Genetics and Genomics Commons^™

The Role Of Direct-Fed Microbials In Conventional Livestock Production, Joe O. Buntyn, Ty Schmidt, David J. Nisbet, Todd R. Callaway

Department of Animal Science: Faculty Publications

Supplementation of direct-fed microbials (DFM) as a means to improve the health and performance of livestock has generated significant interest over the past 15+ years. A driving force for this increased interest in DFM is to reduce or eliminate the use of low-dose antibiotics in livestock production. This increased attention toward DFM supplementation has generated an extensive body of research. This effort has resulted in conflicting reports. Although there has been considerable variation in the design of these studies, one of the main causes for this lack of consistency may be attributed to the variation in the experimental immune challenge …

Determination Of Yolk Contamination In Liquid Egg White Using Raman Spectroscopy, K. Cluff, G. Konda Naganathan, D. Jonnalagada, I. Mortensen, R. Wehling, Jeyamkondan Subbiah

Department of Animal Science: Faculty Publications

Purified egg white is an important ingredient in a number of baked and confectionary foods because of its foaming properties. However, yolk contamination in amounts as low as 0.01% can impede the foaming ability of egg white. In this study, we used Raman spectroscopy to evaluate the hypothesis that yolk contamination in egg white could be detected based on its molecular optical properties. Yolk contaminated egg white samples (n = 115) with contamination levels ranging from 0% to 0.25% (on weight basis) were prepared. The samples were excited with a 785 nm laser and Raman spectra from 250 to 3,200 …

Biogeographical Patterns In The Hard-Tick Genus Amblyomma Koch 1844 (Acari: Ixodidae), Matthew H. Seabolt

College of Graduate Studies: Theses & Dissertations

Amblyomma Koch is a genus of hard-ticks with approximately 130 species. Its geographical range is typical for organisms with a Gondwanan origin. A majority of these species are endemic to the Neo- and Afrotropical regions, with the remaining taxa dispersed throughout Southeast Asia, Australia and the Pacific islands. Based on this distribution, we hypothesize that the genus dispersal patterns will mirror the fragmentation and continental drift of the Gondwanan supercontinent. Maximum parsimony, maximum likelihood, Bayesian inference and node-dating analyses of nuclear 18S rDNA gene sequences reveal a more recent origin and radiation patterns within the genus and suggest that Amblyomma …

A Mechanistic Study Of An Ipsc Model For Leigh’S Disease Caused By Mtdna Mutataion (8993 T>G), John P. Galdun

Theses and Dissertations

Mitochondrial diseases encompass a broad range of devastating disorders that typically affect tissues with high-energy requirements. These disorders have been difficult to diagnose and research because of the complexity of mitochondrial genetics, and the large variability seen among patient populations. We have devised and carried out a mechanistic study to generate a cell based model for Leigh’s disease caused by mitochondrial DNA mutation 8993 T>G. Leigh’s disease is a multi-organ system disorder that depends heavily on the mutation burden seen within various tissues. Using new reprogramming and sequencing technologies, we were able to show that Leigh’s disease patient fibroblasts …

Power Analysis In Applied Linear Regression For Cell Type-Specific Differential Expression Detection, Edmund Glass

Theses and Dissertations

The goal of many human disease-oriented studies is to detect molecular mechanisms different between healthy controls and patients. Yet, commonly used gene expression measurements from any tissues suffer from variability of cell composition. This variability hinders the detection of differentially expressed genes and is often ignored. However, this variability may actually be advantageous, as heterogeneous gene expression measurements coupled with cell counts may provide deeper insights into the gene expression differences on the cell type-specific level. Published computational methods use linear regression to estimate cell type-specific differential expression. Yet, they do not consider many artifacts hidden in high-dimensional gene expression …

Genomic Comparisons And Genome Architecture Of Divergent Trypanosoma Species, Katie Bradwell

Theses and Dissertations

Virulent Trypanosoma cruzi, and the non-pathogenic Trypanosoma conorhini and Trypanosoma rangeli are protozoan parasites with divergent lifestyles. T. cruzi and T. rangeli are endemic to Latin America, whereas T. conorhini is tropicopolitan. Reduviid bug vectors spread these parasites to mammalian hosts, within which T. rangeli and T. conorhini replicate extracellularly, while T. cruzi has intracellular stages. Firstly, this work compares the genomes of these parasites to understand their differing phenotypes. Secondly, genome architecture of T. cruzi is examined to address the effect of a complex hybridization history, polycistronic transcription, and genome plasticity on this organism, and study its highly …

Synthetic Biology For Autotrophic And Heterotrophic Production Of Ethanol, Nathanael Braselton

Electronic Theses and Dissertations

Growing energy demand and rising levels of greenhouse gases has put massive strain on the global environment. Alternatives to fossil fuels are being developed in an attempt to curb climate change. Biotechnology has made large strides in order to create a completely renewable energy source by genetically modifying microbes to produce biofuels and other “green” high value compounds. In this thesis project, (1) E. coli ATCC9637 (E. coli W) was genetically modified to produce bioethanol from beet juice which contains mainly sucrose. The ethanol productivity by engineered E. coli W was 18.8 mg/L/H/OD₆₀₀.
(2) Cyanobacterium Anabaena sp. PCC7120 …

Plasma-Activated Air Mediates Plasmid Dna Delivery In Vivo, Chelsea M. Edelblute, Loree C. Heller, Muhammad A. Malik, Anna Bulysheva, Richard Heller

Bioelectrics Publications

Plasma-activated air (PAA) provides a noncontact DNA transfer platform. In the current study, PAA was used for the delivery of plasmid DNA in a 3D human skin model, as well as in vivo. Delivery of plasmid DNA encoding luciferase to recellularized dermal constructs was enhanced, resulting in a fourfold increase in luciferase expression over 120 hours compared to injection only (P < 0.05). Delivery of plasmid DNA encoding green fluorescent protein (GFP) was confirmed in the epidermal layers of the construct. In vivo experiments were performed in BALB/c mice, with skin as the delivery target. PAA exposure significantly enhanced luciferase expression levels 460-fold in exposed sites compared to levels obtained from the injection of plasmid DNA alone (P < 0.001). Expression levels were enhanced when the plasma reactor was positioned more distant from the injection site. Delivery of plasmid DNA encoding GFP to mouse skin was confirmed by immunostaining, where a 3-minute exposure at a 10 mm distance displayed delivery distribution deep within the dermal layers compared to an exposure at 3 mm where GFP expression was localized within the epidermis. Our findings suggest PAA-mediated delivery warrants further exploration as an alternative approach for DNA transfer for skin targets.

Thermal Assisted In Vivo Gene Electrotransfer, Amy Donate, Anna Bulysheva, Chelsea Edelblute, Derrick Jung, A. Malik, Siqi Quo, Niculina Burcus, Karl Schoenbach, Richard Heller

Bioelectrics Publications

Gene electrotransfer is an effective approach for delivering plasmid DNA to a variety of tissues. Delivery of molecules with electric pulses requires control of the electrical parameters to achieve effective delivery. Since discomfort or tissue damage may occur with high applied voltage, the reduction of the applied voltage while achieving the desired expression may be an important improvement. One possible approach is to combine electrotransfer with exogenously applied heat. Previous work performed in vitro demonstrated that increasing temperature before pulsing can enhance gene expression and made it possible to reduce electric fields while maintaining expression levels. In the study reported …

Genomics Of Mature And Immature Olfactory Sensory Neuron, Timothy S. Mcclintock

Physiology Research Data

The Excel file contains probabilistic predictions of which genes are expressed in mature versus immature olfactory sensory neurons, versus the sum of all other cell types in the olfactory epithelium. Responses to bulbectomy, which differentially affects mature and immature olfactory sensory neurons, supports these predictions.

Mouse Osns Express 10,000 Genes, Timothy S. Mcclintock

Physiology Research Data

This Excel file (both full and compressed versions are available) contains processed GeneChip microarray data that allows predictions of whether a gene is expressed in mature olfactory sensory neurons of mice.

An Alignment-Free "Metapeptide" Strategy For Metaproteomic Characterization Of Microbiome Samples Using Shotgun Metagenomic Sequencing, Damon H. May, Emma Timmins-Schiffman, Molly P. Mikan, H. Rodger Harvey, Elhanan Borenstein, Brook L. Nunn, William S. Noble

OES Faculty Publications

In principle, tandem mass spectrometry can be used to detect and quantify the peptides present in a microbiome sample, enabling functional and taxonomic insight into microbiome metabolic activity. However, the phylogenetic diversity constituting a particular microbiome is often unknown, and many of the organisms present may not have assembled genomes. In ocean microbiome samples, with particularly diverse and uncultured bacterial communities, it is difficult to construct protein databases that contain the bulk of the peptides in the sample without losing detection sensitivity due to the overwhelming number of candidate peptides for each tandem mass spectrum. We describe a method for …

Genetic Structure And Diversity Of Channel Catfish (Ictalurus Punctatus) In Three Large Midwestern Rivers, Vaclav Alexei Sotola

Masters Theses

Little information is available regarding the genetic structure and diversity of sportfishes in large rivers, which can be vital to continuing the sustainable exploitation of these fisheries. Additionally, impoundments often have vast impacts on riverine systems. These impacts include altering the flow regime, changing the nutrient load, and preventing migratory fish from reaching their spawning grounds. If fishes are prevented from reaching their spawning grounds, their genetic diversity and structuring could begin to change relative to historic measures, potentially decreasing their fitness and ability to survive. I screened microsatellite loci to assess the genetic population structure and diversity of channel …

Vanadium Toxicological Potential Versus Its Pharmacological Activity: New Developments And Research, Agnieszka Ścibior, Juan Llopis, Alvin A. Holder, Mario Altamirano-Lozano

Chemistry & Biochemistry Faculty Publications

Scibior, A., Llopis, J., Holder, A. A., & Altamirano-Lozano, M. (2016). Vanadium toxicological potential versus its pharmacological activity: New developments and research. Oxidative Medicine and Cellular Longevity, 2016, 1-2. doi: 10.1155/2016/7612347

Functional Consequences Of Mtdna Methylation On Mitochondrial Transcription Factor Binding And Transcription Initiation, Elliot N. Burton

Theses and Dissertations

The role of cytosine modifications on nuclear transcription has been well characterized, but the function of DNA methylation in the mitochondrial genome has not been determined. Previous studies conducted by the Taylor laboratory have shown overexpression of the mitochondrial isoform of DNMT1 leads to strand-specific changes in gene expression. Here, we show that increased mtDNMT1 expression leads to an increase in the polycistronic transcript encoding the ND1 and Cox1 sequences. In order to understand the mechanistic basis of these changes, we investigated the effects of CpG methylation in the heavy strand promoter on transcription initiation and TFAM binding. Methylation was …

Characterizing The Oncogenic Properties Of C-Terminal Binding Protein, Evan T. Sumner

Theses and Dissertations

The paralogous C-terminal binding proteins (CtBP) 1 and 2 are evolutionarily conserved transcriptional coregulators that target and disrupt the expression of several genes essential for multiple cellular processes critical to regulating tumor formation. CtBP’s ability to govern the transcription of genes necessary for apoptosis, tumor suppression, invasion/migration and EMT gives rise to its oncogenic activities. Both isoforms of CtBP are found to be overexpressed in cancers including colorectal, pancreatic, ovarian, and breast, with higher levels correlating to lower overall median survival. Although multiple lines of evidence suggest CtBP plays a role in tumorigenesis, it has never been formally characterized as …

Conserved Intramolecular Interactions Maintain Myosin Interacting-Heads Motifs Explaining Tarantula Muscle Super-Relaxed State Structural Basis, Lorenzo Alamo, Dan Qi, Willy Wriggers, Antonio Pinto, Jingui Zhu, Aivett Bilbao, Richard E. Gillilan, Songnian Hu, Raúl Padrón

Mechanical & Aerospace Engineering Faculty Publications

Tarantula striated muscle is an outstanding system for understanding the molecular organization of myosin filaments. Three-dimensional reconstruction based on cryo-electron microscopy images and single-particle image processing revealed that, in a relaxed state, myosin molecules undergo intramolecular head head interactions, explaining why head activity switches off. The filament model obtained by rigidly docking a chicken smooth muscle myosin structure to the reconstruction was improved by flexibly fitting an atomic model built by mixing structures from different species to a tilt-corrected 2-nm three-dimensional map of frozen-hydrated tarantula thick filament. We used heavy and light chain sequences from tarantula myosin to build a …

High And Dry: Post-Fire Tree Seedlingestablishment In Subalpine Forestsdecreases With Post-Fire Drought Andlarge Stand-Replacing Burn Patches, Brian J. Harvey, Daniel C. Donato, Monica G. Turner

Aspen Bibliography

Aim: Climate warming and increased wildfire activity are hypothesized to catalyse biogeographical shifts, reducing the resilience of fire-prone forests world-wide. Two key mechanisms underpinning hypotheses are: (1) reduced seed availability in large stand-replacing burn patches, and (2) reduced seedling establishment/survival after post-fire drought. We tested for regional evidence consistent with these mechanisms in an extensive fire-prone forest biome by assessing post-fire tree seedling establishment, a key indicator of forest resilience.

Location: Subalpine forests, US Rocky Mountains.

Methods: We analysed post-fire tree seedling establishment from 184 field plots where stand-replacing forest fires were followed by varying post-fire climate conditions. Generalized linear …

Sample Size Estimation For Genomics Experiments With Dependent End Points, Desmond Koomson

Open Access Theses & Dissertations

In typical genomics studies involving numerous association tests of gene mutations with a disease, error rate control via multiplicity adjustment is paramount because even if all genes were to be non-differentially associated, we would still make some false positives. Many methods exist that incorporate the control of multiplicity for normally distributed endpoints in sample size estimation, but none addresses the issue for non-normally correlated endpoints.

One common practice in the literature is to assume an equal correlation among all differentially associated or expressed genes, thereby using the generalized binomial or beta-binomial model to compute the comparison-wise power of detecting these …

The Role Of Capillaries In The Lesser Ailments Of Old Age And In Alzheimer's Disease And Vascular Dementia: The Potential Of Pro-Therapeutic Angiogenesis, Charles T. Ambrose

Microbiology, Immunology, and Molecular Genetics Faculty Publications

Apart from chronic diseases (arthritis, diabetes, etc.), old age is generally characterized by three lesser ailments: muscle weakness, minor memory lapses, and cold intolerance. This trio of complaints may have a common, underlying cause, namely, the age-associated reduced microcirculation in muscles, brain, skin, and elsewhere in the body. The Angiogenesis Hypothesis proposes that old age is in part a deficiency disease due to the decline in angiogenic (AG) factors, resulting in a reduced capillary density (CD) throughout the body. Over fifty published papers document waning levels of AG factors and/or decreased CD in various organ systems of aged animals and …

Causes And Consequences Of Variation In Female Mate Choice And Its Relation To Sexual Conflict In Drosophila Melanogaster, David Cs Filice

Theses and Dissertations (Comprehensive)

Female mate choice is a significant driving force of evolutionary change and can explain the evolution of exaggerated male traits and/or displays, and dimorphism between the sexes. Females are thought to choose mates based on the greatest provision of direct or indirect benefits. Despite this, we often still see substantial individual variation in female mate choice behaviours both within and across populations. Recent studies suggest that female mate choice is a complex decision-making process that involves many context-dependent factors. However, the precise sources of this variation, such as previous mating experience, are not completely understood. In Drosophila melanogaster, mating …

Recapitulating Cross-Species Transmission Of Sivcpz To Humans Using Humanized-Blt Mice, Zhe Yuan, Guobin Kang, Fangrui Ma, Wuxun Lu, Wenjin Fan, Christine M. Fennessey, Brandon F. Keele, Qingsheng Li

Nebraska Center for Virology: Faculty Publications

The origins of HIV-1 have been widely accepted to be the consequence of simian immunodeficiency viruses from wild chimpanzees (SIVcpz) crossing over to humans. However, there has not been any in vivo study of SIVcpz infection of humans. Also, it remains largely unknown why only specific SIVcpz strains have achieved cross-species transmission and what transmission risk might exist for those SIVcpz strains that have not been found to infect humans. Closing this knowledge gap is essential for better understanding cross-species transmission and predicting the likelihood of additional cross-species transmissions of SIV into humans. Here we show hu-BLT mice are susceptible …

High Glucose Induces Reactivation Of Latent Kaposi’S Sarcoma-Associated Herpesvirus, Fengchun Ye, Yan Zeng, Jingfeng Sha, Tiffany Jones, Kurt Kuhne, Charles Wood, Shou-Jiang Gao

Nebraska Center for Virology: Faculty Publications

High prevalence of Kaposi’s sarcoma (KS) is seen in diabetic patients. It is unknown if the physiological condition of diabetes contributes to KS development. We found elevated levels of viral lytic gene expression when Kaposi’s sarcoma-associated herpesvirus (KSHV) infected cells were cultured in high glucose medium. To demonstrate the association between high glucose and KSHV replication, we xeno29

grafted telomerase-immortalized human umbilical vein endothelial cells that are infected with KSHV (TIVE-KSHV) into hyperglycemic and normal nude mice. The injected cells expressed significantly higher levels of KSHV lytic genes in hyperglycemic mice than in normal mice. We further demonstrated that high …

Persistent Low-Level Replication Of Sivδnef Drives Maturation Of Antibody And Cd8 T Cell Responses To Induce Protective Immunity Against Vaginal Siv Infection, Sama Adnan, R. Keith Reeves, Jacqueline Gillis, Fay E. Wong, Yi Yu, Jeremy V. Camp, Qingsheng Li, Michelle Connole, Yuan Li, Michael Piatak Jr., Jeffrey D. Lifson, Wenjun Li, Brandon F. Keele, Pamela A. Kozlowski, Ronald C. Desrosiers, Ashley T. Haase, R. Paul Johnson

Nebraska Center for Virology: Faculty Publications

Defining the correlates of immune protection conferred by SIVΔnef, the most effective vaccine against SIV challenge, could enable the design of a protective vaccine against HIV infection. Here we provide a comprehensive assessment of immune responses that protect against SIV infection through detailed analyses of cellular and humoral immune responses in the blood and tissues of rhesus macaques vaccinated with SIVΔnef and then vaginally challenged with wild-type SIV. Despite the presence of robust cellular immune responses, animals at 5 weeks after vaccination displayed only transient viral suppression of challenge virus, whereas all macaques challenged at weeks 20 and 40 post-SIVΔnef …

Characterization Of Insertion Sequence Is605 In Halanaerobium Hydrogeniformans, Michael C. Sadler

Masters Theses

"Insertion sequences are the smallest prokaryotic transposable elements. These genes play a significant evolutionary role by promoting genome plasticity. Insertion sequences are highly diverse elements that have largely been uncharacterized. As such, the ability to accurately identify, annotate, and infer genomic impact of insertion sequences is lacking. The study of new insertion sequences contributes knowledge to their annotation and evolution. Halanaerobium hydrogeniformans is a unique organism with an abnormally high number of insertion sequences. A family of insertion sequences, IS200/605, showed several interesting distinctions from other elements in the genome, including severe open reading frame degradation, and was characterized in …

The Behavioral, Biochemical And Genetic Effects Of Sleep Deprivation In Zebrafish (Danio Rerio), Jade Catherine Boykin

College of Graduate Studies: Theses & Dissertations

Vertebrate sleep is a universal phenomenon and encompasses an array of conserved behavioral and physiological characteristics. Studies of sleep in humans have shown that sleep deprivation leads to adverse effects to human health and additional stress. Teleosts have emerged as a useful model species to study the vertebrate stress response, given its stress axis has high levels of homology with the mammals, including humans. For this study, the behavior of zebrafish (Danio rerio) subjected to acute (24 hours) and chronic (20 days) extended light exposure was monitored and whole-body cortisol was analyzed as an indication of activation of …

A Comprehensive Benchmarking Study Of Protocols And Sequencing Platforms For 16s Rrna Community Profiling, Rosalinda D’Amore, Umer Zeeshan Ijaz, Melanie Schirmer, John G. Kenny, Richard Gregory, Alistair C. Darby, Migun Shakya

Dartmouth Scholarship

In the last 5 years, the rapid pace of innovations and improvements in sequencing technologies has completely changed the landscape of metagenomic and metagenetic experiments. Therefore, it is critical to benchmark the various methodologies for interrogating the composition of microbial communities, so that we can assess their strengths and limitations. The most common phylogenetic marker for microbial community diversity studies is the 16S ribosomal RNA gene and in the last 10 years the field has moved from sequencing a small number of amplicons and samples to more complex studies where thousands of samples and multiple different gene regions are interrogated. …

Ecology Of Two Reintroduced Black Bear Populations In The Central Appalachians, Sean Mccarthy Murphy

Theses and Dissertations--Animal and Food Sciences

Reintroduced populations are vulnerable to demographic and environmental stochasticity, deleterious genetic effects, and reduced population fitness, all of which can increase extinction probability. Population viability is principle to determining the status of reintroduced populations and for guiding management decisions. To attempt to reestablish black bear (Ursus americanus) populations in the central Appalachians, two reintroductions using small founder groups occurred during the 1990s in the Big South Fork area along the Kentucky-Tennessee border (BSF) and in the Jefferson National Forest along the Kentucky-Virginia border (KVP). My objectives were to estimate demographic and genetic parameters, and to evaluate long-term viability …

Endohelminth Parasites Of Some Midwater And Benthopelagic Stomiiform Fishes From The Northern Gulf Of Mexico, Michael J. Andres, Mark S. Peterson, Robin M. Overstreet

Gulf and Caribbean Research

: Mesopelagic fishes represent significant ecological links between mesozooplankton and the larger pelagic squids, fishes, and marine mammals. As such, these fishes also play a significant role as intermediate or paratenic hosts for parasites that require a crustacean intermediate host and mature in marine mammals or pelagic fishes. We examined a total of 208 individuals representing 5 species of Sternoptychidae and 88 individuals representing 2 species of Phosichthyidae from 20 locations in the northern Gulf of Mexico (nGOM). Six of the 7 species we examined are mesopelagic and one species was benthopelagic. We found the larval stages of Anisakis brevispiculata …

Draft Genome Sequences For Seven Streptococcus Parauberis Isolates From Wild Fish In The Chesapeake Bay, Ashley Haines, Emily Nebergall, Elvira Besong, Kimaya Council, Onaysha Lambert, David Gauthier

Biological Sciences Faculty Publications

Streptococcus parauberis is a pathogen of cattle and fish, closely related Streptococcus uberis and Streptococcus iniae. We report the genomes of seven S. parauberis strains recovered from striped bass (Morone saxatilis) in the Chesapeake Bay. The availability of these genomes will allow comparative genomic analysis of Chesapeake Bay S. parauberis strains versus S. parauberis cultured from other animal hosts and geographic regions.