Jose V. Lopez

Jose V. Lopez is an American-Filipino molecular biologist. He has been faculty and professor of biology at Nova Southeastern University (NSU).[1] in Dania Beach FL since 2007.

Jose V. Lopez
AwardsHalmos College Professor of the Year
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 worksNuclear mitochondrial transposition, cat mitochondrial genome sequence, molecular genetics of Orbicella sibling species, marine sponge genetics, GIGA, microbiomes
Notable ideastransposition of mitochondrial DNA

His doctoral dissertation involved the characterization of transpositions of mitochondrial DNA into the nuclei of cats and the naming of NUMT (nuclear mitochondrial DNAs) as a common evolutionary genomics phenomenon.[2] Subsequent work has involved the application of molecular genetics to symbiosis and marine biology research (e.g. corals and sponges). Lopez is also known for co-founding the Global Invertebrate Genomics Alliance (GIGA) community of scientists,[3] participating in the Porifera Tree of Life and Earth Microbiome Projects and raising the awareness of microbiological concepts for potential extraterrestrial mesocosm simulation, modeling, and colonization.[4]

Career

Lopez obtained his bachelor's degree at the Georgia Institute of Technology. He then earned a Master of Science degree focused on molecular biology at the Florida State University (under J. Herbert Taylor; former and deceased National Academy of Science Member), and his doctorate in Environmental Biology and Public Policy at George Mason University in Fairfax VA studying the evolution of mitochondrial DNA and its transpositions into cellular nuclei ("NUMT") in feline nuclear genomes in the National Cancer Institute's Laboratory of Genomics Diversity under Stephen J. O’Brien (current National Academy of Sciences member) in Frederick MD. Dr. Lopez then applied his molecular evolutionary training in postdoctoral appointments with Dr. Nancy Knowlton (current National Academy of Sciences member) characterizing the Orbicella (formerly Montastraea) annularis coral sibling species complex at the Smithsonian Tropical Research Institute in Panama, and marine sponge genetics with Dr. Shirley Pomponi at Harbor Branch Oceanographic Institute in Ft Pierce, FL. 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 ChangingSeas TV.[5] 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,[6] microbiome ecology,[7][8] genomics, forensics, metagenomics of oil-exposed organisms, conservation genomics[9] and systematics/phylogenetics. Professor Lopez is part of the Deep Pelagic Nekton Dynamics (DEEPEND) Consortium of the Gulf of Mexico 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. Two major themes that appear consistently throughout Lopez's research are symbiosis and biological diversity at multiple levels.

The Global Invertebrate Genomics Alliance (GIGA)

Professor Lopez has a proclivity to collaborate and so the forming of GIGA provided a natural progression. The mission of GIGA is 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 genome sequencing project, Genomes10K, Lopez moved to form GIGA in 2013.[11] This involved reaching out to a large and diverse community of invertebrate biologists, who mostly supported the concept. Then 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 and sequence the whole genomes of 1.5 million eukaryotes, the bulk of multicellular biodiversity on the earth. GIGA has now elected a new slate of officers in order to register as a not-for-profit entity in 2020. Lopez will serve as GIGA's first president.

Sponges, Microbial Symbionts and Microbial Communities

Studying marine sponges indirectly led to marine microbes, since Lopez had no formal training in microbiology. Sponge biology was fascinating from various scientific perspectives: microbes are the oldest living organisms while sponges represent one of the oldest groups on the metazoan evolutionary tree; sponges host diverse microbial symbionts which could the original source of the many natural products isolated from the phylum. The latter aspect sparked an interest in natural microbial communities (“microbiomes”) which has expanded to several other ecosystems and host models in later years.

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 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. Nonetheless, Lopez applied the burgeoning culture-independent molecular tools that arose from the Woese revolution of rRNA-based bacterial systematics[15]. Eventually molecular based identifications expanded to local marine ecosystems as predictors of water quality, human skin microbiomes as possible forensic tools, Myotis bat feces to test for potential microbiome effects on longevity, and the Lake Okeechobee watershed of Florida.

Life

Lopez's parents are University of Philippines graduates, clinical pathologist Ernesto G. and Rosario Lopez, who first met each other in Binghamton New York.[16] He is married to Amy Doyle of Plantation FL.

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References
  1. "Halmos College of Natural Sciences and Oceanography at NSU". cnso.nova.edu. Retrieved 2019-03-01.
  2. 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. doi:10.1007/BF00163806 (inactive 2020-01-12). PMID 7932781.
  3. 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.
  4. Lopez, Jose V; Peixoto, Raquel S; Rosado, Alexandre S (22 August 2019). "Inevitable future: space colonization beyond Earth with microbes first". FEMS Microbiology Ecology. 95 (10). doi:10.1093/femsec/fiz127. PMC 6748721. PMID 31437273.
  5. "ChangingSeas.TV Sponge documentary (episode 801)". www.changingseas.tv/.
  6. 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.
  7. 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". Microbiol-Open. 4(3);. 4 (3): 390–408. doi:10.1002/mbo3.245. PMC 4475383. PMID 25740409.CS1 maint: extra punctuation (link)
  8. 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.
  9. 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.
  10. 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.
  12. i5K Consortium. (2013). "The i5K Initiative: advancing arthropod genomics for knowledge, human health, agriculture, and the environment". J. Heredity. 104 (5): 595–600. doi:10.1093/jhered/est050. PMC 4046820. PMID 23940263. Retrieved 20 October 2019.
  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. doi:10.1073/pnas.1720115115. PMC 5924910. PMID 29686065.
  14. Wilkinson, Clive (1987). "Significance of microbial symbionts in sponge evolution and ecology". Symbiosis.
  15. Pace, Norm (1997). "A molecular view of microbial diversity and the biosphere". Science. 276 (5313): 734–740. doi:10.1126/science.276.5313.734.
  16. Nancy Wiltsie (24 September 1961). "Filipino tradition followed at Quedding-Lopez wedding". Binghamton Sun-Bulletin.

Category:American molecular biologists Category:Scientists

  • The Global Invertebrate Genomics Alliance - GIGA
  • DEEPEND consortium
  • Porifera Tree of Life Project
  • Other Publications
  • Unpublished Essays


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