Biology Commons^™

Humanized Mouse Models Of Hiv Infection, Paul W. Denton, J. Victor Garcia

Biology Faculty Publications

Because of the limited tropism of HIV, in vivo modeling of this virus has been almost exclusively limited to other lentiviruses such as SIV that reproduce many important characteristics of HIV infection. However, there are significant genetic and biological differences among lentiviruses and some HIV-specific interventions are not effective against other lentiviruses in non-human hosts. For these reasons much emphasis has recently been placed on developing alternative animal models that support HIV replication and recapitulate key aspects of HIV infection and pathogenesis in humans. Humanized mice, CD34+ hematopoietic progenitor cell transplanted immunodeficient mice and in particular mice also implanted with …

Variation, Systematics, And Relationships Of The Leptodactylus Bolivianus Complex (Amphibia: Anura: Leptodactylidae), W. Ronald Heyer, Rafael O. De Sá

Biology Faculty Publications

Heyer, W. Ronald, and Rafael O. de Sá. Variation, Systematics, and Relationships of the Leptodactylus bolivianus Complex (Amphibia: Anura: Leptodactylidae). Smithsonian Contributions to Zoology, number 635, viii + 58 pages, 21 figures, 20 tables, 2011.—The Leptodactylus bolivianuscomplex has been considered to consist of one or two species, L. bolivianus alone or L. bolivianus and L. insularum. Detailed morphological analyses were undertaken to evaluate variation in the complex, which ranges from Costa Rica through Panama, across northern South America in the river valleys draining to the Caribbean, and throughout much of the Amazon basin with southern limits in Bolivia. Members of …

Flowering Phenology Change And Climate Warming In Southwestern Ohio, Ryan Mcewan, Robert J. Brecha, Donald R. Geiger, Grace P. John

Biology Faculty Publications

Global surface temperature has increased markedly over the last 100 years. This increase has a variety of implications for human societies, and for ecological systems. One of the most obvious ways ecosystems are affected by global climate change is through alteration of organisms’ developmental timing (phenology). We used annual botanical surveys that documented the first flowering for an array of species from 1976 to 2003 to examine the potential implications of climate change for plant development. The overall trend for these species was a progressively earlier flowering time. The two earliest flowering taxa (Galanthus and Crocus) also exhibited the strongest …

Dissimilatory Nitrate Reductionpathways In An Oligotrophic Aquatic Ecosystem: Spatial And Temporal Trends, I. J. Washbourne, C. L. Crenshaw, Michelle A. Baker

Biology Faculty Publications

Elevated nitrate (NO₃⁻) concentrations can cause eutrophication, which may lead to harmful algal blooms, loss of habitat and reduction in biodiversity. Denitrification, a dissimilatory process that removes NO₃⁻ mainly as dinitrogen gas (N₂), is believed to be the dominant NO₃⁻ removal pathway in aquatic ecosystems. Evidence suggests that a less well-studied process, dissimilatory nitrate reduction to ammonium (DNRA), which retains nitrogen (N) in the system, may also be important under favorable conditions. Using stable isotope tracers in sealed microcosms, we measured the potential for NO₃⁻ losses due to DNRA …

Simple Structural Differences Between Coding And Noncodingdna, Kenneth J. Locey, Ethan P. White

Biology Faculty Publications

Background

The study of large-scale genome structure has revealed patterns suggesting the influence of evolutionary constraints on genome evolution. However, the results of these studies can be difficult to interpret due to the conceptual complexity of the analyses. This makes it difficult to understand how observed statistical patterns relate to the physical distribution of genomic elements. We use a simpler and more intuitive approach to evaluate patterns of genome structure.

Methodology/Principal Findings

We used randomization tests based on Morisita's Index of aggregation to examine average differences in the distribution of purines and pyrimidines among coding and noncoding regions of 261 …

De Novo Characterization Of The Gametophyte Transcriptome In Bracken Fern, Pteridium Aquilinum, J. P. Der, M. S. Barker, N. J. Wickett, C. W. Depamphilis, Paul G. Wolf

Biology Faculty Publications

Because of their phylogenetic position and unique characteristics of their biology and life cycle, ferns represent an important lineage for studying the evolution of land plants. Large and complex genomes in ferns combined with the absence of economically important species have been a barrier to the development of genomic resources. However, high throughput sequencing technologies are now being widely applied to non-model species. We leveraged the Roche 454 GS-FLX Titanium pyrosequencing platform in sequencing the gametophyte transcriptome of bracken fern (Pteridium aquilinum) to develop genomic resources for evolutionary studies.

The Evolution Of Chloroplast Genes And Genomes In Ferns, Paul G. Wolf, J. P. Der, A. M. Duffy, J. B. Davidson, A. L. Grusz, K. M. Pryer

Biology Faculty Publications

Most of the publicly available data on chloroplast (plastid) genes and genomes come from seed plants, with relatively little information from their sister group, the ferns. Here we describe several broad evolutionary patterns and processes in fern plastid genomes (plastomes), and we include some new plastome sequence data. We review what we know about the evolutionary history of plastome structure across the fern phylogeny and we compare plastome organization and patterns of evolution in ferns to those in seed plants. A large clade of ferns is characterized by a plastome that has been reorganized with respect to the ancestral gene …

The Selaginella Genome Identifies Changes In Gene Content Associated With The Evolution Of Vascular Plants, J. A. Banks, T. Nishiyama, M. Hasebe, J. L. Bowman, M. Gribskov, C. Depamphilis, Paul G. Wolf

Biology Faculty Publications

Vascular plants appeared ~410 million years ago, then diverged into several lineages of which only two survive: the euphyllophytes (ferns and seed plants) and the lycophytes. We report here the genome sequence of the lycophyte Selaginella moellendorffii (Selaginella), the first nonseed vascular plant genome reported. By comparing gene content in evolutionarily diverse taxa, we found that the transition from a gametophyte- to a sporophyte-dominated life cycle required far fewer new genes than the transition from a nonseed vascular to a flowering plant, whereas secondary metabolic genes expanded extensively and in parallel in the lycophyte and angiosperm lineages. Selaginella differs in …

Functional Characterization Of Putative Cilia Genes By High-Content Analysis, Cary Lai, Nidhi Gupta, Xiaohui Wen, Linda Rangell, Ben Chih, Andrew S. Peterson, J Fernando Bazan, Li Li, Suzie J. Scales

Biology Faculty Publications

Cilia are microtubule-based protrusions from the cell surface that are involved in a number of essential signaling pathways, yet little is known about many of the proteins that regulate their structure and function. A number of putative cilia genes have been identified by proteomics and comparative sequence analyses, but functional data are lacking for the vast majority. We therefore monitored the effects in three cell lines of small interfering RNA (siRNA) knockdown of 40 of these genes by high-content analysis. We assayed cilia number, length, and transport of two different cargoes (membranous serotonin receptor 6-green fluorescent protein [HTR6-GFP] and the …

Quantifying The Impact Of Gene Flow On Phenotype-Environment Mismatch: A Demonstration With The Scarlet Monkeyflower Mimulus Cardinalis, John R. Paul, Seema N. Sheth, Amy L. Angert

Biology Faculty Publications

Geographic range margins offer testing grounds for limits to adaptation. If range limits are concordant with niche limits, range expansions require the evolution of new phenotypes that can maintain populations beyond current range margins. However, many species' range margins appear static over time, suggesting limits on the ability of marginal populations to evolve appropriate phenotypes. A potential explanation is the swamping gene flow hypothesis, which posits that asymmetrical gene flow from large, well-adapted central populations prevents marginal populations from locally adapting. We present an empirical framework for combining gene flow, environment, and fitness-related phenotypes to infer the potential for maladaptation, …

Relative Changes In Krillabundance Inferred From Antarctic Fur Seal, T. Huang, L. Sun, John M. Stark, Y. Wang, Z. Cheng, Q. Yang, S. Sun

Biology Faculty Publications

Antarctic krill Euphausia superba is a predominant species in the Southern Ocean, it is very sensitive to climate change, and it supports large stocks of fishes, seabirds, seals and whales in Antarctic marine ecosystems. Modern krill stocks have been estimated directly by net hauls and acoustic surveys; the historical krill density especially the long-term one in the Southern Ocean, however, is unknown. Here we inferred the relative krill population changes along the West Antarctic Peninsula (WAP) over the 20th century from the trophic level change of Antarctic fur seal Arctocephalus gazella using stable carbon (d13C) and nitrogen (d15N) isotopes of …

Description Of The Tadpole Of Proceratophrys Renalis (Miranda-Ribeiro, 1920) (Anura: Cycloramphidae), Filipe Augusto C. Do Nascimento, Barnagleison S. Lisboa, Gabriel O. Skuk, Rafael O. De Sá

Biology Faculty Publications

The tadpole of Proceratophrys renalis is described based on specimens from Maceió, State of Alagoas, northeastern Brazil. At stage 35 the body is slightly dorso-ventrally depressed, ovoid in lateral, dorsal, and ventral views. Oral disc is ventral with lateral emarginations, surrounded by a single row of marginal papillae with a large gap on the upper labium. Labial tooth row formula is 2(2)/3(1 ). The analysis of internal oral anatomy revealed two possible characters that readily distinguish P. renalis from P. boiei, supporting the recent resurrection of P. renal is. Comparisons with available descriptions of the larvae for other species in …

Ecology And Transmission Of Buruli Ulcer Disease: A Systematic Review, Richard W. Merritt, Edward D. Walker, Pamela L. C. Small, John R. Wallace, Paul D. R. Johnson, Mark Eric Benbow, Daniel A. Boakye

Biology Faculty Publications

Buruli ulcer is a neglected emerging disease that has recently been reported in some countries as the second most frequent mycobacterial disease in humans after tuberculosis. Cases have been reported from at least 32 countries in Africa (mainly west), Australia, Southeast Asia, China, Central and South America, and the Western Pacific. Large lesions often result in scarring, contractual deformities, amputations, and disabilities, and in Africa, most cases of the disease occur in children between the ages of 4–15 years. This environmental mycobacterium, Mycobacterium ulcerans, is found in communities associated with rivers, swamps, wetlands, and human-linked changes in the aquatic environment, …

Muscle Receptor Organs In The Crayfish Abdomen: A Student Laboratory Exercise In Proprioception, Bonnie Leksrisawat, Ann S. Cooper, Allison B. Gilberts, Robin L. Cooper

Biology Faculty Publications

The primary purpose of this experiment is to demonstrate primary sensory neurons conveying information of joint movements and positions as proprioceptive information for an animal. An additional objective of this experiment is to learn anatomy of the preparation by staining, dissection and viewing of neurons and sensory structures under a dissecting microscope. This is performed by using basic neurophysiological equipment to record the electrical activity from a joint receptor organ and staining techniques. The muscle receptor organ (MRO) system in the crayfish is analogous to the intrafusal muscle spindle in mammals, which aids in serving as a comparative model that …

Physiological Recordings Of High And Low Output Nmjs On The Crayfish Leg Extensor Muscle, Wenhui Wu, Robin L. Cooper

Biology Faculty Publications

We explain in detail how to expose and conduct electrophysiological recordings of synaptic responses for high (phasic) and low (tonic) output motor neurons innervating the extensor muscle in the walking leg of a crayfish. Distinct differences are present in the physiology and morphology of the phasic and tonic nerve terminals. The tonic axon contains many more mitochondria, enabling it to take a vital stain more intensely than the phasic axon. The tonic terminals have varicosities, and the phasic terminal is filiform. The tonic terminals are low in synaptic efficacy but show dramatic facilitated responses. In contrast, the phasic terminals are …

Maple Syrup: A Sweet Springtime Lesson, Stephen G. Saupe, Sarah Gainey

Biology Faculty Publications

No abstract provided.

Osteology, Natural History Notes, And Phylogenetic Relationships Of The Poorly Known Caribbean Frog Leptodactylus Nesiotus (Anura, Leptodactylidae), María Laura Ponssa, Michael J. Jowers, Rafael O. De Sá

Biology Faculty Publications

The Leptodactylus melanonotus group consists of 15 species, but references to skeletal characters are available for only three species: L. leptodactyloides, L. melanonotus, and L. diedrus. Leptodactylus nesiotus is a member of the melanonotus group known only from the type locality, Bonasse swamp, on the Southwestern peninsula of Trinidad, Trinidad and Tobago. This species has been categorized as vulnerable given its restricted distribution. Herein, we report the adult osteology of L. nesiotus, the skeletal characters are compared with the available data from other Leptodactylus species. A phylogenetic analysis recovers a paraphyletic L. melanonotus group relative to the L. …

Evolutionary History And Taxonomy Of The Cuscuta Umbellata Complex (Convolvulaceae): Evidence Of Extensive Hybridization From Discordant Nuclear And Plastid Phylogenies, Mihai Costea, Saša Stefanović

Biology Faculty Publications

The Cuscuta umbellata complex is one of the 15 major clades recently circumscribed in C. subg. Grammica. Most of its members occur in North AMerican and the Caribbean (C. desmouliniana, C. lacerata, C. lacerata, C. leptantha, C. liliputana, C. odontolepsis, C. polyanthemos, C. tuberculata, C. umbellata), but three species (C. acuta, C. membranacea, C. umbellata) grow in South America, and one (C. hyalina) is found as a native species in India, Pakistan and Eastern to South Africa. Basic morphology, scanning electron microscopy and …

A Novel Multifunctional Oligonucleotide Microarray For Toxoplasma Gondii, Amit Bahl, Paul H. Davis, Michael Behnke, Florence Dzierszinski, Manjunatha Jagalur, Feng Chen, Dhanasekaran Shanmugam, Michael W. White, David Kulp, David S. Roos

Biology Faculty Publications

Background: Microarrays are invaluable tools for genome interrogation, SNP detection, and expression analysis, among other applications. Such broad capabilities would be of value to many pathogen research communities, although the development and use of genome-scale microarrays is often a costly undertaking. Therefore, effective methods for reducing unnecessary probes while maintaining or expanding functionality would be relevant to many investigators.

Results: Taking advantage of available genome sequences and annotation for Toxoplasma gondii (a pathogenic parasite responsible for illness in immunocompromised individuals) and Plasmodium falciparum (a related parasite responsible for severe human malaria), we designed a single oligonucleotide microarray capable of supporting …

Impact Of Interdisciplinary Undergraduate Research In Mathematics And Biology On The Development Of A New Course Integrating Five Stem Disciplines, Lester Caudill, April L. Hill, Kathy Hoke, Ovidiu Z. Lipan

Biology Faculty Publications

Funded by innovative programs at the National Science Foundation and the Howard Hughes Medical Institute, University of Richmond faculty in biology, chemistry, mathematics, physics, and computer science teamed up to offer first- and second-year students the opportunity to contribute to vibrant, interdisciplinary research projects. The result was not only good science but also good science that motivated and informed course development. Here, we describe four recent undergraduate research projects involving students and faculty in biology, physics, mathematics, and computer science and how each contributed in significant ways to the conception and implementation of our new Integrated Quantitative Science course, a …

Dorsal Eye Selector Pannier (Pnr) Suppresses The Eye Fate To Define Dorsal Margin Of The Drosophila Eye, Sarah M. Oros, Meghana Tare, Madhuri Kango-Singh, Amit Singh

Biology Faculty Publications

Axial patterning is crucial for organogenesis. During Drosophila eye development, dorso-ventral (DV) axis determination is the first lineage restriction event. The eye primordium begins with a default ventral fate, on which the dorsal eye fate is established by expression of the GATA-1 transcription factor pannier (pnr). Earlier, it was suggested that loss of pnr function induces enlargement in the dorsal eye due to ectopic equator formation. Interestingly, we found that in addition to regulating DV patterning, pnr suppresses the eye fate by downregulating the core retinal determination genes eyes absent (eya), sine oculis (so) and dacshund (dac) to define the …

The Identity Of The Crackling, Luminescent Frog Of Suriname (Rana Typhonia Linnaeus, 1758) (Amphibia, Anura), E. O. Lavilla, José A. Langone, José M. Padial, Rafael O. De Sá

Biology Faculty Publications

Review of the literature and recently available field notes from the collector of the type allows a reconsideration of the identity of the Linnaean name Rana typhonia. We provide evidence to demonstrate that the Linnaean species is neither a bufonid nor an Asiatic ranid, but a Neotropical hylid. Subsequently, we consider Rana typhonia as an older synonym of Rana venulosa Laurenti, 1768, redescribing its holotype under the new combination, Trachycephalus typhonius (Linnaeus, 1758).

Conidia But Not Yeast Cells Of The Fungal Pathogen Histoplasma Capsulatum Trigger A Type I Interferon Innate Immune Response In Murine Macrophages, Diane O. Inglis, Charlotte A. Berkes, Davina R. Hocking Murray, Anita Sil

Biology Faculty Publications

Histoplasma capsulatum is the most common cause of fungal respiratory infections and can lead to progressive disseminated infections, particularly in immunocompromised patients. Infection occurs upon inhalation of the aerosolized spores, known as conidia. Once inside the host, conidia are phagocytosed by alveolar macrophages. The conidia subsequently germinate and produce a budding yeast-like form that colonizes host macrophages and can disseminate throughout host organs and tissues. Even though conidia are the predominant infectious particle for H. capsulatum and are the first cell type encountered by the host during infection, very little is known at a molecular level about conidia or about …

Herbivore And Fungal Pathogen Exclusion Aects The Seed Production Of Four Common Grassland Species, Timothy L. Dickson, Charles E. Mitchell

Biology Faculty Publications

Insect herbivores and fungal pathogens can independently affect plant fitness, and may have interactive effects. However, few studies have experimentally quantified the joint effects of insects and fungal pathogens on seed production in non-agricultural populations. We examined the factorial effects of insect herbivore exclusion (via insecticide) and fungal pathogen exclusion (via fungicide) on the population-level seed production of four common graminoid species (Andropogon gerardii, Schizachyrium scoparium, Poa pratensis, and Carex siccata) over two growing seasons in Minnesota, USA. We detected no interactive effects of herbivores and pathogens on seed production. However, the seed production of …

The Identity Of Zachaenus Roseus Cope, 1890 (Anura: Species Inquirenda), Esteban O. Lavilla, J. J. Nuñez, F. E. Rabanal, José A. Langone, Rafael O. De Sá

Biology Faculty Publications

Zachaenus roseus Cope, 1890, has puzzled systematists working in southern South America. A single individual, the holotype, has ever been collected and this specimen is in extremely poor preservation condition. Herein, the precise location of the type locality of Z. roseus is determined based on a historical review of the literature. Furthermore, following a careful comparison with all species that inhabit the southern austral forest, and that could potentially correspond to Zachaenus roseus, we conclude that this taxon is placed in the synonymy of Eupsophus calcaratus (Günther, 1881)

Integrative Genomic Approaches Highlight A Family Of Parasite-Specific Kinases That Regulate Host Responses, Lucia Peixoto, Feng Chen, Omar S. Harb, Paul H. Davis, Daniel P. Beiting, Catie Small Brownback, Dinkorma Ouloguem, David S. Roos

Biology Faculty Publications

Apicomplexan parasites release factors via specialized secretory organelles (rhoptries, micronemes) that are thought to control host cell responses. In order to explore parasite-mediated modulation of host cell signaling pathways, we exploited aphylogenomic approach to characterize the Toxoplasma gondii kinome, defining a 44 member family of coccidian-specific secreted kinases, some of which have been previously implicated in virulence. Comparative genomic analysis suggests that ‘‘ROPK’’ genes are under positive selection, and expression profiling demonstrates that most are differentially expressed between strains and/or during differentiation. Integrating diverse genomic-scale analyses points to ROP38 as likely to be particularly important in parasite biology. Upregulating expression …

A Major Role For Mammals In The Ecology Of Mycobacterium Ulcerans, Janet A. Fyfe, Caroline J. Lavender, Kathrine A. Handasyde, Alistair R. Legione, Carolyn R. O'Brien, Timothy P. Stinear, Sacha J. Pidot, Torsten Seemann, Mark Eric Benbow, John R. Wallace, Christina Mccowan, Paul D. R. Johnson

Biology Faculty Publications

Background: Mycobacterium ulcerans is the causative agent of Buruli ulcer (BU), a destructive skin disease found predominantly in sub-Saharan Africa and south-eastern Australia. The precise mode(s) of transmission and environmental reservoir(s) remain unknown, but several studies have explored the role of aquatic invertebrate species. The purpose of this study was to investigate the environmental distribution of M. ulcerans in south-eastern Australia.

Meditation Acutely Improves Psychomotor Vigilance, And May Decrease Sleep Need, Prashant Kaul, Jason Passafiume, Craig R. Sargent, Bruce F. O'Hara

Biology Faculty Publications

BACKGROUND: A number of benefits from meditation have been claimed by those who practice various traditions, but few have been well tested in scientifically controlled studies. Among these claims are improved performance and decreased sleep need. Therefore, in these studies we assess whether meditation leads to an immediate performance improvement on a well validated psychomotor vigilance task (PVT), and second, whether longer bouts of meditation may alter sleep need.

METHODS: The primary study assessed PVT reaction times before and after 40 minute periods of mediation, nap, or a control activity using a within subject cross-over design. This study utilized novice …

Microarray Analysis Of A Salamander Hopeful Monster Reveals Transcriptional Signatures Of Paedomorphic Brain Development, Robert B. Page, Meredith A. Boley, Jeramiah J. Smith, Srikrishna Putta, Stephen R. Voss

Biology Faculty Publications

Background

The Mexican axolotl (Ambystoma mexicanum) is considered a hopeful monster because it exhibits an adaptive and derived mode of development - paedomorphosis - that has evolved rapidly and independently among tiger salamanders. Unlike related tiger salamanders that undergo metamorphosis, axolotls retain larval morphological traits into adulthood and thus present an adult body plan that differs dramatically from the ancestral (metamorphic) form. The basis of paedomorphic development was investigated by comparing temporal patterns of gene transcription between axolotl and tiger salamander larvae (Ambystoma tigrinum tigrinum) that typically undergo a metamorphosis.

Results

Transcript abundances from whole brain …

Avoidance Of Skeletal Muscle Atrophy In Spontaneous And Facultative Hibernators, Clark Cotton, Henry J. Harlow

Biology Faculty Publications

Smooth and skeletal muscle changes were compared from overwintering white-tailed prairie dogs, spontaneous hibernators that undergo regular, low-temperature torpor bouts, and black-tailed prairie dogs, facultative hibernators that use sporadic, moderate-temperature torpor bouts. The objectives were to assess the abilities of these two species with dramatically different torpor patterns (1) to conserve skeletal muscle morphology, protein, and strength and (2) to use labile protein in the small intestine and liver during the winter season of reduced activity and food intake. Mass and protein concentration of the extensor digitorum longus (EDL), soleus, liver, and small intestine, as well as skeletal muscle strength …