A5076394173- Bacterial Genetics and Biotechnology
- Genomics and Phylogenetic Studies
- Enzyme Structure and Function
- Microbial Metabolic Engineering and Bioproduction
- Microbial Community Ecology and Physiology
- Gene Regulatory Network Analysis
- Protist diversity and phylogeny
- RNA and protein synthesis mechanisms
- Bacteriophages and microbial interactions
- Protein Structure and Dynamics
- Listeria monocytogenes in Food Safety
- Genomics and Chromatin Dynamics
- Advanced Proteomics Techniques and Applications
- Bioinformatics and Genomic Networks
- CRISPR and Genetic Engineering
- Viral Infectious Diseases and Gene Expression in Insects
- Gene expression and cancer classification
- RNA modifications and cancer
- Cancer Research and Treatments
- DNA Repair Mechanisms
- Microbial bioremediation and biosurfactants
- Bacterial biofilms and quorum sensing
- Gaussian Processes and Bayesian Inference
- Endoplasmic Reticulum Stress and Disease
- Heat shock proteins research
Duke University
2016-2025
Institut thématique Génétique, génomique et bioinformatique
2023
Center for Systems Biology
2014-2015
Durham University
2012
Institute for Systems Biology
2007-2010
University of Washington
2002-2010
Cedars-Sinai Medical Center
2008
Seattle University
2007
Environmental Molecular Sciences Laboratory
2005
Pacific Northwest National Laboratory
2005
Transcriptome-wide time series expression profiling is used to characterize the cellular response environmental perturbations. The first step analyzing transcriptional data often cluster genes with similar responses. Here, we present a nonparametric model-based method, Dirichlet process Gaussian mixture model (DPGP), which jointly models clusters and temporal dependencies processes. We demonstrate accuracy of DPGP in comparison state-of-the-art approaches using hundreds simulated sets. To...
Article16 June 2009Open Access Prevalence of transcription promoters within archaeal operons and coding sequences Tie Koide Institute for Systems Biology, Seattle, WA, USAPresent address: Departamento de Bioquímica e Imunologia, Faculdade Medicina Ribeirão Preto, Universidade São Paulo, Brazil. E-mail: [email protected]Search more papers by this author David J Reiss USA Search Christopher Bare Wyming Lee Pang Marc T Facciotti Department Biomedical Engineering UC Davis Genome Center, One...
The production of outer membrane vesicles by Gram-negative bacteria has been well documented; however, the mechanism behind biogenesis these remains unclear. Here a high-throughput experimental method and systems-scale analysis was conducted to determine vesiculation values for whole genome knockout library Escherichia coli mutant strains (Keio collection). resultant dataset quantitatively recapitulates previously observed phenotypes implicates nearly 150 new genes in process vesiculation....
Microbial growth curves are used to study differential effects of media, genetics, and stress on microbial population growth. Consequently, many modeling frameworks exist capture measurements. However, current models designed quantify under conditions for which has a specific functional form. Extensions these required the perturbations, often exhibit nonstandard curves. Rather than assume forms experimental we developed general robust model using Gaussian process (GP) regression. GP...
Different weak organic acids have significant potential as topical treatments for wounds infected by opportunistic pathogens that are recalcitrant to standard treatments. These long been used bacteriostatic compounds in the food industry, and some cases already being clinic. The effects of different vary with pH, concentration, specific acid used, but no studies date on any examined detailed interactions between these key variables a controlled systematic way. We therefore comprehensively...
Microbial cells must continually adapt their physiology in the face of changing environmental conditions. Archaea living extreme conditions, such as saturated salinity, represent important examples resilience. The model salt-loving organism Haloferax volcanii exhibits remarkable plasticity its morphology, biofilm formation, and motility response to variations nutrients cell density. However, mechanisms regulating these lifestyle transitions remain unclear. In prior research, we showed that...
Timely regulation of carbon metabolic pathways is essential for cellular processes and to prevent futile cycling intracellular metabolites. In Halobacterium salinarum, a hypersaline adapted archaeon, sugar-sensing TrmB family protein controls gluconeogenesis other biosynthetic pathways. Notably, Hbt. salinarum does not utilize carbohydrates energy, uncommon among Haloarchaea. We characterized TrmB-family transcriptional regulator in saccharolytic generalist, Haloarcula hispanica, investigate...
ABSTRACT Archaeal molecular biology has been a topic of intense research in recent decades as their role global ecosystems, nutrient cycles, and eukaryotic evolution comes to light. The hypersaline-adapted archaeal species Halobacterium salinarum Haloferax volcanii serve important model organisms for understanding genomics, genetics, biochemistry, part because efficient tools enable genetic manipulation. As result, the number strains circulation among haloarchaeal community increased...
The potential functions have been investigated of two proteins in Deinococcus radiodurans R1 predicted to be involved the maintenance and integrity S layer: hexagonally packed intermediate (Hpi) protein, SlpA (DR2577), a homologue an S-layer protein Thermus thermophilus. Deletion hpi gene had little effect on structure cell envelope or shear- solvent-induced stress responses. However, deletion slpA caused substantial alterations structure, significant defect resistance solvent shear stresses...
Article16 June 2009Open Access A single transcription factor regulates evolutionarily diverse but functionally linked metabolic pathways in response to nutrient availability Amy K Schmid Institute for Systems Biology, Seattle, WA, USA Search more papers by this author David J Reiss Min Pan Tie Koide USAPresent address: E-mail: [email protected]Search Nitin S Baliga Corresponding Author Department of Microbiology, University Washington, Information Schmid1, Reiss1, Pan1, Koide1 and 1,2...
Adjustment of physiology in response to changes oxygen availability is critical for the survival all organisms. However, chronology events and regulatory processes that determine how when environmental tension result an appropriate cellular not well understood at a systems level. Therefore, transcriptome, proteome, ATP, growth were analyzed halophilic archaeon generate temporal model describes drive transition between organism’s two opposing cell states anoxic quiescence aerobic growth....
Abstract Background Previous work has shown that the hypersaline-adapted archaeon, Halobacterium salinarum NRC-1 , is highly resistant to oxidative stress caused by exposure hydrogen peroxide, UV, and gamma radiation. Dynamic alteration of gene regulatory network (GRN) been implicated in such resistance. However, molecular functions transcription proteins involved this response remain unknown. Results Here we have reanalyzed several existing GRN systems biology datasets for H. identify...
Summary Co‐ordinating metabolism and growth is a key challenge for all organisms. Despite fluctuating environments, cells must produce the same metabolic outputs to thrive. The mechanisms underlying this ‘growth homeostasis’ are known in bacteria eukaryotes, but remain unexplored archaea. In model archaeon H alobacterium salinarum , transcription factor TrmB regulates enzyme‐coding genes diverse pathways response glucose. However, . thought not catabolize To resolve discrepancy, we...
In all three domains of life, organisms use nonspecific DNA-binding proteins to compact and organize the genome as well regulate transcription on a global scale. Histone is primary eukaryotic nucleoprotein, its evolutionary roots can be traced archaea. However, not archaea this protein DNA-packaging component, raising questions regarding role histones in archaeal chromatin function. Here, quantitative phenotyping, transcriptomic, proteomic assays were performed deletion overexpression...
Networks of interacting transcription factors are central to the regulation cellular responses abiotic stress. Although architecture many such networks has been mapped, their dynamic function remains unclear. Here we address this challenge in archaea, microorganisms possessing that resemble those both eukaryotes and bacteria. Using genome-wide DNA binding location analysis integrated with gene expression cell physiological data, demonstrate a bacterial-type factor (TF), called RosR, five...
Histones, ubiquitous in eukaryotes as DNA-packing proteins, find their evolutionary origins archaea. Unlike the characterized histone proteins of a number methanogenic and themophilic archaea, previous research indicated that HpyA, sole encoded model halophile Halobacterium salinarum, is not involved DNA packaging. Instead, it was found to have widespread but subtle effects on gene expression maintain wild type cell morphology. However, precise function halophilic histone-like remain...
The relatively small numbers of proteins and fewer possible post-translational modifications in microbes provide a unique opportunity to comprehensively characterize their dynamic proteomes. We have constructed PeptideAtlas (PA) covering 62.7% the predicted proteome extremely halophilic archaeon Halobacterium salinarum NRC-1 by compiling approximately 636 000 tandem mass spectra from 497 spectrometry runs 88 experiments. Analysis PA with respect biophysical properties constituent peptides,...
Because iron toxicity and deficiency are equally life threatening, maintaining intracellular levels within a narrow optimal range is critical for nearly all known organisms. However, regulatory mechanisms that establish homeostasis not well understood in organisms dwell environments at the extremes of pH, temperature, salinity. Under conditions limited iron, extremophile Halobacterium salinarum, salt-loving archaeon, mounts specific response to scavenge growth. We have identified...
Gene regulatory networks (GRNs) are critical for dynamic transcriptional responses to environmental stress. However, the mechanisms by which GRN regulation adjusts physiology enable stress survival remain unclear. Here we investigate functions of transcription factors (TFs) within global stress-tolerant archaeal microorganism Halobacterium salinarum. We measured growth phenotypes a panel TF deletion mutants in high temporal resolution under heat shock, oxidative stress, and low-salinity...
Halobacterium salinarum are halophilic archaea that display directional swimming in response to various environmental signals, including light, chemicals and oxygen. In Hbt. salinarum, the building blocks (archaellins) of archaeal apparatus (the archaellum) N-glycosylated. However, physiological importance archaellin N-glycosylation remains unclear. Here, a tetrasaccharide comprising hexose three hexuronic acids decorating five archaellins was characterized by mass spectrometry. Such...
Despite intense recent research interest in archaea, the scientific community has experienced a bottleneck study of genome-scale gene expression experiments by RNA-seq due to lack commercial and specifically designed rRNA depletion kits. The high rRNA:mRNA ratio (80–90%: ~10%) prokaryotes hampers global transcriptomic analysis. Insufficient ribodepletion results low sequence coverage mRNA, therefore, requires substantially higher number replicate samples and/or sequencing reads achieve...