Rui Wang Similar Datasets
Project description:Platelet concentrates (PCs) represent a blood transfusion product with a major concern for safety as their storage temperature (20-24ºC) allows bacterial growth, and their maximum storage time period (less than a week) precludes complete microbiological testing. Pathogen inactivation technologies (PITs) provide an additional layer of safety to the blood transfusion products from known and unknown pathogens (such as bacteria, viruses and parasites). In this context, PITs (such as Mirasol Pathogen Reduction Technology -PRT-) have been developed and are implemented in many countries. However, several studies have shown in vitro that Mirasol PRT induces a certain level of platelet shape change, hyperactivation, basal degranulation and increased oxidative damage during storage. It has been suggested that Mirasol PRT might accelerate what has been described as the platelet storage lesion (PSL), but supportive molecular signatures have not been obtained. We aimed at dissecting the influence of both variables, i.e. Mirasol PRT and storage time, at the proteome level. We present comprehensive proteomics data analysis of Control PCs and PCs treated with Mirasol PRT at storage days 2, 6 and 8. Our workflow was set to perform proteomics analysis using a gel-free and label-free quantification (LFQ) approach. Semi-quantification was based on LFQ signal intensities of identified proteins using MaxQuant/Perseus software platform. We identified marginal differences between Mirasol PRT and control PCs during storage. However, those significant changes at the proteome level were specifically related to the functional aspects previously described to affect platelets upon Mirasol PRT, and in addition, the effect of Mirasol PRT on the platelet proteome appeared not to be exclusively due to an accelerated or enhanced PSL. In summary, semi-quantitative proteomics allows to discern between proteome changes due to Mirasol PRT or PSL, and proves to be a methodology suitable to phenotype platelets in an unbiased manner, in various physiological contexts.
2018-03-23 | PXD008119 | Pride
Project description:This series represents the complete series of the human 293h media depleted storage on agarose / rehydration condition course analysis. Samples include Control, monolayer; Control, monolayer/full recovery, antibiotics; Spheroid, no storage; two week storage/0hr recovery; two week storage/full recovery; four week storage/0hr recovery; six week storage/0hr recovery. Keywords = 293h cells Keywords = desiccation Keywords = rehydration Keywords = spheroid Keywords = stabilization Keywords = ambient temperature Keywords: other
2005-08-01 | GSE1364 | GEO
Project description:Bacteria regulate their cellular resource allocation to enable their fast growth-adaptation to a variety of environmental niches. We studied the ribosomal allocation, growth and expression profile of two sets of fast-growing mutants of Escherichia coli K-12 MG1655. Mutants with 3 copies of the stronger ribosomal RNA operons grew faster than the wild-type strain in minimal media and show similar phenotype to previously studied rpoB mutants. All of them displayed increased ribosomal content, a longer diauxic shift and a reduced activity of the aceBAK operon, indicative of repressed gluconeogenic pathways. Transcriptomic profiles of fast-growing mutants showed common downregulation of hedging functions and upregulated growth functions. Proteome allocation estimations showed an increase in the growth-related proteome for fast-growing strains, but not an increased cellular budget for recombinant protein production. These results show that two different regulatory perturbations (rRNA promoters or rpoB mutations) increasing ribosomal allocation optimize the proteome for growth with a concomitant fitness cost.
2022-02-21 | GSE180830 | GEO
Project description:This series represents the complete series of the human 293h media depleted storage on agarose / rehydration condition course analysis. Samples include Control, monolayer; Control, monolayer/full recovery, antibiotics; Spheroid, no storage; two week storage/0hr recovery; two week storage/full recovery; four week storage/0hr recovery; six week storage/0hr recovery.
2008-06-11 | E-GEOD-1364 | biostudies-arrayexpress
Project description:Human breast milk (HBM) is the ideal source of nutrients for infants and is rich in microRNA (miRNA). In recent years, expressed breast milk feeding rather than direct breastfeeding is becoming increasingly prevalent for various reasons. HBM requires storage and processing, which can cause various changes in the ingredients. We investigated how the miRNAs in HBM change due to processes often used in real life. HBM samples collected from 10 participants were each divided into 7 groups according to the storage temperature, thawing method, and storage period. And we analyzed the miRNA changes in each group. Significant changes in expression of several miRNAs were confirmed when HBM were heated by microwave immediately after collection, stored at room temperature for 1 week, or frozen for 1 week. Changes in expression were also dependent on the frozen period or thawing method. However, there was no change in the miRNA expression in all samples refrigerated for 1 week. The expression of miRNA can change depending on the diverse processing, storage, and thawing methods of breast milk, and refrigerated storage may be an ideal method to maintain a state of miRNA.
2022-11-03 | GSE216940 | GEO
Project description:Tardigrades contain characteristic free-floating body cavity cells that are also called storage cells. To investigate the cell-specific expression patterns of tardigrade-unique genes, the expression levels of dissected storage cells are compared to those of the whole body.
2023-01-04 | GSE212632 | GEO
Project description:Proteome-wide determinants of co-translational chaperone binding in bacteria
| PRJNA1238275 | ENA
Project description:Investigate the effect of storage conditions of tumor specimens on the proteome and phosphoproteome profiling
| PRJNA477672 | ENA
Project description:Three storage conditions were compared in 293T cells: (1) 37C (control), (2) 4C overnight, and (3) -80C storage followed by liquid nitrogen preservation. Either cold storage induced significant alterations in cell diameter, circularity, and proteome composition. This study highlights the importance of preserving cells under viable conditions to maintain the integrity of the proteome and underscore the necessity of optimizing cell storage protocols to ensure accurate representation of the cellular proteome, particularly in the context of SCP studies. By elucidating the intricate interplay between storage conditions, cellular morphology, and protein expression, this study contributes valuable insights towards advancing SCP methodologies and enhancing our understanding of cellular heterogeneity.
2024-06-26 | MSV000095162 | MassIVE
Project description:The genome sequence is the “blue-print of life”, but proteomics is required to relate this blue-print of life to the actual physiology of living cells. Because of their low complexity – only about 2.000 proteins make a Staphylococcus aureus cell viable – bacteria are excellent model systems to identify the entire protein assembly of a living organism. Many of the studies on physiological proteomics of bacteria, however, still rely on 2D gel-based technologies that visualize only a minor part of the proteome. In this study it will be shown that the majority of proteins expressed in the Gram-positive human pathogen S. aureus can be identified and even quantified by a combination of gel-based and gel-free approaches, the latter having undergone formidable improvements over the last 10 years. S. aureus has been the model of choice for our proteomic studies, because it combines high pathogenicity with increasing antibiotic resistance, which calls for new leads in the development of anti-staphylococcal therapy. On the way towards the entire proteome of S. aureus, we analysed four subproteomic fractions: cytosolic proteins, membrane-bound proteins, cell-surface associated and extracellular proteins, the two latter fractions containing most of the virulence factors. To obtain quantitative results, we compared growing cells and non-growing/stationary phase cells using the 15N metabolic labelling approach. With almost 2.000 proteins, 80 % of the expressed proteome was identified and even quantified in growing and non-growing cells. A comprehensive inventory of the entire protein assembly during the two physiologically distinct states is presented, which integrates data ranging from gene expression to subcellular localization. Three major protein classes were distinguished: (i) Proteins induced in the stationary phase only (ii) Vegetative proteins, no longer synthesized but stable in the stationary phase (iii) Vegetative proteins, no longer required in non-growing cells and finally degraded. This quantitative proteomics approach for growing/non-growing cells, which represents a proof-of-principle for whole-cell physiological proteomics, can now be extended to address particular infection-relevant physiological states. Importantly, the present model study represents the highest coverage of a bacterial proteome so far (except low complexity bacteria). It thus paves the way towards a new understanding of cell physiology and pathophysiology of S. aureus and related pathogenic bacteria, opening a new era in infection-related research on this crucial pathogen. For the DNA-microarray experiment RNA was extracted from two independently grown cultures. One was grown in 14N labelled BioExpress medium and the other in 15N labelled BioExpress medium. Samples of exponentially growing cells (OD600=0.5) and of cell at 5h after entry into stationary phase were harvested from every culture. Equal amounts of all four RNAs were pooled and the pool was used as common reference (Cy3-labeld) for the four sample RNAs (Cy3). Thus, in total four hybridizations, one for each sample versus the common reference, were performed.
2009-11-11 | E-GEOD-15060 | biostudies-arrayexpress