Laboratory for Genomic Effects on Nature by Environmental Stressors (GENES)
Research Interest
Coral Bleaching
Philippine coral reefs have the highest biodiversity in the world. Coral reefs contribute PHP 67.5 billion annually for the Philippine economy by creating coral reef fisheries, attracting tourists, protecting Philippine coastal communities from erosion, and by creating jobs for over a million small scale fishers and the poor. Alarmingly, Philippine coral reefs also experience the world’s highest threat level to extinction by climate change and manmade pollutants. Philippine government policy makers state that they can do little to protect this national treasure and resource citing the lack of suitable metrics to help guide policy and the protection of reefs and coastal ecosystems.
The Laboratory for Genomic Effects on Nature by Environmental Stressors studies the molecular mechanisms by which anthropogenic pollutants induce coral bleaching in order to identify new and superior metrics that can pinpoint and stop pollutants before rather than after irreversible bleaching and damage to coral reefs occur. We are approaching this through several projects.
Identification of field-validated stress-specific molecular biomarkers associated with bleaching of clownfish-hosting sea anemones
Study site
We identified Puerto Princesa Bay as one of the world’s ideal study sites to study coral bleaching since it has healthy coral reefs adjacent to an area experiencing sudden and explosive urbanization. Because many of the pollutants are new, Puerto Princesa Bay allows us to disambiguate the complexities of the environment and identify new point sources of manmade pollution for identification of field-validated stress-specific biomarkers.
Study organism
We study clownfish-hosting sea anemones in the field which are much easier to find and identify during the limited underwater airtime throughout SCUBA. Clownfish-hosting sea anemones, like hard coral, are Cnidarians that experience bleaching through the same mechanisms. Unlike hard coral, which for technical reasons are notoriously difficult to study underwater, clownfish-hosting sea anemones enable us to track and profile hundreds of samples in one field study. Help Nemo help us to save our coral reefs!
Field work
GPS mapping of bleached and unbleached clownfish-hosting sea anemones in Puerto Princesa Bay, Palawan
We track and profile hundreds of bleached and unbleached clownfish-hosting sea anemones encountered in a single field survey by scientific reconnaissance dives. Join our laboratory and enjoy hundreds of fun dives for free!
Sonar mapping
In addition to profiling molecular changes in the context of 2-dimensional maps of environmental parameters, we map the sea bottom to obtain 3-dimensional insights into the causes of bleaching. For example, there could be more bleaching within this underwater channel from sediments carrying farming chemicals after rain events.
Laboratory work
Aquarium studies
In parallel to our field studies, we conduct laboratory aquarium studies on both clownfish-hosting sea anemones and a model sea anemone with controlled amounts of stressor. Combining our laboratory experiments with the field studies yield cross-validating results with real-world relevance.
Genomics, Metagenomics, and Transcriptomics
We use the high-throughput technologies at the Philippine Genome Center to profile changes in DNA and RNA in response to bleach-inducing stressors in order to identify biomarkers. These biomarkers help us to understand the biological mechanisms involved in bleaching. The biomarkers can also be used to develop molecular diagnostic kits that that will help guide policy makers and coastal ecosystem managers.
Proteomics
We also look for proteins that can be used as stress-specific biomarkers for the onset of bleaching.
Metabolomics
We also study metabolic biomarkers that can be used as stress-specific biomarkers for the onset of bleaching.
Computational analysis
GIS
A significant part of our work involves computational analysis of our field work through Graphical Information Systems software. Geospatial mapping of our GPS-referenced sea anemones, sonar maps, multiparameter surveys, satellite imagery, and our terrestrial surveys gives us insights by interpreting molecular results in the context of the environment over space and time.
Bioinformatics
High-throughput technologies such as genomics, metagenomics, transcriptomics, proteomics and metabolomics generate millions of data points that must be analyzed. Bioinformatics transforms these data into knowledge which in turn can be turned into action.
Cambrian Explosion
A side project is our interest in the Cambrian Explosion resulted in a sudden burst in biodiversity of marine life 500 million years ago. Complex organisms such as trilobites suddenly appeared. We have a hypothesis that a disease-causing environmental stressor catalyzed the Cambrian Explosion which can be bioinformatically tested by mining the ever-growing phylogeny of genomic databases.
