NCBI GEO: archive for gene expression and epigenomics data sets: 23-year update.

The Gene Expression Omnibus (GEO) is an international public repository that archives gene expression and epigenomics data sets generated by next-generation sequencing and microarray technologies. Data are typically submitted to GEO by researchers in compliance with widespread journal and funder mandates to make generated data publicly accessible. The resource handles raw data files, processed data files and descriptive metadata for over 200 000 studies and 6.5 million samples, all of which are indexed, searchable and downloadable. Additionally, GEO offers web-based tools that facilitate analysis and visualization of differential gene expression. This article presents the current status and recent advancements in GEO, including the generation of consistently computed gene expression count matrices for thousands of RNA-seq studies, and new interactive graphical plots in GEO2R that help users identify differentially expressed genes and assess data set quality. The GEO repository is built and maintained by the National Center for Biotechnology Information (NCBI), a division of the National Library of Medicine (NLM), and is publicly accessible at https://www.ncbi.nlm.nih.gov/geo/.

Efeito do treino com restrição de fluxo sanguíneo versus treino resistido de alta intensidade sobre a força de indivíduos sedentários: um ensaio clínico controlado e randomizado / Blood flow restriction training versus high-intensity resistance training in sedentary individuals: a randomized controlled trial

Objetivos: comparar os efeitos do treino com restrição de flux o sanguíneo com o treino resistido de alta intensidade no ganho de força e hipertrofia. Material e métodos: n este ensaio clínico randomizado e controlado, 24 homens sedentários foram randomizados em do is grupo s: treino com restrição de fluxo sanguíneo ou treino resistido de alta intensidade. Ambos os grupos realizaram 10 sessões de exercício de preensão manual até com 3 séries de exercícios até a falha, sendo que o grupo com treino de restrição de fluxo sanguíneo realizou com 30% da carga máxima obtida no teste de 1 repetição máxima, enquanto que o grupo de alta intensidade realizou com 80% da carga. T odo s o s voluntários foram avaliados e reavaliados a dinamometriade preensão manual e a perimetria de antebraço. Os dados foram tabulados e analisados no statistical package for the social sciences, utilizando o teste t-student, e o não paramétrico u de mann whitney, adotando a significância de 5% (α = 0,05). Resultados: para o desfecho força, identificou-se que tanto o grupo que treino com restrição do fluxo, quanto o grupo que treinou com alta intensidade tiveram aumentos significativos (p= 0,005 e 0,026, respectivamente). Já em relação ao aumento da circunferência, notou-se que somente o treino de restrição do flux o se mostrou estatisticamente quando comparado o aumento entre os grupos (p= 0,00 1). Conclusão: foi possível concluir que o treinamento com restrição do fluxo sanguíneo mostrou eficaz tanto para o ganho de força, quanto para o aumento de circunferência, apresentando vantagens quando comparado ao grupo de treinamento resistido com alta intensidade...(AU)

Objectives: to compare the effects of blood flow restriction trainin g wit h h igh in tensity resistance training on strength gain and hypertrophy. Material and methods: in this randomized controlled trial, 24 sedentary men were randomized into two groups: restricted blood flow training or high inten sity resistance training. Both groups performed 10 handgrip exercise sessions up to 3 sets of exercises un t il failure, and the group with blood flow restriction training performed with 3 0 % o f t he m ax imum lo ad obtained in the 1-repetition maximum test, while the high intensity group performed with 80% of the load. All volunteers were assessed and reassessed by handgrip dynamometry and forearm perimetry. Data were tabulated and analyzed in the statistical package for the social sciences, using the t-studen t test an d t he non-parametric mann whitney u test, adopting the significance of 5% (α = 0.05). Results: for the stren gth outcome, it was found that both the flow restriction training group and the high intensity train in g gro up had significant increases (p = 0.005 and 0.026, respectively). Regarding the increase in circumference, it was noted that only the flow restriction training was statistically when compared to the increase bet ween the groups (p = 0.001). Conclusion: it was concluded that training with blood flow restriction was effective for both strength gain and circumference increase, presenting advantages when compared to the high intensity resistance training group...(AU)

Dissatisfaction with body image and associated factors in adult women / Insatisfação com a imagem corporal e fatores associados em mulheres adultas

ABSTRACT Objective To associate body image with sociodemographic profile, lifestyle, anthropometry and health conditions in adult women. Methods Prevalence study, conducted in a probabilistic cluster sample (n=35 Primary Education Schools) conducted in 2016 with 633 teachers. Sociodemographic characteristics were evaluated; morbidities, anthropometric variables; subjective health issues; lifestyle and self-reported morbidities. Results The prevalence of body image dissatisfaction was 48.7%. There was a greater chance of dissatisfaction among older women who have children, unsatisfactory lifestyle, are overweight, with poor health/poor self-perception of health, and the presence of depressive symptoms. Women who had a poor lifestyle had a four-fold greater chance of dissatisfaction with body appearance (Odds Ratio=4.193) than women who had a satisfactory lifestyle. Conclusion The results revealed that almost half of the adult women surveyed in this study reported dissatisfaction with their body image. This outcome indicates the need for interventions and program implementation related to body image dissatisfaction among women.

RESUMO Objetivo Esta pesquisa buscou associar imagem corporal com perfil sociodemográfico, estilo de vida, antropometria e condições de saúde em mulheres adultas. Métodos Um estudo de prevalência foi conduzido em uma amostra probabilística por conglomerados (n=35 Escolas da Educação Básica de Ensino), no ano de 2016, com 633 professoras. Foram avaliadas características sociodemográficas, morbidades, variáveis antropométricas, questões subjetivas em saúde, estilo de vida e morbidades autorreferidas. Resultados A prevalência de insatisfação com a imagem corporal foi de 48,7%. Houve maior chance de insatisfação entre as mulheres com maior idade, filhos, estilo de vida insatisfatório, acima do peso, autopercepção ruim/péssima de sua saúde e presença de sintomas depressivos. Mulheres que apresentaram estilo de vida insatisfatório tiveram probabilidade quatro vezes maior de insatisfação com a aparência corporal (Odds Ratio=4,193) do que as com estilo de vida satisfatório. Conclusão Os resultados revelaram que quase metade das mulheres adultas pesquisadas neste estudo relatou ter insatisfação com a imagem corporal. Esses resultados indicam a necessidade de intervenções e de implementação de programas relacionados à insatisfação com a imagem corporal entre as mulheres.

H+ and Pi Byproducts of Glycosylation Affect Ca2+ Homeostasis and Are Retrieved from the Golgi Complex by Homologs of TMEM165 and XPR1.

Glycosylation reactions in the Golgi complex and the endoplasmic reticulum utilize nucleotide sugars as donors and produce inorganic phosphate (Pi) and acid (H+) as byproducts. Here we show that homologs of mammalian XPR1 and TMEM165 (termed Erd1 and Gdt1) recycle luminal Pi and exchange luminal H+ for cytoplasmic Ca2+, respectively, thereby promoting growth of yeast cells in low Pi and low Ca2+ environments. As expected for reversible H+/Ca2+ exchangers, Gdt1 also promoted growth in high Ca2+ environments when the Golgi-localized V-ATPase was operational but had the opposite effect when the V-ATPase was eliminated. Gdt1 activities were negatively regulated by calcineurin signaling and by Erd1, which recycled the Pi byproduct of glycosylation reactions and prevented the loss of this nutrient to the environment via exocytosis. Thus, Erd1 transports Pi in the opposite direction from XPR1 and other EXS family proteins and facilitates byproduct removal from the Golgi complex together with Gdt1.

NCBI GEO: archive for functional genomics data sets--update.

The Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) is an international public repository for high-throughput microarray and next-generation sequence functional genomic data sets submitted by the research community. The resource supports archiving of raw data, processed data and metadata which are indexed, cross-linked and searchable. All data are freely available for download in a variety of formats. GEO also provides several web-based tools and strategies to assist users to query, analyse and visualize data. This article reports current status and recent database developments, including the release of GEO2R, an R-based web application that helps users analyse GEO data.

New regulators of a high affinity Ca2+ influx system revealed through a genome-wide screen in yeast.

The bakers' yeast Saccharomyces cerevisiae utilizes a high affinity Ca(2+) influx system (HACS) to survive assaults by mating pheromones, tunicamycin, and azole-class antifungal agents. HACS consists of two known subunits, Cch1 and Mid1, that are homologous and analogous to the catalytic α-subunits and regulatory α2δ-subunits of mammalian voltage-gated calcium channels, respectively. To search for additional subunits and regulators of HACS, a collection of gene knock-out mutants was screened for abnormal uptake of Ca(2+) after exposure to mating pheromone or to tunicamycin. The screen revealed that Ecm7 is required for HACS function in most conditions. Cycloheximide chase experiments showed that Ecm7 was stabilized by Mid1, and Mid1 was stabilized by Cch1 in non-signaling conditions, suggesting they all interact. Ecm7 is a member of the PMP-22/EMP/MP20/Claudin superfamily of transmembrane proteins that includes γ-subunits of voltage-gated calcium channels. Eleven additional members of this superfamily were identified in yeast, but none was required for HACS activity in response to the stimuli. Remarkably, many dozens of genes involved in vesicle-mediated trafficking and protein secretion were required to prevent spontaneous activation of HACS. Taken together, the findings suggest that HACS and calcineurin monitor performance of the membrane trafficking system in yeasts and coordinate compensatory processes. Conservation of this quality control system in Candida glabrata suggests that many pathogenic species of fungi may utilize HACS and calcineurin to resist azoles and other compounds that target membrane biosynthesis.

NCBI GEO: archive for functional genomics data sets--10 years on.

A decade ago, the Gene Expression Omnibus (GEO) database was established at the National Center for Biotechnology Information (NCBI). The original objective of GEO was to serve as a public repository for high-throughput gene expression data generated mostly by microarray technology. However, the research community quickly applied microarrays to non-gene-expression studies, including examination of genome copy number variation and genome-wide profiling of DNA-binding proteins. Because the GEO database was designed with a flexible structure, it was possible to quickly adapt the repository to store these data types. More recently, as the microarray community switches to next-generation sequencing technologies, GEO has again adapted to host these data sets. Today, GEO stores over 20,000 microarray- and sequence-based functional genomics studies, and continues to handle the majority of direct high-throughput data submissions from the research community. Multiple mechanisms are provided to help users effectively search, browse, download and visualize the data at the level of individual genes or entire studies. This paper describes recent database enhancements, including new search and data representation tools, as well as a brief review of how the community uses GEO data. GEO is freely accessible at http://www.ncbi.nlm.nih.gov/geo/.

NCBI GEO: archive for high-throughput functional genomic data.

The Gene Expression Omnibus (GEO) at the National Center for Biotechnology Information (NCBI) is the largest public repository for high-throughput gene expression data. Additionally, GEO hosts other categories of high-throughput functional genomic data, including those that examine genome copy number variations, chromatin structure, methylation status and transcription factor binding. These data are generated by the research community using high-throughput technologies like microarrays and, more recently, next-generation sequencing. The database has a flexible infrastructure that can capture fully annotated raw and processed data, enabling compliance with major community-derived scientific reporting standards such as 'Minimum Information About a Microarray Experiment' (MIAME). In addition to serving as a centralized data storage hub, GEO offers many tools and features that allow users to effectively explore, analyze and download expression data from both gene-centric and experiment-centric perspectives. This article summarizes the GEO repository structure, content and operating procedures, as well as recently introduced data mining features. GEO is freely accessible at http://www.ncbi.nlm.nih.gov/geo/.

NCBI GEO: mining tens of millions of expression profiles--database and tools update.

The Gene Expression Omnibus (GEO) repository at the National Center for Biotechnology Information (NCBI) archives and freely disseminates microarray and other forms of high-throughput data generated by the scientific community. The database has a minimum information about a microarray experiment (MIAME)-compliant infrastructure that captures fully annotated raw and processed data. Several data deposit options and formats are supported, including web forms, spreadsheets, XML and Simple Omnibus Format in Text (SOFT). In addition to data storage, a collection of user-friendly web-based interfaces and applications are available to help users effectively explore, visualize and download the thousands of experiments and tens of millions of gene expression patterns stored in GEO. This paper provides a summary of the GEO database structure and user facilities, and describes recent enhancements to database design, performance, submission format options, data query and retrieval utilities. GEO is accessible at http://www.ncbi.nlm.nih.gov/geo/

One-hybrid screens at the Saccharomyces cerevisiae HMR locus identify novel transcriptional silencing factors.

In Saccharomyces cerevisiae, genes located at the telomeres and the HM loci are subject to transcriptional silencing. Here, we report results of screening a Gal4 DNA-binding domain hybrid library for proteins that cause silencing when targeted to a silencer-defective HMR locus.

A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome.

The high degree of similarity between the mouse and human genomes is demonstrated through analysis of the sequence of mouse chromosome 16 (Mmu 16), which was obtained as part of a whole-genome shotgun assembly of the mouse genome. The mouse genome is about 10% smaller than the human genome, owing to a lower repetitive DNA content. Comparison of the structure and protein-coding potential of Mmu 16 with that of the homologous segments of the human genome identifies regions of conserved synteny with human chromosomes (Hsa) 3, 8, 12, 16, 21, and 22. Gene content and order are highly conserved between Mmu 16 and the syntenic blocks of the human genome. Of the 731 predicted genes on Mmu 16, 509 align with orthologs on the corresponding portions of the human genome, 44 are likely paralogous to these genes, and 164 genes have homologs elsewhere in the human genome; there are 14 genes for which we could find no human counterpart.