Genetics and Genomics Commons^™

Case Study: Producer Concerns And Perceptions Regarding The Effect Of Methane On Cattle Production And The Environment: A Survey Of Nebraska Producers, B. M. Boyd, A. Jones, Lisa Franzen-Castle, K. Jenkins, Richard J. Rasby, Matt K. Luebbe, Richard R. Stowell, Samodha C. Fernando, Galen E. Erickson

Department of Animal Science: Faculty Publications

Enteric methane production from cattle and its effect on climate change has been a topic of debate. Multiple studies have explored methods to reduce cattle enteric methane production while simultaneously improving performance. However, most strategies developed have not been widely implemented by cattle producers. Knowledge of producer concerns and perceptions on methane production from cattle and its effect on the environment may be limited. Therefore, the objectives of this survey were to determine what Nebraska producers know about methane production by cattle and how it affects performance and to determine whether different age groups, regions of Nebraska, and production size …

Development Of A Row-Crop Tractor Data Acquisition System, James Roeber, Santosh Pitla, Roger M. Hoy, Joe D. Luck

Department of Animal Science: Faculty Publications

Numerous advancements in machinery performance on row-crop agricultural tractors have been made in recent years. Currently, the Organisation for Economic Co-operation and Development (OECD) only tests predetermined points (E.g., max. power, max. torque) for drawbar and hydraulic power. This method of testing has been used for many years with the tractor at a steady state which is usually not typical of row-crop operations. A data acquisition system (DAQ) was designed that records implement energy consumption (E.g., drawbar loading, PTO power, and hydraulic power). The system used a LabVIEW program and a compact data acquisition system (cDAQ) to record data from …

An Application Of Mesh Enrichment Analysis In Livestock, Gota Morota, F. Moreno, James L. Petersen, Daniel C. Ciobanu, K. Tsuyuzaki, I. Nikaido

Department of Animal Science: Faculty Publications

An integral part of functional genomics studies is to assess the enrichment of specific biological terms in lists of genes found to be playing an important role in biological phenomena. Contrasting the observed frequency of annotated terms with those of the background is at the core of overrepresentation analysis (ORA). Gene Ontology (GO) is a means to consistently classify and annotate gene products and has become a mainstay in ORA. Alternatively, Medical Subject Headings (MeSH) offers a comprehensive life science vocabulary including additional categories that are not covered by GO. Although MeSH is applied predominantly in human and model organism …

Optimizing The Use Of Fibrous Residues In Beef And Dairy Diets, James C. Macdonald, G. E. Erickson, P. J. Kononoff, T. J. Klopfenstein

Department of Animal Science: Faculty Publications

Increased corn prices over the past decade have altered land use away from traditional forage in favor of corn. Accordingly, beef and dairy producers have had to adopt non-traditional forage resources into their production systems, many of which have become available as a result of increased corn production. Byproducts of the wet and dry milling industries have been used to replace both corn and forage in beef and dairy diets. Byproducts containing corn bran have large amounts of readily digestible hemicellulose. The use of byproducts may increase milk production, ADG, and G:F in dairy, beef growing, and beef finishing diets, …

Microbial Diversity And Activity In The Nematostella Vectensis Holobiont: Insights From 16s Rrna Gene Sequencing, Isolate Genomes, And A Pilot-Scale Survey Of Gene Expression, Jia Y. Har, Tim Helbig, Ju H. Lim, Samodha C. Fernando, Adam M. Reitzel, Kevin Penn, Janelle R. Thompson

Department of Animal Science: Faculty Publications

We have characterized the molecular and genomic diversity of the microbiota of the starlet sea anemone Nematostella vectensis, a cnidarian model for comparative developmental and functional biology and a year-round inhabitant of temperate salt marshes. Molecular phylogenetic analysis of 16S rRNA gene clone libraries revealed four ribotypes associated with N. vectensis at multiple locations and times. These associates include two novel ribotypes within the ε-Proteobacterial order Campylobacterales and the Spirochetes, respectively, each sharing 99% 16S rRNA identity with Endozoicomonas elysicola and Pseudomonas oleovorans, respectively. Species-specific PCR revealed that these populations persisted in N. vectensis asecually propagated under laboratory …

Sheep Updates 2015 - Moora, Bruce Mullen, Kate Pritchett, Kimbal Curtis, Daniel Real, Jaq Pearson, Lynne Bradshaw, Geoff Lindon, Katherine Davies, Kevin Hepworth, Stephen Lee, Dawson Bradford, Lucy Anderton, Jackie Jarvis, Ben Patrick

Sheep Updates

This session covers thirteen papers from different authors:

1. The Sheep Industry Business Innovation project, Bruce Mullan, Sheep Industry Development Director, Department of Agriculture and Food, Western Australia

2. Western Australian sheep stocktake, Kate Pritchett and Kimbal Curtis, Research Officers, Department of Agriculture and Food, Western Australia

3. Tedera - a perenial forage legume to reduce your supplementary feeding in summer and autumn, Dr. Daniel Real, Senior Plant Breeder, Department of Agriculture and Food, Western Australia

4. National Livestock Identification System (NLIS) for sheep and goats - what is the NLIS database? Jac Pearson, Biosecurity Officer, Department of Agriculture and …

Sheep Updates 2015 - Katanning, Bruce Mullan, Kate Pritchett, Kimbal Curtis, Chris Wilcox, Mike Hyder, Leigh Sonnerman, Lynne Bradshaw, Geoff Lindon, Katherine Davies, Joe Young, Stephen Lee, Ian Robertson, Lucy Anderton, Hayley Norman, Ed Barrett-Lennard, Jackie Jarvis, Ben Patrick

Sheep Updates

This session covers fourteen papers from different authors:

1. The Sheep Industry Business Innovation project, Bruce Mullan, Sheep Industry Development Director, Department of Agriculture and Food, Western Australia

2. Western Australian sheep stocktake, Kate Pritchett and Kimbal Curtis, Research Officers, Department of Agriculture and Food, Western Australia

3. Wool demand and supply - short term volatility, long term opportunities, Chris Wilcox, Principal of Poimena Analysis

4. Lifetime management for maternal ewes, Mike Hyder, Research Officer, Department of Agriculture and Food, Western Australia

5. National Livestock Identification System (NLIS) for sheep and goats - what is the NLIS database? Leigh Sonnermann, …

Cellular Defects Caused By Hypomorphic Variants Of The Bloom Syndrome Helicase Gene Blm, Vivek M. Shastri, Kristina H. Schmidt

Molecular Biosciences Faculty Publications

BACKGROUND: Bloom syndrome is an autosomal recessive disorder characterized by extraordinary cancer incidence early in life and an average life expectancy of ~27 years. Premature stop codons in BLM, which encodes a DNA helicase that functions in DNA double-strand-break repair, make up the vast majority of Bloom syndrome mutations, with only 13 single amino acid changes identified in the syndrome. Sequencing projects have identified nearly one hundred single nucleotide variants in BLM that cause amino acid changes of uncertain significance.

METHODS AND RESULTS: Here, in addition to identifying five BLM variants incapable of complementing certain defects of Bloom syndrome cells, …

Exogenous Administration Of Lipids To Steers Alters Aspects Of The Innate Immune Response To Endotoxin Challenge, Nicole C. Burdick Sanchez, Jeffery A. Carroll, Janet R. Donaldson, Joe O. Buntyn, Ty B. Schmidt

Department of Animal Science: Faculty Publications

This study examined the effects of increasing energy availability from both dextrose and lipid treatments on the proinflammatory response to LPS in Holstein steers. Steers were randomly assigned to one of three groups: saline at 0.5 ml/ kg body weight (Control) or 50% dextrose [0.5 ml/kg body weight (Dextrose) to mimic calm cattle’s response to LPS] administered immediately prior to LPS (0.5 mg/kg body weight at 0 h) or continuous lipid emulsion infusion from –1 to 6 h [Intralipid 20% (Baxter, Deerfield, IL USA); 0.5 ml/kg/hr (Lipid) to mimic temperamental cattle]. Concentrations of non-esterified fatty acids (NEFA) were greater in …

Mesh Ora Framework: R/Bioconductor Packages To Support Mesh Over-Representation Analysis, Koki Tsuyuzaki, Gota Morota, Manabu Ishii, Takeru Nakazato, Satoru Miyazaki, Itoshi Nikaido

Department of Animal Science: Faculty Publications

Background: In genome-wide studies, over-representation analysis (ORA) against a set of genes is an essential step for biological interpretation. Many gene annotation resources and software platforms for ORA have been proposed. Recently, Medical Subject Headings (MeSH) terms, which are annotations of PubMed documents, have been used for ORA. MeSH enables the extraction of broader meaning from the gene lists and is expected to become an exhaustive annotation resource for ORA. However, the existing MeSH ORA software platforms are still not sufficient for several reasons.

Results: In this work, we developed an original MeSH ORA framework composed of six types of …

A Cooperative Study On The Standardized Total-Tract Digestible Phosphorus Requirement Of Twenty-Kilogram Pigs, O. Adeola, M. J. Azain, S. D. Carter, T. D. Crenshaw, M. J. Estienne, B. J. Kerr, M. D. Lindemann, C. V. Maxwell, P. S. Miller, M. C. Shannon, E. Van Heugten

Department of Animal Science: Faculty Publications

A cooperative study comprising growth performance, bone mineralization, and nutrient balance experiments was conducted at 11 stations to determine the standardized total-tract digestible (STTD) P requirement of 20-kg pigs using broken-line regression analysis. Monocalcium phosphate and limestone were added to a corn–soybean meal–based diet at the expense of cornstarch to establish 6 concentrations of STTD P from 1.54 to 5.15 g/kg in increments of 0.62 g/kg at a constant Ca:total P of 1.52:1.0. Diets were fed to 936 pigs (average initial BW of 19 kg) in 240 pens for 20 replicate pens of barrows and 20 replicate pens of gilts …

Yield And Forage Value Of A Dual-Purpose Bmr-12 Sorghum Hybrid, Melinda K. Yerka, Andrea K. Pederson, J. J. Toy, Galen E. Erickson, Jeffrey F. Pedersen, Rob B. Mitchell

Department of Animal Science: Faculty Publications

Grain sorghum [Sorghum bicolor (L.) Moench] is an important crop for rainfed production systems with 2.7 million ha grown in the United States in 2013. The brown-midrib (bmr) mutations, especially bmr-12, have resulted in low stover lignin and high fiber digestibility without reducing grain yield in some sorghum lines. However, the effect of the bmr trait on beef cattle (Bos taurus) performance when grazing crop residue is unknown. Our objectives were to validate previous small-plot results reporting no grain yield difference between near-isogenic bmr-12 (BMR) and wild-type control (CON) A Wheatland × R

Tx430 …

Cattle With Increased Severity Of Bovine Respiratory Disease Complex Exhibit Decreased Capacity To Protect Against Histone Cytotoxicity, J. A. Matera, B. K. Krehbiel, J. A. Hernandez Gifford, D. L. Step, C. R. Krehbiel, C. A. Gifford

Department of Animal Science: Faculty Publications

Bovine respiratory disease complex (BRDC) is the leading cause of morbidity and mortality in feedlot cattle. Significant inflammation and lesions are often observed in lungs of infected cattle. During acute inflammatory responses, histones contribute to mortality in rodents and humans and serum proteins can protect against histone-induced cytotoxicity. We hypothesized that cattle experiencing chronic or fatal cases of BRDC have reduced ability to protect against cytotoxic effects of histones. Serum samples were collected from 66 bull calves at the time of normal feedlot processing procedures. Animals were retrospectively assigned to groups consisting of calves never treated for BRDC (control [CONT]; …

The Effects Of Technology Use In Feedlot Production Systems On Feedlot Performance And Carcass Characteristics, C. L. Maxwell, B. C. Wilson, C. F. O'Neill, B. K. Wilson, C. G. Hixon, C. L. Haviland, A. N. Grimes, M. S. Calvo-Lorenzo, D. L. Vanoverbeke, G. G. Mafi, C. J. Richards, D. L. Step, B. P. Holland, C. R. Krehbiel

Department of Animal Science: Faculty Publications

The objectives of this study were to examine the effects of feedlot production systems with and without the use of a β-adrenergic agonist compared to an all-natural production program on feedlot performance and carcass characteristics. Crossbred beef steers (n = 336; initial BW = 379 ± 8 kg) were randomized to 1 of 3 treatments in a randomized complete block design (RCBD; 14 steers/pen; 8 pens/treatment). Treatments consisted of an all-natural treatment (NAT), a conventional treatment (CONV), and a conventional treatment with a β-agonist (CONV-Z). All treatments were fed the same basal diet with NAT cattle receiving no growth promoting …

Large Dsdna Chloroviruses Encode Diverse Membrane Transport Proteins, Gerhard Thiel, Timo Greiner, David Dunigan, Anna Moroni

James Van Etten Publications

Many large DNA viruses that infect certain isolates of chlorella-like green algae (chloroviruses) are unusual because they often encode a diverse set of membrane transport proteins, including functional K+ channels and aquaglyceroporins as well as K+ transporters and calcium transporting ATPases. Some chloroviruses also encode putative ligand-gated-like channel proteins. No one protein is present in all of the chloroviruses that have been sequenced, but the K+ channel is the most common as only two chloroviruses have been isolated that lack this complete protein. This review describes the properties of these membrane-transporting proteins and suggests possible physiological functions and evolutionary histories …

Gene Expression And Alzheimer's Disease: Evaluation Of Gene Expression Patterns In Brain And Blood For An Alzheimer's Disease Mouse Model, Amanda Hazy

Senior Honors Theses

Previous studies have established a causative role for altered gene expression in development of Alzheimer’s disease (AD). These changes can be affected by methylation and miRNA regulation. In this study, expression of miRNA known to change methylation status in AD was assessed by qPCR. Genome-wide expression changes were determined by RNA-sequencing of mRNA from hippocampus and blood of control and AD mice. The qPCR data showed significantly increased expression of Mir 17 in AD, and sequencing data revealed 230 genes in hippocampus, 58 genes in blood, and 8 overlapping genes showing significant differential expression (p value ≤ 0.05). Expression data …

The Role Of Rnai In Downregulation Of Physcomitrella Patens Defense Genes And The Preliminary Steps Of Peg Mediated Transformation Of Mosses, Adam Beswick

Undergraduate Honors Thesis Collection

When attacked by a pathogen, the moss Physcomitrella patens will undergo both a hypersensitive response (HR) as well as a systematic acquired resistance (SAR) response. The SAR response turns on genes that ready the plant for future pathogen attacks. The hormone jasmonic acid (JA) is one of the products of SAR response in P. patens. In this study interference RNA (RNAi) was used to decrease gene expression of the allene oxide cyclase (ACe) gene, a key gene in the production pathway of JA. Using quantitative reverse transcriptase polymerase chain reaction (qRT-PCR), RNAi was found to significantly lower ACC gene levels …

Quaking Aspen At The Residential-Wildland Interface: Elk Herbivory Hinders Forest Conservation., Paul C. Rogers, Allison Jones, James Catlin, James Shuler, Arthur Morris, Michael R. Kuhns

Aspen Bibliography

T: Quaking aspen (Populus tremuloides) forests are experiencing numerous impediments across North America. In the West, recent drought, fire suppression, insects, diseases, climate trends, inappropriate management, and ungulate herbivory are impacting these high biodiversity forests. Additionally, ecological tension zones are sometimes created at residential-wildland interfaces with divergent management directives. For example, private conservation reserves bordering public land may be degraded from browsing where game species find refuge from hunting and plentiful forage. We examined putative herbivore impacts to nearly pure aspen forests at Wolf Creek Ranch (WCR), a sparsely developed residential landscape in northern Utah. Forty-three one-hectare monitoring …

Altered Fire Regimes And The Persistence Of Quaking Aspen In The Rocky Mountains: A Literature Review, Aaron Rosenblum

Aspen Bibliography

The persistence of quaking aspen (Populus tremuloides Michx.) is of significant importance to land managers in the Rocky Mountain region. Fire suppression in the past century has been implicated as a mechanism influencing aspen population dynamics, as aspen are generally considered an early seral disturbance adapted species. The heterogeneity of aspen community assemblages and fire regimes makes it difficult to discern what the result of fire suppression has been at large spatial and temporal scales. Decision makers should investigate the questions at hand at the stand level in their study location to best determine the mechanisms at play, as well …

Long-Term Vegetation Change In Utah's Henry Mountains: A Study In Repeat Photography, Charles E. Kay

Aspen Bibliography

An extensive search was conducted of archival and other sources to locate as many historical photographs as possible for the Henry Mountains in south-central Utah. Those images were then taken into the field, the original camera stations relocated, and modern pictures made of the historical scenes to evaluate long-term vegetation change and land management activities. In all, 626 repeat photo sets were compiled—608 by the author and 18 by Earl Hindley. This book includes 126 photo sets that were representative of the areas studied.