Field studies and the IACUC: protocol review, oversight, and occupational health and safety considerations

Field studies involving animals, like other institutional research endeavors, are regulated and evaluated by an IACUC to insure that the protocols employed in those studies are consistent with the most humane care and use of animals. Unlike many other on-site research projects, however, field studies present unique logistical and other challenges to IACUC evaluation. The authors explore many of these challenges, including the special protocol considerations and idiosyncratic occupational health and safety concerns characteristic of field-study reviews.     

Identification and isolation of a Castellaniella species important during biostimulation of an acidic nitrate- and uranium-contaminated aquifer

Immobilization of uranium in groundwater can be achieved through microbial reduction of U(VI) to U(IV) upon electron donor addition. Microbial community structure was analyzed in ethanol-biostimulated and control sediments from a high-nitrate (>130 mM), low-pH, uranium-contaminated site in Oak Ridge, TN. Analysis of small subunit (SSU) rRNA gene clone libraries and polar lipid fatty acids from sediments revealed that biostimulation resulted in a general decrease in bacterial diversity. Specifically, biostimulation resulted in an increase in the proportion of Betaproteobacteria (10% of total clones in the control sediment versus 50 and 79% in biostimulated sediments) and a decrease in the proportion of Gammaproteobacteria and Acidobacteria. Clone libraries derived from dissimilatory nitrite reductase genes (nirK and nirS) were also dominated by clones related to Betaproteobacteria (98% and 85% of total nirK and nirS clones, respectively). Within the nirK libraries, one clone sequence made up 59 and 76% of sequences from biostimulated sediments but only made up 10% of the control nirK library. Phylogenetic analysis of SSU rRNA and nirK gene sequences from denitrifying pure cultures isolated from the site indicate that all belong to a Castellaniella species; nearly identical sequences also constituted the majority of biostimulated SSU rRNA and nirK clone libraries. Thus, by combining culture-independent with culture-dependent techniques, we were able to link SSU rRNA clone library information with nirK sequence data and conclude that a potentially novel Castellaniella species is important for in situ nitrate removal at this site.     

Prevalence of enterotoxigenic Clostridium perfringens Isolates in Pittsburgh (Pennsylvania) area soils and home kitchens

In the United States and Europe, food poisoning due to Clostridium perfringens type A is predominantly caused by C. perfringens isolates carrying a chromosomal enterotoxin gene (cpe). Neither the reservoir for these isolates nor the point in the food chain where these bacteria contaminate foods is currently understood. Therefore, the current study investigated whether type A isolates carrying a chromosomal cpe gene are present in two potential reservoirs, i.e., soil and home kitchen surfaces. No C. perfringens isolates were recovered from home kitchen surfaces, but most surveyed soil samples contained C. perfringens. The recovered soil isolates were predominantly type A, but some type C, D, and E soil isolates were also identified. All cpe-positive isolates recovered from soil were genotyped as type A, with their cpe genes on cpe plasmids rather than the chromosome. However, two cpe-positive soil isolates did not carry a classical cpe plasmid. Both of those atypical cpe-positive soil isolates were sporulation capable yet failed to produce C. perfringens enterotoxin, possibly because of differences in their upstream promoter regions. Collectively these results suggest that neither soil nor home kitchen surfaces represent major reservoirs for type A isolates with chromosomal cpe that cause food poisoning, although soil does appear to be a reservoir for cpe-positive isolates causing non-food-borne gastrointestinal diseases.     

Genome sequence of the cellulolytic gliding bacterium Cytophaga hutchinsonii

The complete DNA sequence of the aerobic cellulolytic soil bacterium Cytophaga hutchinsonii, which belongs to the phylum Bacteroidetes, is presented. The genome consists of a single, circular, 4.43-Mb chromosome containing 3,790 open reading frames, 1,986 of which have been assigned a tentative function. Two of the most striking characteristics of C. hutchinsonii are its rapid gliding motility over surfaces and its contact-dependent digestion of crystalline cellulose. The mechanism of C. hutchinsonii motility is not known, but its genome contains homologs for each of the gld genes that are required for gliding of the distantly related bacteroidete Flavobacterium johnsoniae. Cytophaga-Flavobacterium gliding appears to be novel and does not involve well-studied motility organelles such as flagella or type IV pili. Many genes thought to encode proteins involved in cellulose utilization were identified. These include candidate endo-beta-1,4-glucanases and beta-glucosidases. Surprisingly, obvious homologs of known cellobiohydrolases were not detected. Since such enzymes are needed for efficient cellulose digestion by well-studied cellulolytic bacteria, C. hutchinsonii either has novel cellobiohydrolases or has an unusual method of cellulose utilization. Genes encoding proteins with cohesin domains, which are characteristic of cellulosomes, were absent, but many proteins predicted to be involved in polysaccharide utilization had putative D5 domains, which are thought to be involved in anchoring proteins to the cell surface.     

Cue combination and the effect of horizontal disparity and perspective on stereoacuity

Relative depth judgments of vertical lines based on horizontal disparity deteriorate enormously when the lines form part of closed configurations (Westheimer, 1979). In studies showing this effect, perspective was not manipulated and thus produced inconsistency between horizontal disparity and perspective. We show that stereoacuity improves dramatically when perspective and horizontal disparity are made consistent. Observers appear to use unhelpful perspective cues in judging the relative depth of the vertical sides of rectangles in a way not incompatible with a form of cue weighting. However, 95% confidence intervals for the weights derived for cues usually exceed the a-priori [0-1] range.     

Constitutive polymorphic cyanogenesis in the Australian rainforest tree, Ryparosa kurrangii (Achariaceae)

Cyanogenesis, the liberation of volatile hydrogen cyanide from endogenous cyanide-containing compounds, is a proven plant defence mechanism and the particular cyanogens involved have taxonomic utility. The cyclopentenoncyanhydrin glycoside gynocardin was the only cyanogen isolated from foliar tissue of the rare Australian rainforest tree, Ryparosa kurrangii (Achariaceae). Mechanical damage simulating foliar herbivory did not induce a significant increase in the expression of cyanogenesis over a 24h period, indicating cyanogenic herbivore defence in R. kurrangii is constitutive. The cyanogenic potential of mature leaves was quantitatively polymorphic between trees in a natural population, ranging from 0.54 to 4.77 mg CN g(-1) dry wt leaf tissue.     

Investigating early hominin dispersal patterns: developing a framework for climate data integration

An investigation using the Stepping Out model of early hominin dispersal out of Africa is presented here. The late arrival of early hominins into Europe, as deduced from the fossil record, is shown to be consistent with poor ability of these hominins to survive in the Eurasian landscape. The present study also extends the understanding of modelling results from the original study by Mithen and Reed (2002. Stepping out: a computer simulation of hominid dispersal from Africa. J. Hum. Evol. 43, 433-462). The representation of climate and vegetation patterns has been improved through the use of climate model output. This study demonstrates that interpretative confidence may be strengthened, and new insights gained when climate models and hominin dispersal models are integrated.     

Paleontological Patterns, Macroecological Dynamics and the Evolutionary Process

Here we consider evolutionary patterns writ large in the fossil record. We argue that Darwin recognized but downgraded or de-emphasized several of these important patterns, and we consider what a renewed emphasis on these patterns can tell us about the evolutionary process. In particular, one of the key patterns we focus on is the role geographic isolation plays in fomenting evolutionary divergence; another one of the key patterns is stasis of species; the final pattern is turnovers, which exist at several hierarchical scales, including regional ecosystem replacement and pulses of speciation and extinction. We consider how each one of these patterns are related to the dynamic of changing ecological and environmental conditions over time and also investigate their significance in light of other concepts including punctuated equilibria and hierarchy theory. Ultimately, we tie each of these patterns into a framework involving macroecological dynamics and the important role environmental change plays in shaping evolution from the micro- to macroscale.     

On the Nature and Significance of Variability in Lions (Panthera leo)

Although the lion is one of nature’s best-known species, much remains to be learned about its variability. Recently documented variation in genetics, morphology, ecology and behavior help to explain its adaptability and illustrate the inter-dependencies of biological responses at different organizational scales.     

Use of the 16S-23S rDNA internal transcribed spacer of Roseovarius crassostreae for epizootiological studies of juvenile oyster disease (JOD)

Juvenile oyster disease (JOD) in Crassostrea virginica is caused by the marine bacterium Roseovarius crassostreae. Although the 16S rRNA genes of the bacterial isolates exhibit little variation, 2 genetic signatures (GSI and GSII) may be discerned by Ava I digestion of the 16S-23S internal transcribed spacer (ITS). In this study we analyzed isolates from JOD epizootics throughout the northeastern USA (including affected adults for the first time) to better understand how oyster populations encounter and become affected by the pathogen. Isolates from a given epizootic usually had the same ITS signature; however, the involvement of both genetic signatures was occasionally detected, even within the same oyster. Sequencing was used to localize the variable Ava I site to a 100 bp region of low sequence identity, and detection of additional base changes resulted in the identification of 11 distinct genotypes. One genotype was found only in Martha's Vineyard, Massachusetts, USA and persisted in JOD survivors. Two genotypes were associated with Maine epizootics, and both were believed to be unique to that region until 2004, when one was detected in Martha's Vineyard among oysters that had survived colonization by the local genotype. Apparent competition between those 2 genotypes was also detected among a population of juveniles. Five genotypes were found only in New York, and the other 3 were isolated from both New York and from around Cape Cod, Massachusetts. Relationships between the geographic occurrence and phylogenetic relatedness of genotypes were compared with regional current patterns to identify possible mechanisms controlling their distribution.