Project description:Geobacteraceae transfer electrons from a donor such as acetate to an electron acceptor such as Fe(III) or U(VI). Geobacter uraniireducens is found in uranium-contaminated sites and plays an important role in in situ bioremediation. In this experiment, gene expression was compared between G. uraniireducens cultures grown in sediments from a uranium contaminated site amended with acetate and cultures grown in acetate/fumarate medium. Keywords: two-condition comparison
2008-10-20 | GSE10920 | GEO
Project description:soil of uranium mining tailings
Project description:G. uraniireducens was isolated from a subsurface site in Rifle, CO undergoing in situ uranium bioremediation. Sediments from the Rifle site were heat-sterilized, amended with acetate to simulate in situ bioremediation conditions, and inoculated with G. uraniireducens. Gene transcript abundance in these cells using sediment Fe(III) and Mn(IV) oxides as the electron acceptor were compared with transcript levels in cells grown with fumarate as the electron acceptor. Additional comparisons were made between cells grown on synthetic Fe(III) or Mn(IV) oxides and cells grown on fumarate. 3 biological replicates hybridized in duplicate
Project description:Despite the fact that deep sea mining is becoming more popular nowadays in terms of obtaining metals ores for daily life purposes, its potential impact to the deep sea habitat, which is originally stable and converse, stills remains uncertain. In order to estimate and regulate the imapct of deep sea mining activities, an in-situ exposure experiment is performed to observe the change in proteomics expression of the deep-sea scvangers, Abyssorchomene distinctus, to copper exposure. This project aims to suggest a potenial protein bio-marker in Abyssorchomene distinctus to assess the impact of mining activities towards deep sea organisms and also discuss the potential application of other deep sea in-situ exposure experiment in the future.
Project description:To investigate the chromatin structure surrounding human RNA polymerase II (Pol II) transcription on host and viral genomes, chromatin immunoprecipitation (ChIP) was performed following digestion of HCMV infected primary human foreskin fibroblasts (HFFs) with DNA Fragmentation Factor (DFF). DFF is a human endonuclease responsible for cleaving between nucleosomes during apoptosis. We found that utilizing DFF as the front end for ChIP-Seq in place of sonication or Micrococcal nuclease (MNase) offered new insights into the connections between active transcription and the local chromatin on the host and that these connections were completely absent on the HCMV genome.
Project description:Molecular Elasticity and Adjustment of Drought Recovery Dynamics of 14N- and 15N-fertilized Legume Medicago truncatula. Climate change in conjunction with population growth necessitates a systems biology approach to characterize plant drought response and a more thorough understanding of the underlying molecular mechanisms. During drought stress and recovery, the metabolome and proteome regulate and are regulated through diverse mechanisms including synthesis and degradation. In order to study this complex regulation network, a front-end multilevel analysis is presented for the first time, investigating protein turnover, regulatory classes of proteins and metabolites as well as post translational ubiquitination of a target set of proteins during a severe stress and recovery scenario in the model legume Medicago truncatula. Evidence for enhanced translational proteome regulation was observed during drought recovery and functional clusters of differentially dynamic phases during the course of recovery were defined. The data give novel insights into molecular elasticity that enable recovery of drought stressed plants. Additionally, these results offer putative targets and metabolic pathways for future plant-bioengineering towards enhanced drought stress tolerance.
Project description:G. uraniireducens was isolated from a subsurface site in Rifle, CO undergoing in situ uranium bioremediation. Sediments from the Rifle site were heat-sterilized, amended with acetate to simulate in situ bioremediation conditions, and inoculated with G. uraniireducens. Gene transcript abundance in these cells using sediment Fe(III) and Mn(IV) oxides as the electron acceptor were compared with transcript levels in cells grown with fumarate as the electron acceptor. Additional comparisons were made between cells grown on synthetic Fe(III) or Mn(IV) oxides and cells grown on fumarate.
Project description:Invasive tumor front (the tumor-host interface) is vitally important in malignant cell progression and metastasis. Tumor cell interactions with resident and infiltrating host cells and with the surrounding extracellular matrix and secreted factors ultimately determine the fate of the tumor. In this study we focus on the invasive tumor front, making an in-depth characterization of reticular fiber scaffolding, infiltrating immune cells, gene expression and methylation profiles of classified aggressive primary uterine adenocarcinomas and leiomyosarcomas.
Project description:Invasive tumor front (ITF, the tumor-host interface) is vitally important in malignant cell progression and metastasis. Tumor cell interactions with resident and infiltrating host cells and with the surrounding extracellular matrix and secreted factors ultimately determine the fate of the tumor. Herein we focus on the invasive tumor front, making an in-depth characterization of reticular fiber scaffolding, infiltrating immune cells, gene expression and epigenetic profiles of classified aggressive primary uterine adenocarcinomas (uADC) and leiomyosarcomas (uLMS).
