Project description:We identified RNA binding motif protein 47 (RBM47) as a target gene of transforming growth factor (TGF)-beta in mammary gland epithelial cells (NMuMG cells) that have undergone the epithelial-to-mesenchymal transition (EMT). TGF-beta repressed RBM47 expression in NMuMG cells and lung cancer cell lines. Expression of RBM47 correlated with good prognosis in patients with lung, breast, and gastric cancer. RBM47 suppressed the expression of cell metabolism-related genes, which were the direct targets of nuclear factor erythroid 2-related factor 2 (Nrf2; also known as NFE2L2). RBM47 bound to KEAP1 and Cullin3 mRNAs, and knockdown of RBM47 inhibited their protein expression, which led to enhanced binding of Nrf2 to target genomic regions. Knockdown of RBM47 also enhanced the expression of some Nrf2 activators, p21/CDKN1A and MafK induced by TGF-beta. Both mitochondrial respiration rates and the side population cells in lung cancer cells increased in the absence of RBM47. Our findings, together with the enhanced tumor formation and metastasis of xenografted mice by knockdown of the RBM47 expression, suggested tumor suppressive roles for RBM47 through the inhibition of Nrf2 activity. Effect of shRNA for RBM47 and TGF-beta on gene expression was evaluated by RNA-seq and RBM47-bound RNAs were identified by RIP-seq in A549 cells.
Project description:Exposure to particulate matter (PM) has been associated with deficits in lung function growth among children in Western countries. However, few studies have explored this association in developing countries, where PM levels are often substantially higher.Children (n = 3273) 6-12 years of age were recruited from 8 schools in 4 Chinese cities. The lung function parameters of forced vital capacity (FVC) and forced expiratory volume in 1 second (FEV1) were measured using computerized spirometers twice a year for up to 3 years (1993-1996). Dichotomous samplers placed in each schoolyard were used to measure PM2.5 and PM10 (PM with diameter ? 2.5 ?m and ? 10 ?m, respectively). Multivariable generalized estimating equations were used to examine the association between the quarterly average PM levels and lung function growth during the period of follow-up.Annual average PM2.5 and PM10 levels in the 4 cities ranged from 57 to 158 ?g/m and 95 to 268 ?g/m, respectively. In multivariable models, an increase of 10 ?g/m of PM2.5 was associated with decreases of 2.7 mL FEV1 (95% confidence interval = -3.5 to -2.0), 3.5 mL FVC (-4.3 to -2.7), 1.4 mL/year FEV1 growth (-1.8 to -0.9), and 1.5 mL/year FVC growth (-2.0 to -1.0). Similar results were seen with PM10 exposure.Exposure to ambient particulate matter was associated with decreased growth in lung function among Chinese children.
Project description:In order to identify how MnTE-2-PyP affects p300 association to chromatin genome-wide, we performed a p300 chromatin Immunoprecipitation assay followed by Next Generation Sequencing on PC3 cells treated with or without MnTE-2-PyP one hour post-irradiation (Figure 3A). Based on the called peaks near genes, we predicted that HIF-1βand CREB transcription factors were associating DNA less in the presence of MnTE-2-PyP. DNA was ChIP-Fixed from Pc3 cells treated with 20 Gy radiation and with and without T2E drug. There are 2 biological replicates of PC3 untreated cells and 3 biological replicates of PC3 cells treated with MnTE-2-PyP. There are two corresponding input samples for the biological replicates.
Project description:Trypanosomatids such as Leishmania, Trypanosoma brucei and Trypanosoma cruzi belong to the order Kinetoplastida and are the source of many significant human and animal diseases. Current treatment is unsatisfactory and is compromised by the rising appearance of drug resistant parasites. Novel and more effective chemotherapeutics are urgently needed to treat and prevent these devastating diseases, which relies on the identification of essential, parasite specific targets that are absent in the host. Lipids constitute essential components of the cell and carry out multiple critical functions from building blocks of biological membranes to regulatory roles in signal transduction, organellar biogenesis, energy storage, and virulence. The recent technological advances of lipidomics has facilitated the broadening of our knowledge in the field of cellular lipid content, structure, functions, and metabolic pathways.This review highlights the application of lipidomics (i) in the characterization of the lipidome of kinetoplastid parasites or of their subcellular structure(s), (ii) in the identification of unique lipid species or metabolic pathways that can be targeted for novel drug therapies, (iii) as an analytic tool to gain a deeper insight into the roles of specific enzymes in lipid metabolism using genetically modified microorganisms, and (iv) in deciphering the mechanism of action of anti-microbial drugs on lipid metabolism. Lastly, an outlook stating where the field is evolving is presented.Lipidomics has contributed to the expanding knowledge related to lipid metabolism, mechanism of drug action and resistance, and pathogen-host interaction of trypanosomatids, which provides a solid basis for the development of better anti-parasitic pharmaceuticals.
Project description:The quality (color, tenderness, juiciness, protein content, and fat content) of poultry meat is closely linked to age, with older birds typically exhibiting increased intramuscular fat (IMF) deposition. However, specific lipid metabolic pathways involved in IMF deposition remain unknown. To elucidate the mechanisms underlying lipid changes, we conducted a study using meat geese at 2 distinct growth stages (70 and 300 d). Our findings regarding the approximate composition of the meat revealed that as the geese aged 300 d, their meat acquired a chewier texture and displayed higher levels of IMF. Liquid chromatography-mass spectrometry (LC-MS) was employed for lipid profiling of the IMF. Using a lipid database, we identified 849 lipids in the pectoralis muscle of geese. Principal component analysis and orthogonal partial least squares discriminant analysis were used to distinguish between the 2 age groups and identify differential lipid metabolites. As expected, we observed significant changes in 107 lipids, including triglycerides, diglycerides, phosphatidylethanolamine, alkyl-glycerophosphoethanolamine, alkenyl-glycerophosphoethanolamine, phosphatidylcholine, phosphatidylinositol, lysophosphatidylserine, ceramide-AP, ceramide-AS, free fatty acids, cholesterol lipids, and N-acyl-lysophosphatidylethanolamine. Among these, the glyceride molecules exhibited the most pronounced changes and played a pivotal role in IMF deposition. Additionally, increased concentration of phospholipid molecules was observed in breast muscle at 70 d. Unsaturated fatty acids attached to lipid side chain sites enrich the nutritional value of goose meat. Notably, C16:0 and C18:0 were particularly abundant in the 70-day-old goose meat. Pathway analysis demonstrated that glycerophospholipid and glyceride metabolism were the pathways most significantly associated with lipid changes during goose growth, underscoring their crucial role in lipid metabolism in goose meat. In conclusion, this work provides an up-to-date study on the lipid composition and metabolic pathways of goose meat and may provide a theoretical basis for elucidating the nutritional value of goose meat at different growth stages.
Project description:To demonstrate that the P. multistriata gene MRP3 is responsible for sex determination, we overexpressed it in a mating type minus strain. The transgenic strain generated displayed sex reversal and behaved like a strain of the opposite mating type. In this study, we compared the gene expression profile of the wild type versus the transformed strain.
Project description:In this study, we have investigated the physiological consequences of PHB (poly(3-hydroxybutyrate)) synthesis in H. seropedicae by characterising the trancriptional changes in a mutant strain lacking phaC1 gene which codes for the PHA synthase enzyme essential for the last step in the synthesis of PHB. To do this experiment both wild type (SmR1) and phaC1 mutant were cultured on Nfb-Malate-HP media suplemented with 20 mM of ammonium chloride under 30 Celsius degrees and 120 rpm shaking rate until the late log-phase (O.D600 = 1.0), when the peak of PHB production is observed. The cultures obtained as above were harvested for RNA extraction and transcriptome analysis.
Project description:Alcoholic fatty liver disease (AFLD) is characterized by lipid accumulation and inflammation and can progress to cirrhosis and cancer in the liver. AFLD diagnosis currently relies on histological analysis of liver biopsies. Early detection permits interventions that would prevent progression to cirrhosis or later stages of the disease. Herein, we have conducted the first comprehensive time-course study of lipids using novel state-of-the art lipidomics methods in plasma and liver in the early stages of a mouse model of AFLD, i.e., Lieber-DeCarli diet model. In ethanol-treated mice, changes in liver tissue included up-regulation of triglycerides (TGs) and oxidized TGs and down-regulation of phosphatidylcholine, lysophosphatidylcholine, and 20-22-carbon-containing lipid-mediator precursors. An increase in oxidized TGs preceded histological signs of early AFLD, i.e., steatosis, with these changes observed in both the liver and plasma. The major lipid classes dysregulated by ethanol play important roles in hepatic inflammation, steatosis, and oxidative damage. Conclusion: Alcohol consumption alters the liver lipidome before overt histological markers of early AFLD. This introduces the exciting possibility that specific lipids may serve as earlier biomarkers of AFLD than those currently being used.
Project description:Glycosphingolipids (GSLs) contain one or more sugars that are attached to a sphingolipid moiety, usually to a ceramide, but in rare cases also to a sphingoid base. A large structural heterogeneity results from differences in number, identity, linkage, and anomeric configuration of the carbohydrate residues, and also from structural differences within the hydrophobic part. GSLs form complex cell-type specific patterns, which change with the species, the cellular differentiation state, viral transformation, ontogenesis, and oncogenesis. Although GSL structures can be assigned to only a few series with a common carbohydrate core, their structural variety and the complex pattern are challenges for their elucidation and quantification by mass spectrometric techniques. We present a general overview of the application of lipidomics for GSL determination. This includes analytical procedures and instrumentation together with recent correlations of GSL molecular species with human diseases. Difficulties such as the structural complexity and the lack of standard substances for complex GSLs are discussed.