Proteome analysis of human gastric cardia adenocarcinoma by laser capture microdissection

<p>Abstract</p> <p>Background</p> <p>The incidence of gastric cardiac adenocarcinoma (GCA) has been increasing in the past two decades in China, but the molecular changes relating to carcinogenesis have not been well characterised.</p> <p>Methods</p> <p>In this study, we used a comparative proteomic approach to analyse the malignant and nonmalignant gastric cardia epithelial cells isolated by navigated laser capture microdissection (LCM) from paired surgical specimens of human GCA.</p> <p>Results</p> <p>Twenty-seven spots corresponding to 23 proteins were consistently differentially regulated. Fifteen proteins were shown to be up-regulated, while eight proteins were shown to be down-regulated in malignant cells compared with nonmalignant columnar epithelial cells. The identified proteins appeared to be involved in metabolism, chaperone, antioxidation, signal transduction, apoptosis, cell proliferation, and differentiation. In addition, expressions of HSP27, 60, and Prx-2 in GCA specimens were further confirmed by immunohistochemical and western blot analyses.</p> <p>Conclusion</p> <p>These data indicate that the combination of navigated LCM with 2-DE provides an effective strategy for discovering proteins that are differentially expressed in GCA. Such proteins may contribute in elucidating the molecular mechanisms of GCA carcinogenesis. Furthermore, the combination provides potential clinical biomarkers that aid in early detection and provide potential therapeutic targets.</p

A Framework For Detecting Noncoding Rare-Variant associations of Large-Scale Whole-Genome Sequencing Studies

Large-scale whole-genome sequencing studies have enabled analysis of noncoding rare-variant (RV) associations with complex human diseases and traits. Variant-set analysis is a powerful approach to study RV association. However, existing methods have limited ability in analyzing the noncoding genome. We propose a computationally efficient and robust noncoding RV association detection framework, STAARpipeline, to automatically annotate a whole-genome sequencing study and perform flexible noncoding RV association analysis, including gene-centric analysis and fixed window-based and dynamic window-based non-gene-centric analysis by incorporating variant functional annotations. In gene-centric analysis, STAARpipeline uses STAAR to group noncoding variants based on functional categories of genes and incorporate multiple functional annotations. In non-gene-centric analysis, STAARpipeline uses SCANG-STAAR to incorporate dynamic window sizes and multiple functional annotations. We apply STAARpipeline to identify noncoding RV sets associated with four lipid traits in 21,015 discovery samples from the Trans-Omics for Precision Medicine (TOPMed) program and replicate several of them in an additional 9,123 toPMed samples. We also analyze five non-lipid toPMed traits

Correlation between Transit-Oriented Development (TOD), Land Use Catchment Areas, and Local Environmental Transformation

Transit-oriented development (TOD) has been recognised as a sustainable planning approach and that is typically designed for a whole city. Individual land use characteristics and the causations have often been ignored. Therefore, the primary objective of this study was to explore the factors that influence the land use catchment area (LCA) characteristics at a station neighborhood level. First, it contributes a methodology to measure the LCA by introducing a new concept. The density gradient was introduced to generate the scale and compactness degree of each station. Second, it provides a theoretical framework for understanding the causes of different LCAs. The partial least squares (PLS) regression model was employed to explore the accessibility effects. By analysing density gradient curves, it reveals that stations grew to fit the negative exponential function. Regarding the scale and form degree of LCAs, the impact of accessibility before and after a station construction have been corroborated. Moreover, the effects of facilities function before construction, distance from main roads, and elevated stations have been emphasized. The results provide support for a more sophisticated concept of catchment area relating to land use at the level of an individual TOD station, while shedding light on the benefits of those engaged in the future design of TOD with due consideration of the local physical environments

Diversification rate shifts in the Cape Floristic Region: The right traits in the right place at the right time

Species diversity patterns are the product of diversification rate variation, but the factors influencing changes in diversification rates are poorly known. Radiation is thought to be the result of ecological opportunity: the right traits in the right environment at the right time. We test this in the Cape Floristic Region (CFR) of South Africa, in which pyrophytic heathland (fynbos) and non-pyrophytic Afromontane forest occur interdigitated. We infer transitions from forest to fynbos in three Cape clades (Penaeaceae, Phyliceae and Diosmeae) and test if they are associated with diversification rate shifts and the evolution of functional traits linked to fire, high insolation and seasonal drought. We estimate diversification rate shifts using maximum likelihood and use phylogenetic comparative methods to show that forest to fynbos shifts were associated with decreases in leaf area and specific leaf area and preceded or coincided with increases in diversification rates. Furthermore, we show that Penaeaceae, Phyliceae and Diosmeae species are typical members of their vegetation types in terms of their traits. The diversification rate shifts of Penaeaceae and Phyliceae are dated to the Miocene, when postulated aridification-driven changes in the CFR fire regimes may have triggered expansion of the fynbos at the cost of forest, providing an ecological opportunity for the diversification of fynbos lineages

Data from: On the complexity of triggering evolutionary radiations

Recent developments in phylogenetic methods have made it possible to reconstruct evolutionary radiations from extant taxa, but identifying the triggers of radiations is still problematic. Here, we propose a conceptual framework to explore the role of variables that may impact radiations. We classify the variables into extrinsic conditions vs intrinsic traits, whether they provide background conditions, trigger the radiation, or modulate the radiation. We used three clades representing angiosperm phylogenetic and structural diversity (Ericaceae, Fagales and Poales) as test groups. We located radiation events, selected variables potentially associated with diversification, and inferred the temporal sequences of evolution. We found 13 shifts in diversification regimes in the three clades. We classified the associated variables, and determined whether they originated before the relevant radiation (backgrounds), originated simultaneously with the radiations (triggers), or evolved later (modulators). By applying this conceptual framework, we establish that radiations require both extrinsic conditions and intrinsic traits, but that the sequence of these is not important. We also show that diversification drivers can be detected by being more variable within a radiation than conserved traits that only allow occupation of a new habitat. This framework facilitates exploration of the causative factors of evolutionary radiations

Fagales_fossil

Fagales fossils used in the analysi

White Mountain Apache texts

PM631.Z77, ISO 639-3 : apl, White Mountain Apache dialect--Texts, Apache language

Data from: Fossils and a large molecular phylogeny show that the evolution of species richness, generic diversity and turnover rates are disconnected

The magnitude and extent of global change during the Cenozoic are remarkable, yet the impacts of these changes on biodiversity and the evolutionary dynamics of species diversification remain poorly understood. To investigate this question we combine palaeontological and neontological data for the angiosperm order Fagales, an ecologically important clade of c. 1370 species of trees with an exceptional fossil record. We show differences in patterns of accumulation of generic diversity, species richness, and turnover rates for Fagales. Generic diversity evolved rapidly from the Late Cretaceous and peaked in the Eocene or Oligocene. Turnover rates were high during periods of extreme global climate change, but relatively low when the climate remained stable. Species richness accumulated gradually throughout the Cenozoic, possibly at an accelerated pace after the Middle Miocene. Species diversification was into new environments: Quercoids radiating in Oligocene subtropical seasonally arid habitats, Casuarinaceae in Australian pyrophytic biomes, and Betula into late Neogene holarctic habitats. These radiations were counterbalanced by regional extinctions in late-Neogene mesic warm-temperate forests. Thus overall diversification at species level is linked to regional radiations of clades with appropriate ecologies exploiting newly available habitats

Fossils and a large molecular phylogeny show that the evolution of species richness, generic diversity, and turnover rates are disconnected

v.75(2015