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WP 1: Acquisition of equipment

 

 

Objectives
  • To purchase state-of-the-art equipment to critically improve the infrastructure of IMBG in the areas of
    • a) genomics (automated Sanger-based sequencer, highthroughput Real Time PCR for SNP genotyping),
    • b) phenotyping and systematics (3D micro-CT tomographic system),
    • c) ex situ and
    • d) in situ biological in vivo monitoring and experimentation (experimental facilities) and
    • e) data storage, processing and distribution [hardware for biodiversity data collection, storage and analysis at multiple levels (genomic, taxonomic, community)]
  • To install the equipment and make it fully operational

 

Description of work

Genomic and morphological approaches constitute two fundamental components of biodiversity research that can be automated, as proposed here, thus allowing data collection at the community and ecosystem level. State-of-the-art equipment already exists at IMBG. Additional equipment will be purchased in order to optimize research applications at all levels of data collection.

Equipment for genetic/genomic analysis comprises a Sanger based sequencer (Task 1.1) and a highthroughput dual TaqMan OpenArray System for SNP genotyping and gene expression (Task 1.2). Automatic high prevision phenotypic data will be collected by application of a Micro-CT tomography (Task 1.3).
Nevertheless, the above do not address the biological facet of biodiversity. To address this point, the following approaches will be used:

Experimental facilities in the laboratory (Task 1.4) will allow fine control of experimental conditions for detailed studies of the biology, physiology, population dynamics, and the genetic basis of biological differences. This valuable experimental setting still does not cover the study of biodiversity in the natural environment, nor does it give information of natural communities’ interactions. This will be studied in the natural environment, where organisms and communities will be studied by use of an innovative BBLsampler (Task 1.5).

All the biological data in the field will be coupled with continuous monitoring of physical parameters obtained by a moored data buoy (Task 1.6)

By combining the DNA and morphological data and analysis with biological data collection, in controlled
and in natural settings, IMBG will offer the whole range of ways to study biodiversity, putting it in a coherent methodological and interpretative framework. This will be achieved by integration of data based on considerable computation capacity, based on purchase of a computer cluster for parallel computation comprising 96 CPUs and storage capacity of 12 TB (Task 1.7).

 

Tasks

Task 1.1: Purchase of sequencing equipment.

A state of the art Sanger-technology sequencer will be purchased (ABI 3730xl with 96 capillaries) to replace the previous model (ABI3700) operating in IMBG, which has become obsolete because its production, service and consumables ceased. A Sanger technology sequencer such as ABI3730 that produces long reads is indispensable for small to medium scale sequencing and microsatellite genotyping, but it is also perfectly combined with Roche 454-FLX sequencer, recently implemented in IMBG, for finishing genomes by closing gaps in genomes assembled from shotgun sequencing.

Expected cost: 90,000 € for a refurbished system.

 

Task 1.2: Purchase of a dual TaqMan OpenArray System for SNP genotyping and gene expression.

The Applied Biosystems dual TaqMan OpenArray System is a highthroughput system which can be used for detection of single nucleotide polymorphisms (SNPs) in multiplexed assays and for gene expression quantitation.

Expected cost: 150,000 €


Task 1.3:
Purchase of a Micro-CT tomograph.

A micro-CT tomograph will be purchased, with resolution of a micro-metre scale, which practically means that even the fine structure of the morphological characters may be perfectly observed in any individual from phyto- and zooplankton to macro- and even mega-fauna. The tomograph produces 3-D graphical representations of the scanned object, which is a particularly important feature in accurate species identification. More importantly, they do not make use of covering material (e.g. platinum), a feature, which makes them highly desirable for the scanning of type-material stored in museums.

Expected cost: 240,000 €.


Task 1.4.
Purchase of an experimental aquarium system (large scale bioreactor).

Bioreactor systems are being used for the ex situ experimental cultivation of marine organisms. These systems use separate enclosures for the enrichment of water and for food production thus enabling the control of suspended food concentration in the major enclosure with the cultivated organisms. They have been used successfully for the experimental cultivation of filter-feeding invertebrates such as sponges, bryozoans, bivalves, ascidians and filter-feeding crustaceans. The experimental aquarium culture system will be equipped by a network of sensors dedicated to the continuous monitoring of the internal environmental conditions, e.g. pH, oxygen, temperature, and salinity. Metabolic wastes and other inhibitory excreted metabolites will be removed from the recycle flow by passing the water through biofilters containing naturally developed microbial populations. Total water volume of the major
enclosure area will be 1,5 m3.

Expected cost: 40,000 €.

Task 1.5. Up-grade of the innovative BBL sampling towed sledge system of IMBG.

In the framework of a European funded project coordinated by IMBG (DG. XIV, Study Project 1999/036) an innovative towed sledge sampling system has been developed for the study of biodiversity of the Benthic Boundary Layer. Despite the fact that successful application of this system has been made within the continental shelf area, today there is a need to up-grade it. The up-graded version will be equipped with three pairs of water sampling bottles, three horizontal plankton nets with opening-closing doors and a colour underwater camera.. The gear will be connected to the towing research vessel by means of a 1000 m long heavy-duty umbilical cable that will be purchased in order to replace the 300 m long existing one. Flow-meters will be mounted in front of the net in order to estimate the volume of the filtered water. An odometer will be mounted at the rear part of the sledge for the continuous measurement of the distance travelled. Finally, a frame with a colour video camera will be attached on the top of the sledge in order to monitor the sampling performance of the gear.

Expected cost: 40,000 €

Task 1.6. Purchase of a moored data buoy.

This field large scale facility will be installed in the UnderwaterBiotechnological Laboratory area and data will be conveyed to the receiving IMBG land facilities via VHF in real-time. The unit will be used for the long term support of all the in-situ experiments via the long-term monitoring of the meteorological conditions at the sea surface level (wind speed and direction, air temperature and pressure, relative humidity, solar and infrared (IR) radiation) as well as of major hydrological and oceanographic parameters throughout the water column (wave height and period, current speed and direction, temperature, salinity, turbidity, pH, oxygen, and conductivity of water).

Expected cost: 115,000 €.

Task 1.7: Purchase of hardware.

A Beowulf cluster architecture will be setup with 12 nodes of 8 Xeon (3gHz and 16GB RAM) core each (96 CPUs in total) interconnected with 10GigE and a Storage Area Network of 12TB. In some more detail, the whole system will comprise: 

  • a) Twelve Dell Poweredge nodes (dual Quad Xeon 3GHz,156GB RAM) at an estimated cost of 4,000 € each (48,000 € total),
  • b) 10GigE connection system (card and switch) for interconnecting the nodes (25,500 €) and
  • c) a storage system such as a AoE SAN storage device of 12 TB estimated (24,000 €).

Expected cost: 97,500 €.

 

It should be noted that HCMR’s practice is to depreciate all its fixed assets on the year of its obtainment.