Lactic acid bacterial LC-MS/MS
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Q Exactive
ORGANISM(S): Lactobacillus Plantarum Subsp. Plantarum P-8
SUBMITTER: 
Jie Yu
LAB HEAD: Heping Zhang
PROVIDER: PXD010054 | Pride | 2020-01-09
REPOSITORIES: pride
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| P17071.pep.xml | Pepxml | |||
| P17071.prot.xml | Xml | |||
| P17071_F1.raw | Raw | |||
| P17071_F10.raw | Raw | |||
| P17071_F2.raw | Raw |
Items per page: 5 1 - 5 of 13 |
Similar Datasets
Project description:To identify the downstream targets of macrophages that mediate tumor metastasis, we first established a highly metastatic cell line, named SCC7-M, then we performed proteomics analysis using the tumor tissue from mice bearing SCC7 and SCC7-M tumors.
2024-05-24 | PXD048866 | Pride
Project description:Lactic acid bacteria (LAB) are Gram-positive, acid-tolerant bacteria that have long been used in food fermentation and are generally recognized as safe (GRAS). LAB are a part of a normal microbiome and act as probiotics, improving the gastrointestinal microbiome and health when consumed. An increasing body of research has shown the importance of the microbiome on both mucosal immune heath and immune response to pathogens and oral vaccines. Currently, there are few approved mucosal vaccines, and most are attenuated viruses or bacteria, which necessitates cold chain, carries the risk of reversion to virulence, and can have limited efficacy in individuals with poor mucosal health. On account of these limitations, new types of mucosal vaccine vectors are necessary. There has been increasing interest and success in developing recombinant LAB as next generation mucosal vaccine vectors due to their natural acid and bile resistance, stability at room temperature, endogenous activation of innate and adaptive immune responses, and the development of molecular techniques that allow for manipulation of their genomes. To enhance the immunogenicity of these LAB vaccines, numerous adjuvant strategies have been successfully employed. Here, we review these adjuvant strategies and their mechanisms of action which include: Toll-like receptor ligands, secretion of bacterial toxins, secretion of cytokines, direct delivery to antigen presenting cells, and enterocyte targeting. The ability to increase the immune response to LAB vaccines gives them the potential to be powerful mucosal vaccine vectors against mucosal pathogens.
| S-EPMC6963626 | biostudies-literature
Project description:Toxoplasma gondii is a widely prevalent parasite of animals and humans that causes a broad spectrum of conditions ranging from asymptomatic or mild cold-like infections to abortion, severe ocular disease, encephalitis, and sometimes death. It is a member of the phylum Apicomplexa that also includes such significant human pathogens as Plasmodium spp. and Cryptosporidium spp. causing malaria and diarrheal disease, respectively. The toxoplasma cell has a multilayered pellicle: under the plasma membrane lies the inner membrane complex (IMC) comprised of flat membrane sacks supported by cortical microtubules and a meshwork of cytoskeletal filaments. The IMC acts as a mechanical barrier for membrane vesicles trafficking to and from the plasma membrane, necessitating the existence of dedicated cites for endo- and exocytosis where the IMC is interrupted. One such site is located at the apical end of the cell where the contents of the apical secretory organelles is exocytosed upon invasion. However, endocytosis in Toxoplasma and other apicomplexans is poorly understood, although conspicuous invaginations of the plasma membrane observed microscopically have been dubbed the micropore and postulated to be involved in endocytosis. We found that the endocytic markers including the subunits α and μ of the AP2 adaptor complex, dynamin-related protein C (DrpC), an Eps15 homology domain-containing protein, and the kelch-domain protein K13 localise to distinct persistent foci in the pellicle of Toxoplasma. Another type of persistent punctate structures found in the IMC are the enigmatic apical annuli whose function is completely unknown. We have discovered a new component of the annuli which is a putative LMBR1 family region protein embedded into the plasma membrane. Our experiments indicate that this protein – and annuli by extension – has a role in exocytosis. To better understand the molecular composition of these endocytic and exocytic structures and gain an insight into their function, we genetically fused them with a promiscuous bacterial biotin-ligase BirA* and used them as baits in proximity-dependent biotin identification experiments (BioID). We employed TMT10plex labelling and MS3-level tandem mass spectrometry with synchronous precursor selection (SPS-MS3) to achieve accurate quantification of multiple samples. Several hundred proteins have been identified and quantified in three biological replicates for every bait and the parental cell line control. Proteins significantly enriched in the BirA*-tagged cells relative to the control have been identified using linear modelling with LIMMA.
2023-04-17 | PXD034193 | Pride
Project description:To support the development of a dynamic in vitro human pharmacokinetic/pharmacodynamic simulation model for biofilm-mediated infections and study stability of meropenem, an LC-MS/MS method for the determination of meropenem in Luria Bertani (LB) media was developed and validated in an API2000 LC-MS/MS system. A partial validation was also performed in M9 media. Sample aliquots of 100μL (or 25μL for M9 media) were mixed with the internal standard (IS) ceftazidime and filtered. The filtrate was directly injected onto a C8 column eluted with ammonium formate (10mM, pH 4) and acetonitrile (0.1% formic acid) in a gradient mode. ESI(+) and MRM with ion pair m/z 384→68 for meropenem and m/z 547→468 for the IS were used for quantification. The calibration curve concentration range was 50 to 25,000ng/mL. The recovery was over 98%. In LB media, significant signal suppression was observed throughout the time period of detection when compared with mobile phase solvents, but the matrix effect was compensated well with the IS. In M9 media, much less signal suppression was observed. The method is simple, fast, and reliable. Using the method, stability of meropenem in LB and M9 media were tested. No significant degradation was observed for at least 8h in both LB media (37°C) and M9 media (30°C), but more than 15% degradation was observed overnight (∼20h). The method was transferred to an API5000 LC-MS/MS system using meropenem-d6 as the IS.
| S-EPMC4104812 | biostudies-literature
Project description:FLT3 is the most frequently mutated gene in AML â up to 40% of AML harbor an activating mutation within FLT3 gene. Though AML is a relatively rare disease, such a high mutability rate, as observed with FLT3 gene, is striking. To elucidate the molecular background of this phenomenon, we have established nine unique FLT3/ITD - carrying 32D cell lines and a set of controls, and subjected them to whole genome expression analysis and 2DE LC/MS proteomics. Data obtained on this so far largest set of ITD mutants indicates that in comparison to the wild type FLT3 expressing 32D cells and transduction controls, FLT3/ITD positive cells exhibit less mature expression profiles resembling ST-HSC and MkEP/CMP/LMPP progenitors. We hypothesize that FLT3/ITD might contribute not only to the proliferative advantage of FLT3/ITD positive cells, but also to their reprogramming towards less differentiated stages, thus strengthening their malignant properties. This finding might explain the pronounced mutation rate of the aberrantly expressed FLT3 gene in AML, and, also, the inferior prognosis of FLT3/ITD positive AML patients. Moreover, the microarray data has revealed biological differences among individual ITD variants â a finding supporting the recent clinical data on the prognostic impact of the size of individual ITDs. Keywords: genetic modification Nine stable 32D cell lines harboring unique human FLT3/ITD mutants, two parental 32 cell lines, two 32D stable cell lines harboring cloning vector only, and two 32D cell lines stably expressing human wild type FLT3 were subjected to the microarray analysis.
2010-04-08 | E-GEOD-12766 | biostudies-arrayexpress
Project description:This study aims to investigate fermentative metabolites in probiotic vegetable juice from four crop varieties (Brassica oleracea var. capitata, B. oleracea var. italica, Daucus carota L., and Beta vulgaris) and their antioxidant properties. Vegetable juice was inoculated with two lactic acid bacteria (LAB) (Companilactobacillus allii WiKim39 and Lactococcus lactis WiKim0124) isolated from kimchi and their properties were evaluated using untargeted UPLC-QTOF-MS/MS and GC-MS. The samples were also evaluated for radical (DPPH• and OH•) scavenging activities, lipid peroxidation, and ferric-reducing antioxidant power. The fermented vegetable juices exhibited high antioxidant activities and increased amounts of total phenolic compounds. Fifteen compounds and thirty-two volatiles were identified using UPLC-QTOF-MS/MS and GC-MS, respectively. LAB fermentation significantly increased the contents of d-leucic acid, indole-3-lactic acid, 3-phenyllactic acid, pyroglutamic acid, γ-aminobutyric acid, and gluconic acid. These six metabolites showed a positive correlation with antioxidant properties. Thus, vegetable juices fermented with WiKim39 and WiKim0124 can be considered as novel bioactive health-promoting sources.
| S-EPMC8614894 | biostudies-literature
Project description:The aim of this study was to determine the effects of six common commercial lactic acid bacteria (LAB) additives [A1, Lactobacillus plantarum, L. buchneri, and Enterococcus faecalis; A2, L. plantarum and L. casei; A3, L. plantarum and L. buchneri; A4, L. plantarum, L. buchneri, L. casei, and Pediococcus acidilactici; A5, L. plantarum (producing feruloyl esterase); and A6, L. buchneri, P. acidilactici, β-glucanase, and xylanase] on the bacterial community and fermentation quality of alfalfa silage. Alfalfa was harvested at the squaring stage, wilted in the field for 24 h, and ensiled without any additives (Control) or with A1, A2, A3, A4, A5, or A6. Microbial counts, bacterial community, fermentation parameters, and nutritional composition were determined after ensiling for 90 days. The total abundance of LAB genera on alfalfa pre-ensiling was 0.38% in bacterial community. The abundances of Lactobacillus, Enterococcus, and Pediococcus in the Control silage were 42.18, 40.18, and 8.09% of abundance, respectively. The abundances of Lactobacillus in A1-, A2-, A3-, A4-, and A5-treatments were 89.32, 92.93, 92.87, 81.12, and 80.44%, respectively. The abundances of Pediococcus and Lactobacillus in A6-treatment were 70.14 and 24.86%, respectively. Compared with Control silage, LAB-treated silage had lower pH and less ammonia nitrogen and water-soluble carbohydrates concentrations (p < 0.05). Further, the A5- and A6-treatments contained lower neutral detergent fiber, acid detergent fiber, and hemicellulose than other treatments (p < 0.05). Overall, LAB genera were presented as minor taxa in alfalfa pre-ensiling and as dominant taxa in alfalfa silage. Adding LAB additives improved the fermentation quality and altered the bacterial community of alfalfa silage. The main bacterial genera in Control silage were Lactobacillus, Enterococcus, and Pediococcus. Lactobacillus dominated the bacterial communities of A1-, A2-, A3-, A4-, and A5-treatments, while Pediococcus and Lactobacillus were dominant bacterial genera in A6-treatment. Inoculating A5 and A6 degraded the fiber in alfalfa silage. It is necessary to ensile alfalfa with LAB inoculants.
| S-EPMC9073077 | biostudies-literature
Project description:The objective is to obtain miRNA representative signatures both in plasma and bronchoalveolar cell fraction that could serve as biomarker in respiratory diseases. The identification of new less invasive biomarkers is necessary to improve the detection and prognostic outcome of respiratory pathological processes. The measurement of miRNA expression through less invasive techniques such as plasma and serum have been suggested to analysis of several lung malignancies including lung cancer. These studies are assuming a common deregulated miRNA expression both in blood and lung tissue. The present study aimed to obtain miRNA representative signatures both in plasma and bronchoalveolar cell fraction that could serve as biomarker in respiratory diseases. we have compared circulating plasma miRNA with the bronchoalveolar cell fraction-derived miRNA patterns from 10 patients with several lung disease using a RT-qPCR assay.
2011-10-20 | E-GEOD-33045 | biostudies-arrayexpress
Project description:The lysis and extraction of soluble bacterial proteins from cells is a common practice for proteomics analyses, but insoluble bacterial biomasses are often left behind. Here, we show that with triflic acid treatment, the insoluble bacterial biomass of Gram- and Gram+ bacteria can be rendered soluble. We use LC-MS/MS shotgun proteomics to show that bacterial proteins in the soluble and insoluble postlysis fractions differ significantly. Additionally, in the case of Gram- Pseudomonas aeruginosa, triflic acid treatment enables the enrichment of cell-envelope-associated proteins. Finally, we apply triflic acid to a human microbiome sample to show that this treatment is robust and enables the identification of a new, complementary subset of proteins from a complex microbial mixture.
| S-EPMC7108958 | biostudies-literature
Project description:To investigate effects of single-walled carbon nanohorns (SWCNHs) om total expression profile of tomato seeds and plants we introduced SWCNHs in MS agar medium in concentration of 25 ug/ml Objectives for this study included the identification of genes that were up or down-regulated at the transcriptional level in tomato seeds and seedlings in response to SWCNHs Seeds (1 day on medium) and 11-days old seedlings of wild type tomato seedlings (cv. Micro-Tom) growing on regular MS agar medium or MS medium supplemented with carbon nanohorns (25 ug/ml) were selected for RNA extraction and hybridization on Affymetrix microarrays. Keywords: stress responses
2015-01-01 | E-GEOD-57541 | biostudies-arrayexpress