Project description:Differential analysis of Methylobacterium extorquens DM4 in methanol versus dichloromethane condition using shotgun label free MS1 quantification approach
Project description:The leaf extract of T. indica had been reported to posses high phenolic content and showed high antioxidant activities. However, scientific data on the molecular mechanisms underlying the beneficial properties of the leaf extract are still lacking. In this study, the effects of the leaf extract on the expression of genes in cultured HepG2 cells were investigated using microarray technology. The leaf extract significantly regulated the expression of genes involved with consequential impact on the coagulation system, cholesterol biosynthesis, xenobiotic metabolism signaling and antimicrobial response. HepG2 cells were seeded and treated with an IC20 concentration of the methanol leaf extract of T. indica for 24 h. Following this, cells were trypsinized and then preciptated by centrifugation. Cells were washed with phosphate buffer saline (PBS) before total cellular RNA (tcRNA) were extracted from the cells. tcRNA from both untreated and T. indica leaf-treated HepG2 cells were selected for RNA extraction and hybridization on Affymetrix microarrays. All experiments were done in triplicate. The microarray analysis was performed on Affymetrix Human Gene 1.0 S.T Array according to the manufacturer's protocol. The gene sets were then subjected to analysis of variance (ANOVA) in the Partek Genomics Suite software to determine significantly expressed genes which was set according to P value less than 0.05 and fold change difference of equal to or greater than 1.5.
Project description:This project is a proteomic comparison of Hyphomicrobium sp. MC8b grown with dichloromethane or with methanol. The datasets were obtained using the annotated genome of Hyphomicrobium sp. MC8b.
Project description:We carried out a prospective, longitudinal, single-center, observational cohort study of patients with confirmed acute methanol poisoning that were treated in hospitals during a mass methanol poisoning outbreak in the Czech Republic in 2012. Venous blood for proteomic analysis was obtained from 24 patients with confirmed acute methanol poisoning upon admission to the hospital (group M (“Methanol”)) with heparin administration for hemodialysis and ethanol or fomepizole administration as the antidote to block ADH. In the follow-up group of survivors of methanol poisoning (group S (“Survivors”)), venous blood samples for proteomic analysis were obtained from 46 patients during the examination, which took place 4 years after discharge from the hospital. For the control group not exposed to methanol, 24 healthy subjects were recruited (group C, “Controls”). Blood samples were spun, the serum was separated, and the samples were frozen to −80 °C until the analyses. Blood serum samples were depleted of most abundant serum proteins using Agilent MARS 14 column, samples fractionated and fractions containing proteins of interest precipitated. Samples were analyzed using LC-MS/MS Thermo Orbitrap Fusion (UHPLC-ESI-Q-OT-qIT) and identified proteins with differential expression.
Project description:This project is a proteomic comparison of Hyphomicrobium sp. MC8b grown with dichloromethane or with methanol. The datasets were obtained using a pan-proteomic database built by merging the predicted proteomes from the annotated genomes of 13 Hyphomicrobium strains.
Project description:Introduction: The application of single-cell RNA sequencing has greatly improved our under-standing of various cellular and molecular mechanisms involved in physiological and pathophysi-ological processes. However, obtaining living cells for this technique can be difficult under certain conditions. To solve this problem, the methanol fixation method appeared as a promising alternative for routine clinical use. Materials and Methods: In this study, we selected two AML samples that had been fixed in methanol for 12–18 months. Once the cells were rehydrated, these samples were subjected to single-cell RNA sequencing. We then compared the results obtained from these samples with those obtained from the same samples cryopreserved in DMSO. Results: We used a previously validated methanol fixation protocol to perform scRNA-seq on DMSO cryopreserved cells and cells fixed in methanol for more than one year. Preliminary results show that methanol fixation induces some genetic and transcriptional modification compared with DMSO cryopreservation but remains a valuable method for single-cell analysis of primary human leukemia cells. Conclusions: The initial findings from this study highlight certain resemblances in methanol fixation over a 12-month period and cryopreservation with DMSO, along with associated transcriptional level modifications. However, we observed genetic degradation in the fixation condition when extending beyond one year. Despite certain study limitations, it is evident that short-term methanol fixation can be effec-tively used for leukemia blast samples. Its ease of implementation holds the potential to simplify the integration of this technique into routine clinical practice.
Project description:We recently showed that methanol emitted by wounded plants might function as a signaling molecule for plant-to-plant and plant-to-animal communications. In mammals, methanol is considered a poison because the enzyme alcohol dehydrogenase (ADH) converts methanol into toxic formaldehyde. However, the detection of methanol in the blood and exhaled air of healthy volunteers suggests that methanol may be a chemical with specific functions rather than a metabolic waste product. Using a genome-wide analysis of the mouse brain, we demonstrated that an increase in blood methanol concentration led to a change in the accumulation of mRNAs from genes primarily involved in detoxification processes and regulation of the alcohol/aldehyde dehydrogenases gene cluster. Removal of the intestine significantly decreased the rate of methanol addition to the plasma and suggested that the gut flora may be involved in the endogenous production of methanol. Liver mRNA quantification showed changes in the accumulation of mRNAs from genes involved in cell signalling and detoxification processes. We hypothesized that endogenous methanol acts as a regulator of homeostasis by controlling the mRNA synthesis
Project description:The leaf extract of T. indica had been reported to posses high phenolic content and showed high antioxidant activities. However, scientific data on the molecular mechanisms underlying the beneficial properties of the leaf extract are still lacking. In this study, the effects of the leaf extract on the expression of genes in cultured HepG2 cells were investigated using microarray technology. The leaf extract significantly regulated the expression of genes involved with consequential impact on the coagulation system, cholesterol biosynthesis, xenobiotic metabolism signaling and antimicrobial response.