DNA

Congrats to Vicky Suarez-Ulloa on completing a great PhD!!!

Posted by | DNA, Epigenetics, FIU, Graduate student, Marine Biology, Omics, Oysters, Red Tides, Research, Toxicology | No Comments

Victoria Suarez-Ulloa defended her PhD dissertation last week with perfect scores!, this completes a very productive stage in her academic trajectory with 10 papers published, several presentations in international conferences and most importantly, a postdoctoral position already lined up in Europe to continue working with population epigenomics. Vicky, we’re really proud of you and wish you the best for the future!!!

Eastern oyster epigenetics work accepted in Aquatic Toxicology!

Posted by | DNA, Epigenetics, FIU, Histones, Marine Biology, Oysters, Red Tides, Toxicology | No Comments

Our latest work “Effects of Florida Red Tides on histone variant expression and DNA methylation in the Eastern oyster Crassostrea virginica” has been accepted for publication in the journal Aquatic Toxicology (3.557 impact factor, ranked 3/104 in Marine & Freshwater Biology). The unformatted version of the paper is available at http://www.sciencedirect.com/science/article/pii/S0166445X17300760 and HERE. This work was developed by our lab at FIU (Environmental Epigenetics group, Dept. Biology, Institute of Water and Environment, CREST Center for Aquatic Chemistry and Environment) in collaboration with the Ecotoxicology Lab (SERC) and the University of Vigo, in Spain. We also collaborated with Rookery Bay National Estuarine Research Reserve during this research. Our results provide a basis to better understand how Florida Red Tides affect oysters and epigenetic mechanisms participating in their responses to environmental stress, opening new avenues to incorporate environmental epigenetics approaches into management and conservation programs. We are currently building on this work in collaboration with Mote Marine Lab as well as with aquaculture stakeholders in south and central Florida.

Heatmap color

Back from SETAC world 2017 in Orlando

Posted by | Conference, DNA, Epigenetics, Graduate student, Marine Biology, Oysters, Red Tides, Research, Toxicology | No Comments

Last week we had the chance of participating in a session focused on environmental epigenetics in the world congress of the Society of Environmental Toxicology and Chemistry. It was really great to see so many people interested in using epigenetic approaches to address environmental problems, involving a wide range of new model organisms encompassing environmental and ecological relevance. From our side, we presented works investigating the epigenetic modifications involved in responses to Florida Red tides in Eastern oysters (talk by Dr. Eirin-Lopez), the different genetic networks activated during responses (Victoria Suarez-Ulloa) as well as the first results from our most recent efforts to elucidate the epigenetic mechanisms underlying coral responses to nutrient stress in the ocean (Javier Rodriguez-Casariego). Overall, we left with a great feeling and looking forward to see environmental epigenetics grow and its links with ecology, toxicoloy and physiology being further explored in the future!img_4039

Dr. Eirin-Lopez at Ocean Life Series 2016

Posted by | Chromatin, Conference, corals, DNA, Education, Epigenetics, FIU, Marine Biology, Outreach | No Comments

Dr. Eirin-Lopez will be presenting the conference “The Epigenetics Revolution Reaches the Ocean” next Friday, April 15th, at the Murray E. Nelson Government Center in Key Largo, FL. A meet & greet will take place at 6 pm, followed by the conference at 7 pm. We’re looking forward to meet our Friends Of The Key Largo Cultural Center.

 

Congratulations to Gabriel (Lu) Diaz on getting a McNair Award!

Posted by | Awards, DNA, Education, FIU, Marine Biology | No Comments

Our own Gabriel (Lu) Diaz is a new Fellow in the 2016 Ronald E. McNair Post Baccalaureate Achievement Program (mcnairscholars.com), BIG congratulations!!! The McNair Scholars Program is a federal TRIO program funded at 151 institutions across the United States and Puerto Rico by the U.S. Department of Education. It is designed to prepare undergraduate students for doctoral studies through involvement in research and other scholarly activities. McNair participants are either first-generation college students with financial need, or members of a group that is traditionally underrepresented in graduate education and have demonstrated strong academic potential. The goal of the McNair Scholars Program is to increase graduate degree awards for students from underrepresented segments of society. The induction ceremony will take place next Tuesday, March 29th at 6pm, in the MMC Campus at FIU.

gabriel_diaz_600x400

Our last work has been just published today on Peer J!

Posted by | Bioinformatics, DNA, Marine Biology, Omics, Red Tides, Research, Toxicology | No Comments

Victoria (Vicky) Suarez-Ulloa, a Graduate Student at Chromevol, has led our last paper entitled “Unbiased high-throughput characterization of mussel transcriptomic responses to sublethal concentrations of the biotoxin okadaic acid”, published today in the journal Peer J. In this work we have collaborated with researchers from UK and Spain characterizing the genes involved in responses to the effects of marine biotoxins. In the pictures below you can see the now traditional “hanging ceremony” of the paper reprint below the corresponding poster (presented at the Gordon Conference in Ecological and Evolutionary Genomics last summer) in the hallway near our lab. Vicky was fortunate enough to count with the help and indications of three gentleman during this operation.

Congrats!!!

IMG_3201

IMG_3200

IMG_3204

 

It’s all too much for me to take …

Posted by | Cytogenetics, DNA, Genetics, Marine Biology, Red Tides, Research, Toxicology | No Comments

… when it comes to marine biotoxins!!!

For more than a decade now, we have been studying the effect of pollution on the genome of marine invertebrates, notably the genotoxic effect of marine biotoxins produced during harmful algal blooms. However, while the toxic effect of these compounds is well known, little is known about how much of them is needed and for how long to produce DNA damage. That is precisely what our own Veronica Prego-Faraldo has been studying during the last 2 years.

vero_600x400

In a paper published today in the Journal of Toxicology and Environmental Health, Part A (78:814-824. Jul. 2015. View PDF), she provides in vitro evidence supporting the harmful effect of the biotoxin okadaic acid a low concentrations in specific tissues of bivalve molluscs. This work constitutes the first report investigating the early genotoxic effect of this biotoxin, which soon will be followed by complementary in vivo analyses in the mussel Mytilus.

Environmental epigenetics meets marine invertebrates

Posted by | Chromatin, DNA, Epigenetics, Histones, Marine Biology, Omics, Toxicology | No Comments

Environmental epigenetics investigates the cause-effect relationships between specific environmental factors and the subsequent epigenetic modifications triggering adaptive responses in the cell. Given the dynamic and potentially reversible nature of the different types of epigenetic marks, environmental epigenetics constitutes a promising venue for developing fast and sensible biomonitoring programs. Indeed, several epigenetic biomarkers have been successfully developed and applied in traditional model organisms (e.g., human and mouse). Nevertheless, the lack of epigenetic knowledge in other ecologically and environmentally relevant organisms has hampered the application of these tools in a broader range of ecosystems, most notably in the marine environment.

Fortunately, that scenario is now changing thanks to the growing availability of complete reference genome sequences along with the development of high-throughput DNA sequencing and bioinformatic methods. Altogether, these resources make the epigenetic study of marine organisms (and more specifically marine invertebrates) a reality.

vicky_600x400rodri_600x400We have built on this knowledge to develop a review/perspectives paper on this topic, recently published in the journal Marine Pollution Bulletin. This work (conducted by Victoria Suarez-Ulloa and Rodrigo Gonzalez-Romero, grad student and postdoc at Chromevol, respectively) provides a timely perspective highlighting the extraordinary potential of environmental epigenetic analyses as a promising source of rapid and sensible tools for pollution biomonitoring, using marine invertebrates as sentinel organisms. This strategy represents an innovative, groundbreaking approach, improving the conservation and management of natural resources in the oceans.

 

is it a boy or a girl?

Posted by | DNA, Evolution, Genetics, Molecular biology, Research | No Comments

Sex determination is an extraordinarily complex mechanism. During this process, signals of different nature (genetic, epigenetic, environmental, etc.) interact with each other, often in a hierarchical manner, to produce a male or a female embryo. Historically, the study of sex determination has relied on insect models (specially the fruit fly Drosophila) due to their short generation time as well as to the presence of very well developed genetic toolkits.

Ulovené pri rieke ved¾a domu

Ten years ago we started a collaboration focused on this topic with the laboratory of Dr. Lucas Sanchez at the CIB-CSIC (Spanish Research Council, Madrid), investigating the evolution of the different components (proteins and genes) of the sex determination cascade in insects. Our latest results on this subject have been published this week by the journal Genetics. In this work we describe an unusual variation in the sex determination mechanism of sciara flies (gnats). More specifically, we find that the gene doublesex (responsible for discriminating between male-specific and female-specific developmental plans) does not seem to play that role in these insects, as suggested by the presence of non sex-specific doublesex transcripts in both males and females. This feature sets Sciara apart from other insects, revealing not only their divergent nature but also the extreme plasticity of sex determination mechanisms in nature.