Rapid Development of Intestinal Type Gastric Adenocarcinoma

Intestinal type gastric adenocarcinoma is felt to develop over a protracted time period through a series of defined steps. Several potential risk factors for the development of gastric cancer have been identified, including a family history of gastric cancer and Helicobacter pylori infection. We present the case of a patient with neither risk factor who progressed in a 14 month time frame from histologically normal gastric mucosa to early stage intestinal type gastric adenocarcinoma in the setting of diffuse gastric intestinal metaplasia and atrophic gastritis. This patient's presentation conflicts with our current understanding of the development of intestinal type gastric adenocarcinoma

Fire and climate: contrasting pressures on tropical Andean timberline species

Department of Biological Sciences; Florida Institute of Technology; Melbourne FL USA Department of Biological Sciences; Florida Institute of Technology; Melbourne FL USA Department of Biological Sciences; Florida Institute of Technology; Melbourne FL USA Geography, College of Life & Environmental Sciences; University of Exeter; Exeter UK Department of Biological Sciences; Florida Institute of Technology; Melbourne FL USA CEPSAR; The Open University; Milton Keynes UK Instituto de Geología; Universidad Nacional Autónoma de México; Ciudad Universitaria; Mexico City Mexico Department of Forest and Soil Sciences; University of Natural Resources and Life Sciences Vienna; Vienna Austria Department of Biology and Center for Energy; Environment and Sustainability; Wake Forest University; Winston Salem NC USACopyright © 2015 John Wiley & Sons Ltd.Aim: The aim was to test competing hypotheses regarding migration of the Andean timberline within the last 2000 years. Location: The upper forest limit in Manu National Park, Peru. Methods: A randomized stratified design provided 21 soil profiles from forested sites just below the timberline, 15 from puna grassland sites just above the timberline and 15 from the transitional habitat at the puna–forest boundary. From each profile a surface sample (hereafter modern) and a sample from the base of the organic horizon (hereafter historical) were collected. Pollen and charcoal were analysed from the modern and historical layers of the 51 soil profiles. A chronological framework was provided by 24 14C dates. Data were ordinated as modern and historical groups and the temporal trends illustrated by Procrustes rotation. Results: The organic layer from the soil profiles represented the last 600–2000 years. Fire was much more abundant in all habitat types (puna, transitional and forested) in the modern compared with the historical groups. Samples that had historically been in puna just above the timberline showed encroachment by woody species. Samples that had been forested were still classified as forest but their composition had become more transitional. Sites that were transitional appeared to represent a new or expanded class of sites that was far less abundant historically. Main conclusions: Our results are consistent with ongoing warming causing an upslope migration of species, although not necessarily of the timberline. Weedy fire-tolerant species are spreading upslope, creating a transitional forest, softening the boundary between forest and puna. Simultaneously, fire introduced to improve grazing outside the park has increasingly penetrated the forest and is causing the upper timberline to shift towards more fire-tolerant and weedy species. Consequently, both the form of the ecotone between forest and grassland and the species composition of these forests is changing and is expected to continue to change, representing a shifting baseline for what is considered to be natural.Gordon and Betty Moore Foundation Andes-to-Amazon programmeBlue Moon FundNational Science Foundatio

Interethnic diversity of NAT2 polymorphisms in Brazilian admixed populations

<p>Abstract</p> <p>Background</p> <p>N-acetyltransferase type 2 (Nat2) is a phase II drug- metabolizing enzyme that plays a key role in the bioactivation of aromatic and heterocyclic amines. Its relevance in drug metabolism and disease susceptibility remains a central theme for pharmacogenetic research, mainly because of its genetic variability among human populations. In fact, the evolutionary and ethnic-specific SNPs on the <it>NAT2 </it>gene remain a focus for the potential discoveries in personalized drug therapy and genetic markers of diseases. Despite the wide characterization of <it>NAT2 </it>SNPs frequency in established ethnic groups, little data are available for highly admixed populations. In this context, five common <it>NAT2 </it>SNPs (<it>G191A</it>, <it>C481T</it>, <it>G590A</it>, <it>A803G </it>and G<it>857A</it>) were investigated in a highly admixed population comprised of Afro-Brazilians, Whites, and Amerindians in northeastern Brazil. Thus, we sought to determine whether the distribution of <it>NAT2 </it>polymorphism is different among these three ethnic groups.</p> <p>Results</p> <p>Overall, there were no statistically significant differences in the distribution of <it>NAT2 </it>polymorphism when Afro-Brazilian and White groups were compared. Even the allele frequency of <it>191A</it>, relatively common in African descendents, was not different between the Afro-Brazilian and White groups. However, allele and genotype frequencies of <it>G590A </it>were significantly higher in the Amerindian group than either in the Afro-Brazilian or White groups. Interestingly, a haplotype block between <it>G590A </it>and <it>A803G </it>was verified exclusively among Amerindians.</p> <p>Conclusions</p> <p>Our results indicate that ethnic admixture might contribute to a particular pattern of genetic diversity in the <it>NAT2 </it>gene and also offer new insights for the investigation of possible new <it>NAT2 </it>gene-environment effects in admixed populations.</p

Transcriptome profiling of grapevine seedless segregants during berry development reveals candidate genes associated with berry weight

Indexación: Web of Science; PubMedBackground Berry size is considered as one of the main selection criteria in table grape breeding programs. However, this is a quantitative and polygenic trait, and its genetic determination is still poorly understood. Considering its economic importance, it is relevant to determine its genetic architecture and elucidate the mechanisms involved in its expression. To approach this issue, an RNA-Seq experiment based on Illumina platform was performed (14 libraries), including seedless segregants with contrasting phenotypes for berry weight at fruit setting (FST) and 6–8 mm berries (B68) phenological stages. Results A group of 526 differentially expressed (DE) genes were identified, by comparing seedless segregants with contrasting phenotypes for berry weight: 101 genes from the FST stage and 463 from the B68 stage. Also, we integrated differential expression, principal components analysis (PCA), correlations and network co-expression analyses to characterize the transcriptome profiling observed in segregants with contrasting phenotypes for berry weight. After this, 68 DE genes were selected as candidate genes, and seven candidate genes were validated by real time-PCR, confirming their expression profiles. Conclusions We have carried out the first transcriptome analysis focused on table grape seedless segregants with contrasting phenotypes for berry weight. Our findings contributed to the understanding of the mechanisms involved in berry weight determination. Also, this comparative transcriptome profiling revealed candidate genes for berry weight which could be evaluated as selection tools in table grape breeding programs.http://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-016-0789-

Characterizing genomic alterations in cancer by complementary functional associations.

Systematic efforts to sequence the cancer genome have identified large numbers of mutations and copy number alterations in human cancers. However, elucidating the functional consequences of these variants, and their interactions to drive or maintain oncogenic states, remains a challenge in cancer research. We developed REVEALER, a computational method that identifies combinations of mutually exclusive genomic alterations correlated with functional phenotypes, such as the activation or gene dependency of oncogenic pathways or sensitivity to a drug treatment. We used REVEALER to uncover complementary genomic alterations associated with the transcriptional activation of β-catenin and NRF2, MEK-inhibitor sensitivity, and KRAS dependency. REVEALER successfully identified both known and new associations, demonstrating the power of combining functional profiles with extensive characterization of genomic alterations in cancer genomes

Association between Selected Oral Pathogens and Gastric Precancerous Lesions

We examined whether colonization of selected oral pathogens is associated with gastric precancerous lesions in a cross-sectional study. A total of 119 participants were included, of which 37 were cases of chronic atrophic gastritis, intestinal metaplasia, or dysplasia. An oral examination was performed to measure periodontal indices. Plaque and saliva samples were tested with real-time quantitative PCR for DNA levels of pathogens related to periodontal disease (Porphyromonas gingivalis, Tannerella forsythensis, Treponema denticola, Actinobacillus actinomycetemcomitans) and dental caries (Streptococcus mutans and S. sobrinus). There were no consistent associations between DNA levels of selected bacterial species and gastric precancerous lesions, although an elevated but non-significant odds ratio (OR) for gastric precancerous lesions was observed in relation to increasing colonization of A. actinomycetemcomitans (OR = 1.36 for one standard deviation increase, 95% Confidence Interval = 0.87–2.12), P. gingivalis (OR = 1.12, 0.67–1.88) and T. denticola (OR = 1.34, 0.83–2.12) measured in plaque. To assess the influence of specific long-term infection, stratified analyses by levels of periodontal indices were conducted. A. actinomycetemcomitans was significantly associated with gastric precancerous lesions (OR = 2.51, 1.13–5.56) among those with ≥ median of percent tooth sites with PD≥3 mm, compared with no association among those below the median (OR = 0.86, 0.43–1.72). A significantly stronger relationship was observed between the cumulative bacterial burden score of periodontal disease-related pathogens and gastric precancerous lesions among those with higher versus lower levels of periodontal disease indices (p-values for interactions: 0.03–0.06). Among individuals with periodontal disease, high levels of colonization of periodontal pathogens are associated with an increased risk of gastric precancerous lesions

A genetic algorithm-Bayesian network approach for the analysis of metabolomics and spectroscopic data: application to the rapid detection of Bacillus spores and identification of Bacillus species

Background The rapid identification of Bacillus spores and bacterial identification are paramount because of their implications in food poisoning, pathogenesis and their use as potential biowarfare agents. Many automated analytical techniques such as Curie-point pyrolysis mass spectrometry (Py-MS) have been used to identify bacterial spores giving use to large amounts of analytical data. This high number of features makes interpretation of the data extremely difficult We analysed Py-MS data from 36 different strains of aerobic endospore-forming bacteria encompassing seven different species. These bacteria were grown axenically on nutrient agar and vegetative biomass and spores were analyzed by Curie-point Py-MS. Results We develop a novel genetic algorithm-Bayesian network algorithm that accurately identifies sand selects a small subset of key relevant mass spectra (biomarkers) to be further analysed. Once identified, this subset of relevant biomarkers was then used to identify Bacillus spores successfully and to identify Bacillus species via a Bayesian network model specifically built for this reduced set of features. Conclusions This final compact Bayesian network classification model is parsimonious, computationally fast to run and its graphical visualization allows easy interpretation of the probabilistic relationships among selected biomarkers. In addition, we compare the features selected by the genetic algorithm-Bayesian network approach with the features selected by partial least squares-discriminant analysis (PLS-DA). The classification accuracy results show that the set of features selected by the GA-BN is far superior to PLS-DA

Performance of CMS muon reconstruction in pp collision events at sqrt(s) = 7 TeV

The performance of muon reconstruction, identification, and triggering in CMS has been studied using 40 inverse picobarns of data collected in pp collisions at sqrt(s) = 7 TeV at the LHC in 2010. A few benchmark sets of selection criteria covering a wide range of physics analysis needs have been examined. For all considered selections, the efficiency to reconstruct and identify a muon with a transverse momentum pT larger than a few GeV is above 95% over the whole region of pseudorapidity covered by the CMS muon system, abs(eta) < 2.4, while the probability to misidentify a hadron as a muon is well below 1%. The efficiency to trigger on single muons with pT above a few GeV is higher than 90% over the full eta range, and typically substantially better. The overall momentum scale is measured to a precision of 0.2% with muons from Z decays. The transverse momentum resolution varies from 1% to 6% depending on pseudorapidity for muons with pT below 100 GeV and, using cosmic rays, it is shown to be better than 10% in the central region up to pT = 1 TeV. Observed distributions of all quantities are well reproduced by the Monte Carlo simulation.Comment: Replaced with published version. Added journal reference and DO