Lab Members


Ph.D student
Andia sm

Andia Chaves-Fonnegra

Email: andiachaves@gmail.com

Dissertation: Increase of excavating sponges on Caribbean coral reefs: reproduction, dispersal and coral deterioration.

My general research interests include: marine ecology, population genetics and chemical ecology. My PhD thesis project consists of determining how far excavating sponges are able to expand and disperse on Florida and Caribbean coral reefs. To answer these questions I am utilizing population genetics and ecological approaches. I also plan to look at reproductive aspects and temperature effect on sponges and associated microbes.

In addition, I colaborate in the Porifera tree of life Project. Besides marine sponges and corals, I like to work and volunteer in coastal and seabirds projects.

Masters Students
Andia sm

Jignasa Patel (Jigu)

Email: jp1445@nova.edu

Thesis project: Seasonal variation in meta-transcriptome profiles of the marine sponge, Axinella corrugata and its microbial consortia: A 454 pyrosequencing approach.

Currently, I am studying the seasonal variation in meta-transcriptome profiles of the marine sponge, Axinella corrugata and its microbial consortia: A 454 pyrosequencing approach. This project will help me learn new molecular techniques and get conversant with latest bioinformatics. I am employed as a graduate assistant with PorTOL (Porifera Tree Of Life) project and also worked as a research specialist with the Broward County Sea Turtle Conservation Program. My other pursuits include studying marine microbiology, bioluminescence of jellyfish, and volunteering for various organizations and events.

Andia sm

Dawn Formica

Email: df539@nova.edu

Thesis project: Seasonal fluctuations of microbial population structure in the subtropical marine sponge Amphimedon compressa.

I graduated from Eckerd College with a B.S. in Marine Biology. I am now pursuing my Masterfs degree in Marine Biology at NSU. My main interest is studying seasonal fluctuations of microbial community structure in the subtropical marine sponge, Amphimedon compressa, to understand how factors, such as temperature, salinity, nitrite, and nitrate levels play a role in the interactions between sponges and their endosymbionts.

I am also involved in the Poriferan Tree of Life project (PorTol).

In addition, my many interests include volunteering with the Marine Animal Rescue Society and sea turtle conservation work.

Andia sm

Emily Smith

Email: es874@nova.edu

Thesis project: Impact of oil spill on sponges and their microbial community.

The aim of my Masterfs thesis project is to assess the impact of the recent Deepwater Horizon oil spill in the Gulf of Mexico on sponge species and their associated microbial communities. Using transcriptomics and metagenomics, we can trace the direct impact of crude oil and dispersants on both sponge physiology (a marker of reef health) and microbial community dynamics (a marker of water quality). My project goal is to determine how the dilution of oil and dispersant affect sponge gene expression and their microbiota by comparing archived sponge samples from the collection at Harbor Branch Oceanographic Institute-FAU and freshly collected sponges of the same species from the Gulf of Mexico directly impacted by the oil spill. Sponge tissue mRNA will be extracted and used to determine effects of oil on sponge physiology and gene expression. Electron microscopy, fluorescent in-situ hybridization (FISH) and quantitative real-time PCR (qPCR) experiments will be used to validate sequence based results.
Research Interests: Endangered species research, conservation biology and genetics, wildlife biology, population biology, ecology.

Andia sm

Sebastian Basile

Email: sb1349@nova.edu

Thesis project: Base Composition Analysis and Codon Usage Bias of Demosponges

For my research, I am interested in the codon bias in Porifera. Synonymous codons encode the same amino acids, but are not used randomly. This codon bias is seen universally and varies across phyla, organisms, and genes within a given genome. My study of possible codon bias will provide a background into the selective pressures acting upon sponge genotypes, suggest optimum codons and base composition preferences to facilitate future primer design, and assist in the overall goals of the lab's PorTol project (The Porifera Tree of Life www.PorTol.org).

Andia sm

Tandace Burkhart

Email: tandace@nova.edu

Thesis project: The search for novel sponge genes: bioinformatics analysis of gene expression in multiple sponges.

My research interests include genetics, bioinformatics analysis and sponge microbial community profiling. Through the use of several bioinformatics tools, such as MG-RAST, Genbank and SEED annotation, I am examining the functional and evolutionary relationships of expressed sponge genes to other eukaryotes and searching for novel genes. This study may indicate phylogenetic markers or orthologous genes that could be amplified via PCR. The results of this study will help develop a greater understanding of gene expression in multiple sponges. I am interested in utilizing new bioinformatics analyses to discover novel information from marine gene expression.

Former Graduate Students
  Patricia Anne Waikel
MSC 2010
Email: waikel@nova.edu
Thesis: Sponges, symbionts and secondary metabolites: connections characterized by molecular and metagenomic approaches.
  Crystal A. Conway
MSC 2010
Email: cconway@nova.edu
Thesis: Study of secondary metabolite gene expression in marine microbial co-cultures using qPCR.
  Ewelina Rubin
MSC 2009
Email: ewelina@nova.edu
Thesis: Scleractinian coral recruitment to reefs physically damaged by ship groundings.
  Karita Negandhi
MSC 2009
Email: negandhi@nova.edu
Thesis: Microbial Communities with Emphasis on Coral Disease-Associated Bacteria within Florida Reef Sponges.

Farquhar Undergraduate Students
Sebastian Jofre - Porifera tree of life Project (Portol) 2010-11
Case Warshall, Estefania Niewialkouski - Coral symbionts 2011
Samia Quadri- Excavating sponges project 2010
Crystal Romero - Comparison of sponge RNA extractions 2010
Stephanie Bromante, Jillian Gormley - Study of marine sponge viruses 2009
Justin Piancentino, Shilpa Kailas - Bacterial fingerprinting and genomic data mining 2009
Vanessa Pierre, Mishaal Rehman- Analysis of microbial symbionts 2009
Fidel Maceda, Naoko Kurata - Molecular biodiversity survey of marine fungus 2008-09

Jesse Secord - Excavating sponges ecology and genetics project 2011
Case Warshall - Coral microbe project January-March 2011
Estefania Niewialkouski - Coral microbe project January-March 2011
Paola Velez - Excavating sponges ecology and genetics project 2010

Current Lab Projects
Porifera tree of life Project (Portol)
Excavating sponges ecology and genetics
Effect of oil spills on sponges and microbes
Sponge genomics and metatranscriptomes
Bioinformatics and genomic data mining