDB databases as well as a …