Genetics and Genomics Commons^™

Effects Of Reactive Oxygen Species On Life History Traits Of Caenorhabditis Elegans, Samson William Smith

Dissertations and Theses

Evolutionary life history theory predicts that tradeoffs among fitness-related phenotypes will occur as a result of resource limitations and/or physiological constraints. Such tradeoffs are defined as the cost(s) incurred on one component of fitness (e.g., reproduction) by the increased expression of another fitness-related trait (e.g., longevity). Only recently have researchers begun to investigate the mechanistic bases of life history tradeoffs. A recent proposal is that reactive oxygen species (ROS) have a central role in shaping life history traits and tradeoffs. Research on disparate animal taxa has highlighted strong correlations between oxidative stress resistance and fitness-related life history traits, for example. …

Antibody Responses To Lytic And Latent Human Herpesvirus 8 Antigens Among Hiv-Infected Patients In Central China, Tiejun Zhang, Na He, Yingying Ding, Qingwu Jiang, Charles Wood

Nebraska Center for Virology: Faculty Publications

Human herpesvirus 8 (HHV8) is an important opportunistic infection of HIV/AIDS. However, very little is known about antibody seropositivities to HHV8 lytic and latent antigens among HIVinfected patients in China. Therefore, a cross-sectional study was conducted to explore HHV8 serostatus among 316 HIV-infected patients in a rural area of central China. The antibody seropositivity to HHV8 ORF65 (lytic) and LANA (latent) antigens was 12.7% and 10.4%, respectively. Patients who were naïve to antiretroviral therapy (ART) were more likely to be seropositive for antibodies to ORF65 (OR: 3.79; 95% CI: 1.71–8.42) and LANA (OR: 3.77; 95% CI: 1.55–9.14) than patients receiving …

Triticum Mosaic Poacevirus Enlists P1 Rather Than Hc-Pro To Suppress Rna Silencing-Mediated Host Defense, Satyanarayana Tatineni, Feng Qu, Ruhui Li, Thomas Jack Morris, Roy French

Nebraska Center for Virology: Faculty Publications

Triticum mosaic virus (TriMV) is the type species of the newly established Poacevirus genus in the family Potyviridae. In this study, we demonstrate that in contrast to the helper component- proteinase (HC-Pro) of Potyvirus species, the P1 proteins of TriMV and Sugarcane steak mosaic poacevirus function in suppression of RNA silencing (SRS). TriMV P1 effectively suppressed silencing induced by single- or double-stranded RNAs (ss/ds RNAs), and disrupted the systemic spread of silencing signals at a step after silencing signal production. Interestingly, contrary to enhanced SRS activity of potyviral HC-Pro by co-expression with P1, the presence of TriMV HC-Pro reduced …

Chloroviruses: Not Your Everyday Plant Virus, James L. Van Etten, David D. Dunigan

Nebraska Center for Virology: Faculty Publications

Viruses infecting higher plants are among the smallest viruses known and typically have four to ten protein-encoding genes. By contrast, many viruses that infect algae (classified in the virus family Phycodnaviridae) are among the largest viruses found to date and have up to 600 protein- encoding genes. This brief review focuses on one group of plaque-forming phycodnaviruses that infect unicellular chlorella-like green algae. The prototype chlorovirus PBCV-1 has more than 400 protein-encoding genes and 11 tRNA genes. About 40% of the PBCV-1 encoded proteins resemble proteins of known function including many that are completely unexpected for a virus. In many …

Subunit Organization Of The Membrane-Bound Hiv-1 Envelope Glycoprotein Trimer, Youdong Mao, Liping Wang, Christopher Gu, Alon Herschhorn, Shi-Hua Xiang, Hillel Haim, Xinzhen Yang, Joseph Sodroski

Nebraska Center for Virology: Faculty Publications

The trimeric human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein (Env) spike is a molecular machine that mediates virus entry into host cells and is the sole target for virus-neutralizing antibodies. The mature Env spike results from cleavage of a trimeric gp160 precursor into three gp120 and three gp41 subunits. Here we describe an ~11-Å cryo-EM structure of the trimeric HIV-1 Env precursor in its unliganded state. The three gp120 and three gp41 subunits form a cage-like structure with an interior void surrounding the trimer axis. Interprotomer contacts are limited to the gp41 transmembrane region, the torus-like gp41 ectodomain, and …

Genome Sequence Of Strain Himb55, A Novel Marine Gammaproteobacterium Of The Om60/Nor5 Clade, Megan Huggett, Michael Rappe

Research outputs 2012

Strain HIMB55 is a phylogenetically unique member of the OM60/NOR5 clade of the Gammaproteobacteria isolated from coastal seawater of Kaneohe Bay on the northeastern shore of Oahu, Hawaii, by extinction culturing in seawater-based oligotrophic medium. Here we present the genome sequence of strain HIMB55, including genes for bacteriochlorophyll-based phototrophy.

Oxygenation Properties And Oxidation Rates Of Mouse Hemoglobins That Differ In Reactive Cysteine Content, Jay F. Storz, Roy E. Weber, Angela Fago

Jay F. Storz Publications

House mice (genus Mus) harbor extensive allelic variation at two tandemly duplicated genes that encode the β-chain subunits of adult hemoglobin (Hb). Alternative haplotypes differ in the level of sequence divergence between the two β-globin gene duplicates: the Hbb^d and Hbb^p haplotypes harbor two structurally distinct β-globin genes, whereas the Hbb^s haplotype harbors two β-globin duplicates that are identical in sequence. One especially salient difference between the s-type Hbs relative to the d- and p-type Hbs relates to the number of reactive β-chain cysteine residues. In addition to the highly conserved cysteine residue …

Regulatory Changes Contribute To The Adaptive Enhancement Of Thermogenic Capacity In High-Altitude Deer Mice, Zachary A. Cheviron, Gwendolyn C. Bachman, Alex D. Connaty, Jay F. Storz

Jay F. Storz Publications

In response to hypoxic stress, many animals compensate for a reduced cellular O₂ supply by suppressing total metabolism, thereby reducing O₂ demand. For small endotherms that are native to high-altitude environments, this is not always a viable strategy, as the capacity for sustained aerobic thermogenesis is critical for survival during periods of prolonged cold stress. For example, survivorship studies of deer mice (Peromyscus maniculatus) have demonstrated that thermogenic capacity is under strong directional selection at high altitude. Here, we integrate measures of whole-organism thermogenic performance with measures of metabolic enzyme activities and genomic transcriptional profiles to …

Genetic Diversity Of Neotropical Myotis (Chiroptera: Vespertilionidae) With An Emphasis On South American Species, Roxanne J. Larsen, Michelle C. Knapp, Hugh H. Genoways, Faisal Ali Anwarali Khan, Peter A. Larsen, Don E. Wilson, Robert J. Baker

University of Nebraska State Museum: Mammalogy Papers

Background: Cryptic morphological variation in the Chiropteran genus Myotis limits the understanding of species boundaries and species richness within the genus. Several authors have suggested that it is likely there are unrecognized species-level lineages of Myotis in the Neotropics. This study provides an assessment of the diversity in New World Myotis by analyzing cytochrome-b gene variation from an expansive sample ranging throughout North, Central, and South America. We provide baseline genetic data for researchers investigating phylogeographic and phylogenetic patterns of Myotis in these regions, with an emphasis on South America.

Methodology and Principal Findings: Cytochrome-b sequences were …

Widespread Triploidy In Western North American Aspen (Populus Tremuloides), Karen E. Mock, Colin M. Callahan, M. Nurul Islam-Faridi, John D. Shaw, Hardeep S. Rai, Stewart C. Sanderson, Carol A. Rowe, Ronald J. Ryel, Michael D. Madritch, Richard S. Gardner, Paul G. Wolf

Aspen Bibliography

No abstract provided.

Cryptic Distant Relatives Are Common In Both Isolated And Cosmopolitan Genetic Samples, Brenna M. Henn, Lawrence S. Hon, J. Michael Macpherson, Nicholas Eriksson, Serge Saxonov, Itsik Pe'er, Joanna Mountain

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Although a few hundred single nucleotide polymorphisms (SNPs) suffice to infer close familial relationships, high density genome-wide SNP data make possible the inference of more distant relationships such as 2nd to 9th cousinships. In order to characterize the relationship between genetic similarity and degree of kinship given a timeframe of 100–300 years, we analyzed the sharing of DNA inferred to be identical by descent (IBD) in a subset of individuals from the 23andMe customer database (n = 22,757) and from the Human Genome Diversity Panel (HGDP-CEPH, n = 952). With data from 121 populations, we show that the average amount …

Successful Genotyping Of Microsatellites In The Woolly Mammoth, Yasuko Ishida, Alfred L. Roca, Stephen Fratpietro, Alex D. Greenwood

Biological Sciences Faculty Publications

Genetic analyses using ancient DNA from Pleistocene and early Holocene fossils have largely relied on mitochondrial DNA (mtDNA) sequences. Among woolly mammoths, Mammuthus primigenius, mtDNA analyses have identified 2 distinct clades (I and II) that diverged 1-2 Ma. Here, we establish that microsatellite markers can be effective on Pleistocene samples, successfully genotyping woolly mammoth specimens at 2 loci. Although significant differentiation at the 2 microsatellite loci was not detected between 16 clade I and 4 clade II woolly mammoths, our results demonstrate that the nuclear population structure of Pleistocene species can be examined using fast-evolving nuclear microsatellite markers.

Identification Of Cellular Functions Of Cardiolipin As Physiological Modifiers Of Barth Syndrome, Amit Shridhar Joshi

Wayne State University Dissertations

Cardiolipin (CL) is an anionic phospholipid synthesized in the mitochondrial inner membrane. Perturbation of CL metabolism leads to Barth syndrome (BTHS), a life threatening genetic disorder. I utilized genetic, biochemical and cell biological approaches in yeast to elucidate the cellular functions of CL. Understanding the functions of CL is expected to shed light on the pathology and possible treatments for BTHS.

BTHS is caused by mutations in TAZ1, which encodes a CL remodeling enzyme called tafazzin. BTHS patients exhibit a wide range of clinical presentations, indicating that physiological modifiers influence the BTHS phenotype. A targeted synthetic lethality screen was performed …

Development And Application Of Methods Used To Source Prehistoric Southwestern Maize: A Review, Larry Benson

United States Geological Survey: Staff Publications

Archaeological cobs free of mineral contaminants should be used to source the soils in which they were grown. Mineral contaminants often contain much higher concentrations of metals than vegetal materials and can alter a cob’s apparent metal and heavy-isotope content. Cleaning a cob via immersion in an acid solution for more than a few minutes will result in the incongruent and sometimes complete leaching of metals, including strontium (Sr), from the cob. When using ⁸⁷Sr/⁸⁶Sr to determine the location of potential agriculture fields, it is best to either integrate several depth-integrated soil samples or to integrate several …

Patterns Of Population Structure And Historical Dispersal In Squaloid Sharks: A Species-Level Approach Using Molecular Markers, Ana Christina Pimenta Verissimo

Dissertations, Theses, and Masters Projects

Squaloids (Order Squaliformes) are a highle diverse group of mostly deepwater habitats (> 200 m). Many species are regularly caught in commercial fisheries worldwide but their low productivity and correspondingly low intrinsic rebound potentials make them particularly vulnerable to population depletion and overexploitation. of special concern to fisheries management and conservation efforts are the spiny dogfish Squalus acanthias, the leafscale gulper shark Centrophorus squamosus and the Portuguese dogfish Centroscymnus coelolepis. These taxa have recently been declared overfished in several parts of each species' distribution but management efforts have been made to recover the "stocks" without a good understanding of the …

Pando Clone (World's Largest Living Organism?) History And Evaluation : Case Study For Revalidation, Allen V. Henningson

Aspen Bibliography

No abstract provided.

Inheritance Of Humeral Spotting In The Croaking Gourami (Osphronemidae: Trichopsis Vittatus), Jack Frankel, Lisa Alder-Golden, Andre Porter

Department of Biology Faculty Publications

The croaking gourami (Trichopsis vittatus) exhibits two phenotypes associated with humeral spotting. Fish possess a prominent, dark humeral patch or spot located behind the operculum or lack this spotting pattern. Segregation patterns observed from the progenies of eleven different crosses support the hypothesis that the inheritance of humeral spotting in T. vittatus is controlled by the action of a single autosomal locus, with complete dominance of the allele controlling the spotted phenotype.

Decision Memo: Pando Aspen Clone Restoration Project, Kurt Robins

Aspen Bibliography

The Pando Clone is located in Township 26 South, Range 1 East, Sections 24 and 25 about 1 mile southwest of the Lakeside Resort on State Highway 25 and about 1 mile due east of Mallard Bay at the southwest corner of Fish Lake (see map). The Pando Clone is the largest aspen clone in the world and the largest (most massive) single living organism in existence that has been discovered to date (Grant, 1993; DeWoody et al, 2008). It encompasses approximately 106 acres and is estimated to weigh in excess of 13 million pounds (Grant, 1993). This clone is …

Dna Secondary Structures And Their Contribution To Mutagenesis In B. Subtilis Stationary Phase Cells, Carmen Vallin, Holly Anne Martin, Christian Ross, Ronald Yasbin, Eduardo Robleto

McNair Poster Presentations

It is widely known and accepted that the cause of many mutations in cells are generated during the replication process of actively dividing cells, however more recent research has shown that mutations also arise in non growing conditions, a phenomenon known as stationary phase mutagenesis. Much of what is known come from studies in eukaryotic and bacterial models. It has been proposed that in non-growing cells, the process of transcription plays an important role in mutagenesis. We test the hypothesis that DNA secondary structures, formed during transcription, promote mutagenesis. The transcription-generated structures are speculated to be prone to by blocking …

Design Of A Distributed Hadoop Solution For The Multiple Sequence Alignment Algorithm: Clustal Omega, Jurate Daugelaite

Theses

Multiple Sequence Alignment (MSA) of DNA and protein sequences is one of the most essential techniques in the fields of molecular biology, computational biology and bioinformatics. It aids the identification and prediction of three dimensional structures, primary functions and evolutionary relatedness amongst groups of species, organisms, and genes. Since as the completion of the Human Genome Project and with the advent of sequencing initiatives such as the Genome 10K project, the rate of genome sequencing has increased exponentially, producing vast amounts of DNA and protein sequences. MSA algorithms, when applied to such sequence data, can identify common homology, structure and …