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Universidade Nacional da Irlanda em Galway -- Ciência sem Fronteiras
PhD Project Template
PI name & contact details:
School:
Dr Gerard Fleming
Microbiology, School of Natural Sciences, NUIGalway. Ireland
Email: ger.fleming@nuigalway.ie
Tel: +353 91 493562
School of Natural Sciences
Has project been agreed with head (or
nominee) of proposed registration
school?
YES
Research Centre / group
affiliation:
Research group / centre website:
Infectious Disease and Immunity Cluster
PI website / link to CV:
http://www.nuigalway.ie/microbiology/dr__gerard_fleming.
html
http://www.nuigalway.ie/microbiology/moru.html
http://ncbes.eurhost.net/infectious-disease.aspx
Co-Supevisor (Prof. Deniz
Tasdemir)
http://www.nuigalway.ie/chemistry/level2/staff/DenizTasd
emir/dtresearch.html
Brief summary of PI research / research group / centre activity (2 or 3 lines max):
If you are already involved in relevant scholarly activities relating to Brazil, please mention them here.
Research includes: Culture of deep sea microorganisms under extreme hydrostatic pressures,
Bioactive metabolites from deep sea environments
Title & brief description of PhD project (suitable for publication on web):
Screening for Novel Antimicrobials in Deep-Sea Microorganisms: A Culture-Based Approach Under
in-situ Conditions of Hydrostatic Pressure
The continued development of microbial resistance to antibiotics, in conjunction with few new
antibiotics coming to market has placed a renewed emphasis for the biodiscovery of novel quorumsensing antimicrobials. The marine environment harbours the largest repository of microorganisms
on the planet and offers potential for the discovery of new genera of microorganisms with novel
antimicrobial properties. The deep sea (c.a. 4000m) is representative of an extreme oligotrophic
environment of low temperatures and high hydrostatic pressure. We propose to use a culturedependent approach to the isolation of microorganisms from the deep sea waters and sediment.
This approach (as opposed to a metagenomic pipeline) will facilitate the isolation of keystone
microbial populations which can translate and correctly fold and export proteins under similar
conditions to those found in the deep sea. Enrichments waters will be carried out in pressure vessels
at in-situ pressures to enhance the enrichment of piezophilic microorganisms. A novel pressureretaining and semi-continuous culture system (which we have developed) will be employed to
facilitate the directed selection of populations of microorganisms with specific physiological
characteristics amenable to the production of antimicrobial peptides. These organisms (single
species or consortia) will be isolated and characterised using molecular techniques. Whole-cell and
cell-filter extracts will be screened for antibacterial/antifungal and anti-biofilm activity. The most
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Universidade Nacional da Irlanda em Galway -- Ciência sem Fronteiras
bioactive extracts will be fermented in large scale and extracted. The chemical constituents of the
extract will be purified and antimicrobial potentials will be determined by means of growth
inhibition studies with clinically-relevant type strains The chemical structure of bioactive principle(s)
will be elucidated by high resolution NMR, MS and LC-MS techniques.
Unique selling points of PhD project in NUI Galway:
NuI Galway offers a four-year Structured `PhD programme – with added learning structures to enhance the
scientific researcher. This enables the candidate to achieve a holistic approach to his/her degree and build
competencies and skill which augment their research undertaking.
Within NUIGalway, Dr Fleming’s Microbial Oceanography Research Unit has extensive expertise in growing
microorganisms under extreme hydrostatic pressure and members have participated in International
collaborations/ cruises to the Atlantic, Mediterranean and Southern Ocean. Collaborators include British
Antarctic Survey; CRP, Spain; NIOZ-MEE, Netherlands; NIOO-CEMO, Netherlands; CNRS, France; University of
Ghent, Belgium; PUM, Italy; HCMR, Greece and Department of Marine Zoology, Senkenberg, Germany.
Dr. Fleming’s Multi-disciplinary approach to Marine Biotechnology/biodiscovery as evidenced by membership
of:
 Biodiversity: Patterns & Processes Cluster, Ryan Institute, NUI.,Galway
 Marine and Coastal Processes Cluster, Ryan Institute, NUI.,Galway
 Member Aquaculture, Biotechnology, & Biodiscovery Cluster, Ryan Institute, NUI.,Galway
Dr. Fleming’s Group leads a dynamic and focus led group with a multidisciplinary approach to research. The
ethos of the group is one of fostering the researcher so she/he can realise her/his full potential as a creative
and productive scientist. Dr. Fleming has over thirty-year’s experience of working with chemostat culture and
has advanced chemostat culture facilities. He has published widely in the field and has well established links
with Industry in the use of this medium for selection and enrichment purposes.
Deniz Tasdemir is established professor of marine biodiscovery with long experience in natural product
chemistry and drug discovery. She holds expertise in extraction, metabolite profiling, isolation and structure
elucidation as well as biological activity assessment of diverse classes of natural molecules from marine
macro- or microorganisms. She is the lead PI of the Beaufort Marine Biodiscovery Project and also involved in
Nutramara Marine Functional Food Initiative. She has shiptime access to research vessel Celtic Explorer and
the Holland I Deepwater ROV (Remotely Operated Vehicle) that will enable the collection of marine sediments
which harbor microorganisms capable of producing novel molecules. Prof. Tasdemir’s group and the School of
Chemistry have state of the art infrastructure equipped with HPLC, UPLC-MS, high resolution NMR, LC-MS, Xray crystalography facilities.
This multidisciplinary project is very likely to pave the way for discovery of novel antibiotics.
Name & contact details for project queries, if different from PI named above:
Please indicate the graduates of which disciplines that should apply:
BSc in Pharmacy, B.Sc in Biological Science; B.Sc in Microbiology; B.Sc in Molecular Biology; B.Sc.
in Fermentation Technology
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Universidade Nacional da Irlanda em Galway -- Ciência sem Fronteiras
Ciência sem Fronteiras / Science Without Borders Priority Area:
Please indicate the specific programme priority area under which the proposed PhD project fits- choose only
one (tick box):
Engineering and other technological areas
Pure and Natural Sciences (e.g. mathematics, physics, chemistry)/Physical Sciences (Mathematics,
Physics, Chemistry, Biology and Geosciences)
Health and Biomedical Sciences / Clinical, Pré-clinical and Health Sciences
Information and Communication Technologies (ICTs), Computing
Aerospace
Pharmaceuticals
Sustainable Agricultural Production
Oil, Gas and Coal
Renewable Energy
Minerals, Minerals Technology
Biotechnology
Nanotechnology and New Materials
Technologies for Prevention and Mitigation of Natural Disasters
Bioprospecting and Biodiversity
X
Marine Sciences
Creative Industry
New technologies in constructive engineering
Please indicate which of the following applies to this project (referring to Science Without Borders
arrangements):
Suitable only as a Full PhD (Y/N): _ __Y__
Available to candidates seeking a Sandwich PhD arrangement (Y/N): _Y_