Ontology highlight
ABSTRACT:
PROVIDER: PRJNA886312 | ENA |
REPOSITORIES: ENA
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Project description:RNA from stem containing first node and internodes during dough stage was considered for the above purpose. Satabdi, (popularly known as Minikit) most popular cultivar of West Bengal and Palman, another high yielding variety were considered for microarray analysis for comparison to each other. Two rice genotypes were grown in identical conditions (same field with contaminated ground water) to obtain the most meaningful conclusion. Dough stage was considered as variation in arsenic accumulation among the genotypes starts during dough stage to maturity. Plant tissues were collected from stem for transcriptomic analysis as expression profiling of such tissue in response to arsenic would be most useful as arsenic transport/loading in grain was assumed to be controlled by arsenic translocation behavior at inter vascular level or from xylem to phloem. Satabdi accumulates more than twice of arsenic in brown rice (0.346 mg/kg) than that of Palman (0.156 mg/kg) whereas accumulation in straw (2.07 mg/kg) was approximately less than half of the Palman (4.491 mg/kg)
2014-01-17 | E-MTAB-2106 | biostudies-arrayexpress
Project description:Zika virus (ZIKV) is a mosquito-transmitted positive-sense RNA virus in the family Flaviviridae. ZIKV infections are associated with neurodevelopmental deficiencies termed Congenital Zika Syndrome. ZIKV strains are grouped into three phylogenetic lineages: East African, West African, and Asian, which contains the American lineage. RNA virus genomes exist as genetically-related sequences. The heterogeneity of these viral populations is implicated in viral fitness, and genome diversity is correlated to virulence. This study examines genetic diversity of representative ZIKV strains from all lineages utilizing next generation sequencing (NGS). Inter-lineage diversity results indicate that ZIKV lineages differ broadly from each other; however, intra-lineage comparisons of American ZIKV strains isolated from human serum or placenta show differences in diversity when compared to ZIKVs from Asia and West Africa. This study describes the first comprehensive NGS analysis of all ZIKV lineages and posits that sub-consensus-level diversity may provide a framework for understanding ZIKV fitness during infection.
2018-12-31 | E-MTAB-5945 | biostudies-arrayexpress
Project description:Chronic exposure to arsenic is associated with dermatological and non-dermatological disorders. Consumption of arsenic contaminated drinking water results in accumulation of arsenic in liver, spleen, kidneys, lungs and gastrointestinal tract. Although, arsenic is cleared from these sites, a substantial amount of residual arsenic is left in keratin-rich tissues such as skin. Epidemiological studies on arsenic suggest the association of skin cancer upon arsenic exposure, however, the exact mechanism of arsenic induced carcinogenesis is not completely understood. We have developed a cell line-based model to understand the molecular mechanisms involved in arsenic mediated toxicity and carcinogenicity. Human skin keratinocyte cell line, HaCaT was exposed to 100nM sodium arsenite for six months. We observed an increase in the basal ROS levels in arsenic exposed cells along with the increase in anti-apoptotic proteins. SILAC-based quantitative proteomics approach resulted in the identification and quantitation of 2,181 proteins of which 39 proteins were found to be overexpressed (≥2-fold) and 56 downregulated (≤2-fold) upon chronic arsenic exposure. Our study provides comprehensive insights into the molecular basis of chronic arsenic exposure on skin.
2017-01-02 | PXD001645 | Pride
Project description:We performed label-free proteomics in C. elegans to define and quantify changes in the ubiquitinated (Ub)-proteome during the aging process. More specifically, we compared wild-type worms at the first day of adulthood with young (day 5), mid-age (day 10) and aged adults (day 15). Moreover, we assessed protein levels of age-matched long-lived genetic models of dietary restriction (eat-2(ad1116)) and reduced insulin/IGF-1 signaling (daf-2(e1370)).
2021-05-26 | PXD025128 | Pride
Project description:We describe the alterations in DNA methylation around the promoter region and the impact on gene expression in HaCaT cells during the transformation process caused by chronic exposure to arsenic. Nucleic acids were extracted at the beginning of treatment and at weeks 0, 5, 15, and 25. Cell cultures with the same passage (week 25) and no arsenic treatment served as controls.
2019-11-02 | E-MTAB-7972 | biostudies-arrayexpress