Digital Commons Network^™

Granite Rock Outcrops: An Extreme Environment For Soil Nematodes?, Erin Austin, Katharine Semmens, Charles Parsons, Amy M. Treonis

Biology Faculty Publications

We studied soil nematode communities from the surface of granite flatrock outcrops in the eastern Piedmont region of the United States. The thin soils that develop here experience high light intensity and extreme fluctuations in temperature and moisture and host unique plant communities. We collected soils from outcrop microsites in Virginia (VA) and North Carolina (NC) in various stages of succession (Primitive, Minimal, and Mature) and compared soil properties and nematode communities to those of adjacent forest soils. Nematodes were present in most outcrop soils, with densities comparable to forest soils (P > 0.05). Nematode communities in Mature and Minimal soils …

Range Expansions And New Breeding Records Of Birds In Tamaulipas, Mexico, Timothy Brush

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Biology)

Breeding birds of riparian forests and other habitats in the Ciudad Victoria area were studied, mainly in June 2003 and 2006. Olivaceous woodcreeper (Sittasomus griseicapillus), mangrove swallow (Tachycineta albilinea), and scrub euphonia (Euphonia affinis; nesting) extended their range north to the Ciudad Victoria area. Western kingbird (Tyrannus verticalis) nested for the first time in Tamaulipas and occurred south to the Ciudad Victoria area, and European starlings (Sturnus vulgaris) nested in south-central Tamaulipas for the first time. Great curassow (Crax rubra) and crested guan (Penelope purpurascens) were rediscovered in the Ciudad Victoria area for the first time since 1909. Distributions of …

Small Mammals In Portions Of Great Basin National Park Susceptible To Groundwater Withdrawal: Diversity And Stable Isotope Perspectives, Bryan T. Hamilton

Theses and Dissertations

To support population growth in Las Vegas, Nevada, large scale increases in groundwater pumping are planned across the state. This pumping could affect riparian areas in Great Basin National Park by lowering groundwater levels, reducing stream flows, and xerifying riparian vegetation. Great Basin National Park (GBNP) is mandated to manage its resources unimpaired for future generations. Loss of biodiversity is unacceptable under this mandate. If groundwater levels are reduced beyond a threshold, aquatic and riparian diversity would be lost, but the effects on small mammal communities are less clear. To provide baseline information and to consider the effects of groundwater …

Survival Of The Misfits : Why Most Sperm Are Duds & Other Interesting Tales Of Evolution, Deby L. Cassill, Nelson Poynter Memorial Library.

USF St. Petersburg Campus Faculty Publications

Speaker: Dr. Deby Cassill

Landscape Genomics And Biased Fst Approaches Reveal Single Nucleotide Polymorphisms Under Selection In Goat Breeds Of North-East Mediterranean, Lorraine Pariset, Stephane Joost, Paolo Ajmone Marsan, Alessio Valentini, Econogene Consortium

Biological Sciences Faculty Publications

Background: In this study we compare outlier loci detected using a F_st based method with those identified by a recently described method based on spatial analysis (SAM). We tested a panel of single nucleotide polymorphisms (SNPs) previously genotyped in individuals of goat breeds of southern areas of the Mediterranean basin (Italy, Greece and Albania). We evaluate how the SAM method performs with SNPs, which are increasingly employed due to their high number, low cost and easy of scoring.

Results: The combined use of the two outlier detection approaches, never tested before using SNP polymorphisms, resulted in the …

Avian Incubation Inhibits Growth And Diversification Of Bacterial Assemblages On Eggs, Matthew D. Shawkey, Mary K. Firestone, Eoin L. Brodie, Steven R. Beissinger

Biology Faculty Research

Microbial infection is a critical source of mortality for early life stages of oviparous vertebrates, but parental defenses against infection are less well known. Avian incubation has been hypothesized to reduce the risk of trans-shell infection by limiting microbial growth of pathogenic bacteria on eggshells, while enhancing growth of commensal or beneficial bacteria that inhibit or competitively exclude pathogens. We tested this hypothesis by comparing bacterial assemblages on naturally incubated and experimentally unincubated eggs at laying and late incubation using a universal 16S rRNA microarray containing probes for over 8000 bacterial taxa. Before treatment, bacterial assemblages on individual eggs from …

Accumulation Of Rhodopsin In Late Endosomes Triggers Photoreceptor Cell Degeneration, Yashodhan Chinchore, Amitavo Mitra, Patrick J. Dolph, Norbert Perrimon

Dartmouth Scholarship

Progressive retinal degeneration is the underlying feature of many human retinal dystrophies. Previous work using Drosophila as a model system and analysis of specific mutations in human rhodopsin have uncovered a connection between rhodopsin endocytosis and retinal degeneration. In these mutants, rhodopsin and its regulatory protein arrestin form stable complexes, and endocytosis of these complexes causes photoreceptor cell death. In this study we show that the internalized rhodopsin is not degraded in the lysosome but instead accumulates in the late endosomes. Using mutants that are defective in late endosome to lysosome trafficking, we were able to show that rhodopsin accumulates …

Desiccation Survival In An Antarctic Nematode: Molecular Analysis Using Expressed Sequenced Tags, Byron J. Adams, Bishwo N. Adhikari, Diana H. Wall

Faculty Publications

Background: Nematodes are the dominant soil animals in Antarctic Dry Valleys and are capable of surviving desiccation and freezing in an anhydrobiotic state. Genes induced by desiccation stress have been successfully enumerated in nematodes; however we have little knowledge of gene regulation by Antarctic nematodes which can survive multiple environmental stresses. To address this problem we investigated the genetic responses of a nematode species, Plectus murrayi, that is capable of tolerating Antarctic environmental extremes, in particular desiccation and freezing. In this study, we provide the first insight into the desiccation induced transcriptome of an Antarctic nematode through cDNA library construction …

Correlation Between Animal And Mathematical Models For Prostate Cancer Progression, Zdzislaw Jackiewiczy, Cheryl L. Jorcyk, Mikhail K. Kolev, Barbara Zubik-Kowal

Biology Faculty Publications and Presentations

This work demonstrates that prostate tumour progression in vivo can be analysed by using solutions of a mathematical model supplemented by initial conditions chosen according to growth rates of cell lines in vitro. The mathematical model is investigated and solved numerically. Its numerical solutions are compared with experimental data from animal models. The numerical results confirm the experimental results with the growth rates in vivo.

Induction Of Microrna-221 By Platelet-Derived Growth Factor Signaling Is Critical For Modulation Of Vascular Smooth Muscle Phenotype, Brandi N. Davis, Aaron C. Hilyard, Peter H. Nguyen, Giorgio Lagna, Akiko Hata

Biology

The platelet-derived growth factor (PDGF) signaling pathway is a critical regulator of animal development and homeostasis. Activation of the PDGF pathway leads to neointimal proliferative responses to artery injury; it promotes a switch of vascular smooth muscle cells (vSMC) to a less contractile phenotype by inhibiting the SMC-specific gene expression and increasing the rate of proliferation and migration. The molecular mechanism for these pleiotropic effects of PDGFs has not been fully described. Here, we identify the microRNA-221 (miR-221), a small noncoding RNA, as a modulator of the phenotypic change of vSMCs in response to PDGF signaling. We demonstrate that miR-221 …

Species Delimitation In Lemurs: Multiple Genetic Loci Reveal Low Levels Of Species Diversity In The Genus Cheirogaleus, Linn F. Groeneveld, David W. Weisrock, Rodin M. Rasoloarison, Anne D. Yoder, Peter M. Kappeler

Biology Faculty Publications

BACKGROUND: Species are viewed as the fundamental unit in most subdisciplines of biology. To conservationists this unit represents the currency for global biodiversity assessments. Even though Madagascar belongs to one of the top eight biodiversity hotspots of the world, the taxonomy of its charismatic lemuriform primates is not stable. Within the last 25 years, the number of described lemur species has more than doubled, with many newly described species identified among the nocturnal and small-bodied cheirogaleids. Here, we characterize the diversity of the dwarf lemurs (genus Cheirogaleus) and assess the status of the seven described species, based on phylogenetic and …

Observations Of Flotsam Entrapment In The Northern Diamond-Backed Watersnake (Nerodia R. Rhombifer), Jason Ortega, Frederic Zaidan

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Biology)

—Small areas of protected land may act as islands of suitable habitat surrounded by human development. Although these areas receive protection, we have observed one way that the surrounding human population can still endanger the welfare of its inhabitants. During our observations of the Northern Diamond-backed Watersnake (Nerodia r. rhombifer) in a semi-protected nature park surrounded by human development, we encountered 13 individuals entangled with flotsam. Of the 220 juvenile through adult snakes that we captured, 12 were encircled by various types of objects (e.g., finger cots; latex sheaths that cover a single digit, dental elastics, and plastic bottle neck …

Development, Implementation And Evaluation Of A Data-Assimilative Ocean Forecasting System Off The Central California Coast, Yi Chao, Zhijin Li, John Farrara, James C. Mcwilliams, James Bellingham, Xavier Capet, Francisco Chavez, Jei-Kook Choi, Russ Davis, Jim Doyle, David M. Fratantoni, Peggy Li, Patrick Marchesiello, Mark A. Moline, Jeff Paduan, Steve Ramp

Biological Sciences

The development and implementation of a real-time ocean forecast system based on the Regional Ocean Modeling System (ROMS) off the coast of central California are described. The ROMS configuration consists of three nested modeling domains with increasing spatial resolutions: the US West coastal ocean at 15-km resolution, the central California coastal ocean at 5 km, and the Monterey Bay region at 1.5 km. All three nested models have 32 vertical sigma (or terrain-following) layers and were integrated in conjunction with a three-dimensional variational data assimilation algorithm (3DVAR) to produce snapshots of the ocean state every 6 h (the reanalysis) and …

Bioluminescence To Reveal Structure And Interaction Of Coastal Planktonic Communities, Mark A. Moline, Shelley M. Blackwell, James F. Case, Steven H.D. Haddock, Christen M. Herren, Cristina M. Orrico, Eric Terrill

Biological Sciences

Ecosystem function will in large part be determined by functional groups present in biological communities. The simplest distinction with respect to functional groups of an ecosystem is the differentiation between primary and secondary producers. A challenge thus far has been to examine these groups simultaneously with sufficient temporal and spatial resolution for observations to be relevant to the scales of change in coastal oceans. This study takes advantage of general differences in the bioluminescence flash kinetics between planktonic dinoflagellates and zooplankton to measure relative abundances of the two groups within the same-time space volume. This novel approach for distinguishing these …

The Most Widely Publicized Gender Problem In Human Genetics, William D. Stansfield, Matthew A. Carlton

Biological Sciences

In two-child families containing at least one boy, the expected probability that such a family has two boys is 1/3, provided that the boy/girl (B/G) ratio is 1.0 and the population to which they belong has a binomial distribution of BB, (BG + GB), and GG families. It is commonly known that in most human populations the sex ratio at birth (i.e., the ratio of the number of boys to the number of girls) is greater than 1.0. Teachers and textbook writers seldom discuss the more realistic expected distributions in populations where the sex ratio is greater than 1.0. We …

Synthesis: Evolutionary Ecology Of Microbial Wars: Within-Host Competition And (Incidental) Virulence, Sam Brown, Fredrik Inglis, François Taddei

Biology Department Faculty Works

Invading an occupied niche is a formidable ecological challenge, and one of particular human importance in the context of food-borne microbial pathogens. We discuss distinct categories of invader-triggered environmental change that facilitate invasion by emptying their niche of competitors. Evidence is reviewed that gut bacteria use such strategies to manipulate their environment (via bacteriocins, temperate phage viruses or immuno-manipulation) at the expense of their competitors are reviewed. The possible virulence implications of microbial warfare among multiple co-infecting strains are diverse. Killing competitors can reduce virulence by reducing overall microbial densities, or increase virulence if for example the allelopathic mechanism involves …

Evolutionary Ecology Of Microbial Wars: Within-Host Competition And (Incidental) Virulence, Sam Brown, R Inglis, François Taddei

Biology Department Faculty Works

Invading an occupied niche is a formidable ecological challenge, and one of particular human importance in the context of food-borne microbial pathogens. We discuss distinct categories of invader-triggered environmental change that facilitate invasion by emptying their niche of competitors. Evidence is reviewed that gut bacteria use such strategies to manipulate their environment (via bacteriocins, temperate phage viruses or immuno-manipulation) at the expense of their competitors are reviewed. The possible virulence implications of microbial warfare among multiple co-infecting strains are diverse. Killing competitors can reduce virulence by reducing overall microbial densities, or increase virulence if for example the allelopathic mechanism involves …

Ecological Specialization In A Spatially Structured Population Of The Thermophilic Cyanobacterium Mastigocladus Laminosus, Scott R. Miller, Carin Williams, Aaron L. Strong, Darla Carvey

Biological Sciences Faculty Publications

Laboratory evolution experiments suggest the potential for microbial populations to contribute significant ecological variation to ecosystems, yet the functional importance of genetic diversity within natural populations of microorganisms is largely unknown. Here, we investigated the distribution of genetic and phenotypic variation for a population of the cyanobacterium Mastigocladus laminosus distributed along the temperature gradient of White Creek, Yellowstone NP. A total of 153 laboratory strains were directly isolated from five sites with mean annual temperatures ranging between 39 and 54 C. Genetic characterization at four nitrogen metabolism genes identified 15 closely related lineages in the population sample. These lineages were …

A Preliminary Study Of The Diversity And Temporal Patterns Of Abundance Of Tachinidae In Southwestern Ohio, Diego J. Inclán, John O. Stireman Iii

Biological Sciences Faculty Publications

Although tachinids are one of the most diverse families of Diptera (Irwin et al. 2003) and represent the largest group of non-hymenopteran parasitoids (Belshaw 1994), the ecology of most species in the family is poorly known. Most of the studies that have focused on tachinids are related to taxonomic descriptions. Currently, our knowledge is very limited in terms of the diversity and distribution of populations across time and space, especially in the Nearctic and Neotropical Regions (Stireman 2008). There have been a number of recent studies focused on diversity and temporal distributions of tachinids in the Palaearctic Region such as …

A Lot About A Little Dot - Lessons Learned From Drosophila Melanogaster Chromosome 4, Nicole Riddle, Christopher Shaffer, Sarah C.R. Elgin

Biology Faculty Research

The fourth chromosome of Drosophila melanogaster has a number of unique properties that make it a convenient model for the study of chromatin structure. Only 4.2 Mb overall, the 1.2 Mb distal arm of chromosome 4 seen in polytene chromosomes combines characteristics of heterochromatin and euchromatin. This domain has a repeat density of ~35%, comparable to some pericentric chromosome regions, while maintaining a gene density similar to that of the other euchromatic chromosome arms. Studies of position-effect variegation have revealed that heterochromatic and euchromatic domains are interspersed on chromosome 4, and both cytological and biochemical studies have demonstrated that chromosome …

Genome-Wide Identification Of H-Ns-Controlled, Temperature-Regulated Genes In Escherichiacoli K-12, Christine A. White-Ziegler, Talya R. Davis

Biological Sciences: Faculty Publications

DNA microarrays demonstrate that H-NS controls 69% of the temperature regulated genes in Escherichia coli K-12. H-NS is shown to be a common regulator of multiple iron and other nutrient acquisition systems preferentially expressed at 37°C and of general stress response, biofilm formation, and cold shock genes highly expressed at 23°C.

Which Sry Locus Is The Hypertensive Y Chromosome Locus?, Monte E. Turner, Joel Farkas, Jeff Dunmire, Daniel Ely, Amy Milsted

Biology Faculty Research

The Y chromosome of the spontaneously hypertensive rat (SHR) contains a genetic component that raises blood pressure compared with the Wistar-Kyoto (WKY) Y chromosome. This research tests the Sry gene complex as the hypertensive component of the SHR Y chromosome. The Sry loci were sequenced in 1 strain with a hypertensive Y chromosome (SHR/Akr) and 2 strains with a normotensive Y chromosome (SHR/Crl and WKY/Akr). Both SHR strains have 7 Sry loci, whereas the WKY strain has 6. The 6 loci in common between SHR and WKY strains were identical in the sequence compared (coding region, 392-bp 5' prime flanking, …

Sexually Antagonistic Selection, Sexual Dimorphism, And The Resolution Of Intralocus Sexual Conflict, Robert M. Cox, Ryan Calsbeek

Dartmouth Scholarship

Males and females share most of their genomes and express many of the same traits, yet the sexes often have markedly different selective optima for these shared traits. This sexually antagonistic (SA) selection generates intralocus sexual conflict that is thought to be resolved through the evolution of sexual dimorphism. However, we currently know little about the prevalence of SA selection, the components of fitness that generate sexual antagonism, or the relationship between sexual dimorphism and current SA selection. We reviewed published studies to address these questions, using 424 selection estimates representing 89 traits from 34 species. Males and females often …

The Gift Of Giving, Jin Park

Lake Union Herald

No abstract provided.

Down And Out. The Functional Effects Of Silencing Calsequestrin 1 Or Deleting Both Calsequestrin Genes In Mammalian Muscle, Leandro Royer, Sandrine Pouvreau, Ying Wang, Gerhard Meissner, Jingsong Zhou, Pompeo Volpe, Alessandra Nori, Robert H. Fitts, James L. W. Bain, Feliciano Protasi, Paul D. Allen, Bjorn Knollmann, Danny R. Riley, Eduardo Rios

Biological Sciences Faculty Research and Publications

No abstract provided.

Establishment Of A Research Colony Of Marmorkrebs, A Parthenogenetic Crayfish Species, Stephanie A. Jimenez, Zen Faulkes

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Biology)

Marmorkrebs, or marbled crayfish, are recently discovered parthenogenetic crayfish. Its origins are unknown, but it has been introduced into natural ecosystems and could become a highly invasive pest species. Marmorkrebs have potential as a model organism for research in many biological fields because they are genetically uniform. A key element of most successful model organisms is maintaining self-sustaining breeding colonies. We report on our efforts find the best conditions for establishing and maintaining a Marmorkrebs breeding colony for research. The colony was founded by four adults of unknown age (P generation). These foundresses were housed communally in standard aquaria and …

Molecular Coevolution Of Pacific Northwest Hantaviruses And Their Host, The Deer Mouse, Peromyscus Maniculatus, Philip Darren Jones

Dissertations and Theses

Sin Nombre virus (SNV, family Bunyaviridae, genus Hantavirus), hosted by the deer mouse, Peromyscus maniculatus (family Cricetidae, Subfamily Neotominae), is the primary etiological agent of Hantavirus pulmonary syndrome (HPS) in the western United States. HPS, with known pathogenicity only to humans and for which there is no cure or prophylaxis, affects the epithelium of the lungs by making the capillaries leaky, thereby resulting in bilateral infiltrates, and eventually leading to respiratory failure and death by drowning in approximately 38% of hospitalized patients.

In the Americas, Peromyscus has been co-evolving with hantaviruses for approximately 12–20 million years, since the first …

Multi-Component Evaluation To Minimize The Spread Of Aquatic Invasive Seaweeds, Harmful Algal Bloom Microalgae, And Invertebrates Via The Live Bait Vector In Long Island Sound, Charles Yarish, Robert Whitlatch, George Kraemer, Senjie Lin

Publications

The goal of the project was to protect guard Long Island Sound from the introduction of non-native organisms that may be imported via fishing bait worms and the seaweed packing material known as wormweed (Ascophyllum nodosum). The project examined bait for non-native invertebrate animals, macroalgae (also known as seaweeds), and harmful, toxin-producing microalgae. Bait was purchased from retail bait shops at locations ranging from northeastern Long Island Sound along the Connecticut shoreline to the southwestern part of the Sound in Long Island. Using a combination of visual and microscopic inspection, and sophisticated molecular biological techniques to detect the presence of …

Protein Nutrition Of Southern Plains Small Mammals: Immune Response To Variation In Maternal And Offspring Dietary Nitrogen, James A. Wilson, Jennifer L. Parsons, Eric E. Jorgensen

Biology Faculty Publications

Maternal nutrition during pregnancy and postnatal offspring nutrition may influence offspring traits. We investigated the effects of maternal and post weaning offspring dietary nitrogen on immune function and hematology in two species of rodent: the hispid cotton rat (Sigmodon hispidus), a primarily herbivorous rodent, and the fulvous harvest mouse (Reithrodontomys fulvescens), an omnivore. These two species responded differently to the same levels of treatment, with cotton rats primarily influenced by maternal diet and harvest mice by post weaning offspring diet. Cotton rats born to mothers on high-nitrogen diets had lower values of mean corpuscle volume and hemoglobin and greater concentrations …

Randomization And In Vivo Selection Reveal A Ggrg Motif Essential For Packaging Human Immunodeficiency Virus Type 2 Rna, Tayyba T. Baig, Jean-Marc Lanchy, J. Stephen Lodmell

Biological Sciences Faculty Publications

The packaging signal (psi) of human immunodeficiency virus type 2 (HIV-2) is present in the 5' noncoding region of RNA and contains a 10-nucleotide palindrome (pal; 5'-392-GGAGUGCUCC) located upstream of the dimerization signal stem-loop 1 (SL1). pal has been shown to be functionally important in vitro and in vivo. We previously showed that the 3' side of pal (GCUCC-3') is involved in base-pairing interactions with a sequence downstream of SL1 to make an extended SL1, which is important for replication in vivo and the regulation of dimerization in vitro. However, the role of the 5' side of pal (5'-GGAGU) was …