Philip D Weyman

Summary

Affiliation: J. Craig Venter Institute
Country: USA

Publications

  1. pmc Assembly of eukaryotic algal chromosomes in yeast
    Bogumil J Karas
    Department of Synthetic Biology and Bioenergy, J, Craig Venter Institute, 10355 Science Center Dr, San Diego, CA 92121, USA
    J Biol Eng 7:30. 2013
  2. pmc Diatom centromeres suggest a mechanism for nuclear DNA acquisition.
    Rachel E Diner
    Proc Natl Acad Sci U S A 114:E6015-E6024. 2017
  3. pmc A broad survey reveals substitution tolerance of residues ligating FeS clusters in [NiFe] hydrogenase
    Isaac T Yonemoto
    Department of Synthetic Biology and Bioenergy, J, Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA 92037, USA
    BMC Biochem 15:10. 2014
  4. pmc Dual organism design cycle reveals small subunit substitutions that improve [NiFe] hydrogenase hydrogen evolution
    Isaac T Yonemoto
    J, Craig Venter Institute, 10355 Science Center Dr, San Diego, CA 92121, USA
    J Biol Eng 7:17. 2013
  5. doi request reprint Assembly of large, high G+C bacterial DNA fragments in yeast
    Vladimir N Noskov
    Department of Synthetic Biology and Bioenergy, J Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA
    ACS Synth Biol 1:267-73. 2012
  6. doi request reprint Transferring whole genomes from bacteria to yeast spheroplasts using entire bacterial cells to reduce DNA shearing
    Bogumil J Karas
    Department of Synthetic Biology and Bioenergy, J Craig Venter Institute, La Jolla, California, USA
    Nat Protoc 9:743-50. 2014
  7. pmc Designer diatom episomes delivered by bacterial conjugation
    Bogumil J Karas
    Synthetic Biology and Bioenergy Group, J Craig Venter Institute, La Jolla, California 92037, USA
    Nat Commun 6:6925. 2015
  8. pmc Refinement of the Diatom Episome Maintenance Sequence and Improvement of Conjugation-Based DNA Delivery Methods
    Rachel E Diner
    Microbial and Environmental Genomics Group, J Craig Venter Institute, La Jolla, CA, USA Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
    Front Bioeng Biotechnol 4:65. 2016
  9. doi request reprint Inactivation of Phaeodactylum tricornutum urease gene using transcription activator-like effector nuclease-based targeted mutagenesis
    Philip D Weyman
    Department of Synthetic Biology and Bioenergy, J Craig Venter Institute, La Jolla, CA, USA
    Plant Biotechnol J 13:460-70. 2015
  10. doi request reprint Strategies for cloning and manipulating natural and synthetic chromosomes
    Bogumil J Karas
    Synthetic Biology and Bioenergy Group, J Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA
    Chromosome Res 23:57-68. 2015

Collaborators

  • Bogumil J Karas
  • Daniel G Gibson
  • Vladimir N Noskov
  • Isaac T Yonemoto
  • Rachel E Diner
  • Hamilton O Smith
  • Andrew E Allen
  • Vincent A Bielinski
  • Christopher L Dupont
  • Nathan C Lian
  • Chari M Noddings
  • Ngocquynh A Nguyen
  • Jeffrey B McQuaid
  • Miguel A Anzelmatti
  • Anthony K Kang
  • Josh L Espinoza
  • Jakob Jansson
  • Jelena Jablanovic
  • Benjamin R Clarkson
  • Thao Amy Nguyen
  • Christopher W Matteri

Detail Information

Publications13

  1. pmc Assembly of eukaryotic algal chromosomes in yeast
    Bogumil J Karas
    Department of Synthetic Biology and Bioenergy, J, Craig Venter Institute, 10355 Science Center Dr, San Diego, CA 92121, USA
    J Biol Eng 7:30. 2013
    ..4 Mb genome sequence that has been assembled into chromosome-sized scaffolds making it an ideal test case for assembly and maintenance of eukaryotic chromosomes in yeast...
  2. pmc Diatom centromeres suggest a mechanism for nuclear DNA acquisition.
    Rachel E Diner
    Proc Natl Acad Sci U S A 114:E6015-E6024. 2017
    ..Thus, simple sequence requirements may enable DNA from foreign sources to persist in the nucleus as extrachromosomal episomes, revealing a potential mechanism for organellar and foreign DNA acquisition...
  3. pmc A broad survey reveals substitution tolerance of residues ligating FeS clusters in [NiFe] hydrogenase
    Isaac T Yonemoto
    Department of Synthetic Biology and Bioenergy, J, Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA 92037, USA
    BMC Biochem 15:10. 2014
    ....
  4. pmc Dual organism design cycle reveals small subunit substitutions that improve [NiFe] hydrogenase hydrogen evolution
    Isaac T Yonemoto
    J, Craig Venter Institute, 10355 Science Center Dr, San Diego, CA 92121, USA
    J Biol Eng 7:17. 2013
    ..Studies by others altering the medial cluster of a Desulfovibrio fructosovorans hydrogenase from 3Fe-4S to 4Fe-4S resulted in two-fold improved hydrogen evolution activity...
  5. doi request reprint Assembly of large, high G+C bacterial DNA fragments in yeast
    Vladimir N Noskov
    Department of Synthetic Biology and Bioenergy, J Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA
    ACS Synth Biol 1:267-73. 2012
    ..Thus, cloning strategies utilizing yeast recombination with large, high G+C prokaryotic sequences should include yeast origins of replication as a part of the design process...
  6. doi request reprint Transferring whole genomes from bacteria to yeast spheroplasts using entire bacterial cells to reduce DNA shearing
    Bogumil J Karas
    Department of Synthetic Biology and Bioenergy, J Craig Venter Institute, La Jolla, California, USA
    Nat Protoc 9:743-50. 2014
    ..Excluding the time required for preparing starting cultures and for incubating cells to form final colonies, the protocol can be completed in 3 h. ..
  7. pmc Designer diatom episomes delivered by bacterial conjugation
    Bogumil J Karas
    Synthetic Biology and Bioenergy Group, J Craig Venter Institute, La Jolla, California 92037, USA
    Nat Commun 6:6925. 2015
    ..This highly efficient genetic system facilitates high-throughput functional characterization of algal genes and accelerates molecular phytoplankton research. ..
  8. pmc Refinement of the Diatom Episome Maintenance Sequence and Improvement of Conjugation-Based DNA Delivery Methods
    Rachel E Diner
    Microbial and Environmental Genomics Group, J Craig Venter Institute, La Jolla, CA, USA Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
    Front Bioeng Biotechnol 4:65. 2016
    ..The data presented offer additional information regarding the mechanism by which the yeast-derived sequence enables diatom episome maintenance and demonstrate options for flexible vector design. ..
  9. doi request reprint Inactivation of Phaeodactylum tricornutum urease gene using transcription activator-like effector nuclease-based targeted mutagenesis
    Philip D Weyman
    Department of Synthetic Biology and Bioenergy, J Craig Venter Institute, La Jolla, CA, USA
    Plant Biotechnol J 13:460-70. 2015
    ..Numerous high carbon metabolites were enriched in the mutant, implying a breakdown of cellular C and N repartitioning. The presented method improves the molecular toolkit for diatoms and clarifies the role of urease in the urea cycle. ..
  10. doi request reprint Strategies for cloning and manipulating natural and synthetic chromosomes
    Bogumil J Karas
    Synthetic Biology and Bioenergy Group, J Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA
    Chromosome Res 23:57-68. 2015
    ....
  11. pmc Designed surface residue substitutions in [NiFe] hydrogenase that improve electron transfer characteristics
    Isaac T Yonemoto
    J Craig Venter Institute, Synthetic Biology and Bioenergy Group, 4120 Capricorn Lane, La Jolla, CA 92037, USA
    Int J Mol Sci 16:2020-33. 2015
    ..Combining ferredoxin fusion and surface charge modification showed progressively improved activity in an in vitro assay with purified enzyme. ..
  12. pmc Direct transfer of whole genomes from bacteria to yeast
    Bogumil J Karas
    Department of Synthetic Biology and Bioenergy, J Craig Venter Institute, San Diego, California, USA
    Nat Methods 10:410-2. 2013
    ..8 megabases (Mb) into yeast under conditions that promote cell fusion. Moreover, we discovered that removal of restriction endonucleases from donor bacteria resulted in the enhancement of genome transfer...
  13. ncbi request reprint Facile Site-Directed Mutagenesis of Large Constructs Using Gibson Isothermal DNA Assembly
    Isaac T Yonemoto
    J Craig Venter Institute, Synthetic Biology and Bioenergy Group, 4120 Capricorn Lane, La Jolla, CA, 92137, USA
    Methods Mol Biol 1498:359-366. 2017
    ....