CRC proteomic analysis by LC MS/MS
Ontology highlight
ABSTRACT:
INSTRUMENT(S):
ORGANISM(S): Human Gut Metagenome
DISEASE(S): Colon Cancer
SUBMITTER: 
rana abo-hammam
LAB HEAD: Rana Hashem
PROVIDER: PXD037271 | Pride | 2023-08-18
REPOSITORIES: Pride
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| 21P04220001.mzML | Mzml | |||
| 21P04220001.raw | Raw | |||
| 21P04220002.mzML | Mzml | |||
| 21P04220002.raw | Raw | |||
| 21P04220004.mzML | Mzml |
Items per page: 5 1 - 5 of 16 |
Similar Datasets
Project description: Not available
| S-EPMC8262168 | biostudies-literature
Project description:Leaf-cutting ants of the genera Acromyrmex and Atta live in mutualistic symbiosis with a basidiomycete fungus (Leucocoprinus gongylophorus), which they cultivate as fungal gardens in underground nest chambers. The ants provide the fungus with a growth substrate consisting of freshly cut leaf fragments. After new leaf fragments are brought into the nest, the ants chew them into smaller pieces and apply droplets of fecal fluid to the leaf pulp before depositing this mixed substrate in the fungus garden and inoculating it with small tufts of mycelium from older parts of the garden. Previous work has shown that the fecal fluid contains a range of digestive enzymes including proteases, amylases, chitinases, cellulases, pectinases, hemicellulases and laccases, and that most of these enzymes are produced by the fungal symbiont in specialized structures called gongylidia that the ants eat. After ingestion, the enzymes apparently pass unharmed through the alimentary channel of the ants and end up in the fecal fluid. Most likely this complex system is an adaptation of the ant-fungus symbiosis to a herbivorous lifestyle, as the ancient ancestors of the ants and the fungus lived as hunter-gatherers and saprotrophs, respectively. The promise of fecal fluid for getting insight into the molecular adaptations that enables the ant-fungus holosymbiont to live as a herbivore, led us to investigate the fecal fluid proteome using LC-MS/MS in order to get a more comprehensive picture of the repertoire of proteins present.
2021-01-12 | PXD016395 | Pride
Project description:Maternal environment is an important regultor of seed dormancy, but the mechanisms underlying the process are poorly understood. We have found that genes in the circadian clock control dormancy, in part through their regulation of the canonical photoperiod pathway known from research into flowering time control. In this experiment we compare the affects of altering seed maturation temperature or maternal photoperiod on dry seed transcriptomes, and the photoperiod-insenstive ft-1 mutant to wt type Ler. In this way we are identifying gene expression programmes which result from the seed's response to maternal environmental experience. Keywords: Expression profilling by array 12 samples were used in this experiment
2011-04-21 | E-GEOD-28747 | biostudies-arrayexpress
Project description:The interplay of gut microbiota with the kidney system, characteristic to reduced kidney function and increased concentrations of urea in gut; in turn increases bacterial urease activity and generation of uremic toxins. Knowledge on these underlying bidirectional molecular mechanisms is nevertheless still limited. In this exploratory study, fecal proteomics analysis was performed, to investigate this largely unexplored biological material as a source of relevant information reflecting the gut-kidney axis at protein level. Specifically, fecal suspension samples from patients with chronic kidney disease (CKD); CKD1 (n = 12) and CKD4 (n = 17) were analysed by high resolution LC-MS/MS. Protein identification was performed using both the human and bacterial UniProt RefSeq reviewed databases, identifying 701 and 1011 unique proteins, respectively. Differential expression analysis (CKD4/CKD1) revealed significance for human proteins previously associated with reduced saccharolytic fermentation, inflammation and CKD, including pancreatic alpha-amylase and galectin-3-binding protein. Significant changes in bacterial proteins such as glyceraldehyde-3-phosphate dehydrogenase, suggest differential butyrate synthesis in CKD4/CKD1. Quantitatively measured decrease of pancreatic alpha-amylase and butyrate in CKD4/CKD1, supported these hypotheses. In conclusion, this analysis highlighted the presence of inflammation and suggested reduced saccharolytic fermentation affecting butyrate synthesis pathways in later disease stages. Validation by a multi-omics analysis is planned.
2025-06-02 | PXD048778 | Pride
Project description:To explore the molecular mechanism underlying the inflammatory symptoms, we set out to screen S1P interactors using Co-IP and liquid chromatography-tandem mass spectrometry (LC-MS/MS) and identified 29 potential candidates
2022-05-04 | PXD031064 | Pride
Project description:The study is based on the identification of serum protein biomarkers for NT 1. A total of 27 serum samples were collected (16 NT 1 and 11 controls), the altered expression levels of low-abundant proteins (DEPs) associated with narcolepsy type 1 was investigated by comparing the proteomes of the two sample cohorts. DEPs that are revealed to be most related to NT 1 pathogenesis and have high levels of fold changes were further targeted and validated by LC-PRM-MS. Then, the effects of the DEPs were explored by system biology analysis.
2023-05-10 | PXD038248 | Pride
Project description:Morphine causes microbial dysbiosis. In this study we focused on restoration of native microbiota in morphine treated mice and looked at the extent of restoration and immunological consequences of this restoration. Fecal transplant has been successfully used clinically, especially for treating C. difficile infection2528. With our expanding knowledge of the central role of microbiome in maintenance of host immune homeostasis17, fecal transplant is gaining importance as a therapy for indications resulting from microbial dysbiosis. There is a major difference between fecal transplant being used for the treatment of C. difficile infection and the conditions described in our studies. The former strategy is based on the argument that microbial dysbiosis caused by disproportionate overgrowth of a pathobiont can be out-competed by re-introducing the missing flora by way of a normal microbiome transplant. This strategy is independent of host factors and systemic effects on the microbial composition. Here, we show that microbial dysbiosis caused due to morphine can be reversed by transplantation of microbiota from the placebo-treated animals.
2016-06-01 | E-MTAB-3723 | biostudies-arrayexpress
Project description:Elucidation of the mechanism of temperature tolerance in yeast is essential for enhancing cellular robustness of strains, providing more economically and sustainable sound industrial processes. We investigated the differential responses of three distinct Saccharomyces cerevisiae strains, an industrial wine strain, ADY5, a laboratory strain, CEN.PK113-7D and an industrial bioethanol strain, Ethanol Red, grown at sub- (12 ºC) and-supra (39 ºC) optimal temperatures under chemostat conditions, in which specific growth rate–dependent changes are eliminated. In contrast to previous studies, we employed anaerobic conditions, mimicking the industrial processes. The proteomic profile of these strains was performed by SWATH-MS, allowing the quantification of 997 proteins. Our analysis revealed that temperature response differs between the strains, highlighting the precision with which each strain responds to changes in its environment; however, we also found some common responsive proteins among the strains, revealing that the response to temperature involves general stress and specific mechanisms. Overall, sub-optimal temperature conditions involved a higher remodeling of the proteome than supra-optimal temperature. Further, the proteomic data evidenced that the cold response involves a strong repression of translation related proteins as well as induction of amino acid metabolism, together with components related to protein folding and degradation. On the other hand, the high temperature response mainly recruits amino acid metabolism. Our study provides a global and thorough insight into how growth temperature affects yeast proteome, which can be a step forward for research regarding the comprehension and the improvement of yeast thermotolerance.
2021-01-04 | PXD016567 | Pride