A freshwater cyanophage whose genome indicates close relationships to photosynthetic marine cyanomyophages

Bacteriophage S-CRM01 has been isolated from a freshwater strain of Synechococcus and shown to be present in the upper Klamath River valley in northern California and Oregon. The genome of this lytic T4-like phage has a 178,563 bp circular genetic map with 297 predicted protein-coding genes and 33 tRNA genes that represent all 20-amino-acid specificities. Analyses based on gene sequence and gene content indicate a close phylogenetic relationship to the 'photosynthetic' marine cyanomyophages infecting Synechococcus and Prochlorococcus. Such relatedness suggests that freshwater and marine phages can draw on a common gene pool. The genome can be considered as being comprised of three regions. Region 1 is populated predominantly with structural genes, recognized as such by homology to other T4-like phages and by identification in a proteomic analysis of purified virions. Region 2 contains most of the genes with roles in replication, recombination, nucleotide metabolism and regulation of gene expression, as well as 5 of the 6 signature genes of the photosynthetic cyanomyophages (hli03, hsp20, mazG, phoH and psbA; cobS is present in Region 3). Much of Regions 1 and 2 are syntenic with marine cyanomyophage genomes, except that a segment encompassing Region 2 is inverted. Region 3 contains a high proportion (85%) of genes that are unique to S-CRM01, as well as most of the tRNA genes. Regions 1 and 2 contain many predicted late promoters, with a combination of CTAAATA and ATAAATA core sequences. Two predicted genes that are unusual in phage genomes are homologues of cellular spoT and nusG.     

Sister chromatid exchange analysis of the 15q11 region in Prader-Willi syndrome patients

Summary Prader-Willi syndrome (PWS) is a sporadic disorder in which about half of cases have a 15q12 deletion. Although a small number of cases have other rearrangements involving 15q12, the rest of the cases appear to have normal chromosomes. Clinical similarities among all these patients regardless of the karyotype strongly suggests a common etiology. To investigate the nature of this common etiology, we analyzed sister chromatid exchange (SCE) at the 15q11-13 region in 10 PWS patients with the chromosome deletion, 12 PWS patients with normal chromosomes, and 11 normal control individuals. While SCE at the q11-13 region was absent on the 15q12 deleted chromosome, the percentage of SCE on chromosome 15 at q11 was statistically higher for PWS with normal chromosomes (10.1%) compared to that for normal controls (1.9%) and the normal homologue (2.2%) in deleted patients (²=7.7982, df=2, P<0.025). The data suggest relative instability of DNA at the 15q11 region in PWS patients.     

Treatment of HeLa cells with bacterial water extracts inhibits Shigella flexneri invasion

Abstract Pathogenesis mediated by Shigella flexneri requires invasion of the gastrointestinal epithelium. It has been previously shown that HeLa cells challenged with S. flexneri show alterations in their phosphotyrosine-containing protein profile. In this report, we demonstrated that bacterial water extracts (WE) abrogated the invasion of HeLa cells by S. flexneri in a dose-dependent manner. A proteinaceous component of S. flexneri was shown to be responsible for this inhibitory activity. Proteins encoded on the 140-MDa plasmid were not responsible for the observed inhibition. WE from other Gram-negative bacteria also inhibited Shigella invasion of HeLa cells. HeLa cells pretreated with WE showed changes in the profile and the intensity of phosphotyrosine-containing protein bands. These data were consistent with a surface protein component in WE which initiated aberrant host cell signaling at the membrane which may account for the inhibition of bacterial entry.     

Biological and analytical variation of the human sweating response: implications for study design and analysis

Appropriate quantification of analytical and biological variation of thermoregulatory sweating has important practical utility for research design and statistical analysis. We sought to examine contributors to variability in local forearm sweating rate (SR) and sweating onset (SO) and to evaluate the potential for using bilateral measurements. Two women and eight men (26 ± 9 yr; 79 ± 12 kg) completed 5 days of heat acclimation and walked (1.8 l/min VO(2)) on three occasions for 30 min in 40°C, 20% RH, while local SR and SO were measured. Local SR measures among days were not different (2.14 ± 0.72 vs. 2.02 ± 0.79 vs. 2.31 ± 0.72 mg·cm(2)·min(-1), P = 0.19) nor was SO (10.47 ± 2.54 vs. 10.04 ± 2.97 vs. 9.87 ± 3.44 min P = 0.82). Bilateral SR (2.14 ± 0.72 vs. 2.16 ± 0.71 mg·cm(2)·min(-1), P = 0.56) and SO (10.47 ± 2.54 vs. 10.83 ± 2.48 min, P = 0.09) were similar and differences were ≤ 1 SD of day-to-day differences for a single forearm. Analytical imprecision (CV(a)), within (CV(i))-, and between (CV(g))-subjects' coefficient of variation for local SR were 2.4%, 22.3%, and 56.4%, respectively, and were 0%, 9.6%, and 41%, respectively, for SO. We conclude: 1) technologically, sweat capsules contribute negligibly to sweat measurement variation; 2) bilateral measures of SR and SO appear interchangeable; 3) when studying potential factors affecting sweating, changes in SO afford a more favorable signal-to-noise ratio vs. changes in SR. These findings provide a quantitative basis for study design and optimization of power/sample size analysis in the evaluation of thermoregulatory sweating.     

Translational machinery of the chaetognath <Emphasis Type="Italic">Spadella cephaloptera</Emphasis>: a transcriptomic approach to the analysis of cytosolic ribosomal protein genes and their expression

Background  

Chaetognaths, or arrow worms, are small marine, bilaterally symmetrical metazoans. The objective of this study was to analyse ribosomal protein (RP) coding sequences from a published collection of expressed sequence tags (ESTs) from a chaetognath (Spadella cephaloptera) and to use them in phylogenetic studies.     

Quantifying bacterial evolution in the wild: A birthday problem for Campylobacter lineages

Measuring molecular evolution in bacteria typically requires estimation of the rate at which nucleotide changes accumulate in strains sampled at different times that share a common ancestor. This approach has been useful for dating ecological and evolutionary events that coincide with the emergence of important lineages, such as outbreak strains and obligate human pathogens. However, in multi-host (niche) transmission scenarios, where the pathogen is essentially an opportunistic environmental organism, sampling is often sporadic and rarely reflects the overall population, particularly when concentrated on clinical isolates. This means that approaches that assume recent common ancestry are not applicable. Here we present a new approach to estimate the molecular clock rate in Campylobacter that draws on the popular probability conundrum known as the ‘birthday problem’. Using large genomic datasets and comparative genomic approaches, we use isolate pairs that share recent common ancestry to estimate the rate of nucleotide change for the population. Identifying synonymous and non-synonymous nucleotide changes, both within and outside of recombined regions of the genome, we quantify clock-like diversification to estimate synonymous rates of nucleotide change for the common pathogenic bacteria Campylobacter coli (2.4 x 10⁻⁶ s/s/y) and Campylobacter jejuni (3.4 x 10⁻⁶ s/s/y). Finally, using estimated total rates of nucleotide change, we infer the number of effective lineages within the sample time frame–analogous to a shared birthday–and assess the rate of turnover of lineages in our sample set over short evolutionary timescales. This provides a generalizable approach to calibrating rates in populations of environmental bacteria and shows that multiple lineages are maintained, implying that large-scale clonal sweeps may take hundreds of years or more in these species.