Paul Orwin TSSA Fall 2012

Enhances faculty\u27s teaching by attending a conference devoted to university teaching, a high-impact practice, evidence-based practice or a newly developing teaching practice

Characterization and expression analysis of Staphylococcus aureus pathogenicity island 3 - Implications for the evolution of staphylococcal pathogenicity islands

We describe the complete sequence of the 15.9-kb staphylococcal pathogenicity island 3 encoding staphylococcal enterotoxin serotypes B, K, and Q. The island, which meets the generally accepted definition of pathogenicity islands, contains 24 open reading frames potentially encoding proteins of more than 50 amino acids, including an apparently functional integrase. The element is bordered by two 17-bp direct repeats identical to those found flanking staphylococcal pathogenicity island 1. The island has extensive regions of homology to previously described pathogenicity islands, particularly staphylococcal pathogenicity islands 1 and bov. The expression of 22 of the 24 open reading frames contained on staphylococcal pathogenicity island 3 was detected either in vitro during growth in a laboratory medium or serum or in vivo in a rabbit model of toxic shock syndrome using DNA microarrays. The effect of oxygen tension on staphylococcal pathogenicity island 3 gene expression was also examined. By comparison with the known staphylococcal pathogenicity islands in the context of gene expression described here, we propose a model of pathogenicity island origin and evolution involving specialized transduction events and addition, deletion, or recombination of pathogenicity island "modules.

Complementarity of dung beetle species with different functional behaviours influence dung–soil carbon cycling

Decomposition of large ungulate herbivore dung and its subsequent incorporation into the soil play key roles in carbon and nutrient cycling and are important for grassland productivity. Dung beetles contribute to the initial breakdown and transport of organic matter from the dung into the soil but how they interact with the microbial community to modify decomposition processes remains poorly understood. Using a mesocosm experiment, we investigated the individual and interactive effect of two dung beetle species with contrasting functional behaviour (dweller species: Agrilinus ater (De Geer 1774) vs. tunneler species: Typhaeus typhoeus (Linneaus 1758)) on dung C cycling (CO2 fluxes and C transfer through the soil profile) and resultant effects on microbial activity and biomass in the soil. Both dung beetle species contributed significantly to dung removal, reducing the C lost through microbial respiration from the whole mesocosm. However, C concentrations measured in leachates from the mesocosm were only significantly higher in the presence of the tunneler species, indicating that tunnelling activity was required to increase C transfer down the soil profile. The combined effect of the two dung beetle species resulted in the highest soil microbial respiration from the soil and in particular in the 2–10 cm depth increment, suggesting positive complementarity effects between species with different functional behaviour. We conclude that the return of C in the form of dung in grasslands, coupled with the activity of a functionally diverse dung beetle assemblage, could result in short term fluctuations in soil microbial activity with important consequences for soil C cycling

Coordinated surface activities in Variovorax paradoxus EPS

<p>Abstract</p> <p>Background</p> <p><it>Variovorax paradoxus </it>is an aerobic soil bacterium frequently associated with important biodegradative processes in nature. Our group has cultivated a mucoid strain of <it>Variovorax paradoxus </it>for study as a model of bacterial development and response to environmental conditions. Colonies of this organism vary widely in appearance depending on agar plate type.</p> <p>Results</p> <p>Surface motility was observed on minimal defined agar plates with 0.5% agarose, similar in nature to swarming motility identified in <it>Pseudomonas aeruginosa </it>PAO1. We examined this motility under several culture conditions, including inhibition of flagellar motility using Congo Red. We demonstrated that the presence of a wetting agent, mineral, and nutrient content of the media altered the swarming phenotype. We also demonstrated that the wetting agent reduces the surface tension of the agar. We were able to directly observe the presence of the wetting agent in the presence and absence of Congo Red, and found that incubation in a humidified chamber inhibited the production of wetting agent, and also slowed the progression of the swarming colony. We observed that swarming was related to both carbon and nitrogen sources, as well as mineral salts base. The phosphate concentration of the mineral base was critical for growth and swarming on glucose, but not succinate. Swarming on other carbon sources was generally only observed using M9 salts mineral base. Rapid swarming was observed on malic acid, d-sorbitol, casamino acids, and succinate. Swarming at a lower but still detectable rate was observed on glucose and sucrose, with weak swarming on maltose. Nitrogen source tests using succinate as carbon source demonstrated two distinct forms of swarming, with very different macroscopic swarm characteristics. Rapid swarming was observed when ammonium ion was provided as nitrogen source, as well as when histidine, tryptophan, or glycine was provided. Slower swarming was observed with methionine, arginine, or tyrosine. Large effects of mineral content on swarming were seen with tyrosine and methionine as nitrogen sources. Biofilms form readily under various culture circumstances, and show wide variance in structure under different conditions. The amount of biofilm as measured by crystal violet retention was dependent on carbon source, but not nitrogen source. Filamentous growth in the biofilm depends on shear stress, and is enhanced by continuous input of nutrients in chemostat culture.</p> <p>Conclusion</p> <p>Our studies have established that the beta-proteobacterium <it>Variovorax paradoxus </it>displays a number of distinct physiologies when grown on surfaces, indicative of a complex response to several growth parameters. We have identified a number of factors that drive sessile and motile surface phenotypes. This work forms a basis for future studies using this genetically tractable soil bacterium to study the regulation of microbial development on surfaces.</p

Essential Concepts and Learning Outcomes for Cell and Molecular Biology

In the new, transformed Biology BS program for conversion from quarter to semester, multiple faculty will teach varied courses under the “Cell and Molecular” requirement for our program. Our old program required multiple core courses, leading to bottlenecks as students could not get seats in needed classes. We have designed our new program to provide students with options under core categories, providing students more flexibility which should improve time to graduation. Students must take at least ONE of the courses, although students who chose to focus on Cell and Molecular Biology should be able to learn new material in ALL courses. The courses which satisfy the “Cell and Molecular” requirement include Cell Biology, Molecular Biology, Genetics, and Microbiology. For this faculty learning community, we aimed to develop our courses to ensure that ALL courses within the “Cell and Molecular core category cover essential concepts and learning outcomes, but yet remain distinct so that students who want to place emphasis on Cell and Molecular Biology can learn from all the courses. To accomplish this, faculty who teach these courses met together to discuss scholarly articles regarding essential concepts and expected learning outcomes for cell and molecular degree programs. We present here our final reflection and the new syllabi for each of the Category A courses. We conclude our new core category A will cover essential concepts and learning outcomes, but yet remain distinct so that students who want to place emphasis on Cell and Molecular Biology can learn from all the courses

Genome of the Root-Associated Plant Growth-Promoting Bacterium Variovorax paradoxus Strain EPS

Variovorax paradoxus is a ubiquitous betaproteobacterium involved in plant growth promotion, the degradation of xenobiotics, and quorum-quenching activity. The genome of V. paradoxus strain EPS consists of a single circular chromosome of 6,550,056 bp, with a 66.48% G+C content

Complete Genome Sequence of the Metabolically Versatile Plant Growth-Promoting Endophyte Variovorax paradoxus S110

Variovorax paradoxus is a microorganism of special interest due to its diverse metabolic capabilities, including the biodegradation of both biogenic compounds and anthropogenic contaminants. V. paradoxus also engages in mutually beneficial interactions with both bacteria and plants. The complete genome sequence of V. paradoxus S110 is composed of 6,754,997 bp with 6,279 predicted protein-coding sequences within two circular chromosomes. Genomic analysis has revealed multiple metabolic features for autotrophic and heterotrophic lifestyles. These metabolic diversities enable independent survival, as well as a symbiotic lifestyle. Consequently, S110 appears to have evolved into a superbly adaptable microorganism that is able to survive in ever-changing environmental conditions. Based on our findings, we suggest V. paradoxus S110 as a potential candidate for agrobiotechnological applications, such as biofertilizer and biopesticide. Because it has many associations with other biota, it is also suited to serve as an additional model system for studies of microbe-plant and microbe-microbe interactions

Genome of the Root-Associated Plant Growth-Promoting Bacterium Variovorax paradoxus Strain EPS

Variovorax paradoxus is a ubiquitous betaproteobacterium involved in plant growth promotion, the degradation of xenobiotics, and quorum-quenching activity. The genome of V. paradoxus strain EPS consists of a single circular chromosome of 6,550,056 bp, with a 66.48% G+C content

Genes That Influence Swarming Motility and Biofilm Formation in Variovorax paradoxus EPS

Variovorax paradoxus is an aerobic soil bacterium associated with important biodegradative processes in nature. We use V. paradoxus EPS to study multicellular behaviors on surfaces.We recovered flanking sequence from 123 clones in a Tn5 mutant library, with insertions in 29 different genes, selected based on observed surface behavior phenotypes. We identified three genes, Varpa_4665, Varpa_4680, and Varpa_5900, for further examination. These genes were cloned into pBBR1MCS2 and used to complement the insertion mutants. We also analyzed expression of Varpa_4680 and Varpa_5900 under different growth conditions by qPCR.The 29 genes we identified had diverse predicted functions, many in exopolysaccharide synthesis. Varpa_4680, the most commonly recovered insertion site, encodes a putative N-acetyl-L-fucosamine transferase similar to WbuB. Expression of this gene in trans complemented the mutant fully. Several unique insertions were identified in Varpa_5900, which is one of three predicted pilY1 homologs in the EPS genome. No insertions in the two other putative pilY1 homologs present in the genome were identified. Expression of Varpa_5900 altered the structure of the wild type swarm, as did disruption of the chromosomal gene. The swarming phenotype was complemented by expression of Varpa_5900 from a plasmid, but biofilm formation was not restored. Both Varpa_4680 and Varpa_5900 transcripts were downregulated in biofilms and upregulated during swarming when compared to log phase culture. We identified a putative two component system (Varpa_4664-4665) encoding a response regulator (shkR) and a sensor histidine kinase (shkS), respectively. Biofilm formation increased and swarming was strongly delayed in the Varpa_4665 (shkS) mutant. Complementation of shkS restored the biofilm phenotype but swarming was still delayed. Expression of shkR in trans suppressed biofilm formation in either genetic background, and partially restored swarming in the mutant.The data presented here point to complex regulation of these surface behaviors

African Linguistics in Central and Eastern Europe, and in the Nordic Countries

Non peer reviewe