ABSTRACT: Protein complexome analysis of Pseudomonas aeruginosa PAO1 at OD 0.3 in LB media through 10-40% glycerol gradient fractionation in 21 samples.
Project description:A 10 ul drop of B. cinerea spores prepared in half-strength commercial grape juice was placed in the middle of detached Arabidopsis leaves. A cock-borer of 6 mm diameter was used to harvest leaf discs starting from the edge of the lesion (close, 0-6 mm) and the edge of the first disc (away, 6-12 mm) 48 hr after inoculation. Control plants were inoculated with a 10 ul drop of half-strength commercial grape juice with no spores. Three Biological replicates were done of which the third replicate was a dye-swap. In total 12 samples were analyzed. Each array constituted one replicate making six arrays for the whole experiment.
Project description:Bacteria spatially confine cellular processes like protease secretion and signal transduction in membrane platforms termed functional membrane microdomains, which in certain organisational and functional features resemble the lipid rafts of eukaryotic cells. However, a rigorous understanding of their composition, assembly and biological significance is unknown. Here we use the human pathogen methicillin-resistant Staphylococcus aureus (MRSA) to show that the organization of these platforms requires a preferential interaction between unphosphorylated membrane saccharolipids and the scaffold protein flotillin. This interaction leads to their accumulation in specific membrane microdomains concomitantly to the attraction of membrane-associated multimeric complexes, for which flotillin promotes efficient oligomerization. One of these harbored proteins is the penicillin-binding protein PBP2a, responsible for penicillin resistance in MRSA. We took PBP2a as showcase to demonstrate that flotillin mutants are also defective in PBP2a oligomerization and activity. Thus, perturbation of microdomains assembly, using commercially available drugs, interferes with PBP2a oligomerization and causes a relapse of MRSA penicillin resistance in vitro and in vivo, resulting in MRSA infections susceptible to conventional penicillin treatments. Our study shows that bacterial cells organize sophisticated programs for cellular compartmentalization and unravels a novel strategy to develop antimicrobial therapies for multi-drug resistance pathogens.
Project description:To determine interactors of Aurora-A, HA tagged Aurora-A was immunoprecipitated from MV4-11 cells stably expressing HA tagged Aurora-A wild type and compared to MV4-11 cells expressing empty vector.
Project description:Jasmonates is inductively produced as a major plant hormone responsible for defense reactions in plants against both biotic and abiotic stresses, such as pathogen infection and mechanical wounding. We identified JA-inducible genes in the wild-type rice leaves 0 - 4 h after JA treatment using 44k microarray. Expression profiling in the wild-type rice leaves treated with jasmonic acid for 0.5, 1, 2, and 4 h was compared with that in the untreated wild-type rice leaves using two-color method with three biological replicates.
Project description:ForJ, ForF and ForZ are cluster situated regulators of the formicamycin biosynthetic gene cluster in Streptomyces forimcae. This ChIP Sequencing experiment was conducted to identify where in the genome these regulators bind in order to identify which transcripts they might regulate.
Project description:Jasmonates is inductively produced as a major plant hormone responsible for defense reactions in plants against both biotic and abiotic stresses, such as pathogen infection and mechanical wounding. Jasmonoyl isoleucine is known to be a bioactive compound of jasmonate and plays a pivotal role for plant defenses. We identified OsJAR1M-bM-^HM-^Rrelated JA-inducible genes in osjar1 tos17 mutant (osjar1-2) rice leaves 0 - 2 h after JA treatment using 44k microarray. Expression profiling in the wild-type rice leaves treated with jasmonic acid for 0, 0.5, 1, and 2 h was compared with that in the osjar1 mutant leaves treated with jasmonic acid for 0, 0.5, 1, and 2 h using two-color method with three biological replicates.
Project description:22 total proteome samples from E. coli wild type resolved on a glycerol gradient resulting in 20 fractions and a pellet fraction. A lysate sample is given as input control. Further, 2 affinity purification samples comparing YggL-3xFLAG pulldown vs. the wild type is given. In this case, each sample was run on a gel and the lanes cut into 15 gel pieces each.
Project description:Whole genome sequencing (WGS) of tongue cancer samples and cell line was performed to identify the fusion gene translocation breakpoint. WGS raw data was aligned to human reference genome (GRCh38.p12) using BWA-MEM (v0.7.17). The BAM files generated were further analysed using SvABA (v1.1.3) tool to identify translocation breakpoints. The translocation breakpoints were annotated using custom scripts, using the reference GENCODE GTF (v30). The fusion breakpoints identified in the SvABA analysis were additionally confirmed using MANTA tool (v1.6.0).