Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Gut bacterial phytohormone modulates olfactory sensing, chemotaxis and mortality in fruit fly (Drosophila melanogaster): a new dimension to gut-brain axis

ABSTRACT: Aim of the study was to profile and quantify the proteins head region of D. melanogaster that are changing as a result of phytohormone administration. Data-independent acquisition (DIA) bases quantitative proteomics approach were used to achieve this aim. An Orbitrap Fusion Tribrid mass spectrometer (Thermo Fischer Scientific, Bremen, Germany) connected to the Easy- nLC-1200 nanoflow liquid chromatography system (Thermo Scientific) was used for data acquisition.

INSTRUMENT(S): Orbitrap Fusion

ORGANISM(S): Drosophila Melanogaster (fruit Fly)

DISEASE(S): Disease Free

SUBMITTER: Keshava Prasad T. S.

LAB HEAD: T. S. Keshava Prasad

PROVIDER: PXD044924 | Pride | 2024-05-22

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Publications

Comprehensive insights into the impact of bacterial indole-3-acetic acid on sensory preferences in Drosophila melanogaster.

Aziz Raifa Abdul RA Ramesh Poornima P Suchithra Kokkarambath Vannadil KV Stothard Paul P Narayana Vanya Kadla VK Raghu Shamprasad Varija SV Shen Fo-Ting FT Young Chiu-Chung CC Prasad T S Keshava TSK Hameed Asif A

Scientific reports 20240409 1

Several bacteria of environmental and clinical origins, including some human-associated strains secrete a cross-kingdom signaling molecule indole-3-acetic acid (IAA). IAA is a tryptophan (trp) derivative mainly known for regulating plant growth and development as a hormone. However, the nutritional sources that boost IAA secretion in bacteria and the impact of secreted IAA on non-plant eukaryotic hosts remained less explored. Here, we demonstrate significant trp-dependent IAA production in Pseud ...[more]

PMID: 38594449

Similar Datasets

FAS Inhibited Proteomics and Phosphoproteomics Profiling of Colorectal Cancer Spheroids shows Activation of Ferroptotic Death Mechanism

Project description:Colorectal cancer (CRC) is projected to become the third most diagnosed and third most fatal cancer in the United States by 2024, with early onset CRC on the rise. Research is constantly underway to discover novel therapeutics for the treatment of various cancers to improve patient outcomes and survival rates. Recently, fatty acid synthase (FAS) has become a druggable target of interest for the treatment of many different cancers. FAS inhibitors have been developed over the years with mixed success. One such inhibitor, TVB-2640, has gained popularity for its high specificity for FAS and has even entered a phase 1 clinical trial for the treatment of solid tumors. However, the distinct molecular differences that occur upon inhibiting FAS have yet to be understood. Here, we conduct time course proteomics and phosphoproteomics on analyses HCT 116 and HT-29 CRC spheroids inhibited with either a generation 1 (cerulenin) or generation 2 (TVB-2640) FAS inhibitor. Proteins involved in lipid metabolism and cellular respiration were altered in abundance. It was also observed that proteins and enzymes involved in ferroptosis—an iron mediated form of cell death—were altered. These results show HT-29 spheroids exposed to cerulenin or TVB-2640 are undergoing a ferroptotic death mechanism.

2024-08-10 | PXD050987 | Pride

Narrow precursor window for DIA-MS enhances protein identification and quantification

Project description:Data independent acquistion (DIA) is becoming widely as a method of choice in quantitation proteomics due to its high reproducibility and quantitation accuracy at high-throughput fashion. In this project, we systematically evaluated the effect of the selected precursor mass range for DIA-MS on the protein identification and quantification. We show that a narrow precursor window (400-650 m/z) DIA could identify a 34.7% more proteins than a conventional DIA with a wide precursor window of 400-1200 m/z. When combining the three narrow precursor windows (400-650, 650-900, and 900-1200 m/z) DIA-MS analyses, we obtained a 59.4% increase in the number of proteins quantified than a conventional DIA-MS analysis.

2021-10-01 | PXD026965 | Pride

HEK293T_The Label-free DIA-MS nanoproteomics workflow based on empirically corrected spectral library and application for 5000 PBMCs stimulated by LPS

Project description:A refined HEK293T peptide dilution series acquired in DIA mode on Orbitrap Lumos.

2022-04-27 | PXD029738 | Pride

Mapping perturbations in the cellular proteome of OCIAD1 and OCIAD2 knockdown U2OS cells.

Project description:To gain insight into the function of both OCIAD paralogs, we used untargeted quantitative mass spectrometry to compare the whole-cell proteomes of control U2OS cells, U2OS cells with individual or double OCIAD1/OCIAD2 knockdown, and OCIAD1 knockdown cells in which OCIAD1 expression was reintroduced by lentiviral delivery.

2021-05-14 | PXD025573 | Pride

Deep proteome analysis of mouse brains from wild-type, LPS-induced, and drug-treated mice groups

Project description:We studied the effect of bacterial Lipopolysaccharides on inducing neuroinflammation in mice. In addition, we investigated the effect of novel LAT1-utilizing anti-inflammatory derivatives on reversing this LPS-induced neuroinflammation status. Thus, we performed deep proteome analysis of mouse brains after treatment with vehicle, LPS, and LPS with LAT1-utilizing derivatives. The objective is to follow the different inflammatory biomarkers in the mouse brain and explain the inflammatory process after the LPS treatment with and without the LAT1-utilizing prodrugs.

2022-10-25 | PXD030838 | Pride

Mapping the interactome of OCIAD1 in human K562 cells

Project description:Immunoprecipitation of OCIAD1 followed by mass spectrometry analysis to identify binding partners in human cells. To determine the functional significance of OCIAD1 interactors, we also looked for interactions that were modulated by a loss-of-function mutant (F102A).

2021-05-14 | PXD025682 | Pride

Exploring molecular dynamics indicators associated with reproductive performance of Bos indicus cattle in plasma samples through data-independent acquisition mass spectrometry

Project description:Aim of the study was to profile the blood plasma proteome of healthy Bos indicus cattle and use it as a baseline against which to compare different conditions in Bos indicus cattle, such as disease, reproduction associated proteins and pregnancy specific proteins etc. Data-independent acquisition (DIA) bases quantitative proteomics approach coupled to LC-MS/MS methods were used to achieve this aim. An Orbitrap Fusion Tribrid mass spectrometer (Thermo Fischer Scientific, Bremen, Germany) connected to the Easy- nLC-1200 nanoflow liquid chromatography system (Thermo Scientific) was used for data acquisition.

2024-07-15 | PXD034103 | Pride

Novel Events, Gene Model Correction of Mycobacterium Avium by Proteogenomic Analysis

Project description:Mycobacterium avium is one of the prominent disease causing bacteria in humans. It causes lymphadenitis, chronic pulmonary and extrapulmonary and disseminated infections in adults, children and immunocompromised humans. M. avium has ~4,500 predicted gene models, out of which not all are identified at proteomic level. Proteomic database search followed by proteogenomic analysis helps in the correction of gene models, identification of novel exons/genes, variant proteins. As part of this study, we performed proteomic analysis of M. avium cultures by data-dependent acquisition (DDA) and data-independent acquisition (DIA) method followed by proteogenomic analysis of M. avium proteomic data. M. avium culture was subjected to proteomic sample preparation. The resulting peptides were acquired in 120min DDA (12 bRPLC) and DIA method using EASY nLC 1200 liquid chromatogram system coupled to Orbitrap Fusion Tribrid mass spectrometer. The resulting DDA raw files were searched sequentially against the M. avium proteome database, Mycobacterium tuberculosis H37Rv and Ra proteome database (Mtb), M. avium genome six-frame translated proteome and variant proteins database, respectively. The database search result was converted into a spectral library and used for DIA data search for the validation of GSSPs and variant peptides. The database search of M. avium DDA has resulted in the identification of 2,954 M. avium proteins, 128 Mtb proteins, 174 GSSPs (M. avium genome six-frame translated proteome) and 795 SNPs corresponding to 612 proteins (variant proteins database), respectively. The M. avium proteome database search has covered 62.09% of the proteome with the identification of 2,954 proteins out of 4,757 proteins in the database. From the manual categorization of 174 GSSPs, we observed 23 N-terminal extensions, 142 pseudogene coding peptides and one each novel exon and short peptide, respectively.

2023-03-17 | PXD032067 | Pride

Myeloperoxidase is a Critical Mediator of Anthracycline-induced Cardiomyopathy

Project description:The anthracycline doxorubicin is a commonly used chemotherapeutic drug that induces cardiomyopathy in almost 10% of patients. The aim of this study was to examine the role of the leukocyte-derived enzyme Myeloperoxidase (MPO) in pathogenesis of anthracycline-induced Cardiomyopathy (AICM). We performed proteomics on whole heart tissue of MPO-deficient mice on C57BL/6J background and wildtype (WT) littermates seven days after intravenous injection of the anthracycline Doxorubicin (20 mg/kg bodyweight, dissolved in saline) or saline (NaCl).

2023-08-30 | PXD037524 | Pride

Temporal omics analysis in Syrian hamsters unravel cellular effector responses to moderate COVID-19

Project description:Using omics tools with the SARS-CoV-2 infected Syrian hamster as model for COVID-19, along with published datasets from COVID-19 patients, Nouailles et al. present a detailed longitudinal analysis of systemic and pulmonary quantitative and qualitative immune responses in a moderate disease setting. Targeted analysis of the alveolar and microvascular niche revealed a dominant role for monocyte-derived macrophages and endothelial cells regarding early anti-viral genes as well as pro-inflammatory and T cell recruiting chemokine expression. Recruitment of cytotoxic effector T cells coincided with viral clearance. This combined response was favorable for a moderate and self-limited disease course.

2021-06-17 | PXD025164 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data