Human impacts on pig frog (Rana grylio) populations in south Florida wetlands: Harvest, water management and mercury contamination

This study investigated how harvest and water management affected the ecology of the Pig Frog, Rana grylio. It also examined how mercury levels in leg muscle tissue vary spatially across the Everglades. Rana grylio is an intermediate link in the Everglades food web. Although common, this inconspicuous species can be affected by three forms of anthropogenic disturbance: harvest, water management and mercury contamination. This frog is harvested both commercially and recreationally for its legs, is aquatic and thus may be susceptible to water management practices, and can transfer mercury throughout the Everglades food web. ^ This two-year study took place in three major regions: Everglades National Park (ENP), Water Conservation Areas 3A (A), and Water Conservation Area 3B (B). The study categorized the three sites by their relative harvest level and hydroperiod. During the spring of 2001, areas of the Everglades dried completely. On a regional and local scale Pig Frog abundance was highest in Site A, the longest hydroperiod, heavily harvested site, followed by ENP and B. More frogs were found along survey transects and in capture-recapture plots before the dry-down than after the dry-down in Sites ENP and B. Individual growth patterns were similar across all sites, suggesting differences in body size may be due to selective harvest. Frogs from Site A, the flooded and harvested site, had no differences in survival rates between adults and juveniles. Site B populations shifted from a juvenile to adult dominated population after the dry-down. Dry-downs appeared to affect survival rates more than harvest. ^ Total mercury in frog leg tissue was highest in protected areas of Everglades National Park with a maximum concentration of 2.3 mg/kg wet mass where harvesting is prohibited. Similar spatial patterns in mercury levels were found among pig frogs and other wildlife throughout parts of the Everglades. Pig Frogs may be transferring substantial levels of mercury to other wildlife species in ENP. ^ In summary, although it was found that abundance and survival were reduced by dry-down, lack of adult size classes in Site A, suggest harvest also plays a role in regulating population structure. ^

Landscape genetics of Phaedranassa herb. (Amaryllidaceae) in Ecuador

Speciation can be understood as a continuum occurring at different levels, from population to species. The recent molecular revolution in population genetics has opened a pathway towards understanding species evolution. At the same time, speciation patterns can be better explained by incorporating a geographic context, through the use of geographic information systems (GIS). Phaedranassa (Amaryllidaceae) is a genus restricted to one of the world’s most biodiverse hotspots, the Northern Andes. I studied seven Phaedranassa species from Ecuador. Six of these species are endemic to the country. The topographic complexity of the Andes, which creates local microhabitats ranging from moist slopes to dry valleys, might explain the patterns of Phaedranassa species differentiation. With a Bayesian individual assignment approach, I assessed the genetic structure of the genus throughout Ecuador using twelve microsatellite loci. I also used bioclimatic variables and species geographic coordinates under a Maximum Entropy algorithm to generate distribution models of the species. My results show that Phaedranassa species are genetically well-differentiated. Furthermore, with the exception of two species, all Phaedranassa showed non-overlapping distributions. Phaedranassa viridiflora and P. glauciflora were the only species in which the model predicted a broad species distribution, but genetic evidence indicates that these findings are likely an artifact of species delimitation issues. Both genetic differentiation and nonoverlapping geographic distribution suggest that allopatric divergence could be the general model of genetic differentiation. Evidence of sympatric speciation was found in two geographically and genetically distinct groups of P. viridiflora. Additionally, I report the first register of natural hybridization for the genus. The findings of this research show that the genetic differentiation of species in an intricate landscape as the Andes does not necessarily show a unique trend. Although allopatric speciation is the most common form of speciation, I found evidence of sympatric speciation and hybridization. These results show that the processes of speciation in the Andes have followed several pathways. The mixture of these processes contributes to the high biodiversity of the region.

The effects of fertilization and simulated grazing on the community structure of a seagrass bed in South Florida

The importance of resource supply and herbivory in driving competitive interactions among species has been an important but contentious issue within ecology. These variables exhibit different effects on species competition when manipulated in isolation but interact when manipulated together. I tested the direct and interactive effects of nutrient addition and simulated grazing (clipping) on the competitive performance of primary producers and community structure of a seagrass bed in South Florida. One square meter experimental plots were established in a mixed seagrass meadow from August 2007 to July 2009. The experiment was a 3 x 3 factorial experiment: 3 fertility treatments: control, medium (2.4 mg N d−1 and 80 µg P day −1) and high (4.8 mg N d−1 and 160 µg P day−1) x 3 clipping intensities (0, 25% and 50 % biomass removal (G)) x 5 replicates for each treatment = 45 plots). Nutrient additions and simulated grazing were done every two months. Fertilization and simulated grazing decreased sexual reproduction in S. filiforme. Fertilization increased competitive dominance within the primary producers while simulated grazing counteracted this effect by removal of the dominant species. Fertilization ameliorated the negative impacts of simulated grazing while simulated grazing prevented competitive exclusion in the fertilized plots. Nutrient addition and simulated grazing both exerted strong control on plant performance and community structure. Neither bottom up nor top down influences was eliminated in treatments where both factors where present. The effects of fertilization on plant performance were marked under all clipping intensities indicating that the system is regulated by nutrient availability both in the presence or absence of grazers. Clipping effects were strong under both fertilized and unfertilized conditions indicating that the seagrass bed can be simultaneously under top-down control by grazers.

What Google Maps can do for Biomedical Data Dissemination: Examples and a Design Study

Background: Biologists often need to assess whether unfamiliar datasets warrant the time investment required for more detailed exploration. Basing such assessments on brief descriptions provided by data publishers is unwieldy for large datasets that contain insights dependent on specific scientific questions. Alternatively, using complex software systems for a preliminary analysis may be deemed as too time consuming in itself, especially for unfamiliar data types and formats. This may lead to wasted analysis time and discarding of potentially useful data. Results: We present an exploration of design opportunities that the Google Maps interface offers to biomedical data visualization. In particular, we focus on synergies between visualization techniques and Google Maps that facilitate the development of biological visualizations which have both low-overhead and sufficient expressivity to support the exploration of data at multiple scales. The methods we explore rely on displaying pre-rendered visualizations of biological data in browsers, with sparse yet powerful interactions, by using the Google Maps API. We structure our discussion around five visualizations: a gene co-regulation visualization, a heatmap viewer, a genome browser, a protein interaction network, and a planar visualization of white matter in the brain. Feedback from collaborative work with domain experts suggests that our Google Maps visualizations offer multiple, scale-dependent perspectives and can be particularly helpful for unfamiliar datasets due to their accessibility. We also find that users, particularly those less experienced with computer use, are attracted by the familiarity of the Google Maps API. Our five implementations introduce design elements that can benefit visualization developers. Conclusions: We describe a low-overhead approach that lets biologists access readily analyzed views of unfamiliar scientific datasets. We rely on pre-computed visualizations prepared by data experts, accompanied by sparse and intuitive interactions, and distributed via the familiar Google Maps framework. Our contributions are an evaluation demonstrating the validity and opportunities of this approach, a set of design guidelines benefiting those wanting to create such visualizations, and five concrete example visualizations.

The Relationship of Heteroptera Species Richness, Abundance, and Morphology to Elevation Gradients and Land-use Regimes on Mt. Kilimanjaro

Insect biodiversity is unevenly distributed on local, regional, and global scales. Elevation is a key factor in the uneven distribution of insect diversity, serving as a proxy for a host of environmental variables. My study examines the relationship of Heteroptera (true bugs) species diversity, abundance, and morphology to elevational gradients and land-use regimes on Mt. Kilimanjaro, Tanzania, East Africa. Heteroptera specimens were collected from 60 research sites covering an elevational range of 3684m (866-4550m above sea level). Thirty of the sites were classified as natural, while the remaining 30 were classified as disturbed (e.g., agricultural use or converted to grasslands). I measured aspects of the body size of adult specimens and recorded their location of origin. I used regression models to analyze the relationships of Heteroptera species richness, abundance, and body measurements to elevation and land-use regime. Richness and abundance declined with greater elevation, controlling for land use. The declines were linear or logarithmic in form, depending on the model. Richness and abundance were greater in natural than disturbed sites, controlling for elevation. According to an interaction, richness decreased more in natural than disturbed sites with rising elevation. Body length increased as a quadratic function of elevation, adjusting for land use. Body width X length decreased as a logarithmic function of elevation, while leg length/body length decreased as a quadratic function. Leg length/body length was greater in disturbed than natural sites. Interactions indicated that body length and body width X length were greater in natural than disturbed sites as elevation rose, although the general trend was downward. Future research should examine the relative importance of land area, temperature, and resource constraints for Heteroptera diversity and morphology on Mt. Kilimanjaro.

Seasonal activity and road mortality of the snakes of the Pa-Hay-Okee wetlands of Everglades National Park

The current study describes the composition and activity of the snake community of the Pa-hay-okee wetlands of Everglades National Park. The study was conducted from January 1987 to January 1989. Sixteen species were observed, with Thamnophis sauritus, Thamnophis sirtalis, Nerodia fasciata pictiventris, and Agkistrodon piscivorus representing 90.2% of the total sample. The seasonal distribution and activity of the snakes were closely related to fluctuations in the water table. Most activity occurred in the winter months as snakes migrated west following the drying water edge of Shark River Slough. Seventy percent of all snakes observed during this study were either injured or dead on the road. Over 50% of annual mortality occurred during migration. The impact that road mortality is having on the local snake community cannot be ignored. Management options are provided to minimize loss. A comparison is made to the snake community of the Long Pine Key Region of Everglades National Park.

Seasonal variability in microbial methanol utilisation in coastal waters of the western English Channel

Methanol is ubiquitous in seawater and the most abundant oxygenated volatile organic compound (OVOC) in the atmosphere where it influences oxidising capacity and ozone formation. Marine methylotrophic bacteria utilise methanol in seawater both as an energy and/or growth substrate. This work represents the first fully resolved seasonal study of marine microbial methanol uptake dynamics. Rates of microbial methanol dissimilation in coastal surface waters of the UK varied between 0.7 – 11.2 nmol l-1 h-1 and reached a maximum in February. Rates of microbial methanol assimilation varied between 0.04 – 2.64 x 10-2 nmol l-1 h-1 and reached a maximum in August. Temporal variability in microbial methanol uptake rates shows that methanol assimilation and dissimilation display opposing seasonal cycles, although overall <1% of methanol was assimilated. Correlative approaches with 16S rRNA pyrosequencing data suggested that bacteria of the SAR11 clade and Rhodobacterales could be significantly influencing rates of methanol dissimilation and assimilation, respectively, at station L4 in the western English Channel

Seasonal variability in microbial methanol utilisation in coastal waters of the western English Channel

Methanol is ubiquitous in seawater and the most abundant oxygenated volatile organic compound (OVOC) in the atmosphere where it influences oxidising capacity and ozone formation. Marine methylotrophic bacteria utilise methanol in seawater both as an energy and/or growth substrate. This work represents the first fully resolved seasonal study of marine microbial methanol uptake dynamics. Rates of microbial methanol dissimilation in coastal surface waters of the UK varied between 0.7 – 11.2 nmol l-1 h-1 and reached a maximum in February. Rates of microbial methanol assimilation varied between 0.04 – 2.64 x 10-2 nmol l-1 h-1 and reached a maximum in August. Temporal variability in microbial methanol uptake rates shows that methanol assimilation and dissimilation display opposing seasonal cycles, although overall <1% of methanol was assimilated. Correlative approaches with 16S rRNA pyrosequencing data suggested that bacteria of the SAR11 clade and Rhodobacterales could be significantly influencing rates of methanol dissimilation and assimilation, respectively, at station L4 in the western English Channel

Survey on the digenean and monogenean helminthes of clupeidae (teleosts) from southern part of Caspian Sea

The helminthes parasites fauna of 313 specimens of Caspian herrings (Clupeonella cultriventris, Clupeonella engrauliformis, Clupeonella grimmi) caught from catching localities situated in southeast of Caspian Sea Were investigated during winter 2008 until autumn 2009. A total of 3 helminthes species were found. They were including Pseudopentagramma symmetrica from intestine (mid gut, hind gut and cecae) Bunocotyle cingulata in intestine, Mazocreas alosae the only monogenean with Marine origin in the gills of infected specimens. In addition to two zoonotic species including Contracecum sp. and Anisakis sp. in digestive system, muscle and ovary and an Acanthocephal, Corynosoma strumosum in intestine which were previously reported. We can conclude that the main characteristic of the helminthes parasites community of Clupeidae species studied is the dominance of the endoparasites species due mainly to the digenean Pseudopentagramma symmetrica and Bunocotyle cingulata and the relative scarcity of ectohelminthes fauna. In this paper the latest data of helminthes fauna and community ecology of digenean of Clupeidae species are presented and the community structure of Pseudopentagramma symmetrica is discussed.

Characterization of the poxAB operon encoding a class D carbapenemase in Pseudomonas aeruginosa

Pseudomonas aeruginosa is a dreaded opportunistic pathogen that causes severe and often intractable infections in immunocompromised and critically ill patients. This bacterium is also the primary cause of fatal lung infections in patients with cystic fibrosis and a leading nosocomial pathogen responsible for nearly 10% of all hospital-acquired infections. P. aeruginosa is intrinsically recalcitrant to most classes of antibiotics and has the ability to acquire additional resistance during treatment. In particular, resistance to the widely used β-lactam antibiotics is frequently mediated by the expression of AmpC, a chromosomally encoded β-lactamase that is ubiquitously found in P. aeruginosa strains. This dissertation delved into the role of a recently reported chromosomal β-lactamase in P. aeruginosa called PoxB. To date, no detailed studies have addressed the regulation of poxB expression and its contribution to β-lactam resistance in P. aeruginosa. In an effort to better understand the role of this β-lactamase, poxB was deleted from the chromosome and expressed in trans from an IPTG-inducible promoter. The loss of poxB did not affect susceptibility. However, expression in trans in the absence of ampC rendered strains more resistant to the carbapenem β-lactams. The carbapenem-hydrolyzing phenotype was enhanced, reaching intermediate and resistant clinical breakpoints, in the absence of the carbapenem-specific outer membrane porin OprD. As observed for most class D β-lactamases, PoxB was only weakly inhibited by the currently available β-lactamase inhibitors. Moreover, poxB was shown to form an operon with the upstream located poxA, whose expression in trans decreased pox promoter (Ppox) activity suggesting autoregulation. The transcriptional regulator AmpR negatively controlled Ppox activity, however no direct interaction could be demonstrated. A mariner transposon library identified genes involved in the transport of polyamines as potential regulators of pox expression. Unexpectedly, polyamines themselves were able induce resistance to carbapenems. In summary, P. aeruginosa carries a chromosomal-encoded β-lactamase PoxB that can provide resistance against the clinically relevant carbapenems despite its narrow spectrum of hydrolysis and whose activity in vivo may be regulated by polyamines.^