Hellenic Centre for Marine Research (HCMR)

Hellenic Centre for Marine Research (HCMR)

Research Infrastructure affiliation: AQUAEXCEL2020

Location: Heraklion, Crete, Greece

Website address: http://www.imbbc.hcmr.gr

Local Access Officer: Dr. Stavros Chatzifotis (stavros@hcmr.gr), dr. Panagiotis Kasapidis (kasapidi@hcmr.gr)

Description

HCMR -the main advisory body on aquaculture and fisheries in Greece- participate in the Transnational Access (TA) program with the Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC). IMBBC aims to carry out basic and applied research on 1) aquaculture technology, reproduction, rearing, nutrition, welfare, pathology and fish quality 2) diversity of marine and freshwater life, phylogeography and genomics of marine species, development of genomic approaches in fish aquaculture, bioinformatics and interactions of organisms with their environment.

IMBBC has a long-standing experience in converting accumulated knowledge to aquaculture technologies applicable to the private sector, development of genetic tools for parentage assignment, production of genetic maps and QTL analyses of aquaculture species.

In Aqualabs, emphasis is given to hatchery technology, where systems with automated feeding and monitoring of environmental parameters have been installed. A unit of cages is devoted to on-growing experiments and monitoring of feeding behaviour.

The IMBBC's Genomics/Bioinformatics facility has modern equipment, essential for the design and elaboration of research projects in the fields of populations genetics, molecular ecology, phylogeography, genetic improvement and genomics of Mediterranean aquaculture fish, and it is able to perform any necessary genetic analysis under the context of the proposed activity.

Facilities

Aqualabs is an infrastructure organised as a vertical integrated hatchery with pilot scale and small scale experimental rearing facilities well equipped with specialised wet and dry laboratories and more classic infrastructures. The 7 main zones of experimental Access (1700 m2) integrate the up-to date technology in fish larviculture and computerised management and are managed each by a scientist. The ability to work with early life stages of many different species is unique worldwide. Nutritional and digestibility experiments can be performed in 35 tanks of 500 L and 18 tanks of 250 L respectively. Tanks are connected to a recirculation system with the ability of thermoregulation and photoperiod control. A biochemical laboratory equipped with HPLC, HPTLC, GC, Dumas nitrogen analyser, automated fiber analyzer and bomb calorimeter is offered for chemical analysis of samples. The cage unit is unique in the Mediterranean as it offers a variety of high quality experimental facilities for study of nutritional requirements and also the behaviour during the on-growing phase of the most important Mediterranean aquaculture species.

The Genomics/Bioinformatics installations include Next Generation high-throughput genetic analysers [454 FLX & Junior (Roche) and MiSeq (Illumina)], a capillary sequence analyzer ABI 3730xl (for DNA sequencing and genotyping), an arsenal of gradient and real-time PCR machines, a microarray scanner, a TaqMan OpenArray Genotyping System, a QIAcube (Qiagen) nucleic acid extraction system and in general equipment which facilitates and ensures the appropriate conditions for the isolation and the qualitative and quantitative study of the genetic profile of an organism at the level of DNA, RNA and proteins. Last, the institute operates a bioinformatics platform (BioCluster) with 13 worker nodes, 300 CPU cores, 2.5 TB RAM, 112 TB high performance storage (Lustre), 18 TB HA global storage (ZFS/NFS) /home, 40 Gbps Infiniband network.

Services

The Aqualabs infrastructure offers a) Hatchery technology and larviculture, b) Biology and control of larvae-fish development, c) Determination of nutrient and energy requirements and optimization of feeding, use of alternative sources of nutrients, d) Fish behaviour and applications in rearing populations using automated feeding systems, self-feeders, data loggers, video recording and analysis, and e) Production management in cages during grow-out in relation to feeding, behaviour and management.

The IMBBC's Genomics-Bioinformatics infrastructure is a leading institution in the research for fish species for the Mediterranean aquaculture through participation to European research projects and collaborations with the industry. Round the year there is a constant flow of visitors for research and education purposes. The infrastructure pursuits research and innovation in a) phylogenetics, systematics and population genetics, b) the de novo genome analysis, transcriptome sequencing, and analysis of microbial diversity (metagenomics), and c) the development of molecular markers, parentage assignment analyses, construction of genetic maps for target species and potentially also QTL analyses.

Using the facilities:

  • Microscopy (fluorescence, inverted microscope, phase contrast) and stereoscopy equipped for photography, camera and image analysis.
  • Physico-chemical analysis of water with electronic devices or photometer.
  • Microbiology (cooled incubator, laminar flow, deep freezer, cooled centrifuge, colony counter).
  • Biochemistry and nutrition (Dumas, Soxhlet extractor, Hydrolysis unit, fibertec, muffle furnace, oven, GC for fatty acid analysis, bomb calorimeter, HPTLC, LC).
  • Fish Physiology (ELISA, RIA enzymatic methods), haematology, endocrinology, speed vac.
  • Histology (rotary tissue processor 12 stations (histokinette), embedding station, microtome, slide warmer plate, portable bench, top fume hood, staining system).
  • Fish behaviour, ethology, biorhythms and welfare with electronic self-feeders linked to computerised data collector, tagging systems of fish (fish eagle) and cameras.

Support offered

Visitors planning to perform experiments in the IMBBC facilities are asked to provide an experimental plan for their work. TA-users have the same access to the facility, equipment and technical support as any other HCMR researcher. IMBBC does not provide lodging, but restaurants, and hotels are nearby.

Reimbursement procedures

Download here the guide for reimbursement procedures for travel and subsistence in place at HCMR.
Reimbursement procedures will be specified in the User Access Contract. National and institutional rules apply. 
Please contact dr. Panagiotis Kasapidis (kasapidi@hcmr.gr) for further info.