P-Index, A Novel Algorithm for Bibliometric Analysis

Poster presented at Medical Library Association annual meeting, May 2010Describes an algorithm for bibliographic analysi

A Computational Approach to Estimating Nondisjunction Frequency in Saccharomyces cerevisiae.

Errors segregating homologous chromosomes during meiosis result in aneuploid gametes and are the largest contributing factor to birth defects and spontaneous abortions in humans. Saccharomyces cerevisiae has long served as a model organism for studying the gene network supporting normal chromosome segregation. Measuring homolog nondisjunction frequencies is laborious, and involves dissecting thousands of tetrads to detect missegregation of individually marked chromosomes. Here we describe a computational method (TetFit) to estimate the relative contributions of meiosis I nondisjunction and random-spore death to spore inviability in wild type and mutant strains. These values are based on finding the best-fit distribution of 4, 3, 2, 1, and 0 viable-spore tetrads to an observed distribution. Using TetFit, we found that meiosis I nondisjunction is an intrinsic component of spore inviability in wild-type strains. We show proof-of-principle that the calculated average meiosis I nondisjunction frequency determined by TetFit closely matches empirically determined values in mutant strains. Using these published data sets, TetFit uncovered two classes of mutants: Class A mutants skew toward increased nondisjunction death, and include those with known defects in establishing pairing, recombination, and/or synapsis of homologous chromosomes. Class B mutants skew toward random spore death, and include those with defects in sister-chromatid cohesion and centromere function. Epistasis analysis using TetFit is facilitated by the low numbers of tetrads (as few as 200) required to compare the contributions to spore death in different mutant backgrounds. TetFit analysis does not require any special strain construction, and can be applied to previously observed tetrad distributions

Bioremediation of lead using spore surface displayed proteins

Lead is a toxic pollutant very harmful to human health since it accumulates in the body and affects the brain, liver, kidney, and bones. Fetuses can be exposed to lead during pregnancy, which can cause problems with learning later on in the baby’s life. The purpose of this project is to display a lead binding protein on bacterial spore surface for the bioremediation of lead from water. Spores from Bacillus subtilis are very robust and resistant to various harsh environments. Genetically fused to a spore surface protein, the displayed proteins demonstrate enhanced robustness and can be easily produced through sporulation without the need of further purification. PbrR is a regulatory protein that modulates the lead resistance in bacteria. In this project, we fused seven variants of PbrR to the spore surface protein CotC (CotC-PbrRs). The lead binding affinity and specificity of these PbrR variants on the spore surface will be characterized. The robustness of these spores with PbrR will be also evaluated using wastewater samples

Ascospore release and survival in Sclerotinia sclerotiorum

The release and survival of ascospores of a UK Sclerotinia sclerotiorum isolate were studied. Apothecia placed in a spore clock apparatus with different lighting regimes at 15 °C released ascospores continuously with an increasing rate for the duration of experiments (72–84 h). Spore release was not confined to light or dark periods in alternating regimes and occurred in continuous dark or light. Ascospores were released in both saturated air (90–95% rh) and at 65–75% rh. High temperature and rh were detrimental to ascospore survival but spore viability was maintained for longer periods than previously reported. The significance of these results in relation to disease control is discussed

A Laboratory Infection of Alfalfa Weevil, \u3ci\u3eHypera Postica\u3c/i\u3e (Coleoptera: Curculionidae), Larvae With the Fungal Pathogen \u3ci\u3eZoophthora Phytonomi\u3c/i\u3e (Zygomycetes: Entomophthoraceae)

Larvae of the alfalfa weevil, Hypera postica, were infected by an in vitro colony of Zoophthora phytonomi. Two spore types (infective conidia, and resting spores) were produced from infection trials. The spore type produced may be influenced by the physiological state of the larvae. Trials using field collected larvae which would produce diapausing adults formed both conidia and resting spores. Trials using larvae from a nondiapausing colony, however, formed only resting spores

Organic amendment increases arbuscular mycorrhizal fungal diversity in primary coastal dunes

Plastic pots were inserted beneath seedlings of a shallow-rooted C4 grass species, Ischaemum indicum, with and without a root-impenetrable nylon sachet filled with organic matter (OM) amendment, at seven stations along an interrupted belt transect in which plant community and soil chemistry had been previously surveyed. The transect was perpendicular to mean high-water mark (MH-WM) across a primary coastal dune system in Goa, India, where summer monsoon is the predominant weather feature. The Quadrat survey of plant frequency was made in stations when the above-ground biomass was estimated to be highest. Arbuscular mycorrhiza fungal (AMF) spore density and diversity were determined morphologically in amended and control pots soils, and in OM sachet residues, after host-plant desiccation when monsoon rains had ceased. Twenty-seven AM fungal spore morphotypes were isolated from the pots containing OM amended rhizosphere soils, 19 from controls and 14 from OM residues in the sachets. Gigaspora margarita proved to be the dominant spore in all treatments. Eight morphotypes recovered from amended pots were not recovered from the controls. There was an increasing trend in species diversity in amended pots away from MH-WM. Spore recovery from the three regimes showed variable distribution that indicated differing AMF species strategies

Asexual and sexual replication in sporulating organisms

This paper develops models describing asexual and sexual replication in sporulating organisms. Replication via sporulation is the replication strategy for all multicellular life, and may even be observed in unicellular life (such as with budding yeast). We consider diploid populations replicating via one of two possible sporulation mechanisms: (1) Asexual sporulation, whereby adult organisms produce single-celled diploid spores that grow into adults themselves. (2) Sexual sporulation, whereby adult organisms produce single-celled diploid spores that divide into haploid gametes. The haploid gametes enter a haploid "pool", where they may recombine with other haploids to form a diploid spore that then grows into an adult. We consider a haploid fusion rate given by second-order reaction kinetics. We work with a simplified model where the diploid genome consists of only two chromosomes, each of which may be rendered defective with a single point mutation of the wild-type. We find that the asexual strategy is favored when the rate of spore production is high compared to the characteristic growth rate from a spore to a reproducing adult. Conversely, the sexual strategy is favored when the rate of spore production is low compared to the characteristic growth rate from a spore to a reproducing adult. As the characteristic growth time increases, or as the population density increases, the critical ratio of spore production rate to organism growth rate at which the asexual strategy overtakes the sexual one is pushed to higher values. Therefore, the results of this model suggest that, for complex multicellular organisms, sexual replication is favored at high population densities, and low growth and sporulation rates.Comment: 8 pages, 5 figures, to be submitted to Journal of Theoretical Biology, figures not included in this submissio

Surface charge and hydrodynamic coefficient measurements of {\it Bacillus subtilis} spore by Optical Tweezers

In this work we report on the simultaneous measurement of the hydrodynamic coefficient and the electric charge of single {\it Bacillus subtilis} spores. The latter has great importance in protein binding to spores and in the adhesion of spores onto surfaces. The charge and the hydrodynamic coefficient were measured by an accurate procedure based on the analysis of the motion of single spores confined by an optical trap. The technique has been validated using charged spherical polystyrene beads. The excellent agreement of our results with the expected values demonstrates the quality of our procedure. We measured the charge of spores of {\it B. subtilis} purified from a wild type strain and from two isogenic mutants characterized by an altered spore surface. Our technique is able to discriminate the three spore types used, by their charge and by their hydrodynamic coefficient which is related to the hydrophobic properties of the spore surface.Comment: 21 pages 5 figure