Life Sciences Commons^™

Physiologic And Pathologic Profiling Of Clonal Variations, Wing Hing Wong

Arts & Sciences Electronic Theses and Dissertations

This thesis sought to provide a better understanding of clonality in various malignant and non-malignant settings using a variety of genomic analytical tools. Clonality is pre-defined as the presence of a mixed population of cells in which each sub-population has distinct somatic mutation profile. It is a common feature in cancers where subpopulations of cells arise as a result of independent, yet continual acquisition of somatic mutations. The clonal architecture of cancers can be used as a diagnostic and prognostic biomarker as well as to monitor disease progression or resolution. Besides cancer, clonal variability and expansion is also implicated in …

Comparative Genomics Study Reveals Red Sea Bacillus With Characteristics Associated With Potential Microbial Cell Factories (Mcfs), G. Othoum, S. Prigent, A. Derouiche, L. Shi, A. Bokhari, S. Alamoudi, S. Bougouffa, X. Gao, R. Hoehndorf, S. T. Arold, T. Gojobori, H. Hirt, F. F. Lafi, J. Nielsen, V. B. Bajic, I. Mijakovic, M. Essack

All Works

© 2019, The Author(s). Recent advancements in the use of microbial cells for scalable production of industrial enzymes encourage exploring new environments for efficient microbial cell factories (MCFs). Here, through a comparison study, ten newly sequenced Bacillus species, isolated from the Rabigh Harbor Lagoon on the Red Sea shoreline, were evaluated for their potential use as MCFs. Phylogenetic analysis of 40 representative genomes with phylogenetic relevance, including the ten Red Sea species, showed that the Red Sea species come from several colonization events and are not the result of a single colonization followed by speciation. Moreover, clustering reactions in reconstruct …

Changes To North American Butterfly Names, Jing Zhang, Qian Cong, Jinhui Shen, Paul A. Opler, Nick V. Grishin

The Taxonomic Report of the International Lepidoptera Survey

We obtained and analyzed whole genome shotgun sequences of all 845 species of butterflies recorded from Canada and the United States. Genome-scale phylogenetic trees constructed from the data reveal several nonmonophyletic genera and suggest improved classification of species included in these genera. Here, these changes are formalized and 2 subgenera are described: Amblyteria Grishin, subgen. n. (type species Goniloba exoteria Herrich-Schäffer, 1869, parent genus Amblyscirtes Scudder, 1872), and Coa Grishin, subgen. n. (type species Hesperia baracoa Lucas, 1857, parent genus Polites Scudder, 1872). Furthermore, we resurrect 3 genera and 2 subgenera from synonymy, change the rank of 6 currently used …

Promises And Challenges Of Eco-Physiological Genomics In The Field: Tests Of Drought Responses In Switchgrass. Plant Physiology, John T. Lovell, Eugene V. Shakirov, Scott Schwartz, David B. Lowry, Michael J. Aspinwall, Samuel H. Taylor, Jason Bonnette, Juan Diego Palacio-Mejia, Christine V. Hawkes, Philip A. Fay, Thomas E. Juenger

Yevgeniy (Eugene) Shakirov

Identifying the physiological and genetic basis of stress tolerance in plants has proven to be critical to understanding adaptation in both agricultural and natural systems. However, many discoveries were initially made in the controlled conditions of greenhouses or laboratories, not in the field. To test the comparability of drought responses across field and greenhouse environments, we undertook three independent experiments using the switchgrass reference genotype Alamo AP13. We analyzed physiological and gene expression variation across four locations, two sampling times, and three years. Relatively similar physiological responses and expression coefficients of variation across experiments masked highly dissimilar gene expression responses …

The Genomic Landscape Of Molecular Responses To Natural Drought Stress In Panicum Hallii., John T. Lovell, Jerry Jenkins, David B. Lowry, Sujan Mamidi, Avinash Sreedasyam, Xiaoyu Weng, Kerrie Barry, Jason Bonnette, Brandon Campitelli, Chris Daum, Sean P. Gordon, Billie A. Gould, Albina Khasanova, Anna Lipzen, Alice Macqueen, Juan Diego Palacio-Mejía, Christopher Plott, Eugene V. Shakirov, Shengqiang Shu, Yuko Yoshinaga, Matt Zane, Dave Kudrna, Jason D. Talag, Daniel Rokhsar, Jane Grimwood, Jeremy Schmutz, Thomas E. Juenger

Yevgeniy (Eugene) Shakirov

Environmental stress is a major driver of ecological community dynamics and agricultural productivity. This is especially true for soil water availability, because drought is the greatest abiotic inhibitor of worldwide crop yields. Here, we test the genetic basis of drought responses in the genetic model for C4 perennial grasses, Panicum hallii, through population genomics, field-scale gene-expression (eQTL) analysis, and comparison of two complete genomes. While gene expression networks are dominated by local cis-regulatory elements, we observe three genomic hotspots of unlinked trans-regulatory loci. These regulatory hubs are four times more drought responsive than the genome-wide average. Additionally, cis- and trans-regulatory …

Fifty New Genera Of Hesperiidae (Lepidoptera), Qian Cong, Jing Zhang, Jinhui Shen, Nick V. Grishin

Insecta Mundi

Genomic sequencing and analysis of worldwide skipper butterfly (Lepidoptera: Hesperiidae) fauna points to imperfections in their current classification. Some tribes, subtribes and genera as they are circum­scribed today are not monophyletic. Rationalizing genomic results from the perspective of phenotypic characters suggests two new tribes, two new subtribes and 50 new genera that are named here: Ceratrichiini Grishin, trib. n., Gretnini Grishin, trib. n., Falgina Grishin, subtr. n., Apaustina Grishin, subtr. n., Flattoides Grishin, gen. n., Aurivittia Grishin, gen. n., Viuria Grishin, gen. n., Clytius Grishin, gen. n., Incisus Grishin, gen. n., …

Integrating Human Omics Data To Prioritize Candidate Genes., Yong Chen, Xuebing Wu, Rui Jiang

Yong Chen

BACKGROUND: The identification of genes involved in human complex diseases remains a great challenge in computational systems biology. Although methods have been developed to use disease phenotypic similarities with a protein-protein interaction network for the prioritization of candidate genes, other valuable omics data sources have been largely overlooked in these methods.

METHODS: With this understanding, we proposed a method called BRIDGE to prioritize candidate genes by integrating disease phenotypic similarities with such omics data as protein-protein interactions, gene sequence similarities, gene expression patterns, gene ontology annotations, and gene pathway memberships. BRIDGE utilizes a multiple regression model with lasso penalty to …

Genome-Wide Discovery Of Missing Genes In Biological Pathways Of Prokaryotes., Yong Chen, Fenglou Mao, Guojun Li, Ying Xu

Yong Chen

BACKGROUND: Reconstruction of biological pathways is typically done through mapping well-characterized pathways of model organisms to a target genome, through orthologous gene mapping. A limitation of such pathway-mapping approaches is that the mapped pathway models are constrained by the composition of the template pathways, e.g., some genes in a target pathway may not have corresponding genes in the template pathways, the so-called "missing gene" problem.

METHODS: We present a novel pathway-expansion method for identifying additional genes that are possibly involved in a target pathway after pathway mapping, to fill holes caused by missing genes as well as to expand the …

Tracing Evolutionary Footprints To Identify Novel Gene Functional Linkages., Yong Chen, Li Yang, Yunfeng Ding, Shuyan Zhang, Tong He, Fenglou Mao, Congyan Zhang, Huina Zhang, Chaoxing Huo, Pingsheng Liu

Yong Chen

Systematic determination of gene function is an essential step in fully understanding the precise contribution of each gene for the proper execution of molecular functions in the cell. Gene functional linkage is defined as to describe the relationship of a group of genes with similar functions. With thousands of genomes sequenced, there arises a great opportunity to utilize gene evolutionary information to identify gene functional linkages. To this end, we established a computational method (called TRACE) to trace gene footprints through a gene functional network constructed from 341 prokaryotic genomes. TRACE performance was validated and successfully tested to predict enzyme …

Integrated Omics Study Delineates The Dynamics Of Lipid Droplets In Rhodococcus Opacus Pd630., Yong Chen, Yunfeng Ding, Li Yang, Jinhai Yu, Guiming Liu, Xumin Wang, Shuyan Zhang, Dan Yu, Lai Song, Hangxiao Zhang, Congyan Zhang, Linhe Huo, Chaoxing Huo, Yang Wang, Yalan Du, Huina Zhang, Peng Zhang, Huimin Na, Shimeng Xu, Yaxin Zhu, Zhensheng Xie, Tong He, Yue Zhang, Guoliang Wang, Zhonghua Fan, Fuquan Yang, Honglei Liu, Xiaowo Wang, Xuegong Zhang, Michael Q Zhang, Yanda Li, Alexander Steinbüchel, Toyoshi Fujimoto, Simon Cichello, Jun Yu, Pingsheng Liu

Yong Chen

Rhodococcus opacus strain PD630 (R. opacus PD630), is an oleaginous bacterium, and also is one of few prokaryotic organisms that contain lipid droplets (LDs). LD is an important organelle for lipid storage but also intercellular communication regarding energy metabolism, and yet is a poorly understood cellular organelle. To understand the dynamics of LD using a simple model organism, we conducted a series of comprehensive omics studies of R. opacus PD630 including complete genome, transcriptome and proteome analysis. The genome of R. opacus PD630 encodes 8947 genes that are significantly enriched in the lipid transport, synthesis and metabolic, indicating a super …

Rare Degs1 Variant Significantly Alters De Novo Ceramide Synthesis Pathway, Nicholas B. Blackburn, Laura F. Michael, Peter J. Meikle, Juan M. Peralta, Marian Mosior, Scott Mcahren, Hai H. Bui, Melissa A. Bellinger, Corey Giles, Satish Kumar, Ana C. Leandro, Marcio Almeida, Jacquelyn M. Weir, Michael C. Mahaney, Thomas D. Dyer, Laura Almasy, John L. Vandeberg, Sarah Williams-Blangero, David C. Glahn, Ravindranath Duggirala, Mark Kowala, John Blangero, Joanne E. Curran

School of Medicine Publications and Presentations

The de novo ceramide synthesis pathway is essential to human biology and health but genetic influences remain unexplored. The core function of this pathway is the generation of biologically active ceramide from its precursor, dihydroceramide. Dihydroceramides have diverse, often protective, biological roles; conversely, increased ceramide levels are biomarkers of complex disease. To explore the genetics of the ceramide synthesis pathway, we searched for deleterious nonsynonymous variants in the genomes of 1,020 Mexican Americans from extended pedigrees. We identified a Hispanic ancestry−specific rare functional variant, L175Q, in DEGS1, a key enzyme in the pathway that converts dihydroceramide to ceramide. This amino …

The Efficacy Of Whole Human Genome Capture On Ancient Dental Calculus And Dentin, Kirsten A. Ziesemer, Jazmin Ramos-Madrigal, Allison E. Mann, Bernd W. Brandt, Krithivasan Sankaranarayanan, Andrew T. Ozga, Menno Hoogland, Courtney A. Hofman, Domingo C. Salazar-Garcia, Bruno Frohlich, George R. Miller, Anne C. Stone, Mark Aldenderfer, Cecil M. Lewis Jr., Corinne L. Hofman, Christina Warinner, Hannes Schroeder

Andrew Ozga

Objectives

Dental calculus is among the richest known sources of ancient DNA in the archaeological record. Although most DNA within calculus is microbial, it has been shown to contain sufficient human DNA for the targeted retrieval of whole mitochondrial genomes. Here, we explore whether calculus is also a viable substrate for whole human genome recovery using targeted enrichment techniques.

Materials and methods

Total DNA extracted from 24 paired archaeological human dentin and calculus samples was subjected to whole human genome enrichment using in‐solution hybridization capture and high‐throughput sequencing.

Results

Total DNA from calculus exceeded that of dentin in all cases, …

Multi-Omic Understanding Of The Evolution Of Xenobiotic Tolerance In Bacterial Isolates And Communities, Tayte Paul Campbell

Arts & Sciences Electronic Theses and Dissertations

Xenobiotic compounds are any chemicals that are released into an environment by human action and that occur at concentrations higher than found naturally. Xenobiotics, including aromatic compounds and antibiotics, are recalcitrant to degradation because they are often toxic or mutagenic. Despite this toxicity, bacteria account for a large portion of xenobiotic degradation in the environment. Bacteria are able to adapt to these foreign chemicals, gaining increased levels of tolerance and increased rates of xenobiotic degradation. On the strain level, increased tolerance can be caused by mutations in individual cells or through the acquisition of genes from other cells. At the …

Validity Evaluation Of The Genetics And Genomics In Nursing Practice Survey, Alexandra Plavskin, William E. Samuels, Kathleen A. Calzone

Publications and Research

Aim: To psychometrically test the Genetics and Genomics Nursing Practice Survey (GGNPS) for evidence of content, face and construct validity.

Design:This study was a secondary data analysis.

Method: Data collected from the Method for Introducing a New Competency into Nursing Practice (MINC) study were used to evaluate the GGNPS for evidence of construct validity via structural equation modelling and confirmatory factor analysis. Face validity was evaluated via feedback from practicing RNs without specific experience with or knowledge of genetics/genomics. Content validity was evaluated via content expert feedback and assessment of a content validity index.

Results: The thresholds …

Quantifying The Predictability Of Evolution At The Genomic Level In Lycaeides Butterflies, Samridhi Chaturvedi

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Stephen Jay Gould, a great scientist and evolutionary biologists, suggested that if we could replay the tape of life, we would not have observed similar course of events because evolution is stochastic and if affected by several events. Since then, the possibility that evolution is repeatable or predictable has been debated. Studies using large-scale evolution experiments, long-term data for individual populations, and controlled experiments in nature, have demonstrated phenotypic and genetic convergence in several taxa. These studies suggest that despite some randomness, predictable evolutionary patterns can emerge on a large temporal and spatial scale. However, a few cases also exist …

A Csra-Binding, Trans-Acting Srna Of Coxiella Burnetii Is Necessary For Optimal Intracellular Growth And Vacuole Formation During Early Infection Of Host Cells, Shaun Wachter, Matteo Bonazzi,, Kyle Shifflett, Abraham Moses, Rahul Raghavan, Michael F. Minnick

Biology Faculty Publications and Presentations

Coxiella burnetii is an obligate intracellular gammaproteobacterium and zoonotic agent of Q fever. We previously identified 15 small non-coding RNAs (sRNAs) of C. burnetii. One of them, CbsR12 (Coxiella b urnetii small RNA 12), is highly transcribed during axenic growth and becomes more prominent during infection of cultured mammalian cells. Secondary structure predictions of CbsR12 revealed four putative CsrA-binding sites in stem loops with consensus AGGA/ANGGA motifs. We subsequently determined that CbsR12 binds to recombinant C. burnetii CsrA-2, but not CsrA-1, proteins in vitro. Moreover, through a combination of in vitro and cell …

Mixing It Up: The Impact Of Episodic Introgression On The Evolution Of High-Latitude Mesocarnivores, Jocelyn P. Colella

Biology ETDs

At high latitudes, climatic oscillations have triggered repeated episodes of organismal divergence by geographically isolating populations. For terrestrial species, extended isolation in glacial refugia – ice-free regions that enable terrestrial species persistence through glacial maxima – is hypothesized to stimulate allopatric divergence. Alternatively, upon glacial recession, divergent populations expanded from independent glacial refugia and often contacted other diverging populations. In the absence of reproductive isolating mechanisms, this biogeographic process may trigger hybridization and ultimately, gene flow between divergent taxa. My dissertation research aims to understand how these episodic periods of isolation and contact have impacted the evolution of high latitude …

A Method For Improving The Accuracy And Efficiency Of Bacteriophage Genome Annotation, Alicia Salisbury, Philippos K. Tsourkas

Life Sciences Faculty Research

Bacteriophages are the most numerous entities on Earth. The number of sequenced phage genomes is approximately 8000 and increasing rapidly. Sequencing of a genome is followed by annotation, where genes, start codons, and functions are putatively identified. The mainstays of phage genome annotation are auto-annotation programs such as Glimmer and GeneMark. Due to the relatively small size of phage genomes, many groups choose to manually curate auto-annotation results to increase accuracy. An additional benefit of manual curation of auto-annotated phage genomes is that the process is amenable to be performed by students, and has been shown to improve student recruitment …

Oomycete Metabarcoding Reveals The Presence Of Lagenidium Spp. In Phytotelmata, Paula Leoro-Garzon, Andrew J. Gonedes, Isabel Olivera, Aurelien Tartar

Biology Faculty Articles

The oomycete genus Lagenidium, which includes the mosquito biocontrol agent L. giganteum, is composed of animal pathogens, yet is phylogenetically closely related to the well characterized plant pathogens Phytophthora and Pythium spp. These phylogenetic affinities were further supported by the identification of canonical oomycete effectors in the L. giganteum transcriptome, and suggested, mirroring the endophytic abilities demonstrated in entomopathogenic fungi, that L. giganteum may have similarly retained capacities to establish interactions with plant tissues. To test this hypothesis, culture-independent, metabarcoding analyses aimed at detecting L. giganteum in bromeliad phytotelmata (a proven mosquito breeding ground) microbiomes were performed. Two …

Genome Of The Tropical Plant Marchantia Inflexa: Implications For Sex Chromosome Evolution And Dehydration Tolerance, Rose A. Marks, Jeramiah J. Smith, Quentin Cronk, Christopher J. Grassa, D. Nicholas Mcletchie

Biology Faculty Publications

We present a draft genome assembly for the tropical liverwort, Marchantia inflexa, which adds to a growing body of genomic resources for bryophytes and provides an important perspective on the evolution and diversification of land plants. We specifically address questions related to sex chromosome evolution, sexual dimorphisms, and the genomic underpinnings of dehydration tolerance. This assembly leveraged the recently published genome of related liverwort, M. polymorpha, to improve scaffolding and annotation, aid in the identification of sex-linked sequences, and quantify patterns of sequence differentiation within Marchantia. We find that genes on sex chromosomes are under greater …

Identifying Senescence As A Mode Of Chemo Resistance In Ovarian Cancer, Noelle L. Cutter Ph.D., Jennifer Furman, Ryan Frank, Cassandra Greco, Matthrew Lucito

Faculty Works: Biology, Chemistry, and Environmental Studies

Current treatments of ovarian and breast cancer result in chemo resistance all too often. It has been hypothesized that senescence-a dormant condition associated with increased age and apoptosis- may play a role in the development of chemo resistance. We performed an in-vitro study with HOSE (carboplatin-sensitive), SKOV3 (chemo resistant ovarian cancer), and CAMA1 (chemo resistant breast cancer) cell lines, which were exposed to a variety of platinum-based treatments meant to model current cover clinically relevant scenarios in terms of tumor hypoxia. They were then stained for senescence in-vitro using B-gal, and analyzed for proliferation using the Cell Counting Kit 8, …

Genome To Phenome: Improving Animal Health, Production, And Well-Being – A New Usda Blueprint For Animal Genome Research 2018–2027, Caird Rexroad, Jeffrey Vallet, Lakshmi Kumar Matukumalli, James Reecy, Derek Bickhart, Harvey Blackburn, Mark Boggess, Hans Cheng, Archie Clutter, Noelle Cockett, Catherine Ernst, Janet E. Fulton, John Liu, Joan Lunney, Holly Neibergs, Et Al.

Animal, Dairy, and Veterinary Science Faculty Publications

In 2008, a consortium led by the Agricultural Research Service (ARS) and the National Institute for Food and Agriculture (NIFA) published the “Blueprint for USDA Efforts in Agricultural Animal Genomics 2008–2017,” which served as a guiding document for research and funding in animal genomics. In the decade that followed, many of the goals set forth in the blueprint were accomplished. However, several other goals require further research. In addition, new topics not covered in the original blueprint, which are the result of emerging technologies, require exploration. To develop a new, updated blueprint, ARS and NIFA, along with scientists in the …

Nucjuke: A Web Tool For Re-Ranking Crispr-Cas9 Grnas Based On Chromatin Accessibility In Yeast, Gaea Turman

Scholars Week

A variety of papers published in the last decade have suggested that chromatin accessibility could have significant influence over the success of CRISPR-Cas9 experiments in S. cerevisiae; where chromatin accessibility refers to nucleosome presence at a targeted genomic location. It has been found that nucleosome presence can physically impede Cas9 from making a double stranded break at a specific target site, causing a decreased experimental efficiency. We have created a web-tool called NucJuke that seeks to mitigate this problem by categorically re-ranking gRNAs based on having high, partial, or low chromatin accessibility (referring to no nucleosome occupancy, partial nucleosome occupancy, …

Differential Effects Of Influenza Virus Na, Ha Head, And Ha Stalk Antibodies On Peripheral Blood Leukocyte Gene Expression During Human Infection., Kathie-Anne Walters, Ruoqing Zhu, Michael Welge, Kelsey Scherler, Jae-Keun Park, Zainab Rahil, Hao Wang, Loretta Auvil, Colleen Bushell, Min Young Lee, David Baxter, Tyler Bristol, Luz Angela Rosas, Adriana Cervantes-Medina, Lindsay Czajkowski, Alison Han, Matthew J Memoli, Jeffery K Taubenberger, John C Kash

Articles, Abstracts, and Reports

In this study, we examined the relationships between anti-influenza virus serum antibody titers, clinical disease, and peripheral blood leukocyte (PBL) global gene expression during presymptomatic, acute, and convalescent illness in 83 participants infected with 2009 pandemic H1N1 virus in a human influenza challenge model. Using traditional statistical and logistic regression modeling approaches, profiles of differentially expressed genes that correlated with active viral shedding, predicted length of viral shedding, and predicted illness severity were identified. These analyses further demonstrated that challenge participants fell into three peripheral blood leukocyte gene expression phenotypes that significantly correlated with different clinical outcomes and prechallenge serum …

An Assessment Of Combinatorial Transcription Factor Activity At P53 Enhancer Elements, Sylvia Kuang

Biological Sciences

Certain non-coding DNA sequences in the eukaryotic genome regulate gene expression. These non-coding regulatory regions, including promoters and enhancers, are controlled by the binding of multiple transcription factors which act together to regulate gene transcription. The number of potential transcription factor combinations regulating any gene presents a massive experimental challenge. One well-known transcription factor, p53, activates multiple transcription pathways involved in tumor suppression, primarily through engagement with enhancers. p53 is one member of a paralogous transcription factor family, which includes the factor p63. Whereas p53 is involved in tumor suppression, p63 is a transcription factor responsible for maintaining epithelial cell …

Community Oncology Clinicians’ Knowledge, Beliefs, And Attitudes Regarding Genomic Tumor Testing, Eric Anderson, Alexandra Hinton, Kimberly Murray, Hayley Mandeville, Caitlin Gutheil, Leo Waterston, Lee Lucas, Christine Duarte, Christian Thomas, Susan Miesfeldt, Petra Helbig, Andrey Antov, Jens Rueter, Paul Han

Maine Medical Center

Introduction: Genomic tumor testing (GTT) is a new technology that promises to make cancer treatment more precise. However, little is known about clinicians’ knowledge, beliefs, and attitudes regarding GTT, particularly in community oncology settings.

The Relationship Between Uncertainty Tolerance And Oncologists’ Perceptions Of Large-Panel Genomic Tumor Testing, Eric Anderson, Alexandra Hinton, Christine Lary, Kimberly Murray, Leo Waterson, Paul Han, Maine Cancer Genomics Initiative

Maine Medical Center

Introduction:

Large-panel genomic tumor testing (GTT) is a new technology that promises to make cancer treatment more precise, but that currently poses many uncertainties regarding its clinical value and appropriate use. Uncertainty Tolerance (UT), a psychological construct that describes trait-level differences in individuals’ responses to uncertainty, may influence oncologists’ perceptions and attitudes regarding GTT.

Expanded Phenotypic Diagnoses For 24 Recently Named New Taxa Of Hesperiidae (Lepidoptera), Nick V. Grishin

The Taxonomic Report of the International Lepidoptera Survey

Expanded diagnoses by phenotypic characters for the 24 new taxa named in the article "Genomes of skipper butterflies reveal extensive convergence of wing patterns" by Li, W., Cong, Q., Shen, J., Zhang, J., Hallwachs, W., Janzen, D.H. and Grishin, N.V., 2019 and published in the Proceedings of the National Academy of Sciences of the United States of America on March 15, 2019 are provided and illustrated. More detailed diagnoses will help identifying these phylogenetic groups by their wing patterns and shapes and other morphological characters including the structures of antennae and genitalia using this single publication, instead of obtaining the …

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 …