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FOREWORD
001 Letter from President,
University College Dublin
003 Letter from Chair,
Board of Management,
Conway Institute of Biomolecular
and Biomedical Research
004 Foreword by Chief Executive,
Conway Institute of Biomolecular
and Biomedical Research
HIGHLIGHTS
007 Conway Institute Highlights
009 Centre Highlights
012 New Appointments
013 Programme Level Grants
014 High Impact Publications
016 Awards and Events
RESEARCH OUTCOMES
019 Research Outcomes
021 Campus Companies
CONWAY INSTITUTE TODAY
025 Buildings and Technical Services
027 Affymetrix GeneChip Core Technology
029 Real-Time PCR
031 DNA Sequencing and
Oligonucleotide Synthesis Service
032 Proteome Research Centre (PRC)
033 Flow Cytometry Facility
035 Confocal Microscopy and
Digital Imaging Facility
037 Bioinformatics Service
039 Electron Microscopy Laboratory
041 Mass Spectrometry Facility
043 Business and Finance
045 Communications and Education
APPENDIX
049 Publications
067 Grants Awarded
075 Thesis Submissions
079 Conway Institute Seminar Series
081 Committees/Management Structure
083 Contact Us
Contents
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DR HUGH BRADY, PRESIDENT
UNIVERSITY COLLEGE DUBLIN
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The collaborative ethos of the Conway is borne out in the strength of new relationships
with other research institutes across Dublin in the areas of proteomics, neuroscience
and prostate cancer; with industry in the areas of neurodegenerative disorders and core
technology platforms and with the wider community and the secondary education sector
in particular through outreach initiatives such as ScienceWorks.
The building, which will accommodate the Conway Institute’s new Centre for Synthesis
and Chemical Biology (CSCB), began construction in June 2004 and is expected to be
ready for occupancy in September 2005. This 2,500m2 facility will house six state-of-
the-art research laboratories and associated researchers’ space as well as superb
analytical instrumentation facilities including nuclear magnetic resonance (NMR)
spectroscopy and mass spectrometry centres, which will be employed in studies at the
interface between chemistry and biology.
This combination of world-class infrastructural development and high calibre innovative
researchers and students augurs well for the success of the Institute.
Dr Hugh Brady
President
University College Dublin
2004 marked the 150th anniversary of UCD and afforded us a unique opportunity
to both celebrate UCD’s past and contemplate its role in shaping Ireland’s future.
UCD is a great modern Irish university that has played a unique role in the creation
of Ireland’s current success. UCD’s Conway Institute will be key to sustaining this
success. The new knowledge created within the Institute is not only shedding light
on the causation of diseases such as arthritis, diabetes and Alzheimer’s but also
fuelling Ireland’s emerging biotechnology sector.
This annual report summarises the achievements of Conway researchers during the
Institute’s first full year of operation within the new facility. During the reporting
period, eleven Conway investigators received programme level grants. The Conway
Applied Neurotherapeutics Research Group (ANRG), led by Professor Ciaran Regan was
established under a 07.7 million research cluster award from Science Foundation Ireland
(SFI). The combined achievements of 028.6 million in grant income, 270 peer-reviewed
publications and 54 new PhDs bodes well for the future of the Institute.
A special welcome to some new arrivals. Professor Michael Dunn was awarded the first
Science Foundation Ireland Professorship at the Conway Institute. Professor Dunn joins
the Proteomic Research Centre, directed by Professor Stephen Pennington. The work
of their research teams in identifying and implementing proteomic technologies will
make a significant contribution to a variety of international, collaborative, biomedical
research programmes in the cardiovascular, transplantation and neuro-proteomics areas.
Professor Des Higgins, who developed one of the most highly cited and widely used
software programmes in biology, ClustalW, was appointed to the chair of bioinformatics.
His research focuses on protein sequence alignment methods that lead to the development
of software for use in experimental biology. Professors Paul McKeigue and Helen Colhoun
joined the genetic epidemiology area. Their work traces the genes that underlie ethnic
variation in disease risk, based on studying populations of mixed descent. Their current
focus is on the epidemiology of ethnic variation in risk of cardiovascular disease and
diabetes. Towards the end of the year, Professor Des Fitzgerald joined UCD as Vice-
President for Research. Professor Fitzgerald established a new molecular medicine unit
at the Conway where research projects include the investigation of cyclooxygenase
biology in cancer tumour tissue. The unit is also part of the SFI REMEDI and Bloodomics
consortium. The arrival of such an exceptional cohort of scientists to join the existing
high calibre researchers in the Conway Institute gives UCD a strong base on which to
build a world-class reputation.
003 <> 004
MR DENIS BROSNAN, CHAIRMAN
BOARD OF MANAGEMENT
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I am delighted to present the second annual report of the Conway Institute.
The Board of Management of the Conway Institute has overseen the early
development of the Institute since first convening in July 2002.
This annual report shows the achievements of Conway researchers during the first full
year of operation within the new facility. Dr Philip Nolan served as director from May
2003 to May 2004 and, in this time supervised the completion, equipping and occupancy
of the new research building, strengthened the collaborative research ethos of the
Institute and forged strong partnerships with other third level institutions. The Board
wishes Dr Nolan every success in his new post as Registrar of University College Dublin.
Professor Pat Guiry has led the Institute in his capacity as chief executive since May 2004
and we commend him on the success of Institute in this first year of operation.
At this phase of development of the Institute, it is vital that an ongoing, stable
investment in research infrastructure and activity is maintained to ensure growth
and competitiveness. This Board and the Institute will continue to justify this investment
by clearly articulating the successes, benefits and outcomes to date and defining a
strategic plan for the future. I thank the members of the Board for their time and
invaluable input to date.
The objectives of the Conway Institute remain clear: it will be internationally recognised
as an important centre for research in several key areas; it will have a reputation for
excellence in teaching and training; it will form close and productive relationships with
industry and will be acknowledged by the public as an important contributor to our social
and economic development. The achievements outlined in this annual report highlight
the fact that we are on the right track.
Mr Denis Brosnan
Chairman
Board of Management
Conway Institute of Biomolecular and Biomedical Research
This annual report outlines the activities of researchers at the Conway Institute
for the period 1st September 2003 to 30th September 2004; the first full year of
occupancy of the new facility for the majority of researchers. Even prior to this
period, we had achieved many of the key objectives and performance indicators
defined under the funding model of the Programme for Research in Third Level
Institutions. Undoubtedly, the synergies already being created through collaborative
research underpinned by world-class infrastructural support will result in significant
and exciting developments over the coming years.
This slightly extended reporting period will facilitate future reports being in line with
the academic year, which is appropriate to the business of the Institute being carried
out within the operational environs of University College Dublin. The work of the
Institute extends far beyond this location, however. The collaborative ethos of the
Institute is being borne out in the strength of new relationships being forged with other
research institutes across Dublin in areas of proteomics, synthesis and chemical biology,
neuroscience and prostate cancer; with industry in the areas of neurodegenerative
disorders and core technology platforms; and with the secondary education sector and
wider community through outreach initiatives such as ScienceWorks and AccesScience.
Excellence in research is fundamental. In order for that excellence to be of value to
the community, which supports our work, we must continue to engage with partners
and stakeholders in order to pursue our research in a wider context.
Finally, I wish to congratulate all of the staff and students in the Institute for their
work to date and wish them continued success for the future.
Professor Pat Guiry
Chief Executive
Conway Institute of Biomolecular and Biomedical Research
Letter from C
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PROFESSOR PAT GUIRY,
CHIEF EXECUTIVE
Foreword
HIGHLIGHTS
007 Conway Institute Highlights
009 Centre Highlights
012 New Appointments
013 Programme Level Grants
014 High Impact Publications
016 Awards and Events
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The contribution to science of
Professor Edward J Conway, FRS;
one of Ireland’s most distinguished
scientists, first professor of biochemistry
and pharmacology at UCD (1933–1963)
and namesake of the Institute, was
commemorated in the presence of his
daughters and grandchildren. Dr Ronald
Cox, chair of the National Committee For
Science And Engineering Commemorative
Plaques unveiled a plaque dedicated to
Professor EJ Conway, FRS in recognition
of his contribution to science.
ACCESSCIENCE ‘04
Since 1997, the Merville lay seminars
were the foremost public information
forum for science in Ireland. Being
organised for the first time this year
by the Conway Institute, the competition
was expanded to include all Conway
postgraduate research students and
rebranded as AccesScience. Third year
postgraduate students compete to explain
their research without the use of scientific
jargon and six finalists are chosen for the
grand finale in O’Reilly Hall, University
College Dublin.
This year, the event was held on the
evening of May 4th with Mr Pat Kenny,
RTE as the host and a celebrity judging
panel made up of Ms Emma O’Kelly,
education & science correspondent, RTE;
Ms Geraldine Kennedy, editor, The Irish
Times; Mr Michael Keating, former
Tipperary all-Ireland medal winner
and coach; Mr Ronan Wilmot, actor
and director of the New Theatre.
First prize went to Ms Niamh Tuite
for explaining her alternative approach
to toxicity testing. Ms Eavan Daly and
Ms Brid Ryan received second and third
prizes respectively for their research
on neutrophil locomotion and ‘survivin’
breast cancer. The prize for best visual
representation of science went to Mr
Lorcan Allan for his poster on biomaterial.
After making presentations to the
prizewinners, An Tánaiste, Mary Harney
TD commended the efforts of the Conway
Institute to address the issue of making
science accessible to everybody. ‘It is
not enough for scientists to be competent
in their chosen field, they must carry their
enthusiasm for science to the public and to
do this they must be able to communicate
their ideas and discoveries in clear terms
and non-scientific language, a goal
which I am happy to see echoed in the
AccesScience competition’.
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OFFICIAL OPENING
The vision to build a world-class facility
for multidisciplinary, collaborative
research became a reality on September
1st 2003 when the Conway Institute of
Biomolecular & Biomedical Research
opened its doors on the Belfield campus
of University College Dublin. While
the Institute itself has been in virtual
existence since 2000, the research being
carried out by Conway investigators at
various university campus and hospital
sites had been a reality.
To mark the launch of the Conway
Institute of Biomolecular & Biomedical
Research, a series of events were
organised during September 10th–11th
2003 as a celebration of science; past,
present and future.
An Tánaiste, Mary Harney, TD, officially
opened the building on September 11th
2003. Speaking at the official opening
ceremony, the Tánaiste said: ‘The Conway
Institute is a stunning state-of-the-art
facility, which has been realised through
the various government research funding
mechanisms. The Institute is a key
infrastructural investment in the life
sciences/biotechnology sector, and is part
of the infrastructure needed in delivering
Ireland’s strategic objective of developing
world class competence and businesses
built around these technologies’.
‘The Institute is currently retaining the best
young Irish scientists and also attracting
top quality researchers from abroad. It will
undoubtedly play an important role in the
development of the knowledge-based
economy in Ireland for the foreseeable
future. I anticipate and look forward to
the next number of years when Irish
society and the economy will undoubtedly
reap the benefits of this Government
investment’, the Tánaiste added.
Dr Don Thornhill, chairman of the
Higher Education Authority opened the
Festival of Research 2003. The plenary
lecture was delivered by the eminent
chemist, Professor Sir Jack Baldwin
who is professor of organic chemistry
and head of the Dyson Perrins Laboratory,
Oxford University. Knighted in 1997 in
recognition of his services to organic
chemistry, he has published nearly six
hundred research papers and patents and
is making seminal contributions across a
broad spectrum of synthetic, mechanistic
and biological chemistry.
Other international guest speakers
included Professor Norman Maitland,
YCR Cancer Research Unit, University
of York; Professor Saul Tzpori, Tufts
University School of Veterinary Medicine,
USA; Dr Anthony Gershlick, Division of
Cardiology, Glenfield Hospital, UK and
Dr Frank Walsh, senior vice president
and head of discovery research, Wyeth
Research, USA. The Conway Festival of
Research 2003 also featured an exhibition
of scientific posters showcasing the
exciting research being carried out by the
400 researchers across the three centres
of the Conway Institute.
Conw
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(L-R) Dr Philip Nolan, then Director, Conway
Institute; An Tánaiste, Mary Harney,
Dr Art Cosgrove, then President, UCD;
Mr Denis Brosnan, Chairman, Board of
Management of the Conway Institute.
Members of the family of the late
Prof EJ Conway, namesake of the Institute
at a commemorative ceremony to mark his
contribution to science.
AccesScience ’04: (L-R) Brid Ryan, St Vincent’s
University Hospital (3rd); Niamh Tuite,
Dept. of Pharmacology (1st) and Eavan Daly,
Dept. of Medicine & Therapeutics(2nd).
CONWAY INTEGRATIVE BIOLOGY
Launch of the Applied Neurotherapeutic
Research Group
In January 2004, the Conway Applied
Neurotherapeutics Research Group
(ANRG), led by Professor Ciaran Regan
was established under a 7.7 million
research cluster award from Science
Foundation Ireland (SFI), the National
Foundation for Excellence in Scientific
Research. This grant will support a
number of scientists from University
College Dublin, Trinity College Dublin
and the Neuroscience Discovery Group
of Wyeth Research whose research will
focus on disorders of the brain including
Alzheimer’s disease, schizophrenia
and depression.
Wyeth, one of the world’s largest
pharmaceutical companies, has
extensive activities in Ireland including
a current major investment in a new
biopharmaceuticals manufacturing
facility at Grange Castle, Dublin.
Professor Ciaran Regan welcomed the
significant commitment from SFI and
the support of Wyeth saying, ‘We can
now tackle a new area of brain research
and, hopefully, improve upon current
medications and even identify potential
new therapies for these diseases.’
Dr Menelas Pangalos will lead the Wyeth
Neuroscience Discovery Group that will
provide financial support to the project
as well as technology and guidance in
the drug development process. ‘It is a
unique synergy of academic and industrial
talents, and has a good chance of helping
us understand the root causes of these
debilitating diseases of the brain and
uncovering new approaches for us to
better treat patients in the future’,
said Dr Pangalos.
Conway investigators, Dr William
O’Connor and Dr Keith Murphy are also
involved in this initiative, which promises
to increase the knowledge base in this
area of psychiatric and neurological
diseases and lead to potentially
useful treatments.
3rd Annual CIB Symposium
The Centre for Integrative Biology held
its third annual symposium on February
19th 2004 in the Conway Institute.
In addition to local speakers, there were
guest presentations from Professor Denis
Noble, Oxford University, UK; Professor
Frank Strutz, Georg-August University,
Gottingen; Germany, Professor Colin Hill,
University College Cork; Dr Niall Dillon,
Imperial College London, UK and Dr
Eileen Furlong, European Molecular
Biology Laboratory, Heidelberg, Germany.
Launch of the Proteome
Research Centre
The Conway Institute Proteome Research
Centre, under the leadership of Professor
Stephen Pennington was launched with an
opening symposium on June 3–4th 2004.
The programme included lectures from
world-leaders in the field of proteomics
including Professor Denis Hochstrasser,
Geneva University Hospital; Dr Scott
Patterson, Amgen Inc, California and
Professor Daryl Pappin, Proteome
Research Centre, Applied Biosystems,
Framingham, USA.
The new challenge in biomedical science
since the completion of the human
genome has been to discover the function
of proteins encoded by genes. This new
facility has the most diverse mixture of
instrumentation and software available
anywhere in Ireland for the study of
proteins. The major focus of the proteomic
research programme is to identify new
biological markers of disease and possible
targets for therapy.
Professor Stephen Pennington says,
‘We are excited by the potential of the
state-of–the-art instrumentation we
have installed in the Proteome Research
Centre and look forward to the challenge
of applying it to a diverse range of
biomedical research projects to further
our understanding of biological systems
and human diseases’.
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CONWAY SYNTHESIS
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2nd Annual CSCB Symposium
The Centre for Synthesis and Chemical
Biology (CSCB) held its second annual
symposium on December 12th 2003
at the Royal College of Surgeons in
Ireland (RCSI). Over 200 visitors
including academics, postdoctoral,
and postgraduate students attended
the symposium from RCSI, University
College Dublin (UCD), Trinity College
Dublin (TCD) and other Irish universities.
Plenary lectures were presented by
Professors Alois Fürstner Mülheim,
Germany; Marc Lautens, Toronto, Canada;
Nick Farrell, Virginia Commonwealth,
USA; Peter Leadley, Cambridge, UK; Anne
Imberty, CNRS, Grenoble, France and
Carolyn Bertozzi, Berkeley, USA.
CSCB Awarded EU Funding For Asia Link
Project In Medicinal Chemistry
In March 2004, the CSCB was awarded EU
funding through the Asia Link programme
in collaboration with the Universities of
Regensburg, Ulm, HoChiMinh City, Hue,
Shanghai and the KAAD. The aim of
the project Asia Link is a bi-directional
flow of scientific information related
to drug discovery research. To reach this
aim, young researchers from the Asian
partners will receive training and
participate in research projects at the
European institutions, while young
European researchers will gain knowledge
on traditional medicine and plants from
the Asian partners.
CSCB Synthesis Workshop
This annual workshop was held on April
30th 2004 in the department of chemistry.
Professor Tony Barrett from Imperial
College London gave a presentation
entitled ‘Recent advances in the total
synthesis of antibiotic natural products’.
This was preceded by presentations
from CSCB researchers, Dr Stephen
Connon, TCD; Dr Matthias Tacke, UCD;
Dr Mauro Adamo, RCSI and Professor
Pat Guiry, UCD.
Construction of the new CSCB Building
Work commenced on the new building for
the CSCB in June 2004 and the project
will take approximately fourteen months
to complete. The 2,300m2 building will
house state-of-the-art laboratories and
will be linked to the existing building of
the department of chemistry.
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Lead investigators pictured at ANRG launch,
February 2004 (L-R) Dr Mene Pangalos (Wyeth),
Prof Peter Humphries (TCD), Prof Ciaran Regan (UCD),
Dr Billy O’Connor (UCD) and Dr Keith Murphy (UCD).
Pictured at the CSCB Symposium (L-R) Prof Kevin
Nolan, Prof Pat Guiry, Dr Donal O’Shea, Prof Anne
Imberty, Prof Peter Leadlay, Prof Mark Lautens,
Prof Carolyn R. Bertozzi, Dr Paul Murphy, Prof
Nicholas P. Farrell and Prof Alois Furstner.
Image of new CSCB building.
011 <> 012
Professor Des Higgins initiated his SFI
Investigator award on taking up position
as chair of bioinformatics in the Conway
Institute. His project will focus on the
development of protein sequence
alignment methods and will ultimately
provide software for use in experimental
biology. Prof Higgins developed ClustalW,
one of the most highly cited and widely
used programmes in biology.
Professor Helen Colhoun joined the
Conway Institute from University College
London where she held the position of
professor of clinical epidemiology. In her
current role, the research of Prof Colhoun
focuses on the genetic epidemiology
and pathophysiology of diabetes and
cardiovascular diseases.
Professor Paul McKeigue joined the
Conway Institute from the London
School of Hygiene & Tropical Medicine
where he held the position of professor
of metabolic & genetic epidemiology.
His work on genetic epidemiology began
as an extension of his research on ethnic
variation in risks of cardiovascular disease
and diabetes. This led to the development
of methods for exploiting the genetic
structure of admixed populations to
localise genes underlying these ethnic
differences in risk.
Professor Pat Guiry took up position as
chief executive of the Conway Institute in
June 2004. He has been involved with the
Institute since its inception and also holds
an associate professorship in synthetic
organic chemistry within the department
of chemistry in UCD.
Professor Des Fitzgerald took up position
as vice-president for research, UCD during
the report period. He and his research
team joined the Conway Institute from
the Royal College of Surgeons in Ireland.
This molecular medicine unit has a
number of ongoing projects that focus on
novel aspects of cyclooxygenase biology,
which provide the first step in the
generation of prostaglandins.
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CONWAY MOLECULAR MEDICINE
Launch of the Prostate Tumour
Bank Consortium
In April 2004, the Irish Cancer Society
in conjunction with the Dublin Molecular
Medicine Centre (DMMC) launched a
prostate tumour bank consortium. The
aim of the project is to allow scientists and
clinicians from University College Dublin,
Trinity College Dublin and the associated
teaching hospitals; the Mater Misericordiae
University Hospital, St Vincent’s University
Hospital, St James’ Hospital and St Luke’s
Hospital, to examine the samples of
tumours from men with early stage
and advanced stage prostate cancer.
Dr William Watson, senior lecturer
at the department of surgery, Mater
Misericordiae University Hospital and
principal investigator in Conway Molecular
Medicine is one of the three senior
investigators of the prostate cancer
research consortium. He believes the
scheme is an important step in the battle
against the disease. ‘This new research
will allow us to come up with better
markers that will allow us to detect the
disease earlier and with more certainty
than currently possible. And if we detect
the disease earlier, we will have a better
chance of successfully treating and
curing it’, he said.
The prostate cancer consortium hopes to
collect about 300 samples over the next
three years from men who have been
diagnosed with prostate cancer and have
given written consent for their tissue
samples to be deposited in the tumour
bank. These samples will then be screened
for characteristic proteins and compared
to normal tissue. The scientists will then
try to also detect these proteins in the
blood and urine of men with prostate
cancer with the view to identifying a
biological marker for the disease. Earlier
detection of the disease could lead to
more effective treatment regimes.
3rd Annual DMMC Symposium
The 3rd annual symposium of the Dublin
Molecular Medicine Centre was held on
April 21st & 22nd 2004 at the Conway
Institute. Lectures at the meeting were
divided into the areas of apoptosis &
cell cycle, angiogenesis & hypoxia, CNS
disease & development and resolution
of inflammation. In addition to local
speakers from the partner institutions,
there were guest presentations from
Dr Ciaran Morrison, NUI Galway; Dr Angela
Duffy, NUI Galway; Dr Bruno Morgan,
University Hospital of Leicester NHS Trust;
Professor Paul Redmond, Cork University
Hospital; Dr Kari Stefansson, president &
CEO DeCODE Genetics Iceland; Professor
Alan Hall, University College London.
Workshop sessions were also held on
inflammation, therapeutic strategies
in cancer, neuroscience and
immunoregulation.
Conw
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Centre H
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Prof Donal Hollywood and Dr William Watson
pictured at the launch of the Prostate Tumour
Bank Consortium. (Photo courtesy of the Irish
Cancer Society)
013 <> 014
Despite its limitations, we use the
impact factor; a quantitative tool for
ranking, evaluating, categorising,
and comparing journals, in an effort
to identify significant publications.
It is clear that potentially significant
papers may appear in journals, which
are widely regarded as the best in the
field but still have relatively low impact
factors. The publications listed below
are the top five publications by impact
factor from investigators in each of the
three Conway centres. The impact factor
of each journal [in parentheses] was
calculated using the ISI Journal Citation
Reports®: Science Edition 2003.
A complete listing of the publications
during the report period is given in
appendix 1. The names of Conway
principal investigators from the associated
centre are highlighted in bold while those
from a different centre collaborating on a
paper are in italics.
CONWAY SYNTHESIS AND
CHEMICAL BIOLOGY
McManus HA, Guiry PJ: Recent
developments in the application of
oxazoline-containing ligands in
asymmetric catalysis. Chemical Reviews
2004; 104: 4151-202 [20.233]
Aherne A, Kennan A, Kenna PF, McNally N,
Lloyd DG, Alberts IL, Kiang AS, Humphries
MM, Ayuso C, Engel PC, Gu JJ, Mitchell BS,
Farrar GJ, Humphries P: On the molecular
pathology of neurodegeneration in
IMPDH1-based retinitis pigmentosa.
Human Molecular Genetics 2004; 13:
641-50 [8.597]
Polakova M, Pitt N, Tosin M, Murphy P:
Glycosidation reactions of silyl ethers with
conformationally inverted donors derived
from glucuronic acid: Stereoselective
synthesis of glycosides and 2-deoxyglyco-
sides. Angewandte Chemie-International
Edition 2004; 43: 2518-21 [8.427]
Gorman A, Killoran J, O’Shea C, Kenna T,
Gallagher WM, O’Shea DF: In vitro
demonstration of the heavy-atom effect
for photodynamic therapy. Journal of the
American Chemical Society 2004; 126:
10619-31 [6.516]
Byrne B, Carmody M, Gibson E,
Rawlings B, Caffrey P: Biosynthesis
of deoxyamphotericins and deoxyamphot-
eronolides by engineered strains of
Streptomyces nodosus. Chemistry &
Biology 2003; 10: 1215-24 [6.129]
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During the reporting period, eleven
Conway investigators received
programme level grants.
A Science Foundation Ireland cluster
award established the ANRG under the
leadership of Professor Ciaran Regan.
Dr Keith Murphy and Dr William O’Connor
received grants under this award.
Science Foundation Ireland awarded
investigator grants to Dr Bernard Allan
for ‘Role of the PPAR co-activator PGC-1
in the molecular programming of insulin
sensitivity in human skeletal muscle cell’;
Professor Des Higgins for ‘Multiple
alignment method for the genome ERA’;
Dr Paul Murphy for ‘Towards novel
glycoconjuate based therapeutics for
angiogenesis’; Professor Don MacElroy
to appoint Professor Mohamed Al-Rubeai
to the position of SFI investigator in
biochemical engineering.
The inaugural SFI President of Ireland
Young Researcher award was made
to Dr Jens Nielson for ‘Towards an
understanding of enzyme catalysis:
a multidisciplinary informatics-
based approach’.
The Health Research Board awarded
programme grants to Professor Cliona
O’Farrelly for the ‘Characterisation of
hepatitis C induced immunological
subversion and its implications for
treatment response’; Dr Paul Moynagh
for ‘Toll-like receptors in human disease’;
Professor Desmond Fitzgerald for
‘Programme on cell regulation by
cyclooxygenases; novel therapeutic
targets in cancer and inflammation’.
Program
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High Im
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AWARDS
Dr William Gallagher was named the
2004 BACR/AstraZeneca Young Scientist
of the Year. This prestigious award is
given to a scientist under 35 years who
demonstrates excellence in cancer
research. Dr Gallagher’s research
investigates the mechanism and role of a
family of proteins called fibulins in healthy
and diseased states, with particular focus
on the role of fibulin-1 and –4 in cancer.
As part of the award, Dr Gallagher gave
an invited seminar at the 2004 British
Cancer Research Meeting.
Dr Manuela Tosin received the 2004
Royal Irish Academy Award for Young
Chemists, which is given to the best
PhD thesis in this area. Dr Paul Murphy,
department of chemistry and CSCB
supervised Manuela during her post-
graduate studies. The title of her thesis
was ‘Novel Synthetic and Structural
Studies in Carbohydrate Chemistry’.
CONWAY INSTITUTE SOCIAL EVENTS
The first Conway Christmas party was
held in 2003 with a reception and music
in the foyer. The party continued late
into the night at a central Dublin venue.
A midsummer barbecue was organised
for all Conway staff on June 26th 2004.
The afternoon started with ‘team building’
games, music was provided by John Ralph’s
band and resident DJ Luke Millington.
Both events were great opportunities
for researchers to meet socially.
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CONWAY INTEGRATIVE BIOLOGY
Murtagh J, McArdle E, Gilligan E,
Thornton L, Furlong F, Martin F:
Organisation of mammary epithelial
cells into 3D acinar structures requires
glucocorticoid and JNK signaling.
Journal of Cell Biology 2004;
166: 133-43 [12.023]
Laffey JG, Honan D, Hopkins N,
Hyvelin JM, Boylan JF, McLoughlin P:
Hypercapnic acidosis attenuates
endotoxin-induced acute lung injury.
American Journal of Respiratory and
Critical Care Medicine 2004;
169: 46-56 [8.876]
Castilla J, Gutierrez-Adan A, Brun A,
Doyle D, Pintado B, Ramirez MA,
Salguero FJ, Parra B, San Segundo FD,
Sanchez-Vizcaino JM, Rogers M,
Torres JM: Subclinical bovine spongiform
encephalopathy infection in transgenic
mice expressing porcine prion protein.
Journal of Neuroscience 2004;
24: 5063-9 [8.306]
Dolinsky TJ, Nielsen JE, McCammon JA,
Baker NA: PDB2PQR: an automated
pipeline for the setup of Poisson-
Boltzmann electrostatics calculations.
Nucleic Acids Research 2004;
32: W665-W667 [6.575]
Sandi C, Merino JJ, Cordero MI, Kruyt ND,
Murphy KJ, Regan CM: Modulation of
hippocampal NCAM polysialylation and
spatial memory consolidation by fear
conditioning. Biological Psychiatry 2003;
54: 599-607 [6.482]
CONWAY MOLECULAR MEDICINE
Hagen T, Taylor CT, Lam F, Moncada S:
Redistribution of intracellular oxygen in
hypoxia by nitric oxide: Effect on HIF1
alpha. Science 2003; 302: 1975-8 [29.781]
Colhoun HM, Betteridge DJ, Durrington PN,
Hitman GA, Neil HAW, Livingstone SJ,
Thomason MJ, Mackness MI, Charlton-
Menys V, Fuller JH: Primary prevention
of cardiovascular disease with atorvastatin
in type 2 diabetes in the Collaborative
Atorvastatin Diabetes Study (CARDS):
multicentre randomised placebo-controlled
trial. Lancet 2004; 364: 685-96 [18.316]
Brazil DP, Yang ZZ, Hemmings BA:
Advances in protein kinase B signalling:
AKTion on multiple fronts. Trends in
Biochemical Sciences 2004;
29: 233-42 [14.273]
Malcolm A, Leissring R, Wesley Farris,
Alice Y Chang, Dominic M Walsh, Xining
Wu, Xiaoyan Sun, Matthew P Frosch,
Dennis J Selkoe: Enhanced proteolysis
of the amyloid b-protein in vivo prevents
plaque formation, secondary pathology
and premature lethality in APP transgenic
mice. Neuron 2003; 40: 1087-93 [14.109]
Hoggart CJ, Shriver MD, Kittles RA,
Clayton DG, McKeigue PM: Design and
analysis of admixture mapping studies.
American Journal of Human Genetics
2004; 74: 965-78 [11.602]
Awards and E
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High Im
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Enjoying the sunshine at the Conway summer BBQ.
Teamwork at Conway; fun at the summer BBQ.
RESEARCH OUTCOMES
019 Research Outcomes
021 Campus Companies
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The Conway Institute works closely with
NovaUCD, the innovation and technology
transfer centre at UCD, to ensure the
successful commercialisation of UCD’s
research programmes. NovaUCD is
responsible for the implementation of
UCD’s policies relating to intellectual
property and for the provision of advice
on the protection and exploitation of UCD’s
intellectual property. NovaUCD also offers
a supportive environment, business
support programmes, such as the campus
company development programme, and
incubation and other facilities to assist
innovators and entrepreneurs in taking
their ideas from proof-of-principle to
full commercial success. This proactive
policy for the translation of research has
seen many of the principal investigators
within the Conway Institute establishing
links with the biotechnology and
pharmaceutical sectors through
collaborative programmes, licensing
agreements, contract research and
campus companies.
In the past year, Conway investigators
filed four new patents and a further
two patent applications entered the
national/regional phases in various
territories. In addition, two new license
agreements for patents filed by Conway
investigators were concluded with
companies. Overall, six campus companies
have been established and are being
managed with the involvement of Conway
investigators, two of which are housed
within the Conway Institute building
itself. Brief descriptions of these campus
companies are provided overleaf.
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The key performance indicators for
this research institute are defined in
terms of the numbers of peer-reviewed
publications and postgraduate thesis
submissions, the total grant income
awarded to investigators and the extent
of commercialisation activity. The 2004
annual report highlights the research
outcomes for the Conway Institute
during the period from September 1st
2003 to September 30th 2004. The
reporting period was delineated in order
to (a)reflect the research activity from
the first year of operation within the
new facility and (b)align the reporting
period for future reports with that of
the university academic year.
PUBLICATIONS
During the reporting period, there
were 269 publications by Conway
investigators in peer-reviewed journals.
This is comparable to the figures for
the previous year and a remarkable
achievement given that investigators
spent a period of time relocating to the
new facility and establishing their groups
within the Institute. Using the ISI Journal
Citation Reports®: Science Edition 2003,
47% of articles were published in journals
with an impact factor of greater than 3.0.
A full listing of publications can be found
in appendix 1.
GRANT AWARDS
In the reporting period from September
1st 2003 – September 30th 2004, Conway
investigators received grant awards from
external funding agencies amounting
to 28.6 million, of which 21.1 million
was from peer reviewed sources. The
highest percentage of funding came from
Science Foundation Ireland (fig. 1).
Looking at the trend in grant income over
the previous six years, we can see that the
total grant income awarded to Conway
investigators in the first nine months of
2004 already exceeds the total figure for
the previous year (fig. 2). A full listing of
grant awards can be found in appendix 2.
THESIS SUBMISSIONS
There were 54 Doctor of Philosophy
(PhD) thesis submissions by postgraduate
students being supervised by Conway
investigators during the reporting period
from September 1st 2003 – September
30th 2004. In addition, there were
4 Master of Surgery degrees (MCh),
4 Master of Science (MSc) degrees
and 1 Doctor of Medicine (MD) degree
submissions in the same period. A full
listing of student names and thesis titles
can be found in appendix 3.
TECHNOLOGY TRANSFER AND
COMMERCIALISATION
One of the aims of the Conway Institute
is to contribute to the development of
Ireland as a knowledge economy. The
investment in research and education will
yield the dividend of research capacity
and human capital to fuel a growing
biotechnology industry. In this context,
the Conway Institute is committed to
fostering entrepreneurship, facilitating
technology transfer and to developing
strong partnerships with industry.
Research O
utcomes
Science Foundation Ireland 54%
IRC
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T 5
%
Health Research Board 19%
European Union FP6 4%
Enterprise Ireland 4%
Others 9%
Wellcom
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%
Grant Income
0.0
5.0
10.0
15.0
20.0
25.0
1999 2000 2001 2002 2003 2004*
Fig. 1. Peer-reviewed grant income
in the reporting period by funding agency.
Fig. 2. Monetary value of grant income in the past
six years.
* This figure represents grant income for the first
nine months of the year up to and including
September 30th 2004.
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CYTREA
Cytrea is a campus biotechnology
company with a research base in the
department of chemistry at University
College Dublin. The core activity of the
company centres on the development
of modified cyclodextrins as delivery
systems for the controlled release and
targeted delivery of bioactive entities,
with the emphasis being on bio-
pharmaceuticals. Services provided
by the company involve contract research
in the application of Cytrea cyclodextrins,
for example in formulations for delivery
of a drug or in the controlled release of
nutrients in cell culture technology.
Further details are available on the
company website at www.cytrea.ie
Conway Investigator: Dr Raphael Darcy,
Conway Synthesis & Chemical Biology.
ENZOLVE
Enzolve is a biotechnology company,
which is focused on the commercialisation
of novel enzyme products arising from
UCD research particularly in the area of
protein engineering. Enzolve provides
novel enzyme-based solutions (for
example in the areas of diagnostics,
synthesis and food). Enzolve has an
expanding range of products and also
provides consultancy or contract work
on specialised enzyme projects. Enzolve is
located in the Conway Institute building.
Conway Investigator: Prof Paul Engel,
Conway Synthesis & Chemical Biology.
ILDANA BIOTECH
Ildana Biotech provides innovative
solutions for the diagnosis and control
of parasitic diseases in animals. Current
development projects include rapid
‘point of care’ diagnostics for liver fluke
infection, and vaccines for use in the
control of liver fluke infection in farmed
ruminants, and sel louse infestation in
farmed fish. The research aims to provide
new means of disease control for animals
that are effective, consumer friendly, and
promote animal welfare. Ildana Biotech
completed the 2000 NovaUCD campus
company development programme.
Conway Investigator: Prof Grace Mulcahy,
Conway Integrative Biology.
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ANALYTICAL DRUG & DATA
Analytical Drug and Data (ADD) is a
biotechnology company, which provides
rapid and reliable in vivo pharmacological
evaluation of experimental compounds.
This company was founded in 2001 and
completed the 2001 NovaUCD campus
company development programme.
ADD provides three quality services:
- Drug screening: clinical and pre-clinical
microdialysis in intact conscious brain.
- Analytical chemistry: detection of amino
acids in biological samples.
- Consultancy on all aspects related
to the delivery of treatment for
neurological diseases.
Conway Investigator: Dr William
O’Connor, Conway Molecular Medicine.
BERAND
Berand is a new biotechnology company
delivering preclinical profiling of novel
chemical entities. The company was
launched in August 2004 and is located
in the Conway Institute building.
The company was an award winner
on the 2004 NovaUCD campus company
development programme. The company
focuses on the evaluation of promising
drugs directed against neurological
and psychiatric diseases including neuro-
degenerative psychotic conditions, such
as Alzheimer’s disease and schizophrenia.
New chemical entities are evaluated in
our behavioural repertoire that combines
biochemical and cellular read-outs.
Berand aims to generate in-house
intellectual property through the
identification of lead chemicals derived
from cheminformatic database searching.
The company aims to address the growing
need of large pharmaceutical companies
to outsource research and development
(R&D) activities. In parallel to R&D
service provision, Berand carries out
proprietary research into novel therapies
for the treatment of autism and obesity.
Further details are available on the
company website: www.berand.ie
Conway Investigator: Prof Ciarán Regan,
Conway Integrative Biology.
CELTIC CATALYSTS
Celtic Catalysts is a biotechnology/life
sciences company working in the niche
area of chiral catalysis. The company
is commercialising chiral technology,
which has been developed over the past
five years in the department of chemistry,
University College Dublin. Celtic Catalysts
has developed a key piece of intellectual
property, which enables it to make a
vast array (thousands) of chiral catalysts
of a type that has previously been
demonstrated as being industrially viable.
Celtic Catalysts also has the ability to
screen these catalysts in a systematic
and automated way to ascertain which
ones suit a particular industrial process
for the pharmaceutical or fine chemical
industries. The company aims to become
the leading supplier worldwide of chiral
catalysts for industrial use. In 2004, Celtic
Catalysts, which is located in NovaUCD
and completed the 2000 NovaUCD campus
company development programme,
secured significant strategic investment
of 665,000 from 4th Level Ventures and
Enterprise Ireland.
Conway Investigator: Dr Declan Gilheany,
Conway Synthesis & Chemical Biology.
THE CONWAY INSTITUTE TODAY
025 Buildings and Technical Services
027 Affymetrix GeneChip Core Technology
029 Real-Time PCR
031 DNA Sequencing and
Oligonucleotide Synthesis Service
032 Proteome Research Centre (PRC)
033 Flow Cytometry Facility
035 Confocal Microscopy and
Digital Imaging Facility
037 Bioinformatics Service
039 Electron Microscopy Laboratory
041 Mass Spectrometry Facility
043 Business and Finance
045 Communications and Education
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which allows clear communication between
the different groups in each research
laboratory. This facilitates efficient
use of both space and resources among
all groups.
MECHANICAL AND ELECTRONIC
WORKSHOPS, IT SUPPORT,
AND FACILITIES MANAGEMENT
A large, complex and modern building such
as the Conway Institute requires both
facility supports for the infrastructure itself
and dedicated support for the considerable
investment of public money in scientific
equipment. Mr Padraig O’Murchu supervises
the Conway workshops. As part of this
service, Mr Des Butler has responsibility
for the electronics and electrical section.
Major projects undertaken during the
reporting period included the installation
and commissioning of the zebrafish and
xenopus facilities, the commissioning of the
central gas services, the refurbishment of
the biotechnology building, as well as the
considerable ongoing maintenance of
Conway undergraduate and departmental
equipment. Padraig and Des are currently
developing a fault-reporting module to
ensure efficient use of resources and time.
Mr Paul O’Reilly was appointed to the
position of information technology officer
during the reporting period and continues
to provide dedicated IT support to the
Conway research community. Under Paul’s
stewardship, the number of IT related
problems has been greatly reduced.
Paul also oversaw the introduction of
wireless networking into the Conway
and new security systems to protect the
Institute’s critical server infrastructure.
After the move into the new building,
Mr Eric Leonard was appointed facilities
supervisor for the Institute. In this
capacity, he has worked closely with UCD
buildings and services and the Conway
workshops to establish a high standard of
facility management for the large group of
Conway investigators. Mr Melvin Fleming
has recently joined him in this area.
CORE TECHNOLOGY PROGRAMME
To date, the Conway Institute has invested
several million euro in the development
of its core technology programme.
This programme consists of a number
of technologies detailed below. The
equipment is centrally located, properly
maintained and managed by a cohort
of technical staff who provide technical
support to Conway researchers. Training
is provided in sample preparation,
instrument use and depending on the
technology subsequent analysis of raw
data. This allows researchers access to
high value specialised equipment, which
is properly maintained and managed.
Ms Catherine Moss and Ms Alison Murphy
had established the transcriptomics core
technology prior to the opening of the new
facility. Ms Ann Cullen was subsequently
appointed to manage the confocal
microscopy core facility. All three have
developed a robust service with a large
customer base both within the Conway
and the across the wider UCD and DMMC
research communities. During early 2004,
Ms Janet McCormack joined the rapidly
expanding transcriptomics core from the
department of genetics in Trinity College
and Dr Alfonso Blanco from Galicia in
Spain was employed to establish the flow
cytometry service. Mr Brendan Harhen
who was instrumental in setting up the
mass spectroscopy instrumentation
resigned his position to join University
College Galway and has been replaced by
Ms Caitriona Scaife who is on temporary
secondment from the department
of biochemistry.
MICHAEL O’SULLIVAN, ASST. DIRECTOR,
BUILDINGS AND TECHNICAL SERVICES
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THE BIG MOVE: RELOCATING,
EQUIPPING, AND OCCUPYING
Since 2000, the Conway Institute was
operating as a virtual institute with
some 350 researchers working in various
locations both on and off the Belfield
campus as well as from teaching hospital
sites across the wider Dublin area. Once
the new facility was completed in Summer
2003, one of the biggest challenges to
date lay in turning a virtual institute into
one that was fully staffed, equipped and
functional. Considerable planning by a
number of committees went into this task,
which was completed by the end of
October 2003.
The relocating committee prepared and
implemented a logistical plan to transfer
staff, equipment and materials from their
existing sites into the new Institute
building. This group co-ordinated all
aspects of this complex task and also
formed the Conway interim safety
committee under the chairmanship of
Ms Hilda Bohane. A draft safety statement
and an induction manual were produced.
The equipment and occupancy committee
under the chairmanship of Professor
Finian Martin were responsible for
identifying, tendering, purchasing and
commissioning every item of equipment
needed to ensure the Institute was
functional on opening. A special word
of thanks goes to Professor Martin and to
Dr John Baugh who co-ordinated many
aspects of the procurement process and
also to Dr Kathy O’Boyle and Dr Cormac
Taylor who had the considerable task of
ensuring that the Institute fulfilled its
mission of multidisciplinary occupancy
while simultaneously ensuring that
groups of similar research themes were
sited close to each other.
The move to the Conway Institute was
completed with minimum disruption
to research and with most groups
experiencing only a number of days down
time. Again, we would like to acknowledge
the support of the major projects unit
(MPU) and in particular Ms Eliz Dunne
and Mr Eric Leonard.
A WORKING INSTITUTE
After an initial bedding-in process, the
work of the Institute became established
during the reporting period. Management
and operational issues were dealt with in
an efficient and timely manner through
the establishment of wing operational
groups and a building management group.
RESEARCH WINGS
The Conway Institute building design is
based on the principle of multidisciplinary
occupancy supported by shared central
services. The large, open plan laboratories
accommodate up to 430 researchers over
four wings. Research groups vary in size
from two to over thirty people. Each large,
open plan laboratory contains a range of
scientific services including tissue culture
facilities, minus eighty-degree storage
and high-speed centrifugation.
Currently, Dr John Stephens,
Ms Emer Bonham, Ms Philippa Kavanagh
and Mr Paul Rooney manage the day-
to-day operation of each research
laboratory. All four relocated from
other departments within the University
and quickly established strong systems
of administration and management
to support this large and varied group
of Conway investigators. Their areas
of responsibility include occupancy,
equipment purchasing, health and
safety, and technical support to Conway
researchers. A novel system of wing
operation committees have been set up,
Dr John Stephens
Research Wing 2W
Ms Emer Bonham
Research Wing 1W
Ms Philippa Kavanagh
Research Wing 2E
Mr Paul Rooney
Research Wing 1E
Mr Padraig O’Murchu
Workshops Supervisor
Mr Paul O’Reilly
Information Technology Officer
Mr Eric Leonard
Facilities Supervisor
Mr Melvin Fleming
Facilities Officer
Buildings and Technical Services
027 <> 028
SERVICE
The Affymetrix GeneChip core technology
provides technical expertise and advice
to Conway researchers who wish to use
GeneChip microarrays as a tool to advance
their area of research. The service
includes the following,
- Initial meeting to discuss experimental
design and strategy.
- Advice on sample preparation
and provision of protocols.
- Quality assessment of total RNA
and cRNA using the Agilent bioanalyser
- Array hybridisation, washing, staining
and scanning.
- Assessment and monitoring of array
quality and provision of QC report.
- Low level data analysis and data
filtering using GCOS.
- Use of GeneSpring expression analysis
software for high level analysis.
USAGE
This facility has seen an annual growth
in usage since its launch in August 2000.
Usage levels for the last year report
approx 300 chips/annum run on the
system, with 27 users of the facility.
70% of the user profile from this period
is comprised of Conway researchers
from the departments of pharmacology,
biochemistry, medicine & therapeutics,
surgery, and industrial microbiology.
Dublin Molecular Medicine Centre (DMMC)
researchers and collaborators from
external academic institutes contribute
to the remaining 30% of the usage group.
MS ALISON MURPHY
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Ms Alison Murphy manages the
Affymetrix GeneChip core technology,
which was established within the
Conway Institute in August 2000
and has since seen an annual growth
in the number of users availing of the
system. This expert facility is accessible
to researchers who wish to use the
Affymetrix GeneChip platform and
technical support provided to carry
out microarray analysis.
APPLICATIONS
The technology utilises commercial
high-density microarrays to perform
gene expression profiling. GeneChip
expression arrays enable researchers to
simultaneously monitor genome-wide
expression levels or to focus on changes
within a specific set of genes. However,
it is this global view that has contributed
to the understanding of biological
mechanisms of complex diseases and
processes and has also allowed the
discovery of biomarkers and new drug
targets. While the main area of application
of this technology has been in the study
of gene expression, it can also be used
for DNA analysis, using GeneChip
resequencing and genotyping arrays.
INSTRUMENTATION
This fully integrated system consists
of a GeneChip 3000 scanner, automated
Fluidics 400 station, hybridisation
oven and GeneChip workstation with
GCOS Software.
The recently acquired GeneChip 3000
scanner offers significant improvements
in performance such as faster scanning
time, higher resolution scanning, reduction
in noise and a smaller bench footprint.
It also allows the facility to use the
new higher density array designs now
available eg. the human genome HG U133
2.0 Arrays, which enables analysis of over
47,000 transcripts. The 3000 scanner has
been designed to easily adapt to future
hardware and software advances and
emerging applications.
The Hybridisation Oven 640 holds up
to eight probe array cartridge carriers
(each with eight cartridge slots) that
rotate for controlled hybridisation of
up to 64 probe arrays. This unit delivers
precise temperature control for consistent
performance across all probe array
applications.
The Fluidics 400 Station provides
automated washing and staining of probe
array cartridges using specific fluidics
protocols developed for each array type.
Affymetrix GeneChip® Operating
Software (GCOS) provides seamless
control of the fluidics station and scanner.
In addition, GCOS acquires data, manages
sample and experimental information and
provides initial 1st tier data analysis.
Affym
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Fig. 2. Affymetrix GeneChip®.
Fig. 1. Hybridisation of tagged probes to Affymetrix
GeneChip® microarray.
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SERVICE
The real-time PCR core facility offers a
range of services and technical expertise
in this field to Conway investigators, their
collaborators, UCD staff and the wider
academic and industrial communities.
It provides advice on experimental design,
protocols, an assay design and ordering
service, an optimisation and sample
running service and results analysis.
In addition, training is also provided
on sample set-up, instrumentation and
software allowing researchers to carry
out their own PCR runs if required.
USAGE
There are over 90 users of this facility,
with 55 researchers running experiments
in the last year. 95% of these users are
from within the Conway Institute from
various research groups and departments
within the faculties of medicine, science,
veterinary medicine and agri-food and
the environment. The number of real-time
PCR runs carried out in the last year
increased by 42% and this trend seems
set to continue for the foreseeable future.
MS CATHERINE MOSS
Fig. 1. Low density array.
Fig. 2. Taqman Probe.
Fig. 3. Amplification Plot.
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Ms Catherine Moss manages the
real-time PCR core facility, which has
been in operation for over four years.
During this time, there has been a
continual increase in usage of this
facility in terms of customer base
and experiment throughput. The facility
is now equipped with two real-time
PCR systems offering the most up
to date advancements in this rapidly
developing technology.
APPLICATIONS
Real-time PCR is a very sensitive technique
for DNA and RNA quantification. In real-
time PCR, samples are characterised by the
cycle at which significant amplification of
PCR product is first detected rather than
the amount of PCR product accumulated
after a fixed number of cycles.
This technology can be used for both
absolute and relative quantification of
nucleic acids. Absolute quantification
may be used for determining viral load,
gene copy numbers etc, while relative
quantification is used in gene expression
studies. The majority of users of the
facility to date have used relative
quantification of gene expression to
identify biomarkers and therapeutic
targets in a wide range of disease models.
The real-time PCR instrumentation may
also be used for allelic discrimination.
INSTRUMENTATION
The two instruments currently in operation
in this facility are both sequence detection
systems from Applied Biosystems.
These SDS systems are fully integrated
for real-time detection of PCR and
comprise 96 and 384 well thermal
cycling blocks, a laser for the induction
of fluorescence, CCD camera detector
and sequence detection software for
instrument operation and data analysis.
The instruments support Taqman and
Sybr green chemistries.
ABI 7900HT SDS
This instrument was purchased in
January 2004 to support the existing
ABI7700 instrument. The 384 well plate
option of the 7900HT allows higher
throughput and decreased running costs.
This instrument was upgraded in August
2004 to allow the running of low density
arrays. These are microfluidic cards
containing lyophilised pre-optimised
taqman assays with eight sample loading
ports. They are custom formatted by the
researcher from the Applied Biosystems
website (www.appliedbiosystems.ie)
and allow up to 384 genes targets to
be amplified in one PCR run.
The ABI 7700 is currently being replaced
with the new 7900HT FAST model. This
model allows real-time PCR runs to be run
in less than 30 minutes on a 96 well plate
format. Dr Keith Murphy is financing this
trade-in through support received from
Science Foundation Ireland for the Applied
Neurotherapeutics Research Group.
Real-T
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CR
MS CAITRIONA SCAIFE AND
PROFESSOR STEPHEN PENNINGTON
The PRC was launched with an opening
symposium in June 2004. Ms Caitriona
Scaife is the dedicated core technician
for the facility, which is led by Professor
Stephen Pennington. The PRC is
equipped with state-of-the-art
instrumentation and software to support
a number of complementary proteomics
workflows. The resources in the mass
spectrometry laboratory in the PRC
include a MALDI-Tof/Tof mass
spectrometer with autoloader for high
throughput MALDI-MS/MS and off-line
liquid chromatography (LC) MS/MS
workflows. We also have a linear ion
trap electrospray mass sprectrometer
and a linear ion trap electrospray
mass spectrometer coupled to a
Fourier Transform Ion Cyclotron
Resonance detector.
The PRC also has a large separations
laboratory that contains instrumentation
for 1-D gel electrophoresis, 2-D gel
electrophoresis (2-DE), image scanners
including a three colour laser fluorescence
scanner (Typhoon), which supports the
use of the latest three colour difference
in gel electrophoresis (DIGE) 2-DE. LC
based workflows are supported by the
availability of a multi-dimensional LC
system and a nano-LC system. The latter
is coupled to a MALDI target loading robot
to support off-line LC MALDI-MS.
These facilities are used to support
the research projects of groups led
by Professor Stephen Pennington
and Professor Michael Dunn as well
as a range of collaborative biomedical
research projects.
In general, our aims are to apply
proteomics to basic biomedical sciences
and clinical proteomics projects for the
purpose of gaining mechanistic insights
into biological processes, identifying
diagnostic and prognostic biomarkers
of diseases and identifying potential
targets for therapeutic intervention in
human diseases. To achieve this, we are
particularly interested in applying newly
developed leading edge technologies
for proteomics including methods for
quantitative measurement of protein
expression. The latter we are achieving
in close collaboration with Applied
Biosystems who have funded a
Newman scholarship.
Proteom
e Research C
entre (PR
C)
031 <> 032
MS JANET MCCORMACK
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Ms Janet McCormack joined the
transcriptomics core facility in May
2004 in order to support the work of
Ms Alison Murphy and Ms Catherine
Moss in their technologies. In addition,
Janet manages the new sequencing
and oligo-synthesis service for the
Conway Institute. DNA sequencing and
oligonucleotide synthesis are essential
tools used by most of the investigators
within the Conway Institute at some
stage during their research. Therefore,
it was decided to develop a service,
which would assist the researchers in
their endeavours. Outsourcing of the
technical aspect of the service was
determined to be the best way to
achieve this. The Institute negotiated
an attractive package with MWG-THE
Genomic Company in respect of DNA
sequencing and oligo-synthesis
requirements. The service became
functional in late 2004.
APPLICATIONS
There are a broad variety of uses for the
products provided by MWG. In general,
the templates used for sequencing are
either plasmids or PCR products. However,
large library screens or primer walking
of large constructs can also be carried
out. The oligonucleotides can be used for
conventional PCR or real-time quantitative
PCR and the siRNA duplexes can be used
to silence the genes of interest and
examine their expression profile.
SERVICE
The service is co-ordinated and managed
through the transcriptomics core facility.
There are many facets to the service
including:
- Advice on template preparation
and oligonucleotide design.
- Assistance with MWG’s online ordering
system (www.THE-MWG.com).
- Convenient barcode labelling system.
- Provision of a purchase order number.
- Collection of samples for sequencing.
- Courier service for delivery of samples
to MWG.
- Orders can be tracked online through
the MWG website.
- Results are downloadable from the
website in various formats; text, .pdf
and .scf files.
- Administration of the service.
USAGE
Although relatively new, there is
already a good demand for the service.
At present, there are 52 researchers
within the Conway Institute using the
service. Of those, 40 have used the MWG
for sequencing and 27 have ordered
oligonucleotides from MWG. On average,
there are 100 oligonucleotides and 150
sequencing reactions ordered per month.
DN
A Sequencing and
Oligonucleotide Synthesis Service
033 <> 034
COULTER EPICS XL-MCL
This flow cytometer can simultaneously
measure forward scatter, side scatter and
up to four fluorescent dyes using a single
air-cooled laser at 488 nm. It allows the
analysis and study of many parameters of
human and animal cells, marine plankton
and bacteria. The Coulter EPICS XL-MCL
has a multi-tube carousel loader (MCL),
which is an automated sample loader
for this instrument. The MCL uses up
to thirty-two 12 x 75 mm test tubes,
which permits a throughput of up to
100 samples per hour. The fully featured
XL-MCL incorporates positive bar-code
identification and true vortex mixing prior
to aspiration.
BD FACSARIA CELL SORTER
(BD FACSDIVA SOFTWARE)
This is the first fixed-alignment benchtop
high-speed cell sorter. It can acquire up to
70,000 events per second and sort rates
up to 40,000 events per second with high
purity. It is designed with three lasers:
488 nm (blue), 633nm (red) and 407nm
(violet), and a fixed optical alignment
system that allows simultaneous detection
of up to 15 parameters (2 scatter signals
and up to 13 fluorescent parameters).
The 70- and 100- micron nozzle tip sizes
are designed to accommodate most cell
types and to enable sorting at a variety of
pressures and speeds. Two- and four-way
sorting are standard features available for
a variety of bulk collection devices to
accommodate different tube sizes. The
optional automated cell deposition unit
(ACDU) sorts into multiwell plates and
onto microscope slides. The FACSAria has
a refrigeration system that allows cooling
of the sort sample as well as the sort
collection tubes.
USAGE
Graph 1 shows the number of users of the
facility divided by department and graph 2
shows the hours of usage per department.
DR ALFONSO BLANCO
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Dr Alfonso Blanco manages the flow
cytometry facility, which provides
training, instrumentation, technical
expertise, and software for flow
cytometric analyses. Flow cytometers
are systems for the qualitative and
quantitative measurement of biological
and physical properties of cells and
other particles. These properties are
measured when these events pass
through a laser beam in a single-file.
Trained users of the facility prepare and
run their own samples while untrained
users bring prepared samples to
Dr Blanco, who will run them.
APPLICATION
Flow cytometry can be used to measure
intrinsic cell characteristics such as
size, shape, granularity, pigments or
autofluorescence as well as extrinsic
characteristics such as DNA, apoptosis,
necrosis, internal and external receptors
or membrane structure. This has many
applications in human, animals, plants
and microorganisms (yeast, bacteria
and viruses). Examples include studying
the cell cycle in connection with the effects
of drugs and radiations; quantifying
DNA and ploidy determination (in animal
and plant tissues, including tumours);
calculating various cellular parameters
(intracellular pH, Ca2+ concentration,
membrane potential and fluidity);
detecting a wide variety of antigens;
physical sorting of particles like
organelles and chromosomes.
In this laboratory, the most common
applications are those related to DNA
studies: cell cycle, ploidies, apoptosis,
and viability. Another common application
is immunophenotyping, which refers to
the technique of identifying antigens that
help to characterise different kinds of cells.
Antigens are identified using special
antibodies with specific fluorescence that
bind to them specifically. Cell sorting
allows the physical isolation of cell
populations for further procedures:
cell culture, studies of protein or RNA
expression, etc.
Different groups from different research
centres are actually using this facility
to sort cell populations transfected
with a gene of interest coupled with the
green fluorescent protein (GFP). These
transfected cells can be sorted from those
cells that have not been transfected
because they will not express this protein.
INSTRUMENTATION
The new Dako CyanADP 9 colours UV
laser and a Coulter EPICS XL-MCL are
used for routine blood analyses and
research and a BD FACSAria Cell Sorter
for research analyses and for sorting
samples. There is also a workstation
for off-line analysis of flow data.
DAKO CYAN ADP 9 COLOR,
3 LASERS (UV)
The most recent acquisition within the
facility is the CyAn™ ADP high-performance
research flow cytometer. This machine
extends the range of possibilities still
further. It is a premium instrument with
reliable walk-away operation and the
smallest footprint. It has 3 lasers: an
Enterprise II laser-351nm (UV), a 488nm
(blue) and a 635nm semiconductor (red).
It is ideal for handling a diverse range of
applications, with up to 11 parameters:
FSC, SSC and 9 colours: 5 colours from
488, 2 colours from 635, 2 colours from
351. It offers complete compensation
and analysis rates of up to 50,000 events
per second. Summit software version 4.1
is designed with more power, flexibility
and greater ease of use.
Flow
Cytom
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3:30:00 St Vincent’s Hospital
M&
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74
:45
:00
38
:15
:00
Bio
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30:20:00 External TC
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50:15:00 Collaborators TCD
162:30:00 Crumlin Hospital
10:15:00 Zoology16:35:00 Veterinary
Pathology 2:00:00
Pharmacology 36:00:00
Surgery 795:25:00
Molecular and Medicine 5:00:00
Hours of use per department2004–2005
No Hours of Use 1424:50No of Departments 12
2 St Vincent’s Hospital
M&
T 13
4 B
ioch
em
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2 External TC
D
5 Collaborators TCD
2 Crumlin Hospital
2 Zoology
4 Veterinary
Pathology 1
Pharmacology 9
25
Su
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ry
Molecular and Medicine 1
Number of Users per Department2004–2005
No Users 70No of Departments 12
035 <> 036
USAGE
The confocal and digital imaging facility is
administered and managed as a business
unit. As the facility has only been
operational in its present form since March
2004, it was decided to forego full cost
recovery initially in favour of a nominal
fee in order to generate a user base for
the confocal microscope and a null charge
for the use of the live cell imaging system
and the PALM®MicroBeam system. It is
envisaged however, that full cost recovery
will be implemented for all technologies
within the core facility on review in 2005.
To date, there are 67 regular users of the
confocal microscope facility. 95% of these
users are trained, independent users of the
facility; the remaining 5% are assisted users
whereby technical assistance is provided on
a session basis. This number of users has
been generated from an initial user base of
zero in March 2004. It is expected that the
number of independent users will continue
to grow as the technology and new
techniques are developed. All independent
users undergo a three-day in-house
training course, which is organised on
a monthly basis. In any single calendar
month, the number of people awaiting
training exceeds 12-15. It is envisaged
that the demand for the instrument will
continue to grow over the next 12 months
with the potential requirement to purchase
an additional upright microscope, which
would be dedicated to live cell real-time
confocal work.
The PALM®MicroBeam and laser
micromanipulation system has only been
launched as a core technology since
February 2005. There are currently no
charges applied to the system while we
generate a user base. However, it is
envisaged that the technology will be run
on a full cost recovery basis in the future.
Currently, there are four active groups of
users. In January, the monthly usage was
only 4 hours, this rose to 24.75 hours in
February and 184 hours in March. In line
with other core technologies, it is envisaged
that this trend is likely to continue.
Live Cell Imaging Suite
The Conway Institute live cell imaging
suite consists of a Zeiss upright
fluorescent microscope with live cell
incubation capabilities. As well as a
standard live cell imaging incubation
chamber, the microscope has a unique
hypoxic incubation chamber, which
allows cells to be imaged under desired
atmospheric oxygen tensions. The system
has successfully been employed to date
in the visualisation of hypoxia-induced
alterations in morphology as well as the
monitoring of expression and subcellular
localisation of fluorescently labelled
proteins. In the near future, it is intended
to expand the capabilities of the
microscope to encompass FRET analysis.
For information regarding the use of this
scope, please contact Dr Cormac Taylor
MS ANN CULLEN
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Ms Ann Cullen manages the confocal
microscope and digital imaging facility,
which provides access to the core
equipment of the Zeiss LSM 510 UV
META confocal microscope, the Zeiss
live cell imaging system and the PALM®
MicroBeam laser micromanipulation
system for microdissection. The facilities
are available to Conway researchers,
their collaborators, the wider UCD
campus and external academic and
non-academic users on a cost recovery
basis. The facility has been fully
operational within the Conway Institute
since the commissioning of the new
Zeiss confocal microscope in January
2004. Since that date, the facility
has expanded to incorporate other
complimentary microscopy systems.
INSTRUMENTATION
Zeiss LSM 510 UVMETA
Confocal Microscope
The confocal system is the Carl Zeiss
LSM 510 UVMETA system. Depending on
the specific application, you can choose
between the Axiovert 200M and the
Axioskop 2 FSMOT microscopes. Both
microscopes are interchangeable and
supported by LSM software. Since March
2005, a workstation has been provided
with full access to LSM Examiner and LSM
Browser software enabling post acquisition
image analysis with comprehensive data
archiving, import and export functions
for compatibility with all common image
processing programmes. In addition,
free interactive image software can be
downloaded from www.zeiss.co.uk. The
system is equipped with different lasers
emitting a number of lines in the UV and
visible ranges (351, 364, 458, 477, 488,
514, 543, and 633nm lines). The LSM
510META detector facilitates ‘emission
fingerprinting’; a technique for the
detection, spectral separation and
visualisation of multiple fluorescent labels
including fluorophores with overlapping
emission spectra such as CFP, GFP and
YFP, which cannot be separated using
conventional methods. The system can
also be used for other techniques such
as FRET, FRAP etc and ion imaging.
Zeiss Live Cell Imaging System
The live cell imaging system is a Zeiss
Axiovert 200M motorised inverted
microscope for transmitted light,
brightfield, phase contrast and DIC,
and fluorescence. The system includes 10x,
LD20x and Plan Apo100x/1.4 oil objectives,
a motorised xy stage (transferable for
use on the LSM 510 instrument), Z stack,
time lapse, multi channel, mark and find,
extended depth of focus, auto focus.
Temperature, CO2 and O2 control are
provided by microscope and stage
incubators. The live cell imaging system is
fully supported with AxioVision software.
PALM® MicroLaser System
The PALM®MicroBeam and laser micro-
manipulation system is a state-of-the-art
system for precise non-contact laser
based micromanipulation. Using strongly
focused laser light, microscopically small
objects are cut, microdissected, captured,
fused or microinjected with high precision.
It is a highly versatile technique as all
specimen preparations can be used
including live cells. PALM®RoboSoftware
permits any combination of cutting and
catapulting your sample, with or without
the use of PALM®Membrane slides for
collecting morphologically intact cell
areas. Samples are transported to the
collector cap enabling further analysis.
Protocols for DNA, RNA, protein, microarray
and mass spectrometric analysis can be
applied without difficulty. Additional
information on the PALM system can be
obtained from www.palm-microlaser.com.
Confocal M
icroscopy and Digital Im
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Mo
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Physiology
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Veterin
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Ph
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M&T
Chemical Synthesis& Chemical Biology
Chemical Engineering
Biochemistry
St V
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Confocal Microscope Usage2004–2005
037 <> 038
(i) BioConductor leverages the power
of R to specifically address the
statistical issues associated with
microarray data;
(ii) R and BioConductor are free,
open source software;
(iii)the software is under constant
revision, which is released in a more
timely manner than updates to
commercial software;
(iv) new algorithms and approaches to
analysis are implemented rapidly;
(v) routine analytical procedures can
be scripted relatively easily.
Although the R learning curve is steep,
we believe it is worth the time investment
for the reward of flexible, accurate analysis
of data. Furthermore, we provide the
WebBioc package on our website, which
provides a web interface to the most
fundamental packages of BioConductor.
It is anticipated that the range of packages
with which WebBioc will interface will
grow over time. As an alternative to
BioConductor, the Conway has invested
in GeneSpring which is one of the leading
commercial packages for analysis of
microarray data.
During 2005, we anticipate that
proteomics methodologies will produce
vast quantities of data, which will require
a significant bioinformatics input in terms
of storage and analysis. Together with
the Proteomics Research Centre, we
are investigating the most appropriate
solutions with respect to mass
spectrometry, 2-D gel analysis and
SELDI data.
SERVICE
CIBS provides a range of services from
group training courses to custom scripting.
We provide training in bioinformatics both
in the form of courses and one-to-one
sessions on a particular technique. The
inaugural Introduction to Bioinformatics
course took place in March 2005 and was
highly oversubscribed. This will now be
a biannual event and it is recommended
that all new graduate students take the
course. We have also been part of the
Dublin Molecular Medicine Centre
Introduction to Microarray Analysis
course, which we hosted at the Conway
in March 2005.
Conway researchers collaborate with
the CIBS in a variety of ways. Principally,
those researchers who need to analyse
data but lack the necessary expertise
can set up academic collaborations
with CIBS. Similarly, collaborations
can be arranged when software needs
to be developed for a project (eg.
http://actin.ucd.ie/cgi-bin/rs2cm.cgi).
We provide a web interface to BLAST
(http://actin.ucd.ie/blast.html) for
researchers who have datasets, which
they need to query. Access to these
databases is arranged through the
relevant investigator.
DR PEADAR O’GAORA
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Dr Peadar O’Gaora manages the
bioinformatics services in the Institute.
Bioinformatics can be defined as the
storage, retrieval and analysis of
biological data. This description covers
a huge range of disciplines and methods.
The field of bioinformatics developed
with the emergence of sequencing
projects and became a separate discipline
with the advent of high throughput
sequencing and whole genome
sequencing projects. From the relatively
simple problem of finding open reading
frames in sequence data to analysing the
expression pattern of every gene in a cell
under a range of conditions to automated
histological screening of hundreds of
samples, biologists require a level of
familiarity with at least some branch of
bioinformatics. In the absence of such
familiarity, it has become commonplace
within high quality research institutes
to have a local bioinformatics service
to aid with these analyses and storage/
retrieval issues.
The Conway Institute bioinformatics
service (CIBS) provides support for a
range of bioinformatics analyses. We
provide a set of software packages for
sequence analysis as well as expertise and
advice on specialised analysis methods.
APPLICATIONS
Within the Conway Institute, the variety
of bioinformatics applications is very
wide. A single issue, which reaches across
disciplines, is the storage of the vast
amounts of data generated in the core
technologies. To this end, we are putting
in place a storage area network (SAN)
consisting of an array of serial ATA
(SATA) disks with relevant networking
switches and servers for access to data.
As part of the SAN, we will have an online
automated backup system, which will
copy the data saved on the disks to tape
on a regular basis.
A web site has been set up at
http://actin.ucd.ie for delivery of analysis
solutions. We currently provide a web
interface to the EMBOSS bioinformatics
package. This is a freely available, open
source package of approximately 200
programs, which can be used for most
routine bioinformatics applications.
The interface we have chosen is wEMBOSS
developed at the XXX node of EMBNet.
Again, this is freely available, open
source software.
At present, the most common request
for collaboration with CIBS is in the area
of microarray analysis. Most of the data
generated in the transcriptomics facility is
on Affymetrix GeneChips. We recommend
and routinely use BioConductor
(http://bioconductor.org) for analysis
of these datasets for several reasons:
Bioinform
atics Service
Fig. 1. Affymetrix GeneChip®.
039 <> 040
DR DAVID COTTELL
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Dr David Cottell manages the electron
microscopy laboratory, which is an
interfaculty facility within University
College Dublin (UCD). Those wishing to
avail of the resources of the laboratory
may make an application for entry. The
laboratory staff will then comprehensively
train the prospective user in the
appropriate area of microscopy.
INSTRUMENTATION
The laboratory houses three high-res
transmission electron microscopes (TEM),
one scanning electron microscope (SEM)
and one cryo-stage SEM equipped with
a modern elemental analysis system. In
addition, there are four ultramicrotomes,
a cryo-ultramicrotome and a wide range
of SEM ancillary preparation instruments.
Light microscopy analysis is also
well supported.
APPLICATIONS
The diversity of this equipment allows
comprehensive ultrastructural research
to be undertaken in both the material
and biological sciences. This ranges from
ultrathin section analysis of cells and
tissues with detail maximally resolved
at a few nanometres to topographical
studies using scanning electron
microscopy and elemental analysis.
SERVICE
The mission statement of the laboratory
is to (a) provide a comprehensive electron
microscopy facility for the use of all staff
in UCD, (b) provide technical expertise
to assist in the widest possible range
of applications of electron microscopy,
(c) assist research workers in the
development of new or existing
applications of electron microscopy
to their research, (d) encourage staff
and students to become proficient users
of electron microscopes by running
appropriate expert training courses, (e)
provide a high quality electron microscopy
consultancy service for external agencies,
(f) maintain technical awareness in the
field of electron microscopy and to apply
new knowledge to laboratory operations.
USAGE
There were 136 postgraduate and
postdoctoral research projects that
used the electron microscopy facility
during the 2003/2004 academic year.
This graph shows the breakdown of these
figures on a departmental, faculty and
institutional basis.
Electron M
icroscopy Laboratory
Botany 4%
Miscellaneous 13%
Conway Institute 11%
Vet
erin
ary
Schoo
l 4%
Ag
ricu
ltu
re 4
%13
% E
ng
ineerin
g
5% Medicine
2% Zoology2% Physics
12% Geology
25
% C
he
mis
try
Fig. 1. Tecnai (TEM) with tomography.
(B) TEM, x 18,000.
Fig. 2. Renal glomerulus
(A) light microscopy, x 400.
041 <> 042
Liquid chromatography time-of-flight
(LCT) is the other instrument dedicated
for exact mass measurements. With a
mass resolution in 5000-10,000 and with
a lockspray mass feature, the LCT can
determine mass accurate to less than 5-10
parts per million (ppm). The presence
of an ultra-violet detector (photodiode
detector, Waters) in the HPLC system
(Waters 2795) can be used to determine
the molecular masses of compounds
in a mixture. The LCT has a theoretically
unlimited mass scan range and large
biomolecules and/or their interaction
with organic molecules can be analysed.
For more information, see
www.waters.com/WatersDivision/
Contentd.asp?ref=PSTD-5MBEQS
Fig. 1. ES mass spectra showing the chlorine
adducts of molecular masses of a series of
titanocene compounds.
Fig. 2. MS/MS spectrum of a peptide from a mixture
of peptides showing the amino acid sequence.
Fig. 3. Exact mass measurement using
LCT instrument.
DR DILIP RAI
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Dr Dilip Rai manages the mass
spectrometry facility, which is part
of the Centre for Synthesis and Chemical
Biology and located in the department
of chemistry. The MS facility caters
for over 120 users from 20 different
research groups within University
College Dublin (UCD), Royal College
of Surgeons of Ireland (RCSI) and
Trinity College Dublin (TCD). Mass
spectrometry (MS) is a method of choice
to determine mass of a wide variety of
molecules and the facility also provides
information on the fundamentals of MS,
technical advice and interpretation of
the MS data.
APPLICATIONS
By virtue of its sensitivity and speed, MS
plays a key role in the characterisation
of molecules of interest. MS is involved in
high throughput screening and detection
of chemically synthesised molecules.
Reaction monitoring, assessing quality
of library compound and their structural
elucidations are some of the ways in
which MS is applied.
High throughput screening on Quattro
Micro has resulted in simple mass
determination of over 6,000 sample
analyses. Exact mass measurements on
about 10% of the samples that undergo
high throughput screening are performed
on an annual basis. Collaborations on
biological sample analysis are welcomed.
Currently, there are 3 collaborators on
biological samples ranging from human
protein variants to bacterial siderophores.
Tandem mass spectrometry (MS/MS)
techniques are performed to study
reaction mechanisms and for structural
characterisation of molecules either
in a pure form or in a sample mixture.
Non-covalent complexes between
structurally similar and dissimilar species
have been studied.
INSTRUMENTATION
There are currently two mass
spectrometers (Micromass, Waters Corp.
USA) equipped with electrospray (ES)
source. Both instruments have HPLC
online to the ES source.
The Quattro Micro is fully automated with
an open-access server, which provides a
walk-up system where numerous students
and researchers log in their samples and
collect data in less than 2 minutes per
sample. The largest molecular mass on a
single charge that can be detected is 2040
Da. However, if multiply charged, species
of compounds as large as 70,000 Da can
be detected. The maximum number of
samples per batch run is 48. The mass
spectral data from positive and negative
ionisation modes are provided.
The HPLC (Waters 2695) online with the
MS uses acetonitrile:water (60:40 v/v)
flow solvent through a C18 guard column.
Quattro Micro is a tandem quadrupole
mass spectrometer and can be used for
fragmenting target molecules for further
structural analysis. Quattro Micro, can
also perform the parent and neutral loss
scan and enhance the quality of the mass
spectral data. Although the Quattro Micro
is largely used for qualitative measurement,
it can be used for quantitative analysis
under certain conditions.
For more information, see
www.waters.com/WatersDivision/
Contentd.asp?ref=JDRS-5L7P9T
Mass Spectrom
etry Facility
400 405 410 415 420 425 430 435 440 445 450 455 460 465 470 475 480 485 490 495 500 m0
%
0
%
0
100
100
100
%
441.1Scan ES-
5.48e4
Scan ES-4.87e4
Scan ES-1.87e5
439.0
443.1473.0
445.0
475.1472.9
468.1476.8
485.2
469.1467.1
Franz Josef, sample A in DCM20-Aug-2004
DILIP488 1 [2.051]
DILIP489 1 [2.051]
DILIP490 1 [3.008]
100 200 300 400 500 600 700 800 900 1000
SR16LCT20040518DKR273 38 (0.882) 1: TOF MS ES+
2.16e3100486.1454
%
0
196.0199
208.0435
331.1081
366.1075
509.1324
510.1315
549.1563
610.1896
613.1886
684.2142
758.2247898.3537 988.2603
993.2609
m/z
50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 800 850
4ESA1, >7hr digest, 1:500 in 50% ACN
Daughters of 717ES+6.57e5
DILIP280 1 (4.170)x2100
%
0
V72 L
86 129 158
b2171
230
y“2248
258
b3286
300329
b4357
371
414
y“4432 y“5
547
y“6618
717
b6571
b5470 503
m/z
1 2 3 4 5 6 7 <—— b-ions Val Ala Asp Ala Leu Thr Lys 7 6 5 4 3 2 1 <—— y-ions
- - - - - -
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MR PETER MANGAN
BUSINESS AND FINANCE MANAGER
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CENTRALISED STORES
& COMPUTERISED ORDERING
Prior to moving to the new building,
it was decided to centralise the purchasing
function and establish a central Institute
stores, which would consolidate and
process all orders, carry in-house stock,
receive and dispatch all deliveries, provide
a single point of contact with both
suppliers and the University accounts
office, and generally reduce the burden
of procurement for researchers by
providing a high quality professional
central service. The rationale for this
was to take advantage of economies
of scale and centralisation efficiencies
in the procurement process via:
- Reduced administration due to single
consolidated orders being placed
with suppliers rather than multiple
individual orders.
- Removal of burden of invoice processing
from individual researchers.
- Increased bargaining power with
suppliers leading to significant discounts
due to consolidated bulk purchasing.
- Efficient dedicated purchasing/stores
staff with expertise in all aspects of the
procurement process, including goods
handling and accounts maintenance.
- Efficient goods in/out logistics.
- Centralised record-keeping of
all transactions.
- Financial accountability.
- Faster turnaround times from order
placement to receipt of goods.
To enable this centralisation to succeed,
the process of ordering goods needed to
be upgraded from traditional paper-based
requisitioning to a streamlined automated
process. To this end, the Conway Institute,
working with Legacy Web Services Inc,
designed, developed and successfully
implemented a computerised purchase
order requisitioning system (Labstore)
tailored specifically to the requirements
of the Institute, it’s researchers and the
University’s financial systems with which
it integrates.
Feeding through to the central Conway
Institute stores, this user-friendly
web-based system allows researchers
to order goods electronically from their
desktops against one or other of their
designated research accounts. These
individual orders are then grouped
electronically by supplier, allowing
stores’ staff to process the consolidated
orders in an efficient, streamlined
manner. The system maintains detailed
computer records of all transactions
and allows principal investigators to
run statements on all of their research
accounts thereby keeping track of all
orders and account transactions.
Over the period of this report, the Conway
Institute stores has proven to be one
of the most effective and efficient
operational units within the Institute.
Catering for the purchasing requirements
of the entire Institute, turnover in the first
year was over 3 million with in excess of
10,000 individual orders being processed.
The Conway Stores is managed by
Mr John Ralph who is supported by
Mr Derek McCullagh, Mr Luke Millington
and Ms Annette Wallace.
Business and F
inance
Central Stores
Ms Annette Wallace
Mr Derek McCullagh
Mr Luke Millington
Mr John Ralph
Administration
Ms Bairbre Byrne
Ms Verona Patchell
Ms Ann Mooney
Over the next year, John and his team
will expand the range and quantity of
goods held internally in stock, negotiate
improved supplier discounts on behalf
of the Institute and its researchers, and
generate quantitative data on suppliers,
products and performance. This will
enable improved quality of service and
increased value for money to be passed
on to Conway researchers.
CENTRAL ADMINISTRATION
The Conway Institute directorate seeks
to facilitate the day-to-day running
of the Institute by fulfiling central
administration and financial control
functions and providing administrative
support to the Conway research community.
In August 2004, Ms Bairbre Byrne joined
the Conway Institute directorate team,
taking up the position of executive
assistant (finance). In this role, Bairbre
supports the business & finance manager
and is principally responsible for accounts
processing, monitoring and report
generation. Ms Ann Mooney joined the
directorate as personal assistant to
Professor Guiry while also continuing
her role within the Centre for Synthesis
& Chemical Biology.
RECEPTION SERVICES
The Conway Institute operates a central
reception desk, managed by Ms Verona
Patchell, which provides a number of
key services. Apart from front-of-house
receptionist duties, Verona is responsible
for operating the computerised access
card system, maintaining Institute
timetables and booking transport and
accommodation.
SEMINAR & MEETING FACILITIES
The Conway Institute has a lecture
theatre, function area and a number of
dedicated seminar and meeting rooms,
which it makes available both internally
to the Conway/UCD community, and
externally where appropriate. A centralised
booking system is in place for the hire
of these facilities, which is also operated
through the Conway Institute reception
desk by Ms Verona Patchell.
045 <> 046
MS ELAINE QUINN
COMMUNICATIONS & EDUCATION OFFICER
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COMMUNICATIONS
Conway Master Guidelines
As the Conway Institute moved from
being a virtual to an actual entity, the
problem of identity became evident.
With three constituent centres, each
being associated with other third-level
institutions, and affiliated teaching
hospitals, the network of centres,
institutions and affiliated hospitals was
difficult to explain. Each centre plays a
different role within the continuum of the
Conway scientific programme yet it was
important that each would be identifiably
and intrinsically linked to the ‘umbrella’
organisation. The new Conway logo suite
and guidelines allows each centre to
create their individual identity while
clearly defining their place within the
Institute. The overall strength in this
brand creates greater awareness and
recognition of the Conway Institute within
the national and international scientific
community, among funding agencies and
in the public arena.
Conway Website
Part of the development of the Conway
brand included the redesign and
development of the Conway website.
Launched in July 2004, this website
now provides comprehensive information
about the personnel and work of the
Institute. The most challenging task
in relation to any website is maintaining
the currency of information there. It was
for this reason, and to establish strong
internal lines of communication within
an institute of some 450 people, that
we extended this project to include the
development of an intranet. This will
also give individual investigators the
ability to edit their own personal page
on the internet site.
Media Coverage
In order to attract high calibre personnel
as well as potential industrial and
research partners, secure future funding
and encourage political and public
engagement in science, it is vital that
the Conway Institute make people aware
primarily of its existence and secondly of
its status as a centre of excellence. During
the reporting period, there were in excess
of sixty articles in the print media relating
to the work of the Conway Institute and
its personnel. A number of research
stories were also covered in international
specialist journals and on television and
radio in Ireland and the United Kingdom.
RTE film crews have done background
filming in the laboratories of Conway
Institute for programmes such as Would
You Believe, Scope and Undercover.
The state-of-the-art laboratories also
provided a backdrop to a promotional
DVD for the Discover Science &
Engineering initiative.
EDUCATION
Postgraduate Education
The recommendations of both the
Conference of Heads of Irish Universities
(CHIU) and the European Bologna Process
in relation to the design, development
and delivery of postgraduate education
programmes resulted in the complete
restructuring of the existing Conway
postgraduate programme. In preparation
for the academic year 2004/2005,
the education committee (a) developed
a new postgraduate student booklet,
(b) established a new method of
administering the programme in order
to record student progress, supervision
and mentoring and (c) begun the process
of developing course content, which
will incorporate both educational and
professional skills courses for all Conway
affiliated postgraduates.
Com
munications &
Education
AccesScience judges: Emma O’Kelly, Ronan Wilmot,
Geraldine Kennedy, An Tanaiste Mary Harney TD,
Dr Philip Nolan, director Conway Institute and
Michael Keating.
AccesScience contestants Theresa Aherne,
Brid Ryan, Craig Slattery, Karen Tobin,
Eavan Daly, Niamh Tuite.
Ciara O’Hanlon
Executive Assistant
(Comms and Ed)
Grace Sexton
Assistant Communications
and Education Officer
It is hoped that this programme will
equip graduates with the educational
and professional skills required to enable
them to forge successful, independent
research careers in an increasingly
competitive environment.
Seminars
The organisation of the Conway seminar
series is the responsibility of the Conway
seminar committee. Dr Gethin McBean
assumed the role of chairperson on this
committee during the reporting period
and has worked to deliver a stimulating
and informative series of lectures, which
appeal to researchers at every level of
their career. The 2003/2004 series was
re-structured in an attempt to increase
this element of inclusivity. Details of
the lectures in the seminar series during
the reporting period can be found in
appendix 4.
OUTREACH
AccesScience
In 2004, the organisation of the Merville
lay seminars came under the remit of the
Conway Institute. The competition to
explain scientific research without the
jargon is now open to all Conway third
year postgraduates and has been
rebranded as AccesScience. Six post-
graduate students successfully came
through internal heats within the three
centres of the Institute to compete in the
grand finale in O’Reilly Hall, UCD on May
4th 2004. In an evening hosted by Mr Pat
Kenny, RTE and judged by a celebrity
panel, members of the general public
heard about the latest research areas
such as alternative approaches to toxicity
testing and ‘survivin’ breast cancer.
This programme will be more fully
developed in the coming year in an
effort to exploit the full potential of this
outreach opportunity.
In order to accelerate the development of
the Conway outreach programme in line
with the stated objective of the Institute
under the Programme for Research in
Third Level Institutions, Ms Grace Sexton
was employed as assistant communications
and education officer. During the reporting
period, she was instrumental in devising
and implementing a pilot programme of
outreach events for the academic year
2004/2005. Also, during this time,
Ms Ciara O’Hanlon accepted the role
of executive assistant with responsibility
for communications and education.
ScienceWorks
This pilot series of half-day workshops
aimed at transition year students was
launched during National Science Week
(November 7th-14th). One hundred and
thirty pupils from ten secondary schools
across the greater Dublin area attended
these sessions. Conway Uncovered
brought students on a tour of this
world-class facility; Science@Work
took them into the laboratory for some
hands-on practical experiments and in
Pathways2Science they heard about the
many varied and exciting career paths
of members of staff. The success of the
pilot programme was such that advance
bookings have been taken for workshops
in April and November 2005.
APPENDICES
049 Publications
067 Grants Awarded
075 Thesis Submissions
079 Conway Institute Seminar Series
081 Committees/Management Structure
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App
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Boland NA, Casey M, Hynes SJ,
Matthews JW, Muller-Bunz H, Wilkes P:
Preparation of enantiopure biimidazoline
ligands and their use in asymmetric
catalysis. Organic & Biomolecular
Chemistry 2004; 2: 1995-2002
Brazil DP, Yang ZZ, Hemmings BA:
Advances in protein kinase B signalling:
AKTion on multiple fronts. Trends in
Biochemical Sciences 2004; 29: 233-42
Brennan L, Corless M, Hewage C,
Malthouse JPG, McClenaghan NH, Flatt PR,
Newsholme P: C-13 NMR analysis reveals
a link between L-glutamine metabolism,
D-glucose metabolism and gamma-glutamyl
cycle activity in a clonal pancreatic beta-cell
line. Diabetologia 2003; 46: 1512-21
Bresnihan B, Newmark R, Robbins S,
Genant HK: Effects of anakinra monotherapy
on joint damage in patients with rheumatoid
arthritis. Extension of a 24-week
randomized, placebo-controlled trial.
Journal of Rheumatology 2004; 31: 1103-11
Bresnihan B, Kane D: Sonography and
subclinical synovitis. Annals of the
Rheumatic Diseases 2004; 63: 333-4
Bresnihan B, Gogarty M, FitzGerald O,
Dayer JM, Burger D: Apolipoprotein A-I
infiltration in rheumatoid arthritis synovial
tissue: a control mechanism of cytokine
production? Arthritis Research & Therapy
2004; 6: R563-R566
Brooks SJ, Doyle EM, Hewage C,
Malthouse JPG, Duetz W, O’Connor KE:
Biotransformation of halophenols using
crude cell extracts of Pseudomonas
putida F6. Applied Microbiology and
Biotechnology 2004; 64: 486-92
Brown DA, Glass WK, Fitzpatrick NJ,
Kemp TJ, Errington W, Clarkson GJ,
Haase W, Karsten F, Mahdy AH:
Structural variations in dinuclear model
hydrolases and hydroxamate inhibitor
models: synthetic, spectroscopic and
structural studies. Inorganica Chimica
Acta 2004; 357: 1411-36
Brown DA, Cuffe LP, Fitzpatrick NJ, Ryan AT:
A DFT study of model complexes of zinc
hydrolases and their inhibition by
hydroxamic acids. Inorganic Chemistry
2004; 43: 297-302
Bund SJ, Perkins J, Lim CH, Savage D:
Functional evidence that K+ is the non-
nitric oxide, non-prostanoid endothelium-
derived relaxing factor in rat femoral
arteries. Vascular Pharmacology 2003;
40: 23-8
Bund SJ, Lee RMKW: Arterial structural
changes in hypertension: A consideration
of methodology, terminology and
functional consequence. Journal of
Vascular Research 2003; 40: 547-57
Busca P, Paradisi F, Moynihan E,
Maguire AR, Engel PC: Enantio-selective
synthesis of non-natural amino acids using
phenylalanine dehydrogenases modified
by site-directed mutagenesis. Organic &
Biomolecular Chemistry 2004; 2: 2684-91
Butler G, Kenny C, Fagan A, Kurischko C,
Gaillardin C, Wolfe KH: Evolution of the
MAT locus and its Ho endonuclease in
yeast species. Proceedings of the National
Academy of Sciences of the United States
of America 2004; 101: 1632-7
Butler MP, O’Connor JJ, Moynagh PN:
Dissection of tumor-necrosis factor-alpha
inhibition of long-term potentiation (LTP)
reveals a p38 mitogen-activated protein
kinase-dependent mechanism which
maps to early-but not late-phase LTP.
Neuroscience 2004; 124: 319-26
Butler MW, Mullan RH, Schaffer KE,
Crotty TB, Luke DA, Donnelly SC:
Pulmonary cystic hydatid disease in
Ireland. Irish Journal of Medical
Science 2003; 172: 204-5
Byrne B, Carmody M, Gibson E, Rawlings B,
Caffrey P: Biosynthesis of deoxyam-
photericins and deoxyamphoteronolides
by engineered strains of Streptomyces
nodosus. Chemistry & Biology 2003;
10: 1215-24
Byrne LA, Furlong PJ, Gilheany DG:
Easy access to medium rings by entropy/
strain reduction. V. A simple and mild
route to cyclohepta-1, 3-dienes. Synthetic
Communications 2004; 34: 1631-43
Byrne LA, Gilheany DG: Simple syntheses
of seven-membered rings via an entropy/
strain reduction strategy. Synlett 2004;
933-43
Camera M, Frigerio M, Toschi V, Brambilla M,
Rossi F, Cottell DC, Maderna P, Parolari A,
Bonzi R, De Vincenti O, Tremoli E: Platelet
activation induces cell-surface immuno-
reactive tissue factor expression, which
is modulated differently by antiplatelet
drugs. Arteriosclerosis Thrombosis and
Vascular Biology 2003; 23: 1690-6
Casey E, Rishell S, Glennon B, Hamer G:
Engineering aspects of a mixed
methanotrophic culture in a membrane-
aerated biofilm reactor. Water Science
and Technology 2004; 49: 255-62
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Aden U, O’Connor WT, Berman RF: Changes
in purine levels and adenosine receptors in
kindled seizures in the rat. Neuroreport
2004; 15: 1585-9
Aherne A, Kennan A, Kenna PF, McNally N,
Lloyd DG, Alberts IL, Kiang AS,
Humphries MM, Ayuso C, Engel PC, Gu JJ,
Mitchell BS, Farrar GJ, Humphries P:
On the molecular pathology of
neurodegeneration in IMPDH1-based
retinitis pigmentosa. Human Molecular
Genetics 2004; 13: 641-50
Appelbe R, Casey M, Dunne A, Pascarella E:
Stereoselective synthesis of tetralins using
cationic cyclisations.Tetrahedron Letters
2003; 44: 7641-4
Araujo A, Hall WW: Human T-lymphotropic
virus type II and neurological disease.
Annals of Neurology 2004; 56: 10-9
Axford JS, Cunnane G, FitzGerald O,
Bland JM, Bresnihan B, Frears ER:
Rheumatic disease differentiation using
immunoglobulin G sugar printing by high
density electrophoresis. Journal of
Rheumatology 2003; 30: 2540-6
Baird AW, Campion DP, O’Brien L,
Brayden DJ: Oral delivery of pathogens
from the intestine to the nervous system.
Journal of Drug Targeting 2004; 12: 71-8
Balfe P, McCann A, McGoldrick A,
McAllister K, Kennedy M, Dervan P,
Kerin MJ: Estrogen receptor alpha and
beta profiling in human breast cancer.
Ejso 2004; 30: 469-74
Bates JJ, Watson RWG, Glynn CM, O’Neill AJ,
Fitzpatrick JM, Buggy DJ: Aspirin preserves
neutrophil apoptosis after cardiopulmonary
bypass. Shock 2004; 21: 495-9
Beck RBJ, O’Malley M, van Dijk JP, Nolan P,
Stegeman DF: The effects of bipolar
electrode montage on conduction velocity
estimation from the surface electro-
myogram. Journal of Electromyography
and Kinesiology 2004; 14: 505-14
Beddy D, Watson RWG, Fitzpatrick JM,
O’Connell PR: Increased vascular endothelial
growth factor production in fibroblasts
isolated from strictures in patients with
Crohn’s disease. British Journal of Surgery
2004; 91: 72-7
Beddy DJ, Watson WR, Fitzpatrick JM,
O’Connell PR: Critical involvement of stress-
activated mitogen-activated protein
kinases in the regulation of intracellular
adhesion molecule-1 in serosal fibroblasts
isolated from patients with Crohn’s disease.
Journal of the American College of
Surgeons 2004; 199: 234-42
Benito MJ, Murphy E, Murphy EP,
van den Berg WB, FitzGerald O,
Bresnihan B: Increased synovial tissue
NF-kappa B1 expression at sites adjacent
to the cartilage-pannus junction in
rheumatoid arthritis. Arthritis and
Rheumatism 2004; 50: 1781-7
Benkirane-Jessel N, Schwinte P, Falvey P,
Darcy R, Haikel Y, Schaaf P, Voegel JC,
Ogier J: Build-up of polypeptide multilayer
coatings with anti-inflammatory properties
based on the embedding of piroxicam-
cyclodextrin complexes. Advanced
Functional Materials 2004; 14: 174-82
Bird PI, Pak SC, Worrall DM, Bottomley SP:
Production of recombinant serpins in
Escherichia coli. Methods 2004; 32: 169-76
Appendix 1
Peer-Review
ed Publications during the period from
Septem
ber 1st 2003 – September 30th 2004
1.
2.
3.
4.
5.
6.
7.
8.
9.
10.
11.
12.
13.
14.
15.
16.
17.
18.
19.
20.
21.
22.
23.
24.
25.
26.
27.
28.
29.
30.
31.
32.
33.
34.
051 <> 052
Conway BR, Martin R, McKnight AJ,
Savage DA, Brady HR, Maxwell AP:
Role of alpha-adducin DNA polymorphisms
in the genetic predisposition to diabetic
nephropathy. Nephrology Dialysis
Transplantation 2004; 19: 2019-24
Conway BR, Maxwell AP, Savage DA,
Patterson CC, Doran PP, Murphy M,
Brady HR, Fogarty DG: Association between
variation in the actin-binding gene
caldesmon and diabetic nephropathy in
type 1 diabetes. Diabetes 2004; 53: 1162-5
Cookson S, Reen D: IL-15 drives neonatal T
cells to acquire CD56 and become activated
effector cells. Blood 2003; 102: 2195-7
Corbett K, Kelleher S, Rowland M, Daly L,
Drumm B, Canny G, Greally P, Hayes R,
Bourke B: Cystic fibrosis-associated liver
disease: A population-based study. Journal
of Pediatrics 2004; 145: 327-32
Costello DA, Herron CE: A role for
peroxisome proliferator activated receptors
in the ß-amyloid (Aß[1-40]) mediated
impairment of hippocampal long-term
potentiation in vitro. J Physiol 2004; 555P:
Costello DA, Herron CE: The role of c-Jun
N-terminal kinase in the A beta-mediated
impairment of LTP and regulation of
synaptic transmission in the hippocampus.
Neuropharmacology 2004; 46: 655-62
Coyne JD, Dervan PA: Ileal intussuseptus
containing a Meckel’s diverticulum showing
florid localized mucosal angiogenesis and
microcarcinoidosis. Histopathology 2003;
43: 608-9
Coyne JD, Dervan PA, Barr L: High-grade
carcinomas of the breast showing patterns
of mixed ductal and myoepithelial
differentiation (including myoepithelial
cell-rich carcinoma of the breast).
Histopathology 2004; 44: 580-4
Crean JK, Furlong F, Finlay D, Mitchell D,
Conway B, Brady HR, Godson C, Martin F:
Connective tissue growth factor
[CTGF]/CCN2 stimulates mesangial cell
migration through integrated dissolution of
focal adhesion complexes and activation of
cell polarization. Faseb Journal 2004; 18:
Crushell E, Rowland M, Doherty M,
Gormally S, Harty S, Bourke B, Drumm B:
Importance of parental conceptual model
of illness in severe recurrent abdominal
pain. Pediatrics 2003; 112: 1368-72
Cryan SA, Holohan A, Donohue R, Darcy R,
O’Driscoll CM: Cell transfection with
polycationic cyclodextrin vectors. European
Journal of Pharmaceutical Sciences 2004;
21: 625-33
Cryan SA, Donohue R, Ravoo BJ, Darcy R,
O’Driscoll CM: Cationic cyclodextrin
amphiphiles as gene delivery vectors.
Stp Pharma Sciences 2004; 14: 57-62
Cserni G, Amendoeira I, Apostolikas N,
Bellocq JP, Bianchi S, Boecker W,
Borisch B, Connolly CE, Decker T,
Dervan P, Drijkoningen M, Ellis IO,
Elston CW, Eusebi V, Faverly D, Heikkila P,
Holland R, Kerner H, Kulka J, Jacquemier J,
Lacerda M, Martinez-Penuela J, De Miguel C,
Peterse JL, Rank F, Regitnig P, Reiner A,
Sapino A, Sigal-Zafrani B, Tanous AM,
Thorstenson S, Zozaya E, Fejes G, Wells CA:
Discrepancies in current practice of
pathological evaluation of sentinel lymph
nodes in breast cancer. Results of a
questionnaire based survey by the
European Working Group for Breast
Screening Pathology. Journal of Clinical
Pathology 2004; 57: 695-701
Curley AE, Sweet DG, MacMahon KJ,
O’Connor CM, Halliday HL:
Chorioamnionitis increases matrix metallo-
proteinase - 8 levels in bronchoalveolar
lavage fluid from preterm babies. Arch Dis
Child Fetal Neonatal Ed 2004; 89: 61-4
Curran SA, FitzGerald OM, Costello PJ,
Selby JM, Kane DJ, Bresnihan B,
Winchester R: Nucleotide sequencing of
psoriatic arthritis tissue before and during
methotrexate administration reveals a
complex inflammatory T cell infiltrate with
very few clones exhibiting features that
suggest they drive the inflammatory
process by recognizing autoantigens.
Journal of Immunology 2004; 172: 1935-44
Dalton JP, Neill SO, Stack C, Collins P,
Walshe A, Sekiya M, Doyle S, Mulcahy G,
Hoyle D, Khaznadji E, Moire N, Brennan G,
Mousley A, Kreshchenko N, Maule AG,
Donnelly SM: Fasciola hepatica cathepsin
L-like proteases: biology, function, and
potential in the development of first
generation liver fluke vaccines. Int J
Parasitol. 2003; 33: 1173-81
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Casey M, Donnelly JA, Ryan JC, Ushioda S:
Synthesis of bicyclic lactams using novel
Schmidt reactions. Arkivoc 2003; 310-27
Casey M, Keaveney CM: A concise stereo-
controlled formal total synthesis of (+/-)
-podophyllotoxin using sulfoxide chemistry.
Chemical Communications 2004; 184-5
Castilla J, Gutierrez-Adan A, Brun A,
Doyle D, Pintado B, Ramirez MA,
Salguero FJ, Parra B, San Segundo FD,
Sanchez-Vizcaino JM, Rogers M, Torres JM:
Subclinical bovine spongiform
encephalopathy infection in transgenic
mice expressing porcine prion protein.
Journal of Neuroscience 2004; 24: 5063-9
Celli BR, MacNee W, Agusti A, Anzueto A,
Berg B, Buist AS, Calverley PMA,
Chavannes N, Dillard T, Fahy B, Fein A,
Heffner J, Lareau S, Meek P, Martinez F,
McNicholas WT, Muris J, Austegard E,
Pauwels R, Rennard S, Rossi A, Siafakas N,
Tiep B, Vestbo J, Wouters E, ZuWallack R:
Standards for the diagnosis and treatment
of patients with COPD: a summary of the
ATS/ERS position paper. European
Respiratory Journal 2004; 23: 932-46
Chery F, Cronin L, O’Brien JL, Murphy PV:
Synthesis of pepti-domimetics based on
iminosugar and beta-D-glucopyranoside
scaffolds and inhibiton of HIV-protease.
Tetrahedron 2004; 60: 6597-608
Chery F, Murphy PV: Synthesis of an
iminosugar based peptidomimetic
analogue. Tetrahedron Letters 2004;
45: 2067-9
Chuev GN, Fedorov MV: Wavelet algorithm
for solving integral equations of molecular
liquids. A test for the reference interaction
site model. Journal of Computational
Chemistry 2004; 25: 1369-77
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Hitman GA, Neil HAW, Livingstone SJ,
Thomason MJ, Mackness MI,
Charlton-Menys V, Fuller JH: Primary
prevention of cardiovascular disease with
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Connolly DJ, Lacey PM, McCarthy M,
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Guiry PJ: Preparation and resolution of a
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Connolly R, Timoshenko EG, Kuznetsov YA:
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Connolly R, Timoshenko EG, Kuznetsov YA:
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English NJ, MacElroy JMD: Hydrogen
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English NJ, MacElroy JMD: Structural and
dynamical properties of methane clathrate
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English NJ, MacElroy JMD: Theoretical
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Evans ACO: Ovarian follicle growth and
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development during follicular waves in
cattle. Biology of Reproduction 2004;
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Evans ACO, Duffy P, Crosby TF,
Hawken PAR, Boland MP, Beard AP:
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progestagen treatment on estrus
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the breeding season in ewes. Animal
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Fair T: Follicular oocyte growth and
acquisition of developmental competence.
Animal Reproduction Science 2003;
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Fair T, Gutierrez-Adan A, Murphy M,
Rizos D, Martin F, Boland MP, Lonergan P:
Search for the bovine homolog of the
murine Ped gene and characterization
of its messenger RNA expression during
bovine preimplantation development.
Biology of Reproduction 2004; 70: 488-94
Fair T, Murphy M, Rizos D, Moss C, Martin F,
Boland MP, Lonergan P: Analysis of
differential maternal mRNA expression
in developmentally competent and
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Molecular Reproduction and Development
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Feng J, Tamaskovic R, Yang ZZ, Brazil DP,
Merlo A, Hess D, Hemmings BA:
Stabilisation of Mdm2 via decreased
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Journal of Biological Chemistry 2004;
279: 35510-7
Ferguson AC, Adlington RM, Martyres DH,
Rutledge PJ, Cowley A, Baldwin JE:
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Fisher AJ, Donnelly SC, Pritchard G,
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Fleming FJ, Hill ADK, Kavanagh D, Quinn C,
O’Doherty A, Collins CD, McDermott EW,
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Fleming FJ, Hill ADK, Mc Dermott EW,
O’Doherty A, O’Higgins NJ, Quinn CM:
Intraoperative margin assessment and
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Fleming FJ, Hill ADK, McDermott EW,
O’Higgins NJ, Young LS: Differential
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to the estrogen receptor-estrogen response
element by beta-estradiol and 4-hydroxy-
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Fleming FJ, Kavanagh D, Crotty TB,
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Foell D, Kane D, Bresnihan B, Vogl T,
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Dixon G, Nolan J, McClenaghan N, Flatt PR,
Newsholme P: A comparative study of
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Dixon G, Nolan J, McClenaghan NH, Flatt PR,
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Doherty LS, Kiely JL, Lawless G,
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Watson RWG: Differentiation-induced
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Duffy MJ: The urokinase plasminogen
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Duffy P, Crowe MA, Austin EJ, Mihm M,
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Edwards CJ, Connellan J, Wallace PF,
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Edwards CJ, MacHugh DE, Dobney KM,
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Crowe MA: Technical Note: Effect of
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Estimation of a pKa for Protonated
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Gutierrez-Adan A, Rizos D, Fair T,
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Boland MP, Lonergan P: Effect of speed of
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Hagen T, Taylor CT, Lam F, Moncada S:
Redistribution of intracellular oxygen in
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Harte M, O’Connor W: Evidence for a
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Helley-Hickie LP, Kinsella BT: EP1- and
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the human thromboxane A(2) receptor.
British Journal of Pharmacology 2004;
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Herron CE, Schmid AW, Costello DA,
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Godson C, Brady HR: DNA oligonucleotide
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Kidney International 2003; 64: 2079-91
Higham LJ, Kelly PG, Corr DM,
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Higham LJ, Kelly PG, Mueller-Bunz H,
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Hopkins AM, Baird AW, Nusrat A: ICAM-1:
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Howell K, Ooi H, Preston R, McLoughlin P:
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Hughes JM, Bund SJ: Influence of
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Hurley ME, White MJ, Green AJ, Kelleher J:
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Hynes SO, Ferris JA, Szponar B, Wadstrom T,
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Ljungh A, Clyne M, Andersen LP, Moran AP:
Comparative chemical and biological
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Helicobacter 2004; 9: 313-23
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Foley AG, Ronn LCB, Murphy KJ, Regan CM:
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Foley AG, Hedigan K, Roullet P, Moricard Y,
Murphy KJ, Sara SJ, Regan CM: Consolidation
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Foley AG, Gallagher HC, Murphy KJ,
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Foley AG, Murphy KJ, Hirst WD,
Gallagher HC, Hagan JJ, Upton N,
Walsh FS, Regan CM: The 5-HT6
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Fox S, Dunne JP, Tacke M, Gallagher JF:
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Gallagher HC, Bacon CL, Odumeru OA,
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Valproate activates phosphodiesterase-
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Gallagher J, Howlin J, McCarthy C,
Murphy EP, Bresnihan B, FitzGerald O,
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Galvin DJ, Watson RWG, O’Neill A,
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A potential mechanism of bladder
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Garland MR, Lavelle E, Doherty D,
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Glennon JJ, Leenars CHC, Duffy A,
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Golden-Mason L, Douek DC, Koup RA,
Kelly J, Hegarty JE, O’Farrelly C: Adult
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Kelly SN, McKenna TJ, Young LS:
Modulation of steroidogenic enzymes by
orphan nuclear transcriptional regulation
may control diverse production of cortisol
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Kennedy BN, Stearns GW, Smyth VA,
Ramamurthy V, van Eeden F, Ankoudinova
I, Raible D, Hurley JB, Brockerhoff SE:
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during eye morphogenesis. Developmental
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Kerrigan NJ, Dunne EC, Cunningham D,
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in the preparation of novel P-chirogenic
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Tetrahedron Letters 2003; 44: 8461-5
Kiely JL, Nolan P, McNicholas WT:
Intranasal corticosteroid therapy for
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Kiely D, Guiry PJ: Palladium complexes of
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Kiely D, Guiry PJ: A comparison of palladium
complexes of BINAP and diphenylphos-
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Kieran NE, Rabb H: Immune responses in
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Kieran NE, Maderna P, Godson C: Lipoxins:
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Kilmartin B, Reen DJ: HSP60 induces
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Kilroy TG, Cozzi PG, End N, Guiry PJ: The
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Kirwan RP, Crean JK, Fenerty CH, Clark AF,
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proteinase-2 activity in lamina cribrosa
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Klyubin I, Walsh DM, Cullen WK, Fadeeva JV,
Anwyl R, Selkoe DJ, Rowan MJ: Soluble
Arctic amyloid beta protein inhibits
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2004; 19: 2839-46
Komaraiah P, Navratil M, Carlsson M,
Jeffers P, Brodelius M, Brodelius PE,
Kieran PM, Mandenius CF: Growth behavior
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Koppelstaetter C, Jennings P, Ryan MP,
Morin JP, Hartung T, Pfaller W:
Assessment of a new cell culture perfusion
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Boylan JF, McLoughlin P: Hypercapnic
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Lebret T, Watson RWG, Molinie V, O’Neill A,
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Heat shock proteins HSP27, HSP60, HSP70,
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Lemey P, Salemi M, Wang B, Duffy M,
Hall WH, Saksena NK, Vandamme AM:
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Leonard MO, Cottell DC, Godson C,
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Lombardo D, Longo A, Darcy R,
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Jeffers P, Raposo S, Lima-Costa ME,
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Jennings P, Koppelstaetter C, Pfaller W,
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Jones BR, Brennan S, Mooney CT,
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Kamran M, Calcagno AM, Findon H,
Bignell E, Jones MD, Warn P, Hopkins P,
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Kane D, Stafford L, Bresnihan B,
FitzGerald O: A prospective, clinical
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Kane D, Stafford L, Bresnihan B,
FitzGerald O: A classification study of
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‘DIP or not DIP revisited’. Rheumatology
2003; 42: 1469-76
Kane D, Jensen LE, Grehan S, Whitehead AS,
Bresnihan B, FitzGerald O: Quantitation
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pannus junction. Journal of Rheumatology
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Kane D, Balint PV, Gibney R, Bresnihan B,
Sturrock RD: Differential diagnosis of calf
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Kapushesky M, Kemmeren P, Culhane AC,
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Expression Profiler: next generation –
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Kelly AM, Golden-Mason L, McEntee G,
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25: 273-82
Kelly LM, Hill ADK, Kennedy S, Connolly EM,
Ramanath R, Teh S, Dijkstra B, Purcell R,
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2004; 78: 250-6
Verlengia R, Gorjao R, Kanunfre CC,
Bordin S, de Lima TM, Martins EF,
Newsholme P, Curi R: Effects of EPA and
DHA on proliferation, cytokine production,
and gene expression in Raji cells. Lipids
2004; 39: 857-64
Verlengia R, Gorjao R, Kanunfre CC,
Bordin S, de Lima TM, Newsholme P, Curi R:
Genes regulated by arachidonic and oleic
acids in Raji cells. Lipids 2003; 38: 1157-65
Wang Q, Walsh DM, Rowan MJ, Selkoe DJ,
Anwyl R: Ab-induced block of LTP is
mediated via activation of the receptors
mGluR5 and the kinases JNK, Cdk5 and
p38 MAP kinase. Journal of Neuroscience
2004; 24: 3370-8
Watson RWG, Schalken JA:
Future opportunities for the diagnosis
and treatment of prostate cancer.
Prostate Cancer and Prostatic Diseases
2004; 7: S8-S13
Wells CA, Sloane JP, Coleman D, Munt C,
Amendoeira I, Apostolikas N, Bellocq JP,
Bianchi S, Boecker W, Bussolati G,
Connolly CE, Dervan P, Drijkoningen M,
Ellis IO, Elston CW, Eusebi V, Faverly D,
Heikkila P, Holland R, Jacquemier J,
Lacerda M, Martinez-Penuela J, De Miguel C,
Peterse JL, Rank F, Reiner A, Saksela E,
Sigal-Zafrani B, Sylvan M, Borisch B,
Cserni G, Decker T, Kerner H, Kulka J,
Regitnig P, Sapino A, Tanous AM,
Thorstenson S, Zozaya E: Consistency
of staining and reporting of oestrogen
receptor immunocytochemistry within
the European Union – an inter-laboratory
study. Virchows Archiv 2004; 445: 119-28
Wiley J, Lynch T, Lincoln S, Skipper L,
Hulihan M, Gosal D, Bisceglio G, Kachergus J,
Hardy J, Farrer MJ: Parkinson’s disease in
Ireland: Clinical presentation and genetic
heterogeneity in patients with parkin
mutations. Movement Disorders 2004;
19: 677-81
Wilson SJ, Gorelov AV, Rochev YA,
McGillicuddy F, Dawson KA, Gallagher WM,
Keenan AK: Extended delivery of the
antimitotic agent colchicine from thermo-
responsive N-isopropylacrylamide-based
copolymer films to human vascular smooth
muscle cells. Journal of Biomedical
Materials Research Part A 2003;
67A: 667-73
258.
259.
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262.
263.
264.
265.
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267.
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269.
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Appendix 2
Grants Aw
arded during the period fromSeptem
ber 1st 2003 to September 30th 2004
Researcher Contract Total (Euro) Funding Agency Project Title
Dominic Walsh 917,363 Wellcome Trust Neurotoxic mechanisms of amyloid B-protein: INTRA-AB mutations and p35/CdK5 activation
Caroline Herron 13,000 HRB Molecular basis for B-amyloid mediated neurtoxicity on synaptic transmission and long-term potentiation
Evelyn Murphy 98,600 HRB Understanding nuclear orphan receptor function
John Seery 30,000 Irish Lung Foundation HOX genes and inflammation
William Gallagher 74,476 Cancer Research Ireland Functional genomics of breast cancer: A focus on metastasis
Paul Moynagh 132,000 HRB Defining a role for human cactin in Toll-like receptor signalling
William Gallagher 172,410 HRB Malignant melanoma: Functional studies using DNA methyltransferase inhibitors and genetic suppressor element technology
Breandan Kennedy 180,000 HRB In vivo models of human blindness characterised by cone-rod dystrophy
Clare O’Connor 160,017 HRB Functional analysis of different gene expression in IL-8 versus FMLP stimulated neurophils with specific reference to migratory pattern
Margaret Worrall 155,661 HRB Characterisation of the remaining human A-clade serpins
Kevin Malone 10,000 Iarnrod Eireann Suicide on Irish Railways 1990-2000
Patrick Guiry 57,150 IRCSET New tridentate oxazoline- containing ligands for asymetric catalysis
Clare O’Connor 57,150 IRCSET Evaluation of the molecular mechanisms involved in neutrophil migration
Patrick Guiry 57,150 IRCSET Studies in the intramolecular asymmetric Heck reaction
Donal O’Shea 57,150 IRCSET New organolithium addition methodology to diversely functionalised endoles
Tara McMorrow 128,500 HRB Gene regulation and mechanism of epithelial-mesenchymal transdifferentiation (EMT) in a Cyclosporine A -induced model
Patrick Guiry 64,011 HEA/PRTLI Cycle 3
Patrick Guiry 90,600 HEA/PRTLI Cycle 3 Total synthesis of bioactive compounds
Kevin O’Connor 57,150 IRCSET The directed evolution of phenylalanine hydroxylase
Ciaran Regan 57,150 IRCSET Indentification of novel compounds for the treatment of mental illness
R William G Watson 194,854 Irish Cancer Society Development of new diagnostic, prognostic and therapeutic agents in prostate cancer
Catherine Godson 57,150 IRCSET Annexun - 1 stimulated phagocytosis
Torres Sweeney 15,000 Teagasc A comparison of the virulence characteristics of verocytotoxigenic E. Coli O157:H7 isolates from food animals and humans
Torres Sweeney 15,000 Teagasc The use of antisense RNA technology and antibacterial agents for non-pathogenic bacteria for the control of VTEC in water
R William G Watson 266,709 Irish Cancer Society
Declan Gilheany 339,378 Enterprise Ireland Development of P-chiral chemical technology for application in agriculture
Ciaran Regan 331,200 Enterprise Ireland Psychoscreen; looking backwards: A new path for drug discovery in psychopharmacology
Grace Mulcahy 180,981 Enterprise Ireland RNAi-mediated gene silencing, functional expression and biochemical analysis of the aminopeptidases expressed
by the malarial parasite Plasmodium falciparum
Donal O’Shea 90,600 HEA/PRTLI Cycle 3 New molecular fluorescent switches as tools for chemical biology
Paul Engel 40,647 HRB The molecular basis of autosomal dominant retinitis pigmentosa RP10: Studies of IMP dehydrogenase 1
Michael Casey 57,150 IRCSET Novel ligands for asymmetric catalysis
Jana Haase 14,500 HRB Regulation of serotonin transporter function by the neuronal SNARE protein syntaxin 1A
Paul Moynagh 37,050 IRCSET Novel adaptor proteins in Interleukin-1 and Toll-like receptor signalling pathways
Cliona O’Farrelly 552,000 HRB Characterisation Hepatitis C induced immunological subversion and its implications for treatment response
David Easty 5,000 Mater Misericordiae Hospital Pathology of typorine prospuate
Paul Engel 64,011 HEA/PRTLI Cycle 3 New biocatalysts
Geraldine Butler 311,347 Wellcome Trust Genome wide expression and functional analysis in Candida glabrata
Bernard Allan 999,734 Science Foundation Ireland Rule of the PPAR-gamma co-activator PGC-1 in the molecular programming of insulin sensitivity in human skeletal muscle cells.
David MacHugh 15,662 Teagasc Analysis of lengtic diversity in the Galway sheep breed
Brenda Brankin 112,890 Fighting Blindness Effects of Vascular Endothelial Growth Factors, Placental Growth Factor and Endostatin on blood barrier function
Paul Moynagh 248,203 HRB Toll-like receptors in human disease
Amanda McCann 63,704 Cancer Research Ireland E-cadherin promoter methylation status and C-MET/HGF expression levels in transitional cell carcinoma of the bladder
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Researcher Contract Total (Euro) Funding Agency Project Title
Grace Mulcahy 70,619 Enterprise Ireland Vaccine for the control of liver fluke in cattle and sheep
David Brayden 19,117 Pfizer Ltd Interactions of different avermectins with cellular P-glycoprotien efflux systems
Maurice Boland 15,000 Teagasc To evaluate the effects of genetic improvement practices on growth, feed efficiency and carcass composition and meat quality traits in beef animals
William Gallagher 238,975 HRB Clinical proteomics instrumentation
Ciaran Regan 53,730 Alltech Inc. Kentucky, USA Influence of Sel-Plex on cognitive functioning
Des Higgins 946,700 Science Foundation Ireland Multiple alignment method for the Genome ERA
Paul McLoughlin 88,500 HRB Stereological morphometry: Quantitative assessment of disease-induced angiogenesis and tissue remodelling
Andrew Green 0 European Commission-Non Framework Orpahnet
Michael J Duffy 186,720 European Commission FP6 Epigenetic profiling of breast cancer: prognostic and therapeutic applications
Evelyn Murphy 68,559 HRB Understanding nuclear orphan receptor function
John Baugh 49,500 Irish Lung Foundation Human MIF promoter polymorphisms and chronic inflamatory lung disease
Ciaran Regan 1,313,771 Science Foundation Ireland Applied Neurotherapeutics Research Group
Ciaran Regan 2,120,484 Science Foundation Ireland Applied Neurotherapeutics Research Group
Grace Mulcahy 50,000 Food Safety Promotion Board Cyrptosporidium Research Network
Ciaran Regan 36,920 Glaxo Smith Klein R&D The effect of 5-HT compounds in cognition
Keith Murphy 1,739,208 Science Foundation Ireland Applied Neurotherapeutics Research Group
Paul Murphy 824,752 Science Foundation Ireland Towards novel glycoconjuate based therapeutics for angiogenesis
William T O’Connor 1,706,276 Science Foundation Ireland Applied Neurotherapeutics Research Group
Ciaran Regan 321,803 Science Foundation Ireland Applied Neurotherapeutics Research Group
Madeline Murphy 294,065 Wellcome Trust, UK Characterisation of IHG-1, a novel diabetic-associated gene product, which amplifies Tc of B induced signalling
Grace Mulcahy 237,859 Enterprise Ireland Immunodiagnostics for emerging animal and human parasitic disease (IDEP)
William Hall 8,000 Food Safety Promotion Board Epidemiology and molecular analysis of Norovirus outbreaks in Ireland
Lorraine Kyne 33,653 National Institute of Ageing Ageing and the human antibody response to C. difficile
Amanda McCann 5,000 Mater College Postgraduate Molecular profiling of PRA, PRB and ER alpha as an indicator for endocrine therapy in breast cancer
Education & Research
Amanda McCann 5,000 Mater College Postgraduate Characterisation of the Mitotic Assembly Deficient proteins MAD and MAD2 in predicting breast tumour sensitivity
Education & Research to microtubule inhibitor (Taxol/Taxotere) chemotherapy
Paul Malthouse 25,000 Science Foundation Ireland Seventh International Conference on Reaction Mechanisms
Bat Masterson 11,000 EPA Consultancy work in support of the negotiations for a new EU bathing water directive
Leonie Young 56,255 St Vincent’s University Hospital Nuclear transcriptional regulation in breast cancer
Declan Gilheany 3,800 Enterprise Ireland P-chirogenic phosphine/phosphite hybrids as hydroformylation catalysts
Carmel Hensey 163,846 European Commission FP6 The function of the BMP antagonist gremlin in Xenopus eye development
Paul Engel 3,900 Enterprise Ireland Halophile Collaboration Travel Support 2004
Alan Keenan 2,200 Enterprise Ireland Drug-eluting stents: investigation of elution kinetics under dynamic flow and in vivo efficacy
William Gallagher 5,200 Enterprise Ireland Identification of new biomarkers in breast cancer
Bat Masterson 108,000 Alltracel Pharmaceuticals plc Biomolecular actions of microdispersed oxidised cellulose
R William G William 5,000 Mater Misericordiae Hospital The role of methylation in regulating proapaptatic protein resistance in relation to drug resistance in breast cancer
Eoin Casey 2,500 Enterprise Ireland Quantitative investigation of biofilm heterogeneity
Paul Murphy 155,011 European Commission FP6 Receptor clustering promoted by restricted divalent ligands
Declan Gilheany 57,600 Celtic Catalysts Synthesis of P-chiral ligands for use in asymetric catalysis
R William G William 4,000 Mater Misericordiae Hospital Heat shock protein and clinical response to cardiopulmonary bypass
R William G William 14,000 Mater Misericordiae Hospital Can individual variation in neutrophil function predict acute transplant rejection and postoperative infection?
Patrick Guiry 196,163 European Commission FP6 Ligbank
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Researcher Contract Total (Euro) Funding Agency Project Title
Michael Casey 57,150 IRCSET Synthesis of muscarinic receptor antagonists related to himbacine
Seamas Donnelly 152,728 HRB The CATT-repeat polymorphism in human MIF promoter confers genetic susceptibility to enhanced innate responses via upregulation of TLR4 expression
Barry Bresnihan 145,137 HRB Withdrawal of anti-TNF therapy in patients with rheumatoid arthritis in clinical remission
Pat Lonergan 13,600 Science Foundation Ireland
Bernard Allan 12,500 Science Foundation Ireland STAR Supplement
Paul Murphy 129,054 Science Foundation Ireland Stereoselective glycosidation with conformationally inverted donors
Patrick Guiry 168,837 Science Foundation Ireland Quinazoline and oxazoline-containing ligands for asymetric catalysis
William Gallagher 231,256 Science Foundation Ireland The role of fibulin-4 in the tumour growth and angiogenesis
Breandan Kennedy 224,268 Science Foundation Ireland Genome-wide screens for determinants of cone photoreceptor function
Finian Martin 168,350 Science Foundation Ireland Targets of glucocorticoid-JNK signalling in 3D-mammary epithelial cell assemblies
Eoin Casey 166,855 Science Foundation Ireland Investigation of the factors that determine physiological heterogeneity in biofilms
Matthias Tacke 129,640 Science Foundation Ireland Novel titanocene anti-cancer drugs
Caroline Herron 181,815 Science Foundation Ireland Investigation of inflammatory mediators in hippocampal synaptic transmission and plasticity
Tara McMorrow 204,200 Science Foundation Ireland Targets of immune mediated ephitelial-mesenchymal transdifferentiation
Paul Moynagh 212,777 Science Foundation Ireland Viral pellino: A novel regulator of Toll-like receptor signalling?
Evelyn Murphy 199,519 Science Foundation Ireland Modulation of matrix metalloproteinase gene expression by the nuclear orphan receptor NURR1
Derek Brazil 140,238 HRB Glucose and cytokine-induced tubulointerstitial fibrosis in diabetic nephropathy:
a genomic and in vivo approach towards identifying novel therapeutic targets
William Hall 49,941 National Institute of Infectious BSE Pathogenesis
Diseases, Japan
Derek Brazil 10,000 Irish Nephrological Society Investigating the signalling pathways involved in driving diabetic nephropathy
Evelyn Murphy 180,836 HRB Regulation of matrix metalloproteinase gene expression by the orphan receptor NURR1
Mark Rogers 14,000 European Commission FP6 NeuroPrion – Prevention, control, treatment, management and risk analysis of Prion diseases
Seamas Donnelly 60,000 The Cystic Fibrosis Association Macrophage migration inhibitory factor (MIF) and Cystic Fibrosis (CF) disease pathogenesis
of Ireland
Catherine Godson 181,286 HRB The role of ventroptin, a BMP antagonist, in diabetic retinopathy
Peter Rutledge 127,475 Science Foundation Ireland Peptide mimics of nitrile hydratases: crystallographic and mechanistic studies
Michael Ryan 20,000 Irish Nephrological Society Proteomic investigations of kidney and liver transplant rejection
Seamas Donnelly 40,000 Altana Pharma AG, Co. Dublin The CATT repeat polymorphism in human MIF promotor confers genetic susceptibility to enhanced innate responses via upregulation of TLR4 expression
John Baugh 200,835 IRCSET Hypoxic regulation of macrophage migration inhibitory factor and its role in fibroproliferation
Torres Sweeney 15,000 Teagasc Study of DNA polymorphisms and gene expression in candidate genes associated with meat quality, particularly intramuscular fat
Michael P Ryan 238,000 European Commission FP6 Short-term in vitro assays for long term toxicity (predictomics)
R William G Watson 5,000 Mater Misericordiae Hospital Stricture pathogenesis in Crohn’s disease
Philip Newsholme 26,000 European Commission FP6 Coordination action on the aetiology, pathology and prediction of type 1 diabetes in Europe
William Gallagher 18,500 Enterprise Ireland
Jens Erik Nielsen 136,100 HRB Protein kinase activation
John Baugh 133,160 HRB Regulation of macrophage migration inhibitory factor expression
Gethin McBean 121,900 HRB Do novel strucural analogues of MDMA (ecstasy) target monoamine transporters in the central nervous system?
Kevin Malone 79,802 American Foundation for A fMRI study of brain cortical networks involved in future thinking in health and during suicide depression
Suicide Prevention
William Gallagher 57,150 IRCSET Breast cancer metastasis: Biomarkers and functional mediators
Mohamed Al-Rubeai 2,165,489 Science Foundation Ireland Professor Al-Rubeai; SFI Investigator in Biochemical Engineering
Bat Masterson 3,750 EPA Consultancy work in support of the negotiations for a new EU bathing water directive
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ont’d
Researcher Contract Total (Euro) Funding Agency Project Title
Desmond Fitzgerald 13,415 HRB Nano-HPLC machine for high resolution proteomics
Oliver Fitzgerald 165,000 HRB Differential expression of VEGF, PIGF and the VEDF receptors in inflammatory arthritis
Paul Malthouse 57,150 IRCSET Optimising metallo and aspartyl protease inhibition
AnnMarie O’Donoghue 57,150 IRCSET Fluorocarbon bioremediation through mechanistic enzymology and evolution
Wilhelm Risse 57,150 IRCSET Late transition metal catalysed polymerisation of bicyclic and polycyclic olefins
Desmond Fitzgerald 100,000 Cardio Vascular Research Ltd Establishment of a molecular medicine group
Philip Newsholme 121,750 HRB Importance of the malate-aspartate mitochondrial shuttle to pancreatic beta-cell amino acid metabolism
Alan Keenan 19,850 Irish Heart Foundation Local delivery of anti-restenosis therapy: novel systems for simultaneous delivery of a statin and an anti-platelet agent
Philip Nolan 101,387 HRB The development and validation of physiological measures of pre-sleep arousal suitable for use in nursing research
Desmond Fitzgerald 48,958 HRB Cyclooxygenases in hypoxia-induced pulmonary hypertension
Des Higgins 51,336 Wellcome Trust Sanger Institute Setting up an orthologue database for nematode genomes
Desmond Fitzgerald 362,054 HRB Programme on cell regulation by cyclooxygenases; Novel therapeutic targets in cancer and inflammation
Desmond Fitzgerald 62,646 HRB Transcriptome and proteome analysis of platelet phosphoproteins
Desmond Fitzgerald 69,867 HRB Downstream effectors of cyclooxygenase-2 in colorectal cancer
Desmond Fitzgerald 123,587 HRB Regulation of gene expression by Cyclooxygenase-2 in cardiovascular tissue
Desmond Fitzgerald 142,500 HRB Cyclooxygenases in atherosclerosis: exploring the cardiovascular risk of COX-2 inhibitors
Desmond Fitzgerald 176,680 HRB DRAK2 as a novel effector of the anti-neoplastic effects of cyclooxygenase inhibition in colorectal cancer
Mark Crowe 15,000 Teagasc The welfare of animals during transport
Des Higgins 139,689 HRB Mining the human genome for micro-RNAs
William Gallagher 57,150 IRCSET Functional dissection of malignant melanoma.
Dominic Walsh 15,000 Science Foundation Ireland Neurodegeneration Ireland: Molecular Mechanisms of Neurodegeneration
Jens Erik Nielsen 1,199,800 Science Foundation Ireland Towards an understanding of enzyme catalysis: A multidisciplinary informatics-based approach
Michael P Ryan 137,100 HRB Mechanisms of immune mediated epithelial-mesenchymal transdifferentiation (EMT) in human kidney cells
Brian Glennon 57,150 IRCSET Development and optimisation of large-scale mammalian cell culture processes
Declan Gilheany 57,150 IRCSET C-substituted sugars by asymmetric oxidation
Dominic Walsh 83,095 IRCSET Elucidation of the normal function of proteolytic fragments of the APP protein family and their role in Alzheimer’s disease
Amanda McCann 169,252 HRB The significance of S100A4 and other novel candidate EMT markers as key modulators of the metastatic phenotype of TCCB
Grace Mulcahy 57,150 IRCSET Immunomodulation by Fasciola hepatica: Implications for animal health
Eoin Casey 57,449 Enterprise Ireland Development of a novel drug delivery system for biofilm associated infections
Paul McLoughlin 57,150 IRCSET Protective effect of hypercapnic acidosis in acute lung injury: A role for peroxynitrite.
Paul Murphy 78,073 European Commission FP6 LacClusters – Synthesis of clusters containing lactose and their biological and structural evaluation
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Appendix 3
Thesis Subm
issions during the period fromSeptem
ber 1st 2003 – September 30th 2004
Awarded Doctor of Philiosophy (PhD) during the period September 1st 2003 – September 30th 2004
Submission Date Thesis Title
Allen Lorcan Thomas 26/11/03 A Study of Cell-Biomaterial Interaction: N-isopropylacrylamide-based co-polymer films as a model system
Bergin Orla Eileen 18/09/03 Melanoma Progression: A Study of an Isogenic Cell Line Model Series
Breen Darragh 17/11/03 Polymerisations of Cyclic Monomers using Palladium(11), Aluminium(111) and Zinc(11) Catalysts
Byrne Barry Joseph Edward 10/09/04 Production of Novel Polyenes by Engineering Early and Late Stages of Amphotericin Biosynthesis
Canty Mary Jude 23/10/03 Role of the insulin-like growth factor system during the growth of the first follicle wave of the oestrous cycle in beef heifers
Carmody Marie 16/08/04 Engineered Biosynthesis of Novel Polyenes
Carrigan John Bosco 16/12/03 Discovering how a bacterial dehydrogenase selects its coenzyme
Carroll Anne-Marie 13/07/04 Novel Axially Chiral Phosphinamine Ligands for Asymmetric Catalysis
Connolly Ronan Philip 04/11/03 Conformations of Branched Polymers
Costello Derek Anthony 31/08/04 Mechanisms Underlying the Effects of ßAmyloid Peptide on Synaptic Transmission and Plasticity
in the Rat Hippocampal CA1 in Vitro
Curran Orla Marie 03/12/03 Dendritic Cell Priming of Newborn CD4+ Responses: Role of HSP70 as a Model Antigen
Curran Shane Anthony 08/04 Molecular Analysis of an Inflamatory T Cell Repertoire: Towards a New Paradigm in Psoriatic Arthritis
Dean Jonathan William Arthur 02/04 NKR+ Cells in Human Bone Marrow
Dixon Gordon Philip 19/12/03 The Role of Complement Activation, Fatty Acids, Glucose and Amino Acids in the Mechanisms
of Pancreatic Beta Cell Dysfunction Associated with Diabetes
Dolan Vincent 07/11/03 Gremlin and Induced in high glucose-1; two diabetic nephropathy associated genes with roles in development
English Niall J 07/04 Theoretical Studies of the Kinetics of Crystallisation in External Electromagnetic Fields
Fox Shona Mary 10/11/03 Synthesis and Spectroscopic Characterisation of Novel ansa-Metallocenes Using a Rationally Designed Organic Precursor
Gautier Virginie Wilhelmine Marc 16/01/04 Human I-mfa domain-containing protein, HIC, interacts directly with HIV-1 Tat resulting in the cytoplasmic sequestration of Tat
Hanratty Lynsey Sara 03/10/04 Phylogenetic and Molecular Clock Analysis of the Evolution of Human T-cell Lymphotropic Virus type II (HTLV-II)
in an Endemically Infected Kayapo Indian Population of Brazil
Hashim Amna O 26/07/04 Host cell interactions of human and bovine genotypes of Cryptosporidium parvum
Hegarty Nicholas 26/10/04 The Role of Endothelium-Derived Vasoactive Mediators in Chronic Ureteric Obstruction
Howlin Jillian 08/06/04 Differential Gene Expression in the Postnatal Mammary Gland: A Study on CITED1
Kavanagh Caroline Anne 19/12/03 Poly(N-isopropylacylamide/N-tert-butylacrylamide) Co-polymers as Novel Systems for the Delivery
of Vascular Endothelial Growth Factor in the Prevention of Restenosis
Kelly Sinead Norah 10/09/03 Transriptional Regulation of Key Steroidogenic Enzymes in the Human Adrenal Gland
Kelly Zoe 17/06/04 Insights into Tumour Progression via Transcriptomic and Phenotypic Analysis of Isogenic Cell Line Model Systems
Kelly Leanne 31/10/03 Investigation of the Role of N-linked Glycosylation and the Mechanisms of Heterologous and Homologous Desensitization
of the a and ß Isoforms of the Human Thromboxane (TX) A2 Receptor
Kenna Cliona 30/07/04 Analysis of protein-protein interactions of the human T lymphotropic virus (HTLV) regulatory proteins
Kenna Tony 19/04/04 Characterisation of CD1-restricted T cells in Adult Human Liver
Kennedy Eugene 24/02/04 The Human Prism Gene Family: Cloning and Molecular Characterisation
Kilroy Timothy Gerard 23/06/04 Further Studies in the Intermolecular Asymmetric Heck Reaction
Lynch Julie May 07/09/04 Mechanisms of Epithelial Mesenchymal Transition (EMT) in Human Renal Proximal Tubular Cells
Lynn David John 13/02/04 Bioinformatic Discovery & Evolutionary Analysis of Novel Innate Immunity Genes
Maher Declan Joseph 24/10/03 Studies on Ring-opening Olefin Metathesis Polymerisation and Model Reactions for the Addition Polymerisation of Bicyclic Olefins
Mangan Michael William David 10/06/04 Molecular Tool Development and Analysis of Virulence of the Intracellular Pathogen Rhodococcus equi
Matthews Jonathan Winston 09/01/04 Preparation and Applications of Tunable Imidazoline Ligands for Asymmetric Catalysis
McCrohan Oliver 20/04/04 Routes to Tailoring the Substrate Specificity of Phenylalanine Dehydrogenase
McDonnell Ciaran 03/11/03 Studies in Synthetic Carbohydrate Chemistry
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Awarded Doctor of Philiosophy (PhD) during the period September 1st 2003 – September 30th 2004
Submission Date Thesis Title
McManus Helen Anne 18/10/04 The Preparation of Bidentate and Tridentate Oxazoline – Containing Ligands and their Application in Asymmetric Catalysis
McCormack William 29/07/04 Functional studies on non-inhibitory serpins
Mitchell Derick Michael 22/12/03 Lipoxin A4 and Platelet-Derived Growth Factor Receptor Cross-Talk in Human Mesangial Cells
Mulvany Sean 06/07/04 The Role of Neuroplasticity Processes in Cerebellar – Dependent Learning
Nathwani Seema-Maria Mechanisms of Cisplatin-induced Apoptosis in Renal Proximal Tubular Cells
O’Brien Neil Andrew 13/10/03 Mammaglobin in Breast Cancer
O’Donnell Ruairi Aodh 15/10/04 The role of retinoids in memory and sensorimotor function: implications for the aetiology of schizophrenia
O’Rourke Alan Michael Patrick 13/10/04 A Study of Evolving Droplet Size Distributions in Agitated Liquid-Liquid Dispersions
O’Brien Alan 30/04/04 Synthesis of Monosaccharide Conjugates and Oligosaccharides Derived from Heparin and their Biological Properties
O’Meara Sarah Investigation into the Effects of the Novel Farnesyl Protein Transferase Inhibitors and Statins on Intracellular
Signalling and Function of the Prostacyclin Receptor
Pearson Alan Patrick 24/02/04 Scale-related Effects on the Growth of Filamentous Microorganisms
Ryan Aine 06/11/03 Computational and Synthetic Studies of Model Complexes for Mono- and Dinuclear Zinc Hydrolases
and their Inhibition by Hydroxamic acids
Seymour Claire Marie 11/11/03 Neural Cell Adhesion Molecule (NCAM), Fibroblast Growth Factor Receptor, and Cell-Cell Signalling
During Rodent Memory Consolidation
Sharkey Michael 16/07/04 Identification and characterisation of putative serpin genes from human EST and genome sequences
Ting Tung Leung Welfare, Immune Competence, and Pain Management Following Castration of Male Cattle
Tosin Manuela 22/04/04 Novel Synthetic and Structural Studies in Carbohydrates Chemistry
Wall Daniel Martin 12/03 The Role of Lactate and Lipid Metabolising Enzymes in Virulence of the Intracellular Pathogen Rhodococcus equi
Awarded Master of Surgery (MCh) during the period September 1st 2003 – September 30th 2004
Brannigan Ann Neutrophil apoptosis in inflammatory bowel disease
McLornan Lisa The role of PI3-kinase/AKT signaling pathways in prostate cancer
Shaw Colette Role of extra-cellular matrix proteins in Breast Cancer cell survival
Teahan Seamus Diethylmaleate in the treatment of Prostate Cancer
Awarded Master of Science (MSc) during the period September 1st 2003 – September 30th 2004
Bakhiet Salih Expression of Hypoxia Inducible Factor 1 (HIF-1) and Glucose Transporter 1 (Glut-1) in early stage colorectal carcinoma
Burke Lisa The developmental competence of oocytes in dairy heifers and cows
Griffin Wendy The effect of dosing propylene glycol to dairy cows during the early postpartum period or to heifers
on metabolic and developmental parameters related to fertility
Mooney Jean A study of small ruminant lentiviruses in naturally infected Irish goats
Awarded Doctor of Medicine (MD) during the period September 1st 2003 – September 30th 2004
Cooke Fiachra Joseph 22/11/2003 Epigenetic Control of ER and ER Gene Expression in Human Breast Cancer – A gene promoter methylation
and Immunohistochemical study
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March
Dr Grainne Cunningham, Conway Institute
Amino acid dependent changes in pancreatic
beta-cell function.
Dr Helen Roche, Clinical Medicine, Trinity Health
Science Centre, St James’ Hospital
Nutrient regulation of gene expression –
fatty acids & metabolic health.
Professor Philip Calder, Institute of Human
Nutrition, University of Southampton
Omega-3 fatty acids and inflammatory
gene expression.
May
Dr Diarmuid Moloney, Department
of Orthopaedics Cappagh Hospital
Biomaterials in orthopaedic implants.
Dr Eoin Casey, Chemical Engineering UCD
Prof Elizabeth Tanner, Dept of Materials and
Orthopaedics, University of Lund, Sweden.
CONWAY POSTDOCTORAL SEMINARS
Fourth Thursday of Month
January
Dr Steven Verhaegen, Conway Institute
Slices of Time – Time-lapse videomicroscopy
in cell biology.
Dr Christine Costello, Conway Institute
Dissection of Inflammatory Bowel Disease:
pathophysiology using high-density
cDNA microarrays.
February
Dr John Crean, Conway Institute
Connective Tissue Growth Factor:
a multifunctional signalling regulator.
Dr Joanne Gallagher, Conway Institute
Differential Gene Expression in Inflammation
and Resolution in Rheumatoid Arthritis.
March
Dr Francesca Paradisi, Conway Institute
Mutants of phenylalanine dehydrogenase:
versatile biocatalysts for the synthesis
of novel amino acids.
Dr Aedin Culhane, Conway Institute
Integration and analysis of microarray data;
a study of the NCI60 cancer cell line data.
April
Dr Martin Leonard, Conway Institute
Mechanisms of potentiated glucocorticoid
activity in hypoxia.
Dr Katherine Howell, Conway Institute
Role of nitric oxide in hypoxia-induced
angiogenesis in the adult mammalian lung.
May
Dr Sallyann O’Brien, Conway Institute
Biomarker Identification:
A Focus on Breast Cancer.
Dr Derek Brazil, Conway Institute
Signal transduction cascades in diabetes and its
related complications: from brain to kidney and
back again.
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POSTGRADUATE SEMINARS
First Thursday of month
February
Professor Suzi Jarvis, Nanoscale Function Group,
Trinity College Dublin
Investigating Molecular Function
with a Nano-mechanical probe.
Rhona Duane, Conway Institute
The biological evaluation of novel
glycosaminoglycans.
Brid Ryan, Conway Institute
Survivin and breast cancer.
Jonathan Lowther, Conway Institute
Inhibition of papain by a specific
glyoxal inhibit.
March
Simon Keely, Dept of Small Animal
Clinical Studies
In vitro intestinal cell models for assessing
mucoadhesion of polymers.
Derick Mitchell, Conway Institute
Lipoxin and PDGF receptor cross-talk in human
mesangial cells.
Aine Ryan, Department of Chemistry
Mono- and dinuclear zinc complexes as models
for zinc hydrolase enzymes and their inhibition
by hydroxamic acids – a computational and
synthetic study.
Carlo Largiader, Computational and Molecular
Population Genetics Lab, University of Bern
A population genomic approach to detect
patterns of phenotype and genotype correlated
gene expression.
MOLECULAR MEDICINE SEMINAR SERIES
Second Thursday of Month
February
Professor Tariq Sethi, University of Edinburgh, UK
CD98, Integrins & Cancer.
March
Professor Paul Noble, Yale University USA
CD44 & Inflammatory Disease.
April
Dr Fiona Watt, Cancer Research UK
Control of stem cell fate
in mammalian epidermis.
May
Professor Mauro Perretti,
Kennedy Institute UK
The neutrophil annexin-1 system.
June
Professor Noira Whyte,
University of Sheffield UK
Neutrophil apoptosis the innate immune
response to bacterial pathogens.
DISCIPLINE INTEGRATION SEMINAR SERIES
Third Thursday of Month
January
Dr Dominic Walsh, Conway Institute
Alzheimer oligomers – their production,
activity and inhibition.
Dr Veronica Campbell, Dept of Physiology,
Trinity College, Dublin.
Cannabinoids and neural fate.
Professor Brian Robertson,
Dept of Physiology & Pharmacology,
University of Strathclyde
Trails and trials in potassium channel physiology.
Appendix 4
Conw
ay Institute Seminar Series
Decem
ber 1st 2003 – May 30th 2004
081 <> 082
Conway Education Committee
Dr Clare O’Connor [Chair]
Ms Elaine Quinn
Prof Alan Baird
Dr Paula Byrne
Prof Don MacElroy
Dr David MacHugh
Dr Gethin McBean
Dr Amanda McCann
Dr Wim Meijer
Dr Grace Morgan
Dr Paul Moynagh
Prof Cliona O’Farrelly
Dr John O’Connor
Prof Stephen Pennington
Prof Denis Reen
Dr R William G Watson
Conway Seminar Committee
Dr Gethin McBean [Chair]
Dr Derek Brazil
Dr Sean Callanan
Dr Peter Rutledge
Dr Eoin Casey
Dr R William G Watson
Dr Alex Evans
Prof Alan Keenan
Dr Peter Smyth
Conway Outreach Committee
Ms Elaine Quinn [Chair]
Ms Grace Sexton
Ms Ciara O’Hanlon
Dr John Lowry
Dr Ann Marie O’Donoghue
Dr Geraldine Butler
Mr Joe Cremin
Ms Roisin O’Connor
Con
way
Ins
titu
te o
f B
iom
olec
ular
and
Bio
med
ical
Res
earc
hA
nnua
l Rep
ort
2004
|A
ppen
dice
s
Board of Management
Mr Denis Brosnan, formerly Chairman
& CEO of Kerry Group plc (Chair)
Dr John Brown FRS, Dyson Perrins Laboratory,
University of Oxford
Mr Maurice Keane, formerly Group CEO
of Bank of Ireland
Dr Michael Morgan, formerly of
The Wellcome Trust and CEO of the Sanger
Institute, Cambridge
Mr Ronan O’Caoimh, Trinity Biotech Plc
Ms Heather Ann McSharry, Boots Health Care
Prof Catherine Godson, Vice President for
Innovation & Corporate Partnerships, UCD
Prof Boyd Jones, Dean of Veterinary Medicine
Prof Owen Lewis, Dean of Engineering
Prof Michael Kennedy, Dean of Science
Prof Maurice Boland, Dean of Agriculture
Prof Maurice Fitzgerald, Dean of Medicine
Conway Building Management Committee
Mr Michael O’Sullivan [Chair]
Ms Emer Bonham
Dr John Stephens
Mr Paul Rooney
Ms Philippa Kavanagh
Mr Eric Leonard
Mr Melvin Fleming
Mr Paul O’Reilly
Mr Padraig O’Murchu
Ms Hilda Bohane
Mr Joe Cremin
Conway Safety Committee
Mr Michael O’Sullivan [Chair]
Ms Hilda Bohane
Dr Geraldine Butler
Dr Gerard Cagney
Dr William Watson
Dr Geraldine Butler
Mr Melvin Fleming
Dr Christine Costello
Dr Mark Pickering
Dr John Stephens
Mr Ross Collery
Ms Ciara O’Hanlon
Conway Core Technology
Management Committee
Mr Michael O’Sullivan [Chair]
Ms Catherine Moss
Ms Alison Murphy
Ms Janet McCormack
Ms Caitriona Scaife
Dr Alfonso Blanco
Mr George Keating
Dr David Cottell
Dr Peadar O’Gaora
Mr Colin Travis
Appendix 5
Conw
ay Managem
ent Structures
Con
way
Ins
titu
te o
f B
iom
olec
ular
and
Bio
med
ical
Res
earc
hA
nnua
l Rep
ort
2004
|C
onta
ct U
s
Directorate
Professor Pat Guiry, Chief Executive
Conway Institute of Biomolecular
and Biomedical Research,
University College Dublin,
Belfield, Dublin 4, Ireland
Telephone: (+353 1) 716 6700
Fax: (+353 1) 716 6701
Email: [email protected]
Web: www.ucd.ie/conway
Personal Assistant to Chief Executive:
Ms Ann Mooney
Telephone: (+353 1) 716 6702
Email: [email protected]
Assistant Director, Buildings
& Technical Services:
Mr Michael O’Sullivan
Telephone: (+353 1) 716 6705
Email: [email protected]
Business and Finance Manager:
Mr Peter Mangan
Telephone: (+353 1) 716 6704
Email: [email protected]
Communications & Education Officer:
Ms Elaine Quinn
Telephone: (+353 1) 716 6706
Email: [email protected]
Assistant Communications
& Education Officer:
Ms Grace Sexton
Telephone: (+353 1) 716 6922
Email: [email protected]
IT Officer:
Mr Paul O’Reilly
Telephone: (+353 1) 716 6722
Email: [email protected]
Facilities Manager:
Mr Eric Leonard
Telephone: (+353 1) 716 6721
Email: [email protected]
Facilities:
Mr Melvin Fleming
Telephone: (+353 1) 716 6709
Email: [email protected]
Receptionist/Executive Assistant:
Ms Verona Patchell
Telephone: (+353 1) 716 6700
Email: [email protected]
Executive Assistant
(Communications & Education):
Ms Ciara O’Hanlon
Telephone: (+353 1) 716 6720
Email: [email protected]
Executive Assistant (Finance):
Ms Bairbre Byrne
Telephone: (+353 1) 716 6708
Email: [email protected]
Getting Here
The Conway Institute of Biomolecular
& Biomedical Research is located on the
Belfield campus of University College
Dublin, 4 miles south of Dublin city centre
on the N11. Access to the college from the
N11 is via the Belfield flyover.
A detailed map of the campus can be
found on http://www.ucd.ie/maps/
campusmap05.jpg
Contact U
s
