Functional Genomics


The research goal is the identification, with a functional genomic approach, of molecular markers that describe fish response to environmental conditions, nutritional and feeding strategies.

Fish welfare: molecular reponses to stress in fish. 

In addition to several indicators that have been proposed for assessing fish welfare, such as cortisol, haematocrit, blood glucose or total haemoglobin, molecular biomarkers directly indicating gene activity may have the characteristics for being very sensitive and reliable indicators. In this context, we have first determined the sequence of a glucocorticoid receptor (GR) (AY549305) a stress-related gene in a teleost (Dicentrarchus labrax) of high commercial interest for Mediterranean aquaculture, for which only little is known at present about its genomics. GR acts as a ligand-dependent transcription factor to control and regulate gene expression. We have then investigate the impact of  long-term exposure to crowding stress on GR expression levels in the liver of sea bass quantified by real-time RT-PCR. Our study clearly demonstrated that chronic stress by high rearing density affects GR expression, whose levels in the liver decreases inversely with blood cortisol levels. Therefore, GR may be a valid bio-indicator capable of providing useful information about fish welfare.


Hypothetical model of DNA–binding domain of glucocorticoid receptor  


Fish nutrition: studies on the “compensatory growth” in Sea bass.

The exceptional fast growth that farmed fish experience after a feed deprivation period has been called “compensatory growth” or “catch up “ growth. In intensive aquaculture this phenomenon has been studied in order to find a possibility of enhancing feed conversion efficiency. In this context cloning and sequencing of the complete coding sequences of sea bass (Dicentrarchus labrax, L) insulin-like growth factor I (IGF-I) and IGF-II, myostatin and fibroblast growth factor 6 (FGF6), all genetic determinants of skeletal muscle growth, have been carried out. The complete coding sequences of sea bass IGF-I (AY800248), IGF-II (AY839105), FGF6(AY831723) and myostatin (AY838106) were deposited in the GenBank.

Then, the expression profile of IGF-I, IGF-II, myostatin and FGF6 in liver and myotomal muscle, in response to different feeding regimens, has been studied. The expression levels of all aforementioned genes has been quantified by real-time RT-PCR. Nutritional status influenced significantly the IGF-I and II expression levels in liver as well as in muscle, inducing a down-regulation during fasting and an up-regulation during the recovery from fasting. The myostatin expression levels, confirmed the involvement of this gene in the compensatory growth induced by re-feeding. A novel finding was the increase in myostatin mRNA abundance in the muscle of fasted sea bass, indicating that this autocrine/paracrine growth factor has a role in modulating muscle growth in response to different feeding regimens. Unlike the three aforementioned genes, the FGF6 expression pattern did not provide us any clue to its function, as its muscular mRNA levels were not affected whatever the feeding status of the animals was.

Environmental factors: oxygen-regulated gene expression in Sea bass

Low oxygen is prevalent in many aquatic habitats and one response of fish to hypoxia is compensatory changes in gene expression. In mammals this phenomenon is mediated, in part, by the Hypoxia-Inducible Factor (HIF). This transcription factor accumulates at low oxygen, binds to hypoxia response elements of a variety of target genes, and ultimately increases gene expression. In fish, homologues of HIF are present. However the targets of HIF regulation remain largely unknown. In efforts to characterize mechanisms of hypoxia adaptation in marine fish we have isolated  the complete coding sequence of  HIF-1a in sea bass (Dicentrarchus labrax) (DQ171936), which has been deposited in the GenBank. To study the expression patterns of HIF-1a, fish were exposed to severe acute and chronic hypoxia conditions and the mRNA abundance levels were measured by real time PCR in liver and kidney. Upon exposure to acute hypoxia for 3 hours transcription of HIF-1a was significantly upregulated in both tissues, indicating that its mode of regulation is similar to its mammalian homologues.