RELATIVE ABUNDANCE OF phyla ACTINOBACTERIA AND VITAMIN C CONSUMPTION ARE ASSOCIATED WITH DNA METHYLATION.
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE254646 | GEO | 2024/02/02
REPOSITORIES: GEO
Similar Datasets
Project description:RELATIVE ABUNDANCE OF phyla ACTINOBACTERIA AND VITAMIN C CONSUMPTION ARE ASSOCIATED WITH DNA METHYLATION.
| PRJNA1071183 | ENA
Project description:Vitamin K epoxide reductase (VKOR) drives the vitamin K cycle, activating vitamin K-dependent blood clotting factors. VKOR is also the target of the widely used anticoagulant drug, warfarin. Despite VKOR’s pivotal role in coagulation, its structure and active site remain poorly understood. Here, we used multiplexed, sequencing-based assays to measure the effects of 2,695 VKOR missense variants on abundance and 697 variants on activity in cultured human cells.
2020-08-10 | GSE149922 | GEO
Project description:Vitamin C (ascorbate) is a crucial antioxidant and an essential cofactor of biosynthetic and regulatory enzymes. Unlike humans, mice can synthesize vitamin C thanks to the key enzyme gulonolactone oxidase (Gulo). In the present study, we used the Gulo-/- mouse model, which cannot synthesize their own ascorbate to determine the impact of this vitamin on both the transcriptomics and proteomics profiles in the liver. The study included Gulo-/- mouse groups treated with either sub-optimal or optimal vitamin C concentrations in drinking water. We found a distinctive difference in the mRNA and protein profiles as a function of sex between all the mouse groups. Despite this sexual dimorphism, Spearman correlation analyses were conducted to divulge which transcripts and proteins correlated with hepatic vitamin C concentrations in both females and males. Such analysis on transcriptomics data from females and males revealed changes in a wide array of biological processes involved in glucose, lipid, steroid, and glutathione metabolisms as well as in acute-phase response. Furthermore, although several proteins of the mitochondrial complex III significantly correlated with vitamin C concentrations, their corresponding transcripts did not correlate with vitamin C in both females and males. Thus, this side-by-side comparison between transcriptome and proteome supported the view that post-transcriptional processes play a major role in the regulation of cellular respiration in the liver upon vitamin C deficiency. Our findings suggest that transcriptome profiling alone provides an incomplete picture of molecular changes associated with vitamin C deficiency in the liver of mice and examination of changes in protein abundances is essential to unveil variations that are not transcriptionally regulated.
2023-06-01 | GSE233598 | GEO
Project description:Polyribosomal fractions derived from P25 mice were the starting material for IPs of the FMRP protein and associated mRNA. Therefore we wanted to determine the relative abundance of all mRNAs in the starting pool for the IP as a denominator with which to compare the IPed material.
2011-07-21 | GSE26742 | GEO
Project description:Marine Actinobacteria, particularly coral-associated Actinobacteria, have attracted attention recently. In this study, the abundance and diversity of Actinobacteria associated with three types of coral thriving in a thermally stressed coral reef system north of the Arabian Gulf were investigated. Coscinaraea columna, Platygyra daedalea and Porites harrisoni have been found to harbor equivalent numbers of culturable Actinobacteria in their tissues but not in their mucus. However, different culturable actinobacterial communities have been found to be associated with different coral hosts. Differences in the abundance and diversity of Actinobacteria were detected between the mucus and tissue of the same coral host. In addition, temporal and spatial variations in the abundance and diversity of the cultivable actinobacterial communities were detected. In total, 19 different actinobacterial genera, namely Micrococcus, Brachybacterium, Brevibacterium, Streptomyces, Micromonospora, Renibacterium, Nocardia, Microbacterium, Dietzia, Cellulomonas, Ornithinimicrobium, Rhodococcus, Agrococcus, Kineococcus, Dermacoccus, Devriesea, Kocuria, Marmoricola, and Arthrobacter, were isolated from the coral tissue and mucus samples. Furthermore, 82 isolates related to Micromonospora, Brachybacterium, Nocardia, Micrococcus, Arthrobacter, Rhodococcus, and Streptomyces showed antimicrobial activities against representative Gram-positive and/or Gram-negative bacteria. Even though Brevibacterium and Kocuria were the most dominant actinobacterial isolates, they failed to show any antimicrobial activity, whereas less dominant genera, such as Streptomyces, did show antimicrobial activity. Focusing on the diversity of coral-associated Actinobacteria may help to understand how corals thrive under harsh environmental conditions and may lead to the discovery of novel antimicrobial metabolites with potential biotechnological applications.
| S-EPMC4770044 | biostudies-literature
Project description:Background: Malaria is a one of the most important infectious diseases and is caused by parasitic protozoa of the genus Plasmodium. Previously, the quantitative characterization of the P. falciparum transcriptome demonstrated that the strictly controlled progression of these parasites through their intra-erythrocytic developmental cycle is accompanied by a continuous cascade of gene expression. Although such analyses have proven immensely useful, the precise correlations between transcript and protein abundance remain under-scrutinized. Results: Here, we present a quantitative time-course analysis of relative protein abundance for schizont-stage parasites (34-46 hours post-invasion) based on 2D-gel electrophoresis of protein samples labeled with DIGE fluorescent dyes. For this purpose we analyzed parasite samples taken at four-hour intervals from a tightly synchronized culture and established more than 500 individual protein abundance profiles with high temporal resolution and quantitative reproducibility. Approximately half of all profiles exhibit a significant change in abundance and 12% display an expression peak during the observed 12-hour time interval. Intriguingly, identification of 54 protein spots by mass spectrometry revealed that 58% of the corresponding proteins including actin-I, enolase, eIF4A, eIF5A, and several heat shock proteins are represented by more than one isoform, presumably due to post-translational modifications, with the various isoforms of a given protein frequently showing different expression patterns. Furthermore, comparisons with transcriptome data generated from the same parasite samples reveal significant post-transcriptional gene expression regulation. Conclusions: Together, our data indicate that both post-transcriptional and post-translational events are widespread and of presumably great biological significance during the intra-erythrocytic development of P. falciparum. Additional comment: In essence, the microarray data generated in this study is a repeat of the transcriptome analysis described in Bozdech et al., PLoS Biol 2003, 1(1):E5. Differences include (1) an improved set of oligonucleotides [see Hu et al., BMC Bioinformatics 2007, 8:350] used in the study associated with this GEO entry, and (2) the sampling at only four timepoints during the intra-erythrocytic development cycle (schizont stage) to match and complement the samples processed in the concomitant proteomics analysis.
2009-02-23 | GSE13251 | GEO
Project description:Analysis of livers from 74-day old male rats fed vitamin A sufficient or vitamin A deficient diet for 53 days. Either 10ug or 2ug of total RNA used in standard Affymetrix protocol Keywords = rat Keywords = liver Keywords = vitamin A deficiency Keywords: other
2005-06-30 | GSE1600 | GEO
Project description:Polyribosomal fractions derived from P25 mice were the starting material for IPs of the FMRP protein and associated mRNA. Therefore we wanted to determine the relative abundance of all mRNAs in the starting pool for the IP as a denominator with which to compare the IPed material. [mRNA profiling]: We prepared polyribosomes on sucrose gradients in duplicate from 2 FVB WT mice, age P25, and purified RNA from polyribosomal fractions of each of the two gradients.
2011-07-20 | E-GEOD-26742 | biostudies-arrayexpress
Project description:Background: Malaria is a one of the most important infectious diseases and is caused by parasitic protozoa of the genus Plasmodium. Previously, the quantitative characterization of the P. falciparum transcriptome demonstrated that the strictly controlled progression of these parasites through their intra-erythrocytic developmental cycle is accompanied by a continuous cascade of gene expression. Although such analyses have proven immensely useful, the precise correlations between transcript and protein abundance remain under-scrutinized. Results: Here, we present a quantitative time-course analysis of relative protein abundance for schizont-stage parasites (34-46 hours post-invasion) based on 2D-gel electrophoresis of protein samples labeled with DIGE fluorescent dyes. For this purpose we analyzed parasite samples taken at four-hour intervals from a tightly synchronized culture and established more than 500 individual protein abundance profiles with high temporal resolution and quantitative reproducibility. Approximately half of all profiles exhibit a significant change in abundance and 12% display an expression peak during the observed 12-hour time interval. Intriguingly, identification of 54 protein spots by mass spectrometry revealed that 58% of the corresponding proteins including actin-I, enolase, eIF4A, eIF5A, and several heat shock proteins are represented by more than one isoform, presumably due to post-translational modifications, with the various isoforms of a given protein frequently showing different expression patterns. Furthermore, comparisons with transcriptome data generated from the same parasite samples reveal significant post-transcriptional gene expression regulation. Conclusions: Together, our data indicate that both post-transcriptional and post-translational events are widespread and of presumably great biological significance during the intra-erythrocytic development of P. falciparum. Additional comment: In essence, the microarray data generated in this study is a repeat of the transcriptome analysis described in Bozdech et al., PLoS Biol 2003, 1(1):E5. Differences include (1) an improved set of oligonucleotides [see Hu et al., BMC Bioinformatics 2007, 8:350] used in the study associated with this GEO entry, and (2) the sampling at only four timepoints during the intra-erythrocytic development cycle (schizont stage) to match and complement the samples processed in the concomitant proteomics analysis. Four timepoint samples were harvested from a tightly synchronized 6 liter biofermenter culture of P. falciparum during schizont stage (at 34, 38, 42, and 46 hours post-invasion) and compared against a 3D7 RNA reference pool.
2010-05-05 | E-GEOD-13251 | biostudies-arrayexpress