A5041016547- Molecular Biology Techniques and Applications
- Microfluidic and Capillary Electrophoresis Applications
- Gene expression and cancer classification
- Microfluidic and Bio-sensing Technologies
- Bacterial Genetics and Biotechnology
- Genomics and Phylogenetic Studies
- Nanopore and Nanochannel Transport Studies
- Forensic and Genetic Research
- Innovative Microfluidic and Catalytic Techniques Innovation
- Bacteriophages and microbial interactions
- Biosensors and Analytical Detection
- Advanced biosensing and bioanalysis techniques
- Electrowetting and Microfluidic Technologies
- RNA and protein synthesis mechanisms
- Environmental DNA in Biodiversity Studies
- Cancer therapeutics and mechanisms
- Bioinformatics and Genomic Networks
- Microbial Community Ecology and Physiology
- Metabolomics and Mass Spectrometry Studies
- Carcinogens and Genotoxicity Assessment
- Aquaculture disease management and microbiota
- Viral Infectious Diseases and Gene Expression in Insects
- Molecular Communication and Nanonetworks
- Mercury impact and mitigation studies
- Signaling Pathways in Disease
ID Genomics (United States)
2024
Xilinx (United States)
2014-2015
General Electric (Spain)
2005
Silicon Valley University
2005
University of California, Davis
2003
University of Wisconsin–Madison
1989-2002
University of Helsinki
2001
Northwestern University
2001
Stanford University
1990
University of Alabama at Birmingham
1987
Extremely halophilic archaea contain retinal-binding integral membrane proteins called bacteriorhodopsins that function as light-driven proton pumps. So far, capable of generating a chemiosmotic potential in response to light have been demonstrated only archaea. We describe here type rhodopsin derived from bacteria was discovered through genomic analyses naturally occuring marine bacterioplankton. The bacterial encoded the genome an uncultivated γ-proteobacterium and shared highest amino...
A key challenge of analyzing data from high-resolution spatial profiling technologies is to suitably represent the features cellular neighborhoods or niches. Here we introduce covariance environment (COVET), a representation that leverages gene-gene covariate structure across cells in niche capture multivariate nature interactions within it. We define principled optimal transport-based distance metric between COVET niches scales millions cells. Using encode context, developed environmental...
Cultivation‐independent surveys of ribosomal RNA genes have revealed the existence novel microbial lineages, many with no known cultivated representatives. Ribosomal RNA‐based analyses, however, often do not provide significant information beyond phylogenetic affiliation. Analysis large genome fragments recovered directly from communities represents one promising approach for characterizing uncultivated species better. To assess further utility this approach, we constructed large‐insert...
We have developed an approach to classify toxicants based upon their influence on profiles of mRNA transcripts. Changes in liver gene expression were examined after exposure mice 24 model treatments that fall into five well-studied toxicological categories: peroxisome proliferators, aryl hydrocarbon receptor agonists, noncoplanar polychlorinated biphenyls, inflammatory agents, and hypoxia-inducing agents. Analysis 1200 transcripts using both a correlation-based probabilistic resulted...
Rapid DNA typing provides a transformative solution to help forensic laboratories and law enforcement agencies solve prevent crimes. The RapidHIT® System is fully integrated instrument with simplified user interface enabling an operator run the system obtain profile from sample in less than two hours. integration developmental validation of NDIS-approved 24 loci GlobalFiler® Express kit expands capabilities RapidHIT increase discrimination power, reduce adventitious matches, improve...
We report automated DNA sequencing in 16-channel microchips. A microchip prefilled with sieving matrix is aligned on a heating plate affixed to movable platform. Samples are loaded into sample reservoirs by using an eight-tip pipetting device, and the chip docked array of electrodes focal plane four-color scanning detection system. Under computer control, high voltage applied appropriate programmed sequence that injects separates samples. An integrated confocal fluorescent detector...
Short tandem repeat (STR) DNA typing is a global standard for human identification. Current practice involves highly trained forensic analysts, operating in laboratory setting, using multiple instruments to process samples and analyze the data. Here, we report developmental validation of fully integrated automated profiling system, RapidHIT® System, capable producing up five high quality STR profiles with full controls approximately 90min PowerPlex®16 HS RapidHIT chemistry. The system...
Transcriptional profiling via microarrays holds great promise for toxicant classification and hazard prediction. Unfortunately, the use of different microarray platforms, protocols, informatics often hinders meaningful comparison transcriptional data across laboratories. One solution to this problem is provide a low-cost centralized resource that enables researchers share toxicogenomic has been generated on common platform. In an effort create such resource, we developed standardized set...
The rapid in vivo response of both Escherichia coli and Salmonella typhimurium osmoregulated genes to an osmotic upshift was analyzed detail by using chromosomal operon fusions. Within 10 min after the addition 0.3 M NaCl culture medium, differential rates expression S. proU-lac fusion a proP-lac increased 180- 17-fold respectively, while E. ompC-lac 3.4-fold. For all three stimulated promoters, rate maintained until about 40 upshift. Thereafter, proU continued at steady-state that 27-fold...
We have estimated the extent to which relaxation of supercoiling by DNA gyrase inhibitor coumermycin A1 affects gene expression in vivo Salmonella typhimurium. isolated a set Mu d1-8 Lac+ operon fusions random promoters and measured effect on 67 fusions. The differential rate synthesis was increased for 70% decreased 16%, 13% had less than 25% change expression. response found correlate well (P = 0.067) with basal level such that tended stimulate low inhibit those high Since vast majority...
We have studied the in vitro expression of osmoregulated proU promoter Escherichia coli coupled transcription-translation (S-30) extracts as a function osmolality culture medium used to grow cells and salt concentration added extract. These variables represent novel extensions use S-30 investigate gene regulatory phenomena vitro. The concentrations potassium acetate physiologically relevant osmolyte glutamate for maximal are approximately 2-fold higher than these salts providing lacUV5...
ABSTRACT Mercury is a redox-active heavy metal that reacts with active thiols and depletes cellular antioxidants. Active resistance to the mercuric ion widely distributed trait among bacteria results from action of reductase (MerA). Protein phylogenetic analysis MerA in indicated occurrence second distinctive form archaea, which lacked an N-terminal recruitment domain C-terminal tyrosine. To assess distribution forms interacting community comprising members both prokaryotic domains, studies...
The regulation of three Escherichia coli carbon starvation (cst) genes fused to lacZ was examined. Expression these is induced by for a source. role and cyclic AMP (cAMP) availability an altered-function crp mutation were investigated their effect on cst expression in vivo. experiments indicated that cAMP concentrations controlled the absolute one fusion, but other two fusions dependent upon some component not present exponentially growing cells under conditions glucose excess, even when...
The transcriptional activity of the topA gene which codes for topoisomerase I was examined. An in vitro assay determined that P1 promoter dependent on sigma 32 subunit RNA polymerase. four promoters examined by nuclease S1 mapping transcripts during a heat shock. This 32-dependent shown to function as shock promoter, although is not protein. A possible method compensation transcription other maintain level proposed.
Four pseudorevertants of a −10 region lacPmutation were isolated. Three these mutations found to activate nascent promoters. These were: −2 G/C → A/T change (−2A) promoting transcription at position +11, +1 T/A (+1T) initiation +13, and +10 C/G (+1OA) complex series positions. The fourth mutation [a −12 (−12A)] promotes −1. promoters activated by −12A, −2A +1T resembled the canonical sigma 70 promoter sequences. +1OA activity is also dependent upon holoenzyme but can not be readily assigned...
RNA polymerase requires one of a family sigma subunits for specific promoter recognition and initiation. We have developed an in vitro method to define the subunit required by promoter. Mouse monoclonal antibodies either Escherichia coli 70 or 32 Salmonella typhimurium 54 were added E. coupled transcription-translation S-30 extract programed with DNA template containing interest. Using representative lacUV5, glnAP2, rpoDHS promoters as controls, we found that given strongly inhibited...
cya-lac and crp-lac operon fusions were isolated in Salmonella typhimurium by using the phage Mu d1(lac cts Apr). Both transduction reversion analyses have indicated that lac expression is controlled appropriate promoter, e.g., either crpp or cyap. By chromosomal mobilization techniques, we found cya had a clockwise direction of transcription on standard S. map. The could be complemented Escherichia coli F'133, which covers cya, with resultant 17 to 38% decrease expression. Cyclic AMP was...