A new method for detecting chimeras and other anomalies within 16S rRNA sequence records is presented. Using this method, we screened 1,399 sequences from 19 phyla, as defined by the Ribosomal Database Project, release 9, update 22, found 5.0% to harbor substantial errors. Of these, 64.3% were obvious chimeras, 14.3% unidentified sequencing errors, 21.4% highly degenerate. In all, 11 phyla contained accounting 0.8 11% of these phyla. Many (43.1%) formed parental belonging different While...

ABSTRACT A new computer program, called Mallard, is presented for screening entire 16S rRNA gene libraries of up to 1,000 sequences chimeras and other artifacts. Written in the Java language capable running on all major operating systems, program provides a novel graphical approach visualizing phylogenetic relationships among sequences. To illustrate its use, we analyzed most large cloned bacterial submitted public repository during 2005. Defining library as one containing 100 or more 1,200...

ABSTRACT Here we report the first direct counts of soil bacteriophage and show that substantial populations these viruses exist in (grand mean = 1.5 × 10 7 g −1 ), at least 350-fold more than highest numbers estimated from traditional viable plaque counts. Adding pure cultures a Serratia phage to showed counting methods with electron microscopy developed here underestimated added by eightfold. So, assuming natural phages were similarly underestimated, virus averaged 8 , which is equivalent...

We describe PRIMROSE, a computer program for identifying 16S rRNA probes and PCR primers use as phylogenetic ecological tools in the identification enumeration of bacteria. PRIMROSE is designed to data from Ribosomal Database Project (RDP) find potentially useful oligonucleotides with up two degenerate positions. The taxonomic range these, other existing oligonucleotides, can then be explored, allowing rapid suitable oligonucleotides. includes features allow user‐defined sequence databases...

Mytilus species are important in marine ecology and environmental quality assessment, yet their molecular biology is poorly understood. Molecular aspects of reproduction, hybridisation between species, mitochondrial inheritance, skewed sex ratios offspring adaptation to climatic pollution factors priority areas.To start address this situation, expressed genetic transcripts from M. galloprovincialis were pyrosequenced. Transcripts isolated the digestive gland, foot, gill mantle both male...

Pseudomonas aeruginosa is a common opportunistic bacterial pathogen that causes variety of infections in humans. Populations P. are dominated by clones can be isolated from diverse clinical and environmental sources. To determine whether specific associated with corneal infection, we used portable genotyping microarray system to analyze set 63 isolates patients ulcers (keratitis). We then population analysis compare the keratitis wider collection various nonocular identified markers...

Short dysfunctional telomeres are capable of fusion, generating dicentric chromosomes and initiating breakage-fusion-bridge cycles. Cells that escape the ensuing cellular crisis exhibit large-scale genomic rearrangements drive clonal evolution malignant progression. We demonstrate there is an absolute requirement for fully functional DNA ligase III (LIG3), but not IV (LIG4), to facilitate from a telomere-driven crisis. LIG3- LIG4-dependent alternative (A) classical (C) nonhomologous...

Map based cloning in Arabidopsis thaliana can be a difficult and time-consuming process, specifically if the phenotype is subtle scoring labour intensive. Here, we have re-sequenced 120-Mb genome of novel clock mutant early bird (ebi-1) Wassilewskija (Ws-2). We demonstrate utility sequencing backcrossed line limiting number SNPs considered. identify SNP gene AtNFXL-2 as likely cause ebi-1 phenotype.

Ostreococcus tauri virus (OtV-1) is a large double-stranded DNA and prospective member of the family Phycodnaviridae, genus Prasinovirus. OtV-1 infects unicellular marine green alga O. tauri, smallest known free-living eukaryote. Here we present 191 761 base pair genome sequence OtV-1, which has 232 putative protein-encoding 4 tRNA-encoding genes. Approximately 31% viral gene products exhibit similarity to proteins functions in public databases. These include variety unexpected genes, for...

Summary Although the major food‐borne pathogen Campylobacter jejuni has been isolated from diverse animal, human and environmental sources, our knowledge of genomic diversity in C. is based exclusively on or food‐chain‐associated isolates. Studies employing multilocus sequence typing have indicated that some clonal complexes are more commonly associated with particular sources. Using comparative hybridization a collection 80 isolates representing sources complexes, we identified separate...

Anthropogenic endocrine disruptors now contaminate all environments globally, with concomitant deleterious effects across diverse taxa. While most studies on disruption (ED) have focused vertebrates, the superimposition of male sexual characteristics in female dogwhelk, Nucella lapillus (imposex), caused by organotins, provides one clearcut ecological examples anthropogenically induced ED aquatic ecosystems. To identify underpinning mechanisms imposex for this 'nonmodel' species, we combined...

Abstract The commonest tumors associated with neurofibromatosis type 1 (NF1) are benign peripheral nerve sheath tumors, called neurofibromas. Malignant transformation of neurofibromas into aggressive MPNSTs may occur a poor patient prognosis. A cooperative role SUZ12 or EED inactivation, along NF1, TP53, and CDKN2A loss‐of‐function, has been proposed to drive progression MPNSTs. An exome sequencing analysis eight MPNSTs, one plexiform neurofibroma, seven cutaneous was undertaken. Biallelic...

ABSTRACT We describe two prolonged bacteriophage blooms within sugar beet rhizospheres ensuing from an artificial increase in numbers of indigenous soil bacterium. Further, we provide evidence situ competition between these phages. This is the first demonstration such microbial interactions soil. To achieve this, seeds were inoculated with Serratia liquefaciens CP6RS or its lysogen, CP6RS-ly-Φ1. These sown, along uninoculated seeds, 36 field plots arranged a randomized Latin square. The then...

Arcobacter butzleri is considered to be an emerging human foodborne pathogen. The completion of A. genome sequence along with microarray analysis 13 isolates in 2007 revealed a surprising amount diversity amongst from humans, animals and food. In order further investigate diversity, 792 faecal samples were collected cattle on beef dairy farms the North West England. was isolated 42.5% investigated using multilocus typing. An whole sequence, obtained by 454 shotgun sequencing isolate...

Telomeres shorten with each cell division and can ultimately become substrates for nonhomologous end-joining repair, leading to large-scale genomic rearrangements of the kind frequently observed in human cancers. We have characterized more than 1400 telomere fusion events at single-molecule level, using a combination high-throughput sequence analysis together experimentally induced telomeric double-stranded DNA breaks. show that single chromosomal dysfunctional fuse diverse nontelomeric...

Abstract Background Toxoplasma gondii is a zoonotic parasite of global importance. In common with many protozoan parasites it has the capacity for sexual recombination, but current evidence suggests this rarely employed. The population structure dominated by small number clonal genotypes, which exhibit biallelic variation and limited intralineage divergence. Little known genotypes present in Africa despite importance AIDS-associated toxoplasmosis. Results We here extensive sequence analysis...

The Rhynchosporium species complex consists of hemibiotrophic fungal pathogens specialized to different sweet grass including the cereal crops barley and rye. A sexual stage has not been described, but several lines evidence suggest occurrence reproduction. Therefore, a comparative genomics approach was carried out disclose evolutionary relationship identify genes demonstrating potential for cycle. Furthermore, due very young age five currently known, this genus appears be well-suited...

Combined inhibition of phosphatidylinositol 3-kinase (PI3K) and the mammalian target rapamycin (mTOR) complexes may be an efficient treatment for acute leukemia. The primary objective this phase I single center open label study was to determine maximum tolerated dose (MTD) recommended II (RP2D) dual pan-class PI3K mTOR inhibitor BEZ235 in patients with advanced Herein > 18 years age who had relapsed or showed refractory leukemia were treated (orally at 300-400 mg BID (cohort - 1/1)) assess...

Predation by bacteriophages is thought to control bacterial numbers and facilitate gene transfer among bacteria in the biosphere. A thorough understanding of phage population dynamics therefore necessary if their significance natural environments be fully appreciated. Here we describe situ three separate populations predating on species, living surface field-grown sugar beet (Beta vulgaris var. Amethyst), as recorded over a 9-month period. The distributions were different fluctuated...

Background Invasive Non-typhoidal Salmonella (iNTS) are an important cause of bacteraemia in children and HIV-infected adults sub-Saharan Africa. Previous research has shown that iNTS strains exhibit a pattern gene loss resembles host adapted serovars such as Typhi Paratyphi A. enterica serovar Bovismorbificans was common Malawi between 1997 2004. Methodology We sequenced the genomes 14 Malawian four veterinary isolates from UK, to identify genomic variations signs adaptation strains....

Purpose: Duodenal polyposis and cancer are important causes of morbidity mortality in familial adenomatous (FAP) MUTYH-associated (MAP). This study aimed to comprehensively characterize somatic genetic changes FAP MAP duodenal adenomas better understand tumorigenesis these disorders.Experimental Design: Sixty-nine were biopsied during endoscopy 16 10 patients with polyposis. Ten matched blood DNA samples exome sequenced, 42 further underwent targeted sequencing, 47 studied by array...

Fusion of critically short or damaged telomeres is associated with the genomic rearrangements that support malignant transformation. We have demonstrated fundamental contribution DNA ligase 4-dependent classical non-homologous end-joining to long-range inter-chromosomal telomere fusions. In contrast, localized recombinations initiated by sister chromatid fusion are predominantly mediated alternative activity may employ either 3 1. this study, we sought discriminate relative involvement these...

Aberrant activation of the Wnt signalling pathway is required for tumour initiation and survival in majority colorectal cancers. The development inhibitors has been focus multiple drug discovery programs targeting cancer other malignancies associated with aberrant activation. However, progression new clinical entities slow. One challenge lies limited predictive power 2D cell lines because they fail to fully recapitulate intratumoural phenotypic heterogeneity. In particular, relationship...

Eleven strains of Serratia were isolated from different soils and the guts invertebrates characterized by their sensitivity to eight indigenous bacteriophages. They also classified according bacteriocin production sensitivity, BiOLOG plate API 20E strip profiles 16S rRNA sequence information. One strain was thus identified as plymuthica, another fonticola. The remaining shown be closely related proteamaculans subsp. quinovora Grimont et al. 1983 after DNA-DNA cross-hybridization demonstrated...

Aquatic habitats are important potential sites for gene transfer between indigenous bacteria and released genetically engineered microorganisms (GEMs). Legislation governing GEM release, other practical considerations, have resulted in microcosms, of varying complexity, being used to study aquatic environments. This article reviews these with particular emphasis on the more complex designs and, where possible, compares results obtained them situ studies. We conclude that microcosms can give...