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2013

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Reporters For The Analysis Of N-Glycosylation In Candida Albicans, Shahida Shahana, Hector M. Mora-Montes, Luis Castillo, Iryna Bohovych, Chirag C. Sheth, Frank C. Odds, Neil A.R. Gow, Alistair J.P. Brown Jan 2013

Reporters For The Analysis Of N-Glycosylation In Candida Albicans, Shahida Shahana, Hector M. Mora-Montes, Luis Castillo, Iryna Bohovych, Chirag C. Sheth, Frank C. Odds, Neil A.R. Gow, Alistair J.P. Brown

Department of Biochemistry: Faculty Publications

A large proportion of Candida albicans cell surface proteins are decorated post-translationally by glycosylation. Indeed N-glycosylation is critical for cell wall biogenesis in this major fungal pathogen and for its interactions with host cells. A detailed understanding of N-glycosylation will yield deeper insights into host-pathogen interactions. However, the analysis of N-glycosylation is extremely challenging because of the complexity and heterogeneity of these structures. Therefore, in an attempt to reduce this complexity and facilitate the analysis of N-glycosylation, we have developed new synthetic C. albicans reporters that carry a single N-linked glycosylation site derived from Saccharomyces cerevisiae Suc2. These …


Microrna Function In Human Diseases, Sathish Kumar Natarajan, Mary Anne Smith, Cody J. Wehrkamp, Ashley M. Mohr, Justin L. Mott Jan 2013

Microrna Function In Human Diseases, Sathish Kumar Natarajan, Mary Anne Smith, Cody J. Wehrkamp, Ashley M. Mohr, Justin L. Mott

Department of Biochemistry: Faculty Publications

MicroRNAs are emerging as a hot topic in research, and rightfully so. They show great promise as targets of treatment and as markers for common human diseases, such as cancer and metabolic diseases. In this review, we address some of the basic questions regarding micro- RNA function in human disease and the clinical significance of microRNAs. Specifically, micro- RNAs in epigenetics, cancer, and metabolic diseases are discussed, with examples taken from cholangiocarcinoma and nonalcoholic fatty liver disease.


Influence Of Two Herbicides On Soybean Cyst Nematode (Heterodera Glycines) Reproduction On Henbit (Lamium Amplexicaule) Roots, Rodrigo Werle, Mark L. Bernards, Loren J. Giesler, John L. Lindquist Jan 2013

Influence Of Two Herbicides On Soybean Cyst Nematode (Heterodera Glycines) Reproduction On Henbit (Lamium Amplexicaule) Roots, Rodrigo Werle, Mark L. Bernards, Loren J. Giesler, John L. Lindquist

Department of Agronomy and Horticulture: Faculty Publications

Soybean cyst nematode (SCN) is the most yield-limiting pathogen of soybean in the United States. Henbit is a prevalent winter annual weed species in no-till fields and is reported to be an alternative host of SCN. A greenhouse study was conducted to evaluate how the development of SCN on henbit roots was affected by herbicide mode of action and time of herbicide application. Henbit plants were grown in watertight pots placed in a water bath bench that kept soil temperature constant (27 6 1 C) during the study. Ten d after transplanting, pots were inoculated with approximately 1,000 SCN eggs. …


Maternal Environment Effects On Phenolic Defenses In Abutilon Theophrasti Seeds, Brian J. Schutte, Sam E. Wortman, John L. Lindquist, Adam S. Davis Jan 2013

Maternal Environment Effects On Phenolic Defenses In Abutilon Theophrasti Seeds, Brian J. Schutte, Sam E. Wortman, John L. Lindquist, Adam S. Davis

Department of Agronomy and Horticulture: Faculty Publications

A class of phenolic compounds, ortho-dihydroxyphenols (hereafter “o-DHP”), has been implicated with seed survival. Based on expectations of the growth-differentiation balance hypothesis, we predicted that seed o-DHP concentration exhibits a curvilinear response to increasing resource availability in the maternal environment, with maximum o-DHP occurring at moderate resource levels. To test this hypothesis, Abutilon theophrasti seeds were produced under field conditions at two locations. Each location included twelve maternal environments established through factorial combinations of soil compost (+/−), species assemblage (A. theophrasti with and without maize), and soil nitrogen fertilizer (0, 0.5× or 1× local …


Seed Burial Physical Environment Explains Departures From Regional Hydrothermal Model Of Giant Ragweed (Ambrosia Trifida) Seedling Emergence In U.S. Midwest, Adam S. Davis, Sharon Clay, John Cardina, Anita Dille, Frank Forcella, John Lindquist, Christy Sprague Jan 2013

Seed Burial Physical Environment Explains Departures From Regional Hydrothermal Model Of Giant Ragweed (Ambrosia Trifida) Seedling Emergence In U.S. Midwest, Adam S. Davis, Sharon Clay, John Cardina, Anita Dille, Frank Forcella, John Lindquist, Christy Sprague

Department of Agronomy and Horticulture: Faculty Publications

Robust predictions of weed seedling emergence from the soil seedbank are needed to aid weed management. A common seed accession (Illinois) of giant ragweed was buried in replicate experimental gardens over 18 site years in Illinois, Michigan, Kansas, Nebraska, Ohio, and South Dakota to examine the importance of site and climate variability by year on seedling emergence. In a nonlinear mixed-effects modeling approach, we used a flexible sigmoidal function (Weibull) to model giant ragweed cumulative seedling emergence in relation to hydrothermal time accumulated in each site-year. An iterative search method across a range of base temperature (Tb) …


Sbml Qualitative Models: A Model Representation Format And Infrastructure To Foster Interactions Between Qualitative Modelling Formalisms And Tools, Claudine Chaouiya, Duncan Bérenguier, Sarah M. Keating, Aurélien Naldi, Martijn P. Van Iersel, Nicolas Rodriguez, Andreas Dräger, Finja Büchel, Thomas Cokelaer, Bryan Kowal, Benjamin Wicks, Emanuel Gonçalves, Julien Dorier, Michel Page, Pedro T. Monteiro, Axel Von Kamp, Ioannis Xenarios, Hidde De Jong, Michael Hucka, Steffen Klamt, Denis Thieffry, Nicolas Le Novère, Julio Saez-Rodriguez, Tomáš Helikar Jan 2013

Sbml Qualitative Models: A Model Representation Format And Infrastructure To Foster Interactions Between Qualitative Modelling Formalisms And Tools, Claudine Chaouiya, Duncan Bérenguier, Sarah M. Keating, Aurélien Naldi, Martijn P. Van Iersel, Nicolas Rodriguez, Andreas Dräger, Finja Büchel, Thomas Cokelaer, Bryan Kowal, Benjamin Wicks, Emanuel Gonçalves, Julien Dorier, Michel Page, Pedro T. Monteiro, Axel Von Kamp, Ioannis Xenarios, Hidde De Jong, Michael Hucka, Steffen Klamt, Denis Thieffry, Nicolas Le Novère, Julio Saez-Rodriguez, Tomáš Helikar

Department of Biochemistry: Faculty Publications

Background: Qualitative frameworks, especially those based on the logical discrete formalism, are increasingly used to model regulatory and signalling networks. A major advantage of these frameworks is that they do not require precise quantitative data, and that they are well-suited for studies of large networks. While numerous groups have developed specific computational tools that provide original methods to analyse qualitative models, a standard format to exchange qualitative models has been missing.

Results: We present the Systems Biology Markup Language (SBML) Qualitative Models Package (“qual”), an extension of the SBML Level 3 standard designed for computer representation of qualitative …


Selenodb 2.0: Annotation Of Selenoprotein Genes In Animals And Their Genetic Diversity In Humans, Frederic Romagne, Didac Santesmasses, Louise White, Gaurab K. Sarangi, Marco Mariotti, Ron Hübler, Antje Weihmann, Genis Parra, Vadim N. Gladyshev, Roderic Guigo, Sergi Castellano Jan 2013

Selenodb 2.0: Annotation Of Selenoprotein Genes In Animals And Their Genetic Diversity In Humans, Frederic Romagne, Didac Santesmasses, Louise White, Gaurab K. Sarangi, Marco Mariotti, Ron Hübler, Antje Weihmann, Genis Parra, Vadim N. Gladyshev, Roderic Guigo, Sergi Castellano

Department of Biochemistry: Faculty Publications

SelenoDB (http://www.selenodb.org) aims to provide high-quality annotations of selenoprotein genes, proteins and SECIS elements. Selenoproteins are proteins that contain the amino acid selenocysteine (Sec) and the first release of the database included annotations for eight species. Since the release of SelenoDB 1.0 many new animal genomes have been sequenced. The annotations of selenoproteins in new genomes usually contain many errors in major databases. For this reason, we have now fully annotated selenoprotein genes in 58 animal genomes. We provide manually curated annotations for human selenoproteins, whereas we use an automatic annotation pipeline to annotate selenoprotein genes in other animal genomes. …


The Basis For Limited Specificity And Mhc Restriction In A T Cell Receptor Interface, Kurt H. Piepenbrink, Sydney J. Blevins, Daniel R. Scott, Brian M. Baker Jan 2013

The Basis For Limited Specificity And Mhc Restriction In A T Cell Receptor Interface, Kurt H. Piepenbrink, Sydney J. Blevins, Daniel R. Scott, Brian M. Baker

Department of Biochemistry: Faculty Publications

αβ Tcell receptors (TCRs) recognize peptides presented by major histocompatibility complex (MHC) proteins using multiple complementarity-determining region (CDR) loops. TCRs display an array of poorly understood recognition properties, including specificity, crossreactivity and MHC restriction. Here we report a comprehensive thermodynamic deconstruction of the interaction between the A6 TCR and the Tax peptide presented by the class I MHC HLA-A*0201, uncovering the physical basis for the receptor’s recognition properties. Broadly, our findings are in conflict with widely held generalities regarding TCR recognition, such as the relative contributions of central and peripheral peptide residues and the roles of the hypervariable and germline …


Elucidating Causes Of Diporeia Decline In The Great Lakes Via Metabolomics: Physiological Responses After Exposure To Different Stressors, Suman Maity, Amber Jannasch, Jiri Adamec, James M. Watkins, Thomas Nalepa, Tomas O. Höök, Maria S. Sepúlveda Jan 2013

Elucidating Causes Of Diporeia Decline In The Great Lakes Via Metabolomics: Physiological Responses After Exposure To Different Stressors, Suman Maity, Amber Jannasch, Jiri Adamec, James M. Watkins, Thomas Nalepa, Tomas O. Höök, Maria S. Sepúlveda

Department of Biochemistry: Faculty Publications

The benthic macroinvertebrate Diporeia spp. have been extirpated from many areas of the Laurentian Great Lakes, but the mechanisms underlying such declines are not fully understood. Diporeia declines coinciding with the invasion of exotic dreissenid mussels (zebra and quagga) have led to the hypothesis that Diporeia declines are a result of decreased food availability from increasing competition with dreissenids for diatoms. There is additional evidence that Diporeia are negatively affected when in close proximity to dreissenids, probably because of exposure to toxins present in the mussels’ pseudofeces. Diporeia are also known to be sensitive to anthropogenic contaminants (such as polychlorinated …


Candida Albicans Czf1 And Efg1 Coordinate The Response To Farnesol During Quorum Sensing, White-Opaque Thermal Dimorphism, And Cell Death, Melanie L. Langford, Jessica C. Hargarten, Krista D. Patefield, Elizabeth Marta, Jill R. Blankenship, Saranna Fanning, Kenneth W. Nickerson, Audrey L. Atkin Jan 2013

Candida Albicans Czf1 And Efg1 Coordinate The Response To Farnesol During Quorum Sensing, White-Opaque Thermal Dimorphism, And Cell Death, Melanie L. Langford, Jessica C. Hargarten, Krista D. Patefield, Elizabeth Marta, Jill R. Blankenship, Saranna Fanning, Kenneth W. Nickerson, Audrey L. Atkin

School of Biological Sciences: Faculty Publications

Quorum sensing by farnesol in Candida albicans inhibits filamentation and may be directly related to its ability to cause both mucosal and systemic diseases. The Ras1-cyclic AMP signaling pathway is a target for farnesol inhibition. However, a clear understanding of the downstream effectors of the morphological farnesol response has yet to be unraveled. To address this issue, we screened a library for mutants that fail to respond to farnesol. Six mutants were identified, and the czf1Δ/czf1Δ mutant was selected for further characterization. Czf1 is a transcription factor that regulates filamentation in embedded agar and also whiteto- opaque switching. We found …


A Virus-Induced Gene Silencing Method To Study Soybean Cyst Nematode Parasitism In Glycine Max, Pramod K. Kandoth, Robert Heinz, Greg Yeckel, Nathan W. Gross, Parijat S. Juvale, John Hill, Steven A. Whitham, Thomas J. Baum, Melissa G. Mitchum Jan 2013

A Virus-Induced Gene Silencing Method To Study Soybean Cyst Nematode Parasitism In Glycine Max, Pramod K. Kandoth, Robert Heinz, Greg Yeckel, Nathan W. Gross, Parijat S. Juvale, John Hill, Steven A. Whitham, Thomas J. Baum, Melissa G. Mitchum

School of Biological Sciences: Faculty Publications

Background: Bean pod mottle virus (BPMV) based virus-induced gene silencing (VIGS) vectors have been developed and used in soybean for the functional analysis of genes involved in disease resistance to foliar pathogens. However, BPMV-VIGS protocols for studying genes involved in disease resistance or symbiotic associations with root microbes have not been developed.

Findings: Here we describe a BPMV-VIGS protocol suitable for reverse genetic studies in soybean roots. We use this method for analyzing soybean genes involved in resistance to soybean cyst nematode (SCN). A detailed SCN screening pipeline is described.

Conclusions: The VIGS method described here provides …


Reductive Evolution And The Loss Of Pdc/Pas Domains From The Genus Staphylococcus, Neethu Shah, Rosmarie Gaupp, Hideaki Moriyama, Kent M. Eskridge, Etsuko N. Moriyama, Greg A. Somerville Jan 2013

Reductive Evolution And The Loss Of Pdc/Pas Domains From The Genus Staphylococcus, Neethu Shah, Rosmarie Gaupp, Hideaki Moriyama, Kent M. Eskridge, Etsuko N. Moriyama, Greg A. Somerville

School of Biological Sciences: Faculty Publications

Background: The Per-Arnt-Sim (PAS) domain represents a ubiquitous structural fold that is involved in bacterial sensing and adaptation systems, including several virulence related functions. Although PAS domains and the subclass of PhoQ-DcuS-CitA (PDC) domains have a common structure, there is limited amino acid sequence similarity. To gain greater insight into the evolution of PDC/PAS domains present in the bacterial kingdom and staphylococci in specific, the PDC/PAS domains from the genomic sequences of 48 bacteria, representing 5 phyla, were identified using the sensitive search method based on HMM-to-HMM comparisons (HHblits).

Results: A total of 1,007 PAS domains and 686 …


Four Distinct Types Of Dehydration Stress Memory Genes In Arabidopsis Thaliana, Yong Ding, Ning Liu, Laetitia Virlouvet, Jean-Jack Riethoven, Michael E. Fromm, Zoya Avramova Jan 2013

Four Distinct Types Of Dehydration Stress Memory Genes In Arabidopsis Thaliana, Yong Ding, Ning Liu, Laetitia Virlouvet, Jean-Jack Riethoven, Michael E. Fromm, Zoya Avramova

School of Biological Sciences: Faculty Publications

Background: How plants respond to dehydration stress has been extensively researched. However, how plants respond to multiple consecutive stresses is virtually unknown. Pre-exposure to various abiotic stresses (including dehydration) may alter plants’ subsequent responses by improving resistance to future exposures. These observations have led to the concept of ‘stress memory’ implying that during subsequent exposures plants provide responses that are different from those during their first encounter with the stress. Genes that provide altered responses in a subsequent stress define the ‘memory genes’ category; genes responding similarly to each stress form the ‘non-memory’ category.

Results: Using a genome-wide …


Heritability And Inter-Population Differences In Lipid Profiles Of Drosophila Melanogaster, Cornelia J. F. Scheitz, Yu Guo, Angela M. Early, Lawrence G. Harshman, Andrew G. Clark Jan 2013

Heritability And Inter-Population Differences In Lipid Profiles Of Drosophila Melanogaster, Cornelia J. F. Scheitz, Yu Guo, Angela M. Early, Lawrence G. Harshman, Andrew G. Clark

School of Biological Sciences: Faculty Publications

Characterizing and understanding the complex spectrum of lipids in higher organisms lags far behind our analysis of genome and transcriptome sequences. Here we generate and evaluate comprehensive lipid profiles (>200 lipids) of 92 inbred lines from five different Drosophila melanogaster populations. We find that the majority of lipid species are highly heritable, and even lipids with odd-chain fatty acids, which cannot be generated by the fly itself, also have high heritabilities. Abundance of the endosymbiont Wolbachia, a potential provider of odd-chained lipids, was positively correlated with this group of lipids. Additionally, we show that despite years of laboratory …


Regional Contingencies In The Relationship Between Aboveground Biomass And Litter In The World’S Grasslands, Lydia R. O’Halloran, Elizabeth T. Borer, Eric W. Seabloom, Andrew S. Macdougall, Elsa E. Cleland, Rebecca L. Mcculley, Sarah Hobbie, W. Stanley Harpole, Nicole M. Decrappeo, Chengjin Chu, Jonathan D. Bakker, Kendi F. Davies, Guozhen Du, Jennifer Firn, Nicole Hagenah, Kirsten S. Hofmockel, Johannes Knops, Wei Li, Brett A. Melbourne, John W. Morgan, John L. Orrock, Suzanne M. Prober, Carly J. Stevens Jan 2013

Regional Contingencies In The Relationship Between Aboveground Biomass And Litter In The World’S Grasslands, Lydia R. O’Halloran, Elizabeth T. Borer, Eric W. Seabloom, Andrew S. Macdougall, Elsa E. Cleland, Rebecca L. Mcculley, Sarah Hobbie, W. Stanley Harpole, Nicole M. Decrappeo, Chengjin Chu, Jonathan D. Bakker, Kendi F. Davies, Guozhen Du, Jennifer Firn, Nicole Hagenah, Kirsten S. Hofmockel, Johannes Knops, Wei Li, Brett A. Melbourne, John W. Morgan, John L. Orrock, Suzanne M. Prober, Carly J. Stevens

School of Biological Sciences: Faculty Publications

Based on regional-scale studies, aboveground production and litter decomposition are thought to positively covary, because they are driven by shared biotic and climatic factors. Until now we have been unable to test whether production and decomposition are generally coupled across climatically dissimilar regions, because we lacked replicated data collected within a single vegetation type across multiple regions, obfuscating the drivers and generality of the association between production and decomposition. Furthermore, our understanding of the relationships between production and decomposition rests heavily on separate meta-analyses of each response, because no studies have simultaneously measured production and the accumulation or decomposition of …


A Whole-Cell Biosensor For The Detection Of Gold, Carla M. Zammit, Davide Quaranta, Shane Gibson, Anita J. Zaitouna, Christine Ta, Joel Brugger, Rebecca Y. Lai, Gregor Grass, Frank Reith Jan 2013

A Whole-Cell Biosensor For The Detection Of Gold, Carla M. Zammit, Davide Quaranta, Shane Gibson, Anita J. Zaitouna, Christine Ta, Joel Brugger, Rebecca Y. Lai, Gregor Grass, Frank Reith

School of Biological Sciences: Faculty Publications

Geochemical exploration for gold (Au) is becoming increasingly important to the mining industry. Current processes for Au analyses require sampling materials to be taken from often remote localities. Samples are then transported to a laboratory equipped with suitable analytical facilities, such as Inductively Coupled Plasma-Mass Spectrometry (ICP-MS) or Instrumental Neutron Activation Analysis (INAA). Determining the concentration of Au in samples may take several weeks, leading to long delays in exploration campaigns. Hence, a method for the on-site analysis of Au, such as a biosensor, will greatly benefit the exploration industry. The golTSB genes from Salmonella enterica serovar typhimurium are selectively …


Cd20 Antibody Primes B Lymphocytes For Type I Interferon Production, Dongsheng Xu, Andrew Staedman, Luwen Zhang Jan 2013

Cd20 Antibody Primes B Lymphocytes For Type I Interferon Production, Dongsheng Xu, Andrew Staedman, Luwen Zhang

School of Biological Sciences: Faculty Publications

CD20 is a B cell surface marker that is expressed in various stages in B lymphocytes and certain lymphomas. Clinical administration of CD20 antibody, such as rituximab, is used widely to treat human B-cell lymphomas and other diseases. However, CD20 antibody failed to treat systemic lupus erythematosus (SLE or lupus). The reason for the failure is currently unknown. Type I interferons (IFN) are a major component for the host innate immunity, and a key pathogenic factor in lupus. We found that CD20 antibody potentiated human B cells for its production of IFNs in vitro. This function was specific to …


Conformational B-Cell Epitope Prediction On Antigen Protein Structures: A Review Of Current Algorithms And Comparison With Common Binding Site Prediction Methods, Bo Yao, Dandan Zheng, Shide Liang, Chi Zhang Jan 2013

Conformational B-Cell Epitope Prediction On Antigen Protein Structures: A Review Of Current Algorithms And Comparison With Common Binding Site Prediction Methods, Bo Yao, Dandan Zheng, Shide Liang, Chi Zhang

School of Biological Sciences: Faculty Publications

Accurate prediction of B-cell antigenic epitopes is important for immunologic research and medical applications, but compared with other bioinformatic problems, antigenic epitope prediction is more challenging because of the extreme variability of antigenic epitopes, where the paratope on the antibody binds specifically to a given epitope with high precision. In spite of the continuing efforts in the past decade, the problem remains unsolved and therefore still attracts a lot of attention from bioinformaticists. Recently, several discontinuous epitope prediction servers became available, and it is intriguing to review all existing methods and evaluate their performances on the same benchmark. In addition, …


Dna Sequencing Reveals Patterns Of Prey Selection In Migrating Sharp-Shinned Hawks Las Secuencias De Adn Revelan Patrones De Selección De Presas Por Individuos Migratorios De Accipiter Striatus, John Delong, Nancy Cox, Steve Cox, Zachary Hurst, Jeff Smith Jan 2013

Dna Sequencing Reveals Patterns Of Prey Selection In Migrating Sharp-Shinned Hawks Las Secuencias De Adn Revelan Patrones De Selección De Presas Por Individuos Migratorios De Accipiter Striatus, John Delong, Nancy Cox, Steve Cox, Zachary Hurst, Jeff Smith

School of Biological Sciences: Faculty Publications

Prey selection of migrating raptors has been documented only rarely. Here we used a genetic approach to identify avian prey of Sharp-shinned Hawks (Accipiter striatus) migrating through central New Mexico. We identified species by comparing profiles of a section of the 16S rRNA mitochondrial gene extracted from feathers of prey of known species to profiles from feathers of prey found on the feet and beaks of migrating hawks. We also quantified prey availability along the migration route with multi-year sampling by mist net at two sites near the raptor-sampling site. Sharp-shinned Hawks took most prey species in proportion to their …


Global Attracting Equilibria For Coupled Systems With Ceiling Density Dependence, Eric A. Eager, Mary Hebert, Elise Hellwig, Francisco Hernandez, Richard Rebarber, Brigitte Tenhumberg, Bryan Wigianto Jan 2013

Global Attracting Equilibria For Coupled Systems With Ceiling Density Dependence, Eric A. Eager, Mary Hebert, Elise Hellwig, Francisco Hernandez, Richard Rebarber, Brigitte Tenhumberg, Bryan Wigianto

School of Biological Sciences: Faculty Publications

In this paper, we present a system of two difference equations modeling the dynamics of a coupled population with two patches. Each patch can house only a limited number of individuals (called a carrying capacity) because resources like food and breeding sites are limited in each patch. We assume that the population in each patch is governed by a linear model until reaching a carrying capacity in each patch, resulting in map which is nonlinear and not sublinear. We analyze the global attractors of this model.


Creating An Interdisciplinary Research Course In Mathematical Ecology, Glenn Ledder, Brigitte Tenhumberg Jan 2013

Creating An Interdisciplinary Research Course In Mathematical Ecology, Glenn Ledder, Brigitte Tenhumberg

School of Biological Sciences: Faculty Publications

An integrated interdisciplinary research course in biology and mathematics is useful for recruiting students to interdisciplinary research careers, but there are difficulties involved in creating and implementing it. We describe the genesis, objectives, design policies, and structure of the Research Skills in Theoretical Ecology course at the University of Nebraska–Lincoln and discuss the difficulties that can arise in designing and implementing interdisciplinary courses.


An Interdisciplinary Research Course In Theoretical Ecology For Young Undergraduates, Glenn Ledder, Brigitte Tenhumberg, G. Travis Adams Jan 2013

An Interdisciplinary Research Course In Theoretical Ecology For Young Undergraduates, Glenn Ledder, Brigitte Tenhumberg, G. Travis Adams

School of Biological Sciences: Faculty Publications

As part of an interdepartmental effort to attract promising young students to research at the interface between mathematics and biology, we created a course in which groups of recent high school graduates and first-year college students conducted a research project in insect population dynamics. The students set up experiments, collected data, used the data to develop mathematical models, tested their models against further experiments, and prepared their results for dissemination. The course was self-contained in that the lecture portion developed the mathematical, statistical, and biological background needed for the research. A special writing component helped students learn the principles of …


Prevalence And Correlates Of Kaposi’S Sarcoma-Associated Herpesvirus Infection In A Sample Of Men Who Have Sex With Men In Eastern China, T. Zhang, H. Lin, V. Minhas, W. Zhu, Charles Wood, N. He Jan 2013

Prevalence And Correlates Of Kaposi’S Sarcoma-Associated Herpesvirus Infection In A Sample Of Men Who Have Sex With Men In Eastern China, T. Zhang, H. Lin, V. Minhas, W. Zhu, Charles Wood, N. He

School of Biological Sciences: Faculty Publications

This study aimed to determine the seroprevalence of Kaposi’s sarcoma-associated herpesvirus (KSHV) and related factors in men who have sex with men (MSM) in China. A total of 208 subjects were recruited from eastern China from 2008 to 2009. Plasma samples were collected and screened for KSHV, HIV and syphilis. Overall, KSHV seroprevalence was 32.7% in the subjects. About 92.7% of subjects reported having ever had anal sex with a man, of whom 67.8% had receptive anal sex and 77.9% had insertive anal sex. About 93.1% of the study participants reported having had oral sex with a man, of whom …


Widespread Selection Across Coding And Noncoding Dna In The Pea Aphid Genome, Ryan D. Bickel, Joseph P. Dunham, Jennifer A. Brisson Jan 2013

Widespread Selection Across Coding And Noncoding Dna In The Pea Aphid Genome, Ryan D. Bickel, Joseph P. Dunham, Jennifer A. Brisson

School of Biological Sciences: Faculty Publications

Genome-wide patterns of diversity and selection are critical measures for understanding how evolution has shaped the genome. Yet, these population genomic estimates are available for only a limited number of model organisms. Here we focus on the population genomics of the pea aphid (Acyrthosiphon pisum). The pea aphid is an emerging model system that exhibits a range of intriguing biological traits not present in classic model systems. We performed low-coverage genome resequencing of 21 clonal pea aphid lines collected from alfalfa host plants in North America to characterize genome-wide patterns of diversity and selection. We observed an excess …


Role Of Merh In Mercury Resistance In The Archaeon Sulfolobus Solfataricus, James Schelert, Deepak Rudrappa, Tyler Johnson, Paul H. Blum Jan 2013

Role Of Merh In Mercury Resistance In The Archaeon Sulfolobus Solfataricus, James Schelert, Deepak Rudrappa, Tyler Johnson, Paul H. Blum

School of Biological Sciences: Faculty Publications

Crenarchaeota include extremely thermoacidophilic organisms that thrive in geothermal

environments dominated by sulfidic ores and heavy metals such as mercury. Mercuric ion, Hg(II),

inactivates transcription in the crenarchaeote Sulfolobus solfataricus and simultaneously

derepresses transcription of a resistance operon, merHAI, through interaction with the MerR

transcription factor. While mercuric reductase (MerA) is required for metal resistance, the role of

MerH, an adjacent small and predicted product of an ORF, has not been explored. Inactivation of

MerH either by nonsense mutation or by in-frame deletion diminished Hg(II) resistance of mutant

cells. Promoter mapping studies indicated that Hg(II) sensitivity of the merH …


Antelope Mating Strategies Facilitate Invasion Of Grasslands By A Woody Weed, Shivani Jadeja, Soumya Prasad, Suhel Quader, Kavita Isvaran Jan 2013

Antelope Mating Strategies Facilitate Invasion Of Grasslands By A Woody Weed, Shivani Jadeja, Soumya Prasad, Suhel Quader, Kavita Isvaran

School of Biological Sciences: Faculty Publications

Intra and interspecific variation in frugivore behaviour can have important consequences for seed dispersal outcomes. However, most information comes from among-species comparisons, and within-species variation is relatively poorly understood. We examined how large intraspecific differences in the behaviour of a native disperser, blackbuck antelope Antilope cervicapra, influence dispersal of a woody invasive, Prosopis juliflora, in a grassland ecosystem. Blackbuck disperse P. juliflora seeds through their dung. In lekking blackbuck populations, males defend clustered or dispersed mating territories. Territorial male movement is restricted, and within their territories males defecate on dung-piles. In contrast, mixed-sex herds range over large areas …


Predicting Invasion In Grassland Ecosystems: Is Exotic Dominance The Real Embarrassment Of Richness?, Eric W. Seabloom, Elizabeth T. Borer, Yvonne Buckley, Elsa E. Cleland, Kendi Davies, Jennifer Firn, W. Stanley Harpole, Yann Hautier, Eric Lind, Andrew Macdougall, John L. Orrock, Suzanne M. Prober, Peter Andler, Juan Alberti, T. Michael Anderson, Jonathan D. Bakker, Lori A. Biederman, Dana Blumenthal, Cynthia S. Brown, Lars A. Brudvig, Maria Caldeira, Chengjin Chu, Michael J. Crawley, Pedro Daleo, Ellen I. Damschen, Carla M. D'Antonio, Nicole M. Decrappeo, Chris R. Dickman, Guozhen Du, Philip A. Fay, Paul Frater, Daniel S. Gruner, Nicole Hagenah, Andrew Hector, Aveliina Helm, Helmut Hillebrand, Kirsten S. Hofmockel, Hope C. Humphries, Oscar Iribarne, Virginia L. Jin, Adam Kay, Kevin P. Kirkman, Julia A. Klein, Johannes M. H. Knops, Kimberly J. La Pierre, Laura M. Ladwig, John G. Lambrinos, Andrew D. B. Leakey, Qi Li, Wei Li, Rebecca Mcculley, Brett Melbourne, Charles E. Mitchell, Joslin L. Moore, John Morgan, Brent Mortensen, Lydia R. O'Halloran, Meelis Partel, Jesus Pascual, David A. Pyke, Anita C. Risch, Roberto Salguero-Gomez, Mahesh Sankaran, Martin Schuetz, Anna Simonsen, Melinda Smith, Carly Stevens, Lauren L. Sullivan, Glenda M. Wardle, Elizabeth M. Wolkovich, Peter D. Wragg, Justin Wright, Louie Yang Jan 2013

Predicting Invasion In Grassland Ecosystems: Is Exotic Dominance The Real Embarrassment Of Richness?, Eric W. Seabloom, Elizabeth T. Borer, Yvonne Buckley, Elsa E. Cleland, Kendi Davies, Jennifer Firn, W. Stanley Harpole, Yann Hautier, Eric Lind, Andrew Macdougall, John L. Orrock, Suzanne M. Prober, Peter Andler, Juan Alberti, T. Michael Anderson, Jonathan D. Bakker, Lori A. Biederman, Dana Blumenthal, Cynthia S. Brown, Lars A. Brudvig, Maria Caldeira, Chengjin Chu, Michael J. Crawley, Pedro Daleo, Ellen I. Damschen, Carla M. D'Antonio, Nicole M. Decrappeo, Chris R. Dickman, Guozhen Du, Philip A. Fay, Paul Frater, Daniel S. Gruner, Nicole Hagenah, Andrew Hector, Aveliina Helm, Helmut Hillebrand, Kirsten S. Hofmockel, Hope C. Humphries, Oscar Iribarne, Virginia L. Jin, Adam Kay, Kevin P. Kirkman, Julia A. Klein, Johannes M. H. Knops, Kimberly J. La Pierre, Laura M. Ladwig, John G. Lambrinos, Andrew D. B. Leakey, Qi Li, Wei Li, Rebecca Mcculley, Brett Melbourne, Charles E. Mitchell, Joslin L. Moore, John Morgan, Brent Mortensen, Lydia R. O'Halloran, Meelis Partel, Jesus Pascual, David A. Pyke, Anita C. Risch, Roberto Salguero-Gomez, Mahesh Sankaran, Martin Schuetz, Anna Simonsen, Melinda Smith, Carly Stevens, Lauren L. Sullivan, Glenda M. Wardle, Elizabeth M. Wolkovich, Peter D. Wragg, Justin Wright, Louie Yang

School of Biological Sciences: Faculty Publications

Invasions have increased the size of regional species pools, but are typically assumed to reduce native diversity. However, global-scale tests of this assumption have been elusive because of the focus on exotic species richness, rather than relative abundance. This is problematic because low invader richness can indicate invasion resistance by the native community or, alternatively, dominance by a single exotic species. Here, we used a globally replicated study to quantify relationships between exotic richness and abundance in grass-dominated ecosystems in 13 countries on six continents, ranging from salt marshes to alpine tundra. We tested effects of human land use, native …


Geographic Distribution: Anolis Sagrei (Brown Anole). Usa: Florida: Escambia Co., Louis A. Somma Jan 2013

Geographic Distribution: Anolis Sagrei (Brown Anole). Usa: Florida: Escambia Co., Louis A. Somma

Papers in Herpetology

Pensacola: Agriculture Interdiction Station 1-10, Station 19: 1-10 eastbound (30.54519°N, 87.35201°W, WGS84). November 15, 2012. Katrina Simmons and Randal St. Louis. Verified by Kenneth L. Krysko, Florida Museum of Natural History, University of Florida (UF 169126). First county interdiction and westernmost vouchered specimen for the Florida Panhandle (Krysko et al. 2011. Atlas of Amphibians and Reptiles in Florida. Final report, Project Agreement 080l3, Florida Fish and Wildlife Conservation Commission, Tallahassee. 524 pp.). Currently, Anolis sagrei is not known to be established in Escambia County, but is present in adjacent Santa Rosa County and at least 54 other Florida counties (Krysko …


Female Mate Choice For Multimodal Courtship And The Importance Of The Signaling Background For Selection On Male Ornamentation, Jay A. Stafstrom, Eileen A. Hebets Jan 2013

Female Mate Choice For Multimodal Courtship And The Importance Of The Signaling Background For Selection On Male Ornamentation, Jay A. Stafstrom, Eileen A. Hebets

Eileen Hebets Publications

Conspicuous visual ornaments are frequently incorporated into complex courtship displays that integrate signal components from multiple sensory modalities. Mature male Schizocosa crassipes (Walckenaer, 1837) wolf spiders wave, arch, and tap their ornamented forelegs in a visual courtship display that simultaneously incorporates seismic components. To determine the importance of modality-specific signal components in female mate choice, we used a signal ablation design and compared the mating frequency of female-male pairs across signaling environments with manipulated modality-specific transmission properties. We found that the successful transmission of isolated visual or seismic signaling was sufficient for mating success; neither signaling modality was necessary. Additionally, …


Diversification Under Sexual Selection: The Relative Roles Of Mate Preference Strength And The Degree Of Divergence In Mate Preferences, Rafael L. Rodríguez, Janette W. Boughman, David A. Gray, Eileen A. Hebets, Gerlinde Höbel, Laurel B. Symes Jan 2013

Diversification Under Sexual Selection: The Relative Roles Of Mate Preference Strength And The Degree Of Divergence In Mate Preferences, Rafael L. Rodríguez, Janette W. Boughman, David A. Gray, Eileen A. Hebets, Gerlinde Höbel, Laurel B. Symes

Eileen Hebets Publications

The contribution of sexual selection to diversification remains poorly understood after decades of research. This may be in part because studies have focused predominantly on the strength of sexual selection, which offers an incomplete view of selection regimes. By contrast, students of natural selection focus on environmental differences that help compare selection regimes across populations. To ask how this disparity in focus may affect the conclusions of evolutionary research, we relate the amount of diversification in mating displays to quantitative descriptions of the strength and the amount of divergence in mate preferences across a diverse set of case studies of …