POSA: Perl Objects for DNA Sequencing Data Analysis

Background  

Capillary DNA sequencing machines allow the generation of vast amounts of data with little hands-on time. With this expansion of data generation, there is a growing need for automated data processing. Most available software solutions, however, still require user intervention or provide modules that need advanced informatics skills to allow implementation in pipelines.     

Reduced intracellular survival of Helicobacter pylori vacA mutants in comparison with their wild-types indicates the role of VacA in pathogenesis

The vacuolating cytotoxin VacA of Helicobacter pylori plays an important but yet unknown role in pathogenesis. We studied the impact of the vacuolating cytotoxin on H. pylori invasion of and survival within AGS cells (human gastric cell line derived from an antral adenocarcinoma). Isogenic vacA and cagA mutants were constructed in a wild-type clinical isolate H. pylori, AF4. An H. pylori VacA-deficient mutant, AF4(vacA::kan), was cultured in significantly lower numbers from AGS cells after 24 h incubation with gentamicin added to the culture medium than were the type I wild-type strain AF4 (P<0.03) and an isogenic cagA mutant (P<0.01). Complementation of the AF4 vacA mutant with broth culture supernatant from wild-type AF4 improved the intracellular survival of the vacA mutant. We conclude that H. pylori's vacuolating cytotoxin improves the intracellular survival of H. pylori within AGS cells, suggesting the role of the vacuolating cytotoxin in H. pylori pathogenesis.     

Biochemical basis for depressed serum retinol levels in transthyretin-deficient mice

Transthyretin (TTR) acts physiologically in the transport of retinol in the circulation. We previously reported the generation and partial characterization of TTR-deficient (TTR(-)) mice. TTR(-) mice have very low circulating levels of retinol and its specific transport protein, retinol-binding protein (RBP). We have examined the biochemical basis for the low plasma retinol-RBP levels. Cultured primary hepatocytes isolated from wild type (WT) and TTR(-) mice accumulated RBP in their media to an identical degree, suggesting that RBP was being secreted from the hepatocytes at the same rate. In vivo experiments support this conclusion. For the first 11 h after complete nephrectomy, the levels retinol and RBP rose in the circulations of WT and TTR(-) mice at nearly identical rates. However, human retinol-RBP injected intravenously was more rapidly cleared from the circulation (t(12) = 0.5 h for TTR(-) versus t(12) >6 h for WT) and accumulated faster in the kidneys of TTR(-) compared with WT mice. The rate of infiltration of the retinol-RBP complex from the circulation to tissue interstitial fluids was identical in both strains. Taken together, these data indicate that low circulating retinol-RBP levels in TTR(-) mice arise from increased renal filtration of the retinol-RBP complex.     

Dwarfs and Giants: Cannibalism and Competition in Size-Structured Populations

Cannibals and their victims often share common resources and thus potentially compete. Smaller individuals are often competitively superior to larger ones because of size-dependent scaling of foraging and metabolic rates, while larger ones may use cannibalism to counter this competition. We study the interplay between cannibalism and competition using a size-structured population model in which all individuals consume a shared resource but in which larger ones may cannibalize smaller conspecifics. In this model, intercohort competition causes single-cohort cycles when cannibalism is absent. Moderate levels of cannibalism reduce intercohort competition, enabling coexistence of many cohorts. More voracious cannibalism, in combination with competition, produces large-amplitude cycles and a bimodal population size distribution with many small and few giant individuals. These coexisting "dwarfs" and "giants" have very different life histories, resulting from a reversal in importance of cannibalism and competition. The population structure at time of birth determines whether individuals suffer severe cannibalism, with the few survivors reaching giant sizes, or whether they suffer intense intracohort competition, with all individuals remaining small. These model results agree remarkably well with empirical data on perch population dynamics. We argue that the induction of cannibalistic giants in piscivorous fish is a population-dynamic emergent phenomenon that requires a combination of size-dependent cannibalism and competition.     

The use of oxytetracycline as a marker for juvenile cod (Gadus morhua L.)

We examine aspects of marking large numbers of juvenile cod ( Gadus morhua L.) by oxytetracycline (OTC) for cod enhancement experiments. Reared cod were given OTC through the feed and released in a fjord. Control groups were kept in net pens. A total of 93% of the cod became marked. The size of the cod and the percentage marked were inversely related. The location of the mark within each vertebra gradually changed towards the centre as the cod grew and new bone tissue was added. The percentage of marked cod in the control group did not decrease during a period of almost 3 years after marking, although the intensity of the mark gradually declined. After release, we found no indication that the OTC affected growth or survival of the cod. Cod marked as O-group could be distinguished from cod marked as 2-group, from the position of the mark within the vertebra.     

Mitochondrial minicircles in the free-living bodonid Bodo saltans contain two gRNA gene cassettes and are not found in large networks

In trypanosomatids, the majority of the guide (g) RNAs that provide the information for U-insertion/deletion RNA editing are encoded by minicircles that are catenated into large networks. In contrast, in the distantly related cryptobiid Trypanoplasma borreli, gRNA genes appear to reside in large 180-kb noncatenated DNA circles. To shed light on the evolutionary history and function of the minicircle network, we have analyzed minicircle organization in the free-living bodonid Bodo saltans, which is more closely related to trypanosomatids than T. borreli. We identified 1.4-kb circular DNAs as the B. saltans equivalent of minicircles via sequence analysis of 4 complete minicircles, 14 minicircle fragments, and 14 gRNAs. We show that each minicircle harbors two gRNA gene cassettes of opposite polarity residing in variable regions of about 200 nt in otherwise highly conserved molecules. In the conserved region, B. saltans minicircles contain a putative bent helix sequence and a degenerate dodecamer motif (CSB-3). Electron microscopy, sedimentation, and gel electrophoresis analyses showed no evidence for the existence of large minicircle networks in B. saltans, the large majority of the minicircles being present as circular and linear monomers (85-90%) with small amounts of catenated dimers and trimers. Our results provide the first example of a kinetoplastid species with noncatenated, gRNA gene-containing minicircles, which implies that the creation of minicircles and minicircle networks are separate evolutionary events.     

Role of strain type, AGS cells and fetal calf serum in Helicobacter pylori adhesion and invasion assays

In a human gastric biopsy specimen, 30% of adhering Helicobacter pylori strain AF4 (cagA and VacA positive) was associated with adhesion pedestals. In an AGS cell assay, only a few percent of this type I strain was found to be associated with adhesion pedestals. Nevertheless, a larger proportion of the type I strain was found to invade AGS cells (P < 0.03) and to attach with depressions in the AGS cell membrane (P < 0.03) than a type II strain (cagA and VacA negative). Incubation of AGS cells and H. pylori without adding fetal calf serum (FCS) to the culture medium increased actin accumulations (FITC-phalloidin stained) beneath adhering H. pylori, and decreased H. pylori invasion of AGS cells significantly (P < 0.01). However, no increase in the number of adhesion pedestals was observed by electron microscopy. Proteinase K treatment of FCS eliminated the H. pylori invasion promoting effect (P < 0.01). Our results suggest differences in the ability of H. pylori to induce adhesion pedestals in human gastric epithelial cells and in AGS cells, but a correlation between adhesion pedestal formation in vivo and H. pylori invasion in vitro can be speculated. In addition, H. pylori invasion into AGS cells was found to be mediated by proteins in FCS.     

Complete genome sequence of clinical isolate Pantoea ananatis LMG 5342

The enterobacterium Pantoea ananatis is an ecologically versatile species. It has been found in the environment, as plant epiphyte and endophyte, as an emerging phytopathogen, and as a presumptive, opportunistic human pathogen. Here, we report the complete genome sequence of P. ananatis LMG 5342, isolated from a human wound.     

The genome of plant growth-promoting Bacillus amyloliquefaciens subsp. plantarum strain YAU B9601-Y2 contains a gene cluster for mersacidin synthesis

The genome of rhizobacterium Bacillus amyloliquefaciens subsp. plantarum YAU B9601-Y2 was 4.24 Mb in size and harbored 3,991 coding sequences (CDS). Giant gene clusters were dedicated to nonribosomal synthesis of antimicrobial lipopeptides and polyketides. Remarkably, CAU B946 possessed a gene cluster involved in synthesis of mersacidin.