Life Sciences Commons^™

Chip-Seq And Rna-Seq Reveal An Amrz-Mediated Mechanism For Cyclic Di-Gmp Synthesis And Biofilm Development By Pseudomonas Aeruginosa, Christopher J. Jones, David Newsom, Benjamin Kelly, Yasuhiko Irie, Laura K. Jennings, Binjie Xu, Dominique H. Limoli, Joe J. Harrison, Matthew R. Parsek, Peter White, Daniel J. Wozniak

Biology Faculty Publications

The transcription factor AmrZ regulates genes important for P. aeruginosa virulence, including type IV pili, extracellular polysaccharides, and the flagellum; however, the global effect of AmrZ on gene expression remains unknown, and therefore, AmrZ may directly regulate many additional genes that are crucial for infection. Compared to the wild type strain, a ΔamrZ mutant exhibits a rugose colony phenotype, which is commonly observed in variants that accumulate the intracellular second messenger cyclic diguanylate (c-di-GMP). Cyclic di-GMP is produced by diguanylate cyclases (DGC) and degraded by phosphodiesterases (PDE). We hypothesized that AmrZ limits the intracellular accumulation of c-di-GMP through transcriptional repression …

Utilization Of The Invasive Alga Gracilaria Vermiculophylla (Ohmi) Papenfuss By The Native Mud Snail Ilyanassa Obsoleta (Say), Michele Guidone, Christine Newton, Carol S. Thornber

Biology Faculty Publications

The recent invasions of the red alga, Gracilaria vermiculophylla, to the Atlantic and Eastern Pacific Oceans have the potential to significantly alter intertidal and subtidal soft sediment communities. In particular, G. vermiculophylla increases habitat complexity and provides a novel hard substrate in an otherwise two dimensional habitat. Following our observations that the native omnivorous mud snail Ilyanassa obsoleta utilizes G. vermiculophylla for egg capsule deposition, our field surveys demonstrated that the in situ abundance of egg capsules on G. vermiculophylla matched abundances on a native alga Ceramium virgatumandwere at least 11–50 times greater than on all other co-occurring macrophytes. Additionally, …

Direct-To-Consumer Genetic Testing In The College Classroom: Knowledge, Attitudes, And Concerns Of Introductory Biology Students, Nicanor Austriaco

Biology Faculty Publications

Pioneered by companies like 23andMe.com, deCODEme.com, and Navigenics.com, direct-to-consumer genetic testing refers to genetic tests that are marketed directly to consumers via television, print media, or the Internet. This kind of testing provides access to a customer’s genetic information without necessarily involving either a medical health care professional or a genetic counselor in the process. In recent years, a course offered to medical and graduate students at Stanford University has included an option for students to undergo personal genotyping, raising the possibility that direct-to-consumer genetic testing could also be incorporated into undergraduate biology courses to enhance student learning. In this …

Deletion Of Aif1 But Not Of Yca1/Mca1 Protects Saccharomyces Cerevisiae And Candida Albicans Cells From Caspofungin-Induced Programmed Cell Death, Nicanor Austriaco, Christopher Chin, Faith Donaghey, Kathrine Helming, Morgan Mccarthy, Stephen Rogers

Biology Faculty Publications

Caspofungin was the first member of a new class of antifungals called echinocandins to be approved by a drug regulatory authority. Like the other echinocandins, caspofungin blocks the synthesis of β(1,3)-D-glucan of the fungal cell wall by inhibiting the enzyme, β(1,3)-D-glucan synthase. Loss of β(1,3)-D-glucan leads to osmotic instability and cell death. However, the precise mechanism of cell death associated with the cytotoxicity of caspofungin was unclear. We now provide evidence that Saccharomyces cerevisiae cells cultured in media containing caspofungin manifest the classical hallmarks of programmed cell death (PCD) in yeast, including the generation of reactive oxygen species (ROS), the …

A Dichotomous Key For The Identification Of Nine Salmonids Of The Inland Northwest Using Six Diagnostic Skull Bones : And Associated Equations To Estimate Total Length And Weight From Bones Ingested By Piscivores Or Found In Archeological Sites, Aaron G. Stroud, Allan T. Scholz, Fisheries Research Center (Cheney, Wash.)

Biology Faculty Publications

No abstract provided.

Two Honeysuckles: A Tale Of Dr. Jekyll And Mr. Hyde, W. John Hayden

Biology Faculty Publications

There are about 180 species of Lonicera (honeysuckles) widely distributed in the north temperate zone. These are mostly shrubby plants, but in Virginia, we have two species that are woody vines (lianas). These two lianous honeysuckles should be familiar to all Virginia Native Plant Society members. One is this year’s VNPS Wildflower of the Year, Lonicera sempervirens (coral honeysuckle), and the other is Lonicera japonica (Japanese honeysuckle), widely and deservedly reviled as one of our most aggressive invasive exotic species. Together, these two plants make an odd pair, a sort of botanical Dr. Jekyll and Mr. Hyde. What is it, …

Perennial Grasslands Enhance Biodiversity And Multiple Ecosystem Services In Bioenergy Landscapes, Ben P. Werling, Timothy L. Dickson, Rufus Isaacs, Hannah Gaines, Claudio Gratton, Katherine L. Gross, Heidi Liere, Carolyn M. Malmstrom, Timothy D. Meehan, Leilei Ruan, Bruce A. Robertson, G. Philip Robertson, Thomas M. Schmidt, Abbie C. Schrotenboer, Tracy K. Teal, Julianna K. Wilson, Douglas A. Landis

Biology Faculty Publications

Agriculture is being challenged to provide food, and increasingly fuel, for an expanding global population. Producing bioenergy crops on marginal lands—farmland suboptimal for food crops—could help meet energy goals while minimizing competition with food production. However, the ecological costs and benefits of growing bioenergy feedstocks—primarily annual grain crops—on marginal lands have been questioned. Here we show that perennial bioenergy crops provide an alternative to annual grains that increases biodiversity of multiple taxa and sustain a variety of ecosystem functions, promoting the creation of multifunctional agricultural landscapes. We found that switchgrass and prairie plantings harbored significantly greater plant, methanotrophic bacteria, arthropod, …

Measurement Of Hydrodynamic Force Generation By Swimming Dolphins Using Bubble Dpiv, Frank E. Fish, Paul Legac, Terrie M. Williams, Timothy Wei

Biology Faculty Publications

No abstract provided.

Targeted Cytotoxic Therapy Kills Persisting Hiv Infected Cells During Art, Paul W. Denton, Julie M. Long, Stephen W. Wietgrefe, Craig Sykes, Rae Ann Spagnuolo, Olivia D. Snyder, Katherine Perkey, Nancie M. Archin, Shailesh K. Choudhary, Kuo Yang, Michael G. Hudgens, Ira Pastan, Ashley T. Haase, Angela D. Kashuba, Edward A. Berger, David M. Margolis, J. Victor Garcia

Biology Faculty Publications

Antiretroviral therapy (ART) can reduce HIV levels in plasma to undetectable levels, but rather little is known about the effects of ART outside of the peripheral blood regarding persistent virus production in tissue reservoirs. Understanding the dynamics of ART-induced reductions in viral RNA (vRNA) levels throughout the body is important for the development of strategies to eradicate infectious HIV from patients. Essential to a successful eradication therapy is a component capable of killing persisting HIV infected cells during ART. Therefore, we determined the in vivo efficacy of a targeted cytotoxic therapy to kill infected cells that persist despite long-term ART. …

Diffuse Brain Injury Induces Acute Post-Traumatic Sleep, Rachel K. Rowe, Martin Striz, Adam D. Bachstetter, Linda J. Van Eldik, Kevin D. Donohue, Bruce F. O'Hara, Jonathan Lifshitz

Biology Faculty Publications

Objective

Clinical observations report excessive sleepiness immediately following traumatic brain injury (TBI); however, there is a lack of experimental evidence to support or refute the benefit of sleep following a brain injury. The aim of this study is to investigate acute post-traumatic sleep.

Methods

Sham, mild or moderate diffuse TBI was induced by midline fluid percussion injury (mFPI) in male C57BL/6J mice at 9:00 or 21:00 to evaluate injury-induced sleep behavior at sleep and wake onset, respectively. Sleep profiles were measured post-injury using a non-invasive, piezoelectric cage system. In separate cohorts of mice, inflammatory cytokines in the neocortex were quantified …

Circadian Rhythms Affect Electroretinogram, Compound Eye Color, Striking Behavior And Locomotion Of The Praying Mantis Hierodula Patellifera, Aaron E. Schirmer, Frederick R. Prete, Edgar S. Mantes, Andrew F. Urdiales, Wil Bogue

Biology Faculty Publications

Many behaviors and physiological processes oscillate with circadian rhythms that are synchronized to environmental cues (e.g. light onset), but persist with periods of ~24 h in the absence of such cues. We used a multilevel experimental approach to assess whether circadian rhythms modulate several aspects of the visual physiology and behavior of the praying mantis Hierodula patellifera. We used electroretinograms (ERGs) to assess compound eye sensitivity, colorimetric photographic analyses to assess compound eye color changes (screening pigment migration), behavioral assays of responsiveness to computer-generated prey-like visual stimuli and analyses of locomotor activity patterns on a modified treadmill apparatus. Our results …

Cmvil-10 Stimulates The Invasive Potential Of Mda-Mb-231 Breast Cancer Cells, Cendy Valle Oseguera, Juliet Spencer

Biology Faculty Publications

Cancer is the result of unregulated cell growth that leads to tumor formation, and in many cases, metastases. Although there are several risk factors associated with cancer, one area that remains poorly understood is the impact of infectious disease. Human cytomegalovirus (HCMV) is a member of the herpesvirus family that is highly prevalent in the population. HCMV usually causes clinical disease only in immune compromised individuals, but recent evidence suggests that HCMV may be strongly associated with some forms of cancer, particularly glioblastoma and breast cancer. We investigated the possibility that cmvIL-10, a viral cytokine with homology to human IL-10 …

The Dry Box And C-Terminal Domain Of The Human Cytomegalovirus Us27 Gene Product Play A Role In Promoting Cell Growth And Survival, C C. Tu, Juliet Spencer

Biology Faculty Publications

Human cytomegalovirus (HCMV) is a widespread pathogen that can lay dormant in healthy individuals and establish lifelong latent infection. This successful co-existence is facilitated by a number of viral gene products that manipulate host cellular functions and immune responses. Among these immunomodulatory genes are four G-protein coupled receptors (GPCRs) encoded by HCMV, designated US27, US28, UL33, and UL78. Studies have shown the US28 gene product to be a functional chemokine receptor that signals both constitutively and in a ligand-dependent manner, resulting in a wide range of cellular effects. In previous work, we have found that US27 expression results in at …

Lack Of Quantitative Training Among Early-Career Ecologists: A Survey Of The Problem And Potential Solutions, F. Barraquand, T. G. Ezard, P. Søgaard Jørgensen, Naupaka B. Zimmerman, S. Chamberlain, R. Salguero-Gómez, T. J. Curran, T. Poisot

Biology Faculty Publications

Proficiency in mathematics and statistics is essential to modern ecological science, yet few studies have assessed the level of quantitative training received by ecologists. To do so, we conducted an online survey. The 937 respondents were mostly early-career scientists who studied biology as undergraduates. We found a clear self-perceived lack of quantitative training: 75% were not satisfied with their understanding of mathematical models; 75% felt that the level of mathematics was “too low” in their ecology classes; 90% wanted more mathematics classes for ecologists; and 95% more statistics classes. Respondents thought that 30% of classes in ecology-related degrees should be …

Assessing Perceived And Documented Crop Damage In A Tanzanian Village Impacted By Human-Elephant Conflict (Hec), Rebekah R. Hoffmeier-Karimi, Bruce A. Schulte

Biology Faculty Publications

In sub-Saharan Africa human-wildlife conflict (HWC) is a growing conservation issue and human-elephant conflict (HEC) is of special concern. Crop loss to wildlife comprises a main component of HWC. Deterrent methods for crop loss are numerous and such schemes could be more effective by an improved understanding of how farmers’ perceptions align with actual causes of crop loss. Our objective was to compare the perception by farmers of the causes and extent of crop damage to the measured crop damage in fields of maize (Zea mays) using different deterrent methods. We interviewed agriculturalists in the farming village of Miti Mirefu …

Impacts Of Environmental Pressures On The Reproductive Physiology Of Subpopulations Of Black Rhinoceros (Diceros Bicornis Bicornis) In Addo Elephant National Park, South Africa, Elizabeth Freeman, Jordana Meyer, Jed Bird, John Adendorff, Bruce A. Schulte, Rachel Santymire

Biology Faculty Publications

Black rhinoceros are an icon for international conservation, yet little is known about their physiology due to their secretive nature. To overcome these challenges, non-invasive methods were used to monitor rhinoceros in two sections of Addo Elephant National Park, South Africa, namely Addo and Nyathi. These sections were separated by a public road, and the numbers of elephants, predators and tourists were higher in Addo. Faecal samples (n = 231) were collected (from July 2007 to November 2010) from known individuals and analysed for progestagen and androgen metabolite (FPM and FAM, respectively) concentrations. As biotic factors could impact reproduction, …

Fishes Of Eastern Washington: A Natural History, Volume 1, Allan T. Scholz, Tyler Basler, Josh Smith, Judy Mcmillan, Larry Conboy, Eastern Washington University. Department Of Biology., Eastern Washington University. University Graphics.

Biology Faculty Publications

Volume 1 of 4.

CHAPTER 1: INTRODUCTION, CHAPTER 2: CHECKLISTS OF EXTANT AND FOSSIL FISHES FOUND IN EASTERN WASHINGTON, CHAPTER 3: THE DISCOVERERS, CHAPTER 4: GEOLOGY, CHAPTER 5: COLUMBIA RIVER BASIN HYDROLOGY AND FISH DISTRIBUTION IN EASTERN WASHINGTON

Fishes Of Eastern Washington: A Natural History, Volume 2, Allan T. Scholz, Tyler Basler, Josh Smith, Judy Mcmillan, Larry Conboy, Eastern Washington University. Department Of Biology., Eastern Washington University. University Graphics.

Biology Faculty Publications

Volume 2 of 4.

CHAPTER 6: KEY TO FAMILIES OF EASTERN WASHINGTON FISHES, CHAPTER 7: FAMILY PETROMYZONTIDAE: LAMPREYS, CHAPTER 8: FAMILY ACIPENSERIDAE: STURGEON, CHAPTER 9: FAMILY CLUPEIDAE: HERRINGS, CHAPTER 10: FAMILY CYPRINIDAE: CARPS AND MINNOWS, CHAPTER 11: Family Catostomidae: Suckers, CHAPTER 12: FAMILY ICTALURIDAE: BULLHEAD CATFISHES, CHAPTER 13: Family Esocidae: Pikes

Fishes Of Eastern Washington: A Natural History, Volume 3, Allan T. Scholz, Josh Smith, Amanda Maifeld, Judy Mcmillan, Larry Conboy, Eastern Washington University. Department Of Biology., Eastern Washington University. University Graphics.

Biology Faculty Publications

Volume 3 of 4.

CHAPTER 14: FAMILY SALMONIDAE: SALMON, TROUT, CHARR, WHITEFISH AND GRAYLINGS, CHAPTER 15: FAMILY SALMONIDAE (SUBFAMILY COREGONINAE): WHITEFISH, CHAPTER 16: FAMILY SALMONIDAE (SUBFAMILY MONINAE): SALMON, TROUT AND CHARR, CHAPTER 17: FAMILY SALMONIDAE (SUBFAMILY THYMALLINAE): GRAYLINGS

The Unseen World: Environmental Microbial Sequencing And Identification Methods For Ecologists, Naupaka B. Zimmerman, J. Izard, C. Klatt, J. Zhou, E. Aronson

Biology Faculty Publications

Microorganisms inhabit almost every environment, comprise the majority of diversity on Earth, are important in biogeochemical cycling, and may be vital to ecosystem responses to large-scale climatic change. In recent years, ecologists have begun to use rapidly advancing molecular techniques to address questions about microbial diversity, biogeography, and responses to environmental change. Studies of microbes in the environment generally focus on three broad objectives: determining which organisms are present, what their functional capabilities are, and which are active at any given time. However, comprehending the range of methodologies currently in use can be daunting. To provide an overview of environmental …

Revision Of Anacaena Thomson, 1859 Xi. Republic Of The Philippines (Coleoptera: Hydrophilidae), Hendrik Freitag

Biology Faculty Publications

The species of Anacaena THOMSON, 1859 (Coleoptera: Hydrophilidae) of the Republic of the Philippines are revised. Fifteen new species are described: Anacaena albay sp.n., A. amplocomata sp.n., A. apo sp.n., A. balabag sp.n., A. cordillera sp.n., A. davao sp.n., A. destructa sp.n., A. emergens sp.n., A. hemisphaerica sp.n., A. levistriata sp.n., A. philippina sp.n., A. princesa sp.n., A. quezona sp.n., A. sulcata sp.n., and A. zamboangana. All species are endemic to the Philippines, twelve are aquatic, the habitat of three species is unknown. All Philippine species are morphologically similar to other species of the eastern Oriental Region and probably do …

A Mega-Diverse Water Beetle Genus (Coleoptera: Hydraenidae: Hydraena Kugelann) Commonly Overlooked In Southeast Asia And Its Potential Use For Environmental Biomonitoring, Hendrik Freitag

Biology Faculty Publications

This study summarizes the current knowledge of the water beetle genus Hydraena Kugelann in Southeast Asia. The surprising species diversity and endemism rates in Hydraenopsis Janssens, the only subgenus present in Southeast Asia, are discussed. Data of five published Hydraena surveys from the Philippines and Singapore are used to evaluate species richness and the occurrence of species assemblages that are subject to the presence and quality of forests. Species richness was found to be generally higher in old grown forests. Some species appeared to be confined to near-natural forests. The denomination of indicator species is impeded by adequate sampling data, …

Nel Positively Regulates The Genesis Of Retinal Ganglion Cells By Promoting Their Differentiation And Survival During Development, Chizu Nakamoto, Soh-Leh Kuan, Amy Findlay, Elaine Durward, Zhufeng Ouyang, Masaru Nakamoto, Ewa Zakrewska, Takuma Endo

Biology Faculty Publications

For correct functioning of the nervous system, the appropriate number and complement of neuronal cell types must be produced during development. However, the molecular mechanisms that regulate the production of individual classes of neurons are poorly understood. In this study, we investigate the function of the thrombospondin-1–like glycoprotein, Nel (neural epidermal growth factor [EGF]-like), in the generation of retinal ganglion cells (RGCs) in chicks. During eye development, Nel is strongly expressed in the presumptive retinal pigment epithelium and RGCs. Nel overexpression in the developing retina by in ovo electroporation increases the number of RGCs, whereas the number of displaced amacrine …

2014 Virginia Wildflower Of The Year: Coral Honeysuckle, Lonicera Sempervirens, W. John Hayden

Biology Faculty Publications

The flashy red flowers of coral honeysuckle beckon hummingbirds to their sweet nectar. Coral honeysuckle is a twining woody vine, usually climbing on other vegetation but sometimes trailing along the ground; older stems have papery-brown exfoliating bark.

Biotic Mechanisms Of Community Stability Shift Along A Precipitation Gradient, Lauren M. Hallett, Joanna S. Hsu, Elisa E. Cleland, Scott L. Collins, Timothy L. Dickson, Emily C. Farrer, Laureano A. Gherardi, Katherine L. Gross, Richard J. Hobbs, Laura Turnball, Katharine N. Suding

Biology Faculty Publications

Understanding how biotic mechanisms confer stability in variable environments is a fundamental quest in ecology, and one that is becoming increasingly urgent with global change. Several mechanisms, notably a portfolio effect associated with species richness,compensatory dynamics generated by negative species covariance and selection for stable dominant species populations can increase the stability of the overall community. While the importance of these mechanisms is debated, few studies have contrasted their importance in an environmental context. We analyzed nine long-term data sets of grassland species compositiont o investigate how two key environmental factors, precipitation amount and variability, may directly influence community stability …

De Novo Assembly And Analysis Of The Northern Leopard Frog Rana Pipiens Transcriptome, Matthew K. Christenson, Andrew J. Trease, Lakshmi-Prasad Potluri, Andrew Jezewski, Vincent M. Davis, Lindsey A. Knight, Alan Kolok, Paul H. Davis

Biology Faculty Publications

The northern leopard frog Rana (Lithobates) pipiens is an important animal model, being used extensively in cancer, neurology, physiology, and biomechanical studies. R. pipiens is a native North American frog whose range extends from northern Canada to southwest United States, but over the past few decades its populations have declined significantly and is now considered uncommon in large portions of the United States and Canada. To aid in the study and conservation of R. pipiens, this paper describes the first R. pipiens transcriptome. The R. pipiens transcriptome was annotated using Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), …

Fishes Of Eastern Washington: A Natural History, Volume 4, Allan T. Scholz, Josh Smith, Amanda Maifeld, Judy Mcmillan, Larry Conboy, Eastern Washington University. Department Of Biology., Eastern Washington University. University Graphics.

Biology Faculty Publications

Volume 4 of 4.

CHAPTER 6: KEY TO FAMILIES OF EASTERN WASHINGTON FISHES (REVISED), CHAPTER 18: FAMILY PERCOPSIDAE: TROUT-PERCHES, CHAPTER 19: FAMILY GADIDAE: CODS, CHAPTER 20: FAMILY POECILIIDAE: LIVEBEARERS, CHAPTER 21: FAMILY GASTEROSTEIDAE: STICKLEBACKS, CHAPTER 22: FAMILY COTTIDAE: SCULPINS, CHAPTER 23: FAMILY CENTRARCHIDAE: SUNFISHES, CHAPTER 24: FAMILY PERCIDAE: PERCH, CHAPTER 25: FISH WITH RARE OR UNCERTAIN STATUS IN EASTERN WASHINGTON, CHAPTER 26: LIMINOLOGY, WATER QUALITY, AND FISH HABITAT

Genotyping-By-Sequencing For Populus Population Genomics: An Assessment Of Genome Sampling Patterns And Filtering Approaches, M. Schilling, Paul G. Wolf, A. M. Duffy, H. S. Rai, C. A. Rowe, B. A. Richardson, K. E. Mock

Biology Faculty Publications

Continuing advances in nucleotide sequencing technology are inspiring a suite of genomic approaches in studies of natural populations. Researchers are faced with data management and analytical scales that are increasing by orders of magnitude. With such dramatic advances comes a need to understand biases and error rates, which can be propagated and magnified in large-scale data acquisition and processing. Here we assess genomic sampling biases and the effects of various population-level data filtering strategies in a genotyping-by-sequencing (GBS) protocol. We focus on data from two species of Populus, because this genus has a relatively small genome and is emerging …

Production Of Destruxins From Metarhizium Spp. Fungi In Artificial Medium And In Endophytically Colonized Cowpea Plants, P. S. Golo, D. R. Gardner, Michelle M. Grilley, Jon Y. Takemoto, S. B. Krasnoff, M. S. Pires, E. K. K. Férnandes, V. R. Bittencourt, Donald W. Roberts

Biology Faculty Publications

Destruxins (DTXs) are cyclic depsipeptides produced by many Metarhizium isolates that have long been assumed to contribute to virulence of these entomopathogenic fungi. We evaluated the virulence of 20 Metarhizium isolates against insect larvae and measured the concentration of DTXs A, B, and E produced by these same isolates in submerged (shaken) cultures. Eight of the isolates (ARSEF 324, 724, 760, 1448, 1882, 1883, 3479, and 3918) did not produce DTXs A, B, or E during the five days of submerged culture. DTXs were first detected in culture medium at 2–3 days in submerged culture. Galleria mellonella and Tenebrio molitor …

First Report Of Satellite Males During Breeding In Leptodactylus Latrans (Amphibia, Anura), Gabriel Laufer, Noelia Gobel, José M. Mautone, María Galán, Rafael O. De Sá

Biology Faculty Publications

Individual males can adopt alternative mating tactics. The occurrence of satellite males is a common behaviour across anuran taxa (e.g., Lithobates clamitans, Wells, 1977; Anaxyrus cognatus, Krupa, 1989; Dendropsophus ebraccatus, Miyamoto and Cane, 1980; Rhinella crucifer, Forester and Lynken, 1986). Satellite males take peripheral positions to calling males, and adopt alternate mating tactics in an attempt to intercept females that are attracted to calling males (Wells, 2007) to increase their own mating success. Satellite males could have an inexpensive form of mate-locating, avoiding predators, and saving energy (Arak, 1983). Furthermore, this strategy could play an important role in the genetic …