Project description:A study to explore the transcriptome response of hymenophyllum dentatum in a desiccation-rehydration cycle using high-throughput sequencing (Illumina).
Project description:Atelocollagen gel is often used for three-dimensional culture of articular cartilage-derived cells, but further knowledge is needed about the effect of atelocollagen gel on cells. We performed a microarray analysis using human articular cartilage-derived cells cultured in three different methods (2D culture, 3D culture with atelocollagen gel, and 3D culture without atelocollagen gel).
Project description:The Spanish slug, Arion vulgaris, is considered one of the hundred most invasive species in Central Europe. The lack of natural predators can refer to the potential toxicity of slugs. However, no transcriptomic or proteomic study has been done so far in Arion vulgaris. In this study, we present the first investigation of expression profile in Arion vulgaris at the protein level. Two-dimensional (2D) gel electrophoresis and nano-LC-ESI-MS/MS were used to resolve and identify proteins from slug mantel and slug eggs. To facilitate proteomics in non-model organisms, mRNA-derived protein database was used for protein identification.
Project description:Mass spectrometry (MS)-based top-down proteomics (TDP) delineates proteoforms in cells and requires high-resolution proteoform separation. Herein, for the first time, we employed an automated capillary isoelectric focusing-tandem MS (cIEF-MS/MS) system for large-scale TDP of complex proteomes. Single-shot cIEF-MS/MS identified 771 proteoforms from an Escherichia coli (E. coli) proteome consuming only nanograms of proteins. Coupling two-dimensional size exclusion chromatography (SEC)-cIEF, named “gel-free 2D-PAGE”, to ESI-MS/MS enabled the identification of nearly 2000 proteoforms from the E. coli proteome. Label-free quantitative TDP of zebrafish male and female brains using the SEC-cIEF-MS/MS quantified thousands of proteoforms and revealed sex-dependent proteoform profiles in brains. We discovered several proteolytic proteoforms of pro-opiomelanocortin and prodynorphin with significantly higher abundance in male brains as potential endogenous hormone proteoforms. Multi-level quantitative proteomic analyses (TDP and bottom-up proteomics (BUP)) of the brains revealed that majority of proteoforms having statistically significant difference in abundance between genders (TDP) showed no abundance difference at the corresponding protein group level (BUP), which highlights the importance of delineating proteins in a proteoform-specific manner for accurately understanding protein function.
Project description:We obtained accesses to brain tissue and cerebrospinal fluid (CSF) from the only available post- mortem mucolipidosis type IV (MLIV) patient which became available only recently. We performed mass spectrometry (MS)- based proteomics. Our data demonstrate that pathological players detected in Mcoln1-/- mice are also relevant in the human disease. Moreover, we suggest some previously un-known pathological players. We complement this study by using Mcoln1-/- mice, and were able to confirm that many pathological pathways are evident early in disease development, emphasizing the need for early therapeutic intervention.
Project description:The objective of the present investigation was to consider the level of variation in the protein expression patterns of closely related Salmonella serovars, in order to search for protein factors with levels of expression or posttranslational modifications characteristic for each serovar. For the comparative expression analysis we have utilised classic 2D GE approach which revealed several proteins with serovar specific expression as well as proteins which do not alter their expression levels between serovars and strains. The proteins of interest were identified using LC/MS/MS. Keywords: 2D GE, MS/MS