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Immunoprecipitation followed by mass spectropmetry of Plasmodium falciparum Cullin2

ABSTRACT: This study is aim to characterize Plasmodium Cullin2 to find its interacting partners

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Plasmodium Falciparum (isolate 3d7)

TISSUE(S): Blood Cell, Blood

DISEASE(S): Malaria

SUBMITTER: Zeba Rizvi

LAB HEAD: Dr. Puran Singh Sijwali

PROVIDER: PXD040268 | Pride | 2024-02-14

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	Control_for_Cullin2_HA_Exp1a.raw	Raw
	Control_for_Cullin2_HA_Exp1ab.msf	Msf
	Control_for_Cullin2_HA_Exp1b.raw	Raw
	Control_for_Cullin2_HA_Exp2a.raw	Raw
	Control_for_Cullin2_HA_Exp2ab.msf	Msf

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Immunoprecipitation followed by mass spectropmetry of Plasmodium falciparum Cullin1

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CDC50 interacting partners of Plasmodium falcipraum

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Molecular Mechanisms of Master Regulator VqsM mediating Quorum-sensing and Antibiotic Resistance in Pseudomonas aeruginosa

Project description:The Pseudomonas aeruginosa quorum-sensing (QS) systems contribute to bacterial homeostasis and pathogenicity. Although the AraC family transcription factor VqsM has been characterized to control the production of virulence factors and QS signaling molecules, its detailed regulatory mechanisms still remain elusive. Here, we report that VqsM directly binds to the lasI promoter region, and thus regulates its expression. To identify additional targets of VqsM in P. aeruginosa PAO1, we performed chromatin immunoprecipitation followed by high-throughput DNA sequencing (ChIP-seq) which detected 48 enriched loci harboring VqsM-binding peaks in P. aeruginosa genome. The direct regulation of these genes by VqsM has been confirmed by Electrophoretic mobility shift assays (EMSAs) and quantitative real-time polymerase chain reactions (qRT-PCR). A VqsM-binding motif is found by using MEME suite and verified by footprint assays in vitro. In addition, VqsM directly binds to the promoter regions of antibiotic resistance regulator NfxB and the master type III system regulator ExsA. Notably, the vqsM mutant displayed more resistance to two types of antibiotics and promoted bacterial survival in a mouse model, compared to the wild type PAO1 strain. Collectively, this work provides new cues to better understand the detailed regulatory networks of QS systems, T3SS, and antibiotic resistance. Pseudomonas aeruginosa MAPO1 containing empty pAK1900 or pAK1900-VqsM-VSV

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ChIP-Seq analysis of Phytochrome Interacting Factor 5 DNA binding in low R/FR condition

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Genome-wide analysis of Yki and Sd localization in imaginal disks of Drosophila eye by ChIP Seq

Project description:Throughout Metazoa, developmental processes are controlled by a surprisingly limited number of conserved signaling pathways. Precisely how these signaling cassettes were assembled in early animal evolution remains poorly understood, as do the molecular transitions that potentiated the acquisition of their myriad developmental functions. Here we analyze the molecular evolution of the proto-oncogene YAP/Yorkie, a key effector of the Hippo signaling pathway that controls organ size in both Drosophila and mammals. Based on heterologous functional analysis of evolutionarily distant Yap/Yorkie orthologs, we demonstrate that a structurally distinct interaction interface between Yap/Yorkie and its partner TEAD/Scalloped became fixed in the eumetazoan common ancestor. We then combine transcriptional profiling of tissues expressing phylogenetically diverse forms of Yap/Yorkie with ChIP-seq validation in order to identify a common downstream gene expression program underlying the control of tissue growth in Drosophila. Intriguingly, a subset of the newly-identified Yorkie target genes are also induced by Yap in mammalian tissues, thus revealing a conserved Yap-dependent gene expression signature likely to mediate organ size control throughout bilaterian animals. Combined, these experiments provide new mechanistic insights while revealing the ancient evolutionary history of Hippo signaling. We sought to determine Yki and Sd target genes in Drosophila by immunoprecipitation of Yki, sd and RNA polymerase II. Chromatin immunoprecipitation of Yki, sd, and RNA polymerase II from eye disks was performed.

2014-03-01 | E-GEOD-54601 | biostudies-arrayexpress

Identification of dASF/SF2 potential mRNA targets

Project description:Deciphering the role of alternative splicing in developmental processes relies on the identification of key genes whose expression is controlled by splicing regulators throughout growth of a whole organism. Targeting expression of five SR proteins in the developing eye of Drosophila allowed us to show that these splicing factors induce various phenotypic alterations concerning eye organogenesis and viability. Although both dASF/SF2 and B52 caused defects in ommatidia structure, only B52 impairs normal photoreceptor axons projection and neurogenesis in visual ganglia. Consistently, microarray analyses revealed that many of the B52 targets are involved in brain organogenesis and we show that their splicing profile is altered both in B52 loss and gain of function. Conversely, a large proportion of dASF/SF2 targets are involved in eye development. This differential effect argues that SR proteins confer accuracy to developmental gene-expression programs, thus ensuring tissue identity and supporting cell-lineage decisions. Keywords: genetic modification Experiment aimed at identifying dASF/SF2 potential mRNA targets in the Drosophila developing eye Control: GMR X GFP-NLS trangenic larvae The 2 IP- GFP cy3 vs ASF cy5 rep.1 and IP- GFP cy5 vs ASF cy3 rep.1 samples correspond to dye-swap experiments. Two replicates (rep1 and rep2) are included.

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