Life Sciences Commons^™

The Conserved G-Protein Coupled Receptor Fshr-1 Regulates Protective Host Responses To Infection And Oxidative Stress, Elizabeth V. Miller, Leah N. Grandi, Jennifer A. Giannini, Joseph D. Robinson, Jennifer R. Powell

Biology Faculty Publications

The innate immune system’s ability to sense an infection is critical so that it can rapidly respond if pathogenic microorganisms threaten the host, but otherwise maintain a quiescent baseline state to avoid causing damage to the host or to commensal microorganisms. One important mechanism for discriminating between pathogenic and non-pathogenic bacteria is the recognition of cellular damage caused by a pathogen during the course of infection. InCaenorhabditis elegans, the conserved G-protein coupled receptor FSHR-1 is an important constituent of the innate immune response. FSHR-1 activates the expression of antimicrobial infection response genes in infected worms and delays accumulation …

Doing It Again: Repeating Methodology From Published Literature To Learn Field Biology, Laurie Eberhardt

Biology Faculty Publications

Repeatability underpins a basic assumption in science which students must learn in order to evaluate others’ research findings as well as to communicate the results of their own research. By attempting to repeat the methods of published studies, students learn the importance of clear written communication, while at the same time developing research skills. I describe three examples of published field studies that can be used as the basis for course exercises on the repeatability of methodology, as well as field sampling techniques, all grounded in the overall topic of environmental change. Two of the exercises returned students to the …

Maintenance Of Brucellosis In Yellowstone Bison: Linking Seasonal Food Resources, Host-Pathogen Interaction, And Life-History Trade-Offs, John J. Treanor, Chris Geremia, Michael A. Ballou, Duane H. Keisler, Patrick J. White, John J. Cox, Phillip H. Crowley

Biology Faculty Publications

The seasonal availability of food resources is an important factor shaping the life-history strategies of organisms. During times of nutritional restriction, physiological trade-offs can induce periods of immune suppression, thereby increasing susceptibility to infectious disease. Our goal was to provide a conceptual framework describing how the endemic level bovine brucellosis (Brucella abortus) may be maintained in Yellowstone bison based on the seasonality of food resources and the life-history strategies of the host and pathogen. Our analysis was based on active B. abortus infection (measured via bacterial culture), nutritional indicators (measured as metabolites and hormones in plasma), and carcass …

Drosophila Eye Model To Study Neuroprotective Role Of Creb Binding Protein (Cbp) In Alzheimer’S Disease, Timothy Cutler, Ankita Sarkar, Michael Moran, Andrew Steffensmeier, Oorvashi Roy Puli, Greg Mancini, Meghana Tare

Biology Faculty Publications

Background: The progressive neurodegenerative disorder Alzheimer’s disease (AD) manifests as loss of cognitive functions, and finally leads to death of the affected individual. AD may result from accumulation of amyloid plaques. These amyloid plaques comprising of amyloid-beta 42 (Aβ42) polypeptides results from the improper cleavage of amyloid precursor protein (APP) in the brain. The Aβ42 plaques have been shown to disrupt the normal cellular processes and thereby trigger abnormal signaling which results in the death of neurons. However, the molecular-genetic mechanism(s) responsible for Aβ42 mediated neurodegeneration is yet to be fully understood.

Methodology/Principal Findings: We have utilized Gal4/UAS system to …

The Cababc Operon Essential For Biofilm And Rugose Colony Development In Vibrio Vulnificus, Jin Hwan Park, Youmi Jo, Song Yee Jang, Haenaem Kwon, Yasuhiko Irie, Matthew R. Parsek, Myung Hee Kim, Sang Ho Choi

Biology Faculty Publications

A transcriptome analysis identified Vibrio vulnificus cabABC genes which were preferentially expressed in biofilms. The cabABC genes were transcribed as a single operon. The cabA gene was induced by elevated 3′,5′-cyclic diguanylic acid (c-di-GMP) and encoded a calcium-binding protein CabA. Comparison of the biofilms produced by the cabA mutant and its parent strain JN111 in microtiter plates using crystal-violet staining demonstrated that CabA contributed to biofilm formation in a calcium-dependent manner under elevated c-di-GMP conditions. Genetic and biochemical analyses revealed that CabA was secreted to the cell exterior through functional CabB and CabC, distributed throughout the biofilm matrix, and produced …

Burrowing Owls, Pulex Irritans And Plague, James R. Belthoff, Scott A. Bernhardt, Christopher Ball, Michael Gregg, David H. Johnson, Rachel Ketterling, Emily Price, Juliette K. Tinker

Biology Faculty Publications

Western burrowing owls (Athene cunicularia hypugaea) are small, ground-dwelling owls ofwestern North America that frequent prairie dog (Cynomys spp.) towns and other grasslands.As they rely on rodent prey and occupy burrows once or concurrently inhabited by fossorialmammals, the owls often harbor fleas. We examined the potential role of fleas found onburrowing owls in plague dynamics by evaluating prevalence of Yersinia pestis in fleas and inowl blood. During 2012-2013 fleas and blood were collected from burrowing owls in portionsof five states with endemic plague: Idaho, Oregon, Washington, Colorado, and South Dakota.Fleas were enumerated, taxonomically identified, pooled by nest and assayed for …

The Closing Mechanism Of Dna Polymerase I At Atomic Resolution, Bill R. Miller Iii, Loreena S. Beese, Carol A. Parish, Eugene Y. Wu

Biology Faculty Publications

Highlights

• DNA polymerase X-ray structure provides starting structure to investigate closing
• MD simulations provide atomistic details of DNA polymerase closing
• Propose sequence of events in prechemistry DNA polymerase active site assembly
• Identify a conserved histidine as a potential proton acceptor to initiate catalysis

Summary 
DNA polymerases must quickly and accurately distinguish between similar nucleic acids to form Watson-Crick base pairs and avoid DNA replication errors. Deoxynucleoside triphosphate (dNTP) binding to the DNA polymerase active site induces a large conformational change that is difficult to characterize experimentally on an atomic level. Here, we report an X-ray crystal structure of DNA polymerase …

Kidney-Specific Reduction Of Oxidative Phosphorylation Genes Derived From Spontaneously Hypertensive Rat, Jason A. Collett, Jiffin K. Paulose, Vincent M. Cassone, Jeffrey L. Osborn

Biology Faculty Publications

Mitochondrial (Mt) dysfunction contributes to the pathophysiology of renal function and promotes cardiovascular disease such as hypertension. We hypothesize that renal Mt-genes derived from female spontaneously hypertensive rats (SHR) that exhibit hypertension have reduced expression specific to kidney cortex. After breeding a female Okamoto-Aoki SHR (SAP = 188mmHg) with Brown Norway (BN) males (SAP = 100 and 104 mmHg), hypertensive female progeny were backcrossed with founder BN for 5 consecutive generations in order to maintain the SHR mitochondrial genome in offspring that contain over increasing BN nuclear genome. Mt-protein coding genes (13 total) and nuclear transcription factors mediating Mt-gene transcription …

An Exploration Into Fern Genome Space, Paul G. Wolf, Emily B. Sessa, D. Blaine Marchant, Fay-Wei Li, Carl J. Rothfels, Erin M. Sigel, Mathew A. Gitzendanner, Clayton J. Visger, Jo Ann Banks, Douglas E. Soltis, Pamela S. Soltis, Kathleen M. Pryer, Joshua P. Der

Biology Faculty Publications

Ferns are one of the few remaining major clades of land plants for which a complete genome sequence is lacking. Knowledge of genome space in ferns will enable broad-­‐scale comparative analyses of land plant genes and genomes, provide insights into genome evolution across green plants, and shed light on genetic and genomic features that characterize ferns, such as their high chromosome numbers and large genome sizes. As part of an initial exploration into fern genome space, we used a whole genome shotgun sequencing approach to obtain low-­‐density coverage (~0.4X to 2X) for six fern species from the Polypodiales (Ceratopteris, Pteridium, …

The Sea Lamprey Meiotic Map Improves Resolution Of Ancient Vertebrate Genome Duplications, Jeramiah James Smith, Melissa C. Keinath

Biology Faculty Publications

It is generally accepted that many genes present in vertebrate genomes owe their origin to two whole-genome duplications that occurred deep in the ancestry of the vertebrate lineage. However, details regarding the timing and outcome of these duplications are not well resolved. We present high-density meiotic and comparative genomic maps for the sea lamprey (Petromyzon marinus), a representative of an ancient lineage that diverged from all other vertebrates ~550 million years ago. Linkage analyses yielded a total of 95 linkage groups, similar to the estimated number of germline chromosomes (1n ~ 99), spanning a total of 5570.25 cM. …

Beyond Bivariate Correlations: Three-Block Partial Least Squares Illustrated With Vegetation, Soil, And Topography, Daehyun Kim, Thomas J. Dewitt, César S. B. Costa, John A. Kupfer, Ryan W. Mcewan, J. Anthony Stallins

Biology Faculty Publications

Ecologists, particularly those engaged in biogeomorphic studies, often seek to connect data from three or more domains. Using three-block partial least squares regression, we present a procedure to quantify and define bi-variance and tri-variance of data blocks related to plant communities, their soil parameters, and topography. Bi-variance indicates the total amount of covariation between these three domains taken in pairs, whereas tri-variance refers to the common variance shared by all domains. We characterized relationships among three domains (plant communities, soil properties, topography) for a salt marsh, four coastal dunes, and two temperate forests spanning several regions in the world. We …

Spatiotemporal Dynamics Of Coarse Woody Debris In An Old-Growth Temperate Deciduous Forest, Jessica G. Davis, Julia I. Chapman, Shuang-Ye Wu, Ryan W. Mcewan

Biology Faculty Publications

No abstract provided.

Biodiversity Assessment Among Two Nebraska Prairies: A Comparison Between Traditional And Phylogenetic Diversity Indices, Shelly K. Aust, Dakota L. Ahrendsen, P. Roxanne Kellar

Biology Faculty Publications

Conservation of the evolutionary diversity among organisms should be included in the selection of priority regions for preservation of Earth’s biodiversity. Traditionally, biodiversity has been determined from an assessment of species richness (S), abundance, evenness, rarity, etc. of organisms but not from variation in species’ evolutionary histories. Phylogenetic diversity (PD) measures evolutionary differences between taxa in a community and is gaining acceptance as a biodiversity assessment tool. However, with the increase in the number of ways to calculate PD, end-users and decision-makers are left wondering how metrics compare and what data are needed to calculate various metrics.

Distribution Of Three Congeneric Shrub Species Along An Aridity Gradient Is Related To Seed Germination And Seedling Emergence, Liming Lai, Yuan Tian, Yongji Wang, Xuechun Zhao, Lianhe Jiang, Jerry M. Baskin, Carol C. Baskin, Yuanrun Zheng

Biology Faculty Publications

Environmental tolerance of a species has been shown to correlate positively with its geographical range. On the Ordos Plateau, three Caragana species are distributed sequentially along the precipitation gradient. We hypothesized that this geographical distribution pattern is related to environmental tolerances of the three Caragana species during seed germination and seedling emergence stages. To test this hypothesis, we examined seed germination under different temperature, light and water potentials, and monitored seedling emergence for seeds buried at eight sand depths and given different amounts of water. Seeds of C. korshinskii germinated to high percentages at 5 : 15 to 25 : …

When It Comes To Clethra: Roots Matter, W. John Hayden

Biology Faculty Publications

Roots, too often, are out of sight and out of mind, but they are critical for vigorous, healthy plant growth. All plant enthusiasts—including gardeners, farmers, foresters, and naturalists—should think about and appreciate roots if they wish to acquire a holistic understanding of plant biology. This article introduces readers to the mycorrhizal roots of the 2015 VNPS Wildflower of the Year, Clethra alnifolia (Sweet Pepperbush), and explores the diversity of mycorrhizae in a closely related family, Ericaceae.

Serpentine Ecosystem Responses To Varying Water Availability And Prescribed Fire In The U.S. Mid-Atlantic Region, Jessica Schedlbauer

Biology Faculty Publications

No abstract provided.

Comparative Analysis Of The Flexural Stiffness Of Pinniped Vibrissae, Carly C. Ginter Summarell, Sudeep Ingole, Frank E. Fish, Christopher D. Marshall

Biology Faculty Publications

No abstract provided.

Treatment Strategies That Enhance The Efficacy And Selectivity Of Mitochondria-Targeted Anticancer Agents, Josephine S. Modica-Napolitano, Volkmar Weissig

Biology Faculty Publications

Nearly a century has passed since Otto Warburg first observed high rates of aerobic glycolysis in a variety of tumor cell types and suggested that this phenomenon might be due to an impaired mitochondrial respiratory capacity in these cells. Subsequently, much has been written about the role of mitochondria in the initiation and/or progression of various forms of cancer, and the possibility of exploiting differences in mitochondrial structure and function between normal and malignant cells as targets for cancer chemotherapy. A number of mitochondria-targeted compounds have shown efficacy in selective cancer cell killing in pre-clinical and early clinical testing, including …

Nutrient Addition Effects On Tropical Dry Forests: A Mini-Review From Microbial To Ecosystem Scales., J S. Powers, K K. Becklund, M G. Gei, S B. Iyengar, R Meyer, C S. O'Connell, E M. Schilling, C M. Smith, Bonnie G. Waring, L K. Werden

Biology Faculty Publications

Humans have more than doubled inputs of reactive nitrogen globally and greatly accelerated the biogeochemical cycles of phosphorus and metals. However, the impacts of increased element mobility on tropical ecosystems remain poorly quantified, particularly for the vast tropical dry forest biome. Tropical dry forests are characterized by marked seasonality, relatively little precipitation, and high heterogeneity in plant functional diversity and soil chemistry. For these reasons, increased nutrient deposition may affect tropical dry forests differently than wet tropical or temperate forests. Here, we review studies that investigated how nutrient availability affects ecosystem and community processes from the microsite to ecosystem scales …

Gene Expression During The First 28 Days Of Axolotl Limb Regeneration I: Experimental Design And Global Analysis Of Gene Expression, S. Randal Voss, Alex Palumbo, Radha Nagarajan, David M. Gardiner, Ken Muneoka, Arnold J. Stromberg, Antony T. Athippozhy

Biology Faculty Publications

While it is appreciated that global gene expression analyses can provide novel insights about complex biological processes, experiments are generally insufficiently powered to achieve this goal. Here we report the results of a robust microarray experiment of axolotl forelimb regeneration. At each of 20 post-amputation time points, we estimated gene expression for 10 replicate RNA samples that were isolated from 1 mm of heterogeneous tissue collected from the distal limb tip. We show that the limb transcription program diverges progressively with time from the non-injured state, and divergence among time adjacent samples is mostly gradual. However, punctuated episodes of transcription …

The Myb36 Transcription Factor Orchestrates Casparian Strip Formation, Takehiro Kamiya, Monica Borghi, Peng Wang, John M. C. Danku, Lothar Kalmbach, Prashant S. Hosmani, Sadaf Naseer, Toru Fujiwara, Niko Geldner, David E. Salt

Biology Faculty Publications

The endodermis in roots acts as a selectivity filter for nutrient and water transport essential for growth and development. This selectivity is enabled by the formation of lignin-based Casparian strips. Casparian strip formation is initiated by the localization of the Casparian strip domain proteins (CASPs) in the plasma membrane, at the site where the Casparian strip will form. Localized CASPs recruit Peroxidase 64 (PER64), a Respiratory Burst Oxidase Homolog F, and Enhanced Suberin 1 (ESB1), a dirigent-like protein, to assemble the lignin polymerization machinery. However, the factors that control both expression of the genes encoding this biosynthetic machinery and its …

Tissue Specific Reactions To Positional Discontinuities In The Regenerating Axolotl Limb, Malcolm Maden, Daima Avila, Molly Roy, Ashley W. Seifert

Biology Faculty Publications

We investigated cellular contributions to intercalary regenerates and 180^o supernumerary limbs during axolotl limb regeneration using the cell autonomous green fluorescent protein marker and exchanged blastemas between white and green fluorescent protein animals. After distal blastemas were grafted to proximal levels tissues of the intercalary regenerate behaved independently with regard to the law of distal transformation; graft epidermis was replaced by stump epidermis, muscle-derived cells, blood vessels, and Schwann cells of the distal blastema moved proximally to the stylopodium and cartilage and dermal cells conformed to the law. After 180^o rotation, blastemas showed contributions from stump tissues which …

Neurotranscriptome Profiles Of Multiple Zebrafish Strains, Ryan Y. Wong, John Godwin

Biology Faculty Publications

Behavioral displays or physiological responses are often influenced by intrinsic and extrinsic mechanisms in the context of the organism's evolutionary history. Understanding differences in transcriptome profiles can give insight into adaptive or pathological responses.We utilize high throughput sequencing (RNA-sequencing) to characterize the neurotranscriptome profiles in both males and females across four strains of zebrafish (Danio rerio). Strains varied by previously documented differences in stress and anxiety-like behavioral responses, and generations removed from wild-caught individuals. Here we describe detailed methodologies and quality controls in generating the rawRNA-sequencing reads that are publically available in NCBI's Gene Expression Omnibus database (GSE61108).

The Varying Role Of Water Column Nutrient Removal Along River Continua In Contrasting Landscapes, Alexander J. Reisinger, Jennifer L. Tank, Emma J. Rosi-Marshall, Robert O. Hall Jr, Michelle A. Baker

Biology Faculty Publications

Nutrient transformation processes such as assimilation, dissimilatory transformation, and sorption to sediments are prevalent in benthic zones of headwater streams, but may also occur in the water column. The river continuum concept (RCC) predicts that water column processes become increasingly important with increasing stream size. We predicted that water column nutrient uptake increases with stream size, mirroring carbon/energy dynamics predicted by the RCC. We measured water column uptake of ammonium ( NH+4NH4+ ), nitrate ( NO−3NO3− ), and soluble reactive phosphorus (SRP) in 1st through 5th order stream and river reaches (discharge: 50–68,000 L s−1) in three watersheds ranging from …

Characterizing The Neurotranscriptomic States In Alternative Stress Coping Styles, Ryan Y. Wong, Melissa S. Lamm, John Godwin

Biology Faculty Publications

Background: Animals experience stress in many contexts and often successfully cope. Individuals exhibiting the proactive versus reactive stress coping styles display qualitatively different behavioral and neuroendocrine responses to stressors. The predisposition to exhibiting a particular coping style is due to genetic and environmental factors. In this study we explore the neurotranscriptomic and gene network biases that are associated with differences between zebrafish (Danio rerio) lines selected for proactive and reactive coping styles and reared in a common garden environment.

Results: Using RNA-sequencing we quantified the basal transcriptomes from the brains of wild-derived zebrafish lines selectively bred to exhibit the proactive …

Mutations That Separate The Functions Of The Proofreading Subunit Of The Escherichia Coli Replicase, Zakiya Whatley, Kenneth N. Kreuzer

Biology Faculty Publications

The dnaQ gene of Escherichia coli encodes the Ɛ subunit of DNA polymerase III, which provides the 3' - 5' exonuclease proofreading activity of the replicative polymerase. Prior studies have shown that loss of Ɛ leads to high mutation frequency, partially constitutive SOS, and poor growth. In addition, a previous study from our laboratory identified dnaQ knockout mutants in a screen for mutants specifically defective in the SOS response after quinolone (nalidixic acid) treatment. To explain these results, we propose a model whereby, in addition to proofreading, Ɛ plays a distinct role in replisome disassembly and/or processing of stalled replication …

Genetic Changes To A Transcriptional Silencer Element Confers Phenotypic Diversity Within And Between Drosophila Species, Winslow C. Johnson, Alison J. Ordway, Masayoshi Watada, Jonathan N. Pruitt, Thomas M. Williams, Mark Rebeiz

Biology Faculty Publications

The modification of transcriptional regulation has become increasingly appreciated as a major contributor to morphological evolution. However, the role of negative-acting control elements (e.g. silencers) in generating morphological diversity has been generally overlooked relative to positive-acting “enhancer” elements. The highly variable body coloration patterns among Drosophilid insects represents a powerful model system in which the molecular alterations that underlie phenotypic diversity can be defined. In a survey of pigment phenotypes among geographically disparate Japanese populations of Drosophila auraria, we discovered a remarkable degree of variation in male-specific abdominal coloration. In testing the expression patterns of the major pigment-producing enzymes, …

E151 (Sym15), A Pleiotropic Mutant Of Pea (Pisum Sativum L.), Displays Low Nodule Number, Enhanced Mycorrhizae, Delayed Lateral Root Emergence, And High Root Cytokinin Levels, James M.C. Jones, Lindsey Clairmont, Emily S. Macdonald, Catherine A. Weiner, R.J. Neil Emery, Frédérique C. Guinel

Biology Faculty Publications

In legumes, the formation of rhizobial and mycorrhizal root symbioses is a highly regulated process which requires close communication between plant and microorganism. Plant mutants that have difficulties establishing symbioses are valuable tools for unravelling the mechanisms by which these symbioses are formed and regulated. Here E151, a mutant of Pisum sativum cv. Sparkle, was examined to characterize its root growth and symbiotic defects. The symbioses in terms of colonization intensity, functionality of micro-symbionts, and organ dominance were compared between the mutant and wild type. The endogenous cytokinin (CK) and abscisic acid (ABA) levels and the effect of the exogenous …

Genetic Diversity In Oxytocin Ligands And Receptors In New World Monkeys, Dongren Ren, Guoqing Lu, Hideaki Moriyama, Aaryn C. Mustoe, Emily B. Harrison, Jeffrey French

Biology Faculty Publications

Oxytocin (OXT) is an important neurohypophyseal hormone that influences wide spectrum of reproductive and social processes. Eutherian mammals possess a highly conserved sequence of OXT (Cys-Tyr-Ile-Gln-Asn-Cys-Pro-Leu-Gly). However, in this study, we sequenced the coding region for OXT in 22 species covering all New World monkeys (NWM) genera and clades, and characterize five OXT variants, including consensus mammalian Leu⁸-OXT, major variant Pro⁸-OXT, and three previously unreported variants: Ala⁸-OXT, Thr⁸-OXT, and Phe²-OXT. Pro⁸-OXT shows clear structural and physicochemical differences from Leu⁸-OXT. We report multiple predicted amino …

The Hippo Pathway Effector Yki Downregulates Wg Signaling To Promote Retinal Differentiation In The Drosophila Eye, Erika Lynn Wittkorn, Ankita Sarkar, Kristine Garcia, Madhuri Kango-Singh, Amit Singh

Biology Faculty Publications

The evolutionarily conserved Hippo signaling pathway is known to regulate cell proliferation and maintain tissue homeostasis during development. We found that activation of Yorkie (Yki), the effector of the Hippo signaling pathway, causes separable effects on growth and differentiation of theDrosophila eye. We present evidence supporting a role for Yki in suppressing eye fate by downregulation of the core retinal determination genes. Other upstream regulators of the Hippo pathway mediate this effect of Yki on retinal differentiation. Here, we show that, in the developing eye, Yki can prevent retinal differentiation by blocking morphogenetic furrow (MF) progression and R8 specification. …