Genetics and Genomics Commons^™

A Novel Codon-Optimized Siv Gag-Pol Immunogen For Gene-Based Vaccination, Catherine M. Crosby, Eric A. Weaver, Reeti Khare, Michael A. Barry

Nebraska Center for Virology: Faculty Publications

Simian immunodeficiency virus (SIV) is a robust pathogen used in non-human primates to model HIV vaccines. SIV encodes a number of potential vaccine targets. By far the largest and most conserved protein target in SIV is its gag-pol protein that bears many epitopes to drive multivalent immune T cell responses. While gag-pol is an attractive antigen, it is only translated after a frame shift between gag and pol with the effect that gag and pol are expressed at an approximate 10/1 ratio. The codon bias of native lentiviral genes are also mismatched with the abundance of tRNAs in mammalian cells …

Predators Catalyze An Increase In Chloroviruses By Foraging On The Symbiotic Hosts Of Zoochlorellae, John Delong, Zeina Al-Ameeli, Garry A. Duncan, James L. Van Etten, David D. Dunigan Ph. D.

James Van Etten Publications

Virus population growth depends on contacts between viruses and their hosts. It is often unclear how sufficient contacts are made between viruses and their specific hosts to generate spikes in viral abundance. Here, we show that copepods, acting as predators, can bring aquatic viruses and their algal hosts into contact. Specifically, predation of the protist Paramecium bursaria by copepods resulted in a >100-fold increase in the number of chloroviruses in 1 d. Copepod predation can be seen as an ecological “catalyst” by increasing contacts between chloroviruses and their hosts, zoochlorellae (endosymbiotic algae that live within paramecia), thereby facilitating viral population …

Climate Change And The Integrity Of Science, Peter H. Gleick, James L. Van Etten, Members Of The U.S. National Academy Of Sciences

James Van Etten Publications

We are deeply disturbed by the recent escalation of political assaults on scientists in general and on climate scientists in particular. All citizens should understand some basic scientific facts. There is always some uncertainty associated with scientific conclusions; science never absolutely proves anything. When someone says that society should wait until scientists are absolutely certain before taking any action, it is the same as saying society should never take action. For a problem as potentially catastrophic as climate change, taking no action poses a dangerous risk for our planet.

Scientific conclusions derive from an understanding of basic laws supported by …

Predictable Convergence In Hemoglobin Function Has Unpredictable Molecular Underpinnings, Chandrasekhar Natarajan, Federico G. Hoffmann, Roy E. Weber, Angela Fago, Christopher C. Witt, Jay F. Storz

Jay F. Storz Publications

To investigate the predictability of genetic adaptation, we examined the molecular basis of convergence in hemoglobin function in comparisons involving 56 avian taxa that have contrasting altitudinal range limits. Convergent increases in hemoglobin-oxygen affinity were pervasive among high-altitude taxa, but few such changes were attributable to parallel amino acid substitutions at key residues.Thus, predictable changes in biochemical phenotype do not have a predictable molecular basis. Experiments involving resurrected ancestral proteins revealed that historical substitutions have context-dependent effects, indicating that possible adaptive solutions are contingent on prior history. Mutations that produce an adaptive change in one species may represent precluded possibilities …

Incremental Phylogenetics By Repeated Insertions: An Evolutionary Tree Algorithm, Peter Revesz, Zhiqiang Li

School of Computing: Faculty Publications

We introduce the idea of constructing hypothetical evolutionary trees using an incremental algorithm that inserts species one-by-one into the current evolutionary tree. The method of incremental phylogenetics by repeated insertions lead to an algorithm that can be used on DNA, RNA and amino acid sequences. According to experimental results on both synthetic and biological data, the new algorithm generates more accurate evolutionary trees than the UPGMA and the Neighbor Joining algorithms.

Polyandry In The Absence Of Fitness Benefits In A Species With Female-Biased Sexual Size Dimorphism, Marie Claire Chelini, Eileen A. Hebets

Eileen Hebets Publications

Most studies exploring the evolution of female mating systems focus on species in which females are either monandric (mate with a single male) or highly polyandric (mate with multiple males), but less is understood about variation in mating decisions within a species. How and why do females of a single species decide whether or not to copulate with additional mates? In this study we attempt to answer this question in the highly dimorphic crab spider, Mecaphesa celer, whose females may be either monandric or polyandric. We tested three hypotheses: (1) a female’s decision to remate is based on sequential mate …

Mucosal Vaccination By Adenoviruses Displaying Reovirus Sigma 1, Eric A. Weaver, Zenaido T. Camacho, Matthew L. Hillestad, Catherine M. Crosby, Mallory A. Turner, Adam J. Guenzel, Hind J. Fadel, George T. Mercier, Michael A. Barry

Nebraska Center for Virology: Faculty Publications

We previously developed adenovirus serotype 5 (Ad5) vectors displaying the sigma 1 protein from reovirus as mucosal vaccines. Ad5-sigma retargets to JAM-1 and sialic acid, but had 40-fold reduced gene delivery when compared to Ad5. While weaker at transduction, Ad5-sigma generated stronger T cell responses than Ad5 when used for mucosal immunization. New Ad5-fiber-sigma vectors were generated here by varying the number of fiber β-spiral shaft repeats (R) fused between fiber tail and the sigma. Ad5 virions encoding R3, R14, and R20 chimeras were rescued. Increasing chimera length led to their decreasing encapsidation of these proteins in the virions. Ad5-R3 …

Methods To Account For Breed Composition In A Bayesian Gwas Method Which Utilizes Haplotype Clusters, Danielle F. Wilson-Wells

Department of Statistics: Dissertations, Theses, and Student Work

In livestock, prediction of an animal’s genetic merit using genomic information is becoming increasingly common. The models used to make these predictions typically assume that we are sampling from a homogeneous population. However, in both commercial and experimental populations the sire and dam of an individual may be a mixture of different breeds. Haplotype models can capture this population structure.

Two models based on breed specific haplotype clusters where developed to account for differences across multiple breeds. The first model utilizes the breed composition of the individual, while the second utilizes the breed composition from the sire and dam. Haplotype …

Evaluating Mechanisms Of Rna Editing In Plants, Lexis Funk, Weishu Fan, Jeffrey P. Mower

UCARE Research Products

RNA editing is one of several post-transcriptional RNA processes. This process generates RNA and protein diversity in eukaryotes and results in specific amino acid substitutions, deletions, and changes in gene expression levels. It occurs in both plastids and mitochondria and typically involves the changing of specific C to U (cytosine to uracil). Welwitschia belongs to the gymnosperms (a group of seed-producing plants that includes conifers, cycads, Ginkgo, and Gnetales). It has already been substantiated that Welwitschia mirabilis has a major loss of cis-spliced introns and unusual trans-splicing introns. Research in the Mower lab has already proven that ancestral gymnosperm has …

Relationship Between Morphogenesis And Secretion In The Filamentous Fungus Aspergillus Nidulans, Lakshmi Preethi Yerra

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

Filamentous fungi have a long history in biotechnology for the production of food ingredients, pharmaceuticals and enzymes. The advancements made in recent years have earned filamentous fungi such as Aspergillus species a dominant place among microbial cell factories. Although the model fungus A. nidulans has been extensively studied, the genetic and regulatory networks that underlie morphogenesis and development have yet to be fully characterized. The Rho GTPases (Cdc42 and RacA) are one of the most important regulators of the morphogenetic processes among diverse eukaryotic organisms. Although the functions of these GTPases are relatively well-characterized, little is known about their downstream …

Comparative Evolutionary Analysis Of Organellar Genomic Diversity In Green Plants, Weishu Fan

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

The mitochondrial genome (mitogenome) and plastid genome (plastome) of plants vary immensely in genome size and gene content. They have also developed several eccentric features, such as the preference for horizontal gene transfer of mitochondrial genes, the reduction of the plastome in non-photosynthetic plants, and variable amounts of RNA editing affecting both genomes. Different organismal lifestyles can partially account for the highly diverse organellar genomes across the tree of green plants. For example, endosymbiotic and parasitic lifestyles can dramatically affect the genomic architectures of plant mitochondria and plastids. In this study, the organellar genomes of several green plants with atypical …

Sex Chromosome-Wide Transcriptional Suppression And Compensatory Cis-Regulatory Evolution Mediate Gene Expression In The Drosophila Male Germline, Emily L. Landeen, Christina A. Muirhead, Lori Wright, Colin D. Meiklejohn, Daven C. Presgraves

School of Biological Sciences: Faculty Publications

The evolution of heteromorphic sex chromosomes has repeatedly resulted in the evolution of sex chromosome-specific forms of regulation, including sex chromosome dosage compensation in the soma and meiotic sex chromosome inactivation in the germline. In the male germline of Drosophila melanogaster, a novel but poorly understood form of sex chromosome-specific transcriptional regulation occurs that is distinct from canonical sex chromosome dosage compensation or meiotic inactivation. Previous work shows that expression of reporter genes driven by testis-specific promoters is considerably lower—approximately 3-fold or more—for transgenes inserted into X chromosome versus autosome locations. Here we characterize this transcriptional suppression of X-linked …

Comparative Genomics, Transcriptomics, And Physiology Distinguish Symbiotic From Free-Living Chlorella Strains, Cristian F. Quispe, Olivia Sonderman, Maya Khasin, Wayne R. Riekhof, James L. Van Etten, Kenneth Nickerson

Kenneth Nickerson Papers

Most animal–microbe symbiotic interactions must be advantageous to the host and provide nutritional benefits to the endosymbiont. When the host provides nutrients, it can gain the capacity to control the interaction, promote self-growth, and increase its fitness. Chlorella-like green algae engage in symbiotic relationships with certain protozoans, a partnership that significantly impacts the physiology of both organisms. Consequently, it is often challenging to grow axenic Chlorella cultures after isolation from the host because they are nutrient fastidious and often susceptible to virus infection. We hypothesize that the establishment of a symbiotic relationship resulted in natural selection for nutritional and metabolic …

The Maintenance Of Phenotypic Divergence Through Sexual Selection: An Experimental Study In Barn Swallows Hirundo Rustica, Rebecca Safran, Yoni Vortman, Brittany R. Jenkins, Joanna K. Hubbard, Matt Wilkins, Rachel J. Bradley, Arnon Lotem

School of Biological Sciences: Faculty Publications

Previous studies have shown that sexual signals can rapidly diverge among closely related species. However, we lack experimental studies to demonstrate that differences in trait-associated reproductive performance maintain sexual trait differences between closely related populations, in support for a role of sexual selection in speciation. Populations of Northern Hemisphere distributed barn swallows Hirundo rustica are closely related, yet differ in two plumage-based traits: ventral color and length of the outermost tail feathers (streamers). Here we provide experimental evidence that manipulations of these traits result in different reproductive consequences in two subspecies of barn swallow: (H. r. erythrogaster in North …

High-Throughput Screening Of Clinically Approved Drugs That Prime Polyethylenimine Transfection Reveals Modulation Of Mitochondria Dysfunction Response Improves Gene Transfer Efficiencies, Albert Nguyen, Jared P. Beyersdorf, Jean-Jack Riethoven, Angela K. Pannier

Biological Systems Engineering: Papers and Publications

Nonviral gene delivery methods are advantageous over viral vectors in terms of safety, cost, and flexibility in design and application, but suffer from lower gene transfer efficiency. In addition to modifications to nucleic acid design and nonviral carriers, new tools are sought to enhance transfection. Priming is the pharmacological modulation of transfection efficiency and transgene expression, and has demonstrated transfection increase in several compounds, for example, chloroquine and glucocorticoids. To develop a library of transfection priming compounds, a highthroughput screen was performed of the NIH Clinical Collection (NCC) to identify clinical compounds that prime polyethylenimine (PEI) transfection. HEK293T cells were …

Distribution Of Genomic Variation In The Usda Soybean Germplasm Collection And Relationship With Phenotypic Variation, Nonoy Batiller Bandillo

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

The USDA Soybean Germplasm Collection harbors a large stock of genetic diversity with potential to accelerate soybean cultivar development. The extent and nature of favorable alleles contained in the collection are not well known nor is the distribution of genetic variation and how it relates to phenotypic variation. The genotyping of the entire USDA Soybean Germplasm Collection marked the beginning of a systematic exploration of genetic diversity for genetic research and breeding. In this research, we conducted the first comprehensive analysis of population structure on the collection of ~14,400 soybean accessions [Glycine max (L.) Merr. and G. soja Siebold …

Sequencing And Comparative Analysis Of De Novo Genome Assemblies Of Streptomyces Aureofaciens Atcc 10762, Julien S. Gradnigo

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

Streptomyces aureofaciens is a Gram-positive Actinomycete used for commercial antibiotic production. Although it has been the subject of many biochemical studies, no public genome resource was available prior to this project. To address this need, the genome of S. aureofaciens ATCC 10762 was sequenced using a combination of sequencing platforms (Illumina and 454-shotgun). Multiple de novo assembly methods (SGA, IDBA, Trinity, SOAPdenovo2, MIRA, Velvet and SPAdes) as well as combinations of these methods were assessed to determine which provided the most robust assembly. Combination strategies led to a consistent overestimation of the total genome size. Empirical data from targeted PCR …

Divergent Activity Of The Gonadotropin Releasing Hormone Receptor Gene Promoter Among Genetic Lines Of Pigs Is Partially Conferred By Nuclear Factor (Nf)-Kb, Specificity Protein (Sp)1-Like And Gata-4 Binding Sites, Emily A. Mcdonald, Jacqueline E. Smith, Rebecca A. Cederberg, Brett R. White

Department of Animal Science: Faculty Publications

BACKGROUND: Binding of gonadotropin-releasing hormone (GnRH) to its receptor (GnRHR) on gonadotropes within the anterior pituitary gland is essential to reproduction. In pigs, the GnRHR gene is also located near a genetic marker for ovulation rate, a primary determinant of prolificacy. We hypothesized that pituitary expression of the GnRHR gene is alternatively regulated in genetic strains with elevated ovulation rates (Chinese Meishan and Nebraska Index) vs. standard white crossbred swine (Control).

METHODS: Luciferase reporter vectors containing 5118 bp of GnRHR gene promoter from either the Control, Index or Meishan swine lines were generated. Transient transfection of line-specific, full length, deletion …

Description Of Mesocriconema Ericaceum N. Sp. (Nematoda: Criconematidae) And Notes On Other Nematode Species Discovered In An Ericaceous Heath Bald Community In Great Smoky Mountains National Park, Usa, Thomas O. Powers, Peter Mullin, Rebecca Higgins, Timothy Harris, Kirsten S. Powers

Department of Plant Pathology: Faculty Publications

A new species of Mesocriconema and a unique assemblage of plant-parasitic nematodes was discovered in a heath bald atop Brushy Mountain in Great Smoky Mountains National Park. Mesocriconema ericaceum n. sp., a species with males, superficially resembles M. xenoplax. DNA barcoding with the mitochondrial COI gene provided evidence of the new species as a distinct lineage. SEM revealed significant variability in arrangement of labial submedian lobes, plates, and anterior and posterior annuli. Three other nematodes in the family Criconematidae were characterized from the heath bald. Ogma seymouri, when analyzed by statistical parsimony, established connections with isolates from north-eastern Atlantic …

Cooled Perch Effects On Performance And Well-Being Traits In Caged White Leghorn Hens, J Y. Hu, P Y. Hester, M M. Makagon, G Vezzoli, R S. Gates, Y Xiong, H W. Cheng

Department of Animal Science: Faculty Publications

We assessed the effects of chilled water cooling perches on hen performance and physiological and behavioral parameters under “natural” high temperatures during the 2013 summer with a 4-hour acute heating episode. White Leghorns at 16 wk of age (N = 162) were randomly assigned to 18 cages (n = 9) arranged into 3 units. Each unit was assigned to one of the 3 treatments through 32 wk of age: 1) cooled perches, 2) air perches, and 3) no perches. Chilled water (10◦C) was circulated through the cooled perches when cage ambient temperature exceeded 25^◦C. At the age of …

Rnai Induced Knockdown Of A Cadherin-Like Protein (Ef531715) Does Not Affect Toxicity Of Cry34/35ab1 Or Cry3aa To Diabrotica Virgifera Virgifera Larvae (Coleoptera: Chrysomelidae), Sek Yee Tan, Murugesan Rangasamy, Haichuan Wang, Ana Maria Vélez, James Hasler, David Mccaskill, Tao Xu, Hong Chen, Jessica Jurzenski, Matthew Kelker, Xiaoping Xu, Kenneth E. Narva, Blair D. Siegfried

Department of Entomology: Faculty Publications

The western corn rootworm (WCR), Diabrotica virgifera virgifera LeConte, is an important maize pest throughout most of the U.S. Corn Belt. Bacillus thuringiensis (Bt) insecticidal proteins including modified Cry3Aa and Cry34/35Ab1 have been expressed in transgenic maize to protect against WCR feeding damage. To date, there is limited information regarding the WCR midgut target sites for these proteins. In this study, we examined whether a cadherin-like gene from Diabrotica virgifera virgifera (DvvCad; Gen-Bank accession # EF531715) associated with WCR larval midgut tissue is necessary for Cry3Aa or Cry34/ 35Ab1 toxicity. Experiments were designed to examine the sensitivity of WCR to …

Genome-Wide Differentiation In Closely Related Populations: The Roles Of Selection And Geographic Isolation, Rebecca Safran, Elizabeth Scordato, Matt Wilkins, Joanna K. Hubbard, B. R. Jenkins, Tomáš Albrecht, Samuel Flaxman, H. Karaardiç, Yoni Vortman, Arnon Lotem, Patrik Nosil, P. Pap, Sheng-Feng Shen, S.-F. Chan, T. L. Parchman, Nolan C. Kane

School of Biological Sciences: Faculty Publications

Population divergence in geographic isolation is due to a combination of factors. Natural and sexual selection may be important in shaping patterns of population differentiation, a pattern referred to as “isolation by adaptation” (IBA). IBA can be complementary to the well-known pattern of “isolation by distance” (IBD), in which the divergence of closely related populations (via any evolutionary process) is associated with geographic isolation. The barn swallow Hirundo rustica complex comprises six closely related subspecies, where divergent sexual selection is associated with phenotypic differentiation among allopatric populations. To investigate the relative contributions of selection and geographic distance to genome-wide differentiation, …

Identification Of Qtls For Resistance Against Rhizoctonia Solani And Phoma Glycinicola In Soybeans (Glycine Max L. Merr), Herbert Sserunkuma

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

A QTL (Quantitative trait locus) is a chromosome location of a gene controlling a specific phenotypic trait. The trait maybe governed by multiple genes. Fungal pathogens are responsible for over 50% of all soybean diseases. Rhizoctonia solani Kühn causes seedling dumping off, root and hypocotyl rots and other disease in soybeans. Phoma glycinicola de Gruyter & Boerema causes Red leaf blotch disease, predominantly in Sub-Saharan Africa. There is no reported complete resistance against these fungal pathogens in soybeans. Reaction to R.solani is reportedly a quantitative trait controlled by major and minor genes. Three QTLs contributing to reaction to R. solani …

Nocturnal Foraging Enhanced By Enlarged Secondary Eyes In A Net-Casting Spider, Jay A. Stafstrom, Eileen A. Hebets

Eileen Hebets Publications

Animals that possess extreme sensory structures are predicted to have a related extreme behavioral function. This study focuses on one such extreme sensory structure—the posterior median eyes of the net-casting spider Deinopis spinosa. Although past research has implicated the importance of vision in the nocturnal foraging habits of Deinopis, no direct link between vision in the enlarged eyes and nocturnal foraging has yet been made. To directly test the hypothesis that the enlarged posterior median eyes facilitate visually based nocturnal prey capture, we conducted repeated-measures, visual occlusion trials in both natural and laboratory settings. Our results indicate that D. …

Biology, Gene Flow, And Management Of Glyphosate-Resistant Common Waterhemp (Amaranthus Rudis Sauer) In Nebraska, Debalin Sarangi

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

Common waterhemp is the most troublesome weed in the midwestern United States. Growers from Nebraska reported failure to control common waterhemp following sequential applications of glyphosate in glyphosate-tolerant corn and soybean, which led to moderate to severe yield loss; justifying the need to confirm resistance and study the biology and management of common waterhemp. The objectives of this research were: 1) to confirm the presence of glyphosate-resistant (GR) common waterhemp biotypes in Nebraska and to evaluate their sensitivity to herbicides belonging to alternative sites-of-action; 2) to evaluate the response of common waterhemp to water stress; 3) to quantify pollen-mediated gene …

Non-Essentiality Of Alr And Muri Genes In Mycobacteria, Philion L. Hoff, Denise Zinniel, Raúl G. Barletta

UCARE Research Products

Amino acids are the building blocks of life. If DNA is the blueprint, amino acids are the lumber that proteins are built with. Proteins are built with left-handed, L- forms of amino acids. Bacteria have an essential cell wall component that happens to be an exception: peptidoglycan. Bacteria have enzymes called racemases that convert L- amino acid forms into right-handed, D- forms. Amino acids participate in many reactions with keto acids. Transaminases allow conversion between amino acids by transfer of an amino group.

Previous reports claimed there is no D-ala transaminase activity in mycobacteria and thus alr and murI genes …

Cry1f Resistance Among Lepidopteran Pests: A Model For Improved Resistance Management?, Ana María Vélez, Neetha Nanoth Vellichirammal, Juan Luis Jurat-Fuentes, Blair Siegfried

Department of Entomology: Faculty Publications

The Cry1Fa protein from the bacterium Bacillus thuringiensis (Bt) is known for its potential to control lepidopteran pests, especially through transgenic expression in maize and cotton. The maize event TC1507 expressing the cry1Fa toxin gene became commercially available in the United States in 2003 for the management of key lepidopteran pests including the European corn borer, Ostrinia nubilalis, and the fall armyworm, Spodoptera frugiperda. A high-dose/refuge strategy has been widely adopted to delay evolution of resistance to event TC1507 and other transgenic Bt crops. Efficacy of this strategy depends on the crops expressing a high dose of the …

Three-Year Survey Of Abundance, Prevalence And Genetic Diversity Of Chlorovirus Populations In A Small Urban Lake, Cristian F. Quispe, Olivia Sonderman, Anya Seng, Brenna Rasmussen, Garrett Weber, Claire Mueller, David Dunigan, James L. Van Etten

James Van Etten Publications

Inland water environments cover about 2.5 percent of our planet and harbor huge numbers of known and still unknown microorganisms. In this report, we examined water samples for the abundance, prevalence, and genetic diversity of a group of infectious viruses (chloroviruses) that infect symbiotic chlorella-like green algae. Samples were collected on a weekly basis for a period of 24 to 36 months from a recreational freshwater lake in Lincoln, Nebraska, and assayed for infectious viruses by plaque assay. The numbers of infectious virus particles were both host- and site-dependent. The consistent fluctuations in numbers of viruses suggest their impact as …

Analysis Of Morphology And Secretion Mutants In Aspergillus Nidulans, Shelby N. Holaday, Steven D. Harris

UCARE Research Products

Filamentous fungi are important economically and medically due to their capacity to produce secondary metabolites or as human and animal pathogens. The genes and molecular mechanism responsible for secretion is poorly understood. Using classical genetics, we derived temperature sensitive (Ts) fungal mutants in Aspergillis nidulans. These mutants were then analyzed for their secondary metabolite secretion capacity.

In this study, we used the Ts strains of A. nidulans to determine how knockouts affect morphological and protein secretion by examining the phenotypes under the microscope and also by staining the mutants with Congo red staining. Mutants were stained with Congo red to …

Is A Mitochondrial Plasmid Really A Virus?, Mackenzie Strehle

UCARE Research Products

In addition to containing a large and complex mitochondrial genome, the mitochondria of several species of plants have been shown to contain an independent, self-replicating DNA molecule in the form of a plasmid. Plants in the Brassica genus contain a linear plasmid that is approximately 11.6 kilobases in length. The plasmid is characterized by the presence of terminal inverted repeats and covalently bonded proteins at its termini (Handa 2008). The plasmid also contains six ORFs that encode DNA and RNA polymerases and a number of unknown proteins (Figure 1). Currently, both the function of this plasmid and the mechanisms by …