Genetics Commons^™

Genetic Homogeneity Of The Invasive Lionfish Across The Northwestern Atlantic And The Gulf Of Mexico Based On Single Nucleotide Polymorphisms, R. Pérez-Portela, A. Bumford, B. Coffman, S. Wedelich, M. Davenport, Alex Fogg, M.K. Swenarton, F. Coleman, M.A. Johnston, D.L. Crawford, M.F. Oleksiak

Student Publications

Despite the devastating impact of the lionfish (Pterois volitans) invasion on NW Atlantic ecosystems, little genetic information about the invasion process is available. We applied Genotyping by Sequencing techniques to identify 1,220 single nucleotide polymorphic sites (SNPs) from 162 lionfish samples collected between 2013 and 2015 from two areas chronologically identified as the first and last invaded areas in US waters: the east coast of Florida and the Gulf of Mexico. We used population genomic analyses, including phylogenetic reconstruction, Bayesian clustering, genetic distances, Discriminant Analyses of Principal Components, and coalescence simulations for detection of outlier SNPs, to understand …

The Determinants Of Nucleosome Patterns And The Impact Of Phosphate Starvation On Nucleosome Patterns And Gene Expression In Rice, Qi Zhang

LSU Doctoral Dissertations

In eukaryotic cells, DNA is a large molecule that must be greatly condensed to fit within the nucleus. DNA is wrapped around histone proteins to form nucleosomes, which facilitate DNA condensation, but on the other hand, may limit DNA processes. Organisms must respond to environmental stress in order to survive, and one strategy is by remodeling nucleosomes to promote changes in DNA accessibility to alter gene expression. Studies have demonstrated a clear correlation between nucleosome dynamics and transcriptional change in some eukaryotes, however factors that affect nucleosome positioning in plants are largely unknown, and the correlation between nucleosome dynamics and …

Early Limb Patterning In The Direct‐Developing Salamander Plethodon Cinereus Revealed By Sox9 And Col2a1, Ryan R. Kerney, James Hanken, David C. Blackburn

Biology Faculty Publications

Direct‐developing amphibians form limbs during early embryonic stages, as opposed to the later, often postembryonic limb formation of metamorphosing species. Limb patterning is dramatically altered in direct‐developing frogs, but little attention has been given to direct‐developing salamanders. We use expression patterns of two genes, sox9and col2a1, to assess skeletal patterning during embryonic limb development in the direct‐developing salamander Plethodon cinereus. Limb patterning in P. cinereus partially resembles that described in other urodele species, with early formation of digit II and a generally anterior‐to‐posterior formation of preaxial digits. Unlike other salamanders described to date, differentiation of preaxial zeugopodial …

Breeding For Resistance In California Strawberry To Verticillium Dahliae, Zachary Christman

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

This article focuses on breeding resistant strawberries to the fungus Verticillium dahliae, common name Verticillium wilt. This is a serious fungal disease that can result in a loss of 50% or more of a strawberry harvest when grown in infested soil. The main goal is to provide an example of how a cultivar can be made more resistant to a plant pathogen with the use of plant breeding methods.

Since 1930 the University of California, Davis, has been developing strawberry cultivars that are adapted to the agricultural industry and regional farms. Developing cultivars that require fewer inputs are of …

Copy Number Variation In The Porcine Genome Detected From Whole-Genome Sequence, Rebecca Anderson

Honors Program: Senior Projects (Public)

Copy number variations (CNVs) are large insertions, deletions, and duplications in the genome that vary between individuals in a species. These variations are known to impact a broad range of phenotypes from molecular-level traits to higher-order clinical phenotypes. CNVs have been linked to complex traits in humans such as autism, attention deficit hyperactivity disorder, nervous system disorders, and early-onset extreme obesity. In this study, whole-genome sequence was obtained from 72 founders of an intensely phenotyped experimental swine herd at the U.S. Meat Animal Research Center (USMARC) in Clay Center, Nebraska. This included 24 boars (12 Duroc and 12 Landrace) and …

Investigating The Genetic Structure Of Northern Long-Eared Bats In Nebraska, Jonathan Korbitz

UNO Student Research and Creative Activity Fair

Abstract:

The northern long-eared bat (Myotis septentrionalis) is one of many species of hibernating bats in North America affected by a recently discovered fungal disease called white-nose syndrome (WNS). Northern long-eared bats seem to be extremely susceptible to the disease with mass fatalities occurring among populations in eastern North America. Researchers in the eastern distribution of this species have performed mtDNA analysis to identify the population structure of the species; however, genetic analysis has yet to be done in western parts of its distribution. The goal of this study is to create a better understanding of the genetic …

Developing Pennycress ( Thlaspi Arvense ) As A Biodiesel Feedstock Crop And Plant Model System, Michaela Mcginn

Theses and Dissertations

Thlapsi arvense L. (pennycress) is currently being developed as a profitable oilseed-producing winter annual cover crop with extreme cold tolerance and a rapid life cycle that can be grown on fallow farmland throughout the U.S. Midwest Corn Belt, controlling soil erosion and nutrient runoff while serving as an additional source of income for the American farmer without displacing food crops. The research comprising this dissertation demonstrates that pennycress can serve as a user-friendly model system highly similar to Arabidopsis thaliana, and is well-suited for both laboratory and field experimentation, being readily employable in existing growth facilities. After 10 generations of …

Repeat-Associated Non-Aug (Ran) Translation And Other Molecular Mechanisms In Fragile X Tremor Ataxia Syndrome, M. Rebecca Glineburg, Peter K. Todd, Nicolas Charlet-Berguerand, Chantal Sellier

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Fragile X-associated tremor/ataxia syndrome (FXTAS) is a late-onset inherited neurodegenerative disorder characterized by progressive intention tremor, gait ataxia and dementia associated with mild brain atrophy. The cause of FXTAS is a premutation expansion, of 55 to 200 CGG repeats localized within the 5′UTR of FMR1. These repeats are transcribed in the sense and antisense directions into mutants RNAs, which have increased expression in FXTAS. Furthermore, CGG sense and CCG antisense expanded repeats are translated into novel proteins despite their localization in putatively non-coding regions of the transcript. Here we focus on two proposed disease mechanisms for FXTAS: 1) RNA …

Advancing Behavioural Genomics By Considering Timescale, Clare C. Rittschof, Kimberly A. Hughes

Entomology Faculty Publications

Animal behavioural traits often covary with gene expression, pointing towards a genomic constraint on organismal responses to environmental cues. This pattern highlights a gap in our understanding of the time course of environmentally responsive gene expression, and moreover, how these dynamics are regulated. Advances in behavioural genomics explore how gene expression dynamics are correlated with behavioural traits that range from stable to highly labile. We consider the idea that certain genomic regulatory mechanisms may predict the timescale of an environmental effect on behaviour. This temporally minded approach could inform both organismal and evolutionary questions ranging from the remediation of early …

A Model Species For Agricultural Pest Genomics: The Genome Of The Colorado Potato Beetle, Leptinotarsa Decemlineata (Coleoptera: Chrysomelidae), Sean D. Schoville, Yolanda H. Chen, Martin N. Andersson, Joshua B. Benoit, Anita Bhandari, Julia H. Bowsher, Kristian Brevik, Kaat Cappelle, Mei-Ju M. Chen, Anna K. Childers, Christopher Childers, Olivier Christiaens, Justin Clements, Elise M. Didion, Elena N. Elpidina, Patamarerk Engsontia, Markus Friedrich, Inmaculada García-Robles, Richard A. Gibbs, Chandan Goswami, Alessandro Grapputo, Kristina Gruden, Marcin Grynberg, Bernard Henrissat, Emily C. Jennings, Jeffery W. Jones, Megha Kalsi, Sher A. Khan, Abhishek Kumar, Fei Li, Vincent Lombard, Subba Reddy Palli, June-Sun Yoon

Entomology Faculty Publications

The Colorado potato beetle is one of the most challenging agricultural pests to manage. It has shown a spectacular ability to adapt to a variety of solanaceaeous plants and variable climates during its global invasion, and, notably, to rapidly evolve insecticide resistance. To examine evidence of rapid evolutionary change, and to understand the genetic basis of herbivory and insecticide resistance, we tested for structural and functional genomic changes relative to other arthropod species using genome sequencing, transcriptomics, and community annotation. Two factors that might facilitate rapid evolutionary change include transposable elements, which comprise at least 17% of the genome and …

Gene-Based Association Study For Lipid Traits In Diverse Cohorts Implicates Bace1 And Sidt2 Regulation In Triglyceride Levels, Angela Andaleon, Lauren S. Mogil, Heather Wheeler

Bioinformatics Faculty Publications

Plasma lipid levels are risk factors for cardiovascular disease, a leading cause of death worldwide. While many studies have been conducted on lipid genetics, they mainly focus on Europeans and thus their transferability to diverse populations is unclear. We performed SNP- and gene-level genome-wide association studies (GWAS) of four lipid traits in cohorts from Nigeria and the Philippines and compared them to the results of larger, predominantly European meta-analyses. Two previously implicated loci met genome-wide significance in our SNP-level GWAS in the Nigerian cohort, rs34065661 in CETP associated with HDL cholesterol (P = 9.0 × 10⁻¹⁰) and …

A New Toolset For Protein Expression And Subcellular Localization Studies In Citrus And Its Application To Citrus Tristeza Virus Proteins, Amit Levy, Choaa El-Mochtar, Chunxia Wang, Michael M. Goodin, Vladimir Orbovic

Plant Pathology Faculty Publications

Background

Transient gene expression is a powerful tool to study gene function in plants. In citrus, Agrobacterium transformation is the method of choice for transient expression studies, but this method does not work efficiently with many gene constructs, and there is a need for a more robust transient expression system in citrus leaves. Biolistic particle delivery is an alternative to Agrobacterium transformation, and in some plants, such as Arabidopsis, gives higher transformation rates in leaf tissues than Agrobacterium.

Results

Here we describe an improved method for gene expression in epidermal cells of citrus leaves, using the Bio-Rad Helios gene-gun. …

Dna Sequences Of Mitochondrial Cytochrome C Oxidase I (Coi) Genes From Deep Sea Fishes Collected During Deepend Cruise Dp05 From 2017-05-01 To 2017-05-11, Kimberly A. Finnegan, Andrea Bernard, M. Weber, Ron Eytan, Mahmood S. Shivji

DEEPEND Datasets

Deep sea fishes were collected in the northern Gulf of Mexico during DEEPEND cruise DP05 from May 1 to 11, 2017. This dataset contains Genbank accession numbers of DNA sequences of the mitochondrial Cytochrome c oxidase I (COI) gene from fish species collected.

Examination Of Orthologous Genes (Mrub_2518 And B3728, Mrub_2519 And B3727, Mrub_2520 And B3726, Mrub_2521 And B3725) Responsible For Abc Phosphate Transporters In Two Species M. Ruber And E. Coli, Margaret Meyer, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

In this project we investigated the biological function of the genes b3725, b3726, b3727, b3728 and Mrub_2518, Mrub_2519, Mrub_2520 and Mrub_2521 (KEGG map number 02010). We predict that these genes encode the components of a Phosphate ABC transporter: Orthologous genes Mrub_2518 (DNA coordinates 2565359..2566438) and b3728 encodes the periplasmic phosphate binding component; Orthologous genes Mrub_2519 (DNA coordinates 2566499..2567485) and b3727, and Mrub_2520 (DNA coordinates 2567496..2568326) and b3726 encode for the two transmembrane proteins; Orthologous genes Mrub_2521 (DNA coordinates 2568338..2569159) and b3725 encode for the ATP binding protein within the cytoplasm. Within the two species, M. ruber and E. coli, …

Mrub_1325, Mrub_1326, Mrub_1327, And Mrub_1328 Are Orthologs Of B_3454, B_3455, B_3457, B_3458, Respectively Found In Escherichia Coli Coding For A Branched Chain Amino Acid Atp Binding Cassette (Abc) Transporter System, Bennett Tomlin, Adam Buric, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

In this project we investigated the biological function of the genes Mrub_1325, Mrub_1326, Mrub_1327, and Mrub_1328 (KEGG map number 02010). We predict these genes encode components of a Branched Chain Amino Acid ATP Binding Cassette (ABC) transporter: 1) Mrub_1325 (DNA coordinates 1357399-1358130 on the reverse strand) encodes the ATP binding domain; 2) Mrub_1326 (DNA coordinates 1358127-1359899 on the reverse strand) encodes the ATP-binding domain and permease domain; 3) Mrub_1327 (DNA coordinates 1359899-1360930 on the reverse strand) encodes a permease domain; and 4)Mrub_1328 (DNA coordinates 1711022-1712185 on the reverse strand) encodes the substrate binding domain. This system is not predicted to …

Confirmation That Mrub_1751 Is Homologous To E. Coli Xylf, Mrub_1752 Is Homologous To E. Coli Xylh, And Mrub_1753 Is Homologous To E. Coli Xylg, Ben Price, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

In this project we investigated the biological function of the genes Mrub_1751, Mrub_1752 and Mrub_1753 (KEGG map number 02010). We predict these genes encode components of a D-xylose ATP Binding Cassette (ABC) transporter: 1) Mrub_1752 (DNA coordinates 1809004-1810224 on the forward strand) encodes the permease component (aka transmembrane domain), predicted to be an ortholog and 2) Mrub_1753 (DNA coordinates 1810227-1811000 on the forward strand) encodes the ATP-binding domain (aka nucleotide binding domain); and 3) Mrub_1751 (DNA coordinates 1807855-1808892 on the forward strand) encodes the solute binding protein. The ABC-transporter for M. ruber to transport D-xylose is homologous with the transporter …

Mrub_1283, Mrub_1284 And Mrub_1285 Encode For A Glycine/Betaine Abc Transporter And Are Orthologs Of E. Coli Prov, Prow And Prox, Lan Dang, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

ABC transporters are essential for cellular transport; contribute to maintain the homeostasis of the cells. Generally, ABC transporters are multi-subunit; contain essential cytoplasmic factors which are critical to ATP hydrolysis activity. In this paper, we would like to take a closer look to Mrub_1283, Mrub_1284 and Mrub_1285, three consecutive genes in Meiothermus ruber genome. We hypothesize that these genes are in the same operon and encode for ABC glycine/ betaine transporters. To confirm our hypothesis, we utilizes several bioinformatics tools to predict the potential function of Mrub_1283, Mrub_1284 and Mrub_1285 and to search for their orthologs in Escherichia coli genome. …

Mrub_2120, Mrub_2121, Mrub_2122, Mrub_2123 And Mrub_2124 Are Orthologs Of E. Coli Genes B3458, B3457, B3456, B3455 And B3454, Respectively, And Make Up An Operon That Codes For The Branched-Chain Amino Acid Abc Transporter In Meiothermus Ruber Dsm 1279, Aaron Jones, Madelyn Huber, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

In this project we investigated the biological function of the genes Mrub_2120, Mrub_2121, Mrub_2122, Mrub_2123 and Mrub_2124 (KEGG map number 02010). We predict these genes encode components of a branched-chain amino acid ATP Binding Cassette (ABC) transporter: 1) Mrub_2120 (DNA coordinates 2169247-2170416 on the reverse strand) encodes the branched-chain amino acid binding protein that is localized to the periplasm; 2) Mrub_2121 (DNA coordinates 2170433..2171353 on the reverse strand) encodes the first TMD; 3) Mrub_2122 (DNA coordinates 2171365..2172279 on the reverse strand) encodes the second TMD; 4) Mrub_2123 (DNA coordinates 2172276..2173028 on the reverse strand) encodes the first NBD; 5) Mrub_2124 …

Mrub_1675, Mrub_1676, Mrub_1677, And Mrub_1679 Genes Are Orthologs Of B_3458, B_3457, B_3456, And B_3454 Genes In E. Coli, Respectively, Coding For Abc Transporters. Mrub_1678 And B_3455, Though Perform Similar Tasks, Are Not Orthologous, Ravi Patel, Alaina Hofmann, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

In this project we investigated the biological function of the genes Mrub_1675, Mrub_1676, Mrub_1677, and Mrub_1679 (KEGG map number 02010). We predict these genes encode components of a Branched chain amino acid (ABC) transporter: Mrub_1675 (DNA coordinates 1711022..1712185 on the reverse strand) encodes the permease component, Mrub_1676 (DNA coordinates 1712313..1713170) encodes for the NBD (aka nucleotide binding domain), Mrub_1677 (DNA coordinates 1713167..1714075 on the reverse strand) encodes the NBD (aka nucleotide binding domain), Mrub_1678 (DNA coordinates 1713167..1714075 on the reverse strand) encodes the TMD (aka transmembrane domain) and Mrub_1679 (DNA coordinates 1714781..1715485 on the reverse strand) encodes …

Mrub_0680, Mrub_0836, And Mrub_0837 Found To Be Orthologous To E. Coli Ccma, Ccmb, And Ccmc, Respectively, Coding For Abc-Transport Proteins Involved In Cytochrome-C Biogenesis, Sarah N. Church, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

In this project we investigated the biological function of the genes Mrub_0680, Mrub_0836 and Mrub_0837(KEGG map number 02010). We predict these genes encode components of a Heme ATP Binding Cassette (ABC) transporter: 1) Mrub_0836 (DNA coordinates 823734..824399on the reverse strand) encodes the permease component (aka transmembrane domain), predicted to be an ortho; and 2) Mrub_0680(DNA coordinates 659484..660071 on the reverse strand) encodes the ATP-binding domain (aka nucleotide binding domain); and 3) Mrub_0837(DNA coordinates 824570..825262on the reverse strand) encodes the solute binding protein. This gene system encodes a transmembrane exporter and helper proteins which are thought to …