Life Sciences Commons^™

Effects Of Shielding Adenoviral Vectors With Polyethylene Glycol On Vector-Specific And Vaccine-Mediated Immune Responses, Eric A. Weaver, Michael A. Barry

Nebraska Center for Virology: Faculty Publications

Many individuals have been previously exposed to human adenovirus serotype 5 (Ad5). This prior immunity has long been known to hinder its use for gene therapy and as a gene-based vaccine. Given these immunogenicity problems, we have tested whether polyethylene glycol (PEG) can blunt immune effects against Ad5 during systemic and mucosal vaccination. Ad5 vectors were covalently modified with 5-, 20-, and 35-kDa linear PEG polymers and evaluated for their ability to produce immune responses against transgene antigen products and the vector itself. We show that shielding Ad5 with different-sized PEGs generally reduces transduction and primary antibody responses by the …

New Genes Originated Via Multiple Recombinational Pathways In The Β-Globin Gene Family Of Rodents, Frederico Hoffmann, Juan Opazo, Jay F. Storz

Jay F. Storz Publications

Species differences in the size or membership composition of multigene families can be attributed to lineage-specific additions of new genes via duplication, losses of genes via deletion or inactivation, and the creation of chimeric genes via domain shuffling or gene fusion. In principle, it should be possible to infer the recombinational pathways responsible for each of these different types of genomic change by conducting detailed comparative analyses of genomic sequence data. Here, we report an attempt to unravel the complex evolutionary history of the β-globin gene family in a taxonomically diverse set of rodent species. The main objectives were: 1) …

Differential Loss Of Embryonic Globin Genes During The Radiation Of Placental Mammals, Juan C. Opazo, Federico Hoffmann, Jay F. Storz

Jay F. Storz Publications

The differential gain and loss of genes from homologous gene families represents an important source of functional variation among the genomes of different species. Differences in gene content between species are primarily attributable to lineage-specific gene gains via duplication and lineage-specific losses via deletion or inactivation. Here, we use a comparative genomic approach to investigate this process of gene turnover in the β-globin gene family of placental mammals. By analyzing genomic sequence data from representatives of each of the main superordinal clades of placental mammals, we were able to reconstruct pathways of gene family evolution during the basal radiation of …

An Evolutionary Expressed Sequence Tag Analysis Of Drosophila Spermatheca Genes, Adrianne Prokupek, Federico G. Hoffmann, Seong-Il Eyun, Etsuko N. Moriyama, Min Zhou, Lawrence G. Harshman

Papers in Genetics

This study investigates genes enriched for expression in the spermatheca, the long-term sperm storage organ (SSO) of female Drosophila. SSO genes are likely to play an important role in processes of sexual selection such as sperm competition and cryptic female choice. Although there is keen interest in the mechanisms of sexual selection at the molecular level, very little is known about the female genes that are involved. In the present study, a high proportion of genes enriched for expression in the spermatheca are evolving rapidly. Most of the rapidly evolving genes are proteases and genes of unknown function that …

Corn Distillers Dried Grains (Ddgs) For Growing-Finishing Swine, Phillip S. Miller

Department of Animal Science: Faculty Publications

Two-hundred and forty pigs growing-finishing pigs were used to evaluate the feeding value of distillers dried grains with solubles (DDGS). Treatments consisted of 0, 5, 10 and 15% dietary DDGS inclusion. Treatments did not affect average daily gain (ADG), average daily feed intake (ADFI) or gain:feed (G:F) during the grower 1 period (P > 0.05). During the grower 2 period ADG and ADFI linearly decreased as DDGS increased (P < 0.05). No differences among treatments were detected throughout the feeding phase finisher 1 for ADG, ADFI, and G:F (P > 0.05). During the finisher 2 feeding phase, there was a linear reduction in ADG and ADFI in response to dietary DDGS inclusion (P = 0.01). Overall, linear reductions …

Transmembrane Domain Length Of Viral K+ Channels Is A Signal For Mitochondria Targeting, Jorg Balss, Panagiotis Papatheodorou, Mario Mehmel, Dirk Baumeister, Brigitte Hertel, Nicolas Delaroque, Frank C. Chatelain, Daniel L. Minor Jr., James L. Van Etten, Joachim Rassow, Anna Moroni, Gerhard Thiel

James Van Etten Publications

K⁺ channels operate in the plasma membrane and in membranes of organelles including mitochondria. The mechanisms and topogenic information for their differential synthesis and targeting is unknown. This article describes 2 similar viral K⁺ channels that are differentially sorted; one protein (Kesv) is imported by the Tom complex into the mitochondria, the other (Kcv) to the plasma membrane. By creating chimeras we discovered that mitochondrial sorting of Kesv depends on a hierarchical combination of N- and C-terminal signals. Crucial is the length of the second transmembrane domain; extending its C terminus by >2 hydrophobic amino acids redirects Kesv …

Evidence For Contrasting Modes Of Selection At Interacting Globin Genes In The European Rabbit (Oryctolagus Cuniculus), R. Campos, Jay F. Storz, N. Ferrand

Jay F. Storz Publications

In hybrid zones between genetically differentiated populations, variation in locus-specific rates of introgression may reflect adaptation to different environments or adaptation to different genetic backgrounds. The European rabbit, Oryctolagus cuniculus, is well-suited to studies of such hybrid zone dynamics because it is composed of two genetically divergent subspecies that hybridize in a zone of secondary contact in central Iberia. A species-wide survey of allozyme variation revealed a broad range of locus-specific divergence levels (F_ST ranged from 0 to 0.54, mean F_ST = 0.16). Interestingly, the two loci that fell at opposite ends of the distribution of …

Genomic Evidence For Independent Origins Of Β-Like Globin Genes In Monotremes And Therian Mammals, Juan C. Opazo, Federico G. Hoffmann, Jay F. Storz

Jay F. Storz Publications

Phylogenetic reconstructions of the β-globin gene family in vertebrates have revealed that developmentally regulated systems of hemoglobin synthesis have been reinvented multiple times in independent lineages. For example, the functional differentiation of embryonic and adult β-like globin genes occurred independently in birds and mammals. In both taxa, the embryonic β-globin gene is exclusively expressed in primitive erythroid cells derived from the yolk sac. However, the “ε-globin” gene in birds is not orthologous to the ε-globin gene in mammals, because they are independently derived from lineage-specific duplications of a proto β-globin gene. Here, we report evidence that the early and late …

Differential Role Of Nadp+ And Nadph In The Activity And Structure Of Gdp-D-Mannose 4,6-Dehydratase From Two Chlorella Viruses, Floriana Fruscione, Laura Sturla, Garry Duncan, James L. Van Etten, Paola Valbuzzi, Antonio De Flora, Eleonopra Di Zanni, Michela Tonetti

James Van Etten Publications

GDP-D-mannose 4,6-dehydratase (GMD) is a key enzyme involved in the synthesis of 6-deoxyhexoses in prokaryotes and eukaryotes. Paramecium bursaria chlorella virus-1 (PBCV-1) encodes a functional GMD, which is unique among characterized GMDs because it also has a strong stereospecific NADPH-dependent reductase activity leading to GDP-D-rhamnose formation (Tonetti, M., Zanardi, D., Gurnon, J., Fruscione, F., Armirotti, A., Damonte, G., Sturla, L., De Flora, A., and Van Etten, J.L. (2003) J. Biol. Chem. 278, 21559–21565). In the present study we characterized a recombinant GMD encoded by another chlorella virus, Acanthocystis turfacea chlorella virus 1 (ATCV-1), demonstrating that it has the expected dehydratase …

Dissection Of A Qtl Hotspot On Mouse Distal Chromosome 1 That Modulates Neurobehavioral Phenotypes And Gene Expression, Khyobeni Mozhui, Daniel C. Bastiaansen, Thomas Schikorski, Xusheng Wang, Lu Lu, Robert W. Williams

Department of Animal Science: Faculty Publications

A remarkably diverse set of traits maps to a region on mouse distal chromosome 1 (Chr 1) that corresponds to human Chr 1q21–q23. This region is highly enriched in quantitative trait loci (QTLs) that control neural and behavioral phenotypes, including motor behavior, escape latency, emotionality, seizure susceptibility (Szs1), and responses to ethanol, caffeine, pentobarbital, and haloperidol. This region also controls the expression of a remarkably large number of genes, including genes that are associated with some of the classical traits that map to distal Chr 1 (e.g., seizure susceptibility). Here, we ask whether this QTL-rich region on Chr 1 …

Climate Conditions In Bedded Confinement Buildings, Terry L. Mader, Leslie J. Johnson, Tami Brown-Brandl, John Gaughan

Department of Animal Science: Faculty Publications

Confinement buildings are utilized for finishing cattle to allow more efficient collection of animal waste and to buffer animals against adverse climatic conditions. Environmental data were obtained from a 29 m wide x 318 m long, solid floor, bedded confinement building with the long axis oriented east to west. The south side (front) was approximately 8.5 m high and the north (back) side is approximately 5.0 m high with 3.7 m being open (at the top). The opening was closed to within 1.0 m of the top in the winter. In general, low wind speed and/or decreased air movement associated …

Microarray Analysis Reveals Distinctive Signaling Between The Bed Nucleus Of The Stria Terminalis, Nucleus Accumbens, And Dorsal Striatum, Christopher M. Olsen, Yong Pandey, Shirlean Goodwin, Daniel C. Ciobanu, Lu Lu, Thomas R. Sutter, Danny G. Winder

Department of Animal Science: Faculty Publications

Microarray analysis reveals distinctive signaling between the bed nucleus of the stria terminalis, nucleus accumbens, and dorsal striatum. Physiol Genomics 32: 283–298, 2008. First published October 2, 2006; doi:10.1152/physiolgenomics.00224.2006.—To identify distinct transcriptional patterns between the major subcortical dopamine targets commonly studied in addiction we studied differences in gene expression between the bed nucleus of the stria terminalis (BNST), nucleus accumbens (NAc), and dorsal striatum (dStr) using microarray analysis. We first tested for differences in expression of genes encoding transcripts for common neurotransmitter systems as well as calcium binding proteins routinely used in neuroanatomical delineation of brain regions. This a priori …

Rapid Rates Of Lineage-Specific Gene Duplication And Deletion In The Α-Globin Gene Family, Federico G. Hoffmann, Juan C. Opazo, Jay F. Storz

Jay F. Storz Publications

Phylogeny reconstructions of the globin gene families have revealed that paralogous genes within species are often more similar to one another than they are to their orthologous counterparts in closely related species. This pattern has been previously attributed to mechanisms of concerted evolution such as interparalog gene conversion that homogenize sequence variation between tandemly duplicated genes and therefore create the appearance of recent common ancestry. Here we report a comparative genomic analysis of the α-globin gene family in mammals that reveal a surprisingly high rate of lineage-specific gene duplication and deletion via unequal crossing-over. Results of our analysis reveal that …

Quantitative Trait Locus Mapping For Seed Mineral Concentrations In Two Arabidopsis Thaliana Recombinant Inbred Populations, Brian M. Waters, Michael A. Grusak

Department of Agronomy and Horticulture: Faculty Publications

Biofortification of foods, achieved by increasing the concentrations of minerals such as iron (Fe) and zinc (Zn), is a goal of plant scientists. Understanding genes that influence seed mineral concentration in a model plant such as Arabidopsis could help in the development of nutritionally enhanced crop cultivars. Quantitative trait locus (QTL) mapping for seed concentrations of calcium (Ca), copper (Cu), Fe, potassium (K), magnesium (Mg), manganese (Mn), phosphorus (P), sulfur (S), and Zn was performed using two recombinant inbred line (RIL) populations, Columbia (Col) × Landsberg erecta (Ler) and Cape Verde Islands (Cvi) × Ler, grown …

Whole-Plant Mineral Partitioning Throughout The Life Cycle In Arabidopsis Thaliana Ecotypes Columbia, Landsberg Erecta, Cape Verde Islands, And The Mutant Line Ysl1ysl3, Brian M. Waters, Michael A. Grusak

Department of Agronomy and Horticulture: Faculty Publications

Minimal information exists on whole-plant dynamics of mineral flow through Arabidopsis thaliana or on the source tissues responsible for mineral export to developing seeds. Understanding these phenomena in a model plant could help in the development of nutritionally enhanced crop cultivars. A whole-plant partitioning study, using sequential harvests, was conducted to characterize growth and mineral concentrations and contents of rosettes, cauline leaves, stems, immature fruit, mature fruit hulls, and seeds of three WT lines (Col-0, Ler, and Cvi) and one mutant line (Col-0::ysl1ysl3). Shoot mineral content increased throughout the life cycle for all minerals, although tissue-specific …

Molecular Evolution Of Cytochrome B In High- And Low-Altitude Deer Mice (Genus Peromyscus), E.J. Gering, J. C. Opazo, Jay F. Storz

Jay F. Storz Publications

Patterns of amino-acid polymorphism in human mitochondrial genes have been interpreted as evidence for divergent selection among populations that inhabit climatically distinct environments. If similar patterns are mirrored in other broadly distributed mammalian species, then adaptive modifications of mitochondrial protein function may be detected in comparisons among locally adapted populations of a single wide-ranging species, or among closely related species that have adapted to different environments. Here, we test for evidence of positive selection on cytochrome b variation within and among species of the ecologically diverse rodent genus Peromyscus. We used likelihood-based comparisons of synonymous and nonsynonymous substitution rates …

Speciation Within Bonneted Bats (Genus Eumops): The Complexity Of Morphological, Mitochondrial, And Nuclear Data Sets In Systematics, Molly M. Mcdonough, Loren K. Ammerman, Robert M. Timm, Hugh H. Genoways, Peter A. Larsen, Robert J. Baker

University of Nebraska State Museum: Mammalogy Papers

We phylogenetically analyze 705 base pairs of the cytochrome-b gene and 351 amplified fragment length polymorphism (AFLP) bands from populations of the karyotypically variable Wagner’s bonneted bat, Eumops glaucinus, and the Florida bonneted bat, Eumops floridanus (Chiroptera: Molossidae). Three karyotypes have been documented across the range of E. glaucinus, and we report that the karyotype from Cuba is morphologically similar to that from Jamaica. A 4th karyotype is present in specimens from western Ecuador. Three distinct lineages are present in both the cytochrome-b and AFLP trees. One lineage is restricted to western Ecuador and exhibits cytochrome-b …

Development Of An Immunofluorescence Assay Using Recombinant Proteins Expressed In Insect Cells To Screen And Confirm Presence Of Human Herpesvirus 8-Specific Antibodies, Veenu Minhas, Lynsey N. Crosby, Kay L. Crabtree, Saul Phiri, Tendai J. M'Soka, Chipepo Kankasa, William J. Harrington, Charles D. Mitchell, Charles Wood

Nebraska Center for Virology: Faculty Publications

Human herpesvirus 8 (HHV-8), or Kaposi’s sarcoma (KS)-associated herpesvirus, has been linked to all forms of KS. The results of most current serological assays for the detection of HHV-8-specific antibodies have low levels of concordance among themselves. To establish a sensitive and specific testing strategy that can be used to screen for HHV-8-specific antibodies, three HHV-8 proteins, ORF65, ORF73, and K8.1A, were expressed by using baculoviral vectors in insect cells and incorporated into a monoclonal antibodyenhanced immunofluorescence assay (mIFA) termed the Sf9 three-antigen mIFA. The results obtained by this mIFA were compared to those obtained by a standard mIFA with …

Small-Molecule Cd4 Mimics Interact With A Highly Conserved Pocket On Hiv-1 Gp120, Navid Madani, Arne Schön, Amy M. Princiotto, Judith M. Lalonde, Joel R. Cpurter, Takahiro Soeta, Danny Ng, Liping Wang, Evan T. Brower, Shi-Hua Xiang, Young Do Kwon, Chih-Chin Huang, Richard Wyatt, Peter D. Kwong, Ernesto Freire, Amos B. Smith Iii, Joseph Sodroski

Nebraska Center for Virology: Faculty Publications

Human immunodeficiency virus (HIV-1) interaction with the primary receptor, CD4, induces conformational changes in the viral envelope glycoproteins that allow binding to the CCR5 second receptor and virus entry into the host cell. The small molecule NBD-556 mimics CD4 by binding the gp120 exterior envelope glycoprotein, moderately inhibiting virus entry into CD4-expressing target cells, and enhancing CCR5 binding and virus entry into CCR5-expressing cells lacking CD4. Studies of NBD-556 analogues and gp120 mutants suggest that: 1) NBD-556 binds within the Phe 43 cavity, a highly conserved, functionally important pocket formed as gp120 assumes the CD4- bound conformation; 2) the NBD-556 …

The Human Immunodeficiency Virus Type 1 Envelope Confers Higher Rates Of Replicative Fitness To Perinatally Transmitted Viruses Than To Nontransmitted Viruses, Xiaohong Kong, John T. West, Hong Zhang, Danielle M. Shea, Tendai J. M’Soka, Charles Wood

Nebraska Center for Virology: Faculty Publications

Selection of a minor viral genotype during perinatal transmission of human Immunodeficiency virus type 1

(HIV-1) has been observed, but there is a lack of information on the correlation of the restrictive transmission

with biological properties of the virus, such as replicative fitness. Recombinant viruses expressing the enhanced

green fluorescent protein or the Discosoma sp. red fluorescent (DsRed2) protein carrying the V1 to V5

regions of env from seven mother-infant pairs (MIPs) infected by subtype C HIV-1 were constructed, and

competition assays were carried out to compare the fitness between the transmitted and nontransmitted

viruses. Flow cytometry was used to …

Varying Efficiency Of Long-Term Replication Of Papillomaviruses In Saccharomyces Cerevisiae, Adam J. Rogers, Malte Loggen, Karen Lee, Peter C. Angeletti

Nebraska Center for Virology: Faculty Publications

Human papillomaviruses (HPVs) replicate in mitotically active basal keratinocytes. Two virally encoded proteins, E1, a helicase, and E2, a transcription factor, are important players in replication and maintenance of HPV episomes. We previously showed that HPV16 could replicate stably in Saccharomyces cerevisiae [Angeletti, P.C., Kim, K., Fernandes, F.J., and Lambert, P.F. (2002)] and we identified cis-elements that mediate replication and maintenance [J. Virol. 76(7), 3350-3358.; Kim, K., Angeletti, P.C., Hassebroek, E.C., and Lambert, P.F. (2005)]. Here, we demonstrate that although multiple HPV genomes replicate stably in yeast, they do so with differing long-term efficiency; HPV6-Ura3 is replicated at the …

A Versatile Assay For The Identification Of Rna Silencing Suppressors Based On Complementation Of Viral Movement, Jason G. Powers, Tim L. Sit, Feng Qu, T. Jack Morris, Kook-Hyung Kim, Steven A. Lommel

Nebraska Center for Virology: Faculty Publications

The cell-to-cell movement of Turnip crinkle virus (TCV) in Nicotiana benthamiana requires the presence of its coat protein (CP), a known suppressor of RNA silencing. RNA transcripts of a TCV construct containing a reporter gene (green fluorescent protein) (TCV-sGFP) in place of the CP open reading frame generated foci of three to five cells. TCV CP delivered in trans by Agrobacterium tumefaciens infiltration potentiated movement of TCV-sGFP and increased foci diameter, on average, by a factor of four. Deletion of the TCV movement proteins in TCV-sGFP (construct TCVΔ92-sGFP) abolished the movement complementation ability of TCV CP. Other known suppressors of …

Effects Of Shielding Adenoviral Vectors With Polyethylene Glycol On Vector-Specific And Vaccine-Mediated Immune Responses, Eric A. Weaver, Michael A. Barry

Nebraska Center for Virology: Faculty Publications

Many individuals have been previously exposed to human adenovirus serotype 5 (Ad5). This prior immunity has long been known to hinder its use for gene therapy and as a gene-based vaccine. Given these immunogenicity problems, we have tested whether polyethylene glycol (PEG) can blunt immune effects against Ad5 during systemic and mucosal vaccination. Ad5 vectors were covalently modified with 5-, 20-, and 35-kDa linear PEG polymers and evaluated for their ability to produce immune responses against transgene antigen prod- ucts and the vector itself. We show that shielding Ad5 with different-sized PEGs generally reduces transduction and primary antibody responses by …

Ecological Genomics: Understanding Gene And Genome Function In The Natural Environment, M. C. Ungerer, L. C. Johnson, M. A. Herman

School of Biological Sciences: Faculty Publications

The field of ecological genomics seeks to understand the genetic mechanisms underlying responses of organisms to their natural environments. This is being achieved through the application of functional genomic approaches to identify and characterize genes with ecological and evolutionary relevance. By its very nature, ecological genomics is an interdisciplinary field. In this review, we consider the significance of this new area of study from both an ecological and genomic perspective using examples from the recent literature. We submit that by considering more fully an ecological context, researchers may gain additional insights into the underlying genetic basis of ecologically relevant phenotypic …

Analysis Of Wnt Signaling During Caenorhabditis Elegans Postembryonic Development, Samantha Van Hoffelen, Michael A. Herman

School of Biological Sciences: Faculty Publications

Wnts play a central role in the development of many cells and tissue types in all species studied to date. Like many other extracellular signaling pathways, secreted Wnt proteins are involved in many different processes; in C. elegans these include cell proliferation, differentiation, cell migration, control of cell polarity, axon outgrowth, and control of the stem cell niche. Perturbations in Wnt signaling are also key factors in cancer formation, and therefore of interest to oncobiologists. Wnts are secreted glycoproteins, which bind to Frizzled transmembrane receptors and signal either through, or independently of β-catenin. Both β-catenin-dependent (Wnt/β-catenin) and -independent pathways function …