Sampling, Extraction and Identification


Margaret Rae

Research Programmes for Senior Post Doctoral Fellows:

 

Margaret Rae [email- margaret.rae@nuigalway.ie]

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).

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Svenja Heesch

Svenja Heesch [email- svenja.heesch@nuigalway.ie]

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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Research Programmes for PhD Students:

Katrin Hensel [email:-k.hensel2@nuigalway.ie]

Project Title

Wnt signalling in Hydractinia stem cells

Supervision Team

Dr Uri Frank, Prof Mark Johnson

Overview

Wnt signaling is involved in many cellular processes throughout development. A role for Wnt in pluripotent stem cells has been reported previously in mice, but the precise role it fulfils is not well understood. Understanding the gene regulatory network that controls pluripotency would be relevant to normal development, regenerative medicine and cancer. Studying the decision making of pluripotent stem cells is rather difficult as these cells are only present for a very short time window during development in most animals. Hydractinia is a new model organism for studying pluripotency and we have established new approaches to utilize it in a way not feasible with other models.
Hydractinia echinata is a colonial marine hydroid, living on the shell of hermit-crabs. Hydractinia has a short life cycle, provides daily access to embryos, is easy to culture and amenable to genetic manipulation and posses a remarkable regenerative ability. Regeneration is mediated by pluripotent stem cells, which are maintained in the animal throughout the life cycle. The animal has been a model organism for developmental biology and comparative immunology for decades.

Overall project aims

1. Investigate which Wnt-ligand is affecting the i-cells in Hydractinia. 
2. Explore if this Wnt ligand is specific only for i-cells, or if it is also expressed in other cell types. 
3. Carry out functional studies to find out which phenotype can be observed after deregulation of this gene.

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Mónica Moniz [email:-m.barrosjoycemoniz1@nuigalway.ie]

Project Title
Diversity, species concepts and phylogenetic relationships in some taxonomically difficult groups of marine algae

Supervision Team
Prof. Mark Johnson, Dr. Fabio Rindi and Prof. Michael Guiry.

Overview
Marine algae represent a diverse and genetically heterogeneous assemblage of organisms. Their long evolutionary history has been characterized by complex patterns of morphological character evolution, which has been source of great complication for the taxonomy of many groups. The seaweed flora of Ireland includes approximately 500 species, some of which belong to taxonomically difficult genera.

Overall project aims
This project follows two main lines of investigation:    
1- Characterization of species diversity of macroalgal assemblages epibiontic on sponges of Irish shores. This type of assemblages has been very poorly investigated, especially in the Northern hemisphere.
2- Characterization of species boundaries, phylogenetic relationships and biogeography in two selected algal groups present in Ireland:
a) The order Prasiolales (Trebouxiophyceae, Chlorophyta). This is a group of green algae with simple morphology, which includes marine, freshwater and terrestrial members. The Prasiolales are known to possess several metabolites of biotechnological interest, such as polyols, mycosporine-like aminoacids, anti-freezing proteins and bio-adhesives formed by amyloid fibrils
b) Peyssonnelia (Peyssonneliales, Rhodophyta) is a genus of subtidal red algae widespread in temperate and tropical seas, with about 70 species currently recognized. Despite of its abundant occurrence (especially in the Mediterranean), in Europe this genus has been comparatively understudied and its taxonomy still presents major challenges. An unidentified Peyssonnelia sp. from Fiji has recently been shown to contain novel anticancer compounds.

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Christine Morrow

Christine Morrow [email:- christinemorrow@gmail.com]

Project Title

Morphological and molecular systematics of sponges

Supervision Team

Prof. Christine Maggs, Dr Jim Provan, Dr Julia Sigwart, Dr Louise Allcock

Overview

Molecular systematics of sponges in Ireland is still poorly known, with numerous taxonomic, phylogenetic and nomenclatural problems.  There are likely to be many more species than are currently recognized, including cryptic species, providing potential opportunities for biodiscovery.  In the order Hadromerida (which molecular evidence suggests is likely to be polyphyletic or paraphyletic), the family Polymastiidae contains a number of undescribed species in Irish waters, which have little variation in spicule characters. It is probable that some species currently attributed to the genus Polymastia really belong to the genus Sphaerotylus, plus there are two undescribed probable Sphaerotylus species in Ireland. Molecular systematics is the appropriate tool to investigate these observations as the spicules and skeletal architecture are relatively uniform throughout the family. Within the Poecilosclerida, the family Raspailiidae has no chelae, but all other families are characterised by this type of spicule. Previous classifications have suggested that the Raspailiidae are more closely related to the Axinellidae which share a number of characters. The Hemiasterellidae, currently in with Hadromerids, were formerly in the order Axinellida (now abandoned). DNA sequencing data should contribute to the resolution of current controversy over placement of these families.

Overall project aims

This project aims to catalogue all type material relevant to Irish sponge species and prepare slide preparations of them and to sample at  known hotspots of sponge biodiversity in Ireland, particularly at Lough Hyne and Rathlin Island.  A database of collaborators will be compiled who will supply taxa required for dense and appropriate taxon sampling from elsewhere.  To obtain relevant samples worldwide for phylogenetic studies and to compare the morphology and molecular systematics of sponge samples from Ireland and worldwide.

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Carsten Wolff

Project Title

Molecular evolution, ecology and bioactivity of Keratose sponges.

Supervision Team

Dr Grace McCormack, Dr Louise Alcock, Prof Mark Johnson

 

Overview

Dictyo- and dendroceratid sponges have long been targeted as candidates in biodiscovery due to the high incidence of bioactive metabolites.However, these marine sponge species are a group notoriously difficult to classify. Their skeleton lacks siliceous, or calcareous spicules, but is rather made up of a reticulate skeleton containing collagen-based fibres.Due to the existing ambiguities in morphology-based classical systematics and ongoing difficulties in the more recent field of chemo-taxonomy, a focus of this project is on applying molecular methods to investigate phylogenetic relationships if this group of sponges.

Comparing a dictyoceratid sponge species with a representative sponge species of another taxonomic order through a highly parallel 454-based tag sequencing strategy, a comprehensive picture of the in- and epi-floras and faunas and extending to microbial community diversity, can be painted. This may also address possible mechanisms of bioactivity. Screening a variety of extracts of sponges amongst other marine invertebrate and alga species in a series of cancer assays may verify the importance of sponges and/or their symbionts. Further mechanistic studies may investigate the potential for drug-discovery and help explain fundamental strategies, or metabolic pathways.

Overall Objectives

1. To investigate the phylogeny/molecular systematics of selected dictyoceratid and dendroceratid sponges on a variety of spatial scales

2. To explore the microbial diversity associated with sponges and in particular Dysidea fragilis and Haliclona indistincta through metagenomics

3. To explore the biochemical diversity associated with local sponge species including Dysidea fragilis