Towards the identification of flower-specific genes in Citrus spp.

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Citrus sinensis is a perennial woody species, for which genetic approaches to the study of reproductive development are not readily amenable. Here, the usefulness of the CitEST Expressed Sequence Tag (EST) database is demonstrated as a reliable new resource for identifying novel genes exclusively related to Citrus reproductive biology. We performed the analysis of an EST dataset of the CitEST Project containing 4,330 flower-derived cDNA sequences. Relying on bioinformatics tools, sequences exclusively present in this flower-derived sequence collection were selected and used for the identification of Citrus putative flower-specific genes. Our analysis revealed several Citrus sequences showing significant similarity to conserved genes known to have flower-specific expression and possessing functions related to flower metabolism and/or reproductive development in diverse plant species. Comparison of the Citrus flower- specific sequences with all available plant peptide sequences unraveled 247 unique transcripts not identified elsewhere within the plant kingdom. Additionally, 49 transcripts, for which no biological function could be attributed by means of sequence comparisons, were found to be conserved among plant species. These results allow further gene expression analysis and possibly novel approaches to the understanding of reproductive development in Citrus.303S761768Citrus flower cDNA libraryConselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP

Identifying mega‑environments to enhance the use of superior rice genotypes in Panama

El objetivo de este trabajo fue evaluar tres métodos para identificar mega‑ambientes, para optimizar el uso del potencial genético de los cultivares de arroz, durante el proceso de selección, y para hacer recomendaciones sobre siembras comerciales en Panamá. Los datos experimentales fueron obtenidos de los ensayos de productividad de cultivares precoces realizados entre 2006 y 2008. Para lograr la estratificación de los ambientes y definir los mega‑ambientes, se utilizaron los métodos del genotipo vencedor mediante el modelo AMMI1, el modelo biplot GGE y el de conglomerado por el método de Ward, complementado con el biplot GGE. Los tres métodos utilizados identificaron dos mega‑ambientes, donde los cultivares sobresalientes fueron Fedearroz 473 e Idiap 145-05. Hubo una coincidencia de 100% en el agrupamiento del conglomerado x el biplot GGE, mientras que entre conglomerado x AMMI1 y biplot GGE x AMMI1 fue de 95,2%. El genotipo más estable, en ambos mega-ambientes, fue el cultivar Idiap 145-05, lo que indica capacidad de adaptación amplia y específica. La capacidad adaptativa de los genotipos superiores y no las condiciones agroclimáticas de las localidades evaluadas fue responsable de la definición de los mega‑ambientes.The objective of this work was to evaluate three methods to identify mega-environments, in order to optimize the use of the genetic potential of rice cultivars during the selection process and to make recommendations for commercial plantations in Panama. Experimental data were obtained from the test performance, between 2006 and 2008, for early maturing cultivars. To achieve the stratification of environments and define mega‑environments, the winner genotype method by the AMMI1 model, GGE biplot model and cluster by Ward’s method supplemented by GGE biplot were used. The three methods used identified two mega-environments, where the outstanding cultivars were Fedearroz 473 e Idiap 145-05. There was 100% coincidence in the grouping of the cluster x the GGE biplot, with 95.2% coincidence between the AMMI1 x cluster and GGE biplot x AMMI1. The most stable genotype, in both mega-environments, was the Idiap 145‑05 cultivar, which indicates its broad and specific adaptive capacity. The adaptive capacity of the superior genotypes and not the agroclimatic conditions of the assessed localities was responsible for defining the mega-environments.The objective of this work was to evaluate three methods to identify mega-environments, in order to optimize the use of the genetic potential of rice cultivars during the selection process and to make recommendations for commercial plantations in Panama. Experimental data were obtained from the test performance, between 2006 and 2008, for early maturing cultivars. To achieve the stratification of environments and define mega‑environments, the winner genotype method by the AMMI1 model, GGE biplot model and cluster by Ward’s method supplemented by GGE biplot were used. The three methods used identified two mega-environments, where the outstanding cultivars were Fedearroz 473 e Idiap 145-05. There was 100% coincidence in the grouping of the cluster x the GGE biplot, with 95.2% coincidence between the AMMI1 x cluster and GGE biplot x AMMI1. The most stable genotype, in both mega-environments, was the Idiap 145‑05 cultivar, which indicates its broad and specific adaptive capacity. The adaptive capacity of the superior genotypes and not the agroclimatic conditions of the assessed localities was responsible for defining the mega-environments

The stomach cancer pooling (STOP) project: a global consortium of epidemiological studies of gastric cancer, updated to 2021

The assessment of risk factors in cancer etiology is necessary for defining optimal preventive strategies, as well as for identifying high risk individuals, and it is therefore relevant for medical practice and cancer prevention. The Stomach cancer Pooling (StoP) Project is a consortium of epidemiological studies of gastric cancer (GC), established in year 2012. The StoP Project aims to examine the role of lifestyle, environmental and genetic determinants of GC through pooled analyses of subject-level data. The consortium is the major GC dataset globally, including original data from 35 studies – with case–control study design, including 5 nested case–control within cohort studies – conducted in the Americas, Asia and Europe (Table 1), for a total of about 13,500 cases and 32,000 controls, and it is continuously expanding. To date, the StoP Project contributed a detailed quantification of the risk of GC associated to several factors, including cigarette smoking (relative risk, RR, of 1.32 for heavy vs. never smokers), alcohol drinking (RR=1.48 for heavy vs. never drinkers), socio-economic status (RR=0.60 for high vs. low education), selected dietary factors (RR=1.30 for high vs. low meat intake; RR=0.65 for high vs. low vegetables consumption; RR=0.80 for high vs. low citrus fruit; RR=0.67 for high vs. low polyphenols intake) and occupational exposures (RR=1.70 for miners; RR=1.30 for construction workers; RR=1.33 for agricultural and animal husbandry workers; RR=1.41 for blacksmiths and machine-tool operators). Planned future developments are to analyze the role of rare exposures on GC risk and to examine risk factors in understudied patient subgroups (e.g., young onset GC, gastric cardia cancer, etc.); to integrate additional studies from East Asia; to develop a genome-wide modeling of polygenic risk score in GC; to include survival analyses and to apply machine learning methods in GC risk prediction and prognostication

Sleep Duration and Stress Level in the Risk of Gastric Cancer: A Pooled Analysis of Case-Control Studies in the Stomach Cancer Pooling (StoP) Project

The association between sleep and stress and cancer is underinvestigated. We evaluated these factors in association with gastric cancer (GC). Five case-control studies from the Stomach Cancer Pooling (StoP) Project were included. We calculated the odds ratios (ORs) and the corresponding 95% confidence intervals (CIs) for sleep duration and stress level in association with GC through multiple logistic regression models adjusted for several lifestyle factors. The analysis included 1293 cases and 4439 controls, 215 cardia and 919 noncardia GC, and 353 diffuse and 619 intestinal types. Sleep duration of =9 h was associated with GC (OR =1.57, 95% CI = 1.23-2.00) compared to 8 h. This was confirmed when stratifying by subsite (noncardia OR = 1.59, 95% CI = 1.22-2.08, and cardia OR = 1.63, 95% CI = 0.97-2.72) and histological type (diffuse OR = 1.65, 95% CI = 1.14-2.40 and intestinal OR = 1.24, 95% CI = 0.91-1.67). Stress was associated with GC (OR = 1.33, 95% CI = 1.18-1.50, continuous). This relationship was selectively related to noncardia GC (OR = 1.28, 95% 1.12-1.46, continuous). The risk of diffuse (OR = 1.32, 95% CI = 1.11-1.58) and intestinal type (OR = 1.23, 95% CI = 1.07-1.42) were higher when stress was reported. Results for the association between increasing level of stress and GC were heterogeneous by smoking and socioeconomic status (p for heterogeneity = 0.02 and <0.001, respectively). In conclusion, long sleep duration (=9 h) was associated with GC and its subtype categories. Stress linearly increased the risk of GC and was related to noncardia GC.The authors thank the European Cancer Prevention (ECP) Organization for providing support for the StoP Project meetings.This study was supported by the Fondazione AIRC, Associazione Italianaper la Ricerca sul Cancro, Project no. 21378 (Investigator Grant)

Soil-atmosphere exchange of nitrous oxide, methane and carbon dioxide in a gradient of elevation in the coastal Brazilian Atlantic forest

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Soils of tropical forests are important to the global budgets of greenhouse gases. The Brazilian Atlantic Forest is the second largest tropical moist forest area of South America, after the vast Amazonian domain. This study aimed to investigate the emissions of nitrous oxide (N2O), carbon dioxide (CO2) and methane (CH4) fluxes along an altitudinal transect and the relation between these fluxes and other climatic, edaphic and biological variables (temperature, fine roots, litterfall, and soil moisture). Annual means of N2O flux were 3.9 (+/- 0.4), 1.0 (+/- 0.1), and 0.9 (+/- 0.2) ng N cm(-2) h(-1) at altitudes 100, 400, and 1000 m, respectively. On an annual basis, soils consumed CH4 at all altitudes with annual means of -1.0 (+/- 0.2), -1.8 (+/- 0.3), and -1.6 (+/- 0.1) mg m(-2) d(-1) at 100 m, 400 m and 1000 m, respectively. Estimated mean annual fluxes of CO2 were 3.5, 3.6, and 3.4 mu mol m(-2) s(-1) at altitudes 100, 400 and 1000 m, respectively. N2O fluxes were significantly influenced by soil moisture and temperature. Soil-atmosphere exchange of CH4 responded to changes in soil moisture. Carbon dioxide emissions were strongly influenced by soil temperature. While the temperature gradient observed at our sites is only an imperfect proxy for climatic warming, our results suggest that an increase in air and soil temperatures may result in increases in decomposition rates and gross inorganic nitrogen fluxes that could support consequent increases in soil N2O and CO2 emissions and soil CH4 consumption.83733742Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)FAPESP [2005/57549-8]FAPESP [FAPESP 03/12595-7

ZNF804a Regulates Expression of the Schizophrenia-Associated Genes PRSS16, COMT, PDE4B, and DRD2

ZNF804a was identified by a genome-wide association study (GWAS) in which a single nucleotide polymorphism (SNP rs1344706) in ZNF804a reached genome-wide statistical significance for association with a combined diagnosis of schizophrenia (SZ) and bipolar disorder. Although the molecular function of ZNF804a is unknown, the amino acid sequence is predicted to contain a C2H2-type zinc-finger domain and suggests ZNF804a plays a role in DNA binding and transcription. Here, we confirm that ZNF804a directly contributes to transcriptional control by regulating the expression of several SZ associated genes and directly interacts with chromatin proximal to the promoter regions of PRSS16 and COMT, the two genes we find upregulated by ZNF804a. Using immunochemistry we establish that ZNF804a is localized to the nucleus of rat neural progenitor cells in culture and in vivo. We demonstrate that expression of ZNF804a results in a significant increase in transcript levels of PRSS16 and COMT, relative to GFP transfected controls, and a statistically significant decrease in transcript levels of PDE4B and DRD2. Furthermore, we show using chromatin immunoprecipitation assays (ChIP) that both epitope-tagged and endogenous ZNF804a directly interacts with the promoter regions of PRSS16 and COMT, suggesting a direct upregulation of transcription by ZNF804a on the expression of these genes. These results are the first to confirm that ZNF804a regulates transcription levels of four SZ associated genes, and binds to chromatin proximal to promoters of two SZ genes. These results suggest a model where ZNF804a may modulate a transcriptional network of SZ associated genes

Inhibition of PbGP43 expression may suggest that gp43 is a virulence factor in Paracoccidioides brasiliensis

ABSTARCT: Glycoprotein gp43 is an immunodominant diagnostic antigen for paracoccidioidomycosis caused by Paracoccidioides brasiliensis. It is abundantly secreted in isolates such as Pb339. It is structurally related to beta-1,3-exoglucanases, however inactive. Its function in fungal biology is unknown, but it elicits humoral, innate and protective cellular immune responses; it binds to extracellular matrix-associated proteins. In this study we applied an antisense RNA (aRNA) technology and Agrobacterium tumefaciens-mediated transformation to generate mitotically stable PbGP43 mutants (PbGP43 aRNA) derived from wild type Pb339 to study its role in P. brasiliensis biology and during infection. Control PbEV was transformed with empty vector. Growth curve, cell vitality and morphology of PbGP43 aRNA mutants were indistinguishable from those of controls. PbGP43 expression was reduced 80-85% in mutants 1 and 2, as determined by real time PCR, correlating with a massive decrease in gp43 expression. This was shown by immunoblotting of culture supernatants revealed with anti-gp43 mouse monoclonal and rabbit polyclonal antibodies, and also by affinity-ligand assays of extracellular molecules with laminin and fibronectin. In vitro, there was significantly increased TNF-α production and reduced yeast recovery when PbGP43 aRNA1 was exposed to IFN-γ-stimulated macrophages, suggesting reduced binding/uptake and/or increased killing. In vivo, fungal burden in lungs of BALB/c mice infected with silenced mutant was negligible and associated with decreased lung ΙΛ-10 and IL-6. Therefore, our results correlated low gp43 expression with lower pathogenicity in mice, but that will be definitely proven when PbGP43 knockouts become available.