Population Structure and Diversity of Phenazine-1-Carboxylic Acid Producing Fluorescent Pseudomonas spp. from Dryland Cereal Fields of Central Washington State (USA)

Certain strains of the rhizosphere bacterium Pseudomonas fluorescens contain the phenazine biosynthesis operon (phzABCDEFG) and produce redox-active phenazine antibiotics that suppress a wide variety of soilborne plant pathogens. In 2007 and 2008, we isolated 412 phenazine-producing (Phz(+)) fluorescent Pseudomonas strains from roots of dryland wheat and barley grown in the low-precipitation region (<350 mm annual precipitation) of central Washington State. Based on results of BOX-PCR genomic fingerprinting analysis, these isolates, as well as the model biocontrol Phz(+) strain P. fluorescens 2-79, were assigned to 31 distinct genotypes separated into four clusters. All of the isolates exhibited high 16S rDNA sequence similarity to members of the P. fluorescens species complex including Pseudomonas orientalis, Pseudomonas gessardii, Pseudomonas libanensis, and Pseudomonas synxantha. Further recA-based sequence analyses revealed that the majority of new Phz(+) isolates (386 of 413) form a clade distinctly separated from P. fluorescens 2-79. Analysis of phzF alleles, however, revealed that the majority of those isolates (280 of 386) carried phenazine biosynthesis genes similar to those of P. fluorescens 2-79. phzF-based analyses also revealed that phenazine genes were under purifying selection and showed evidence of intracluster recombination. Phenotypic analyses using Biolog substrate utilization and observations of phenazine-1-carboxylic acid production showed considerable variability amongst members of all four clusters. Biodiversity indices indicated significant differences in diversity and evenness between the sampled sites. In summary, this study revealed a genotypically and phenotypically diverse group of phenazine producers with a population structure not seen before in indigenous rhizosphere-inhabiting Phz(+) Pseudomonas spp.     

A molecular phylogenetic analysis of the vampire moths and their fruit-piercing relatives (Lepidoptera: Erebidae: Calpinae)

Within butterflies and moths, adult hematophagy is limited to species within the vampire moth genus Calyptra. These moths are placed within the subfamily Calpinae, whose other members are known to exhibit a broad range of feeding behaviors including those that can be considered 'piercers' of fruits or other hosts and 'tear feeders'. Here, we reconstruct a phylogenetic hypothesis of Calpinae using molecular data to test whether hematophagy in Calyptra arose from plant or animal-related behaviors. We use a Bayesian method of ancestral state reconstruction to determine the most likely feeding behaviors for the subtribes and genera within this lineage.     

Oligomerization of ICP4 and rearrangement of heat shock proteins may be important for herpes simplex virus type 1 prereplicative site formation

Herpes simplex virus type 1 (HSV-1) DNA replication occurs in replication compartments that form in the nucleus by an ordered process involving a series of protein scaffold intermediates. Following entry of viral genomes into the nucleus, nucleoprotein complexes containing ICP4 can be detected at a position adjacent to nuclear domain 10 (ND10)-like bodies. ND10s are then disrupted by the viral E3 ubiquitin ligase ICP0. We have previously reported that after the dissociation of ND10-like bodies, ICP8 could be observed in a diffuse staining pattern; however, using more sensitive staining methods, we now report that in addition to diffuse staining, ICP8 can be detected in tiny foci adjacent to ICP4 foci. ICP8 microfoci contain UL9 and components of the helicase-primase complex. HSV infection also results in the reorganization of the heat shock cognate protein 70 (Hsc70) and the 20S proteasome into virus-induced chaperone-enriched (VICE) domains. In this report we show that VICE domains are distinct but adjacent to the ICP4 nucleoprotein complexes and the ICP8 microfoci. In cells infected with an ICP4 mutant virus encoding a mutant protein that cannot oligomerize on DNA, ICP8 microfoci are not detected; however, VICE domains could still be formed. These results suggest that oligomerization of ICP4 on viral DNA may be essential for the formation of ICP8 microfoci but not for the reorganization of host cell chaperones into VICE domains.     

Estimation of the number of SNP genetic markers required for parentage verification

Formulae were developed to compute exclusion probabilities for parentage confirmation for any number of diallelic markers under the assumption that the minor allele frequency (MAF) varied among markers, but has a uniform distribution. Three scenarios were analysed: a progeny with (1) a single putative parent; (2) two putative parents; and (3) one actual parent and one putative parent. Exclusion probabilities were computed for minimum values for the MAFs of 0.1, 0.2 and 0.3, and required either one or at least two conflicts for exclusion. The numbers of markers required to obtain 99% exclusion probabilities based on a single conflict for the three minimum MAFs were 54, 45 and 39 for scenario 1; 17, 16 and 15 for scenario 2; and 28, 25 and 24 for scenario 3. The requirement of at least two conflicts for exclusion increased the number of markers required by approximately 45% for all three scenarios and all three minimum MAFs. The results obtained by the analytical formulae were very close to results obtained by simulation and to values in the literature for specific marker sets.     

Genetic analysis of the growth rate of Israeli Holstein calves

Weight of male and female Israeli Holstein calves and yearling gain were analyzed on 285 800 records from 105 935 animals from 458 herds recorded between 1994 and 2007. The difference between the sexes increased until around 400 days, at which point the difference between males and females was 110 kg. Yearling gain, defined as 365 × (weight - 35)/age + 35, was greatest for males at approximately 300 days and for females at 225 days. Yearling gain of male and female calves were highly correlated genetically; thus records from both sexes were combined into a joint genetic analysis. Heritability and repeatability were 0.33 and 0.73 in the analysis of both sexes, and similar in the single-sex analyses. Yearling gain is also highly correlated genetically with various measures of mature cow size. Yearling gain was positively correlated with milk, fat, protein production and somatic cell score, but negatively correlated with fertility and cow survival. Yearling gain was also positively correlated with both the sire and maternal grandsire effects on dystocia, but not with calf mortality. The genetic trend for yearling gain was 0.16 kg/year, while phenotypic trends for first and last weighings were both negative.     

Characterization of microsatellite loci in the Hawaiian endemic shrub Schiedea adamantis (Caryophyllaceae) and amplification in related species and genera

Schiedea adamantis is a rare, perennial shrub endemic to the Hawaiian island of Oahu where it consists of a single population. Using a nonradioactive protocol, 12 microsatellite primers were developed that consisted of di-, tri-, penta- and hexanucleotide repeats. Using multiplexed reactions, all but two primers exhibited polymorphism with an average of 3.67 alleles per primer. Most primers also amplified in 28 additional Schiedea species, revealing wide applicability across the genus; eight and nine primers also amplified in Honckenya peploides and Silene lanceolata, respectively, related genera in the Caryophyllaceae. This is the first known report of microsatellite primers developed in Schiedea.