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Research Programmes

Jonathan Kennedy

Research Programmes for Senior Post Doctoral Fellows:

Jonathan Kennedy [email-]

Metagenomic and Culture-based Approaches to Biodiscovery from Sponges

The main objectives of this research project are the utilisation of the sponge microbiota for the biodiscovery of novel bioactive agents and industrially useful enzymes.  Two main approaches are being adopted - a culture-based approach and, as the vast majority of the sponge microbiota are uncultured, a culture-independent or metagenomic approach. 

For the culture-based approach a collection of marine-sponge derived microorganisms are being cultured, catalogued, extracted and assayed for anti-microbial activities.  Following initial assays selected microbes are being studied in more detail to determine the antimicrobial spectrum of activity, the chemical structure of the antibiotic and the genetics of their biosynthesis.

The functional metagenomics approach will enable access to the biochemical and genetic diversity present in the uncultured majority of the sponge microbiota.  For this approach large clone metagenomic libraries utilising customized vectors are being used to enable functional expression in several host strains.  Due to the large numbers of clones required for this approach a robotic colony picking and arraying system are being employed.  Positive clones are being analysed by subcloning, expression, and DNA sequence analysis.


Marlies Mooij [email:-]

Cell Signalling in Marine Microorganisms-Biofilms-Biofouling

Cell signalling systems and the various genes under its control are crucial for bacterial virulence. As such, these signalling systems could serve as novel targets in the development of new therapeutic agents.  Many bacteria use the cell density dependent cell to cell signalling system, quorum sensing (QS) to coordinate their virulence, including, motility, the formation of biofilms and the expression of drug resistance efflux pumps. Therefore, quorum sensing is a promising target for antimicrobial drugs. This work is focusing on Pseudomonas aeruginosa, as a model system. P. aeruginosa is a ubiquitous environmental bacterium that is among the top three opportunistic human pathogens, and has previously been used as a model organism for studying cell signalling. Reporter assays are being used to identify novel QS and biofilm inhibitors from marine sponges and from marine sponge associated microorganisms, which are a rich source for structurally novel biologically active compounds. Functional metagenomic based approaches are also being employed.  In addition a recently established zebrafish facility within the BIOMERIT Research Centre at the Microbiology Department at University College Cork, is employing zebrafish embryos as an in vivo biological model, to screen for drug interventions on bacterial infections, as well as for effects that bioactive compounds may have on the development of the zebrafish embryo.


Margaret Rae

Margaret Rae [email-]

Sampling, Extraction and Identification of Marine Bioactives

The main objectives of this research project are the sampling, extraction and isolation of marine species for the biodiscovery of novel bioactive molecules.   The extracts obtained are then screened against in-house bioassays and also against partner bioassays for bioactivity. 

Once a bioactive has been identified through bioassay screening, its structural characterization must then proceed using tools such as mass spectrometry and nuclear magnetic resonance spectroscopy.


Fraction Collector

This project necessitated the set-up of the Marine Biodiscovery Laboratory at the Marine Institute and development of all the extraction protocols.  The Laboratory not only performs the extractions but also traces and track all the marine specimens, extracts, fractions etc. from sampling and collection right through to bioassay and structural identity. The Laboratory is split into 2 suites – an extraction and a bioassay suite. The Laboratory houses the customised Marine Biodiscovery Database developed by Dr. Helka Folch in Work Package 5 and also the AntiMarin database (comprising data from approximately 55,000 marine compounds).



Helka Folch

Helka Folch [email:-]

Database Construction and Integration

The main objectives of this research project are to manage data  generated by the National Marine Biodiscovery Programme and link the data collected by the project's stakeholders to existing biodiversity, genetic and chemical resources. This has involved the implementation of  the BioDiscovery database hosted at the Marine Institute  to track the flow of samples and extracts among consortium partners and to provide analysis and decision support tools to prioritize active leads in bioactivity screening.


iPhone App

The database system includes tools aimed at the data mining and visualisation of biogeographical, genetic and chemical information that enable the identification of potential biodiversity and bioactivity 'hotspots'.

The purpose of this research project is also to develop innovative environmental monitoring technologies such as the BioDiscovery smartphone app aimed at facilitating the collection and sharing of biodiversity data.


Susan Clarke

Susan Clarke [email:-]

Marine organisms for bone repair

Clinically it remains a challenge to fill large bone defects such as those following tumour resection or revision of joint replacements. Calcium phosphate ceramics have been used as synthetic bone graft materials as they closely resemble the mineral phase of bone; however the clinical results with these commercially available materials leave room for improvement. Porous materials perform better than solid, bulk materials because they allow vascular and bony invasion. We are currently investigating the ability of mineralising marine organisms with porous structures, such as sponges, cuttlefish and red algae, to support bone growth, either directly or when converted to calcium phosphate structures.

SEMs of (a) cuttlefish (Sepia officinalis), (b) sponge (Spongia agaricina), (c) red algae (Corallina officinalis) and (d) coccolithophores (Emiliania huxleyi)demonstrating a range of macro and microporous structures.


Specific projects include:

  1. The in vitro and in vivo evaluation of the ability of a calcium phosphate scaffold derived from a marine sponge template to support bone growth;
  2. The potential of sponges from Irish Waters to act as scaffolds for bone tissue engineering;
  3. Optimisation and in vitro evaluation of red algae-derived ceramic- the calcium carbonate structure of Coralline officinalis is converted to calcium phosphate;
  4. Use of marine sponge-derived collagen to enhance bone substitute materials- specifically to augment the biocompatibility of an injectable cement designed for vertebroplasty and the surgical repair of burst spinal fractures.

Svenja Heesch

Svenja Heesch [email-]

Sampling, Extraction and Identification of Marine Bioactives

This part of Work package 2: "Sampling, Extraction and Identification" explores Irelands high biodiversity of marine macroalgae for biodiscovery. Large macroalgal species are collected in the field and prepared for the extraction of potential bioactive compounds. Small and rare species are isolated and cultivated in the laboratory to produce sufficient biomass for the extraction. Taxonomic identification of the samples is based on morphological and appropriate molecular genetic markers.

Targeted for collecting and screening, and, where appropriate, for taxonomic studies are especially:
1) introduced/invasive species which may be able to outcompete native species due to novel bioactive defense mechanisms.
2) species related to genetic model organisms, such as Ectocarpus siliculosus, as genomic information may aid in the screening for and identification of novel biochemical compounds and pathways.
3) taxa with known bioactivity to identify potential cryptic species complexes which may produce very different bioactive profiles.

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