Population Structure of Clinical and Environmental Vibrio parahaemolyticus from the Pacific Northwest Coast of the United States

Vibrio parahaemolyticus is a common marine bacterium and a leading cause of seafood-borne bacterial gastroenteritis worldwide. Although this bacterium has been the subject of much research, the population structure of cold-water populations remains largely undescribed. We present a broad phylogenetic analysis of clinical and environmental V. parahaemolyticus originating largely from the Pacific Northwest coast of the United States. Repetitive extragenic palindromic PCR (REP-PCR) separated 167 isolates into 39 groups and subsequent multilocus sequence typing (MLST) separated a subset of 77 isolates into 24 sequence types. The Pacific Northwest population exhibited a semi-clonal structure attributed to an environmental clade (ST3, N = 17 isolates) clonally related to the pandemic O3:K6 complex and a clinical clade (ST36, N = 20 isolates) genetically related to a regionally endemic O4:K12 complex. Further, the identification of at least five additional clinical sequence types (i.e., ST43, 50, 65, 135 and 417) demonstrates that V. parahaemolyticus gastroenteritis in the Pacific Northwest is polyphyletic in nature. Recombination was evident as a significant source of genetic diversity and in particular, the recA and dtdS alleles showed strong support for frequent recombination. Although pandemic-related illnesses were not documented during the study, the environmental occurrence of the pandemic clone may present a significant threat to human health and warrants continued monitoring. It is evident that V. parahaemolyticus population structure in the Pacific Northwest is semi-clonal and it would appear that multiple sequence types are contributing to the burden of disease in this region.     

Pathway to domestic natural rubber production: a cradle-to-grave life cycle assessment of the first guayule automobile tire manufactured in the United States

The International Journal of Life Cycle Assessment - Guayule (Parthenium argentatum) is a perennial shrub that can be cultivated in the Southwestern US. It produces natural rubber that could be a...     

Impact of human activities on the reproduction of Hooded Vultures Necrosyrtes monachus in Burkina Faso

During the last decades, the critically endangered Hooded Vulture Necrosyrtes monachus has strongly declined across its African range. Although direct persecution has been suggested as a major cause of this decline, little is known about the impact of humans on reproductive output in West Africa. We studied the impact of human activities on the reproductive output of Hooded Vultures in the Garango area of Burkina Faso. Twenty and 56 nesting attempts were monitored, respectively, during the breeding season in 2013/14 and 2014/15, to determine reproductive success and identify causes of nest failure. Annual breeding success varied between 0.68 and 0.71 chicks fledged per breeding pair per year and productivity was assessed at 0.57 chicks fledged per territorial pair in 2014/15. The main threats imposed by humans were poaching of eggs, chicks and collection of nest materials, leading to 20% (13 out of 64 breeding attempts) of nest failures over the two years. An additional important reason for nest failure was the pruning and (partial) cutting of nest trees. Despite this high level of human interference, we found that Hooded Vulture nest success increased with proximity to human settlements, probably because breeding vultures benefit from protection by people against persecution and disturbance.     

High-frequency generation of conditional mutations affecting Drosophila melanogaster development and life span.

Genome sequencing reveals that a large percentage of Drosophila genes have homologs in humans, including many human disease genes. The goal of this research was to develop methods to efficiently test Drosophila genes for functions in vivo. An important challenge is the fact that many genes function at more than one point during development and during the life cycle. Conditional expression systems such as promoters regulated by tetracycline (or its derivative doxycycline) are often ideal for testing gene functions. However, generation of transgenic animals for each gene of interest is impractical. Placing the doxycycline-inducible ("tet-on") promoter directed out of the end of the P transposable element produced a mobile, doxycycline-inducible promoter element, named PdL. PdL was mobilized to 228 locations in the genome and was found to generate conditional (doxycycline-dependent), dominant mutations at high frequency. The temporal control of gene overexpression allowed generation of mutant phenotypes specific to different stages of the life cycle, including metamorphosis and aging. Mutations characterized included inserts in the alpha-mannosidase II (dGMII), ash1, and pumilio genes. Novel phenotypes were identified for each gene, including specific developmental defects and increased or decreased life span. The PdL system should facilitate testing of a large fraction of Drosophila genes for overexpression and misexpression phenotypes at specific developmental and life cycle stages.     

Host density influences parasitism of the armyworm Pseudaletia unipuncta in agricultural landscapes

Several studies have shown positive responses of parasitism to either host density or landscape complexity. However, no experiments have manipulated host density in landscapes of differing complexity. Here we report the results of a field experiment conducted to determine how host density and agricultural landscape structure jointly affect parasitism and parasitoid diversity of Pseudaletia unipuncta (Haworth) (Lepidoptera: Noctuidae). Parasitism was assessed by experimentally adding P. unipuncta sentinel larvae at low (1 larvae/plant) and high (3 larvae/plant) densities to detect parasitism in commercial cornfields located in a complex and a simple agricultural landscape. The braconid wasps Glyptapanteles militaris (Walsh) and Meteorus spp. accounted for 98.4% of the observed parasitism. Landscape structure did not influence parasitism (80.2% on average) and contrary to expectations, showed a trend towards increased parasitoid richness and diversity in the simple landscape. Increasing host density revealed a trend of increasing parasitoid richness and diversity, and differentially affected parasitism at the parasitoid specific level. G. militaris parasitized a significantly greater proportion of hosts at low host density, while the opposite occurred for Meteorus spp. (primarily M. communis). These offsetting responses of parasitoids resulted in the lack of an overall host density effect on parasitism. The differential response of these parasitoids to host density is discussed in relation to differences in morphological and life history characteristics. Our results suggest that the specific composition of parasitoid assemblages could significantly alter parasitism at different host densities independently of landscape structural complexity.

Zusammenfassung

Verschiedene Untersuchungen haben gezeigt, dass Parasitismus entweder auf die Wirtsdichte oder die Landschaftskomplexität positiv reagiert. Dennoch haben keine Experimente die Wirtsdichte in Landschaften unterschiedlicher Komplexität manipuliert. Hier berichten wir von den Ergebnissen eines Freilandexperiments, das unternommen wurde, um zu bestimmen, wie die Wirtsdichte und die Struktur der Agrarlandschaft gemeinschaftlich die Parasitierung und die Parasitoidendiversität bei Pseudaletia unipuncta (Haworth) (Lepidoptera: Noctuidae) beeinflussen. Die Parasitierung wurde gemessen indem experimentell P. unipuncta Larven in geringen (1 Larve/Pflanze) und hohen (3 Larven/Pflanze) Dichten hinzugefügt wurden, um die Parasitierung in kommerziellen Kornfeldern zu erfassen, die in komplexen und einfachen Agrarlandschaften lagen. 98.4% der Parasitierung entfiel auf die braconiden Wespen Glyptapanteles militaris (Walsh) und Meteorus spp. Die Struktur der Landschaft beeinflusste die Parasitierung nicht (durchschnittlich 80.2%) und zeigte entgegen den Erwartungen einen Trend zu einer erhöhter Parasitoidenartenzahl und -diversität in der einfachen Landschaft. Eine zunehmende Wirtsdichte ließ einen Trend zu einer erhöhten Parasitoidenartenzahl und -diversität erkennen, und sie beeinflusste die Parasitierung auf dem Artenlevel der Parasitoide unterschiedlich. G. militaris parasitierte einen signifikant höheren Anteil der Wirte bei geringen Wirtsdichten, während für Meteorus spp. (vor allem M. communis) das Gegenteil zutraf. Diese sich ausgleichenden Reaktionen der Parasitoide führten zum Fehlen eines Gesamteffekts der Wirtsdichte auf die Parasitierung. Die unterschiedlichen Reaktionen dieser Parasitoide auf die Wirtsdichte werden in Zusammenhang mit Unterschieden in der Morphologie und Lebensweise diskutiert. Unsere Ergebnisse weisen darauf hin, dass die spezifische Zusammensetzung von Ansammlungen von Parasitoiden die Parasitierung bei unterschiedlichen Wirtsdichten unabhängig von der Komplexität der Landschaftsstruktur signifikant verändern könnte.     

A Regional Retrospective Assessment of the Potential Stressors Causing the Decline of the Cherry Point Pacific Herring Run

The Pacific herring stock that spawns at Cherry Point, northwest of Bellingham, WA, has undergone a dramatic decline in the last 20 years. The population decline corresponds with a collapse of the age structure. The Cherry Point area contains three deep water shipping piers, two refineries, an aluminum smelter, and urban development. The Cherry Point Aquatic Reserve was formed initially to protect the spawning habitat of the Cherry Point Pacific herring run. We conducted a retrospective assessment using the relative risk model (RRM) to investigate the causes of the current decline of the Cherry Point run. The RRM combines aspects of the weight-of-evidence (WoE) approach and other methods of establishing causality into a framework that deals with multiple stressors, uncertainty, and spatial scale.

An analysis of the Cherry Point Pacific herring age structure and population dynamics indicates that the loss of reproductive potential of the older age class fish was the population characteristic that led to the decline of the run. Exploitation, habitat alteration and climate change are the risk factors that contribute to the decline of the Cherry Point Pacific herring. The retrospective assessment identified the cyclic nature of climate change, as expressed by the warmer sea surface temperatures associated with a warm Pacific Decadal Oscillation (PDO), as the primary factor altering the dynamics of the Pacific herring. Other factors are ranked accordingly along with the associated uncertainty. Criteria for selecting alternative endpoints for managing the Cherry Point Aquatic Reserve are also provided.

The strengths of the retrospective RRM include its ability to combine a WoE and causality criteria with a multitude of stressors at a regional scale. The difficulties include how to deal with differences in the magnitude of effects, and expressing the uncertainty as distributions.     

Distribution of mutations in human thymidylate synthase yielding resistance to 5-fluorodeoxyuridine

Thymidylate synthase (TS) catalyzes methylation of dUMP to dTMP and is the target of cancer chemotherapeutic agents (e.g. 5-fluorouracil). Here, we used error-prone PCR to mutagenize the full-length human TS cDNA and then selected mutants resistant to 5-fluorodeoxyuridine in a bacterial complementation system. We found that resistant mutants contained 1-5 amino acid substitutions and that these substitutions were located along the entire length of the polypeptide. Mutations were frequent near the active site Cys(195) and in the catalytically important Arg(50) loop; however, many mutations were also distributed throughout the remainder of the cDNA. Mutants containing a single amino acid replacement identified the following 14 residues as unreported sites of resistance: Glu(23), Thr(51), Thr(53), Val(84), Lys(93), Asp(110), Asp(116), Pro(194), Ser(206), Met(219), His(250), Asp(254), Tyr(258), and Lys(284). Many of these residues are distant from the active site and/or have no documented function in catalysis or resistance. We conclude that mutations distributed throughout the linear sequence and three-dimensional structure of human TS can confer resistance to 5-fluorodeoxyuridine. Our findings imply that long range interactions within proteins affect catalysis at the active site and that mutations at a distance can yield variant proteins with desired properties.     

Production, recovery and immunogenicity of the protective antigen from a recombinant strain of Bacillus anthracis

The protective antigen (PA) is one of the three components of the anthrax toxin. It is a secreted nontoxic protein with a molecular weight of 83 kDa and is the major component of the currently licensed human vaccine for anthrax. Due to limitations found in the existing vaccine formulation, it has been proposed that genetically modified PA may be more effective as a vaccine. The expression and the stability of two recombinant PA (rPA) variants, PA-SNKE-ΔFF-E308D and PA-N657A, were studied. These proteins were expressed in the nonsporogenic avirulent strain BH445. Initial results indicated that PA-SNKE-ΔFF-E308D, which lacks two proteolysis-sensitive sites, is more stable than PA-N657A. Process development was conducted to establish an efficient production and purification process for PA-SNKE-ΔFF-E308D. pH, media composition, growth strategy and protease inhibitors composition were analyzed. The production process chosen was based on batch growth of B. anthracis using tryptone and yeast extract as the only source of carbon, pH control at 7.5, and antifoam 289. Optimal harvest time was 14–18 h after inoculation, and EDTA (5 mM) was added upon harvest for proteolysis control. Recovery of the rPA was performed by expanded-bed adsorption (EBA) on a hydrophobic interaction chromatography (HIC) resin, eliminating the need for centrifugation, microfiltration and diafiltration. The EBA step was followed by ion exchange and gel filtration. rPA yields before and after purification were 130 and 90 mg/l, respectively. The purified rPA, without further treatment, treated with small amounts of formalin or adsorbed on alum, induced, high levels of IgG anti-PA with neutralization activities. Journal of Industrial Microbiology & Biotechnology (2002) 28, 232–238 DOI: 10.1038/sj/jim/7000239 Received 28 August 2001/ Accepted in revised form 20 December 2001     

Probing the nature of H2 activation in catalytic asymmetric hydrogenation

Despite many years of intensive study, the natures of turnover-limiting and enantio-determining steps in catalytic asymmetric hydrogenation of prochiral enamides are poorly understood. An intriguing set of studies involving isotopic labeling distributions in catalytic enamide hydrogenation reactions were reported by Brown and Parker (Organometallics, 1 (1982) 950–956) more than a decade ago. In this paper we report the results of studies re-examining the application of isotopic probes to the catalytic hydrogenation enamides. These results provide some insights into the nature of the H₂ activation step in enamide hydrogenation.