Project description:Exercise stimulates systemic and tissue-specific adaptations that protect against lifestyle related diseases including obesity and type 2 diabetes. Exercise places high mechanical and energetic demands on contracting skeletal muscle, which require finely-tuned protein post-translational modifications involving signal transduction (e.g. phosphorylation) to elicit appropriate short- and long-term adaptive responses. To uncover the breadth of protein phosphorylation events underlying the adaptive responses to endurance exercise and skeletal muscle contraction, we performed global, unbiased mass spectrometry-based phosphoproteomic analyses of skeletal muscle from two rodent models, in situ muscle contraction in rats and treadmill-based endurance exercise in mice.
Project description:We employ RNA-seq of FACS sorted cell populations to identify genes that are enriched in cranial neural crest in relationship to the trunk. Transcriptional profiling of delaminating cranial and trunk neural crest subpopulations.
Project description:Background: Cutaneous squamous cell carcinoma (cSCC) is a common type of skin cancer but there are no comprehensive proteomic studies on this entity. Materials and Methods: We employed liquid chromatography coupled with tandem mass spectrometry (MS/MS) using formalin-fixed paraffin-embedded (FFPE) cSCC material to study the tumor and normal skin tissue proteomes. Ingenuity Pathway Analysis (IPA) was used to interpret the role of altered proteins in cSCC pathophysiology. Results were validated using the Human Protein Atlas and Oncomine database in silico. Results: Of 1,310 unique proteins identified, expression of an average of 144 and 88 proteins were significantly (p<0.05) increased and decreased, respectively, in the tumor samples compared to their normal counterparts. IPA analysis revealed disruptions in proteins associated with cell proliferation, apoptosis, and migration. In silico analysis confirmed that proteins corresponding to 12 antibodies, and genes corresponding to 18 proteins were differentially expressed between the two categories, validating our proteomic measurements. Conclusion: Label-free MS-based proteomics is useful for analyzing FFPE cSCC tissues.
Project description:Adult reproductive diapause is a powerful overwintering strategy for many continental insect species including bumblebees, which enables queens to survive several months through harsh winter conditions and then build new beehives in the following spring. There are few reports regarding the molecular regulatory mechanism of reproductive diapause in Bombus terrestris, which is an important pollinators of wild plants and crops, and our previous researches identified the conditions for reproductive diapause of year-round mass rearing. Here, we performed combined RNA sequencing transcriptomics and quantitative proteomic analyses in different development phases relate to reproductive diapause. According to the overall analysis, we found these differentially expressed proteins/genes act in the citrate cycle, insect hormone biosynthesis, insulin and mTOR signalling pathway. To get better sense of the reproductive diapause regulated mechanism, some genes regulated JH synthesis, insulin/ TOR signal pathway were detected, the BtRheb, BtTOR, BtVg and BtJHAMT had lower expression levels in diapause queens, and the JH III titers levels and some metabolic enzymes activities were significantly up-regulated in found post-diapause queens. After microinjected insulin-like peptides (ILPs) and JH analog (JHA), some indicators shows the significantly changes of hormones, cold tolerance substances, metabolic enzymes and reproduction. Along with other related researches, a reproductive diapause regulated model during B. terrestris year-round mass rearing process was establishment. This study contribute to a comprehensive view and the molecular regulate mechanism of productive diapause in eusocial insect.
Project description:We previously found that rhizobia-inoculation enhanced the soybean's salt tolerance; the transcription factor (TF) GmMYB173 and its downstream gene GmCHS5 dictate soybean’s flavonoid metabolism in response to this stress. For revealing the mechanism of the enhancement, quantitative phosphoproteomics and metabonomic approaches were used to identify phosphoproteins and metabolites that dominant the common pathway between salinity and rhizobia induced response in soybean roots.
Project description:We Have a pancreas MS2/MS3 dataset in this project. We predict all spectra in the datasets via Prosit then rescore. We have 100% FDR maxquant search results, and using percolator we get 1%FDR filtered results with andromeda Scores and another with features extracted from Prosit predictions.
Project description:During aging, senescent cells accumulate in bone marrow and secrete the dysfunctional factors, termed senescence associated secretory phenotype (SASP), which is implied to regulate bone metabolism. To identify the key SASP factors in bone marrow that influence skeletal aging, we analyzed the dysregulated factors in the bone marrow supernatant from young and aged rat through mass spectrometry. In another hand, BMSCs treated with rGCA, transfection of siRNA-Plxnb2 or controls were subjected to global quantitative phosphoproteomic analysis.
Project description:About “MS210144-1 to MS210144-12”: 6 samples: cell body-1#, cell body-2#, cell body-3#, Migrasome-1#, Migrasome-2#, Migrasome-3#, were labeled with tandem mass tags (TMT) reagents and then mixed. These combined TMT-labeled peptides were separated into 12 fractions (shown in list: from MS210144-1 to MS210144-12), then desalted by Sep-Pak columns and separated with a UPLC 3000 system and with an XBridgeTM BEH300 C18 column.
Project description:We created a custom-made microarray for D. montana with 101 genes known to affect traits important in diapause, photoperiodism, reproductive behaviour, circadian clock and stress tolerance in model Drosophila species. This array gave us a chance to filter out genes showing expression changes during photoperiodic reproductive diapause in a species adapted to live in northern latitudes with high seasonal changes. The three samples for the microarray experiments included young females (âyoungâ), 14 days old females cultured under diapause-preventing (âreproducingâ) and 14 days old females cultured under diapause-inducing conditions (âdiapausingâ). Each of these samples had three replicates. The microarray contained 197 unique probe sequences representing 101 candidate genes and seven housekeeping genes. Some of the probes had two copies per array, in which case the averages of their signals were calculated. The Agilent control probes included 77 negative control probes and 200 spike-in probes (10 different probe types, each represented by 20 copies per array).
Project description:CDK4/6 kinase inhibitors have shown great promise in clinical trials in various cancer types and have recently entered clinical trial for advanced prostate cancer. Although patients are expected to respond well to this class of drugs, development of resistance in some patients is anticipated. To pre-empt this and study how prostate cancer may evade CDK4/6 inhibition, new resistance models were generated from LNCaP and LAPC4 prostate cancer cells cells by prolonged culturing in presence of 0.5uM palbociclib. A shotgun phosphoproteomics approach was utilized and integrated with RNA sequencing data to unravel the molecular underpinnings of acquired resistance to palbociclib and resultant broad CDK4/6 inhibitor resistance.