Life Sciences Commons^™

The Use Of Metagenomic Approaches To Analyze Changes In Microbial Communities, Girish Neelakanta, Hameeda Sultana

Biological Sciences Faculty Publications

Microbes are the most abundant biological entities found in the biosphere. Identification and measurement of microorganisms (including viruses, bacteria, archaea, fungi, and protists) in the biosphere cannot be readily achieved due to limitations in culturing methods. A non-culture based approach, called “metagenomics”, was developed that enabled researchers to comprehensively analyse microbial communities in different ecosystems. In this study, we highlight recent advances in the field of metagenomics for analyzing microbial communities in different ecosystems ranging from oceans to the human microbiome. Developments in several bioinformatics approaches are also discussed in context of microbial metagenomics that include taxonomic systems, sequence databases, …

Seasonal Dynamics Of Mesodinium Rubrum In Chesapeake Bay, Matthew D. Johnson, Doane K. Stoecker, Harold G. Marshall

Biological Sciences Faculty Publications

The photosynthetic ciliate Mesodinium rubrum is a common member of coastal phytoplankton communities that is well adapted to low-light, turbid ecosystems. It supports the growth of, or competes with, harmful dinoflagellate species for cryptophyte prey, as well as being a trophic link to copepods and larval fish. We have compiled data from various sources (n = 1063), on the abundance and distribution of M. rubrum in Chesapeake Bay and its tributaries. Because M. rubrum relies on obtaining organelles from cryptophyte algae to maintain rapid growth, we also enumerated cryptophyte algae in the portion of these samples that we collected …

Responses Of Amblyomma Americanum And Dermacentor Variabilis To Odorants That Attract Haematophagous Insects, A. L. Carr, R. M. Roe, C. Arellano, D. E. Sonenshine, C. Schal, C. S. Apperson

Biological Sciences Faculty Publications

Carbon dioxide (CO₂), 1-octen-3-ol, acetone, ammonium hydroxide, L-lactic-acid, dimethyl trisulphide and isobutyric acid were tested as attractants for two tick species, Amblyomma americanum and Dermacentor variabilis (Acari: Ixodidae), in doseresponse bioassays using Y-tube olfactometers. Only CO₂, acetone, 1-octen-3-ol and ammonium hydroxide elicited significant preferences from adult A. americanum, and only CO₂ was attractive to adult D. variabilis. Acetone, 1-octen-3-ol and ammonium hydroxide were separately evaluated at three doses against CO₂ (from dry ice) at a field site supporting a natural population of A. americanum nymphs and adults. Carbon dioxide consistently attracted the …

Ontogenetic Shifts In Resource Allocation: Colour Change And Allometric Growth Of Defensive And Reproductive Structures In The Caribbean Spiny Lobster Panulirus Argus, Joshua R. Anderson, Angelo J. Spadaro, J. Antonio Baeza, Donald C. Behringer

Biological Sciences Faculty Publications

Resource allocation theory predicts a disproportionately large allocation of resources to defensive structures during early ontogeny in organisms that are subject to more intense predation at smaller than at larger body sizes. We tested this prediction on the Caribbean spiny lobster Panulirus argus, which exhibits a negative relationship between predation risk and body size with a high natural mortality of smaller individuals. Independent allometric growth analyses demonstrated that numerous defensive structures (e.g. orbital horns, segments supporting the antenna, the tail fan) display negative allometric growth throughout ontogeny. We interpret these findings as lobsters investing disproportionately more resources to defensive …

Phylogeography Of The Christmas Tree Worm Spirobranchus Corniculatus (Annelida, Serpulidae) From The Coral Triangle, Australia, And Fiji, Abril Iñiguez, Craig J. Starger, Elena Kupriyanova, Demian Willette, Tristan Varman, Joshua A. Drew, Abdul Hamid Toha, Benedict Maralit, Kent E. Carpenter, Paul H. Barber

Biological Sciences Faculty Publications

Christmas Tree Woms is a common name given to a group of large and colourful serpulid polychaetes of the genus Spirobranchus that are obligate symbionts of hermatypic corals commonly found in tropical and subtropical regions world-wide. While current taxonomic species delimitations of these worms are based almost exclusively on the morphology of opercular structures, particularly the number and shape of calcareous opercular horns, high levels of intraspecific variation in this morphological feature have made species boundaries within the genus difficult to resolve. Molecular work to differentiate serpulid worms has long been hampered by the availability of informative markers. Recent work …

Cooperative Breeding And Long-Distance Dispersal: A Test Using Vagrant Records, Caroline L. Rusk, Eric L. Walters, Walter D. Koenig

Biological Sciences Faculty Publications

Cooperative breeding is generally associated with increased philopatry and sedentariness, presumably because short-distance dispersal facilitates the maintenance of kin groups. There are, however, few data on long-distance dispersal in cooperative breeders-the variable likely to be important for genetic diversification and speciation. We tested the hypothesis that cooperative breeders are less likely to engage in long-distance dispersal events by comparing records of vagrants outside their normal geographic range for matched pairs (cooperatively vs. non-cooperatively breeding) of North American species of birds. Results failed to support the hypothesis of reduced long-distance dispersal among cooperative breeders. Thus, our results counter the conclusion that …

Conus: First Comprehensive Conservation Red List Assessment Of A Marine Gastropod Mollusc Genus, Howard Peters, Bethan C. O'Leary, Julie P. Hawkins, Kent E. Carpenter, Callum M. Roberts

Biological Sciences Faculty Publications

Marine molluscs represent an estimated 23% of all extant marine taxa, but research into their conservation status has so far failed to reflect this importance, with minimal inclusion on the authoritative Red List of the International Union for the Conservation of Nature (IUCN). We assessed the status of all 632 valid species of the tropical marine gastropod mollusc, Conus (cone snails), using Red List standards and procedures to lay the groundwork for future decadal monitoring, one of the first fully comprehensive global assessments of a marine taxon. Three-quarters (75.6%) of species were not currently considered at risk of extinction owing …

Habitat Availability And Heterogeneity And The Indo-Pacific Warm Pool As Predictors Of Marine Species Richness In The Tropical Indo-Pacific, Jonnell C. Sanciangco, Kent E. Carpenter, Peter J. Etnoyer, Fabio Moretzsohn

Biological Sciences Faculty Publications

Range overlap patterns were observed in a dataset of 10,446 expert-derived marine species distribution maps, including 8,295 coastal fishes, 1,212 invertebrates (crustaceans and molluscs), 820 reef-building corals, 50 seagrasses, and 69 mangroves. Distributions of tropical Indo-Pacific shore fishes revealed a concentration of species richness in the northern apex and central region of the Coral Triangle epicenter of marine biodiversity. This pattern was supported by distributions of invertebrates and habitat-forming primary producers. Habitat availability, heterogeneity, and sea surface temperatures were highly correlated with species richness across spatial grains ranging from 23,000 to 5,100,000 km(2) with and without correction for autocorrelation. The …

Heritable Melanism And Parasitic Infection Both Result In Black-Spotted Mosquitofish, Lisa Horth, David Gauthier, Wolfgang Vogelbein

Biological Sciences Faculty Publications

Male Gamhusia holhrooki (Eastern Mosquitofish) express a heritable pigmentation polymorphism approximate to 99% of males are silver, and only approximate to 1% have a melanic, black-spotted pattern. Sex-linkage, an autosomal modifier, and temperature control the expression of this heritable melanism. In many teleosts, melanin also accumulates around the site of parasitic invasion. We have identified black-spot disease in wild mosquitofish from their native habitat. Here, we demonstrate convergence upon the black-pigmented phenotype through two means: 1) heritable melanism, and 2) melanic spotting on the silver genotype that results from infection with immature encysted trematodes. Females are silver and express greater …

Does Pitcher Plant Morphology Affect Spider Residency?, Marc A. Milne, Deborah A. Waller

Biological Sciences Faculty Publications

Spiders are often found as residents in association with Sarracenia purpurea ( Purple Pitcher Plant). Many spiders choose web locations based on environmental cues such as vegetation structure and composition, prey density, temperature, and humidity. To determine if spiders use cues from the Purple Pitcher Plant to build their webs, we conducted a field study using variants of the plant that separated various morphological features: nectar, pigment, and the presence of prey. There was no difference in spider residency across all treatments and no difference in male/female or mature/immature residency. Linyphiids were the most common residents, possibly due to pitcher …

Chemical Defense Of An Asian Snake Reflects Local Availability Of Toxic Prey And Hatchling Diet, D. A. Hutchinson, A. H. Savitzky, G. M. Burghardt, C. Nguyen, J. Meinwald, F. C. Schroeder, A. Mori

Biological Sciences Faculty Publications

Species that sequester toxins from prey for their own defense against predators may exhibit population-level variation in their chemical arsenal that reflects the availability of chemically defended prey in their habitat. Rhabdophis tigrinus is an Asian snake that possesses defensive glands in the skin of its neck (nuchal glands'), which typically contain toxic bufadienolide steroids that the snakes sequester from consumed toads. In this study, we compared the chemistry of the nuchal gland fluid of R.tigrinus from toad-rich and toad-free islands in Japan and determined the effect of diet on the nuchal gland constituents. Our findings demonstrate that captive-hatched juveniles …

Cumulative Response Of Ecosystem Carbon And Nitrogen Stocks To Chronic Co2 Exposure In A Subtropical Oak Woodland, Bruce A. Hungate, Paul Dijkstra, Zhuoting Wu, Benjamin D. Duval, Frank P. Day, Alisha L.P. Brown

Biological Sciences Faculty Publications

·Rising atmospheric carbon dioxide (CO₂) could alter the carbon (C) and nitrogen (N) content of ecosystems, yet the magnitude of these effects are not well known. We examined C and N budgets of a subtropical woodland after 11 yr of exposure to elevated CO₂.

·We used open-top chambers to manipulate CO₂ during regrowth after fire, and measured C, N and tracer ¹⁵N in ecosystem components throughout the experiment.

·Elevated CO₂ increased plant C and tended to increase plant N but did not significantly increase whole-system C or N. Elevated CO₂ increased soil …

The Role Of P38 Mapk In The Aetiopathogenesis Of Psoriasis And Psoriatic Arthritis, Athanasios Mavropoulos, Eirini I. Rigopoulou, Christos Liaskos, Dimitrios P. Bogdanos, Lazaros I. Sakkas

Biological Sciences Faculty Publications

The pathogenetic mechanisms responsible for the induction of immune-mediated disorders, such as psoriasis, remain not well characterized. Molecular signaling pathways are not well described in psoriasis, as well as psoriatic arthritis, which is seen in up to 40% of patients with psoriasis. Signaling pathway defects have long been hypothesized to participate in the pathology of psoriasis, yet their implication in the altered psoriatic gene expression still remains unclear. Emerging data suggest a potential pathogenic role for mitogen activated protein kinases p38 (p38 MAPK) extracellular signal-regulated kinase 1/2 (ERK1/2), and c-Jun N-terminal kinase (JNK) in the development of psoriasis. The data …

The Effects Of 11 Yr Of Co2 Enrichment On Roots In A Florida Scrub-Oak Ecosystem, Frank Day, Rachel E. Schroeder, Daniel B. Stover, Alisha L. P. Brown, John R. Butnor, John Dilustro, Bruce A. Hungate, Paul Dijkstra, Benjamn D. Duval, Troy J. Seiler

Biological Sciences Faculty Publications

• Uncertainty surrounds belowground plant responses to rising atmospheric CO₂ because roots are difficult to measure, requiring frequent monitoring as a result of fine root dynamics and long-term monitoring as a result of sensitivity to resource availability.
• We report belowground plant responses of a scrub-oak ecosystem in Florida exposed to 11yr of elevated atmospheric CO₂ using open-top chambers. We measured fine root production, turnover and biomass using minirhizotrons, coarse root biomass using ground-penetrating radar and total root biomass using soil cores.
• Total root biomass was greater in elevated than in ambient plots, and the absolute difference was larger than …

Phytoplankton In Virginia Lakes And Reservoirs, Harold G. Marshall

Biological Sciences Faculty Publications

This study involves a phytoplankton summer/autumn survey in 46 Virginia lakes and reservoirs during 2010-2012. A total of 307 taxa were identified which included several filamentous and colonial cyanabacteria in bloom concentrations. With the exception of one natural lake, the other sites sampled represent impoundments created decades ago, with the majority presently classified as meso- or eutrophic. Among the cyanobacteria were 6 known toxin producers (Anabaena circinalis, Anabaena spiroides, Aphanizomenon flos-aquae, Cylindrospermopsis raciborskii, Limnothrix redekei, and Microcystis aeruginosa). The study characterizes phytoplankton populations in these aging freshwater habitats taken from a large number …

Thalassiosira Spp. Community Composition Shifts In Response To Chemical And Physical Forcing In The Northeast Pacific Ocean, P. Dreux Chappell, Leann P. Whitney, Traci L. Haddock, Susanne Menden-Deuer, Eric G. Roy, Mark L. Wells, Bethany D. Jenkins

Biological Sciences Faculty Publications

Diatoms are genetically diverse unicellular photosynthetic eukaryotes that are key primary producers in the ocean. Many of the over 100 extant diatom species in the cosmopolitan genus Thalassiosira are difficult to distinguish in mixed populations using light microscopy. Here, we examine shifts in Thalassiosira spp. composition along a coastal to open ocean transect that encountered a 3-month-old Haida eddy in the northeast Pacific Ocean. To quantify shifts in Thalassiosira species composition, we developed a targeted automated ribosomal intergenic spacer analysis (ARISA) method to identify Thalassiosira spp. in environmental samples. As many specific fragment lengths are indicative of individual Thalassiosira spp., …

Age-Associated Metabolic And Morphologic Changes In Mitochondria Of Individual Mouse And Hamster Oocytes, Fatma Simsek-Duran, Fang Li, Wentia Ford, R. James Swanson, Howard W. Jones Jr., Frank J. Castora

Biological Sciences Faculty Publications

Background: In human oocytes, as in other mammalian ova, there is a significant variation in the pregnancy potential, with approximately 20% of oocyte-sperm meetings resulting in pregnancies. This frequency of successful fertilization decreases as the oocytes age. This low proportion of fruitful couplings appears to be influenced by changes in mitochondrial structure and function. In this study, we have examined mitochondrial biogenesis in both hamster (Mesocricetus auratus) and mouse (Mus musculus) ova as models for understanding the effects of aging on mitochondrial structure and energy production within the mammalian oocyte.

Methodology/Principal Findings: Individual metaphase …

Historical And Contemporary Dna Indicate Fisher Decline And Isolation Occurred Prior To The European Settlement Of California, Jody M. Tucker, Michael K. Schwartz, Richard L. Truex, Kristine L. Pilgrim, Fred W. Allendorf

Biological Sciences Faculty Publications

Establishing if species contractions were the result of natural phenomena or human induced landscape changes is essential for managing natural populations. Fishers (Martes pennanti) in California occur in two geographically and genetically isolated populations in the northwestern mountains and southern Sierra Nevada. Their isolation is hypothesized to have resulted from a decline in abundance and distribution associated with European settlement in the 1800s. However, there is little evidence to establish that fisher occupied the area between the two extant populations at that time. We analyzed 10 microsatelliteloci from 275 contemporary and 21 historical fisher samples (1880-1920) to evaluate the demographic …

Artifacts And Noise In Dna Profiling, Dan E. Krane

Biological Sciences Faculty Publications

No abstract provided.

Dna Technology In Court, Dan E. Krane

Biological Sciences Faculty Publications

No abstract provided.

Statistical Weights Of Single Source Dna Profiles, Dan E. Krane

Biological Sciences Faculty Publications

No abstract provided.

Generating Forensic Dna Profiles, Dan E. Krane

Biological Sciences Faculty Publications

No abstract provided.

What Can Go Wrong With Dna Profiling, Dan E. Krane

Biological Sciences Faculty Publications

No abstract provided.

Observer Effects In Dna Profiling, Dan E. Krane

Biological Sciences Faculty Publications

No abstract provided.

Statistical Weights Of Mixed Dna Profiles, Dan E. Krane

Biological Sciences Faculty Publications

Presentation recording from December 2012 can be found at http://youtu.be/daRBTopFA1A.

Part of the Forensic DNA Profiling Video Series.

Implications Of Database Searches For Dna Profiling Statistics, Dan E. Krane

Biological Sciences Faculty Publications

No abstract provided.

Models Of Experimental Competitive Intensities Predict Home And Away Differences In Invasive Impact And The Effects Of An Endophytic Mutualist, Sa Xiao, Ragan M. Callaway, George Newcombe, Erik T. Aschehoug

Biological Sciences Faculty Publications

Understanding the role of competition in the organization of communities is limited in part by the difficulty of extrapolating the outcomes of small-scale experiments to how such outcomes might affect the distribution and abundance of species. We modeled the community-level outcomes of competition, using experimentally derived competitive effects and responses between an exotic invasive plant, Centaurea stoebe, and species from both its native and nonnative ranges and using changes in these effects and responses elicited by experimentally establishing symbioses between C. stoebe and fungal endophytes. Using relative interaction intensities (RIIs) and holding other life-history factors constant, individual-based and spatially explicit …

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 Knowlton, Tien Ming Lee, Charles A. Munn, Somchai Nimnuan, B. Z. Nizam, Gillaume Péron, V. V. Robin, Amanda D. Rodewald, Paul G. Rodewald, Robert L. Thomson, Pranav Trivedi, Steven L. Van Wilgenburg, Kartik Shanker

Biological Sciences 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 …

Biochemical Reconstitution Of Hemorrhagic-Fever Arenavirus Envelope Glycoprotein-Mediated Membrane Fusion, Celestine J. Thomas, Sundaresh Shankar, Hedi E. Casquilho-Gray, Joanne York, Stephen Sprang, Jack H. Nunberg

Biological Sciences Faculty Publications

The membrane-anchored proteins of enveloped viruses form labile spikes on the virion surface, primed to undergo large-scale conformational changes culminating in virus-cell membrane fusion and viral entry. The prefusion form of these envelope glycoproteins thus represents an important molecular target for antiviral intervention. A critical roadblock to this endeavor has been our inability to produce the prefusion envelope glycoprotein trimer for biochemical and structural analysis. Through our studies of the GPC envelope glycoprotein of the hemorrhagic fever arenaviruses, we have shown that GPC is unique among class I viral fusion proteins in that the mature complex retains a stable signal …

Projected Climate Change Impacts On The Hydrology And Temperature Of Pacific Northwest Rivers, Huan Wu, John S. Kimball, Marketa M. Elsner, Nate Mantua, Robert F. Adler, Jack Arthur Stanford

Biological Sciences Faculty Publications

A dominant river-tracing-based streamflow and temperature (DRTT) model was developed by coupling stream thermal dynamics with a source-sink routing model. The DRTT model was applied using 1/16 degree (similar to 6 km) resolution gridded daily surface meteorology inputs over a similar to 988,000 km(2) Pacific Northwest (PNW) domain to produce regional daily streamflow and temperature simulations from 1996 to 2005. The DRTT results showed favorable performance for simulation of daily stream temperature (mean R-2 = 0.72 and root-mean-square error = 2.35 degrees C) and discharge (mean R-2 = 0.52 and annual relative error 14%) against observations from 12 PNW streams. …