A5047302232- RNA and protein synthesis mechanisms
- Microbial Community Ecology and Physiology
- Photosynthetic Processes and Mechanisms
- Genomics and Phylogenetic Studies
- Evolution and Genetic Dynamics
- RNA modifications and cancer
- Tuberculosis Research and Epidemiology
- Mathematical Biology Tumor Growth
- Mycobacterium research and diagnosis
- Algal biology and biofuel production
- Gene Regulatory Network Analysis
- Microbial Metabolic Engineering and Bioproduction
- Protist diversity and phylogeny
- Single-cell and spatial transcriptomics
- Bacterial Genetics and Biotechnology
- Evolutionary Game Theory and Cooperation
- Multiple Myeloma Research and Treatments
- Bioinformatics and Genomic Networks
- Coral and Marine Ecosystems Studies
- Protein Degradation and Inhibitors
- Cancer-related molecular mechanisms research
- Hemoglobin structure and function
- CRISPR and Genetic Engineering
- Glioma Diagnosis and Treatment
- Bacteriophages and microbial interactions
Institute for Systems Biology
2014-2025
InSysBio (Russia)
2018-2025
Systems Biology Institute
2024
Seattle University
2021
North Seattle College
2015
Biomed Research Institute
2014
Lawrence Berkeley National Laboratory
2013
University of Pennsylvania
2003-2010
Zero to Three
2008
Abstract Mycobacterium tuberculosis (MTB) infects 30% of all humans and kills someone every 20–30 s. Here we report genome-wide binding for ~80% predicted MTB transcription factors (TFs), assayed global expression following induction each TF. The DNA-binding network consists ~16,000 events from 154 TFs. We identify >50 TF-DNA consensus motifs >1,150 promoter-binding directly associated with proximal gene regulation. An additional ~4,200 are in promoter windows represent strong...
Patescibacteria, also known as the candidate phyla radiation (CPR), are a diverse group of bacteria that constitute disproportionately large fraction microbial dark matter. Its few cultivated members, belonging mostly to Saccharibacteria, grow epibionts on host Actinobacteria. Due lack suitable tools, genetic basis this lifestyle and other unique features Patescibacteira remain unexplored. Here, we show Saccharibacteria exhibit natural competence, exploit property for their manipulation....
Abstract Background Mycobacterium tuberculosis senses and responds to the shifting hostile landscape of host. To characterize underlying intertwined gene regulatory network governed by approximately 200 transcription factors M. , we have assayed global transcriptional consequences overexpressing each factor from an inducible promoter. Results We cloned overexpressed 206 in identify signature each. identified 9,335 183 factors, providing evidence regulation for 70% genome. These signatures...
Corals from the northern Red Sea, in particular Gulf of Aqaba (GoA), have exceptionally high bleaching thresholds approaching >5℃ above their maximum monthly mean (MMM) temperatures. These elevated are thought to be due historical selection, as corals passed through warmer Southern Sea during recolonization Arabian Sea. To test this hypothesis, we determined thermal tolerance GoA versus central (CRS) Stylophora pistillata using multi-temperature acute stress assays determine thresholds....
AIR data sharing is integral to spur research reproducibility, promote reuse, and accelerate research.However, the first step in using these assets -discovering that they exist -is compounded by problems incentives, standardization, coordination of efforts.In 2023, National Institutes Health (NIH) implemented their updated Data Sharing Policy, which mandates timely all NIH-funded data.However, for policy shift culture, improve several changes must happen.In a companion piece 1 , we present...
Mycobacterium tuberculosis senses and responds to the shifting hostile landscape of host. To characterize underlying intertwined gene regulatory network governed by approximately 200 transcription factors M. tuberculosis, we have assayed global transcriptional consequences overexpressing each factor from an inducible promoter. We cloned overexpressed 206 in identify signature each. identified 9,335 183 factors, providing evidence regulation for 70% genome. These signatures agree well with...
Significance Nature is full of species that cooperate in mutually beneficial interactions to survive. Some are completely dependent on such relationships. How and why does this specialization evolve? We show as the bacterium Desulfovibrio vulgaris evolved for 1,000 generations conditions forcing cooperation with archaeon Methanococcus maripaludis , it lost a key metabolic trait would be required grow alone most environments. Large subpopulations lacking capacity respire sulfate 13 21...
Algae accumulate lipids to endure different kinds of environmental stresses including macronutrient starvation. Although this response has been extensively studied, an in depth understanding the transcriptional regulatory network (TRN) that controls transition into lipid accumulation remains elusive. In study, we used a systems biology approach elucidate program coordinates nitrogen starvation-induced metabolic readjustments drive Chlamydomonas reinhardtii.We demonstrate starvation triggered...
The resilience of Mycobacterium tuberculosis (MTB) is largely due to its ability effectively counteract and even take advantage the hostile environments a host. In order accelerate discovery characterization these adaptive mechanisms, we have mined compendium 2325 publicly available transcriptome profiles MTB decipher predictive, systems-scale gene regulatory network model. resulting modular organization 98% all genes within this was rigorously tested using two independently generated...
Mycobacterium tuberculosis (MTB) is a pathogenic bacterium responsible for 12 million active cases of (TB) worldwide. The complexity and critical regulatory components MTB pathogenicity are still poorly understood despite extensive research efforts. In this study, we constructed the first systems-scale map transcription factor (TF) binding sites their target proteins in MTB. We FLAG-tagged overexpression constructs 206 TFs MTB, used ChIP-seq to identify genome-wide events surveyed global...
ABSTRACT Copper is an essential micronutrient used as a metal cofactor by variety of enzymes, including cytochrome c oxidase (Cox). In all organisms from bacteria to humans, cellular availability and insertion copper into target proteins are tightly controlled due its toxicity. The major subunit Cox contains atom that required for catalytic activity. Previously, we identified CcoA (a member facilitator superfamily transporters) component cbb 3 -type production in the Gram-negative,...
Abstract Biomedical datasets are increasing in size, stored many repositories, and face challenges FAIRness (findability, accessibility, interoperability, reusability). As a Consortium of infectious disease researchers from 15 Centers, we aim to adopt open science practices promote transparency, encourage reproducibility, accelerate research advances through data reuse. To improve our computational tools, evaluated metadata standards across established biomedical repositories. The vast...
Poor prognosis and drug resistance in glioblastoma (GBM) can result from cellular heterogeneity treatment-induced shifts phenotypic states of tumor cells, including dedifferentiation into glioma stem-like cells (GSCs). This rare tumorigenic cell subpopulation resists temozolomide, undergoes proneural-to-mesenchymal transition (PMT) to evade therapy, drives recurrence. Through inference transcriptional regulatory networks (TRNs) patient-derived GSCs (PD-GSCs) at single-cell resolution, we...
Article22 November 2011Open Access Niche adaptation by expansion and reprogramming of general transcription factors Serdar Turkarslan Baliga Lab, Institute for Systems Biology, Seattle, WA, USA Search more papers this author David J Reiss Goodwin Gibbins Wan Lin Su Min Pan Christopher Bare L Plaisier Nitin S Corresponding Author Department Microbiology, University Washington, Molecular Cellular Biology Program, Information Turkarslan1, Reiss1, Gibbins1, Su1, Pan1, Bare1, Plaisier1 1,2,3...
Frataxin (Yfh1 in yeast) is a conserved protein and deficiency leads to the neurodegenerative disease Friedreich's ataxia. critical for Fe-S cluster assembly mitochondria, interacting with other components of machinery, including cysteine desulfurase Nfs1, Isd11 Isu1 scaffold protein. Yeast methionine isoleucine substitution (M141I), which E. coli amino acid inserted at this position, corrected most phenotypes that result from lack Yfh1 yeast. This suppressor behaved as genetic dominant....
Climate change has caused drastic declines in corals. As sessile organisms, response to shifting environmental conditions may include changes gene expression, epigenetic modifications, or the microbiome, but as of yet, a common mechanism stress response, alternative splicing (AS), been under-explored Using short-term acute thermal assays, we investigated patterns AS scleractinian coral Acropora cervicornis during and subsequent overnight recovery phase from low (33°C), medium (35°C), high...
Climate change has caused drastic declines in corals. As sessile organisms, corals acclimate to environmental shifts through genome-wide changes gene expression, epigenetic modifications, and alterations microbiome composition. However, alternative splicing (AS), a conserved mechanism of stress response many been under-explored Using short-term acute thermal assays, we investigated patterns AS the scleractinian coral Acropora cervicornis during low (33°C), medium (35°C), high (37°C) heat...
During cytochrome c maturation (Ccm), the DsbA-dependent thio-oxidative protein-folding pathway is thought to introduce a disulphide bond into haem-binding motif of apocytochromes c. This believed be reduced through thio-reductive involving Ccm components CcdA (DsbD), CcmG and CcmH. Here, we show in Rhodobacter capsulatus that absence DsbA levels were decreased or putative glutathione transporter CydDC was not needed for Ccm. decrease due overproduction periplasmic protease DegP as secondary...