Life Sciences Commons^™

A Study Of Correlations Between The Definition And Application Of The Gene Ontology, Yuji Mo

Computer and Electronics Engineering: Dissertations, Theses, and Student Research

When using the Gene Ontology (GO), nucleotide and amino acid sequences are annotated by terms in a structured and controlled vocabulary organized into relational graphs. The usage of the vocabulary (GO terms) in the annotation of these sequences may diverge from the relations defined in the ontology. We measure the consistency of the use of GO terms by comparing GO's defined structure to the terms' application. To do this, we first use synthetic data with different characteristics to understand how these characteristics influence the correlation values determined by various similarity measures. Using these results as a baseline, we found that …

Efficacy Of Genetically Modified Bt Toxins Against Insects With Different Genetic Mechanisms Of Resistance, Bruce E. Tabashnik, Fangneng P. Huang, Mukti N. Ghimire, B. Rogers Leonard, Blair D. Siegfried, Murugesan Rangasamy, Yajun Yang, Yidong Wu, Linda J. Gahan, David G. Heckel, Alejandro Bravo, Mario Soberón

Department of Entomology: Faculty Publications

Transgenic crops that produce Bacillus thuringiensis (Bt) toxins are grown widely for pest control, but insect adaptation can reduce their efficacy. The genetically modified Bt toxins Cry1AbMod and Cry1AcMod were designed to counter insect resistance to native Bt toxins Cry1Ab and Cry1Ac. Previous results suggested that the modified toxins would be effective only if resistance was linked with mutations in genes encoding toxin-binding cadherin proteins. Here we report evidence from five major crop pests refuting this hypothesis. Relative to native toxins, the potency of modified toxins was > 350-fold higher against resistant strains of Plutella xylostella and Ostrinia nubilalis …

Msh1 Influence On Plant Mitochondrial Genome Recombination And Phenotype In Tobacco, Peibei Sun

School of Biological Sciences: Dissertations, Theses, and Student Research

Plant mitochondrial genomes are composed of unusually complex structures, due to active recombination at numerous repeated sequences in the genome. The maintenance of mitochondrial genome stability is under the control of identifiable nuclear genes. In plants, three nuclear genes (MSH1, RECA3 and OSB1) have been shown to participate in recombination surveillance and the suppression of illegitimate recombination in mitochondria. Disruption of these loci in Arabidopsis results in reproducible mitochondrial genome rearrangements. We demonstrated that repeat-mediated de novo recombination was also enhanced in both Arabidopsis and tobacco during passage through in vitro culture. Furthermore, in vitro conditions led …

Heritable Epigenetic Variation Among Maize Inbreds, Steve R. Eichten, Ruth A. Swanson, James C. Schnable, Amanda J. Waters, Peter J. Hermanson, Sanzhen Liu, Cheng-Ting Yeh, Yi Jia, Karla Gendler, Michael Freeling, Patrick S. Schnable, Matthew W. Vaughn, Nathan M. Springer

Department of Agronomy and Horticulture: Faculty Publications

Epigenetic variation describes heritable differences that are not attributable to changes in DNA sequence. There is the potential for pure epigenetic variation that occurs in the absence of any genetic change or for more complex situations that involve both genetic and epigenetic differences. Methylation of cytosine residues provides one mechanism for the inheritance of epigenetic information. A genome-wide profiling of DNA methylation in two different genotypes of Zea mays (ssp. mays), an organism with a complex genome of interspersed genes and repetitive elements, allowed the identification and characterization of examples of natural epigenetic variation. The distribution of DNA methylation …

Species D Adenoviruses As Oncolytics Against B-Cell Cancers, Christopher Y. Chen, Julien S. Senac, Eric A. Weaver, Shannon M. May, Diane F. Jelinek, Philip Greipp, Thomas Witzig, Michael A. Barry

Nebraska Center for Virology: Faculty Publications

Purpose: Oncolytic viruses are self-amplifying anticancer agents that make use of the natural ability of viruses to kill cells. Adenovirus serotype 5 (Ad5) has been extensively tested against solid cancers, but less so against B-cell cancers because these cells do not generally express the coxsackie and adenoviral receptor (CAR). To determine whether other adenoviruses might have better potency, we "mined" the adenovirus virome of 55 serotypes for viruses that could kill B-cell cancers.

Experimental Design: Fifteen adenoviruses selected to represent Ad species B, C, D, E, and F were tested in vitro against cell lines and primary patient B-cell cancers …

Use Of Natural Variation Reveals Core Genes In The Transcriptome Of Iron-Deficient Arabidopsis Thaliana Roots, Ricardo J. Stein, Brian M. Waters

Department of Agronomy and Horticulture: Faculty Publications

Iron (Fe) is an essential mineral micronutrient for plants and animals. Plants respond to Fe deficiency by increasing root uptake capacity. Identification of gene networks for Fe uptake and homeostasis could result in improved crop growth and nutritional value. Previous studies have used microarrays to identify a large number of genes regulated by Fe deficiency in roots of three Arabidopsis ecotypes. However, a large proportion of these genes may be involved in secondary or genotype-influenced responses rather than in a universal role in Fe uptake or homeostasis. Here we show that a small percentage of the Fe deficiency transcriptome of …

Gata-Family Transcription Factors In Magnaporthe Oryzae, Cristian F. Quispe

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

The filamentous fungus, Magnaporthe oryzae, responsible for blast rice disease, destroys around 10-30% of the rice crop annually. Infection begins when the specialized infection structure, the appressorium, generates enormous internal turgor pressure through the accumulation of glycerol. This turgor acts on a penetration peg emerging at the base of the cell, causing it to breach the leaf surface allowing its infection.

The enzyme trehalose-6- phosphate synthase (Tps1) is a central regulator of the transition from appressorium development to infectious hyphal growth. In the first chapter we show that initiation of rice blast disease requires a regulatory mechanism involving an …

Comparison Of Adenoviruses As Oncolytics And Cancer Vaccines In An Immunocompetent B Cell Lymphoma Model, Eric A. Weaver, Christopher Y. Chen, Shannon M. May, Mary E. Barry, Michael A. Barry

Nebraska Center for Virology: Faculty Publications

We have screened human adenoviruses (Ads) for oncolytic activity against a variety of mouse and hamster cell lines and have found a number that are susceptible to a variety of Ad serotypes. A20 lymphoma is derived from BALB/c mice and is susceptible to infection and killing by a variety of human Ads. A20 is also a suitable cancer vaccine model, because these cells express a unique immunoglobulin variable region that can be targeted by vaccination. To compare Ads as cancer vaccines versus Ads as oncolytics, A20 tumors were initiated in immunocompetent BALB/c mice. Mice immunized with first-generation Ad5 expressing the …

Herbicide-Resistant Risk Assessment: Response Of Common Nebraska Weeds To Dicamba Dose, Roberto J. Crespo

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

Dicamba-resistant soybeans are being developed to provide an additional herbicide mechanism of action that can be used in soybean, and to provide a tool to help manage or mitigate the evolution of other herbicide-resistant weed populations. The objectives of this thesis were to assess the risk of common Nebraska weeds developing resistance to dicamba, quantify baseline dose-response to dicamba of high-risk weed species, and survey the variability in dicamba dose-response among populations of those species. Twenty-five weed scientists were asked to estimate the risk likelihood of ten weed species evolving resistance to dicamba following the commercialization of dicamba-resistant soybean. Palmer …

Generation Of A Kupffer Cell-Evading Adenovirus For Systemic And Liver-Directed Gene Transfer, Reeti Khare, Shannon M. May, Francesco Vetrini, Eric A. Weaver, Donna Palmer, Amanda Rosewell, Nathan Grove, Philip Ng, Michael A. Barry

Nebraska Center for Virology: Faculty Publications

As much as 90% of an intravenously (i.v.) injected dose of adenovirus serotype 5 (Ad5) is absorbed and destroyed by liver Kupffer cells. Viruses that escape these cells can then transduce hepatocytes after binding factor X (FX). Given that interactions with FX and Kupffer cells are thought to occur on the Ad5 hexon protein, we replaced its exposed hypervariable regions (HVR) with those from Ad6. When tested in vivo in BALB/c mice and in hamsters, the Ad5/6 chimera mediated >10 times higher transduction in the liver. This effect was not due to changes in FX binding. Rather, Ad5/6 appeared to …

Native And European Haplotypes Of Phragmites Australis (Common Reed) In The Central Platte River, Nebraska, Diane L. Larson, Susan M. Galatowitsch, Jennifer L. Larson

Great Plains Research: A Journal of Natural and Social Sciences

Phragmites australis (common reed) is known to have occurred along the Platte River historically, but recent rapid increases in both distribution and density have begun to impact habitat for migrating sandhill cranes and nesting piping plovers and least terns. Invasiveness in Phragmites has been associated with the incursion of a European genotype (haplotype M) in other areas; determining the genotype of Phragmites along the central Platte River has implications for proper management of the river system. In 2008 we sampled Phragmites patches along the central Platte River from Lexington to Chapman, NE, stratified by bridge segments, to determine the current …

The Human Gut Microbiome: Ecology And Recent Evolutionary Changes, Jens Walter, Ruth Ley

Department of Food Science and Technology: Faculty Publications

The human gastrointestinal tract is divided into sections, allowing digestion and nutrient absorption in the proximal region to be separate from the vast microbial populations in the large intestine, thereby reducing conflict between host and microbes. In the distinct habitats of the gut, environmental filtering and competitive exclusion between microbes are the driving factors shaping microbial diversity, and stochastic factors during colonization history and in situ evolution are likely to introduce intersubject variability. Adaptive strategies of microbes with different niches are genomically encoded: Specialists have smaller genomes than generalists, and microbes with environmental reservoirs have large accessory genomes. A shift …

Population Genetics Of The Western Bean Cutworm (Striacosta Albicosta Smith) Across The United States, Erica Lindroth

Department of Entomology: Dissertations, Theses, and Student Research

The western bean cutworm, Striacosta albicosta (Smith), is a secondary pest of maize (Zea mays L.) and dry beans (Phaseolus vulgaris L.) in the western United States. Recently, this insect has undergone a major territory expansion into the eastern US and has become a pest throughout much of the Corn Belt. This study was instigated to examine the population genetics of this pest to facilitate control and resistance management, as well as to shed light on the current habitat expansion. To this end, western bean cutworm individuals were collected from 28 different locations across the traditional and expanded …

Phylogenetic Diversification Of The Globin Gene Superfamily In Chordates, Jay F. Storz, Juan C. Opazo, Federico G. Hoffmann

Jay F. Storz Publications

Phylogenetic reconstructions provide a means of inferring the branching relationships among members of multigene families that have diversified via successive rounds of gene duplication and divergence. Such reconstructions can illuminate the pathways by which particular expression patterns and protein functions evolved. For example, phylogenetic analyses can reveal cases in which similar expression patterns or functional properties evolved independently in different lineages, either through convergence, parallelism, or evolutionary reversals. The purpose of this article is to provide a robust phylogenetic framework for interpreting experimental data and for generating hypotheses about the functional evolution of globin proteins in chordate animals. To do …

Expression And Purification Of Recombinant Hemoglobin In Escherichia Coli, Chandrasekhar Natarajan, Xiaoben Jiang, Angela Fago, Roy E. Weber, Hideaki Moriyama, Jay F. Storz

Jay F. Storz Publications

Background: Recombinant DNA technologies have played a pivotal role in the elucidation of structure-function relationships in hemoglobin (Hb) and other globin proteins. Here we describe the development of a plasmid expression system to synthesize recombinant Hbs in Escherichia coli, and we describe a protocol for expressing Hbs with low intrinsic solubilities. Since the alpha- and beta-chain Hbs of different species span a broad range of solubilities, experimental protocols that have been optimized for expressing recombinant human HbA may often prove unsuitable for the recombinant expression of wildtype and mutant Hbs of other species.

Methodology/Principal Findings: As a test case …

Analysis Of Long-Term Selection (28 Generations) For Reproduction, Growth, And Carcass Traits In Swine, Wan-Ling Hsu

Department of Animal Science: Dissertations, Theses, and Student Research

The objectives were 1) to estimate responses from 28 generations of selection for increased pigs born alive (BA) with additional selection for increased 180 d weight (WT) and longissimus muscle area (LMA) and decreased backfat (BF) in the last eight generations, 2) to estimate genetic parameters for an array of traits, and 3) to investigate whether a plateau in response for BA has occurred. All lines were derived from the same Large White/Landrace composite population. Index selection for ovulation rate and embryo survival (G0-11) was initiated in L2 in 1981; L1 was selected randomly control line for L2 (G0-23). L2 …

Screening Synteny Blocks In Pairwise Genome Comparisons Through Integer Programming, Haibao Tang, Eric Lyons, Brent S. Pedersen, James C. Schnable, Andrew H. Paterson, Michael Freeling

Department of Agronomy and Horticulture: Faculty Publications

Background:

It is difficult to accurately interpret chromosomal correspondences such as true orthology and paralogy due to significant divergence of genomes from a common ancestor. Analyses are particularly problematic among lineages that have repeatedly experienced whole genome duplication (WGD) events. To compare multiple “subgenomes” derived from genome duplications, we need to relax the traditional requirements of “one-to-one” syntenic matchings of genomic regions in order to reflect “one-to-many” or more generally “many-to-many” matchings. However this relaxation may result in the identification of synteny blocks that are derived from ancient shared WGDs that are not of interest. For many downstream analyses, we …

Advances And Future Challenges In Adenoviral Vector Pharmacology And Targeting, Reeti Khare, Christopher Y. Chen, Eric A. Weaver, Michael A. Barry

Nebraska Center for Virology: Faculty Publications

Adenovirus is a robust vector for therapeutic applications, but its use is limited by our understanding of its complex in vivo pharmacology. In this review we describe the necessity of identifying its natural, widespread, and multifaceted interactions with the host since this information will be crucial for efficiently redirecting virus into target cells. In the rational design of vectors, the notion of overcoming a sequence of viral “sinks” must be combined with re-targeting to target populations with capsid as well as shielding the vectors from pre-existing or toxic immune responses. It must also be noted that most known adenoviral pharmacology …

Genes Identified By Visible Mutant Phenotypes Show Increased Bias Toward One Of Two Subgenomes Of Maize, James C. Schnable, Michael Freeling

Department of Agronomy and Horticulture: Faculty Publications

Not all genes are created equal. Despite being supported by sequence conservation and expression data, knockout homozygotes of many genes show no visible effects, at least under laboratory conditions. We have identified a set of maize (Zea mays L.) genes which have been the subject of a disproportionate share of publications recorded at MaizeGDB. We manually anchored these ‘‘classical’’ maize genes to gene models in the B73 reference genome, and identified syntenic orthologs in other grass genomes. In addition to proofing the most recent version 2 maize gene models, we show that a subset of these genes, those that …

Dose–Sensitivity, Conserved Non-Coding Sequences, And Duplicate Gene Retention Through Multiple Tetraploidies In The Grasses, James C. Schnable, Brent S. Pedersen, Sabarinath Subramaniam, Michael Freeling

Department of Agronomy and Horticulture: Faculty Publications

Whole genome duplications, or tetraploidies, are an important source of increased gene content. Following whole genome duplication, duplicate copies of many genes are lost from the genome. This loss of genes is biased both in the classes of genes deleted and the subgenome from which they are lost. Many or all classes are genes preferentially retained as duplicate copies are engaged in dose sensitive protein–protein interactions, such that deletion of any one duplicate upsets the status quo of subunit concentrations, and presumably lowers fitness as a result. Transcription factors are also preferentially retained following every whole genome duplications studied. This …

Isolation By Distance Explains Genetic Structure Of Buggy Creek Virus, A Bird-Associated Arbovirus, Abinash Padhi, Amy T. Moore, Mary Bomberger Brown, Jerome E. Foster, Martin Pfeffer, Charles R. Brown

School of Natural Resources: Faculty Publications

Many of the arthropod-borne viruses (arboviruses) show extensive genetic variability and are widely distributed over large geographic areas. Understanding how virus genetic structure varies in space may yield insight into how these pathogens are adapted to and dispersed by different hosts or vectors, the relative importance of mutation, drift, or selection in generating genetic variability, and where and when epidemics or epizootics are most likely to occur. However, because most arboviruses tend to be sampled opportunistically and often cannot be isolated in large numbers at a given locale, surprisingly little is known about their spatial genetic structure on the local …

Giant Viruses, James L. Van Etten

James Van Etten Publications

The common view of viruses, mostly true, is of tiny burglars that sneak into cells, grab the biosynthetic controls and compel the cell to make huge numbers of progeny that break out of the cell and keep the replication cycle going. Viruses are supposed to be diminutive even compared to cells that are just a micrometer (1,000 nanometers) in diameter. They are supposed to travel light, making do with just a few well-adapted genes.

In 1992, a new microorganism was isolated from a power-plant cooling tower in Bradford, England, where Timothy Robotham, a microbiologist at Leeds Public Health Laboratory, was …

Minimal Art: Or Why Small Viral K+ Channels Are Good Tools For Understanding Basic Structure And Function Relations, Gerhard Thiel, Dirk Baumeister, Indra Schroeder, Stefan M. Kast, James L. Van Etten, Anna Moroni

James Van Etten Publications

Some algal viruses contain genes that encode proteins with the hallmarks of K+ channels. One feature of these proteins is that they are less than 100 amino acids in size, which make them truly minimal for a K+ channel protein. That is, they consist of only the pore module present in more complex K+ channels. The combination of miniature size and the functional robustness of the viral K+ channels make them ideal model systems for studying how K+ channels work. Here we summarize recent structure/function correlates from these channels, which provide insight into functional properties such as gating, pharmacology and …

Functional Hak/Kup/Kt-Like Potassium Transporter Encoded By Chlorella Viruses, Timo Greiner, José Ramos, Maria C. Alvarez, James Gurnon, Ming Kang, James L. Van Etten, Anna Moroni, Gerhard Thiel

James Van Etten Publications

Chlorella viruses are a source of interesting membrane transport proteins. Here we examine a putative K+ transporter encoded by virus FR483 and related chlorella viruses. The protein shares sequence and structural features with HAK/KUP/KT-like K+ transporters from plants, bacteria and fungi. Yeast complementation assays and Rb+ uptake experiments show that the viral protein, termed HAKCV (high-affinity K+ transporter of chlorella virus), is functional, with transport characteristics that are similar to those of known K+ transporters. Expression studies revealed that the protein is expressed as an early gene during viral replication, and proteomics data indicate that it is not packaged in …

Field Introgression Of Diabrotica Barberi And Diabrotica Longicornis (Coleoptera: Chrysomelidae) Based On Genetic And Morphological Characters, Laura A. Campbell, Thomas L. Clark, Pete L. Clark, Lance Meinke, John E. Foster

Department of Entomology: Faculty Publications

Diabrotica barberi Smith & Lawrence and Diabrotica longicornis (Say) (Coleoptera: Chrysomelidae) are considered to be sister species, and it has been proposed that the two species may hybridize under field conditions. The objective of this study was to examine genetic and morphological characters of D. barberi and D. longicornis for evidence of field introgression. Both species were collected from sympatric and allopatric areas. Amplified fragment length polymorphisms and morphological characters (color and head capsule width) were used to examine variation within and among populations of D. barberi and D. longicornis. Relatively little of the overall …

Regulation Of The Latency–Reactivation Cycle By Products Encoded By The Bovine Herpesvirus 1 (Bhv-1) Latency-Related Gene, Clinton Jones, Leticia Frizzo Da Silva, Devis Sinani

School of Veterinary and Biomedical Sciences: Faculty Publications

Like other α-herpesvirinae subfamily members, the primary site for bovine herpesvirus 1 (BHV-1) latency is ganglionic sensory neurons. Periodically BHV-1 reactivates from latency, virus is shed, and consequently virus transmission occurs. Transcription from the latency-related (LR) gene is readily detected in neurons of trigeminal ganglia (TG) of calves or rabbits latently infected with BHV-1. Two micro-RNAs and a transcript encompassing a small open reading frame (ORF-E) located within the LR promoter can also be detected in TG of latently infected calves. A BHV-1 mutant that contains stop codons near the beginning of the first open reading frame (ORF2) within the …

Effects Of Restricting Energy During The Gilt Developmental Period On Growth And Reproduction Of Lines Differing In Lean Growth Rate: Responses In Feed Intake, Growth, And Age At Puberty, P. S. Miller, R. Moreno, R. K. Johnson

Department of Animal Science: Faculty Publications

The overall objective was to compare reproductive performance through 4 parities of gilts developed with ad libitum access to feed or with restriction of energy to 75% of ad libitum intake. Effects on growth and pubertal development are reported. The experiment was a 2 × 2 factorial with 661 gilts. One-half of the gilts (n = 330) were allowed ad libitum access to feed from weaning to breeding at 235 d of age (AL), and 331 littermates were developed with ad libitum access to feed to 123 d of age and then restricted to 75% of ad libitum intake to …

Banf1 Is Required To Maintain The Self-Renewal Of Both Mouse And Human Embryonic Stem Cells, Jesse L. Cox, Sunil K. Mallanna, Briana D. Ormsbee, Michelle Desler, Matthew S. Wiebe, Angie Rizzino

Nebraska Center for Virology: Faculty Publications

Self-renewal is a complex biological process necessary for maintaining the pluripotency of embryonic stem cells (ESCs). Recent studies have used global proteomic techniques to identify proteins that associate with the master regulators Oct4, Nanog, and Sox2 in ESCs or in ESCs during the early stages of differentiation. Through an unbiased proteomic screen, Banf1 was identified as a Sox2- associated protein. Banf1 has been shown to be essential for worm and fly development but, until now, its role in mammalian development and ESCs has not been explored. In this study, we examined the effect of knocking down Banf1 on ESCs. We …

Developmental Regulation Of Hemoglobin Synthesis In The Green Anole Lizard Anolis Carolinensis, Jay F. Storz, Federico G. Hoffmann, Juan C. Opazo, Thomas J. Sanger, Hideaki Moriyama

Jay F. Storz Publications

Tetrapod vertebrates possess multiple alpha- and beta-like globin genes that are ontogenetically regulated, such that functionally distinct hemoglobin (Hb) isoforms are synthesized during different stages of development. The alpha- and beta-like globin genes of amphibians, birds and mammals are differentially expressed during embryonic development and postnatal life, but little is known about the developmental regulation of globin gene expression in non-avian reptiles. Here we report an investigation into the developmental regulation of Hb synthesis in the green anole lizard Anolis carolinensis. We tested two hypotheses derived from comparative genomic studies of the globin gene clusters in tetrapod vertebrates. First, …

Evolutionary Origins Of Oxygen Sensing In Animals, Kalle T. Rytkönen, Jay F. Storz

Jay F. Storz Publications

All animal life requires molecular oxygen as the terminal electron acceptor in aerobic energy production. A lack of oxygen can reduce the rate of energy production, whereas an excess of oxygen leads to the accumulation of toxic reactive oxygen species. Hence, animals have evolved sophisticated mechanisms with which to monitor and respond to fluctuations in oxygen availability, in order to maintain cellular homeostasis. In all animal taxa examined so far, the maintenance of physiological oxygen homeostasis is mediated by the oxygen-dependent post-translational hydroxylation of a heterodimeric transcription factor, termed hypoxia-inducible factor (HIF; Kaelin & Ratcliffe, 2008). The hydroxylation reaction is …