Life Sciences Commons^™

Ethylene, A Hormone At The Center-Stage Of Nodulation, Frédérique C. Guinel

Biology Faculty Publications

Nodulation is the result of a beneficial interaction between legumes and rhizobia. It is a sophisticated process leading to nutrient exchange between the two types of symbionts. In this association, within a nodule, the rhizobia, using energy provided as photosynthates, fix atmospheric nitrogen and convert it to ammonium which is available to the plant. Nodulation is recognized as an essential process in nitrogen cycling and legume crops are known to enrich agricultural soils in nitrogenous compounds. Furthermore, as they are rich in nitrogen, legumes are considered important as staple foods for humans and fodder for animals. To tightly control this …

First Report Of Invasive Crane Fly, Tipula Oleracea, In Utah, A Van Dyke, Ricardo A. Ramirez, B A. Mcgraw

Biology Faculty Publications

The known range of the common crane fly (Tipula oleracea L.) is expanding in the western US, as adults were captured (by me) in Utah while emerging and flying over golf course rough. Adults were collected at The Ridge Golf Course in West Valley City on 15 September, 2014, and identified by Dr. Benjamin McGraw at the Pennsylvania State University Turfgrass Entomology Lab in University Park, PA. Crane fly larvae (known as leather jackets for their tough skin) were previously found (again, by me) with the help of golf course superintendent Brian Roth on 4 August, 2012 damaging putting greens …

Supplementation Of H1n1pdm09 Split Vaccine With Heterologous Tandem Repeat M2e5x Virus-Like Particles Confers Improved Cross-Protection In Ferrets, Nedzad Music, Adrian J. Reber, Min-Chul Kim, Ian A. York, Sang-Moo Kang

Biology Faculty Publications

Current influenza vaccines induce strain-specific immunity to the highly variable hemagglutinin (HA) protein. It is therefore a high priority to develop vaccines that induce broadly cross-protective immunity to different strains of influenza. Since influenza A M2 proteins are highly conserved among different strains, five tandem repeats of the extracellular peptide of M2 in a membrane-anchored form on virus- like particles (VLPs) have been suggested to be a promising candidate for universal influenza vaccine. In this study, ferrets were intramuscularly immunized with 2009 H1N1 split HA vaccine (“Split”) alone, influenza split vaccine supplemented with M2e5x VLP (“Split+M2e5x”), M2e5x VLP alone (“M2e5x”), …

Temporal And Spatial Dynamics Of Scaling-Specific Features Of A Gene Regulatory Network In Drosophila, Honggang Wu, Renjie Jiao, Manu, Jun Ma

Biology Faculty Publications

A widely appreciated aspect of developmental robustness is pattern formation in proportion to size. But how such scaling features emerge dynamically remains poorly understood. Here we generate a data set of the expression profiles of six gap genes in Drosophila melanogasterembryos that differ significantly in size. Expression patterns exhibit size-dependent dynamics both spatially and temporally. We uncover a dynamic emergence of under-scaling in the posterior, accompanied by reduced expression levels of gap genes near the middle of large embryos. Simulation results show that a size-dependent Bicoid gradient input can lead to reduced Krüppel expression that can have long-range and …

Positional Plasticity In Regenerating Amybstoma Mexicanum Limbs Is Associated With Cell Proliferation And Pathways Of Cellular Differentiation, Catherine D. Mccusker, Antony Athippozhy, Carlos Diaz-Castillo, Charless Fowlkes, David M. Gardiner, S. Randal Voss

Biology Faculty Publications

BACKGROUND: The endogenous ability to dedifferentiate, re-pattern, and re-differentiate adult cells to repair or replace damaged or missing structures is exclusive to only a few tetrapod species. The Mexican axolotl is one example of these species, having the capacity to regenerate multiple adult structures including their limbs by generating a group of progenitor cells, known as the blastema, which acquire pattern and differentiate into the missing tissues. The formation of a limb regenerate is dependent on cells in the connective tissues that retain memory of their original position in the limb, and use this information to generate the pattern …

Administration Of Panobinostat Is Associated With Increased Il-17a Mrna In The Intestinal Epithelium Of Hiv-1 Patients, Ane Bjerg Christensen, Anders Dige, Johan Vad-Nielsen, Christel R. Brinkmann, Mia Bendix, Lars Østergaard, Martin Tolstrup, Ole S. Søgaard, Thomas A. Rasmussen, Jens Randel Nyengaard, Jørgen Agnholt, Paul W. Denton

Biology Faculty Publications

Intestinal CD4+ T cell depletion is rapid and profound during early HIV-1 infection.This leads to a compromised mucosal barrier that prompts chronic systemic inflammation.The preferential loss of intestinal T helper 17 (Th17) cells in HIV-1 disease is a driver of the damage within the mucosal barrier and of disease progression.Thus, understanding the effects of new therapeutic strategies in the intestines has high priority. Histone deacetylase (HDAC) inhibitors (e.g., panobinostat) are actively under investigation as potential latency reversing agents in HIV eradication studies. These drugs have broad effects that go beyond reactivating virus, including modulation of immune pathways. We examined colonic …

Filtering With A Drill Pump: An Efficient And Cost Effective Method To Collect Suspended Sediment And Filtrate, Julia E. Kelso, Michelle A. Baker

Biology Faculty Publications

Water quality monitoring programs across multiple disciplines use total suspended solids (TSS), and volatile suspended solids (VSS), to assess potential impairments of surface water and groundwater. While previous methods for instream filtering have been developed, the need for rapid, cost-effective, high volume sampling has increased with the need to verify and supplement data produced by sondes and instantaneous data loggers. We present an efficient method to filter water instream with a portable drill pump that results in reduced sample processing time, and potentially reduced error associated with sample transportation, preservation, contamination, and homogenization. This technical note outlines the advantages of …

Conserved Molecular Underpinnings And Characterization Of A Role For Caveolin-1 In The Tumor Microenvironment Of Mature T-Cell Lymphomas, Tyler A. Herek, Timothy D. Shew, Heather N. Spurgin, Christine E. Cutucache

Biology Faculty Publications

Neoplasms of extra-thymic T-cell origin represent a rare and difficult population characterized by poor clinical outcome, aggressive presentation, and poorly defined molecular characteristics. Much work has been done to gain greater insights into distinguishing features among malignant subtypes, but there also exists a need to identify unifying characteristics to assist in rapid diagnosis and subsequent potential treatment. Herein, we investigated gene expression data of five different mature T-cell lymphoma subtypes (n = 187) and found 21 genes to be up- and down-regulated across all malignancies in comparison to healthy CD4+ and CD8+ T-cell controls (n = 52). From these results, …

Initial Characterization Of The Large Genome Of The Salamander Ambystoma Mexicanum Using Shotgun And Laser Capture Chromosome Sequencing, Melissa C. Keinath, Vladimir A. Timoshevskiy, Nataliya Y. Timoshevskaya, Panagiotis A. Tsonis, S. Randal Voss, Jeramiah J. Smith

Biology Faculty Publications

Vertebrates exhibit substantial diversity in genome size, and some of the largest genomes exist in species that uniquely inform diverse areas of basic and biomedical research. For example, the salamander Ambystoma mexicanum (the Mexican axolotl) is a model organism for studies of regeneration, development and genome evolution, yet its genome is ~10× larger than the human genome. As part of a hierarchical approach toward improving genome resources for the species, we generated 600 Gb of shotgun sequence data and developed methods for sequencing individual laser-captured chromosomes. Based on these data, we estimate that the A. mexicanum genome is ~32 Gb. …

Seed Germination Ecology Of The Cold Desert Annual Isatis Violascens (Brassicaceae): Two Levels Of Physiological Dormancy And Role Of The Pericarp, Yuan M. Zhou, Juan J. Lu, Dun Y. Tan, Carol C. Baskin, Jerry M. Baskin

Biology Faculty Publications

The occurrence of various species of Brassicaceae with indehiscent fruits in the cold deserts of NW China suggests that there are adaptive advantages of this trait. We hypothesized that the pericarp of the single-seeded silicles of Isatis violascens restricts embryo expansion and thus prevents germination for 1 or more years. Thus, our aim was to investigate the role of the pericarp in seed dormancy and germination of this species. The effects of afterripening, treatment with gibberellic acid (GA₃) and cold stratification on seed dormancy-break were tested using intact silicles and isolated seeds, and germination phenology was monitored in …

Riparian Plant Isotopes Reflect Anthropogenic Nitrogen Perturbations: Robust Patterns Across Land Use Gradients, Steven J. Hall, Rebecca L. Hale, Michelle A. Baker, David R. Bowling, James R. Ehleringer

Biology Faculty Publications

Riparian plants incorporate nitrogen (N) from aquatic, terrestrial, and atmospheric sources, and their stable isotope compositions (δ¹⁵ N) may reflect land use impacts on N sources and transformations over scales of sites to watersheds. We surveyed leaf δ¹⁵ N values of 11 common riparian tree, shrub, and herbaceous species from 20 streams and rivers spanning three fifth-order watersheds in northern Utah, USA (n - 255 sites and 819 leaf samples). Streams spanned undeveloped montane forests to suburban, urban, and agricultural lands. Mean species-specific differences in leaf δ¹⁵N values were relatively small within sites (1.2 ± 2.2‰), …

There's Much Left To Learn: Clethra's Chromosomes, W. John Hayden

Biology Faculty Publications

Many would argue that chromosomes, genes, and DNA form the ineluctable essence of modern biology. Not only do these fundamental components of living cells provide moment-to-moment instructions by which cells carry out basic life processes, they also control inheritance of characteristics from one generation to the next. These essential functions of DNA stem from its repetitive structure. Hugely long DNA molecules are built from just four components, referenced by their singleletter abbreviations, A, C, G, and T. It is the specific sequence of these As, Cs, Gs, and Ts that constitutes the coded information of DNA. Moreover, molecular biologists have …

Molecular Phylogeny And Systematics Of Spider Wasps (Hymenoptera: Pompilidae): Redefining Subfamily Boundaries And The Origin Of The Family, Caleb T. Walker, J. Rodriguez, M. S. Wasbauer, Carol D. Von Dohlen, James P. Pitts

Biology Faculty Publications

Spider wasps (Hymenoptera: Pompilidae) constitute a monophyletic family supported by numerous morphological and behavioural traits. The subfamilial and tribal classifications, however, have a history of conflicting and confusing designations and nomenclature. Here, we reconstruct a molecular phylogeny of Pompilidae from Bayesian and maximum-likelihood analyses of four nuclear molecular markers (elongation factor-1 ë± F2 copy, long-wavelength rhodopsin, RNA polymerase II, and 28S ribosomal RNA). A Bayesian divergence-time estimation analysis was performed using four calibration points and an ancestral-area reconstruction was performed with a Bayesian binary Markov chain Monte Carlo method. New relationships are recovered, and new subfamilial delimitations are proposed and …

Monoaminergic Tone Supports Conductance Correlations And Stabilizes Activity Features In Pattern Generating Neurons Of The Lobster, Panulirus Interruptus, Wulf-Dieter C. Krenz, Anna R. Parker, Edmund William Rodgers, Deborah J. Baro

Biology Faculty Publications

Experimental and computational studies demonstrate that different sets of intrinsic and synaptic conductances can give rise to equivalent activity patterns. This is because the balance of conductances, not their absolute values, defines a given activity feature. Activity-dependent feedback mechanisms maintain neuronal conductance correlations and their corresponding activity features. This study demonstrates that tonic nM concentrations of monoamines enable slow, activity-dependent processes that can maintain a correlation between the transient potassium current (IA ) and the hyperpolarization activated current (Ih ) over the long-term (i.e., regulatory change persists for hours after removal of modulator). Tonic 5 nM DA acted through an …

Alum Adjuvant Enhances Protection Against Respiratory Syncytial Virus But Exacerbates Pulmonary Inflammation By Modulating Multiple Innate And Adaptive Immune Cells, Ki-Hye Kim, Young-Tae Lee, Hye Suk Hwang, Young-Man Kwon, Yu-Jin Jung, Youri Lee, Jong Seok Lee, Yu-Na Lee, Soojin Park, Sang-Moon Kang

Biology Faculty Publications

Respiratory syncytial virus (RSV) is well-known for inducing vaccine-enhanced respiratory disease after vaccination of young children with formalin-inactivated RSV (FI-RSV) in alum formulation. Here, we investigated alum adjuvant effects on protection and disease after FIRSV immunization with or without alum in comparison with live RSV reinfections. Despite viral clearance, live RSV reinfections caused weight loss and substantial pulmonary inflammation probably due to high levels of RSV specific IFN-γ+IL4-, IFN-γ-TNF-α+, IFN-γ+ TNF-α- effector CD4 and CD8 T cells. Alum adjuvant significantly improved protection as evidenced by effective viral clearance compared to unadjuvanted FI-RSV. However, in contrast to unadjuvanted FI-RSV, alum-adjuvanted FI-RSV …

Constraints On The Evolution Of Phenotypic Plasticity: Limits And Costs Of Phenotype And Plasticity, C. J. Murren, Josh R. Auld, H. Callahan, C. K. Ghalambor, C. A. Handelsman, M. A. Heskel, J. G. Kingsolver, H. J. Maclean, J. Masel, H. Maughan, D. W. Pfennig, R. A. Relyea, S. Seiter, E. Snell-Rood, U. K. Steiner, C. D. Schlichting

Biology Faculty Publications

No abstract provided.

Introduction To The Symposium-Unsteady Aquatic Locomotion With Respect To Eco-Design And Mechanics, Frank E. Fish, Paolo Domenici

Biology Faculty Publications

No abstract provided.

A Newly Discovered Bordetella Species Carries A Transcriptionally Active Crispr-Cas With A Small Cas9 Endonuclease, Yury V. Ivanov, Nikki Shariat, Karen B. Register, Bodo Linz, Israel Rivera, Kai Hu, Edward G. Dudley, Eric T. Harvill

Biology Faculty Publications

Background

Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated genes (cas) are widely distributed among bacteria. These systems provide adaptive immunity against mobile genetic elements specified by the spacer sequences stored within the CRISPR.

Methods

The CRISPR-Cas system has been identified using Basic Local Alignment Search Tool (BLAST) against other sequenced and annotated genomes and confirmed via CRISPRfinder program. Using Polymerase Chain Reactions (PCR) and Sanger DNA sequencing, we discovered CRISPRs in additional bacterial isolates of the same species of Bordetella. Transcriptional activity and processing of the CRISPR have been assessed via RT-PCR.

Results

Here we …

Book Reviews, Robert D. Aldridge, Michael B. Thompson, Malorie M. Hayes, Rafael O. De Sá, Christopher G. Lowe

Biology Faculty Publications

Reproductive Biology and Phylogeny of Lizards and Tuatara. J. L. Rheubert, D. S. Siegel, and S. E. Trauth (Eds.). 2014. CRC Press. ISBN 9781466579866. 760 p. $143.96 (hardcover).—

According to the authors, this book was intended to summarize the current knowledge of phylo- geny and reproduction of the Lepidosauria. I believe the authors have achieved their goal. Many of the chapters in this book are derived from presentations that took place at the Symposium on Reproductive Biology of Lizards at the Joint Meeting of Ichthyologists and Herpetologists held in Chattanooga, Tennessee in 2014. Although the majority of the authors are …

Metabolism, Gas Exchange, And Carbon Spiraling In Rivers, Robert O. Hall Jr, Jennifer L. Tank, Michelle A. Baker, Emma J. Rosi-Marshall, Erin R. Hotchkiss

Biology Faculty Publications

Ecosystem metabolism, that is, gross primary productivity (GPP) and ecosystem respiration (ER), controls organic carbon (OC) cycling in stream and river networks and is expected to vary predictably with network position. However, estimates of metabolism in small streams outnumber those from rivers such that there are limited empirical data comparing metabolism across a range of stream and river sizes. We measured metabolism in 14 rivers (discharge range 14–84 m3 s−1) in the Western and Midwestern United States (US). We estimated GPP, ER, and gas exchange rates using a Lagrangian, 2-station oxygen model solved in a Bayesian framework. GPP ranged from …

Clinically Available Medicines Demonstrating Anti-Toxoplasma Activity, Andrew J. Neville, Sydney J. Zach, Xiaofang Wang, Joshua L. Larson, Abigail K. Judge, Lisa A. Davis, Jonathan L. Vennerstrom, Paul H. Davis

Biology Faculty Publications

Toxoplasma gondii is an apicomplexan parasite of humans and other mammals, including livestock and companion animals. While chemotherapeutic regimens, including pyrimethamine and sulfadiazine regimens, ameliorate acute or recrudescent disease such as toxoplasmic encephalitis or ocular toxoplasmosis, these drugs are often toxic to the host. Moreover, no approved options are available to treat infected women who are pregnant. Lastly, no drug regimen has shown the ability to eradicate the chronic stage of infection, which is characterized by chemoresistant intracellular cysts that persist for the life of the host. In an effort to promote additional chemotherapeutic options, we now evaluate clinically available …

The Depsipeptide Romidepsin Reverses Hiv-1 Latency In Vivo, Ole S. Søgaard, Mette E. Graversen, Steffen Leth, Rikke Olesen, Christel R. Brinkmann, Sara K. Nissen, Anne Sofie Kjaer, Mariane H. Schleimann, Paul W. Denton, William J. Hey-Cunningham, Giuseppe Pantaleo, Kim Krogsgaard, Maja Sommerfelt, Remi Fromentin, Nicolas Chomont, Thomas A. Rasmussen, Lars Østergaard, Martin Tolstrup

Biology Faculty Publications

Pharmacologically-induced activation of replication competent proviruses from latency in the presence of antiretroviral treatment (ART) has been proposed as a step towards curing HIV-1 infection. However, until now, approaches to reverse HIV-1 latency in humans have yielded mixed results. Here, we report a proof-of-concept phase Ib/IIa trial where 6 aviremic HIV-1 infected adults received intravenous 5 mg/m2 romidepsin (Celgene) once weekly for 3 weeks while maintaining ART. Lymphocyte histone H3 acetylation, a cellular measure of the pharmacodynamic response to romidepsin, increased rapidly (maximum fold range: 3.7–7.7 relative to baseline) within the first hours following each romidepsin administration. Concurrently, HIV-1 transcription …

Translational Training For Tomorrow’S Environmental Scientists, Mark W. Brunson, Michelle A. Baker

Biology Faculty Publications

Environmental science exists to seek solutions to problems related to human-nature interactions. Unfortunately, in many cases, environmental research findings are not effectively used because scientists are not able to convey their knowledge effectively to policy makers and the public, and/or because the questions they address are not directly linked to the answers stakeholders need. To address this issue, Schlesinger (2010) called for development of a “translational ecology” that would be understandable and usable by decision-makers, interest groups, and citizens. A barrier to usable science is that researchers are not usually trained to be translational. We convened a multi-disciplinary group of …

Transcriptomic Variation Of Hepatopancreas Reveals The Energy Metabolism And Biological Processes Associated With Molting In Chinese Mitten Crab, Eriocheir Sinensis, Shu Huang, Jun Wang, Wucheng Yue, Jiao Chen, Sarah Gaughan, Weiqun Lu, Guoqing Lu, Chenghui Wang

Biology Faculty Publications

Molting is a critical developmental process for crustaceans, yet the underlying molecular mechanism is unknown. In this study, we used RNA-Seq to investigate transcriptomic profiles of the hepatopancreas and identified differentially expressed genes at four molting stages of Chinese mitten crab (Eriocheir sinensis). A total of 97,398 transcripts were assembled, with 31,900 transcripts annotated. Transcriptomic comparison revealed 1,189 genes differentially expressed amongst different molting stages. We observed a pattern associated with energy metabolism and physiological responses during a molting cycle. In specific, differentially expressed genes enriched in postmolt were linked to energy consumption whereas genes enriched in intermolt were related …

Disruption Of Daily Rhythms By High-Fat Diet Is Reversible, Katrina L. Branecky, Kevin D. Niswender, Julie S. Pendergast

Biology Faculty Publications

In mammals a network of circadian clocks coordinates behavior and physiology with 24-h environmental cycles. Consumption of high-fat diet disrupts this temporal coordination by advancing the phase of the liver molecular clock and altering daily rhythms of eating behavior and locomotor activity. In this study we sought to determine whether these effects of high-fat diet on circadian rhythms were reversible. We chronically fed mice high-fat diet and then returned them to low-fat chow diet. We found that the phase of the liver PERIOD2::LUCIFERASE rhythm was advanced (by 4h) and the daily rhythms of eating behavior and locomotor activity were altered …

Can The Results Of Biodiversity-Ecosystem Productivity Studies Be Translated To Bioenergy Production?, Timothy L. Dickson, Katherine L. Gross

Biology Faculty Publications

Biodiversity experiments show that increases in plant diversity can lead to greater biomass production, and some researchers suggest that high diversity plantings should be used for bioenergy production. However, many methods used in past biodiversity experiments are impractical for bioenergy plantings. For example, biodiversity experiments often use intensive management such as hand weeding to maintain low diversity plantings and exclude unplanted species, but this would not be done for bioenergy plantings. Also, biodiversity experiments generally use high seeding densities that would be too expensive for bioenergy plantings. Here we report the effects of biodiversity on biomass production from two studies …

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 …

Mechanisms Of Cross-Protection By Influenza Virus M2-Based Vaccines, Yu-Na Lee, Min-Chul Kim, Young-Tae Lee, Yu-Jin Kim, Sang-Moo Kang

Biology Faculty Publications

Current influenza virus vaccines are based on strain-specific surface glycoprotein hemagglutinin (HA) antigens and effective only when the predicted vaccine strains and circulating viruses are well-matched. The current strategy of influenza vaccination does not prevent the pandemic outbreaks and protection efficacy is reduced or ineffective if mutant strains emerge. It is of high priority to develop effective vaccines and vaccination strategies conferring a broad range of cross protection. The extracellular domain of M2 (M2e) is highly conserved among human influenza A viruses and has been utilized to develop new vaccines inducing cross protection against different subtypes of influenza A virus. …

Cross Protection Against Influenza A Virus By Yeast-Expressed Heterologous Tandem Repeat M2 Extracellular Proteins, Yu-Na Lee, Min-Chul Kim, Young-Tae Lee, Hye Suk Hwang, Jongsang Lee, Cheol Kim, Sang-Moon Kang

Biology Faculty Publications

The influenza M2 ectodomain (M2e) is well conserved across human influenza A subtypes, but there are few residue changes among avian and swine origin influenza A viruses. We expressed a tandem repeat construct of heterologous M2e sequences (M2e5x) derived from human, swine, and avian origin influenza A viruses using the yeast expression system. Intramuscular immunization of mice with AS04-adjuvanted M2e5x protein vaccines was effective in inducing M2e-specific antibodies reactive to M2e peptide and native M2 proteins on the infected cells with human, swine, or avian influenza virus, mucosal and systemic memory cellular immune responses, and cross-protection against H3N2 virus. Importantly, …