A5055757605- RNA and protein synthesis mechanisms
- CRISPR and Genetic Engineering
- Metalloenzymes and iron-sulfur proteins
- Genomics and Phylogenetic Studies
- RNA Interference and Gene Delivery
- Advanced biosensing and bioanalysis techniques
- Electrocatalysts for Energy Conversion
- Bacteriophages and microbial interactions
- Enzyme Catalysis and Immobilization
- Bacterial Genetics and Biotechnology
- Monoclonal and Polyclonal Antibodies Research
- Algorithms and Data Compression
- DNA and Nucleic Acid Chemistry
- Bacterial Infections and Vaccines
- Hydrogen Storage and Materials
- Veterinary Pharmacology and Anesthesia
- Gene Regulatory Network Analysis
- Biosensors and Analytical Detection
- Human-Animal Interaction Studies
- Nanopore and Nanochannel Transport Studies
- Peer-to-Peer Network Technologies
- Microbial Fuel Cells and Bioremediation
- Escherichia coli research studies
- Enzyme Production and Characterization
- RNA modifications and cancer
Michigan State University
1993-2017
Michigan United
2015-2016
Rutgers, The State University of New Jersey
2013-2015
Kyoto University
2011-2013
Stanford University
2007-2010
<ns3:p>The khmer package is a freely available software library for working efficiently with fixed length DNA words, or k-mers. provides implementations of probabilistic k-mer counting data structure, compressible De Bruijn graph representation, partitioning, and digital normalization. implemented in C++ Python, under the BSD license at <ns3:ext-link xmlns:ns4="http://www.w3.org/1999/xlink" ext-link-type="uri"...
Abstract [FeFe] hydrogenases catalyze the reversible reduction of protons to molecular hydrogen (Adams (1990); Biochim Biophys Acta 1020(2): 115–145) and are significant interest for biological production fuel. They complex proteins with active sites containing iron, sulfur, carbon monoxide cyanide ligands (Peters et al. (1998); Science 282(5395): 1853–1858). Maturation enzymes have been identified (Posewitz (2004); J Biol Chem 279(24): 25711–25720), but complete mechanisms not yet...
Background [FeFe] hydrogenase enzymes catalyze the formation and dissociation of molecular hydrogen with help a complex prosthetic group composed common elements. The development energy conversion technologies based on these renewable catalysts has been hindered by their extreme oxygen sensitivity. Attempts to improve directed evolution have failed for want screening platform capable throughputs high enough adequately sample heavily mutated DNA libraries. In vitro compartmentalization (IVC)...
Comprehensive sequence-function mapping involves detailing the fitness contribution of every possible single mutation to a gene by comparing abundance each library variant before and after selection for phenotype interest. Deep sequencing DNA allows frequency reconstruction tens thousands variants in experiment, yet short read lengths current sequencers makes it challenging probe genes encoding full-length proteins. Here we extend scope maps entire protein sequences with modular, universal...
Background [FeFe] hydrogenases are metalloenzymes involved in the anaerobic metabolism of H2. These proteins distinguished by an active site cofactor known as H-cluster. This unique [6Fe–6S] complex contains multiple non-protein moieties and requires several maturation enzymes for its assembly. The pathways biochemical precursors H-cluster biosynthesis have yet to be elucidated. Principal Findings We report vitro system which, first time, chemical additives enhance hydrogenase activation,...
Background [FeFe] hydrogenase enzymes catalyze the production and dissociation of H2, a potential renewable fuel. Attempts to exploit these catalysts in engineered systems have been hindered by biotechnologically inconvenient properties natural enzymes, including their extreme oxygen sensitivity. Directed evolution has used improve characteristics range catalysts, but largely unsuccessful for hydrogenases because lack convenient screening platforms. Methodology/Principal Findings Here we...
The introduction of multiple genes into cells is increasingly required for understanding and engineering biological systems. Small-molecule–responsive transcriptional regulation has been widely used to control transgene expression. In contrast, methods specific simultaneous with a single regulatory protein remain undeveloped. this report, we describe method quantitatively tuning the expression transgenes translational protein. A that binds RNA motif inserted in 5′-untranslated region (UTR)...
Next-generation DNA sequencing has revolutionized the study of biology. However, short read lengths dominant instruments complicate assembly complex genomes and haplotype phasing mixtures similar sequences. Here we demonstrate a method to reconstruct sequences individual nucleic acid molecules up 11.6 kilobases in length from (150-bp) reads. We show that our can construct 99.97%-accurate synthetic reads bacterial, plant, animal genomic samples, full-length mRNA human cancer cell lines, HIV...
Significance The ability to construct novel proteins from basic principles of molecular structure is the fundamental goal protein design. This particularly challenging in case β-barrel outer membrane proteins, where our understanding rules governing and function lags behind that other classes proteins. Here, we took a step toward architecture by focusing on outward-facing amino acid positions contact cell membrane. We replaced membrane-facing surface OmpA with new surfaces designed resemble...
Abstract We describe a scalable and cost-effective sgRNA synthesis workflow that reduces costs by over 70% through the use of large pools microarray-derived oligos encoding unique spacers. These sub-pool are assembled into full-length dsDNA templates via Golden Gate Assembly before in vitro transcription with T7 RNA polymerase. RNA-seq analysis reveals severe biases spacer representation, some spacers being highly overrepresented while others completely absent. Consistent previous studies,...
Adenylate cyclase toxin (ACT) is an important Bordetella pertussis virulence factor that not included in current acellular vaccines. We previously demonstrated immunization with the repeat-in-toxin (RTX) domain of ACT elicits neutralizing antibodies mice and discovered first two to neutralize activities by occluding receptor-binding site. Here, we fully characterize these their epitopes. Both bind low nanomolar affinity cross-react homologues produced B. parapertussis bronchiseptica....
Summary Pentobarbital alone, pentobarbital plus 1% lidocaine solution, 2% and 3% solution were each used to euthanatize 6 dogs. For dog, time between the beginning of injection euthanasia following events was recorded: collapse, onset apnea, flat-line electrocardiogram, electroencephalogram, loss palpable heartbeat, pulse. Any signs pain or discomfort also recorded. There no significant differences among groups except for electrocardiogram. Dogs euthanatized with alone had significantly...
Abstract Next-generation DNA sequencing has revolutionized the study of biology. However, short read lengths dominant instruments complicate assembly complex genomes and haplotype phasing mixtures similar sequences. Here we demonstrate a method to reconstruct sequences individual nucleic acid molecules up 11.6 kilobases in length from (150-bp) reads. We show that our can construct 99.97%-accurate synthetic reads bacterial, plant, animal genomic samples, full-length mRNA human cancer cell...