Genetics and Genomics Commons^™

Low-Abundance Resistant Mutations In Hiv-1 Subtype C Antiretroviral Therapy-Naïve Individuals As Revealed By Pyrosequencing, Sandra Gonzalez, Damien C. Tully, Clement Gondwe, Charles Wood

Nebraska Center for Virology: Faculty Publications

Given the recent scale-up of antiretroviral therapy (ART) in sub-Saharan Africa, we sought to determine how often and at what levels do drug-resistant mutant variants exist in ART-naïve HIV subtype C infected individuals. Samples from 10 ART-naïve Zambian individuals were subjected to ultra-deep pyrosequencing (UDPS) to characterize the frequency of low-abundance drug resistance mutations in the pol gene. Low-abundance clinically relevant variants were detected for nucleoside reverse transcriptase inhibitors (NRTIs), non-nucleoside reverse transcriptase inhibitors (NNRTIs) and protease inhibitors (PIs) in eight of the ten subjects. Intermediate to high-level resistance was predicted for the majority of NRTIs. Mutations conferring resistance to …

Clade C Hiv-1 Isolates Circulating In Southern Africa Exhibit A Greater Frequency Of Dicysteine Motif-Containing Tat Variants Than Those In Southeast Asia And Cause Increased Neurovirulence, Vasudev R. Rao, Ujjwal Neogi, Joshua S, Talboom, Ligia Padilla, Mustafizur Rahman, Cari Fritz-French, Sandra Gonzalez-Ramirez, Anjali Verma, Charles Wood, Ruth M. Ruprecht, Udaykumar Ranga, Tasnim Azim, Vinayaka R. Prasad

Nebraska Center for Virology: Faculty Publications

Background: HIV-1 Clade C (Subtype C; HIV-1C) is responsible for greater than 50% of infections worldwide. Unlike clade B HIV-1 (Subtype B; HIV-1B), which is known to cause HIV associated dementia (HAD) in approximately 15% to 30% of the infected individuals, HIV-1C has been linked with lower prevalence of HAD (0 to 6%) in India and Ethiopia. However, recent studies report a higher prevalence of HAD in South Africa, Zambia and Botswana, where HIV-1C infections predominate. Therefore, we examined whether Southern African HIV-1C is genetically distinct and investigated its neurovirulence. HIV-1 Tat protein is a viral determinant of neurocognitive dysfunction. …

Global Neuroaids Roundtable, Jeymohan Joseph, Cristian L. Achim, Michael J. Boivin, Bruce J. Brew, David B. Clifford, Deborah A. Colosi, Ronald J. Ellis, Robert K. Heaton, Amadou Gallo-Diop, Igor Grant, Georgette D. Kanmogne, Mahendra Kumar, Scott Letendre, Thomas D. Marcotte, Avindra Nath, Carlos A. Pardo, Robert H. Paul, Lynn Pulliam, Kevin Robertson, Walter Royal Iii, Ned Sacktor, Pasiri Sithinamsuwan, Davey M. Smith, Victor Valcour, Brian Wigdahl, Charles Wood

Nebraska Center for Virology: Faculty Publications

In May 2012, the Division of AIDS Research at the National Institute of Mental Health (NIMH) organized the “Global NeuroAIDS Roundtable” in conjunction with the 11th International Symposium on Neurovirology and the 2012 Conference on HIV in the Nervous System. The meeting was held in New York, NY, USA and brought together NIMH-funded investigators who are currently working on projects related to the neurological complications of AIDS (NeuroAIDS) in Africa, Asia, Eastern Europe, and Latin America in order to provide an opportunity to share their recent findings and discuss the challenges encountered within each country. The major goals of the …

The Effect Of Myostatin Genotype On Body Temperature During Extreme Temperature Events, J. T. Howard, Stephen D. Kachman, Merlyn K. Nielsen, Terry L. Mader, Matthew L. Spangler

Department of Animal Science: Faculty Publications

Extreme heat and cold events can create deleterious physiological changes in cattle as they attempt to cope. The genetic background of animals can influence their response to these events. The objective of the current study was to determine the impact of myostatin genotype (MG) on body temperature during periods of heat and cold stress. Two groups of crossbred steers and heifers of unknown pedigree and breed fraction with varying percentages of Angus, Simmental, and Piedmontese were placed in a feedlot over 2 summers and 2 winters. Before arrival, animals were genotyped for the Piedmontese-derived myostatin mutation (C313Y) to determine their …

Review: Life-Cycle, Total-Industry Genetic Improvement Of Feed Efficiency In Beef Cattle: Blueprint For The Beef Improvement Federation, Merlyn K. Nielsen, M. D. Macneil, J. C. M. Dekkers, D. H. Crews Jr., T. A. Rathje, R. Mark Enns, R. L. Weaber

Department of Animal Science: Faculty Publications

On a life-cycle basis, beef animals are able to consume large amounts of low-cost, low-quality forages relative to higher-cost concentrates compared with pigs and chickens. However, of the 3, beef is still more expensive to produce on a cost–per–edible pound basis. Accordingly, there is need for genetic programs and management changes that will improve efficiency, sustainability, and profitability of beef production. Options include improving reproductive rate, reducing feed used for maintenance, or both, while not reducing output. A goal for improving efficiency of feed utilization is to reduce the amount or proportion of feed used for maintenance. Such reduction is …

Genetic Evaluation Of Days To Harvest In Crossbred Lambs, R. M. Lewis, G. C. Marquez, M. H. Davies, D. R. Notter, Rainer Roehe, L. Bünger, G. Simm

Department of Animal Science: Faculty Publications

Days to harvest (DTH) is the number of days a lamb is fed before reaching a target level of fatness. Although economically relevant, this trait has not been thoroughly evaluated in sheep. Most lambs harvested in the United Kingdom are crossbreds sired by purebred terminal sires, with Charollais, Suffolk, and Texel most commonly used. Sires from these breeds were selected on an index designed to increase lean growth while constraining fat. The purpose of this research was to 1) evaluate the effects of index selection in terminal sires on DTH and 2) evaluate the feasibility of incorporating DTH into genetic …

No Evidence For A Relationship Between Hemolymph Ecdysteroid Levels And Female Reproductive Behavior In Schizocosa Wolf Spiders, Reed M. Stubbendieck, Anthony J. Zera, Eileen A. Hebets

Eileen Hebets Publications

This study used radioimmunoassay (RIA) to explore the relationship between levels of hemolymph ecdysteroids and female reproductive behavior in Schizocosa wolf spiders. Specifically, we investigated the relationship between circulating ecdysteroid concentrations in females and 1) likelihood to copulate, or female receptivity [Experiment I— Schizocosa avida (Walckenaer 1837)], 2) time post copulation (Experiment 2— Schizocosa rovneri Uetz & Dondale 1979) and 3) exposure to conspecific male courtship (Experiment 3— Schizocosa uetzi Stratton 1997). In Experiment 1, we expected higher levels of circulating ecdysteroids in receptive versus unreceptive females, based upon prior research demonstrating an increase in receptivity following injections of 20-hydroexyedysone …

Transcriptome Characterization And Detection Of Gene Expression Differences In Aspen (Populus Tremuloides), Hardeep S. Rai, Karen E. Mock, Bryce A. Richardson, Richard C. Cronn, Katherine J. Hayden, Jessica W. Wright, Brian J. Knaus, Paul G. Wolf

Aspen Bibliography

No abstract provided.

Wolf Creek Ranch Aspen Monitoring Report, Paul C. Rogers, Allison Jones, James Catlin, James Shuler, Arthur Morris, Michael Kuhns

Aspen Bibliography

In the summer of 2012 we undertook a landscape assessment of aspen forest conditions at Wolf Creek Ranch (WCR) near Kamas, Utah. Using a geographic information system (GIS) coverage of predicted aspen coverage, fifty systematically selected field "plots" were located and mapped with aspen stands around WCR. Seven plots were eventually discarded from our survey due to lack of aspen cover. Volunteer field crews, mostly WCR homeowners, collected aspen data documenting tree sizes, height/age groups, diameters, reproduction, mortality, browse levels, and browse animal use levels.

Comparison Of Molecular Breeding Values Based On Within- And Across-Breed Training In Beef Cattle, Stephen D. Kachman, Matthew L. Spangler, Gary L. Bennett, Kathryn J. Hanford, Larry Kuehn, Warren M. Snelling, R. M. Thallman, Mahdi Saatchi, Dorian J. Garrick, R. D. Schnabel, Jeremy F. Taylor, E. John Pollak

Department of Animal Science: Faculty Publications

Background: Although the efficacy of genomic predictors based on within-breed training looks promising, it is necessary to develop and evaluate across-breed predictors for the technology to be fully applied in the beef industry. The efficacies of genomic predictors trained in one breed and utilized to predict genetic merit in differing breeds based on simulation studies have been reported, as have the efficacies of predictors trained using data from multiple breeds to predict the genetic merit of purebreds. However, comparable studies using beef cattle field data have not been reported.

Methods: Molecular breeding values for weaning and yearling weight …

Nitrogen Input Effects On Herbage Accumulation And Presence Of Pasture Plant Species, John A. Guretzky, Walter Schacht, Laura Snell, Jonathan Soper, Stephanie Moore, Andrea Watson

Department of Animal Science: Faculty Publications

Long-term responses of pasture plant species to management strategies that vary amount and form of N inputs form a knowledge gap. Our objective was to determine how supplementation of grazing beef cattle (Bos taurus) with corn (Zea mays L.) dried distillers grains plus solubles (DDGS) in unfertilized pasture (SUPP) affects annual herbage accumulation and presence of plant species and functional groups relative to unsupplemented beef cattle on unfertilized (CONT) and N-fertilized (FERT) smooth bromegrass (Bromus inermis Leyss.) pasture. We addressed this objective in the sixth (2010) and seventh (2011) years of a long-term experiment in eastern …

Characterization Of Three Chlorella Sorokiniana Strains In Anaerobic Digested Effluent From Cattle Manure, Naoko Kobayashi, Eric A. Schacht, Austin Barnes, Andrea K. Watson, Julian N. Rosenberg, Galen Erickson, George A. Oyler

Department of Animal Science: Faculty Publications

Chlorella sorokiniana CS-01, UTEX 1230 and UTEX 2714 were maintained in 10% anaerobic digester effluent (ADE) from cattle manure digestion and compared with algal cultivation in Bold’s Basal Medium (BBM). Biomass of CS-01 and UTEX 1230 in ADE produced similar or greater than 280 mg/L after 21 days in BBM, however, UTEX 2714 growth in ADE was suppressed by more than 50% demonstrating a significant species bias to synthetic compared to organic waste-based media. The highest accumulation of protein and starch was exhibited in UTEX 1230 in ADE yielding 34% and 23% ash free dry weight (AFDW), respectively, though fatty …

Effect Of Rate Of Body Weight Gain In Steers During The Stocker Phase. I. Growth, Partitioning Of Fat Among Depots, And Carcass Characteristics Of Growing-Finishing Beef Cattle, E. D. Sharman, P. A. Johnson, C. P. Mcmurphy, A. J. Garmyn, B. J. Pye, G. G. Mafi, C. L. Goad, W. A. Phillips, J. D. Starkey, C. R. Krehbiel, G. W. Horn

Department of Animal Science: Faculty Publications

Two experiments were conducted to examine the effect of growth rate to similar age or BW on fat deposition in stocker cattle grazing dormant native range (DNR) or winter wheat pasture (WP). In each experiment, fall-weaned Angus steers were randomly allotted to 1 of 4 stocker production programs: 1) control, 1.02 kg/d of a 40% CP cottonseed mealbased supplement during grazing of DNR (CON); 2) corn/soybean meal-based supplement fed at 1% of BW during grazing of DNR (CORN); 3) grazing WP at a high stocking rate to achieve a low rate of BW gain (LGWP); and 4) grazing WP at …

Bioinformatics Analysis Of Transcriptome Dynamics During Growth In Angus Cattle Longissimus Muscle, Sonia J. Moisa, Daniel W. Shike, Daniel E. Graugnard, Sandra L. Rodriquez-Zas, Robin E. Everts, Harris A. Lewin, Dan B. Faulkner, Larry L. Berger, Juan J. Loor

Department of Animal Science: Faculty Publications

Transcriptome dynamics in the longissimus muscle (LM) of young Angus cattle were evaluated at 0, 60, 120, and 220 days from early-weaning. Bioinformatic analysis was performed using the dynamic impact approach (DIA) by means of Kyoto Encyclopedia of Genes and Genomes (KEGG) and Database for Annotation, Visualization and Integrated Discovery (DAVID) databases. Between 0 to 120 days (growing phase) most of the highly-impacted pathways (eg, ascorbate and aldarate metabolism, drug metabolism, cytochrome P450 and Retinol metabolism) were inhibited. The phase between 120 to 220 days (finishing phase) was characterized by the most striking differences with 3,784 differentially expressed genes (DEGs). …

Changes In Cell Morphology And The Cellular Localization Of Protein Kinase Dsk1 In Schizosaccharomyces Pombe In Response To Butylated Hydroxyanisole, Jacqueline T. Humphries

Scripps Senior Theses

Dsk1 is the Schizosaccharomyces pombe functional homolog of human SRPK1, an SR protein kinase that regulates localization and function of SR protein splicing factors involved in transcription, alternative splicing, and mRNA export. It has been shown that a Dsk1 deletion strain of S. pombe is sensitive to exposure to butylated hydroxyanisole (BHA), a phenol derivative commonly used as a food preservative. Little is known about how BHA interacts with cells on a functional level, although it has been shown to be cytotoxic and tumorigenic. The aims of this thesis are to study the effect of BHA on eukaryotic cells and …

A Virus-Encoded Potassium Ion Channel Is A Structural Protein In The Chlorovirus Paramecium Bursaria Chlorella Virus 1 Virion, Giulia Romani, Adrianna Piotrowski, Stefan Hillmer, James Gurnon, James L. Van Etten, Anna Morani, Gerhard Thiel, Brigitte Hertel

James Van Etten Publications

Most chloroviruses encode small K+ channels, which are functional in electrophysiological assays. The experimental finding that initial steps in viral infection exhibit the same sensitivity to channel inhibitors as the viral K+ channels has led to the hypothesis that the channels are structural proteins located in the internal membrane of the virus particles. This hypothesis was questioned recently because proteomic studies failed to detect the channel protein in virions of the prototype chlorovirus Paramecium bursaria chlorella virus 1 (PBCV-1). Here, we used a mAb raised against the functional K+ channel from chlorovirus MA-1D to search for the viral K+ channel …

Potassium Ion Channels: Could They Have Evolved From Viruses?1[W], Gerhard Thiel, Anna Moroni, Guillaume Blanc, James L. Van Etten

James Van Etten Publications

Cells communicate among themselves by electrical activity. Sophisticated membrane-embedded proteins, called ion channels, catalyze rapid, selective, and regulated ion fluxes across membranes (Hille, 2001). The resulting membrane currents are responsible for neuronal activity and the systemic propagation of electrical signals in animals. The activity of some channels is important for muscle movement in animals or growth in plants; other channels sense the concentration of physiological signals and modulate key processes in all kinds of eukaryotic cells. Among the many diverse ion channels in higher organisms, K+ channels are among the most important. One feature of K+ channels is that they …

A Path To Success? A Review Of Evolution, Development, And The Predictable Genome By David L. Stern, Hope Hollocher, Charles H. Pence, Grant Ramsey, Michelle M. Wirth

Faculty Publications

No abstract provided.

Delivering Genetic Education And Genetic Counseling For Rare Diseases In Rural Brazil, A.X. Acosta, K Abe-Sandes, R Giugliani, Alan H. Bittles

Research outputs 2013

Brazil is the largest country in Latin America, with an ethnically diverse, Portuguese-speaking and predominantly Roman Catholic population of some 194 million. Universal health care is provided under the Federal Unified Health System (Sistema Único de Saúde) but, as in many other middle and low income countries, access to medical genetics services is limited in rural and remote regions of the country. Since there is no formally recognized Genetic Counseling profession, genetic counseling is provided by physicians, trained either in medical genetics or a related clinical discipline. A comprehensive medical genetics program has been established in Monte Santo, an inland …

Biogeography And Phylogeny Of Aigarchaeota, A Novel Phylum Of Archaea, Gisele Braga Goertz, Brian P. Hedlund

McNair Poster Presentations

‘Aigarchaeota’ is a candidate phylum of Archaea known only by 16S rRNA gene fragments from cultiva­tion-independent microbial surveys and a single composite genome from Candidatus ‘Caldiarchaeum sub­terraneum’, an inhabitant of a subterranean gold mine in Japan. Gene sequences associated with ‘Aigarchaeo­ta’ have been found in a variety of geothermal habits, however a comprehensive analysis of the phylogeny and distribution of ‘Aigarchaeota’ has not yet been done. Public databases were mined for 16S rRNA gene sequences related to known ‘Aigarchaeota’ and a combination of approaches were used to rigorously define the phylogenetic boundaries of the phylum, investigate its distribution, and …