David W. Deamer

David Wilson Deamer (born April 21, 1939) is an American biologist and Research Professor of Biomolecular Engineering at the University of California, Santa Cruz. Deamer has made significant contributions to the field of membrane biophysics. His work led to a novel method of DNA sequencing and a more complete understanding of the role of membranes in the origin of life.

David W. Deamer

Ph.D.
David W. Deamer
Born (1939-04-21) April 21, 1939
Santa Monica, CA
NationalityUnited States
OccupationBiologist
AwardsGuggenheim Fellow, 1985
Academic background
EducationDuke University (B.Sc. 1961)
The Ohio State University (Ph.D. 1965)
Alma materThe Ohio State University
ThesisThe effect of alkaline earth ions on fatty acid and phospholipid monolayers (1965)
Doctoral advisorDavid Cornwell
Academic work
DisciplineBiophysicist
InstitutionsUniversity of California, Santa Cruz
Notable ideasnanopore sequencing

He was awarded a Guggenheim Fellowship in 1985, which supported research at the Australian National University in Canberra to investigate organic compounds in the Murchison meteorite. He served as the president of the International Society for the Study of the Origin of Life, 2013 - 14.

Early life

Deamer's father, also David, worked at Douglas Aircraft in Santa Monica, California during and after World War II while his mother Zena cared for Deamer and his two brothers, Richard and John. In 1952, the family moved to Ohio, where the three brothers attended Westerville High School. In 1957, Deamer submitted his research on self-organizing protozoa to the Westinghouse Science Talent Search and was among the 40 winners who were invited to Washington DC that year. He was awarded a full scholarship to Duke University, where he completed a bachelor's degree in Chemistry in 1961.[1]

Deamer went on to earn a PhD in Physiological Chemistry in 1965 at the Ohio State University School of Medicine. His advisor was David Cornwell, a lipid biochemist, so Deamer focused on calcium interactions with fatty acid and phospholipid monolayers, finishing in 1965. During his time as a graduate student Deamer married Jane, and their first son Mark was born in 1963.

Deamer began post-doctoral research with Lester Packer and Daniel Branton at the University of California, Berkeley in 1965, where he learned techniques of electron microscopy. Deamer and Branton demonstrated that the freeze-etch method split the lipid bilayer of membranes to reveal integral proteins for the first time, and their paper was published in Science in 1967. In the same year Deamer accepted a faculty position at the University of California, Davis, where he spent the next 27 years. Annabeth and Nicholas were added to the family in 1969 and 1977. The marriage ended in 1991.

In 1992 Deamer married Olof Einarsdottir, a professor in the Department of Chemistry and Biochemistry, and moved his laboratory to the University of California, Santa Cruz in 1994. The couple have two children, Asta born in 1995 and Stella born in 2000.

Research

As a young professor at UC Davis, Deamer continued to work with electron microscopy, revealing for the first time particles related to functional ATPase enzymes within the membranes of sarcoplasmic reticulum.[2] After spending sabbaticals in England at the University of Bristol in 1971 and with Alec Bangham in 1975, Deamer became interested in liposomes. Conversations with Bangham inspired his research on the role of membranes in the origin of life, and in 1985 Deamer demonstrated that the Murchison carbonaceous meteorite contained lipid-like compounds that could assemble into membranous vesicles.[3] Deamer described the significance of self-assembly processes in his 2011 book First Life.[4] In collaborative work with Mark Akeson, a post-doctoral student at the time, the two established methods for monitoring proton permeation through ion channels such as gramicidin.[5] In 1989, while returning from a scientific meeting in Oregon, Deamer conceived that it might be possible to sequence single molecules of DNA by using an imposed voltage to pull them individually through a nanoscopic channel. The DNA sequence could be distinguished by the specific modulating effect of the four bases on the ionic current through the channel. In 1993, he and Dan Branton initiated a research collaboration with John Kasianowitz at NIST to explore this possibility with the hemolysin channel, and in 1996 published the first paper demonstrating that nanopore sequencing may be feasible.[6] George Church at Harvard had independently proposed a similar idea, and Church, Branton and Deamer decided to initiate a patent application which was awarded in 1998.[7] Mark Akeson joined the research effort in 1997, and in 1999 published a paper showing that the hemolysin channel, now referred to as a nanopore, could distinguish between purine and pyrimidine bases in single RNA molecules.[8] In 2007, Oxford Nanopore Technologies (ONT) licensed the patents describing the technology[9] and in 2014 released the MinION nanopore sequencing device to selected researchers. The first publications appeared in 2015, one of which used the MinION to sequence E. coli DNA with 99.4% accuracy relative to the established 5.4 million base pair genome.[10] Despite earlier skepticism, nanopore sequencing is now accepted as a viable third generation sequencing method.[11][12][13][14] The original 1996 paper has been cited over 2000 times in the scientific literature, and in 2017, twenty one years later, a Google search for nanopore sequencing returned 226,000 results.

Other Publications

Deamer is also the co-author with science writer Wallace Kaufman of a sci-fi novel, The Hunt for FOXP5: A Genomic Mystery Novel (Springer, 2016). Through characters in American universities and Kazakhstani science and politics the authors explore the ethical complexity of editing human genes.

gollark: Oh, and elliptic curve crypto keys I guess, those are small.
gollark: You could only really do stuff like bruteforce hashes.
gollark: Good luck putting Siri on it. I meant that it'd have 1024 bytes of memory or something.
gollark: Wait, that's exploitable, oh no.
gollark: Presumably if the supertask doesn't converge it will just refuse to run.

References
  1. Deamer, D.W.; Branton, D. (1967). "Fracture planes in an ice-bilayer model membrane system". Science. 158 (3801): 655–657. Bibcode:1967Sci...158..655D. doi:10.1126/science.158.3801.655. PMID 4860951.
  2. Deamer, D.W.; Baskin, R.J. (1969). "Ultrastructure of sarcoplasmic reticulum preparations". Journal of Cell Biology. 42: 296–307. CiteSeerX 10.1.1.281.3389. doi:10.1083/jcb.42.1.296.
  3. Deamer, D.W. (1985). "Boundary structures are formed by organic compounds of the Murchison carbonaceous chondrite". Nature. 317 (6040): 792–794. doi:10.1038/317792a0.
  4. Deamer, David (2011). First life : discovering the connections between stars, cells, and how life began. Berkeley, CA, US: University of California Press. ISBN 9780520274457. OCLC 727950391.
  5. US patent 5795782, Church, George; Deamer, David W.; Branton, Daniel; Baldarelli, Richard; Kasianowicz, John, "Characterization of Individual Polymer Molecules Based on Monomer-Interface Interactions", issued August 18, 1998, assigned to President and Fellows of Harvard College
  6. Akeson, M.; Deamer, D.W. (1991). "Proton conductance in the gramicidin water wire: Model for proton conductance in the FoF1 ATPase?". Biophysical Journal. 60: 101–109. doi:10.1016/s0006-3495(91)82034-3. PMC 1260042. PMID 1715764.
  7. Kasianowicz, J.; Brandin, E.; Branton, D.; Deamer, D.W. (1996). "Characterization of individual polynucleotide molecules using a membrane channel" (PDF). Proceedings of the National Academy of Sciences USA. 93 (24): 13770–13773. Bibcode:1996PNAS...9313770K. doi:10.1073/pnas.93.24.13770. PMC 19421. PMID 8943010.
  8. Akeson, M.; Branton, D.; Kasianowicz, J.J.; Brandin, E.; Deamer, D.W. (1999). "Microsecond time-scale discrimination among polycytidylic acid, polyadenylic acid, and polyuridylic acid as homopolymers or as segments within single RNA molecules". Biophysical Journal. 77 (6): 3227–3233. Bibcode:1999BpJ....77.3227A. doi:10.1016/s0006-3495(99)77153-5. PMC 1300593. PMID 10585944.
  9. "Oxford Nanopore Technology". Retrieved 17 December 2015.
  10. Loman, N.J.; Quick, J.; Simpson, J.T. (2015). "A complete bacterial genome assembled de novo using only nanopore sequencing data". Nature Methods. 12 (8): 733–735. doi:10.1038/nmeth.3444. PMID 26076426.
  11. Regalado, Antonio; Quick, J.; Simpson, J.T. (2014-09-17). "Radical New DNA Sequencer Finally Gets into Researchers' Hands". MIT Technology Review. Retrieved 2019-03-26.
  12. Hayden, Antonio; Quick, J.; Simpson, J.T. (2015). "Pint-sized DNA sequencer impresses first users". Nature. 521 (7550): 15–16. Bibcode:2015Natur.521...15C. doi:10.1038/521015a. PMID 25951262.
  13. Zon, Jerry; Quick, J.; Simpson, J.T. (2015-09-15). "Nanopore Sequencing: 20 Years On". Zone in With Zon: What's Trending in Nucleic Acid Research. Retrieved 2019-03-26.
  14. Krol, Aaron; Quick, J.; Simpson, J.T. (2014-12-22). "Nanopore Sequencing Is Here to Stay". Bio-IT World. Retrieved 2019-03-26.

[1]

  1. The Hunt for FOXP5: A Genomic Mystery Novel, Wallace Kaufman and David Deamer, Springer, 2016, ISBN 978-3-319-28960-1
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