A5036063971- Bioinformatics and Genomic Networks
- Genetics, Aging, and Longevity in Model Organisms
- Microbial Metabolic Engineering and Bioproduction
- Epigenetics and DNA Methylation
- RNA and protein synthesis mechanisms
- Cancer-related gene regulation
- RNA modifications and cancer
- Ubiquitin and proteasome pathways
- CRISPR and Genetic Engineering
- Computational Drug Discovery Methods
- Cellular transport and secretion
- Genomics and Phylogenetic Studies
- Wnt/β-catenin signaling in development and cancer
- Advanced Proteomics Techniques and Applications
- Animal Genetics and Reproduction
- RNA Research and Splicing
- Hedgehog Signaling Pathway Studies
- Brucella: diagnosis, epidemiology, treatment
- Bacteriophages and microbial interactions
- Fungal and yeast genetics research
- Histone Deacetylase Inhibitors Research
- Protein Kinase Regulation and GTPase Signaling
- Genetics and Neurodevelopmental Disorders
- Protein Structure and Dynamics
- Advanced biosensing and bioanalysis techniques
University of Michigan
2011-2022
Michigan United
2019
Cedars-Sinai Medical Center
2018
Harvard University
2003-2013
Dana-Farber Cancer Institute
2003-2013
Harvard University Press
2002-2009
Ghent University
2008
Center for Systems Biology
2004-2008
Massachusetts General Hospital
2005
University of Namur
2004
To initiate studies on how protein-protein interaction (or "interactome") networks relate to multicellular functions, we have mapped a large fraction of the Caenorhabditis elegans interactome network. Starting with subset metazoan-specific proteins, more than 4000 interactions were identified from high-throughput, yeast two-hybrid (HT=Y2H) screens. Independent coaffinity purification assays experimentally validated overall quality this Y2H data set. Together already described and interologs...
Current yeast interactome network maps contain several hundred molecular complexes with limited and somewhat controversial representation of direct binary interactions. We carried out a comparative quality assessment current data sets, demonstrating that high-throughput two-hybrid (Y2H) screening provides high-quality interaction information. Because large fraction the remains to be mapped, we developed an empirically controlled mapping framework produce “second-generation” high-quality, Y2H...
The recently completed Caenorhabditis elegans genome sequence allows application of high-throughput (HT) approaches for phenotypic analyses using RNA interference (RNAi). As large data sets become available, “phenoclustering” strategies can be used to begin understanding the complex molecular networks involved in development and other biological processes. current HT-RNAi resources represent a great asset profiling but are limited by lack flexibility. For instance, existing do not take...
RNA interference (RNAi) of target genes is triggered by double-stranded RNAs (dsRNAs) processed conserved nucleases and accessory factors. To identify the genetic components required for RNAi, we performed a genome-wide screen using an engineered RNAi sensor strain Caenorhabditis elegans . The identified 90 genes. These included Piwi/PAZ proteins, DEAH helicases, binding/processing factors, chromatin-associated DNA recombination nuclear import/export 11 known machinery. We demonstrate that...
The advent of systems biology necessitates the cloning nearly entire sets protein-encoding open reading frames (ORFs), or ORFeomes, to allow functional studies corresponding proteomes. Here, we describe generation a first version human ORFeome using newly improved Gateway recombinational approach. Using Mammalian Gene Collection (MGC) resource as starting point, report successful 8076 ORFs, representing at least 7263 genes, mini-pools PCR-amplified products. These were assembled into 1.1...
Caenorhabditis elegans SKN-1 (ortholog of mammalian Nrf1/2/3) is critical for oxidative stress resistance and promotes longevity under reduced insulin/IGF-1–like signaling (IIS), dietary restriction (DR), normal conditions. inducibly activates genes involved in detoxification, protein homeostasis, other functions response to stress. Here we used genome-scale RNA interference (RNAi) screening identify mechanisms that prevent inappropriate target gene expression non-stressed We identified 41...
Bacteria of the Brucella genus are facultative intracellular class III pathogens. These bacteria able to control trafficking their vacuole, presumably by use yet unknown translocated effectors. To identify such effectors, we used a high-throughput yeast two-hybrid screen interactions between putative human phagosomal proteins and predicted spp. proteins. We identified specific interaction small GTPase Rab2 protein named RicA. This was confirmed GST-pull-down with GDP-bound form Rab2. A...
Abstract Background The retinoblastoma tumor suppressor (Rb) acts in a conserved pathway that is deregulated most human cancers. Inactivation of the single Rb-related gene Caenorhabditis elegans, lin-35 , has only limited effects on viability and fertility, yet causes changes cell-fate cell-cycle regulation when combined with inactivation specific other genes. For instance, Rb synthetic multivulva (synMuv) class B gene, which phenotype inactivated simultaneously A or C synMuv gene. Results...
Src homology 3 (SH3) domains bind peptides to mediate protein–protein interactions that assemble and regulate dynamic biological processes. We surveyed the repertoire of SH3 binding specificity using peptide phage display in a metazoan, worm Caenorhabditis elegans , discovered it structurally mirrors budding yeast Saccharomyces cerevisiae . then mapped interactome stringent two‐hybrid compared with equivalent map for yeast. found resembles analogous network because is significantly enriched...
Abstract Background Human T-cell leukemia virus type 1 (HTLV-1) and 2 both target T lymphocytes, yet induce radically different phenotypic outcomes. HTLV-1 is a causative agent of Adult (ATL), whereas HTLV-2, highly similar to HTLV-1, causes no known overt disease. HTLV gene products are engaged in dynamic struggle activating antagonistic interactions with host cells. Investigations focused on one or few genes have identified several human factors interacting viral proteins. Most the...
Article13 October 2017Open Access Source DataTransparent process RBPJ/CBF1 interacts with L3MBTL3/MBT1 to promote repression of Notch signaling via histone demethylase KDM1A/LSD1 Tao Xu Department Pathology, University Michigan Medical School, Ann Arbor, MI, USA Search for more papers by this author Sung-Soo Park Benedetto Daniele Giaimo Institute Biochemistry, Giessen, Germany Daniel Hall Molecular Genetics, Biochemistry and Microbiology, Cincinnati College Medicine, Cincinnati, OH,...
The bacteria of the Brucella genus are responsible for a worldwide zoonosis called brucellosis. They belong to α-proteobacteria group, as many other that live in close association with eukaryotic host. Importantly, Brucellae mainly intracellular pathogens, and molecular mechanisms their virulence still poorly understood. Using complete genome sequence melitensis , we generated database protein-coding open reading frames (ORFs) constructed an ORFeome library 3091 Gateway Entry clones, each...
The phosphatidylinositol 3-kinase-mammalian target of rapamycin (PI3K-mTOR) pathway plays pivotal roles in cell survival, growth, and proliferation downstream growth factors. Its perturbations are associated with cancer progression, type 2 diabetes, neurological disorders. To better understand the mechanisms action regulation this pathway, we initiated a large scale yeast two-hybrid screen for 33 components PI3K-mTOR pathway. Identification 67 new interactions was followed by validation...