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Groundwater metagenome

ABSTRACT: D2O SIP (Hainich CZO H41)

PROVIDER: PRJNA357979 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR5119617_1.fastq.gz	Fastqsanger.gz
	SRR5119617_2.fastq.gz	Fastqsanger.gz
	SRR5120060_1.fastq.gz	Fastqsanger.gz
	SRR5120060_2.fastq.gz	Fastqsanger.gz
	SRR5120051_1.fastq.gz	Fastqsanger.gz

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Lockdown, caregiving, and antiviral gene regulation in macaques

Project description:Previous research has linked perceived social isolation (loneliness) to reduced antiviral immunity, but the immunologic effects of the objective social isolation imposed by pandemic “shelter in place” (SIP) policies is unknown. We assessed the immunologic impact of SIP by relocating 21 adult male rhesus macaques from 2000 sq-m field cage communities of 70-132 other macaques to 2 wks of individual housing in indoor shelters. SIP was associated with down-regulation of Type I interferon (IFN) antiviral gene expression. This effect emerged within the first 48 hrs of SIP, persisted for at least 2 wks, and abated within 4 wks of return to social housing. A subsequent round of SIP in the presence of a novel juvenile macaque abrogated this effect. These results identify a significant adverse effect of SIP social isolation on antiviral immune regulation in circulating immune cells and they suggest a potential behavioral strategy for ameliorating such effects by promoting pro-social engagement during SIP.

2021-07-28 | GSE174065 | GEO

Electron acceptor-dependent identification of key anaerobic toluene degraders at a tar-oil contaminated aquifer by Pyro-SIP

Project description:Bioavailability of electron acceptors is probably the most limiting factor in the restoration of anoxic, contaminated environments. The oxidation of contaminants such as aromatic hydrocarbons, particularly in aquifers, often depends on the reduction of ferric iron or sulphate. We have previously detected a highly active fringe zone beneath a toluene plume at a tar-oil contaminated aquifer in Germany, where a specialized community of contaminant degraders co-dominated by Desulfobulbaceae and Geobacteraceae had established. Although on-site geochemistry links degradation to sulphidogenic processes, dominating catabolic (benzylsuccinate synthase alpha-subunit, bssA) genes detected in situ appeared more related to those of Geobacter spp. Therefore, a stable isotope probing (SIP) incubation of sediment samples with 13C7-toluene and comparative electron acceptor amendment was performed. We introduce pyrosequencing of templates from SIP microcosms as a powerful new strategy in SIP gradient interpretation (Pyro-SIP). Our results reveal the central role of Desulfobulbaceae for sulphidogenic toluene degradation in situ, and affiliate the detected bssA genes to this lineage. This, and the absence of 13C-labelled DNA of Geobacter spp. in SIP gradients preclude their relevance as toluene degraders in situ. In contrast, Betaproteobacteria related to Georgfuchsia spp. became labelled under iron-reducing conditions. Furthermore, secondary toluene degraders belonging to the Peptococcaceae detected in both treatments suggest the possibility of functional redundancy amongst anaerobic toluene degraders on site.

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Project description:We developed an adaptation to Split-Pool Recognition of Interactions by Tag Extension (SPRITE) called SPRITE-immunoprecipitation (SIP), which enables us to map genome-wide higher-order interactions that are coupled with the protein of interest. In this study we generated SIP data fo H3K4me3 and pan-promoter mark. We generated SIP maps in two mammalian cell types – mouse embryonic stem cells (mES) and mouse bone marrow derived dendritic cells.

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Effect of D2O on S. pombe gene expression

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Project description:This dataset was obtained from the authors of Starke et al. (2020, Journal of Proteomics 222: 103791, https://doi.org/10.1016/j.jprot.2020.103791). Sample labels: 1 - High fiber diet inoculum 2 - High protein diet inoculum 3,4,5 - High fiber + unlabeled water 6,7,8 - High protein + unlabeled water 9,10,11 - High fiber + 25% of 99.9 atom% D2O 12,13,14 - High protein + 25% of 99.9 atom% D2O 15,16,17 - High fiber + 25% of 99.0 atom% H218O 18,19,20 - High protein + 25% of 99.0 atom% H218O Direct quote from the original article describing the dataset. “…the impact of specific diets on a defined microbial community derived from a human fecal sample was to be determined. The defined community was chosen to provide a stable in vitro setup that could be useful for future microbiome research. Briefly, the microbial community was grown in a heavy fiber and a heavy protein diet in addition to 25% heavy water, either as D2O or H218O. A dosage of 25% isotopically labeled water was chosen by trial-and-error to yield sufficient incorporation into protein but avoid the reduction of activity of individual organisms. A difference in growth medium formulation, representing a high-fiber diet and a high-protein diet, was utilized to evaluate shifts in microbial activity. We chose to assess these diets because high-protein, low-carbohydrate interventions represent a popular weight-loss strategy and because we expected a strong effect on the synthesis of amino acids by this comparison. After an incubation time of 12 h, the proteins were analyzed for label-free quantitation (metaproteomics) and incorporation of isotopes (protein-SIP), each in triplicates….”

2022-12-30 | PXD024291 | Pride

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