Gene expression responses to acute and chronic heat stress in the common reef-building coral Pocillopora verrucosa

Global climate change is impacting coral reefs worldwide, with approximately 19% of reefs being permanently degraded, 15% showing symptoms of imminent collapse, and 20% at risk of becoming critically affected in the next few decades. This alarming level of reef degradation is mainly due to an increase in frequency and intensity of natural and anthropogenic disturbances. Recent evidence has called into question whether corals have the capacity to acclimatize or adapt to climate changes and some groups of corals showed inherent physiological tolerance to environmental stressors. The aim of the present study was to evaluate mRNA expression patterns underlying differences in thermal tolerance in specimen of the common reef-building coral Pocillopora verrucosa collected at different locations in Bangka Island waters (North Sulawesi, Indonesia). Part of the experimental work was carried out at the CoralEye Reef Research Outpost (Bangka Island). This includes sampling of corals at selected sites and at different depths (3 and 12 m) as well as their experimental exposure to an increased water temperature under controlled conditions for 3 and 7 days. Levels of mRNAs encoding ATP synthase (ATPs) NADH dehydrogenase (NDH) and a 70kDa Heat Shock Protein (HSP70) were evaluated by quantitative real time PCR. Transcriptional profiles evaluated under field conditions suggested an adaptation to peculiar local environmental conditions in corals collected at different sites and at the low depth. Nevertheless, high–depth collected corals showed a less pronounced site-to-site separation suggesting more homogenous environmental conditions. Exposure to an elevated temperature under controlled conditions pointed out that corals adapted to the high depth are more sensitive to the effects of thermal stress, so that reacted to thermal challenge by significantly over-expressing the selected gene products. Being continuously exposed to fluctuating environmental conditions, low-depth adapted corals are more resilient to the stress stimulus, and indeed showed unaffected or down-regulated mRNA expression profiles. Overall these results highlight that transcriptional profiles of selected genes involved in cellular stress response are modulated by natural seasonal temperature changes in P. verrucosa. Moreover, specimens living in more variable habitats (low-depth) exhibit higher basal HSP70 mRNA levels, possibly enhancing physiological tolerance to environmental stressors.

An integrated system for building and running reproducible research

Our generation of computational scientists is living in an exciting time: not only do we get to pioneer important algorithms and computations, we also get to set standards on how computational research should be conducted and published. From Euclid’s reasoning and Galileo’s experiments, it took hundreds of years for the theoretical and experimental branches of science to develop standards for publication and peer review. Computational science, rightly regarded as the third branch, can walk the same road much faster. The success and credibility of science are anchored in the willingness of scientists to expose their ideas and results to independent testing and replication by other scientists. This requires the complete and open exchange of data, procedures and materials. The idea of a “replication by other scientists” in reference to computations is more commonly known as “reproducible research”. In this context the journal “EAI Endorsed Transactions on Performance & Modeling, Simulation, Experimentation and Complex Systems” had the exciting and original idea to make the scientist able to submit simultaneously the article and the computation materials (software, data, etc..) which has been used to produce the contents of the article. The goal of this procedure is to allow the scientific community to verify the content of the paper, reproducing it in the platform independently from the OS chosen, confirm or invalidate it and especially allow its reuse to reproduce new results. This procedure is therefore not helpful if there is no minimum methodological support. In fact, the raw data sets and the software are difficult to exploit without the logic that guided their use or their production. This led us to think that in addition to the data sets and the software, an additional element must be provided: the workflow that relies all of them.