Genetics and Genomics Commons^™

Genetic Variation And Possible Mechanisms Driving The Evolution Of Worldwide Fig Mosaic Virus Isolates, Jeewan Jyot Walia, Anouk Willemsen, Eminur Elci, Kadriye Caglayan, Bryce W. Falk, Luis Rubio

Nebraska Center for Virology: Faculty Publications

Fig mosaic virus (FMV) is a multipartite negative-sense RNA virus infecting fig trees worldwide. FMV is transmitted by vegetative propagation and grafting of plant materials, and by the eriophyid mite Aceria ficus. In this work, the genetic variation and evolutionary mechanisms shaping FMV populations were characterized. Nucleotide sequences from four genomic regions (each within the genomic RNAs 1, 2, 3, and 4) from FMV isolates from different countries were determined and analyzed. FMV genetic variation was low, as is seen for many other plant viruses. Phylogenetic analysis showed some geographically distant FMV isolates which clustered together, suggesting long-distance migration. …

Risk Factors For Early Childhood Infection Of Human Herpesvirus-8 In Zambian Children: The Role Of Early Childhood Feeding Practices, Kay L. Crabtree, Janet M. Wojcicki, Veenu Minhas, David R. Smith, Chipepo Kankasa, Charles D. Mitchell, Charles Wood

Nebraska Center for Virology: Faculty Publications

Background—Human herpesvirus-8 (HHV-8) infection in early childhood is common throughout sub-Saharan Africa with prevalence increasing throughout childhood. Specific routes of transmission have not been clearly delineated, though HHV-8 is present in high concentrations in saliva.

Methods—To understand the horizontal transmission of HHV-8 within households to children we enrolled for cross-sectional analysis, 251 households including 254 children, age two and under, in Lusaka, Zambia. For all children, plasma was screened for HHV-8 and HIV-1 and health and behavioral questionnaires were completed. Multi-level logistic regression analysis was conducted to assess independent factors for HHV-8 infection in children.

Results—Risk factors for HHV-8 infection …

Turnip Crinkle Virus Coat Protein Inhibits The Basal Immune Response To Virus Invasion In Arabidopsis By Binding To The Nac Transcription Factor Tip, Teresa Donze, Feng Qu, Paul Twigg, T. Jack Morris

Nebraska Center for Virology: Faculty Publications

Turnip crinkle virus (TCV) has been shown to interact with a NAC transcription factor, TIP, of Arabidopsis thaliana, via its coat protein (CP). This interaction correlates with the resistance response manifested in TCV-resistant Arabidopsis ecotype Di-17. We report that failure of a mutated CP to interact with TIP triggered the corresponding TCV mutant (R6A) to cause more severe symptoms in the TCV-susceptible ecotype Col-0. We hypothesized that TCV regulates antiviral basal immunity through TIP-CP interaction. Consistent with this hypothesis, we found that the rate of accumulation of R6A was measurably slower than wild-type TCV over the course of an …

High-Sulfur In Beef Cattle Diets: A Review, M. E. Drewnoski, D. J. Pogge, S. L. Hansen

Department of Animal Science: Faculty Publications

While many cattle feeding areas in the United States have long dealt with high sulfate water, increased feeding of ethanol co-products such as distillers grains with solubles to beef cattle has led to a corresponding increase in dietary sulfur. As a result, sulfur metabolism in the ruminant has been the focus of many research studies over the past ten years, and advances in our knowledge have been made. Excessive sulfur in cattle diets may have implications on trace mineral absorption, dry matter intake, and overall cattle growth. This review will focus on what we have learned about the metabolism of …

Qtls Associated With Dry Matter Intake, Metabolic Mid-Test Weight, Growth And Feed Efficiency Have Little Overlap Across 4 Beef Cattle Studies, Mahdi Saatchi, Jonathan E. Beever, Jared E. Decker, Dan B. Faulkner, Harvey C. Freetly, Stephanie L. Hansen, Helen Yampara-Iquise, Kristen A. Johnson, Stephen D. Kachman, Monty S. Kerley, Jaewoo Kim, Daniel D. Loy, Elisa Marques, Holly L. Neibergs, E. John Pollak, Robert D. Schnabel, Christopher M. Seabury, Daniel W. Shike, W. M. Snelling, Matthew L. Spangler, Robert L. Weaber, D. J. Garrick, Jeremy F. Taylor

Department of Animal Science: Faculty Publications

Background: The identification of genetic markers associated with complex traits that are expensive to record such as feed intake or feed efficiency would allow these traits to be included in selection programs. To identify large-effect QTL, we performed a series of genome-wide association studies and functional analyses using 50 K and 770 K SNP genotypes scored in 5,133 animals from 4 independent beef cattle populations (Cycle VII, Angus, Hereford and Simmental × Angus) with phenotypes for average daily gain, dry matter intake, metabolic mid-test body weight and residual feed intake.

Results: A total of 5, 6, 11 and 10 significant …

Variation In Time And Magnitude Of Immune Response And Viremia In Experimental Challenges With Porcine Circovirus 2b, Taylor B. Engle, Erin E. Jobman, Timonthy W. Moural, Autumn M. Mcknite, Justin W. Bundy, Sarah Y. Barnes, Emily H. Davis, Judith A. Galeota, Thomas E. Burkey, Graham S. Plastow, Stephen D. Kachman, Daniel C. Ciobanu

Department of Animal Science: Faculty Publications

Background: Porcine circovirus 2 is the primary agent responsible for inducing a group of associated diseases known as Porcine Circovirus Associated Diseases (PCVAD), which can have detrimental effects on production efficiency as well as causing significant mortality. The objective of this study was to evaluate variation in viral replication, immune response and growth across pigs (n = 974) from different crossbred lines. The approach used in this study was experimental infection with a PCV2b strain of pigs at an average of 43 days of age.

Results: The sequence of the PCV2b isolate used in the challenge was similar with a …

Quantitative Trait Loci For Energy Balance Traits In An Advanced Intercross Line Derived From Mice Divergently Selected For Heat Loss, Larry J. Leamy, Kari Elo, Merlyn K. Nielsen, Stephanie R. Thorn, William Valdar, Daniel Pomp

Department of Animal Science: Faculty Publications

Obesity in human populations, currently a serious health concern, is considered to be the consequence of an energy imbalance in which more energy in calories is consumed than is expended. We used interval mapping techniques to investigate the genetic basis of a number of energy balance traits in an F₁₁ advanced intercross population of mice created from an original intercross of lines selected for increased and decreased heat loss. We uncovered a total of 137 quantitative trait loci (QTLs) for these traits at 41 unique sites on 18 of the 20 chromosomes in the mouse genome, with X-linked QTLs …

Sudden Aspen Decline Report For Spruce Beetle Epidemic And Aspen Decline Management Response Eis, Jim Worrall, Suzanne Marchetti, Gerald E. Rehfeldt

Aspen Bibliography

Aspen is an important component of GMUG’s forests. Over 288,000 ha (712,000 acres) of aspendominated forest type (TAA) occur across the GMUG (Table 1). Just over half (55%) of the aspen forest type is outside wilderness and roadless areas.

Litter Deposition And Nitrogen Return In Rotationally Stocked Smooth Bromegrass Pastures, John A. Guretzky, Walter H. Schacht, Ana B. Wingeyer, Terry J. Klopfenstein, Andrea K. Watson

Department of Animal Science: Faculty Publications

Understanding how management systems impact nutrient cycling is important to pasture sustainability. From 2010 to 2011, we investigated how supplementation of beef cattle (Bos taurus) with corn (Zea mays L.) dried distillers grains plus solubles (DDGS) on unfertilized, rotationally stocked smooth bromegrass (Bromus inermis Leyss.) pasture (SUPP) affected the litter pool, residual herbage mass, litter deposition, and litter quality relative to unsupplemented beef cattle rotationally stocked on unfertilized control (CONT) and N-fertilized (FERT) smooth bromegrass pastures. As hypothesized based on management for greater herbage mass and animal demand during the grazing season, litter deposition was 48% …

Soil Organic Matter And Root And Rhizome Responses To Management Strategies In Smooth Bromegrass Pastures, John A. Guretzky, Ana B. Nuttelman, Walter H. Schacht, Terry J. Klopfenstein, Andrea K. Watson

Department of Animal Science: Faculty Publications

Soil organic matter (SOM) is a key component of pasture production. This is study investigated how management strategies that varied amount and form of N input in a long-term experiment affected concentrations and stocks of total-soil organic C and N, particulate organic carbon (POC), particulate organic nitrogen (PON), root and rhizome mass, C and N contents in topsoil of smooth bromegrass (Bromus inermis Leyss.) pastures with silty clay loam soils in a wet (2010) and dry (2012) year. Management strategies included: (i) unfertilized pasture grazed with unsupplemented beef cattle (CONT); (ii) unfertilized pasture grazed with dried distillers grains plus …

Analysis Of 28 Generations Of Selection For Reproduction, Growth, And Carcass Traits In Swine, W. L. Hsu, Rodger K. Robinson

Department of Animal Science: Faculty Publications

Selection (28 generations, G) in a Large White–Landrace composite population for traits aimed at increasing live pigs born per litter (BA), with additional selection for increased 180-d weight (WT180) and longissimus muscle area (LMA) and decreased back fat (BF10) in the last 8 generations, was practiced. Objectives herein were to estimate genetic and phenotypic responses and genetic parameters (n = 1,883 to 54,174) and to investigate whether a plateau in response for BA occurred. Line 2 (L2) was selected for an index of ovulation rate and embryo survival (G0 to G11), fully formed pigs (FF) per litter (G12 to 14), …

Comparative Digestibility By Cattle Versus Sheep: Effect Of Forage Quality, S. A. Soto-Navarro, R. Lancaster, C. Sankey, B. M. Capitan, B. P. Holland, L. A. Balstad, C. R. Krehbiel

Department of Animal Science: Faculty Publications

The objective was to determine the effect of forage quality on apparent total tract digestibility and ruminal fermentation in cattle versus sheep. Five yearling English crossbred (Hereford × Angus) steers (440.4 ± 35.6 kg of initial BW) and 5 yearling whiteface (Rambouillet × Columbia × Debouillet) wethers (44.4 ± 4.6 kg of initial BW), each fitted with a ruminal cannula, were randomly assigned to 1 of 3 forage sources within ruminant specie, and the study was conducted over 3 periods. For forage source, both animal and period served as the blocking factor with all forage sources represented once within each …

Effects Of Beef Production System On Animal Performance And Carcass Characteristics, C. L. Maxwell, C. R. Lopez, B. K. Wilson, B. T. Johnson, B. C. Bernhard, C. F. O'Neill, D. L. Vanoverbeke, G. G. Mafi, D. L. Step, C. J. Richards

Department of Animal Science: Faculty Publications

The objective of this study was to evaluate conventional (CONV) and natural (NAT) beef production systems from annual pasture through finishing through grazing. Beef steers (n = 180, initial BW = 250 ± 19 kg) were assigned randomly to 2 treatments in the pasture phase. Steers were implanted with 40 mg of trenbolone acetate (TBA), 8 mg estradiol, and 29 mg tylosin tartrate (CONV), or received no implant (NAT). Steers on the 2 treatments grazed wheat or cereal rye for 109 d. Conventional steers had an 18.5% improvement in ADG (1.22 vs. 1.03 kg/d, P < 0.01) and a heavier final BW (385 vs. 366 kg, P < 0.01) compared with NAT steers. Following the pasture phase, steers (n = 160 steers, 5 steers/pen, 8 pens/treatment) were assigned to a 2 × 2 factorial in the feedlot phase. Production system (NAT vs. CONV) was maintained from the pasture phase, and the second factor was 7 vs. 12% low-quality roughage (DM basis, LOW vs. HIGH). During finishing, CONV steers were given 120 mg of TBA and 24 mg estradiol at processing, fed monensin and tylosin, and fed zilpaterol hydrochloride for the last 20 d of the experiment. There were no program × roughage level interactions (P > 0.07). The CONV steers ate …

System And Method For Analyzing Properties Of Meat Using Multispectral Imaging, Jeyamkondan Subbiah, Chris Richard Calkins, Ashok Kumor Samal, Govindarajan Konda Naganathan

Department of Animal Science: Faculty Publications

A system and method for obtaining multispectral images of fresh meat at predetermined wavelength bands at a first time, subjecting the images to analysis in an image analysis system comprising a computer programmed to perform such analysis, and outputting a forecast of meat tenderness at a later point in time. Predetermined key wavelength bands are precorrelated with a high degree of prediction of meat tenderness and/or other properties of meat and are used in the multispectral system and method. A system and method for determining the key wavelengths is also disclosed. The multispectral imaging system and method is suitable for …

Western Immunoblotting In Avian Shell Gland Sample Immunoblotting Methods1, K.K. Hansen, R.J. Kittok, Gautam Sarath, Mary M. Beck

Department of Animal Science: Faculty Publications

Avian shell gland tissue was subjected to Western blot analysis using anti-human estrogen receptor- α antibody H222. Initial attempts to obtain consistent, high-quality blots were unsuccessful because, as it turned out, excessive lipid in tissue preparations interfered with protein separation. Incremental additions of acetone eventually proved to be the critical step in solubilizing lipids and allowing consistent separation of bands on gels. A detailed description of the methodology is presented.

Short-Term Effects Of Lower Oil Dried Distillers Grains With Solubles In Laying Hen Rations, Sheila E. Scheideler, Kathy Hanford, Brett Kreifels

Department of Animal Science: Faculty Publications

Extraction of oil from dried distillers grains has become a common practice among US ethanol producers. The valuable oil has been diverted to markets other than poultry feed, leaving new dried distillers grains with solubles (DDGS) products higher in fiber and purportedly lower in ME. This study compared 3 DDGS products with 10.3, 7.3, or 5.2% ether extract, respectively, with a corn-soy control ration in young Bovan laying hens for a feeding period from 20 to 33 wk of age. The DDGS was fed at the rate of 20% of the ration. Lower oil content of DDGS had no effect …

Ficotylus Laselvae N. Sp. (Tylenchomorpha: Anguinidae) Associated With Ficus Colubrinae In Costa Rica, Robin M. Giblin-Davis, Natsumi Kanzaki, Kerrie A. Davies, Weimin Ye, Yongsan Zeng, Barbara J. Center, Alejandro Esquivel, Thomas O. Powers

Department of Plant Pathology: Faculty Publications

Ficotylus laselvae n. sp. was recovered from under the bracts of figs (syconia) of Ficus colubrinae from La Selva, Costa Rica, during a survey of nematode rainforest biodiversity and is described herein. This is only the second report of an association between the nematode suborder Tylenchina and the sycones of figs. Previous reports of most nematode associates of the sycones of figs have been from the lumen and involved transmission by female fig wasp pollinators (Agaonidae) during pollination/oviposition (e.g., Schistonchus and Parasitodiplogaster spp.). The association between F. laselvae n. sp. and Ficus colubrinae may involve an invertebrate host, …

Viruses As Nanoparticles: Structure Versus Collective Dynamics, S. Sirotkin, A. Mermet, M. Bergoin, V. Ward, James L. Van Etten

James Van Etten Publications

In order to test the application of the “nanoparticle” concept to viruses in terms of low-frequency dynamics, large viruses (140–190 nm) were compared to similar-sized polymer colloids using ultra-small-angle x-ray scattering and very-low-frequency Raman or Brillouin scattering. While both viruses and polymer colloids show comparable highly defined morphologies, with comparable abilities of forming self-assembled structures, their respective abilities to confine detectable acoustic vibrations, as expected for such monodisperse systems, differed. Possible reasons for these different behaviors are discussed.

Viruses Infecting Marine Picoplancton Encode Functional Potassium Ion Channels, Fenja Siotto, Corinna Martin, Oliver Rauh, James L. Van Etten, Indra Schroeder, Anna Moroni, Gerhard Thiel

James Van Etten Publications

Phycodnaviruses are dsDNA viruses, which infect algae. Their large genomes encode many gene products, like small K+ channels, with homologs in prokaryotes and eukaryotes. Screening for K+ channels revealed their abundance in viruses from fresh-water habitats. Recent sequencing of viruses from marine algae or from salt water in Antarctica revealed sequences with the predicted characteristics of K+ channels but with some unexpected features. Two genes encode either 78 or 79 amino acid proteins, which are the smallest known K+ channels. Also of interest is an unusual sequence in the canonical α-helixes in K+ channels. Structural prediction algorithms indicate that the …

The Role Of Angiotensinogen In Atherosclerosis And Obesity, Congqing Wu

Theses and Dissertations--Nutritional Sciences

Angiotensinogen is the only known precursor in the renin-angiotensin system, a hormonal system best known as an essential regulator of blood pressure and fluid homeostasis. Angiotensinogen is sequentially cleaved by renin and angiotensin- converting enzyme to generate angiotensin II. As the major effector peptide, angiotensin II mainly function through angiotensin type 1 receptor.

Angiotensin-converting enzyme inhibitors, angiotensin receptor blockers, and more recently renin inhibitors are widely known as the 3 classic renin-angiotensin system inhibitory drugs against hypertension and atherosclerosis. Here, we developed an array of regents to explore the effects of angiotensinogen inhibition. First, we demonstrated that genetic deficiency of …

Structural And Functional Characterization Of The Mbd2-Nurd Co-Repressor Complex, Megha Desai

Theses and Dissertations

The MBD2-NuRD co-repressor complex is an epigenetic regulator of the developmental silencing of embryonic and fetal β-type globin genes in adult erythroid cells as well as aberrant methylation-dependent silencing of tumor suppressor genes in neoplastic diseases. Biochemical characterization of the MBD2-NuRD complex in chicken erythroid cells identified RbAp46/48, HDAC1/2, MTA1/2/3, p66α/β, Mi2α/β and MBD2 to comprise this multi-protein complex.

In the work presented in Chapter 2, we have pursued biophysical and molecular studies to describe a previously uncharacterized domain of human MBD2 (MBD2_IDR). Biophysical analyses show that MBD2_IDR is an intrinsically disordered region (IDR). Despite this inherent …

Characterization And Identification Of Novel Regulators Of The Synthesis Of Phospholipids, Cunqi Ye

Wayne State University Dissertations

Phospholipids are the most abundant lipids in cell membranes. The synthesis of phospholipids is crucial for cellular membrane biogenesis and nearly all aspects of cellular processes. Understanding the regulation of synthesis of phospholipids is beneficial to our fundamental knowledge of cell biology as well as human health.

Regulation of the synthesis of phospholipids is intensively studied in the yeast S. cerevisiae. Most notably, the synthesis of phospholipids is coordinated with the synthesis of inositol, a precursor of inositol-containing lipids, by controlling expression of the genes encoding phospholipid biosynthetic enzymes. In addition to this well-characterized regulatory circuit controlled by the …

Investigating The Interactions Between Cyanobacteria And Vibrio Parahaemolyticus, Caroline E. Ward

Honors Theses and Capstones

One well-known pathogen that has been the topic of many recent studies is Vibrio parahaemolyticus, which causes thousands of foodborne illnesses a year, mostly from the ingestion of raw or undercooked oysters. It has been shown cyanobacteria can act as a long-term reservoir of Vibrio cholerae, another pathogenic Vibrio, by encasing the cells within mucilaginous sheaths during which Vibrios enter a viable but non-culturable state. In this study we investigated the interaction of V. parahaemolyticus with cyanobacteria to determine whether cyanobacteria aid in the longevity and survival of V. parahaemolyticus. We found that non-pathogenic V. parahaemolyticus …

Regulation Of Immune Response Genes By Vitamin D In Mammary Epithelial Cells With An Emphasis On Cd14, Katrina Marie Simmons

Legacy Theses & Dissertations (2009 - 2024)

Vitamin D is primarily known for its role in bone health, however recently vitamin D has been identified as a potent immunomodulator. Most research studying the effects of vitamin D on immune properties have focused on immune cells. Few have evaluated how vitamin D affects the immune functions of barrier epithelial cells, such as human mammary epithelial (HME) cells, that are exposed to pathogens both locally and systemically. The goals of the studies described in this thesis were to comprehensively and mechanistically evaluate the immune effects of vitamin D metabolites, 1α,25-dihydroxyvitamin D (1,25D) and 25-hydroxyvitamin D (25D), on HME cells. …

Regulation Of Ty1 Retrovirus-Like Transposon Rna Localization And Translation, Ryan Joseph Palumbo

Legacy Theses & Dissertations (2009 - 2024)

Replication of the Ty1 retrovirus-like transposon of the yeast Saccharomyces cerevisiae is stringently regulated to reduce the frequency of deleterious retrotransposition events. However, under stress conditions, Ty1 retrotransposition can lead to adaptive genomic alterations. To characterize host regulation of Ty1 retrotransposition, I analyzed ribosome profiling data and showed that Ty1 RNA is efficiently translated. Moreover, the ribosome biogenesis factors BUD21, DBP7, HCR1, LOC1, MRT4, and PUF6 are required for optimal expression of the Ty1 protein Gag.

Genetic Diversity And Population Structure Of Brook Trout (Salvelinus Fontinalis) In A Remote Adirondack Watershed, Spencer A. Bruce

Legacy Theses & Dissertations (2009 - 2024)

In conservation genetics, the importance of understanding how historical and contemporary processes have contributed to geographic patterns of genetic structure is key to preserving diversity. In New York State there are currently eleven remaining known populations of native brook trout (Salvelnius fontinalis) that inhabit the watersheds for which they are named. These populations are known as "heritage strains", and are currently managed under regulations set by the New York State Department of Environmental Conservation.

Molecular Actions Of The Vitamin D Receptor In Breast Cancer, Erika Laporta

Legacy Theses & Dissertations (2009 - 2024)

1,25-Dihydroxyvitamin D (1,25D) exerts anti-cancer actions through the vitamin D receptor (VDR) but the specific targets that mediate these effects remain to be defined. In these studies, growth and genomic responses to 1,25D were evaluated in a cellular model system derived from mammary tumors generated in VDR knockout (KO) and wildtype (WT) mice. WT145 cells (derived from WT tumors) expressed VDR and were growth inhibited by 1,25D, whereas KO240 cells (derived from VDRKO tumors) lacked VDR and were not growth inhibited by 1,25D. KO240 cell clones stably expressing VDR (KOhVDR cells) were sensitized to 1,25D mediated growth arrest. Genomic profiling …

Heritable Health: An Exploration Of Parental Epigenetics And Their Impact On Individual And Public Health, Brittany F. Hayes 14

Honor Scholar Theses

None

Multiple Roles For Hoxa3 In Regulating Thymus And Parathyroid Differentiation And Morphogenesis In Mouse, Jena L. Chojnowski, Kyoko Masuda, Heidi A. Trau, Kirk Thomas, Mario Capeechi, Nancy R. Manley

Natural Sciences Faculty Publications

Hoxa3 was the first Hox gene to be mutated by gene targeting in mice and is required for the development of multiple endoderm and neural crest cell (NCC)-derived structures in the pharyngeal region. Previous studies have shown that the Hoxa3 null mutant lacks third pharyngeal pouch derivatives, the thymus and parathyroids by E18.5, and organ-specific markers are absent or downregulated during initial organogenesis. Our current analysis of the Hoxa3 null mutant shows that organ-specific domains did undergo initial patterning, but the location and timing of key regional markers within the pouch, including Tbx1, Bmp4 and Fgf8, were altered. …

The Evolutionary Dynamics Of Transcription Factors, Operators, And Their Target Genes Across Prokaryotes, Marc Del Grande

Theses and Dissertations (Comprehensive)

In prokaryotes, transcriptional regulation commonly involves a transcription factor (TF) binding to a particular conserved sequence of nucleotides (operator). Binding elicits a transcriptional response, either activation or repression. The evolution of gene regulation has been identified as a primary driver of species diversity, making it an important area of research. This work examined the dynamics of the interactions between TFs and operators, and TFs and their primary target genes in attempt to assess the rapid evolution of transcriptional regulatory networks (TRNs) across a diverse set of prokaryotes. Using software packages, operator sequences from Escherichia coli K12 were compared to every …