A5023307207- Algal biology and biofuel production
- RNA and protein synthesis mechanisms
- Microbial Metabolic Engineering and Bioproduction
- RNA modifications and cancer
- Bacterial Genetics and Biotechnology
- RNA Research and Splicing
- Microbial Community Ecology and Physiology
- Marine and coastal ecosystems
- Genomics and Phylogenetic Studies
- Biofuel production and bioconversion
- Aquatic Ecosystems and Phytoplankton Dynamics
- Enzyme Production and Characterization
- CRISPR and Genetic Engineering
- Minerals Flotation and Separation Techniques
- Viral Infections and Immunology Research
- Gene Regulatory Network Analysis
- Photosynthetic Processes and Mechanisms
- Enzyme Catalysis and Immobilization
- Marine and coastal plant biology
- Microplastics and Plastic Pollution
- Viral Infectious Diseases and Gene Expression in Insects
- Agriculture, Soil, Plant Science
- Biomedical and Engineering Education
- RNA regulation and disease
- Nuclear Materials and Properties
Los Alamos National Laboratory
2015-2025
Howard Hughes Medical Institute
2007
University of Utah
2007
Northwestern University
2004-2006
Allegheny College
1998-2002
University of Colorado Boulder
2001
Among the most formidable challenges to algal biofuels is ability harvest algae and extract intracellular lipids at low cost with a positive energy balance. In this monograph, we construct two paradigms that contrast requirements costs of conventional cutting-edge Harvesting Extraction (H&E) technologies. By application parity criterion moderate condition reference state, an energy–cost paradigm created allows 1st stage harvesting technologies be compared easy National Alliance for Advanced...
In 2010, when the National Alliance for Advanced Biofuels and Bioproducts (NAABB) consortium began, little was known about molecular basis of algal biomass or oil production. Very few genome sequences were available efforts to identify best-producing wild species through bioprospecting approaches had largely stalled after U.S. Department Energy's Aquatic Species Program. This lack knowledge included how reduced carbon partitioned into storage products like triglycerides starch role played by...
Optical melting was used to determine the stabilities of 11 small RNA oligomers defined secondary structure as a function magnesium ion concentration. The included helices composed Watson–Crick base pairs, GA tandem GU and loop E motifs (both eubacterial eukaryotic). effect concentration on stability interpreted in terms two simple models. first assumes an uptake metal upon duplex formation. second nonspecific electrostatic attraction ions oligomer. For all oligomers, except E, data could...
When different mutations were introduced into the anticodon loop and at position 73 of YFA2, a derivative yeast tRNA(Phe), single tRNA body was misacylated with 13 amino acids. The affinities these tRNAs for Thermus thermophilus elongation factor Tu (EF-Tu).GTP determined using ribonuclease protection assay. A range 2.5 kcal/mol in binding energies observed, clearly demonstrating that EF-Tu specifically recognizes side chain esterified acid. Furthermore, this specificity can be altered by...
Energy-efficient and scalable harvesting lipid extraction processes must be developed in order for the algal biofuels bioproducts industry to thrive. The major challenge is handling of large volumes cultivation water concentrate low amounts biomass. For extraction, energy cost drivers are associated with disrupting algae cell wall drying biomass before solvent lipids. Here we review research development conducted by Harvesting Extraction Team during 3-year National Alliance Advanced Biofuels...
To identify high productivity strains for microalgal biofuels generation, the maximum specific growth rate of 38 was measured as a function salinity (i.e., 5, 15, and 35 PSU) temperature at 8 temperatures along linear gradient from ca. 5 to 45 °C) determine most suitable medium best growing season, respectively, outdoor raceway pond cultivation. The following were evaluated: Agmenellum quadruplicatum UTEX 2268, Anabaena sp. ATCC 33081, Arthrospira fusiformis 2721, platensis 3086, Chlorella...
Photosynthetic microbes are considered promising biofactories for transforming inorganic carbon from the atmosphere into a renewable source of chemicals and precursors industrial interest; however, there continues to be need strains that demonstrate high productivity, environmental robustness, potential genetically manipulated. Genome sequencing biochemical characterization culture collection microalgae strains, as well isolation previously unidentified environment or mixed cultures, bring...
Two innovative culturing systems, the LED-lighted and temperature-controlled 800 liter indoor raceways at Pacific Northwest National Laboratory (PNNL) Phenometrics environmental Photobioreactors™ (ePBRs) were evaluated in terms of their ability to accurately simulate microalgae growth performance outdoor cultures subjected fluctuating sunlight water temperature conditions. When repeating a 60-day pond culture experiment (batch semi-continuous two dilution rates) conducted Arizona with...
Robust fluorescence-based biosensors are emerging as critical tools for high-throughput strain improvement in synthetic biology. Many developed model organisms where sophisticated biology also well established. However, industrial biochemical production often employs microbes with phenotypes that advantageous a target process, and may fail to directly transition outside the host which they developed. In particular, losses sensitivity dynamic range of sensing occur, limiting application...
Product inhibition is a frequent bottleneck in industrial enzymes, and testing mutations to alleviate product via traditional methods remains challenging as many variants need be tested against multiple substrate concentrations. Further, screening are conducted vitro, resulting enzyme may perform differently vivo the context of whole-cell metabolism regulation. In this study, we address these two problems by establishing high-throughput method an industrially relevant enzyme, chorismate...
Thermodynamic parameters are reported for hairpin formation in 1 M NaCl by RNA sequences of the type GGXANmAYCC, where XY is wobble base pair, GU or UG, and underlined loop three to eight nucleotides. A nearest-neighbor analysis indicates free energy dependent upon size closing pair. Hairpin loops closed UG pairs on average 1.3 kcal/mol less stable than hairpins pairs. The have approximately same stability as AU/UA pairs, while 0.7 more GC/CG These results, combined with model previously...
Microalgae could become an important resource for addressing increasing global demand food, energy, and commodities while helping to reduce atmospheric greenhouse gases. Even though Chlorophytes are generally regarded safe human consumption, there is still much we do not understand about the metabolic biochemical potential of microscopic algae. The aim this study was evaluate biofuel candidate strains Chlorella Scenedesmus produce bioactive metabolites when grown under nutrient depletion...
Targeted mutagenesis of a promoter or gene is essential for attaining new functions in microbial and protein engineering efforts. In the burgeoning field synthetic biology, heterologous genes are expressed host organisms. Similarly, natural designed proteins mutagenized at targeted positions screened gain-of-function mutations. Here, we describe methods to attain complete randomization controlled mutations promoters genes. Combinatorial libraries one hundred thousands tens millions variants...
To investigate the accuracy of a model [Giese et al., 1998, Biochemistry37:1094-1100 and Mathews 1999, JMol Biol 288:911-940] that predicts stability RNA hairpin loops, optical melting studies were conducted on sets hairpins previously determined to have unusually stable thermodynamic parameters. Included tetraloops GNRA UNCG (where N is any nucleotide R purine), hexaloops with UU first mismatches, loop iron responsive element, CAGUGC. The experimental values for loops are in excellent...
Although some experiments suggest that the ribosome displays specificity for identity of esterified amino acid its aminoacyl-tRNA substrate, a study measuring dissociation rates several misacylated tRNAs containing GAC anticodon from A site showed little indication such specificity. In this article, an expanded set and two 2'-deoxynucleotide-substituted mRNAs are used to demonstrate presence lower threshold in k(off) values aa-tRNA binding site. When tRNA binds sufficiently well reach...
Until recently, engineering strategies for altering gene expression have focused on transcription control using strong inducible promoters or one of several methods to knock down wasteful genes. Recently, synthetic riboregulators been developed translational regulation expression. Here, we report a new modular riboregulator class that has the potential finely tune protein and independently concentration each enzyme in an engineered metabolic pathway. This development is important because...
Whole-cell biosensors provide a convenient detection tool for the high-throughput screening of genetically engineered biocatalytic activity. But establishing biosensor an anthropogenic molecule requires both custom transporter and transcription factor. This results in unavoidable "Catch-22" situation which activity cannot be easily confirmed without established functional host organism. We overcame this type circular problem while developing adipic acid (ADA) sensor. First, leveraging...