Wikipedia

Jose V. Lopez

Jose V. Lopez is an American-Filipino Molecular Biologist. He has been a faculty member and Professor of Biology at Nova Southeastern University (NSU)[1] in Dania Beach, Florida, since 2007. Lopez has contributed as a co-founder of the Global Invertebrate Genomics Alliance (GIGA), a community of scientists. He has also participated in the "Porifera—Tree of Life," "Earth Microbiome," and Earth BioGenome projects.

Jose V. Lopez
Academic background
Alma materGeorgia Tech
Florida State University
George Mason University
Thesis (1995)
Doctoral advisorStephen J. O'Brien
InfluencesCharles Darwin, Alan Watts, Henry David Thoreau/Walden, Lynn Margulis, Benjamin Franklin
Academic work
InstitutionsSmithsonian Institution
Harbor Branch Oceanographic Institution
Main interestsevolution, genomics, symbiosis, systematics microbiology,
Notable ideastransposition of mitochondrial DNA

Education

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Lopez obtained his bachelor's degree at the Georgia Institute of Technology.[citation needed] He later earned a Master of Science degree focused on molecular biology at the Florida State University[citation needed] and his doctorate in Environmental Biology and Public Policy at George Mason University in Fairfax, supervised by Stephen J. O'Brien.[2] His doctoral dissertation involved the characterization of transpositions of mitochondrial DNA into the nuclei of cats and the naming of NUMT (nuclear mitochondrial DNA) as a common evolutionary genomics phenomenon.[3] Subsequent work has involved the application of molecular genetics to symbiosis and marine biology research (e.g. corals and sponges).

Career

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Lopez applied his molecular evolutionary training in postdoctoral appointments with Nancy Knowlton, characterizing the Orbicella (formerly Montastraea) annularis coral sibling species complex at the Smithsonian Tropical Research Institute in Panama, and marine sponge genetics with Shirley Pomponi at Harbor Branch Oceanographic Institute in Ft. Pierce.[citation needed] The latter allowed him to use Johnson Sea-Link submersible technology to investigate deep-sea sponges and corals. Lopez's research on marine sponges has been featured in a South Florida PBS documentary "Sponges: are they the oldest animal in the sea?" on Changing Seas TV.[4] While at NSU's Halmos College of Natural Sciences and Oceanography, his laboratory has applied genomics tools to address various specific questions in marine invertebrate-microbial symbiosis,[5] microbiome ecology,[6][7] genomics, forensics, metagenomics of oil-exposed organisms, conservation genomics,[8] and systematics/phylogenetics. Lopez was part of the Deep Pelagic Nekton Dynamics (DEEPEND) Consortium of the Gulf of Mexico, led by marine biologist Tracey T. Sutton, to better understand food webs and pelagic microbial distributions in the deep Gulf of Mexico after the Deepwater Horizon oil spill. Lopez has served as an associate editor for the Journal of Heredity since 2008. In 2018, he was awarded an NSU President's Distinguished Professor Award.[9]

Lopez co-founded the Global Invertebrate Genomics Alliance (GIGA),[10] which seeks to promote research and student training into the genomics of marine and aquatic invertebrate animals.[10] After some initial consultations with geneticist Stephen J. O'Brien and seeing the success of the first whole taxa-driven genome sequencing project, Genome10K, Lopez, and collaborators moved to form GIGA in 2013.[11] This involved reaching out to a diverse community of invertebrate biologists, who mostly supported the concept. Support to fund a maiden workshop was provided by the American Genetics Association. GIGA focuses mostly on aquatic animals but has similar problems (relatively inaccessible, small individual animals, low input DNA for sequencing) to the larger invertebrate consortium, Insect5K (i5K).[12] Both GIGA and i5K now help comprise a "network of networks" as part of the Earth BioGenome Project (EBP),[13] launched in December 2018 to try to sequence the whole genomes of 1.5 million eukaryotes.

Besides the well-known symbiosis,[14] Lopez initially hypothesized that sponge microbiomes could serve as indicators for the communities in their immediate seawater environment since sponges are filter feeders. This hypothesis was later proven to be only partially correct (see the high vs. low microbial abundance classification of sponges (HMA, LMA), as growing evidence indicated that many sponge species carry their own adapted symbionts).[15]

Lopez applied the culture-independent molecular tools that arose from the Woeseian revolution of ribosomal RNA-based bacterial systematics.[16] Eventually, molecular identifications expanded to local marine ecosystems as predictors of water quality, human skin microbiomes as possible forensic tools,[17] Myotis bat feces to test for potential microbiome effects on longevity,[18] and the Lake Okeechobee watershed of Florida.

He is the author of the book "Assessments and Conservation of Biological Diversity from Coral Reefs to the Deep Sea," which approaches deep sea marine biodiversity through perspectives on genetics, microbiology, and evolution.[19]

Personal life

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Lopez's parents are University of the Philippines graduates, clinical pathologist Ernesto G. and Rosario Lopez, who first met each other in Binghamton, New York.[20] He is married to Amy Doyle of Plantation, Florida.[citation needed]

References

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  1. ^ "Halmos College of Natural Sciences and Oceanography at NSU". cnso.nova.edu. Retrieved 2019-03-01.
  2. ^ Lopez, Jose (1995-04-01). "Molecular Evolution of Numt, a Recent Transfer and Tandem Amplification of Mitochondrial DNA into the Nuclear Genome of the Domestic Cat (Felis catus)". Oceanography Faculty Theses and Dissertations.
  3. ^ Lopez, J. V.; Yuhki, N.; Masuda, R.; Modi, W.; O'Brien, S. J. (1994). "Numt, a recent transfer and tandem amplification of mitochondrial DNA to the nuclear genome of the domestic cat". Journal of Molecular Evolution. 39 (2): 174–90. Bibcode:1994JMolE..39..174L. doi:10.1007/BF00163806. PMID 7932781. S2CID 22165470.
  4. ^ "ChangingSeas.TV Sponge documentary (episode 801)". www.changingseas.tv/. 14 December 2023.
  5. ^ Thomas, Torsten (2016). "The Global Sponge Microbiome: Symbiosis Insights Derived From A Basal Metazoan Phylum". Nature Communications. 7 (11870): 11870. doi:10.1038/ncomms11870. PMC 4912640. PMID 27306690.
  6. ^ Campbell, Alexandra; Fleisher, Jay; Sinigalliano, Christopher; White, James; Lopez, Jose (2015). "Dynamics of marine bacterial community diversity of the coastal waters of the reefs, inlets, and wastewater outfalls of Southeast Florida". MicrobiologyOpen. 4 (3): 390–408. doi:10.1002/mbo3.245. PMC 4475383. PMID 25740409.
  7. ^ O'Connell, Lauren; Gao, Song; Fleisher, Jay; Lopez, Jose (2018). "Fine Grained Compositional Analysis of Port Everglades Inlet Microbiome Using High Throughput DNA Sequencing". PeerJ. 6: e4671. doi:10.7717/peerj.4671. PMC 5947159. PMID 29761039.
  8. ^ Lopez, Jose; Kamel, Bishoy; Medina, Monica; Collins, Timothy; Baums, Illiana (2019). "Multiple Facets of Marine Invertebrate Conservation Genomics. Annual Review of Animal Biosciences". Annual Review of Animal Biosciences. 7: 473–497. doi:10.1146/annurev-animal-020518-115034. PMID 30485758. S2CID 54103492.
  9. ^ "Halmos Faculty Wins President's Distinguished Professor of the Year | NSU Newsroom". nsunews.nova.edu. Retrieved 2022-04-02.
  10. ^ a b GIGA Community of Scientists; Bracken-Grissom, H.; Collins, A. G.; Collins, T.; Crandall, K.; Distel, D.; Dunn, C.; Giribet, G.; Haddock, S.; Knowlton, N.; Martindale, M.; Medina, M.; Messing, C.; O'Brien, S. J.; Paulay, G.; Putnam, N.; Ravasi, T.; Rouse, G. W.; Ryan, J. F.; Schulze, A.; Wörheide, G.; Adamska, M.; Bailly, X.; Breinholt, J.; Browne, W. E.; Diaz, M. C.; Evans, N.; Flot, J. F.; Fogarty, N.; et al. (2014). "The Global Invertebrate Genomics Alliance (GIGA): Developing Community Resources to Study Diverse Invertebrate Genomes". Journal of Heredity. 105 (1): 1–18. doi:10.1093/jhered/est084. PMC 4072906. PMID 24336862.
  11. ^ Koepfli, Klaus-Peter; Paten, Benedict; Genome 10K Community of Scientists (2015). "The Genome 10K Project: a way forward". Annu. Rev. Anim. Biosci. 3 (5): 57–111. doi:10.1146/annurev-animal-090414-014900. PMC 5837290. PMID 25689317.{{cite journal}}: CS1 maint: numeric names: authors list (link)
  12. ^ i5K Consortium. (2013). "The i5K Initiative: advancing arthropod genomics for knowledge, human health, agriculture, and the environment". Journal of Heredity. 104 (5): 595–600. doi:10.1093/jhered/est050. PMC 4046820. PMID 23940263.{{cite journal}}: CS1 maint: numeric names: authors list (link)
  13. ^ Lewin, Harris; Robinson, Gene; Kress, John; Baker, William (2018). "Earth BioGenome Project: Sequencing life for the future of life". Proceedings of the National Academy of Sciences. 115 (17): 4325–4333. Bibcode:2018PNAS..115.4325L. doi:10.1073/pnas.1720115115. PMC 5924910. PMID 29686065.
  14. ^ Wilkinson, Clive (1987). "Significance of microbial symbionts in sponge evolution and ecology". Symbiosis.
  15. ^ Thomas, Torsten; Moitinho-Silva, Lucas; Lurgi, Miguel; Björk, Johannes R.; Easson, Cole; Astudillo-García, Carmen; Olson, Julie B.; Erwin, Patrick M.; López-Legentil, Susanna; Luter, Heidi; Chaves-Fonnegra, Andia; Costa, Rodrigo; Schupp, Peter J.; Steindler, Laura; Erpenbeck, Dirk (2016-06-16). "Diversity, structure and convergent evolution of the global sponge microbiome". Nature Communications. 7 (1): 11870. Bibcode:2016NatCo...711870T. doi:10.1038/ncomms11870. ISSN 2041-1723. PMC 4912640. PMID 27306690.
  16. ^ Pace, Norm (1997). "A molecular view of microbial diversity and the biosphere". Science. 276 (5313): 734–740. doi:10.1126/science.276.5313.734. PMID 9115194.
  17. ^ Hampton-Marcell, Jarrad T.; Lopez, Jose V.; Gilbert, Jack A. (March 2017). "The human microbiome: an emerging tool in forensics". Microbial Biotechnology. 10 (2): 228–230. doi:10.1111/1751-7915.12699. ISSN 1751-7915. PMC 5328825. PMID 28244273.
  18. ^ Hughes, Graham M.; Leech, John; Puechmaille, Sébastien J.; Lopez, Jose V.; Teeling, Emma C. (2018-01-08). "Is there a link between aging and microbiome diversity in exceptional mammalian longevity?". PeerJ. 6: e4174. doi:10.7717/peerj.4174. ISSN 2167-8359. PMC 5764031. PMID 29333342.
  19. ^ Lopez, Jose V (2023). Assessments and Conservation of Biological Diversity from Coral Reefs to the Deep Sea. Elsevier Science. ISBN 9780128241127.
  20. ^ Nancy Wiltsie (24 September 1961). "Filipino tradition followed at Quedding-Lopez wedding". Binghamton Sun-Bulletin.
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