Faculty & Staff Profiles

Jose Victor LopezDr. Joe Lopez faculty photo

Professor
joslo@nova.edu
Google Scholar Page
https://plus.google.com/u/0/101028193304378626073/posts (current lab page)
www.nova.edu/ocean/lopez/microlab (previous lab page)

Education
Area(s) of Research

Our laboratory conducts molecular biology, systematics and microbiological research on various marine invertebrates, including corals, marine sponges and their symbiotic microbes.

Evolution underpins much of this research as it does all of biology; in turn, variation and the genetic code underpin biological evolution. Therefore, our research has been focused on characterizing various dimensions of the change and diversity at the genetic and cellular levels. This variation ultimately translates to variation among populations, within and between species and higher taxa.

Sponges represent the oldest metazoan phylum, having existed since at least the Cambrian period 500 million years ago. Even longer still is the evolutionary time frame (over 3 billion years) of diverse single cellular microorganisms.

PorTolTogether these and other organismal groups, comprise major lineages on our Earth's Tree of Life. In this context, our lab has been involved in a National Science Foundation project called Assembling the Tree of Life (or AToL) that aims to assign and map portions of the planet's biodiversity (from species to families to phyla etc) onto a virtual tree or phylogeny showing discrete lineages and relationships among the organisms (http://www.phylo.org/atol/pdf_docs/atol.pdf). To generate the most robust phylogeny possible, multiple laboratories and collaborators will join together to sequence the most informative gene sequences from representative taxa, integrate molecular and non-molecular (e.g. morphological, ecological, behavioral etc) datasets, and run computer analyses that will attempt to derive the best estimate of actual branching orders and relationships among the organisms

Within this program, our lab is part of the Porifera Tree of Life (PorToL) collaborative project that is currently studying the taxonomy and evolutionary relationships among sponges and the phylum's context with the rest of Metazoa.

Another current thread of research is developing model marine organisms. Because sponges are sessile, often long term residents of the benthos, they may also serve as important indicators for environmental change. In this regard, doctoral student and recent L'Oreal recipient, Andia Chaves Fonnegra has an ongoing project that is characterizing the reproduction, recruitment and biogeography of the coral excavating sponge, Cliona delitrix. This sponge grows and eventually kills the coral colonies that it settles upon, and thus modes or reproduction and distribution in the Caribbean region that may or may not be related to climate change, are being determined.

Similarly, and as part of a Florida Institute of Oceanography grant, resulting from the Deepwater Horizon oil spill disaster, our laboratory has collaborated with Florida International University and Florida Atlantic University's Harbor Branch Oceanographic Institute to test the effects of oil and dispersant on sponges and their microbial symbionts. Past collaborations with FAU-HBOI led to the construction of a marine microbial database http://hbmmd.hboi.edu/index.htm.

Other aspects of my research involve molecular evolution, horizontal gene transfer (http://www.wikigenes.org/e/art/e/117.html), gene expression and the application of next generation DNA sequencing for metagenomics (http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000667) and transcriptomics. These technical advances have helped spawn a new initiatives from the human microbiome to the "Earth Microbiome Project", which promises to reveal more diversity and related important functions of microbes (www.earthmicrobiome.org). We hope to participate actively in this project, and also quickly release novel gene sequence data generated by high throughput methods soon after it is generated by public funding.

With the advances of next generation DNA sequencing, our lab has helped spearhead the recent initiative called "The Global Invertebrate Genomics Alliance" or GIGA.  In this long range project, we hope to join other invertebrate biologists in forming a community dedicated to comparing and understanding the broad spectrum of invertebrate genomes in an evolutionary and ecological contexts.  More details at Giga.Nova.edu

 

Current Graduate students

PhD

Andia Chaves Fonnegra - Increase of excavating sponges on Caribbean coral reefs: reproduction, dispersal and coral deterioration

Current Masters Students

Renee Potens - Genetic Analysis of Seasonal Fluctuations in Microbial Symbiont Diversity of the South Florida Marine Sponge Amphimedon compressa

Rebecca Mulheron - Microbial Community Assemblages found with Sponge Orange Band Disease in Xestospongia muta (Large Barrel Sponge).

Dawn Formica - Seasonal fluctuations of microbial population structure in the subtropical marine sponge Amphimedon compressa

Alexandra Campbell - Genetic sequence characterization of marine bacterial diversity from South Florida waters over space and time

Shira Jaye Anteby - Investigation of Regulatory and Hypothetical Genes in Marine Microbes Roseobacter denitrificans Och114 and Oceanobacillus iheyensis HTE831: A Site-Directed Mutagenesis

Jonathan Lanzas - The Current State of Next-Generation Sequencing

Lauren O'Connell - Compositional Analysis of the Port Everglades Inlet (Broward County, FL) Microbiome Using Next Generation Sequencing Technology Emily Powell  - Estimate of Genome Sizes in Marine Invertebrates by Flow Cytometry

Emily Powell

Past Students

Diana Aranda - Spatial and temporal variations of enterococci levels on sub-tropical recreational beaches: a historical analysis.

Emily Smith - Developing marine sponges as biological indicators for oil and chemical dispersant impacts

Tandace Burkhart - Mining genetic databases for new gene discovery

Jignasa Patel - Seasonal variation in meta-transcriptome profiles of the marine sponge, Axinella corrugata and its microbial consortia: A pyrosequencing approach

Karita Negandhi - Microbial Communities with Emphasis on Coral Disease-Associated Bacteria within Florida Reef Sponges Microbial Communities with Emphasis on Coral Disease-Associated Bacteria within Florida Reef Sponges

Crystal Conway - Study Of Secondary Metabolite Gene Expression In Marine Microbial Co-Cultures Using Quantitative Real-Time Pcr

Patricia Waikel - Analysis of a partial expressed sequence tag (est) library and differential expression of genes in biochemical morphotypes of the marine sponge Discodermia dissoluta

Denise Hemphill - Hydrothermal Geology at Meridiani Planum, Mars, and the Possibility of a Marker for Microbial Life in the Iron Oxyhydroxide, Schwertmannite

GIGA Community of Scientists.  2014. The Global Invertebrate Genome Alliance (GIGA): Developing Community Resources to Study Diverse Invertebrates. Journal of Heredity. 105:1-18. http://m.jhered.oxfordjournals.org/content/105/1/1.full

Richards V.P, Grieg, TW, Fair, P.A., McCullough, S.D,  Politz, C., Natoli, A., Driscoll, C., David, V., Hoelzel, AR, Bossart, G.D., Lopez, J. V. 2013. Patterns of Population Structure for Inshore Bottlenose Dolphins along the Eastern United States. Journal of Heredity. 104 (6): 765-778. doi: 10.1093/jhered/est070. http://jhered.oxfordjournals.org/content/104/6/765.abstract

Hill, M., Hill, A., Lopez, J., Pomponi, S., J.V., Reed, J., Tarver, Redmond, N., Diaz, M.C., Boury-Esnault, N., Cardenas, P., Reiswig, H., Dohrmann, M., Morrow, C. Rubin, E., Chaves-Fonnegra, A., Patel, J., Formica, D., Danka, E., De Laine,B-O.,Pohlmann, D., Richie, S., di Stefano, M., Russell , Z., Peterson, K. J., Pisani, D., Thacker, R., Collins, A., 2013. Nuclear housekeeping genes help resolve demosponge relationships and taxonomy. PLoS ONE 8(1): e50437. doi:10.1371/journal.pone.0050437

Hoffmann, M, Monday, S.R., McCarthy, P.J., Lopez, J.V., Fischer, M. and Brown, E.W. Genetic and phylogenetic evidence for horizontal gene transfer among ecologically disparate groups of marine Vibrio. Cladistics. 46-64. View entire paper.

White, J, Patel, J., Ottesen, A., Arce, C., Blackwelder, P., Lopez, J.V. Pyrosequencing of microbes within Axinella corrugata sponges; Diversity seasonal variability, PLoS ONE 7(6): e38204.doi:10.1371/journal.pone.0038204; View entire paper.

Hoffmann M, Monday SR, Allard MW, Strain EA, Whittaker P, Naum M, McCarthy PJ, Lopez JV, Fischer M, Brown EW. (2012) Vibrio carribeanicus sp. Nov., isolated from marine sponge Scleritoderma cyanea. International Journal of Systematic Evol Microbiology. In Press. View entire paper.

Conway, C.A., Esiobu , N., Lopez, J.V. (2012) Co-cultures of Pseudomonas aeroginosa and Roseobacter denitrificans reveal shifts in gene expression levels compared to solo cultures . The Scientific World Journal. Veiw Entire Paper

Lopez, J.V. Ledger, A. Santiago-Vazquez, L.Z, Pop, M., Sommer, D.D.,Ranzer, L., Feldman, A. Kerr, R.G. 2011. Suppression subtractive hybridization PCR isolation of cDNAs from a Caribbean soft coral Electronic Journal of Biotechnology, Vol. 13, no. 5. View entire paper

Negandhi, K., Blackwelder, P.L, Ereskovsky, A.V., Lopez, J.V. (2010). Florida Reef Sponges Harbor Coral Disease-Associated microbes. Symbiosis 51: 117 - 129. View entire paper

Hoffman, M. Fischer, M. Ottesen, A. McCarthy, P.J., Lopez, J.V., Brown, E. Monday. S. (2010). Population dynamics of Vibrio spp. Associated with Marine sponge microcosms. ISME Journal 4(12):1608-12. Epub 2010 Jul 1. View entire paper.

Rubin E.T., Lopez, J.V., Gilliam, D.S., Dodge, R.E., Kosmynin, V.N., Moulding, A.L. (2010). Scleractinian coral recruitment patterns to reefs physically damaged by ship groundings. Proc 11th ICRS. Pp. 326-330. View entire paper.

Lopez, J.V., Ranzer, L.,. Ledger, A., Schoch, B., A. Duckworth, P.J. McCarthy, R.G. Kerr. (2010). Comparison of Bacterial Diversity within the Coral Reef Sponge, Axinella corrugata, and the Encrusting Coral Erythropodium caribaeorum. Proc 11th ICRS. Pp. 1355-1359. View entire paper.

Lopez, J.V., Mouzon, B., McCarthy, P.J., Kerr, R. (2009). The many faces of gene expression profiling: Transcriptome analyses applied towards elucidating marine organismal interactions and metabolism. Textbook on Molecular Biotechnology. IK International Publishing House Pvt. Ltd Amity University Uttar Pradesh (AUUP), ISBN 978-93-80026-37-4. Pp 287-304. View entire paper

Roberto Perez, Li Liu, Jose Lopez, Tianying An and Kathleen S. Rein (2008). Diverse Bactierial PKS sequence derived from Okadaic acid-producing dinoflagellates. Marine Drugs. 6:164-179. View entire paper.

Ranzer, L.K., Brück, TB., Brück, WM., Lopez, J.V., Kerr , RG (2009). A New Prokaryotic Farnesyldiphosphate Synthase from the octocoral, Eunicea Fusca: Differential Display, Inverse PCR, Cloning And Characterization. Marine Biotech. 11(1):62 View entire paper.

Cassler, M., Winegar, R. , McCarthy, P.J., Pomponi, S.A., Peterson, C.L, Wright, A.E, Lopez, J.V. (2008). Use of Real-Time qPCR to quantify members of the unculturable heterotrophic bacterial community in a deep sea marine sponge, Vetulina sp. Microbial Ecology 55:384-394. View entire paper

Park, Y.C, Gunasekera, S., McCarthy, P.J., Lopez. J.V., and Wright, A.E. (2006). New Metabolites from the Marine Derived Fungus Chromocleista sp. Isolated from the Deep-Water Sediment Sample Collected in the Gulf of Mexico. J. Natl Products 69:580-584.

Lopez, J.V. (2006). Some preservation techniques for (deep water) coral samples. In Deep-sea Coral Collection Protocols. (Ed. Peter Etnoyer SD Cairns, JA Sanchez, J Reed, S Brooke, A Baco-Taylor, L Watling et al.). NOAA Technical Memorandum NMFS-OPR-28 NOAA Office of Ocean Exploration. US Dept. Commerce, 45 pp. View entire paper

Snyder, RV , Guerrero, M., Sinigalliano, C., Winshell, J, Perez, R., Lopez, J.V., and K. S. Rein. (2005). Localization of polyketide synthase encoding genes to the toxic dinoflagellate Karenia brevis. Phytochemistry 66:1767-1780. (HBOI 1607). View entire paper

Gunasekera, A., Sfanos, K.A, McCarthy, P.J., Lopez, J.V. (2005). HBMMD: an enhanced database of the microorganisms associated with deeper water marine invertebrates. Applied Microbiol. Biotechnol. (2005) Jan;66(4):373-376. Epub (2004) Nov 16. View entire paper.

Sfanos, K.A.S., Harmody, D.K., McCarthy, P.J., Dang, P., Pomponi, S.A. and Lopez J.V. (2005). A Molecular Systematic Survey of Cultured Microbial Associates of Deep Water Marine Invertebrates. View entire paper

Sandell, K.A., Peterson, C.L., Harmody, D.K., McCarthy, P.J., Pomponi, S.A., Lopez, J.V. (2004). Molecular systematic survey of sponge - derived marine microbes. 6th International Sponge Conference Proceedings. Boll. Mus Ist. Univ. Genova. 68:579-585.

Lopez, J.V., (2003) Naturally mosaic operons for secondary metabolite biosynthesis: Variability and putative horizontal transfer of discrete catalytic domains in the epothilone polyketide synthase locus. Mol Genet Genomics 270:420-431. View entire paper

Enright, E., Lopez, J.V., Peterson, C.L., Pomponi, S.A. (2002). Cloning and characterization of two cyclin dependent kinase (CDK) homologues from the marine sponge, Axinella corrugata. (2002) Boll. Mus Ist. Univ. Genova 66-67:63.

Takabayashi, M., Carter, D.A., Lopez, J.V., Guldberg, O.H. (2003). Genetic Variation of the scleractinian coral, Stylophora pistillata, from Western Pacific reefs. Coral Reefs 22: 17-22.

Snyder, R.V, Gibbs, P. D. L. , Palacios, A., Abiy, L , Dickey, R., Lopez, J.V., Rein, K.S (2003). Polyketide Synthase Genes from Marine Dinoflagellates. Marine Biotechnology. 5:1-12. View entire paper

Sandell, K.A., Peterson, C.L., Harmody, D.K., McCarthy, P.J., Pomponi, S.A., Lopez, J.V. (2002). Molecular systematic survey of sponge -derived marine microbes. Abstract. Boll. Mus Ist. Univ. Genova 66-67:172.

Lopez, J.V., Peterson, C.L., Willoughby, R., Wright, A.E., Enright, E., Zoladz, S., Pomponi, S.A. (2002).Characterization of genetic markers for in vitro cell line identification of the marine sponge, Axinella corrugata. Journal of Heredity. 93:27-36. View entire paper.

Lopez, J.V., Peterson, C.L., Morales, F., Brown, L. (2000). Molecular Studies of Caribbean Biodiversity In The Field: Indian River Lagoon, Fl And Andros Island, Bahamas. Proceedings of MarCuba (2000), Dec 4- 8, (2000). CD version. Intergovernmental Oceanographic Commission of UNESCO, Havana, Cuba.

Lopez, J.V., Peterson, C.L., Morales, F., Brown, L. (2000). Molecular Studies of Biodiversity in the Field: Andros Island Flora and Fauna in the New Millennium. Bahamas Journal of Science. Bahamas Journal of Science. 8:32-41. View entire paper.

Lopez, J.V., McCarthy, P.J., Janda, K.E.,Willoughby, R., Pomponi, S.A. (1999) Molecular techniques reveal wide phyletic diversity of heterotrophic microbes associated with the sponge genus Discodermia (Porifera:Demospongiae). Proceedings of the 5th International Sponge Symposium. Memoirs of the Queensland Museum. 44: 329-341. Brisbane ISSN 0079-8835. View entire paper

Lopez, J.V., Kersanach, R., Rehner, S.A., Knowlton, N. (1999) Molecular determination of species boundaries in corals: Genetic analysis of the Montastraea annularis complex using amplified fragment length polymorphisms and a microsatellite marker. Biol. Bull. 196:80-93. View entire paper.

Pomponi, S.A., Willoughby, R., Wright, A.E., Pecorella, C., Lopez, J. V., Samples, G. (1998) In vitro production of marine-derived compounds. In New Developments in Marine Biotechnology (Eds. Y.Le Gal and H.O. Halvorson) Plenum Press, New York. Pp. 73 - 76

Lopez, J.V., Knowlton, N. (1997) Discrimination of the species of the Montastraea annularis complex with multiple genetic loci. Proceedings of the 8th International Coral Reef Symposium, Rep. of Panama. 2:1613-1618. View entire paper

Lopez, J.V., Stephens, J.C, O'Brien, S.J. (1997) The long and short of nuclear mitochondrial lineages. Trends Ecol. Evol. 12(3):114

Lopez, J.V., Culver, M., Stephens, J.C., Johnson, W.E., O'Brien, S.J. (1997) Rates of nuclear and cytoplasmic mitochondrial sequence divergence in mammals. Mol Biol and Evol. 14(3):277-286. View entire paper.

Masuda, R., Lopez, J.V., Pecon-Slattery, J., Yuhki, N. O'Brien, S.J. (1996) Estimating the phylogeny of the Felidae with two mitochondrial gene sequences. Molecular Phylogenetics and Evolution 6(3):351.

Lopez, J.V., Cevario, S., O'Brien, S.J. (1996) Complete nucleotide sequences of the domestic cat (Felis catus) mitochondrial genome and a transposed mtDNA tandem repeat (Numt) in the nuclear genome. Genomics 33:229-246. View entire paper

Lopez, J.V. (1994) Taking a cat map: whole genome analysis by supercomputer. In Computational Biomedical Research (Monograph) NCI-Biological Supercomputing Center, NCI-FCRDC.

Hoelzel, A.R., Lopez, J.V., Dover, G.A., O'Brien, S.J. (1994) Rapid evolution of a heteroplasmic repetitive region in the mitochondrial control region of carnivores. J. Mol. Evol. 39:191-199.

Lopez, J.V., Yuhki, N., Modi, W., Masuda, R., O'Brien, S.J. (1994) Numt, a recent transfer and tandem amplification of mitochondrial DNA in the nuclear genome of the domestic cat. J. Mol. Evol. 39:171-190. View entire paper

Dipaolo, J.A., Woodworth, C.A., Popescu, N.C., Koval, D.L., Lopez, J.V., Doniger, J. (1990). HSV-2-induced tumorigenicity in HPV16-immortalized human genital keratinocytes. Virology 177:777-779.