Genetics and Genomics Commons^™

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 …

High Rate Of Recent Transposable Element–Induced Adaptation In Drosophila Melanogaster, Josefa Gonzalez, Kapa Lenkov, Mikhail Lipatov, J. Michael Macpherson, Dmitri A. Petrov

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Although transposable elements (TEs) are known to be potent sources of mutation, their contribution to the generation of recent adaptive changes has never been systematically assessed. In this work, we conduct a genome-wide screen for adaptive TE insertions in Drosophila melanogaster that have taken place during or after the spread of this species out of Africa. We determine population frequencies of 902 of the 1,572 TEs in Release 3 of the D. melanogaster genome and identify a set of 13 putatively adaptive TEs. These 13 TEs increased in population frequency sharply after the spread out of Africa. We argue that …

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 …

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 …

The Dynamic Evolutionary History Of The Bananaquit (Coereba Flaveola) In The Caribbean Revealed By A Multigene Analysis, Eva Bellemain, Eldredge Bermingham, Robert Ricklefs

Biology Department Faculty Works

BackgroundThe bananaquit (Coereba flaveola) is a small nectivorous and frugivorous emberizine bird (order Passeriformes) that is an abundant resident throughout the Caribbean region. We used multi-gene analyses to investigate the evolutionary history of this species throughout its distribution in the West Indies and in South and Middle America. We sequenced six mitochondrial genes (3744 base pairs) and three nuclear genes (2049 base pairs) for forty-four bananaquits and three outgroup species. We infer the ancestral area of the present-day bananaquit populations, report on the species' phylogenetic, biogeographic and evolutionary history, and propose scenarios for its diversification and range expansion.ResultsPhylogenetic concordance between …

Advancing Epidemiological Science Through Computational Modeling: A Review With Novel Examples, Scott M. Duke-Sylvester, Eli N. Perencevich, Jon P. Furuno, Leslie A. Real, Holly Gaff

Biological Sciences Faculty Publications

Computational models have been successfully applied to a wide variety of research areas including infectious disease epidemiology. Especially for questions that are difficult to examine in other ways, computational models have been used to extend the range of epidemiological issues that can be addressed, advance theoretical understanding of disease processes and help identify specific intervention strategies. We explore each of these contributions to epidemiology research through discussion and examples. We also describe in detail models for raccoon rabies and methicillin-resis-tant Staphylococcus aureus, drawn from our own research, to further illustrate the role of computation in epidemiological modeling.

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 …

Validation Case Study : Treatment Effectiveness In Aspen Vegetation Type : A Comparison Of Two Types Of Treatments On The Manti-La Sal National Forest, Diane M. Cote

Aspen Bibliography

No abstract provided.

Ancient Dna Identification Of Early 20th Century Simian T-Cell Leukemia Virus Type 1, Sebastien Calvignac, Jean-Michel Terme, Shannon M. Hensley, Pierre Jalinot, Alex D. Greenwood, Catherine Hanni

Biological Sciences Faculty Publications

The molecular identification of proviruses from ancient tissues (and particularly from bones) remains a contentious issue. It can be expected that the copy number of proviruses will be low, which magnifies the risk of contamination with retroviruses from exogenous sources. To assess the feasibility of paleoretrovirological studies, we attempted to identify proviruses from early 20th century bones of museum specimens while following a strict ancient DNA methodology. Simian T-cell leukemia virus type 1 sequences were successfully obtained and authenticated from a Chlorocebus pygerythrus specimen. This represents the first clear evidence that it will be possible to use museum specimens to …

Genome-Wide Compensatory Changes Accompany Drug-Selected Mutations In The Plasmodium Falciparum Crt Gene, Hongying Jiang, Jigar J. Patel, Ming Yi, Jianbing Mu, Jinhui Ding, Robert Stephens, Roland A. Cooper, Michael T. Ferdig, Xin-Zhuan Su

Biological Sciences Faculty Publications

Mutations in PfCRT (Plasmodium falciparum chloroquine-resistant transporter), particularly the substitution at amino acid position 76, confer chloroquine (CQ) resistance in P. falciparum. Point mutations in the homolog of the mammalian multidrug resistance gene (pfmdr1) can also modulate the levels of CQ response. Moreover, parasites with the same pfcrt and pfmdr1 alleles exhibit a wide range of drug sensitivity, suggesting that additional genes contribute to levels of CQ resistance (CQR). Reemergence of CQ sensitive parasites after cessation of CQ use indicates that changes in PfCRT are deleterious to the parasite. Some CQR parasites, however, persist in the …

The Meaning Of Race In The Dna Era: Science, History And The Law, Christian Sundquist

Articles

The meaning of “race” has changed dramatically over time. Early theories of race assigned social, intellectual, moral and physical values to perceived physical differences among groups of people. The perception that race should be defined in terms of genetic and biologic difference fueled the “race science” of the Eighteenth and Nineteenth centuries, during which time geneticists, physiognomists, eugenicists, anthropologists and others purported to find scientific justification for denying equal treatment to non-white persons. Nazi Germany applied these understandings of race in a manner which shocked the world, and following World War II the concept of race increasingly came to be …

Multifactor Effects And Evidence Of Potential Interaction Between Complement Factor H Y402h And Loc387715 A69s In Age-Related Macular Degeneration, Sanna P. Seitsonen, Päivi Onkamo, Gang Peng, Momiao Xiong, Petri V. Tommila, Päivi H. Ranta, Juha M. Holopainen, Jukka A. Moilanen, Tapani Palosaari, Kai Kaarniranta, Seppo Meri, Ilkka R. Immonen, Irma E. Järvelä

Student and Faculty Publications

BACKGROUND: Variants in the complement cascade genes and the LOC387715/HTRA1, have been widely reported to associate with age-related macular degeneration (AMD), the most common cause of visual impairment in industrialized countries. METHODS/PRINCIPAL FINDINGS: We investigated the association between the LOC387715 A69S and complement component C3 R102G risk alleles in the Finnish case-control material and found a significant association with both variants (OR 2.98, p = 3.75 x 10(-9); non-AMD controls and OR 2.79, p = 2.78 x 10(-19), blood donor controls and OR 1.83, p = 0.008; non-AMD controls and OR 1.39, p = 0.039; blood donor controls), respectively. Previously, …

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 …

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 …

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 …