Life Sciences Commons^™

A Dna-Binding Peroxiredoxin Of Coxiella Burnetii Is Involved In Countering Oxidative Stress During Exponential-Phase Growth, Linda D. Hicks, Rahul Raghavan, James M. Battisti, Michael F. Minnick

Biological Sciences Faculty Publications

Coxiella burnetii is a Gram-negative, obligate intracellular bacterial pathogen that resides within the harsh, acidic confines of a lysosome-like compartment of the host cell that is termed a parasitophorous vacuole. In this study, we characterized a thiol-specific peroxidase of C. burnetii that belongs to the atypical 2-cysteine subfamily of peroxiredoxins, commonly referred to as bacterioferritin comigratory proteins (BCPs). Coxiella BCP was initially identified as a potential DNA-binding protein by two-dimensional Southwestern (SW) blots of the pathogen's proteome, probed with biotinylated C. burnetii genomic DNA. Confirmation of the identity of the DNA-binding protein as BCP (CBU_0963) was established by matrix-assisted laser …

A Toolkit For Rapid Gene Mapping In The Nematode Caenorhabditis Briggsae, Daniel C. Koboldt, Julia E. Staisch, Bavithra Thillainathan, Karen Haines, Scott Everet Baird, Helen M. Chamberlin, Eric S. Haag, Raymond D. Miller, Bhagwati P. Gupta

Biological Sciences Faculty Publications

Background

The nematode C. briggsae serves as a useful model organism for comparative analysis of developmental and behavioral processes. The amenability of C. briggsae to genetic manipulations and the availability of its genome sequence have prompted researchers to study evolutionary changes in gene function and signaling pathways. These studies rely on the availability of forward genetic tools such as mutants and mapping markers.

Results

We have computationally identified more than 30,000 polymorphisms (SNPs and indels) in C. briggsae strains AF16 and HK104. These include 1,363 SNPs that change restriction enzyme recognition sites (snip-SNPs) and 638 indels that range between 7 …

Evaluating Forensic Dna Evidence, Dan E. Krane

Biological Sciences Faculty Publications

No abstract provided.

Establishing Parameters For Objective Interpretation Of Dna Profile Evidence, Dan E. Krane

Biological Sciences Faculty Publications

No abstract provided.

The Loss Of Species: Mangrove Extinction Risk And Geographic Areas Of Global Concern, Beth A. Polidoro, Kent E. Carpenter, Lorna Collins, Norman C. Duke, Aaron M. Ellison, Joanna C. Ellison, Elizabeth J. Farnsworth, Edwino S. Fernando, Kandasamy Kathiresan, Nico E. Koedam, Suzanne R. Livingstone, Toyohiko Miyagi, Gregg E. Moore, Vien Ngoc Nam, Jin Eong Ong, Jurgenne H. Primavera, Serverino G. Salmo, Jonnell C. Sanciango, Sukristijono Sukardjo, Yamin Wang, Jean Wan Hong Yong

Biological Sciences Faculty Publications

Mangrove species are uniquely adapted to tropical and subtropical coasts, and although relatively low in number of species, mangrove forests provide at least US $1.6 billion each year in ecosystem services and support coastal livelihoods worldwide. Globally, mangrove areas are declining rapidly as they are cleared for coastal development and aquaculture and logged for timber and fuel production. Little is known about the effects of mangrove area loss on individual mangrove species and local or regional populations. To address this gap, species-specific information on global distribution, population status, life history traits, and major threats were compiled for each of the …

Funding Needed For Assessments Of Weed Biological Control, John L. Maron, Dean E. Pearson, Stephen M. Hovick, Walter P. Carson

Biological Sciences Faculty Publications

No abstract provided.

The Ontogeny Of Muscle Structure And Locomotory Function In The Long-Finned Squid Doryteuthis Pealeii, J. T. Thompson, I. K. Bartol, A. E. Baksi, P. S. Krueger

Biological Sciences Faculty Publications

Understanding the extent to which changes in muscle form and function underlie ontogenetic changes in locomotory behaviors and performance is important in understanding the evolution of musculoskeletal systems and also the ecology of different life stages. We explored ontogenetic changes in the structure, myosin heavy chain (MHC) expression and contractile properties of the circular muscles that provide power for jet locomotion in the long-finned squid Doryteuthis pealeii. The circular muscle fibers of newly hatched paralarvae had different sizes, shapes, thick filament lengths, thin: thick filament ratio, myofilament organization and sarcoplasmic reticulum (SR) distribution than those of adults. Viewed in …

Isoform-Specific Regulation And Localization Of The Coxsackie And Adenovirus Receptor In Human Airway Epithelia, Katherine J.D.A. Excoffon, Nicholas D. Gansemer, Matthew E. Mobily, Philip H. Karp, Kalpaj R. Parekh, Joseph Zabner

Biological Sciences Faculty Publications

Adenovirus is an important respiratory pathogen. Adenovirus fiber from most serotypes co-opts the Coxsackie-Adenovirus Receptor (CAR) to bind and enter cells. However, CAR is a cell adhesion molecule localized on the basolateral membrane of polarized epithelia. Separation from the lumen of the airways by tight junctions renders airway epithelia resistant to inhaled adenovirus infection. Although a role for CAR in viral spread and egress has been established, the mechanism of initial respiratory infection remains controversial. CAR exists in several protein isoforms including two transmembrane isoforms that differ only at the carboxy-terminus (CAR^Ex7 and CAR^Ex8). We found low-level …

Vesicular Calcium Regulates Coat Retention, Fusogenicity, And Size Of Pre-Golgi Intermediates, Marvin Bentley, Deborah C. Nycz, Ashwini Joglekar, Ismene Fertschai, Roland Malli, Wolfgang F. Graier, Jesse C. Hay

Biological Sciences Faculty Publications

The significance and extent of Ca(2+) regulation of the biosynthetic secretory pathway have been difficult to establish, and our knowledge of regulatory relationships integrating Ca(2+) with vesicle coats and function is rudimentary. Here, we investigated potential roles and mechanisms of luminal Ca(2+) in the early secretory pathway. Specific depletion of luminal Ca(2+) in living normal rat kidney cells using cyclopiazonic acid (CPA) resulted in the extreme expansion of vesicular tubular cluster (VTC) elements. Consistent with this, a suppressive role for vesicle-associated Ca(2+) in COPII vesicle homotypic fusion was demonstrated in vitro using Ca(2+) chelators. The EF-hand-containing protein apoptosis-linked gene 2 …

Use Of Rpsl As A Counterselectable Marker In Borrelia Burgdorferi, Dan Drecktrah, Miles J. Douglas, D. Scott Samuels

Biological Sciences Faculty Publications

We have demonstrated that rpsL, encoding the S12 protein of the small ribosomal subunit, can be used as a counterselectable marker in Borrelia burgdorferi, the causative agent of Lyme disease. Mutations in rpsL confer streptomycin resistance. Streptomycin susceptibility is dominant in an rpsL merodiploid, and streptomycin selects for the loss of wild-type rpsL carried in trans. This is the first description of a counterselectable marker in B. burgdorferi.

Probable Causes Of Increasing Brucellosis In Free-Ranging Elk Of The Greater Yellowstone Ecosystem, P. C. Cross, E. K. Cole, A. P. Dobson, W. H. Edwards, K. L. Hamlin, Gordon Luikart, A. D. Middleton, B. M. Scurlock, P. J. White

Biological Sciences Faculty Publications

While many wildlife species are threatened, some populations have recovered from previous Overexploitation, and data linking these population increases with disease dynamics are limited. We present data suggesting that free-ranging elk (Cervus elaphus) are a maintenance host for Brucella abortus in new areas of the Greater Yellowstone Ecosystem (GYE). Brucellosis seroprevalence in free-ranging elk increased from 0-7% in 1991-1992 to 8 20% in 2006-2007 in four of six herd units around the GYE. These levels of brucellosis are comparable to some herd units where elk are artificially aggregated on supplemental feeding grounds. There are several possible mechanisms for this increase …

Merits And Limits Of Ecosystem Protection For Conserving Wild Salmon In A Northern Coastal British Columbia River, Aaron C. Hill, Thomas S. Bansak, Bonnie K. Ellis, Jack Arthur Stanford

Biological Sciences Faculty Publications

Loss and degradation of freshwater habitat reduces the ability of wild salmon populations to endure other anthropogenic stressors such as climate change, harvest, and interactions with artificially propagated fishes. Preservation of pristine salmon rivers has thus been advocated as a cost-effective way of sustaining wild Pacific salmon populations. We examine the value of freshwater habitat protection in conserving salmon and fostering resilience in the Kitlope watershed in northern coastal British Columbia—a large (3186 km²) and undeveloped temperate rainforest ecosystem with legislated protected status. In comparison with other pristine Pacific Rim salmon rivers we studied, the Kitlope is characterized …

Functional Convergence In Reduced Genomes Of Bacterial Symbionts Spanning 200 My Of Evolution, John P. Mccutcheon, Nancy A. Moran

Biological Sciences Faculty Publications

The main genomic changes in the evolution of host-restricted microbial symbionts are ongoing inactivation and loss of genes combined with rapid sequence evolution and extreme structural stability; these changes reflect high levels of genetic drift due to small population sizes and strict clonality. This genomic erosion includes irreversible loss of genes in many functional categories and can include genes that underlie the nutritional contributions to hosts that are the basis of the symbiotic association. Candidatus Sulcia muelleri is an ancient symbiont of sap-feeding insects and is typically coresident with another bacterial symbiont that varies among host subclades. Previously sequenced Sulcia …

Are Forested Buffers An Effective Conservation Strategy For Riparian Fauna? An Assessment Using Meta-Analysis, Laurie B. Marczak, Takashi Sakamaki, Shannon L. Turvey, Isabelle Deguise, Sylvia L. R. Wood, John S. Richardson

Biological Sciences Faculty Publications

Historically, forested riparian buffers have been created to provide protection for aquatic organisms and aquatic ecosystem functions. Increasingly, new and existing riparian buffers are being used also to meet terrestrial conservation requirements. To test the effectiveness of riparian buffers for conserving terrestrial fauna, we conducted a meta-analysis using published data from 397 comparisons of species abundance in riparian buffers and unharvested (reference) riparian sites. The response of terrestrial species to riparian buffers was not consistent between taxonomic groups; bird and arthropod abundances were significantly greater in buffers relative to unharvested areas, whereas amphibian abundance decreased. Edge-preferring species were more abundant …

Diversity Of Interactions: A Metric For Studies Of Biodiversity, Lee A. Dyer, Thomas R. Walla, Harold F. Greeney, John O. Stireman Iii, Rebecca F. Hazen

Biological Sciences Faculty Publications

Multitrophic interactions play key roles in the origin and maintenance of species diversity, and the study of these interactions has contributed to important theoretical advances in ecology and evolutionary biology. Nevertheless, most biodiversity inventories focus on static species lists, and prominent theories of diversity still ignore trophic interactions. The lack of a simple interaction metric that is analogous to species richness is one reason why diversity of interactions is not examined as a response or predictor variable in diversity studies. Using plant-herbivore-enemy trophic chains as an example, we develop a simple metric of diversity in which richness, diversity indices (e.g., …

Cellular And Molecular Dissection Of Pluripotent Adult Somatic Stem Cells In Planarians, Norito Shibata, Labib Rouhana, Kiyokazu Agata

Biological Sciences Faculty Publications

Freshwater planarians, Plathelminthes, have been an intriguing model animal of regeneration studies for more than 100 years. Their robust regenerative ability is one of asexual reproductive capacity, in which complete animals develop from tiny body fragments within a week. Pluripotent adult somatic stem cells, called neoblasts, assure this regenerative ability. Neoblasts give rise to not only all types of somatic cells, but also germline cells. During the last decade, several experimental techniques for the analysis of planarian neoblasts at the molecular level, such as in situ hybridization, RNAi and fluorescence activated cell sorting, have been established. Moreover, information about genes …

Saving Saba Bank: Policy Implications Of Biodiversity Studies, Paul C. Hoetjes, Kent E. Carpenter

Biological Sciences Faculty Publications

Saba Bank has always been an area of special importance to the neighboring island of Saba in the Netherlands Antilles. Sabans traditionally fished on the Bank as far back as 1907, but increasing foreign fishing pressures on the Bank in the 1970s and 1980s forced many Saban fishermen out. Concerns were compounded by the suspicion that shipping was also damaging the benthic habitat of the bank. Fishery legislation, enacted in 1996, brought an end to unlicensed fishing and established Coast Guard enforcement on the Bank, but also led to protests from neighboring countries that previously fished on the Bank.Research was …

The Impact Of Conservation On The Status Of The World's Vertebrates, Michael Hoffmann, Craig Hilton-Taylor, Ariadne Angulo, Monika Böhm, Thomas M. Brooks, Stuart H. M. Butchart, Kent E. Carpenter, Janice Chanson, Beth A. Polidoro, Jonnell C. Sanciangco

Biological Sciences Faculty Publications

Using data for 25,780 species categorized on the International Union for Conservation of Nature Red List, we present an assessment of the status of the world's vertebrates. One-fifth of species are classified as Threatened, and we show that this figure is increasing: On average, 52 species of mammals, birds, and amphibians move one category closer to extinction each year. However, this overall pattern conceals the impact of conservation successes, and we show that the rate of deterioration would have been at least one-fifth again as much in the absence of these. Nonetheless, current conservation efforts remain insufficient to offset the …

Micro-Environment And Plant Assemblage Structure On Virginia's Barrier Island "Pimple" Dunes, Brett A. Mcmillan, Frank P. Day

Biological Sciences Faculty Publications

“Pimple” dunes are small, rounded coastal dunes that form along major dune ridges of the barrier islands along the Eastern Shore of Virginia. Although most pimple dunes are small structures ranging between 10 and 20 m in diameter, they have distinct plant assemblages that replicate the upland ecotones of their barrier islands. We examined the relationship between microenvironment, edaphic factors, and plant assemblage structure on pimple dunes. Water availability was an obvious major ecological driver, but we also tested other environmental factors that may correlate with plant assemblage structure. We found distinct assemblage types that segregated themselves by habitat type: …

Small-Mammal Seed Predation Limits The Recruitment And Abundance Of Two Perennial Grassland Forbs, Mary Bricker, Dean Pearson, John L. Maron

Biological Sciences Faculty Publications

Although post-dispersal seed predators are common and often reduce seed density, their influence on plant population abundance remains unclear. On the one hand, increasing evidence suggests that many plant populations are seed limited, implying that seed predators could reduce plant abundance. On the other hand, it is generally uncertain whether the magnitude of seed limitation imposed by granivores is strong enough to overcome density-dependent processes that could compensate for seed loss at later stages. We examined the impact of seed predation by small mammals, primarily deer mice (Peromyscus maniculatus), on seedling recruitment and subsequent plant establishment of two …

Building A Mechanistic Understanding Of Predation With Gps-Based Movement Data, Evelyn Merrill, Ha˚Kan Sand, Barbara Zimmermann, Heather Mcphee, Nathan Webb, Mark Hebblewhite, Peter Wabakken, Jacqueline L. Frair

Biological Sciences Faculty Publications

Quantifying kill rates and sources of variation in kill rates remains an important challenge in linking predators to their prey. We address current approaches to using global positioning system (GPS)-based movement data for quantifying key predation components of large carnivores. We review approaches to identify kill sites from GPS movement data as a means to estimate kill rates and address advantages of using GPS-based data over past approaches. Despite considerable progress, modelling the probability that a cluster of GPS points is a kill site is no substitute for field visits, but can guide our field efforts. Once kill sites are …

Chloroquine Susceptibility And Reversibility In A Plasmodium Falciparum Genetic Cross, Jigar J. Patel, Drew Thacker, John C. Tan, Perri Pleeter, Lisa Checkley, Joseph M. Gonzales, Bingbing Deng, Paul D. Roepe, Roland A. Cooper, Michael T. Ferdig

Biological Sciences Faculty Publications

Mutations in the Plasmodium falciparum chloroquine (CQ) resistance transporter (PfCRT) are major determinants of verapamil (VP)-reversible CQ resistance (CQR). In the presence of mutant PfCRT, additional genes contribute to the wide range of CQ susceptibilities observed. It is not known if these genes influence mechanisms of chemosensitization by CQR reversal agents. Using quantitative trait locus (QTL) mapping of progeny clones from the HB3 x Dd2 cross, we show that the P. falciparum multidrug resistance gene 1 (pfmdr1) interacts with the South-East Asia-derived mutant pfcrt haplotype to modulate CQR levels. A novel chromosome 7 locus is predicted to contribute …

Quantitative Pcr Assay For Mycobacterium Pseudoshottsii And Mycobacterium Shottsii And Application To Environmental Samples And Fishes From The Chesapeake Bay, D. T. Gauthier, K. S. Reece, J. Xiao, M. W. Rhodes, H. I. Kator, R. J. Latour, C. F. Bonzek, J. M. Hoenig, W. K. Vogelbein

Biological Sciences Faculty Publications

Striped bass (Morone saxatilis) in the Chesapeake Bay are currently experiencing a very high prevalence of mycobacteriosis associated with newly described Mycobacterium species, Mycobacterium pseudoshottsii and M. shottsii. The ecology of these mycobacteria outside the striped bass host is currently unknown. In this work, we developed quantitative real-time PCR assays for M. pseudoshottsii and M. shottsii and applied these assays to DNA extracts from Chesapeake Bay water and sediment samples, as well as to tissues from two dominant prey of striped bass, Atlantic menhaden (Brevoortia tyrannus) and bay anchovy (Anchoa mitchilli). Mycobacterium …

Spawning-Related Movements Of Barred Sand Bass Paralabrax Nebulifer, In Southern California: Interpretations From Two Decades Of Historical Tag And Recapture Data, E. T. Jarvis, Christi Linardich, C. F. Valle

Biological Sciences Faculty Publications

During the 1960s and 1990s, the California Department of Fish and Game tagged 8,634 barred sand bass in southern California, and 972 fish (11%) were recaptured. Tag returns suggest barred sand bass are transient aggregate spawners that form spawning aggregations consisting of both resident and migrant individuals. Spawning residency at a historic spawning location was estimated by the frequency of returns over time; most same-year returns (82%, n  =  141) were recaptured within a 7 to 35-day period. The maximum recapture distance was 92 km. The average (± SD) non-spawning season recapture distance from peak spawning season tagging locations was …

Ancient Dna Analyses Exclude Humans As The Driving Force Behind Late Pleistocene Musk Ox (Ovibos Moschatus) Population Dynamics, Paula F. Campos, Eske Willerslev, Andrei Sher, Ludovic Orlando, Erik Axelsson, Alexei Tikhonov, Kim Aaris-Sorensen, Alex D. Greenwood, Ralf-Dietrich Kahlke, Pavel Kosintsev

Biological Sciences Faculty Publications

The causes of the late Pleistocene megafaunal extinctions are poorly understood. Different lines of evidence point to climate change, the arrival of humans, or a combination of these events as the trigger. Although many species went extinct, others, such as caribou and bison, survived to the present. The musk ox has an intermediate story: relatively abundant during the Pleistocene, it is now restricted to Greenland and the Arctic Archipelago. In this study, we use ancient DNA sequences, temporally unbiased summary statistics, and Bayesian analytical techniques to infer musk ox population dynamics throughout the late Pleistocene and Holocene. Our results reveal …

Biodiversity Assessment Of The Fishes Of Saba Bank Atoll, Netherlands Antilles, Jeffrey T. Williams, Kent E. Carpenter, James L. Van Tassell, Paul Hoetjes, Wes Toller, Peter Etnoyer, Michael Smith

Biological Sciences Faculty Publications

Biodiversity surveys were conducted on Saba Bank, Netherlands Antilles, to assess ichthyofaunal richness and to compare with published surveys of other Caribbean localities. The primary objective was to estimate the total species richness of the Saba Bank ichthyofauna. A variety of sampling techniques was utilized to survey the fish species of both the visually accessible megafauna and the camouflaged and small-sized species comprising the cryptic ichthyofauna. Based on results presented herein, the number of species known on Saba Bank is increased from 42 previously known species to 270 species. Expected species-accumulation curves demonstrate that the current estimate of species richness …

Morphological Differences Among Eyeless Amphipods In The Genus Stygobromus Dwelling In Different Subterranean Habitats, David C. Culver, John R. Holsinger, Mary C. Christman, Tanja Pipan

Biological Sciences Faculty Publications

The amphipod genus Stygobromus occurs in a variety of subterranean habitats in North America, including caves, phreatic (groundwater) lakes, and superficial subterranean habitats (seeps and epikarst). The habitats share the absence of light but differ in other features, such as pore size of the habitat, available food, and degree of seasonality. Measurements of body size, antennal size, and antennal segment number of type specimens were compared for 56 species occurring in the eastern United States. Except for differences in body size, differences among species in the four different habitats were not significant. Body size was related to relative pore size …

Conservation Status And Habitat Use Of The West Virginia Spring Salamander (Gyrinophilus Subterraneus) And Spring Salamander (G. Porphyriticus) In General Davis Cave, Greenbrier Co., West Virginia, Matthew L. Niemiller, Michael S. Osbourn, Dante B. Fenolio, Thomas K. Pauley, Brian T. Miller, John R. Holsinger

Biological Sciences Faculty Publications

The West Virginia Spring Salamander (Gyrinophilus subterraneus) is one of four obligate cave-dwelling species of plethodontid salamanders found east of the Mississippi River in the United States. This species is endemic to a single cave system; General Davis Cave, in Greenbrier Co., West Virginia, where it is syntopic with the closely-related Spring Salamander (G. porphyriticus). Accordingly, the West Virginia Spring Salamander is a species of critical conservation concern. Because of it's conservation status and lack of data regarding the ecology and life history, particularly about population trends, we present data on relative abundance of and habitat …

Don't Diss Integration: A Comment On Ricklefs's Disintegrating Communities, Rob W. Booker, Ragan M. Callaway, Lohengrin A. Cavieres, Zaal Kikvidze, Christopher J. Lortie, Richard Michalet, Francisco I. Pugnaire, Alfonso Valiente-Banuet, Thomas G. Whitham

Biological Sciences Faculty Publications

No abstract provided.

Evaluating Forensic Dna Evidence, Dan E. Krane

Biological Sciences Faculty Publications

No abstract provided.