GNPS_Amazon urbanization skin and environmental samples
Ontology highlight
ABSTRACT: MS/MS data were collected from skin of Amazon individuals and from their houses (walls and floors of living room, bedroom, kitchen and bathroom).
Project description:MS/MS data were collected from skin of Amazon individuals and from their houses (walls and floors of living room, bedroom, kitchen and bathroom).
Project description:Human death marks the end of organismal life under conditions such that the components of the human body continue to be alive. Such postmortem cellular survival depends on the nature (Hardy scale) of human death. Slow and expected death typically result from terminal illnesses and includes a prolonged terminal phase of life. As such organismal death process unfolds, do cells of the human body adapt for postmortem cellular survival? Organs with low energy cost-of-living, such as the skin, are better suited for postmortem cellular survival. In this work, the effect of different durations of terminal phase of human life on postmortem changes in cellular gene expression was investigated using RNA sequencing data of 701 human skin samples from the Genotype-Tissue Expression database. Longer terminal phase (slow-death) was associated with a more robust induction of survival pathways (PI3K-Akt signaling) in postmortem skin. Such cellular survival response was associated with the upregulation of embryonic developmental transcription factors such as FOXO1, FOXO3, ATF4 and CEBPD. Upregulation of PI3K-Akt signaling was independent of sex or duration of death-related tissue ischemia. Analysis of single nucleus RNA-seq of post-mortem skin tissue specifically identified the dermal fibroblast compartment to be most resilient as marked by adaptive induction of PI3K-Akt signaling. Prospective studies depicted hypomethylation of PI3K-Akt signaling genes in slow compared to fast human death. Compared to fast death, slow death also induced angiogenic pathways in the dermal endothelial cell compartment of postmortem human skin. In contrast, specific pathways supporting functional properties of the skin as an organ were downregulated following slow death. Such pathways included melanogenesis and those representing the skin extracellular matrix. Efforts to understand the significance of death as a biological variable in influencing the transcriptomic composition of surviving component tissues has far-reaching implications including rigorous interpretation of experimental data collected from the dead and mechanisms involved in transplant-tissue obtained from dead donors.
Project description:Total RNA was purified from keratinocytes isolated from FFPE arsenic-induced skin lesion samples collected from individuals exposed to high concentrations of arsenic exceeding 50 ppb in drinking water in Murshidibad district of West Bengal, India.
Project description:A gene expression profiling sub-study was conducted in which skin biopsy samples were collected from 85 patients with moderate-to-severe psoriasis who were participating in ACCEPT, an IRB-approved Phase 3, multicenter, randomized trial. This analysis identified 4,175 probe-sets as being significantly modulated in psoriasis lesions (LS) compared with matched biopsies of non-lesional (NL) skin.
Project description:In plastic and reconstructive surgery, mechanical stretch (MS) forces are frequently used to stimulate skin regeneration in order to produce additional skin for repairing tissue defects. Fibroblast activation in response to MS is crucial for skin growth during skin expansion. While its function in skin expansion is unknown, interleukin 11 (IL11) has been described as a cytokine that is increased in response to mechanical stimuli. In this study, we demonstrated that the expression of IL11 and IL11 receptor alpha subunit (IL11RA) was significantly increased in dermal fibroblasts (DFs) of the well-regenerated expanded skins (ESs) in human and mouse samples. However, IL11 was relatively lacking in the poorly-regenerated human ESs. Through the inhibition of IL11 signaling, MS-induced fibroblast proliferation, extracellular matrix (ECM) production, and myofibroblast activation were all inhibited in vitro. Consistently, depletion of IL11 signaling in vivo reduced skin regeneration during skin expansion, as evidenced by decreased dermal thickness and inhibited fibroblast function. Notably, transcriptomic analysis revealed that MS stimulation induced the upregulation of pathways associated with cell proliferation, collagen synthesis, stress response, and cell activation, whereas these pathways were downregulated in the IL11RA knockdown group. Mechanistically, we discovered that WNT5B acts as a downstream regulator of IL11-mediated cell activation in the presence of MS. Finally, the administration of recombinant IL11 via intradermal injection into mice significantly promoted fibroblast activation and halted the reduction in dermal thickness that occurred during skin expansion. In summary, our study demonstrated that IL11 signaling plays a crucial role in the activation of fibroblasts induced by MS, making it a promising target for clinical application in enhancing skin regeneration during skin expansion.
Project description:The aim of this study was to develop a suitable method to preserve fecal samples for metaproteomics analyses when flash-freezing is not an option. Fecal samples were collected from conventional adult C57BL/6 mice and combined into a fecal master mix. The fecal master mix was then split into 48 subsamples that were subjected to different preservation treatments. The following six preservation methods were tested: flash-freezing in liquid nitrogen followed by storage at -80°C, immersion in RNAlater® and storage at room temperature, immersion in RNAlater® and immediate storage at -80°C, immersion in 95% ethanol and storage at room temperature, immersion in a RNAlater-like buffer “NAP buffer” and storage at room temperature, and immersion in an autoclaved RNAlater-like buffer “Autoclaved NAP buffer” and storage at room temperature. Proteins were extracted from the samples after being stored for 1 and 4 weeks. There were 4 replicates per treatment and time-point. Samples were analyzed by LC-MS/MS and the data were analyzed with Proteome Discoverer against a large database of mouse microbiota protein sequences.
Project description:Psoriasis, a prevalent chronic inflammatory skin disease, affects over 100 million individuals globally and is increasingly acknowledged as a systemic condition impacting the heart, blood vessels, and joints. A substantial body of research highlights a strong correlation between the severity of psoriasis and an elevated risk of cardiovascular diseases. Notably, treatments that alleviate dermatological symptoms have also been shown to reduce the formation of coronary plaques. Adipose tissue, functioning as a significant endocrine organ, secretes pro-inflammatory mediators that perpetuate the chronic low-grade inflammation typical of obesity. To investigate the molecular changes in adipose tissue associated with psoriasis, we collected subcutaneous adipose tissue samples from both psoriatic lesion skin (LS, n=8) and peripheral non-lesional skin (NLS, n=8), and conducted comprehensive transcriptomic analyses.
Project description:Single cell RNA sequencing of embryonic mouse dorsolateral skin were microdissected. All live cells were collected and submitted in bulk for droplet-based cDNA library preparation (9000 cells/sample)
Project description:To broaden our understanding of the gene expression common to volar skin, we biopsied the dorsum of the hand, palm, dorsum of the foot and sole and collected miRNA for chip anlayses total of 16 skin biopsy samples with 4 repeats from distinct individuals of each site: dorsum of hand, palm, dorstum of foot and sole