Project description:ETFDH (electron transfer flavoprotein ubiquinone oxidoreductase) is a 64 kDa protein monomer located in the inner mitochondrial membrane, in charge of transferring the electrons received from the electron transfer flavoprotein ETF to the Coenzyme Q (Q). Pathological mutations in ETFDH lead to Multiple Acyl-CoA Dehydrogenase Deficiency (MADD; OMIM #231680). C2C12 cells lacking ETFDH were analysed by TMT analysis and compared to wt cells.
Project description:Mitochondrial Ca2+ ([Ca2+]M) uptake through its Ca2+ uniporter (MCU) is central to many cell functions such as bioenergetics, spatiotemporal organization of Ca2+ signals, and apoptosis. MCU activity is regulated by several intrinsic proteins including MICU1, MICU2, and EMRE. While significant details about the role of MICU1, MICU2, and EMRE in MCU function have emerged recently, a key challenge for the future experiments is to investigate how these regulatory proteins modulate mitochondrial Ca2+ influx through MCU in intact cells under pathophysiological conditions. This is further complicated by the fact that several variables affecting MCU function change dynamically as cell functions. To overcome this void, we develop a data-driven model that closely replicates the behavior of MCU under a wide range of cytosolic Ca2+ ([Ca2+]C), [Ca2+]M, and mitochondrial membrane potential values in WT, MICU1 knockout (KO), and MICU2 KO cells at the single mitochondrion and whole-cell levels. The model is extended to investigate how MICU1 or MICU2 KO affect mitochondrial function. Moreover, we show how Ca2+ buffering proteins, the separation between mitochondrion and Ca2+-releasing stores, and the duration of opening of Ca2+-releasing channels affect mitochondrial function under different conditions. Finally, we demonstrate an easy extension of the model to single channel function of MCU.
Project description:A mutant of L. plantarumWCFS1 (deletion of lp_2991) was compared with the wildtype grown in standard MRS broth. Cells were sampled at OD1 for mRNA extraction. Knockout vs wildtype. Technical replicates (same mRNA isolation) used for a dye swap.
Project description:Transcriptional profiling of S. thermophilus LMD-9 wild-type compared to the isogenic mutant strain CB052 (deletion of mecA, STER_0216) for the identification of the MecA regulon. Cells were grown in THB medium supplemented with glucose 1% (THBG) and sampled at OD600 = 0.4 for mRNA extraction wild-type vs knockout, 2 WT biological replicates (one used as technical replicate for a dye swap), 2 KO biological replicates (one used as technical replicate for a dye swap)
Project description:Transcriptional profiling of S. thermophilus LMD-9 wild-type compared to the isogenic mutant strain CB003 (deletion of comX, STER_0189) for the identification of the ComX regulon. Cells were grown in CDM medium supplemented with lactose 1% (CDML) and sampled at OD600 = 0.4 for mRNA extraction wild-type vs knockout, 2 WT biological replicates (one used as technical replicate for a dye swap), 2 KO biological replicates (one used as technical replicate for a dye swap)
Project description:Transcriptional profiling of S. thermophilus LMD-9 wild-type compared to the isogenic mutant strain CB0082 (deletion of hdiR, STER_0918) for the identification of the HdiR regulon. Cells were grown in CDM medium supplemented with lactose 1% (CDML) and sampled at OD600 = 0.4 for mRNA extraction wild-type vs knockout, 2 WT biological replicates (one used as technical replicate for a dye swap), 2 KO biological replicates (one used as technical replicate for a dye swap)
Project description:Mutations in the E3 ubiquitin ligase Mkrn3 are associated with precocious puberty in humans. In order to determine the targets of Mkrn3, we performed a TMT-based proteomic analysis of Mkrn3 WT vs KO mouse brains.
Project description:LRRC23 is required for stablizing the sperm axonemal structure. Mass spectrometry analysis was carried out to compare the proteome of Lrrc23 WT and KO sperm.
Project description:The 2-OG-Fe(II) dioxygenase family are critical for cellular adaptation to changes in oxygen concentration. We found that cells with OGFOD1 gene silencing in this family showed resistance to cell death under ischemia, and cDNA microarray analysis of OGFOD1 knockout human cells revealed downregulation of ATPAF1. Although reintroduction of the OGFOD1 wild-type gene to OGFOD1 KO cells restored ATPAF1 mRNA levels, the catalytically inactive OGFOD1 mutant did not.