Life Sciences Commons^™

Genomics Of A Metamorphic Timing Qtl: Met1 Maps To A Unique Genomic Position And Regulates Morph And Species-Specific Patterns Of Brain Transcription, Robert B. Page, Meredith A. Boley, D. Kevin Kump, S. Randal Voss

Biology Faculty Publications

Very little is known about genetic factors that regulate life history transitions during ontogeny. Closely related tiger salamanders (Ambystoma species complex) show extreme variation in metamorphic timing, with some species foregoing metamorphosis altogether, an adaptive trait called paedomorphosis. Previous studies identified a major effect QTL (met1) for metamorphic timing and expression of paedomorphosis in hybrid crosses between the biphasic Eastern tiger salamander (Ambystoma tigrinum tigrinum) and the paedomorphic Mexican axolotl (Ambystoma mexicanum). We used existing hybrid mapping panels and a newly created hybrid cross to map the met1 genomic region and determine the …

Reconstruction Of Family-Level Phylogenetic Relationships Within Demospongiae (Porifera) Using Nuclear Encoded Housekeeping Genes, Malcolm Hill, April L. Hill, Et. Al.

Biology Faculty Publications

Background: Demosponges are challenging for phylogenetic systematics because of their plastic and relatively simple morphologies and many deep divergences between major clades. To improve understanding of the phylogenetic relationships within Demospongiae, we sequenced and analyzed seven nuclear housekeeping genes involved in a variety of cellular functions from a diverse group of sponges.

Methodology/Principal Findings: We generated data from each of the four sponge classes (i.e., Calcarea, Demospongiae, Hexactinellida, and Homoscleromorpha), but focused on family-level relationships within demosponges. With data for 21 newly sampled families, our Maximum Likelihood and Bayesian-based approaches recovered previously phylogenetically defined taxa: Keratosa^p, Myxospongiae …

Trichoptera Of Mindoro, The Philippines I. New Species And Records From The Baroc River Catchment, Roxas, Oriental Mindoro (Insecta, Trichoptera), Hendrik Freitag, Wolfram Mey

Biology Faculty Publications

The study of a collection of caddisflies from Mindoro yielded a total of 34 species. Eight species proved to be unknown taxa and are described in the present article as: Rhyacophila crenophysetis spec. nov., Agapetus parallelaria spec. nov., Stactobia roxasi spec. nov., Paduniella vicentis spec. nov., Paduniella prodita spec. nov., Psychomyia taugadensis spec. nov., Tinodes hypoplectis spec. nov., and Ecnomus biundularia spec. nov. A list of all collected species is provided.

A New Intertidal Shore Bug (Heteroptera: Saldidae) From The Philippines, Hendrik Freitag, Herbert Zettel, Clister V. Pangantihon

Biology Faculty Publications

Salduncula carmencitae sp.n. is described, its habitus and the paramere and parandria of the male are illustrated. This shore bug was found on Mindanao Island, the Philippines, in the intertidal zone. Habitat and behaviour of the species are briefly described. The distinguishing diagnostic characters of species of Salduncula Brown, 1954 are discussed.

Ancyronyx Erichson, 1847 (Coleoptera, Elmidae) From Mindoro, Philippines, With Description Of The Larvae And Two New Species Using Dna Sequences For The Assignment Of The Developmental Stages, Hendrik Freitag

Biology Faculty Publications

Ancyronyx buhid sp. n. and Ancyronyx tamaraw sp. n. are described based on adults and larvae, matched using their cox1 or cob DNA sequence data. Additional records of Ancyronyx schillhammeri Jäch, 1994 and Ancyronyx minerva Freitag & Jäch, 2007 from Mindoro are listed. The previously unknown larva of Ancyronyx schillhammeri is also described here, aided by cox1 data. The new species and larval stages are described in detail and illustrated by SEM and stacked microscopic images. Keys to the adult and larval Ancyronyx species of Mindoro and an updated checklist of Philippine Ancyronyx species are provided. The usefulness as bioindicators, …

Hydraena (Hydraenopsis) Ateneo, New Species (Coleoptera, Hydraenidae) And Other Aquatic Polyphaga From A Small Habitat Patch In A Highly Urbanized Landscape Of Metro Manila, Philippines, Hendrik Freitag

Biology Faculty Publications

Seven species of Hydraenidae, Hydrophilidae and Elmidae are recorded from temporary freshwater habitats at the Ateneo de Manila University Campus in the metropolitan area of Manila, Philippines. They were identified as Enochrus (Lumetus) fragiloides d’Orchymont, Helochares (Hydrobaticus) lepidus d’Orchymont, Helochares (Helochares) pallens (MacLeay), Hydraena (Hydraenopsis) scabra d’Orchymont, Hydraena (Hydraenopsis) palawanensis Freitag & Jäch (new record for Luzon Island), Stenelmis sp. A further hydraenid species was unknown to science and is newly described: Hydraena (Hydraenopsis) ateneo Freitag, sp. n. Aedeagus, gonocoxite, spermatheca, and female tergite X are illustrated by …

2013 Virginia Wildflower Of The Year: Redbud, Cercis Canadensis, W. John Hayden

Biology Faculty Publications

Redbuds are small trees or shrubs that may attain heights of 10 m or so. Leaves are alternate and two-ranked, simple, entire, deciduous, broadly cordate, with an acute apex, 611 cm long, 712 cm wide, and palmately veined. Petioles have two swollen pulvini, one at its connection with the stem, the other at its junction with the leaf blade.

Pushing Taxonomy To Extiction?, Alessandro Minelli, Annemarie Ohler, Erna Aescht, Aaron Bauer, Lucio Bonato, Roger Bour, Marcelo Rodrigues De Carvalho, Rafael O. De Sá, Et Al.

Biology Faculty Publications

Can we describe all species on Earth before they disappear? We argue that this is possible only by endowing taxonomy with professional manpower and appropriate material resources as required by big science.

Contrary to Costello et al.’s (CMS) (1) statements, taxonomy is not an easy discipline accessible to all through a smartphone. It requires exhaustive training and long familiarity with field, specimens and literature (2).

CMS’s argument is framed in terms of species numbers, but different, non-overlapping species concepts apply to bacteria, brambles and birds (3,4,5): “the species” as common unit of biodiversity does not exist (6).

Even ignoring this …

Comparative Study Of Environmental Factors Influencing Motor Task Learning And Memory Retention In Sighted And Blind Crayfish, Sonya M. Bierbower, Zhanna P. Shuranova, Kert Viele, Robin L. Cooper

Biology Faculty Publications

In classical conditioning, an alteration in response occurs when two stimuli are regularly paired in close succession. An area of particular research interest is classical conditioning with a chemical signal and visual and/or tactile stimuli as the unconditional stimuli, to test manipulative and motor behaviors in a learning paradigm. A classical learning task chamber was developed to examine learning trends in a sighted surface-dwelling crayfish, Procambarus clarkii, and in a blind cave-dwelling crayfish, Orconectes australis packardi. We examined whether learning is influenced by environmental factors and/or reliance on different primary sensory modalities. Crayfish were trained to manipulate a large, cumbersome …

Genomics Of A Metamorphic Timing Qtl: Met1 Maps To A Unique Genomic Position And Regulates Morph And Species-Specific Patterns Of Brain Transcription, Robert B. Page, Meredith A. Boley, David K. Kump, Stephen R. Voss

Biology Faculty Publications

Very little is known about genetic factors that regulate life history transitions during ontogeny. Closely related tiger salamanders (Ambystoma species complex) show extreme variation in metamorphic timing, with some species foregoing metamorphosis altogether, an adaptive trait called paedomorphosis. Previous studies identified a major effect quantitative trait locus (met1) for metamorphic timing and expression of paedomorphosis in hybrid crosses between the biphasic Eastern tiger salamander (Ambystoma tigrinum tigrinum) and the paedomorphic Mexican axolotl (Ambystoma mexicanum). We used existing hybrid mapping panels and a newly created hybrid cross to map the met1 genomic region and …

Pre-Binding Sites In The Mdr Of Cll: Potential Tumor Suppressor Regulation, Christine E. Cutucache, Javeed Iqbal, Philip Bierman, Robert Gregory Bociek, Dennis D. Weisenburger, Shantaram S. Joshi

Biology Faculty Publications

Chronic lymphocytic leukemia [CLL] is the most common adult leukemia and is heterogeneous in clinical presentation. CLL cases present with various chromosomal aberrations, including 11q23, 14q32, 17p, and trisomy 12, with the most common abnormality being deletion of 13q14 [1]. Although monoallelic deletion of 13q14 is common, there is a subset of patients who have complete nullisomy at 13q14, a locus that has been hypothesized to contribute to CLL pa thogenesis [2] due to loss of tumor suppressors [DLEU and miR-15a/16-1].We hypothesized that deletion of both copies of 13q14 would lead to uncontrollable proliferation …

Sensitivity Of Grassland Plant Community Composition To Spatial Vs. Temporal Variation In Precipitation, Elsa E. Cleland, Scott L. Collins, Timothy L. Dickson, Emily C. Farrer, Katherine L. Gross, Laureano A. Gherardi, Lauren M. Hallett, Richard J. Hobbs, Joanna S. Hsu, Laura Turnball, Katharine N. Suding

Biology Faculty Publications

Climate gradients shape spatial variation in the richness and composition of plant communities. Given future predicted changes in climate means and variability, and likely regional variation in the magnitudes of these changes, it is important to determine how temporal variation in climate influences temporal variation in plant community structure. Here, we evaluated how species richness, turnover, and composition of grassland plant communities responded to interannual variation in precipitation by synthesizing long-term data from grasslands across the United States. We found that mean annual precipitation (MAP) was apositive predictor of species richness across sites, but a positive temporal relationship between annual …

Characterization Of The Asian Citrus Psyllid Transcriptome, Justin Reese, Matthew K. Christenson, Nan Leng, Surya Saha, Brandi Cantarel, Magdalen Lindeberg, Cecilia Tamborindeguy, Justin Maccarthy, Andrew J. Trease, Steven V. Ready, Vincent M. David, Courtney Mccormick, Christian Haudenschild, Shunsheng Han, Shannon L. Johnson, Kent S. Shelby, Hong Huang, Blake R. Bextine, Robert G. Shatters, David G. Hall, Paul H. Davis, Wayne B. Hunter

Biology Faculty Publications

The Asian citrus psyllid, Diaphorina citri Kuwayama (Hemiptera: Psyllidae) is a vector for the causative agents of Huanglongbing, which threatens citrus production worldwide. This study reports and discusses the first D. citri transcriptomes, encompassing the three main life stages of D. citri, egg, nymph and adult. The transcriptomes were annotated using Gene Ontology (GO) and insecticide-related genes within each life stage were identified to aid the development of future D. citri insecticides. Transcriptome assemblies and other sequence data are available for download at the International Asian Citrus Psyllid Genome Consortium website [http://psyllid.org/download] and at NCBI [http://www.ncbi.nlm.nih.gov/bioproject/29447].

In Vivo Analysis Of Highly Conserved Nef Activities In Hiv-1 Replication And Pathogenesis, Richard L. Watkins, Wei Zou, Paul W. Denton, John F. Krisko, John L. Foster, J. Victor Garcia

Biology Faculty Publications

Background: The HIV-1 accessory protein, Nef, is decisive for progression to AIDS. In vitro characterization of the protein has described many Nef activities of unknown in vivo significance including CD4 downregulation and a number of activities that depend on Nef interacting with host SH3 domain proteins. Here, we use the BLT humanized mouse model of HIV-1 infection to assess their impact on viral replication and pathogenesis and the selection pressure to restore these activities using enforced in vivo evolution.

Results: We followed the evolution of HIV-1LAI (LAI) with a frame-shifted nef (LAINeffs) during infection of BLT mice. LAINeffs …

Salamander Hox Clusters Contain Repetitive Dna And Expanded Non-Coding Regions: A Typical Hox Structure For Non-Mammalian Tetrapod Vertebrates?, Stephen Randal Voss, Srikrishna Putta, John A. Walker, Jeremiah J. Smith, Nobuyasu Maki, Panagiotis A. Tsonis

Biology Faculty Publications

Hox genes encode transcription factors that regulate embryonic and post-embryonic developmental processes. The expression of Hox genes is regulated in part by the tight, spatial arrangement of conserved coding and non-coding sequences. The potential for evolutionary changes in Hox cluster structure is thought to be low among vertebrates; however, recent studies of a few non-mammalian taxa suggest greater variation than originally thought. Using next generation sequencing of large genomic fragments (>100 kb) from the red spotted newt (Notophthalamus viridescens), we found that the arrangement of Hox cluster genes was conserved relative to orthologous regions from other vertebrates, but the …

How Species Richness And Total Abundance Constrain The Distribution Of Abundance, Kenneth J. Locey, Ethan P. White

Biology Faculty Publications

The species abundance distribution (SAD) is one of the most intensively studied distributions in ecology and its hollow-curve shape is one of ecology’s most general patterns. We examine the SAD in the context of all possible forms having the same richness (S) and total abundance (N), i.e. the feasible set. We find that feasible sets are dominated by similarly-shaped hollow-curves, most of which are highly correlated with empirical SADs (most R2 values > 75%), revealing a strong influence of N and S on the form of the SAD and an a priori explanation for the ubiquitous hollow-curve. Empirical SADs are often …

Life History, C. W. Fox, Frank J. Messina

Biology Faculty Publications

No abstract provided.

Redbud Cauliflory: The Inside Story, W. John Hayden

Biology Faculty Publications

One of the most distinctive features of redbuds, Cercis canadensis, the 2013 VNPS Wildflower of the Year, is its production of flowers on mature trunks and major branches, a habit termed cauliflory. Redbud flowers also form on young, one-year old twigs; as explained below, twig- and trunk-borne flowers are parts of a single developmental continuum; twigs bearing flowers eventually becoming trunks and large branches that continue to bear flowers.

Horseshoe Crab Eggs: A Rare Resource For Predators In Long Island Sound, Mark Beekey, Jennifer Mattei, Barbara J. Pierce

Biology Faculty Publications

In Delaware Bay, the spawning of several million horseshoe crabs (Limulus polyphemus) coincides with the arrival of migratory shorebirds that feed on their eggs. High horseshoe crab spawning densities and resulting high egg densities drive egg availability and predation rates. At high spawning densities, female horseshoe crabs perturb previously deposited clutches causing eggs to rise to the sediment surface (surface egg densities average 100,000 eggs m^{− 2}). At the surface (0–5 cm), the eggs are quickly depleted by shorebirds and other predators. This interaction between egg density and egg predation has not been explicitly explored on …

A Hunter Virus That Targets Both Infected Cells And Hiv Free Virions: Implications For Therapy, Cody Greer, Gisela García-Ramos

Biology Faculty Publications

The design of 'hunter' viruses aimed at destroying human immunodeficiency virus (HIV) infected cells is an active area of research that has produced promising results in vitro. Hunters are designed to target exposed viral envelope proteins in the membranes of infected cells, but there is evidence that the hunter may also target envelope proteins of free HIV, inducing virus-virus fusion. In order to predict the effects of this fusion on therapy outcomes and determine whether fusion ability is advantageous for hunter virus design, we have constructed a model to account for the possibility of hunter-HIV fusion. The study was based …

Positive Relationships Between Association Strength And Phenotypic Similarity Characterize The Assembly Of Mixed-Species Bird Flocks Worldwide, Hari Sridhar, Umesh Srinivasan, Robert A. Askins, Julio Cesar Canales-Delgadillo, Chao-Chieh Chen, David N. Ewert, George A. Gale, Eben Goodale, Wendy K. Gram, Patrick J. Hart, Keith A. Hobson, Richard L. Hutto, Sarath W. Kotagama, Jessie L. Knowlton, Tien Ming Lee, Charles A. Munn, Somchai Nimnuan, B. Z. Nizam, Guillaume Péron, V. V. Robin, Amanda D. Rodewald, Paul G. Rodewald, Robert L. Thomson, Pranav Trivedi, Steven L. Van Wilgenburg, Kartik Shanker

Biology Faculty Publications

Competition theory predicts that local communities should consist of species that are more dissimilar than expected by chance. We find a strikingly different pattern in a multicontinent data set (55 presence-absence matrices from 24 locations) on the composition of mixed-species bird flocks, which are important sub-units of local bird communities the world over. By using null models and randomization tests followed by meta-analysis, we find the association strengths of species in flocks to be strongly related to similarity in body size and foraging behavior and higher for congeneric compared with noncongeneric species pairs. Given the local spatial scales of our …

Molecular Phylogeny Of Microhylid Frogs (Anura: Microhylidae) With Emphasis On Relationships Among New World Genera, Rafael O. De Sá, Jeffrey W. Streicher, Relebohile Sekonyela, Mauricio C. Forlani, Simon P. Loader, Eli Greenbaum, Stephen Richards, Célio F.B. Haddad

Biology Faculty Publications

Background: Over the last ten years we have seen great efforts focused on revising amphibian systematics. Phylogenetic reconstructions derived from DNA sequence data have played a central role in these revisionary studies but have typically under-sampled the diverse frog family Microhylidae. Here, we present a detailed phylogenetic study focused on expanding previous hypotheses of relationships within this cosmopolitan family. Specifically, we placed an emphasis on assessing relationships among New World genera and those taxa with uncertain phylogenetic affinities (i.e., incertae sedis).

Results: One mitochondrial and three nuclear genes (about 2.8 kb) were sequenced to assess phylogenetic relationships. We utilized an …

Localizing Brain Regions Associated With Female Mate Preference Behavior In A Swordtail, Ryan Y. Wong, Mary E. Ramsey, Molly E. Cummings

Biology Faculty Publications

Female mate choice behavior is a critical component of sexual selection, yet identifying the neural basis of this behavior is largely unresolved. Previous studies have implicated sensory processing and hypothalamic brain regions during female mate choice and there is a conserved network of brain regions (Social Behavior Network, SBN) that underlies sexual behaviors. However, we are only beginning to understand the role this network has in pre-copulatory female mate choice. Using in situ hybridization, we identify brain regions associated with mate preference in female Xiphophorus nigrensis, a swordtail species with a female choice mating system. We measure gene expression in …

Toward The Beginning Of Time: Circadian Rhythms In Metabolism Precede Rhythms In Clock Gene Expression In Mouse Embryonic Stem Cells, Jiffin K. Paulose, Edmund B. Rucker Iii, Vincent M. Cassone

Biology Faculty Publications

The appearance, progression, and potential role for circadian rhythms during early development have previously focused mainly on the suprachiasmatic nucleus (SCN) and peri- and postnatal expression of canonical clock genes. More recently, gene expression studies in embryonic stem cells have shown that some clock genes are expressed in undifferentiated cells; however rhythmicity was only established when cells are directed toward a neural fate. These studies also concluded that a functional clock is not present in ESCs, based solely on their gene expression. The null hypothesis underlying the present study is that embryonic stem cells become rhythmic in both clock gene …

Physiological Epicotyl Dormancy And Recalcitrant Storage Behaviour In Seeds Of Two Tropical Fabaceae (Subfamily Caesalpinioideae) Species, K. M. G. Gehan Jayasuriya, Asanga S. T. B. Wijetunga, Jerry M. Baskin, Carol C. Baskin

Biology Faculty Publications

BACKGROUND AND AIMS: Physiological epicotyl dormancy in which the epicotyl elongates inside the seed before the shoot emerges has been reported for only a few tropical rainforest species, all of which are trees that produce recalcitrant seeds. In studies on seeds of Fabaceae in Sri Lanka, we observed a considerable time delay in shoot emergence following root emergence in seeds of the introduced caesalpinioid legumes Brownea coccinea and Cynometra cauliflora. Thus, our aim was to determine if seeds of these two tropical rainforest trees have physiological epicotyl dormancy, and also if they are recalcitrant, i.e. desiccation sensitive.

METHODOLOGY: Fresh seeds …

Scribble Acts In The Drosophila Fat-Hippo Pathway To Regulate Warts Activity, Shilpi Verghese, Indrayani Waghmare, Hailey Kwon, Katelin Hanes, Madhuri Kango-Singh

Biology Faculty Publications

Epithelial cells are the major cell-type for all organs in multicellular organisms. In order to achieve correct organ size, epithelial tissues need mechanisms that limit their proliferation, and protect tissues from damage caused by defective epithelial cells. Recently, the Hippo signaling pathway has emerged as a major mechanism that orchestrates epithelial development. Hippo signaling is required for cells to stop proliferation as in the absence of Hippo signaling tissues continue to proliferate and produce overgrown organs or tumors. Studies in Drosophila have led the way in providing a framework for how Hippo alters the pattern of gene transcription in target …

Brief Embryonic Strychnine Exposure In Zebrafish Causes Long-Term Adult Behavioral Impairment With Indications Of Embyronic Synaptic Changes, Nicole M. Roy, Brianna Arpie, Joseph Lugo, Elwood Linney, Edward D. Levin, Daniel Cerutti

Biology Faculty Publications

Zebrafish provide a powerful model of the impacts of embryonic toxicant exposure on neural development that may result in long-term behavioral dysfunction. In this study, zebrafish embryos were treated with 1.5mM strychnine for short embryonic time windows to induce transient changes in inhibitory neural signaling, and were subsequently raised in untreated water until adulthood. PCR analysis showed indications that strychnine exposure altered expression of some genes related to glycinergic, GABAergic and glutamatergic neuronal synapses during embryonic development. In adulthood, treated fish showed significant changes in swimming speed and tank diving behavior compared to controls. Taken together, these data show that …

Gene Expression Patterns Specific To The Regenerating Limb Of The Mexican Axolotl, James R. Monaghan, Antony Athippozhy, Ashley W. Seifert, Sri Putta, Arnold J. Stromberg, Malcolm Maden, David M. Gardiner, Stephen R. Voss

Biology Faculty Publications

Salamander limb regeneration is dependent upon tissue interactions that are local to the amputation site. Communication among limb epidermis, peripheral nerves, and mesenchyme coordinate cell migration, cell proliferation, and tissue patterning to generate a blastema, which will form missing limb structures. An outstanding question is how cross-talk between these tissues gives rise to the regeneration blastema. To identify genes associated with epidermis-nerve-mesenchymal interactions during limb regeneration, we examined histological and transcriptional changes during the first week following injury in the wound epidermis and subjacent cells between three injury types; 1) a flank wound on the side of the animal that …

Soil Nematodes And Their Prokaryotic Prey Along An Elevation Gradient In The Mojave Desert (Death Valley National Park, California, Usa), Amy M. Treonis, Kelsey Sutton, Brendan Kavanaugh, Archana Narla, Timothy Mcllarky, Jasmine Felder, Cecilia O'Leary, Megan Riley, Alyxandr Pikus, Sarah Thomas

Biology Faculty Publications

We characterized soil communities in the Mojave Desert across an elevation gradient. Our goal was to test the hypothesis that as soil quality improved with increasing elevation (due to increased productivity), the diversity of soil prokaryotes and nematodes would also increase. Soil organic matter and soil moisture content increased with elevation as predicted. Soil salinity did not correlate to elevation, but was highest at a mid-gradient, alluvial site. Soil nematode density, community trophic structure, and diversity did not show patterns related to elevation. Similar results were obtained for diversity of bacteria and archaea. Relationships between soil properties, nematode communities, and …

Idiosyncratic Responses Of Seagrass Phenolic Production Following Sea Urchin Grazing, Latina Steele, John F. Valentine

Biology Faculty Publications

While chemical defenses can determine plant persistence in terrestrial ecosystems and some marine macroalgae, their role in determining seagrass persistence in areas of intense grazing is unknown. As a first step toward determining if concentrations of feeding deterrents in seagrasses increase following herbivore attacks, we conducted 4 experiments using a common macrograzer (sea urchin Lytechinus variegatus) and 2 phylogenetically divergent seagrass species (Thalassia testudinum and Halodule wrightii). Macrograzer impacts on production of phenolic acids and condensed tannins varied somewhat idiosyncratically with season, urchin density, and distance from urchin damage. In general, phenolic concentrations were higher in both turtlegrass and shoalgrass …