Conway Focus Issue 13 March 2011

As part of his €20,000 prize, Brian will and establish if there is any link to the Centre of Excellence hosts workshop spend a international week in Waters laboratories in process of twinning.

A number of Conway development graduate Irish biopharmaceutical and postdoctoral researchers company, Sigmoid Pharma recently scooped the overall Innovation the Year award have recently been of recognised for at the inaugural Irish Timesin All-Island outstanding research national and Innovation Awards. The life-science SME, international competitions. founded by UCD pharmacology graduate, Dr

results in both academic outputs and the application of research toward clinical product development indigenous companies.”

Manchesterwith where their high value mass

tract is lined with cells that block the contents of the gut from leaking into the intestine. In an IBD patient, this barrier is broken and the contents of the gut leak out into surrounding areas. The research team in UCD Conway used a Addressing model of IBD by applying a newMs class of theand, international guests, Mary drugs asof hydroxylase inhibitors, Duff,known Director Nursing and Ms. Kay were able to almost completely reverse the Connolly, Assistant Director of Nursing for the symptoms of the disease.

spectrometry and specialist Commenting on equipment the Taylor collaboration, Dr advice said, will be at collaboration his disposal.with the Taylor Coulter “The The Participate programme focused on As a European Centre of Excellence, the laboratory clearly demonstrates the potential Ivan Coulter,of has actively collaborated with advanced treatment regimens for RA in the Department Rheumatology in St Vincent’s that can beConroy, realised through focused Dr. Patricia McGowan won the 8th St Dr Judith postgraduate Conway Fellow, Professor Cormac Taylor clinic, including practical aspects of biologic application of basic research.

The development University Hospital was chosen to host an since being granted a Science Foundation Luke’s Young Investigators Award for researcher without Drs Sean Ennis and Sally therapy carried in the accredited infusion of a smart economy will depend on like-minded Bone & Joint Unit expressed their hope that international two-day workshop on March Ireland industry research partnership award Ann Lynch inpartners UCDoptimal School of Medicine her presentation on ‘ADAMs: new “When we applied new drugs to our IBD collaborative identifying opportunities suite that provides care for RA the experience ofthese the multidisciplinary team in 2004.

26th & 27th 2010.

Sponsored by Roche players in breast cancer progression’. A &patients.

Medical Science was one of three model, the gut was tricked into thinking that it and realising basic and applied research In addition to lectures from Conway from St Vincent’s would provide a template for The Irish Times award researcher working recognises the stellar Pharma, the Participate workshop gave was being deprived of oxygen. This activated synergies.

This collaboration, initiated through senior postdoctoral scientists awarded KnomeDISCOVERY™ Fellows, Professors Oliver FitzGerald and innovative performance of Sigmoid Pharma in delegates to reproduce similar care and protective pathways, which in turn prevented a SFI research supplement, highlights the twenty rheumatologists from centres in the Education & Research Centre,in exome and heard comparative Douglassequencing Veale, delegates from clinical their application of research and development. the death of that line the potential that innovative indigenous companies facilities forthe thecells management of RA patients in St Vincent’s University Hospital with analysis packages.

Europe and Australia the07/05/2010 opportunity to 13:12 working The company has developed two new drug nurse aboutcan patient education, May 2010.qxd:Layout 1 copy Pagespecialists 3 gastrointestinal tract,” explained Professor with academia realise.” their respective countries.

Professor Joe Duffy, Dr McGowan technologies, LEDDS™ and SmPill™, which not witness the care of patients with rheumatoid screening and monitoring of biological Taylor. “Our pre-clinical trial data can now Taylor’s collaboration with Sigmoid Pharma has only enhance solubility and permeability received the the Royal Academy of Medicineof Judith will use KnomeDISCOVERY™ inform the next phase Sigmoid Pharma product therapies. arthritis (RA) at St Vincent’s. certainly been successful by these metrics with theIreland drug but can deliver it to targeted locations in bronze medal and €1000. development pipeline”. in her research on facio-audiothree co-authored publications to date in two of Back row (L-R): Dr John O’Connor, Gen Sec RAMI and in the gastrointestinal tract, including the symphalangism (FAS), a rare InUCD addition to Conway the product thatDrisPatrick currently in the highest ranking scientific journals in the SBBS and Institute; Buckley, colon.

Brian Morrissey, PhD student with developmental syndrome.

Workingof the RCSI, finalist; Dr Patricia McGowan, UCD SBBS is phase II clinical studies, Sigmoid Pharma field, Gastroenterology and Proceeding The SigmoidStephen Pharma-Taylor collaboration is and ConwayaInstitute, winner 8th Stformulation Luke’s Young of Professors Pennington and John with two Irish families each as with setthe developing LEDDS™-enabled National Academy of Sciences, wella as facilitating the development of a new Investigators Award; Dr Antoinette Powell, TCD, finalist; the hydroxylase inhibitor generation proprietary innovative products Armstrong (St Luke’s Hospital) won of tripletsofwhere only two children are therapeutic approach for the treatment of Mr Tom Walsh, President RAMI. Frontto row (L-R):about Prof dimethyloxaloylglycine (DMOG) bring and the creation high-skilled jobs.FAS, she the Waters postgraduate ‘identical’ twinsofand both have inflammatory bowel disease symposium (IBD) by bringing Donal Hollywood, Clinical Oncology TCD; effective, safe andProfessor targeted delivery of this competition for demonstrating hopesthan to identify distinctive spelling More 15,000 people in Ireland and together the research methodology of the Dr Catriona O’Sullivan, agent.

Medical Director St Luke’s potential therapeutic millions people worldwide are living with the Taylor group analytical with the proprietary Hospital; Dr Claire Donohoe, TCD, finalist. innovative, ideas through his variantsofthat could cause the disease symptoms IBD today.inCurrent liquid/emulsion An image ofresearch. thedrug frogdelivery peptidesystem, structure central variety of solutions order totherapeutic understand the proteomic options for this chronic debilitating disease are LEDDS®, developed Sigmoid Pharma.team to the work of a UCDbyConway research structural basis for the difference in biological very limited with surgery often being the only was selectedon asthe theaward, front cover image for the Commenting Professor Taylor activity. viable option. The Sigmoid product, currently said, delighted forscientific Dr Coulter and his April “We 2010are edition of the journal, in a phase II clinical study, uniquely enables Thisdelivery particular peptide, isolated from the team and indeed it reflects well our Biochimica et Biophysica Actaon (BBA); oral of aXT-7 powerful drug without partnership. A key driver of successful skin of systemic Silurana tropicalis, shows potential for causing side-effects.

Proteins & Proteomics. scientific research in 2010 is meaningful development as it has impressive isdrug a therapeutic target used in and the theactivity Under normal the gastrointestinal PhD student, Kalyana Venneti tract is lined with cells that block the contents results in bothconditions, academic outputs Irish biopharmaceutical development interaction academia with industry that Peptides inofthe skin of many speciesand of frog against theofof growth ofbowel bacteria and Candida treatment short of the gut from leaking into the intestine. In an application research towardsyndrome, clinical product company, Fellow, Sigmoid Dr Pharma recentlyHewage scooped Conway Chandralal have anti-bacterial and anti-fungal properties IBD patient, this barrier is broken and the development with indigenous companies.” the overall Innovation the Year award at albicans.

However, this potential as an antiwhere nutrients are not being correctly have determined theof3-dimensional as well as the Irish abilityTimes to lyseAll-Island or rupture contents of the gut leak out into surrounding the inaugural absorbed either due to severe solution structure of glucagon-like infective agent isthe restricted by itsintestinal haemolytic Commenting on Taylor collaboration, Dr mammalianAwards. cells. This innate areas. The research team in UCD Conway used Innovation The life-science SME, disease or surgical resection of a large peptide-2 (GLP-2) for the immunity first time activity.said, Coulter “The collaboration with the Taylor protects it from attack.

These properties ofDr a model of IBD and, by applying a new class of founded by UCDmagnetic pharmacology graduate, portion ofclearly the intestine. using nuclear resonance laboratory demonstrates the potential drugs known as hydroxylase inhibitors, were Ivan Coulter, has modelling. actively collaborated frog molecular skin peptides are exciting from visual the with A change the amino acid focused structure of the and This that can beto realised through able to almost completely reverse the Conway Fellow, Professor Cormac Taylor prospect of being developed into was selected as the cover image of “These results a valuable application of basic research.

The development XT-7 peptide canprovide create an analogue that symptoms of the disease. since being granted a Science Foundation therapeutically valuable anti-infective and antithe current1issue of the biochemical of a smart economy will depend like-minded insight into the structural andon functional retains anti-infective properties but without the Ireland industry research partnership May 2010.qxd:Layout copy 07/05/2010 Page in 3humans have Meta-analysis by UCD researchers ledaward by 13:12 collaborative of HIV we nefapplied are critical in new determining studies shown that non “When these drugs tothe ourrate IBD identifying opportunities journal, FEBS Letters. cancer properties ofpartners GLP-2 andactivity. itswith receptor in 2004.agents. complicating haemolytic The single Conway Fellow, Professor Denis Shields has of disease progression.

Denis progression associated gross model, the gut was trickedProfessor into thinking that it and realising was basic andcould applied research interactions, which help in the determined that there is no clear evidence deletions in the nef gene.

Shields believes that searches for modifiers The Irish Times award recognises the stellar amino acidThis substitution (glycine replaced by ConwayasFellow, Dr Chandralal Hewage and his was being deprived of oxygen. This activated of synergies. collaboration, initiated through design of novel therapeutic drugs that Acting an intestinal promoting that particular defectiveofgrowth viral sequences inin progression rates should focus on other innovative performance Sigmoid Pharma protective pathways, whichnow in turn prevented a SFI research supplement, highlights the lysine) improves the therapeutic potential of team carried out molecular modelling of the However, much at of the in the area to may be active theresearch GLP-2 receptor”, agent in the and large bowel, Coverand of April 2010 edition“Systematic of Biochimica evaluation et Biophysica the nef small gene or certain regions of the host viral factors. theirHIV-1 application of research and development. the death of the cells that line the potential that innovative indigenous companies date has been occurring based on observational or case XT-7 peptide its [G4K]XT-7 in a this naturally peptide.

(BBA); Proteins & says Dr Hewage.

GLP-2 promotes theanalogue expansion of the protein play aand significant role in new disease ofActa large quantities ofProteomics. data by bioinformatics The company has developed two drug gastrointestinal tract,” explained Professor working with academia can realise.” studies rather than rigorous, systematic epithelial mucosa and, consequently, progression. can be“Our just pre-clinical as importanttrial in refuting technologies, LEDDS™ and SmPill™, which not Taylor. data can now scientific evaluation.

This work by doctoral Taylor’s collaboration with Sigmoid Pharma has hypotheses thatphase are current in Pharma the literature, as better absorption of nutrients.

It does of only enhance the solubility and permeability Reference inform the next Sigmoid product HIV-infected patients can be categorised on candidatebeen Ravindra Pushker these set outmetrics to certainly successful it is in discovering unknown patterns”, he said. the drug but can deliver it tocell targeted locations this by stimulating crypt proliferation Conformational and molecularby interaction studies with development pipeline”. the basis of the number of years it takes for determine in a substantially larger sample set three co-authored publications to date in two of in thepreventing gastrointestinal tract, including the of glucagon-like peptide-2 with its N-terminal and cell death in the gut them to progress to AIDS. Some patients if any association between disease This research wasproduct fundedthat through Sciencein In addition to the ispeptide-2 currently the highest rankingexists scientific journals in the colon. extracellular receptor domain.

Kalyana C. Venneti, Solution structure of glucagon-like as the epithelium. maintain stable CD4 lymphocyte counts and progression and particular amino acid Foundation Ireland and University College phase II clinical studies, Sigmoid Pharma is field, Gastroenterology and Proceeding the2 Chandralal Hewage. FEBS Letters volume 585 of issue cover image of FEBS Letters, January 2011 do not go on Pharma-Taylor to develop AIDS even after more differences or deletions within the nef gene.

Dublin.

The Sigmoid collaboration is developing a LEDDS™-enabled formulation of National of Sciences, as well as the 21 JanuaryAcademy 2011 Glucagon-like peptide-2 than 10 years infection. (GLP-2) facilitating the of development of a new the hydroxylase inhibitor generation of proprietary innovative On a per patient basis, there was noproducts excess of therapeutic approach for the treatment of dimethyloxaloylglycine (DMOG) to bring about and thepatients creationwith of high-skilled Scientists are curious as to why these longLTNP one or morejobs. defective nef inflammatory bowel disease (IBD) bygraduate bringing A newnonfortnightly forum for Conway decided bywhen the members but is envisaged (thomas.scharzl@ucd.ie and postdoctoral effective, safe and targeted) delivery of this term, progressor (LTNP) patients do not sequences compared toitprogressors.

More 15,000 people in technology Ireland and together the research methodologybeoflaunched the and postdoctoral researchers that itthan willhigh include a mix of researchers, Dr David Gomez Reference: potential therapeutic agent. develop AIDS. This may reflectwill differences in While the frequency of amino acid millions of people worldwide are living with the Taylor group with the proprietary Meta-analysis to test the association HIV-1 Slattery nef amino in May initiative will give earlyoverviews,IBD informal and formal research (david.gomez@ucd.ie) and DrofCraig the host,2010. viral This genetics or environmental replacement at today. particular residues is indicative symptoms Current therapeutic acid differences and deletions with disease progression. liquid/emulsion drug delivery system, factors that could potentially be exploited for of rapid evolvement, permutation testing stage researchers the opportunity to talk about seminars, PhD viva rehearsals and career (craig.slattery@ucd.ie ) invite suggestions for Ravindra Pushker, Jean-Marc Jacquē, Denis C. Shields. options for this chronic debilitating disease are LEDDS®, developed by Sigmoid Pharma. the treatment of the that disease. showed thatwith residues with more replacements Journal of Virology, Apr 2010 p3644-3653 science and issues concern them in an development talks from within and beyond the forum schedule. very limited surgery often being the only tract is lined with cells that block the contents results in both academic outputs and the Irish biopharmaceutical development using single substrate enzyme catalysis metabolism and 1-not dimensional nuclear Conway Fellow, Professor J. Paul G.Taylor than expected were statistically significant.

Commenting on the award, Professor informalinenvironment with refreshments academia.

Forum committee members, PhD viable option.

The Sigmoid product, currently Studies model organisms have shown that ofcan thecheck gut from into theexperimental intestine. In an application of research toward clinical product company, Sigmoid Pharma recently scooped on leaking appropriate magnetic resonance (NMR).

Malthouse has developed three iPhone said, “We are delighted for Dr Coulter and his in a phase II clinical study, uniquely enables provided!

Content for the forum will be student Mr Thomas Schwarzl infection with nef-deficient virus shows an The researchers conclude that current data IBD patient, this barrier is broken and the development with indigenous companies.” the overall Innovation of the Year award at team and indeed it reflects well on our conditions for determining catalytic applications intended as experimental oral delivery of a powerful drug without provides no evidence that individual residues attenuated course ofTimes infection and some contents of the gut leak out into surrounding the inaugural partnership.

A Irish key driver ofAll-Island successful Commenting on the Taylor collaboration, Dr constants using EnzymeQA. The Scientists using NMR in their research planning aids for researchers and causing systemic side-effects. areas. The research team in UCD Conway used Innovation Awards. life-science SME, scientific research inThe 2010 is meaningful Coulter said, collaboration the Taylor ona http:// can avail of “The practical tips on with setting revision aids forpharmacology undergraduate and aapplications model of IBD can and,be by found applying new class of founded by UCD graduate, Under normal conditions, the gastrointestinal interaction of academia with industry that Dr laboratory clearly demonstrates the potential drugs known as hydroxylase inhibitors, were Ivan Coulter, has actively EnzymeQA, collaborated with itunes.apple.com/us/app/enzymeqa/ up experiments such as parameters postgraduate students. that can be realised through focused able to almost completely reverse the Conway Fellow, and Professor Cormac Taylor id412649030?mt=8 and signalofprocessing, interacting with AminoAcidQA NMRQA contain application basic research.

The development symptoms of the disease. being granted a Science Foundation NMR operators and even basic NMR asince series of questions and answers on of a smart economy will depend on like-minded Ireland industry research partnership award “When we applied these new drugs to our IBD collaborative identifying opportunities facts. Thosepartners researchers considering the topics of enzymology, amino acid in 2004. model, the gut was tricked into thinking that it and realising basic and applied research The Irish Times award recognises the stellar was being deprived of oxygen. This activated synergies. This collaboration, initiated through innovative performance of Sigmoid Pharma in protective pathways, which in turn prevented a SFI research supplement, highlights the their application of research and development. the death of the cells that line the potential that innovative indigenous companies The company has developed two new drug Meta-analysis by UCD researchers led by of HIV nef are critical determining the rate studies in humans havecan shown that non gastrointestinal tract,” in explained Professor working with academia realise.” technologies, LEDDS™ and SmPill™, which not Conway Fellow, Professor Denis Shields has of disease Professor Denis progression was associated with gross Taylor.

“Ourprogression. pre-clinical trial data can now Quinn Elaine Taylor’s collaboration with Sigmoid Pharma has only enhancethat the there solubility permeability determined is noand clear evidence of Shieldsthe believes that searches for modifiers of deletions in the nef gene. inform next phase Sigmoid Pharma product Communications & Education Officer certainly been successful by these metrics with the but can deliver itviral to targeted locations thatdrug particular defective sequences in progression pipeline”. rates should now focus on other development However, much of the research in the area to three co-authored publications to date in two of UCD Conway Institute of Biomolecular & Biomedical Research in gastrointestinal including thethe HIV-1 nef gene or tract, certain regionsthe of the host and viral factors. “Systematic evaluation datehighest has been basedscientific on observational case Inofaddition to the product is currently in the ranking journals inorthe colon.

College Dublin protein play a significant role in disease large quantities of University datathat by bioinformatics studies rather than rigorous, systematicof the phase clinical studies, Sigmoid Pharma is field, Gastroenterology and Proceeding Belfield, Dublin 4 progression. can beII just as important in refuting The Sigmoid Pharma-Taylor collaboration is scientificAcademy evaluation.

This work as bywell doctoral developing LEDDS™-enabled ofas National of Sciences, as the hypothesesa that are current in formulation the literature, Ireland facilitating the development of a new Investing in Your Future HIV-infected patients can be categorised on candidate Ravindra Pushker set out products to the inhibitor generation of proprietary innovative it ishydroxylase in discovering unknown patterns”, he said. therapeutic for of theyears treatment offor the basis ofapproach the number it takes determine in a substantially larger sample set dimethyloxaloylglycine (DMOG) to bring about and the creation of high-skilled jobs.

E: elaine.quinn@ucd.ie inflammatory bowel disease (IBD) by bringing them to progress to AIDS. Some patients if any association exists between disease This research wastargeted funded through effective, safe and delivery Science of this T: (+353-1) 716 6706 More than 15,000 people in Ireland and together the research methodology of the maintain stable CD4 lymphocyte counts and progression and particular amino acid Foundation Ireland and University College potential therapeutic agent. millions of people worldwide are living with the F: (+353-1) 716 6701 Taylor the proprietary do not group go on with to develop AIDS even after more differences or deletions within the nef gene.

Dublin. symptoms IBD today. Current therapeutic liquid/emulsion delivery system, W: www.ucd.ie/conway than 10 years ofdrug infection.

On a perfor patient basis, there was nodisease excessare of options this chronic debilitating LEDDS®, developed by Sigmoid Pharma.

Scientists are curious as to why these longLTNP patients with one or more defective nef very limited with surgery often being the only Commenting on the award, Professor term, non- progressor (LTNP) patientsTaylor do not sequences when to progressors. viable option.

Thecompared Sigmoid product, currently

Frog peptide structure selected for journal cover

collaborator Irish Times Innovation New 3-DConway visual of intestinalscoops growth promoting peptideAward

Bioinformatic analysis of HIV progression studies

Launch of Conway postdoctoral & graduate forum

Conway collaborator scoops Times Innovation Award New biochemistry applications forIrish iTunes store

Bioinformatic analysis of HIV progression studies

Success in EU FP7 call March Issue 13101 May2011 2010 Issue september 2007 Issue

Conway collaborator scoops Irish Times Innovation Award Recognising excellence in research

disease (CKD) and improve patient treatment, Conway researchers led by Dr. Tara McMorrow and Professor Michael Ryan have with particular focus on CKD arising from diabetes and hypertension. The multisuccessfully secured €485,500 in funding as disciplinary research consortium has 25 part of an overall award to the Systems May 2010.qxd:Layout 1 copy 07/05/2010 13:12 Page 3 partners (16 universities, 9 industry partners) Biology towards Novel Chronic Kidney from 15 countries and the project is due to run Disease Diagnosis and Treatment (SysKid) for five years. consortium under the European Union FP7 programme.

The UCD Conway team, including postdoctoral researchers Dr. Craig Slattery and Dr. Natalia Syskid (www.SysKid.eu) was established to Martin, will utilise cell culture and animal further our understanding of chronic kidney

models to identify processes involved in early CKD progression and investigate novel strategies for preventing and slowing the progression of the disease. These studies will be integrated with clinical and epidemiological studies across the consortium using systems biology methodologies in order to develop new diagnostic strategies and treatment options to prevent CKD development. Email tara.mcmorrow@ucd.ie for details of a PhD position currently available.

GlycoExtractor advances glycan data manipulation cells, tissues and fluids.

EUROCarbDB, a research infrastructure design Glycomics needs the supporting framework of extensive, well-curated databases and study funded by the EU 6th Framework Commercial packages that support HPLC flexible analytical tools. Currently, this field Programme. Prospective users can access the instruments cannot facilitate the extraction of GlycoExtractor tool on of study lacks the established, large quantities of data. In an effort to alleviate comprehensive and centralised data http://glycobase.nibrt.ie:8080/DemoGlycoExtra this bottleneck within high-throughput collections, standards and information ctor/mainPage. glycomic projects, the NIBRT team have reporting protocols that exist addition within development As latest to the ‘omic’ biomarkers for red meat and vegetable serum levelswith of vitamin are associated is lined cells thatDblock the contents results in both academic outputs and the Referencetract Irishthe biopharmaceutical developed a web-based tool that interfaces Research by Conway Fellow, Dr Oliver the function of worm Arl13b causes the complex traits including diabetes, GlycoExtractor: web-based interface forobesity, high genomics and field proteomics. of theAmarkers gut from of leaking into the intestine. In an application of research toward clinical product company, Sigmoid Pharma recently scooped of science, metabolomics shows intake. with disturbed glucose with the Waters chromatography software throughput processing of HPLC-Glycan data Blacque has revealed new information ciliary membrane to bulge and become mental retardation and even cancer. patient,Matthew this barrier is broken and the indigenous companies.” Natalia V. IBD theNatalia overallArtemenko Innovation of the Year awardpackage at to development improve andwith automate the export Researchers, Dr and Dr nutrition potential in the area of metabolism and cardiovascular disease.

Artemenko, P. Campbell, and Pauline about a gene implicated in Joubert of data to various misshapen as well for as affecting the ability M. of Rudd Journal contents of the gutResearch, leak out2010, into surrounding the inaugural Irish Times All-Island of Proteome 9 (4), pp Matthew Campbell from the National Institute file formats subsequent research.

New research led by Conway Using biofluids and food diaries from 160 Dr Oliver Blacque hopes that these findings Commenting on the Taylor collaboration, Dr 2037–2041 syndrome and related disorders other proteins to properly distribute within areas. The research team in UCD Conway used Innovation Awards.

The cerebellar life-science SME, analysis. The modular ofwere the tool of Bioprocessing Research & Training (NIBRT) is Coulter said,architecture “The collaboration with Fellow, Dr Lorraine Brennan individuals, researchers ablethe to Taylor have developed method to identify will ultimately lead by to aapplying greatera new a“We model of IBD and, class of founded by UCD pharmacology graduate, Drfacilitates characterised byRudd blindness, bone the the ciliary membrane. led by Conway(JSRDs), Fellow, Professor Pauline also manipulation of data from laboratory clearly demonstrates the potential understanding not only JSRDs, butwere also making strides in developing theother use data management identify metabolites associated with people who as respond to of supplementation drugs known hydroxylase inhibitors, Ivan Coulter, hascystic actively collaborated with have developedabnormalities, an open access, web-based systems. kidneys, that can be realised through focused alsodietary found that a fullyfrom functional of closely related ciliopathies such tovitamin almost completely reverse the Conway Fellow, Professor Cormac Taylor of metabolomics toand discover potential They different patterns 33 different able with D with respect to theasmarkers interface that facilitates extraction, querying developmental delay loss of muscle application of basic research.

The development The NIBRT Arl13b team groups. are nowSeveral working tothe integrate symptoms of theand disease. since being granted a Science protein is needed for the normal Meckel Gruber Bardet-Biedl and sharing of dietary HPLC-glycan data The generated biomarkers and ininFoundation food metabolites of the metabolic syndrome.

Thissyndrome, new tone and control. findings of thisGlycoExtractor of a with smartthe economy willofdepend on like-minded EUROCarbDB Ireland industry research partnership award high throughput processes. functioning of a protein transport system in as well as perhaps more common method is a move towards personalised identifying groups of people who were linked to specific food groups.

In “When we applied these new drugs to our IBD collaborative partners identifying opportunities research, provide a comprehensive highin 2004. funded through a Science framework to cilia.

This intraflagellar transport phenotypes model, the and gutassociated was tricked intocilium thinking that it and realising basicpatient and applied research nutrition being in awith position to advise respond specific dietaryof Ireland particular, O-acetlycarnitine wassystem associated models to identify processes involved in early disease (CKD) and improve treatment, Conway researchers ledto by Dr. Tara throughput HPLC data analysis platform for Glycosylation is the most common and Foundation Ireland President The Irish Times award recognises the stellar (IFT) makes contact with theinitiated ciliary through dysfunction such as mental retardation was beinggroups deprived of oxygen.

This on activated synergies.

This collaboration, CKD progression and investigate novel McMorrow diverse and Professor Michael Ryan (PIYRA) have with particular on CKD from structurally post-translational the storage andfocus annotation ofarising experimental specific of people based theirand interventions. with red meat intake and Young Researcher Award to Oliver innovative performance of Sigmoid Pharma in protective pathways, in turn prevented amembrane.

SFI research supplement, highlights the onmultithese results, they strategies obesity. for preventing andwhich slowing the modification proteins.

Morerecently than of allas in diabetes data. integration of Based next generation hypertension.

The successfullyof secured €485,500 in half funding metabolic phenotype rather than more phenylacetylglutamine with vegetable Blacque, were published the Theand their application of research and development. the death the cellsThese that line the will potential that innovative indigenous companies progression of theofdisease. studies gene products haveaward been shown to be lifestyle, genetics bioinformatic tools will further thehas proposed a new working model for Arl13b, disciplinary research consortium 25 part of an overall to has the Systems generic , ‘one size fits all’ approach.”

The link between diet, intake.

The company developed two new drug Journal of Cell Biology.

He notes “That Arl13b associates with ciliary gastrointestinal tract,” explained Professor working with academia can realise.” be integrated with clinical and epidemiological glycosylated.

With many specific glycans or development of unified approaches for universities, 9 industry partners) Biology towards Novel Chronic it functions at the ciliary membrane technologies, LEDDS™ and SmPill™, which not (16where and risk factors forKidney chronic diseases ispartners now Taylor.

“Our pre-clinical trial data can now membranes and is required for cilium across the consortium using systems glycoforms showing potential as cancer handling large scale glycomics data from 15 countries and the project is initiatives duemembrane to run Disease Diagnosis and Treatment (SysKid) One of seven genes associated with JSRDs, to regulate important ciliary Taylor’s collaboration with Sigmoid Pharma studies has only enhance the solubility and permeability of inform theBrennan, next phase Sigmoid Pharma product Lorraine and her colleagues in the a focus international With diet Commenting on these findings, Dr Brennan biology methodologies in order to develop new with applications in been biomarker discovery biomarkers, isthe anof increasing needresearch. to structure/function in both worms and for five consortium there under European FP7 certainly successful by transmembrane these metrics with the drug but can it to targetedknown locations Arl13b codes fordeliver a Union protein already to years. properties such as shape, development pipeline”.

NIBRT researchers Dr Matthew Campbell and Dr Natalia diagnostic strategies and treatment options to UCD Institute of Food & Health and being a major contributory factor to the says, “By identifying these biomarkers, develop high throughput, highly sensitive and mammals demonstrates the remarkable programme. three co-authored publications to date in two of in theroles gastrointestinal tract, including theThe This UCD research wasteam, partially supported by play in the and/or function protein distributions and IFT. ArtemenkoCKD who development. developed GlycoExtractor Conway including postdoctoral Email robust strategies that detail the formation glycome of University College Cork,that are now in the increase in metabolic diseases such as we highest are taking a significant step forward in evolutionary conservation ofishow this small In addition to the product currently in the ranking scientific journals in theprevent colon. of cilia, which hair-like projections researchers Dr. Craig Slattery and Dr. Natalia Syskid (www.SysKid.eu) wasare established to tara.mcmorrow@ucd.ie for details of a PhD phase II clinical studies, Sigmoid Pharma is field, Gastroenterology and Proceeding of the process offunctions.” expanding both of these studies obesity, diabetes and cardiovascular developing theyears novel concept of nutritype.

Up to only 20 ago, many believed G-protein extending from the surface of the cell.Martin, will National utilise cell cultureofand animalas well as the position developing currently available. further our understanding of chronic kidney The Sigmoid Pharma-Taylor collaboration is a LEDDS™-enabled formulation Academy Sciences, to assess applicability in larger cohorts of and, disease, a the reliable dietary assessment The ability a metabolic most cilia totobeproduce redundant cellular profile facilitating the development of a new However, precise molecular details of Reference the hydroxylase inhibitor generation of proprietary innovative products organelles that have fallen victim to in respect of the latter study, to other dietary method is crucial to understanding this link. that reflects patterns of dietary intake therapeutic approach for the treatment of Joubert syndrome Arl13b functions at ciliary what exactly Arl13b is doing in cilia have dimethyloxaloylglycine (DMOG) to bring about and the creation of high-skilled jobs. mammalian evolutionvaluable - a type as of part cellular interventions.

This work has beenoffunded by could be extremely of membranes andand stabilizes protein transport in inflammatory bowel disease (IBD) by bringing effective, safe targeted delivery this remained unclear.

More than 15,000 people in Ireland and Caenorhabditis elegans. Cevik Hori Y, KaplanFood OI, appendix.

We now know that these cellular together the research methodology of the the Irishtherapeutic Department of S, Agriculture, The small molecules or metabolites that dietary assessment in the clinical setting”. potential agent.

Kida K, Toivenon T, Foley-Fisher C, Cottell D, Katada T, people worldwide living Taylor group withstudied the proprietary Blacque’s team the gene within in the cilia antennaeofpresent on nearly are all of ourwith cellsthe and Fisheries. complex processes the likely millions Commenting research, DrBiol.

Kennedy most to die as aIBD result of the raised New research result led byfrom Conway Fellow Dr system, Kontanion K, the Blacque OE. J Cell 2010 Mar 22; symptoms today.

Current therapeutic liquid/emulsion drug delivery of tiny worms (Caenorhabditis elegans) and serve fundamental roles in many cell are influenced both by endogenous As well as gaining insight into the habitual glucose levels seen in diabetes.

Breandán Kennedy indicates that treatment said, “By establishing a robust model for early 188(6):953-69 options for this chronic debilitating disease are LEDDS®, developedframework

by Sigmoid Pharma.

Glycomics needs the supporting cells, tissues and fluids.

EUROCarbDB, a research infrastructure design while inatsex, the University motility andwith sensory functions, including of diabetic blindness should factorscollaborators (such aslook age, genes andofdisease) very dietary patterns of individuals, thistheresearch and late stageby diabetic we would Reference surgery being only of extensive, well-curated databases and study funded the EUretinopathy, 6th Framework Dr Kennedysignalling andlimited his team found thatoften new blood Commenting on the award, Professor Taylor conducted parallel experiments in pathways critical to development. protecting the Tokyo neurons responsible for colour Commercial packages that support HPLC hope to better understand the progression option.

The Sigmoid and exogenous factors (such group have also profiling Programme. Prospective users can access of the flexible analytical tools. Currently, this fieldas diet and vessels andviable the neuronal cellused deathmetabolomic inproduct, diabeticcurrently May 2010.qxd:Layout 1delighted copy 13:12 Page 3 said, “We arejust for07/05/2010 Dr and his vision in the eye and not targeting theCoulter cultured human cells. Together, they instruments cannot facilitate the extraction of enables the disease andtool pave for identifying in amonitor phase II clinical study, uniquely O’Sullivan A, Gibney MJ, Brennan L. Dietary intake Using nuclear magnetic resonance to specific dietary interventions.

GlycoExtractor onthe way of study lacks drugs). the established, retinopathy can arise independently of each It is now not surprising that defects in team indeed it reflects well on our blood vessels confirmed as is and currently the practice. large quantities of data.

In an effort to alleviate oral delivery of a powerful without new drug targets its successful treatment”.

Arl13b patterns arefor reflected in metabolomic profiles: comprehensive and centralised dataproteins uses lipid http://glycobase.nibrt.ie:8080/DemoGlycoExtra In addition, they identified thatdrug cone (NMR) andthat mass spectrometry, cilium structure and function are associated partnership.

A key driver of successful other. this bottleneck within high-throughput causing systemic side-effects. potential role in dietary assessment studies. American anchors to associate with the ciliary photoreceptor collections, standards and information ctor/mainPage. neurons, those involved in that vitamin Nearly 2.5 million people worldwide are blind multivariate analysis of metabolites can There is evidence to suggest D The research was funded through Science scientific research in 2010 is meaningfulglycomic with an the everNIBRT expanding projects, team range have of human Journal Clinical Nutrition 2011 93:314-321. In press reporting protocols that exist within membrane. colour vision and normal used inconditions, daylight, are most due to diabetic retinopathy.

This secondary Reference gastrointestinalFoundation Ireland and the Health Research interaction of academia with industry that provide a chemical profile of activity within aUnder status may a role inthethe developed web-based tool that interfaces andplay syndromes, GlycoExtractor: A web-based interface for high genomics andofproteomics. affected by diseases the high glucose levels. collectively called complication diabetes activates the growth Board. with the Waters chromatography software O’Sullivan A, ofGibney MJ, O Connor cells. development of diseases related to the throughput processing HPLC-Glycan data A, Mion B, Much of the work on the project was carried ciliopathies, which have overlapping clinical of new leaky blood vessels in the eye and is Researchers, Dr Natalia Artemenko and Dr package to features improve and automate the export S, Cashman KD, Flynn A,and Shanahan Artemenko, Matthew P. Campbell, PaulineF, Natalia V. Kaluskar research team made their observations metabolic syndrome.

This syndrome UCD candidate, SebihaThe such as polycystic kidneys andis the responsible forout theby death ofdoctoral photoreceptors, M. Rudd Journal Research, 2010, 9 (4), pp BrennanofL.Proteome (2010) Biochemical and Metabolomic Matthew Campbell from the National Institute of dataa to various file formats subsequent using novel zebrafish model for of diabetes, the neurons that send visual messages to our New findings by this team show that collective name for a group of risk factors Reference: Cevik.

She and her colleagues went on to livers, retinal degeneration, bone 2037–2041 Phenotyping in the Identification of a Vitamin D analysis.

The modular architecture the tool of Bioprocessing Research & Training (NIBRT) which resembles the early stages ofofdiabetic brain.

Predominant coneatphotoreceptor dysfunction a the Metabolic demonstrate in C. elegans how abnormalities, hydrocephalus, as well metabolic profiling of urine candisrupting reflect that occur together and increase riskas ofmodels Arl13b ciliary membrane Responsive Metabotype Markersininof led

by Conway Fellow,led Professor Pauline Rudd also facilitates the manipulation of data from retinopathy in humans.

It is an exciting disease (CKD) and improve patient treatment, to identify processes for involved early Conway researchers

by Dr. Tara hyperglycaemic model of non-proliferative diabetic Syndrome.Molecular Nutrition and Food Research.In dietary patterns ofweb-based individuals. stroke, disease and type CKD IIretinopathy. have developed an open access, otherparticular data management systems. development for thecardiovascular group who now hope to Until now, itand was unclear if Michael the changes tohave The study, progression and investigate novel McMorrow Professor Ryan with focus on CKD arising from Yolanda Alvarez, Jenneth Chen, Alison press DOI 10.1002/mnfr.201000458 interface that facilitates extraction, querying further extend their research and establish vessels and neurons occurred independently of published recently the American Journal diabetes.

Research findings by agroups strategies for Waghorne, preventing and slowing the Reynolds, Nore John J. O’Connor, Breandan diabetes and hypertension.

The multisuccessfully secured €485,500 ininfunding as The NIBRT team are now working to integrate and sharing of which HPLC-glycan dataSystems generated model of late stage diabetic disease. one type of the retinal neuron isin Kennedy. Disease & Mechanisms (2010) will of Models the disease.

These studies Clinical Nutrition, identified two novel working inconsortium this area suggest disciplinary research has 25 that low progression partother of anand overall award to GlycoExtractor withinthe EUROCarbDB high throughput processes. by UCD researchers led partners Meta-analysis by of HIV nef are critical in determining the rate studies humans have shown that non be integrated with clinical and epidemiological (16touniversities, 9 industry partners) Biology towards Novel Chronic Kidney framework provide a was comprehensive highConway Fellow, Professor Denis Shields has of disease progression.using Professor Denis progression associated with gross studies across the consortium systems from 15 countries and the project is due for to run Disease Diagnosis and Treatment (SysKid) throughput HPLC data platform Glycosylation isdetermined the most common that thereand is no clear evidence Shields believesinthat searches for modifiers of deletions in analysis the nef gene. biology methodologies order to develop new for five years. consortiumdiverse under the European Union FP7 structurally post-translational the storage and annotation of experimental that particular defective viral sequences in progression rates should focus on otherin diagnostic strategies and treatment toMSc larger programmes suchnow asoptions the new We introduced 4ofnew advanced core am delighted to welcome you to thedata. The integration programme.ofI proteins. modification More than half of all of next generation However, much the research in the area to the HIV-1 nef gene or certain regions ofThe theUCD Conway team, including postdoctoral hostdevelopment. and viral factors.

“Systematic evaluation prevent CKD Email gene products Conway have been shown be role bioinformatic tools further date haswill been basedthe on case technology modules onobservational a pilot basis or this Focus andtolook forward to working Imaging commencing in by September 2010. protein play a significant of large quantities data researchers Dr. Craig Slattery and Dr. Natalia Syskid (www.SysKid.eu) was established toin disease tara.mcmorrow@ucd.ie forofdetails ofbioinformatics a PhD development of unified approaches for glycosylated.

With many specific glycans or studies rather than rigorous, systematic academic year; those covering principlesposition currently progression. can be justavailable. as important in refuting with you in the comingkidney months!

Martin, will utilise cell culture and animal further our understanding of chronic scale glycomics dataoutputs initiatives glycoforms showing potential as cancer scientific evaluation.

This work byand doctoral tract is lined that with are cellscurrent that block contents results in both academic theapplied Irish biopharmaceutical development handling large in initiatives, thethe and practical aspects ofchemistry imaging and Ihypotheses hope that a number of Icompany, amisdelighted to welcome Dr Ian scooped Barwick, With ainbackground intoward over funding isfrom testament notnew only toliterature, the In anas biomarkers, there an increasing need with biomarker discovery HIV-infected patients can betorecently categorised on applications candidate Ravindra Pushker setclinical out and toproduct of the gut leaking into the intestine. application of research Sigmoid Pharma it is in discovering unknown patterns”, he said. proteomics in in latethe March and willset run researchers Business Development for for 18 years experience pharmaceutical scientific credentials of the investigators NIBRT Dr Matthew Campbell and Dr Natalia As institute anofincreasingly including the researcher forum develop high throughput, highly sensitive and basis of the with number ofManager years it award takes determine inbegan a substantially larger sample IBD patient, thisearly-stage barrier is broken and the development with indigenous companies.” the an overall Innovation the Year at This research was partially supported by from Artemenko who developed GlycoExtractor the Conway, Systems Biology Ireland & industry, Ian comes to UCD Bangor involved but also to the collaborative until mid-June with a further two modules in robust strategies that detail the glycome of them to progress to AIDS. Some patients if any association exists between disease This research was funded through Science contents of in thethis gutissue, leak out the inaugural Irish Times All-Island interdisciplinary research focus and described willinto notsurrounding only Commenting onflow the Taylor collaboration, Dr as areas.

Charles thelife-science directorate team.

University, Wales where he spent years strength manifests maintain Institute stable CD4toThe lymphocyte counts and progressionand and particular amino acid4 place Foundation Ireland and University Collegeused Thethat research team inwith UCDcrossConway Innovation Awards.

SME, genomics cytometry taking expertise in specialist technology platforms, strengthen the community of Conway Coulter said, “The collaboration with the Taylor Ian willgobe in driving our strategic Technical Director for within Intellectual Property do not to develop AIDS even after more differences or deletions thethe nefsummer gene.

Dublin. ainstitutional model of IBDinteractions. and, by applying a new class of founded byonpivotal UCD pharmacology graduate, Dr over week-long periods during laboratory clearly demonstrates the potential we are uniquely placed to participate in the researchers forge new inhibitors, interdisciplinary than Coulter, 10 yearsagenda of infection. drugs known and as hydroxylase were Ivan has actively collaboratedthe with innovation and maximising and Commercialisation. months.

Onand acan per patient basis, there focused was no excess EUROCarbDB, of that be realised through cells, tissues fluids. a research infrastructure design Glycomics needs the supporting framework able almost completely reverse the Conway Fellow, Professor Cormac Taylor impact of ourcurious relationships with industrial education and training ofto the next linkstobut will celebrate heighten Professor Walter Kolchand Scientists are as why these longLTNP patients with one or more defective nef application of basic research.

The development study funded by the Framework of extensive, well-curated databases and symptoms of EU the 6th disease. since beingof granted a Science Foundation partners. Specifically, he aims to The attract Congratulations towill Professors Geraldine generation research scientists. newly Commercial packages that support HPLC awareness of ourusers research innovation Director term,tools. non- progressor (LTNP) patients do not sequences when compared tothis progressors. of a hope smart to economy depend on like-minded We determine from pilot if Programme.

Prospective can and access the flexible analytical Currently, thispartnership field Ireland industry research award new collaborative research funds and Reference: Butler and Denis Shields as they launch instruments cannot facilitate the extraction of develop AIDS. This may reflect differences in While the high frequency of amino acid “When we applied these new drugs to our IBD collaborative partners identifying opportunities PhD programme in Bioinformatics successes. of study lacks launched the2004. established, GlycoExtractor tool to ontest the association in demand for training from within UCD as well Meta-analysis of HIV-1 nef amino identify opportunities for new product/ the Wellcome Trust UCD PhD programme large quantities of data.

In an effort to alleviate the host, viral genetics or environmental replacement at particular residues is indicative model, the gut was tricked into thinking that it and realising basic and applied research Commenting on the research, Kennedy most likely to die as a result of the raised New research and led by Conway Fellow Dr http://glycobase.nibrt.ie:8080/DemoGlycoExtra comprehensive and centralised data acid differences and deletionsDr with disease progression.

Systems Biology recently attracted 80bottleneck as from external academic centres and The Irish Times award recognises the stellar process development with industry this within high-throughput in Computational Infection Biology.

Their factors that could potentially be exploited for of rapid evolvement, permutation testing was being deprived of oxygen.

This activated synergies.

This collaboration, initiated through glucose levels seen in diabetes.

Breandán Kennedy indicates that treatment said, “ByRavindra establishing robust model for early Pushker,aJean-Marc Jacquē, Denis C. Shields. collections, standards and information ctor/mainPage. innovative performance of Sigmoid in Professor WalterAprKolch EU 120 non-EU applicants forPharma up glycomic to 15 will dictate stand-alone delivery projects, the NIBRT team partners. the and treatment of look the disease. showed that residues withhave more replacements Journal of Virology, 2010 p3644-3653 pathways, which inwe turn prevented aindustry SFI research supplement, highlights the of success in securing such competitive of diabeticprotocols blindness should at and lateprotective stage diabetic retinopathy, would reporting that exist within Reference their application of research and development.

Dr Kennedyapotential and his team found that new blood developed web-based tool that interfaces than expected were not statistically significant. the death of the Conway cells that line the that innovative indigenous companies these advanced modules or inclusion within Director, UCD Institute protecting and the studentships. neurons responsible for colour hope to better understand the progression of A web-based interface for high GlycoExtractor: genomics proteomics.

Studies in model organisms have shown that theand The company has developed two new drug vessels the neuronal cell death in diabetic with Waters chromatography software gastrointestinal tract,” Professor working with academia can realise.” processing of HPLC-Glycan throughput vision in the eye and not just targeting the the disease and pave the wayexplained fordata identifying infection with nef-deficient virus shows an The researchers conclude that current data technologies, LEDDS™ and SmPill™, which not retinopathy can arise independently of each Researchers, Artemenko and Dr package to improve and automate the export Natalia V. Taylor.

Artemenko, Matthew P. Campbell, and can Pauline “Ourfor pre-clinical trial data now blood vesselsDr asNatalia is currently the practice. new drug targets its successful treatment”. provides noformats evidence that individual residues attenuated course of infection someof Taylor’s collaboration with Sigmoid hasRudd only enhance the solubility andand permeability of Intoaddition, other. they identified that cone Pharma M. Journal Proteome Research, 2010,Pharma 9 (4), ppproduct data various file for subsequent Matthew Campbell from the National Institute inform of the next phase Sigmoid 2037–2041 certainly been successful by these metrics with the drug but can deliver it to targeted locations photoreceptor neurons, those involved in Nearly 2.5 million people worldwide are blind of Bioprocessing Research & Training (NIBRT) analysis. The modular architecture of the tool The research was funded through Science development pipeline”. three co-authored publications to date in two of the gastrointestinal tract, including thealso colour vision and used in daylight, are most dueby to Conway diabeticin retinopathy.

This secondary led Fellow, Professor Pauline Rudd facilitates the manipulation of data from Foundation Ireland and the Health Research In addition to the product that is currently in the highest ranking scientific journals in the affected bymanagement the high glucose levels. complication ofcolon. diabetes activatesweb-based the growth other data systems. have developed an open access,

Conway collaborator scoops Irish Times Worm research reveals cilia disease geneInnovation functionAward Towards personalised nutrition

Success in EU FP7 call

Zebrafish model gives insights into diabetic blindness GlycoExtractor advances glycan data manipulation

Success in EU FP7 call

Bioinformatic analysis of HIV progression studies

Director’s Message

Conway collaborator scoops Irish Times Innovation Award Director’s Message

GlycoExtractor advances glycan data manipulation

Zebrafish model gives insights into diabetic blindness

UCD CONWAY INSTITUTE OF BIOMOLECULAR & BIOMEDICAL RESEARCH

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Conway collaborator scoops gene Irish Times Innovation Award Novel regulator of photoreceptor expression

Conway collaborator scoops Irish Times Innovation Award ConwayTrust collaborator Irish Times Innovation Award First Welcome fundingscoops for Irish based PhD Programme Irish biopharmaceutical development company, Sigmoid recentlythe scooped For first timePharma in itsdevelopment history, Irishthe biopharmaceutical the overallSigmoid Innovation of therecently Yearfunding award at company, Pharma scooped Welcome Trust has awarded the Irish Times All-Island the inaugural overall of the Year award The at for an IrishInnovation based PhD programme.

Innovation Awards.

The life-science SME, the inaugural Irish Times All-Island UK charitable foundation will provide founded byof UCD graduate, Dr Innovation Awards.

The life-science upwards €3 pharmacology million towards aSME, fourIvan Coulter, haspharmacology actively collaborated with founded by UCD graduate, Dr year structured UCD PhD programme Conway Fellow, Cormac Taylor Ivan Coulter, hasProfessor actively collaborated with in Computational Infection Biology.

Conway Fellow, Professor Cormac Taylor since being granted a Science Foundation since being granted a Science Foundation Ireland industry research partnership award The UCD PhD Programme will contribute Ireland industry research partnership award in 2004. to one of the Wellcome Trust’s major in 2004.

The Irish Times award recognises research challenges, namely tothe stellar The Irish Times recognises the stellarin understand theaward emergence, transmission, innovative performance of Sigmoid Pharma innovative performance of Sigmoid Pharma pathogenesis and control of acute and in their application of research and development. theircompany application research chronic infectious diseasesand atdevelopment. the The hasofdeveloped two new global drug The company LEDDS™ has developed two new which drug not level. technologies, and SmPill™, technologies, LEDDS™ and and SmPill™, which not only enhance the solubility permeability of only enhance the solubility andwill permeability of “The research the drug but canprogramme deliver it to targeted locations the drug but the can deliver to targeted locations investigate basistract, ofit pathogenicity in the gastrointestinal including the in thevirulence gastrointestinal tract, including the and in infectious organisms colon. colon. from viruses (such as human ranging May 2010.qxd:Layout 1 copy 07/05/2010 13:12 immunodeficiency virus (HIV), hepatitis The collaboration is The Sigmoid Sigmoid Pharma-Taylor Pharma-Taylor collaboration is B, and influenza) to bacteria facilitating of aa causing new facilitating the the development development of new malaria, TBapproach and other diseases, therapeutic for major the treatment treatment of and therapeutic approach for the of fungi, which bowel grow disease on indwelling inflammatory (IBD) by bymedical bringing inflammatory bowel disease (IBD) bringing devices,”the says programme director, together methodology of the the together the research research methodology Professor Geraldine Butler, UCDofSchool Taylor group with the proprietary of Biomolecular & Biomedical Science liquid/emulsion drug delivery system, and UCD Conway Institute.

LEDDS®, developed by Sigmoid Pharma.

“The areas ofoninvestigation will Taylor Commenting the award, Professor include response infection, for Drto Coulter and his said, “Wethe arehost delighted identifying therapeutic team and indeed it reflectstargets well on and our partnership. A A key key driver driver of partnership. of successful successful scientific research research in in 2010 scientific 2010 is is meaningful meaningful interaction of of academia academia with interaction with industry industry that that

results in both academic outputs and the application ofnovel research toward product developing drugs.

Oneclinical aspect results in both academic outputs and the development indigenous unique to University College Dublinproduct is application of with research towardcompanies.” clinical that the programme will investigate development indigenous companies.”Dr Commenting with on the Taylor collaboration,

pathogenesis in both animals and man, Coulter said, “The collaboration with the Taylor Commenting on the Taylor collaboration, Dr addressing the ‘One World, One Health’ laboratory clearly demonstrates the potential Coulter said, “The collaboration with the Taylor initiative, linking human, animal and that can beclearly realised through focused laboratory demonstrates the potential environmental health.”

application basic through research.focused The development that can be of realised application of basic research.

The development of a smart economy will depend like-minded Advances in the developmenton of new of a smart economy will depend on like-minded collaborative partners identifying opportunities high-throughput scientific techniques collaborative partners identifying opportunities and realising basicenormous and appliedamounts research have generated and realising basic appliedinitiated research synergies.

This collaboration, through of data relevant toand infectious disease synergies.

Thissupplement, initiated through a SFI research the research that iscollaboration, currently highlights under-utilised, apotential SFIto research supplement, highlights the due a that lackinnovative of methodologies and indigenous companies potential that innovative indigenous suitably trained scientists. working with academia can realise.”companies working with academia can realise.”

Taylor’s collaboration with Sigmoid Pharma has The newcollaboration UCD PhD programme Taylor’s with Sigmoid aims Pharma has certainly been successful by these metrics with to address this by equipping students certainly been successful by these metrics with three co-authored publications to date in two of with skills necessary to negotiate three the co-authored publications to date in two of the highest ranking scientific journals in the the culturalranking and linguistic the highest scientific barriers journals in the field, Gastroenterology andbiological Proceedingand of the the that currently separate Page 3 field, Gastroenterology and Proceeding of National Academy Academyresearch of Sciences, Sciences, as well well as as the the computational disciplines.

National of as generation of of proprietary proprietary innovative innovative products products generation The PhDcreation programme will draw on and the the creation of high-skilled high-skilled jobs. and of jobs.

expertise from across five UCD Schools, MoreUCD thanConway 15,000 people people in Ireland Ireland and More than 15,000 in and the Institute, and the millions of people people worldwide areSystems living with with the the millions of worldwide are living UCD Complex and Adaptive symptoms IBD today.and Current therapeutic Laboratory (CASL) will therapeutic train debilitating disease are are options forto this chronic debilitating disease scientists integrate computational very limitedwith withbiological surgery often being often being the the only only methods research focused viable option. The Sigmoid product, on infectious diseases. product, currently currently in a phase II clinical study, uniquely uniquely enables enables oral delivery powerful drug It will build of onathe success ofwithout the UCD drug without causing causing systemic systemic side-effects. side-effects.

tract is lined with cells that block the contents of theisprogramme gut from intoblock the intestine.

In an PhD in Bioinformatics and tract lined withleaking cells that the contents IBD thisleaking barrier is broken and theIn an Systems Biology funded by the Irish of thepatient, gut from into the intestine. contents ofCouncil the leak out into surrounding Research for is Science, Engineering IBD patient, thisgut barrier broken and the areas.

The team insince UCDsurrounding Conway used & Technology (IRCSET) 2007, and contents of research the gut leak out into aalso model of IBD and,team by applying aConway new class on individual research projects on areas.

The research in UCD usedof infectious disease and bioinformatics asand, hydroxylase inhibitors, wereof adrugs modelknown of IBD by applying a new class funded

by Science Foundation Ireland able toknown almost reverse the drugs ascompletely hydroxylase inhibitors, were grants to participating investigators. able to almost completely the symptoms of the disease. reverse symptoms of the disease.

“When we applied these new drugs to our IBD Professor Denis Shields, UCD School “When we these new drugs to ourthat IBDit model, theapplied gut&was tricked into thinking of Medicine Medical Science, UCD model, theInstitute gut was tricked into thinking that it was being deprived of This Conway & oxygen.

UCD CASL isactivated the was beingdirector deprived oxygen.

This prevented activated protective pathways, which in turn deputy ofofthe programme and protective pathways, which in turn preventedin many Conway Fellows be involved the death of the cells that will line the the death of the cells that line the aspects of delivery. details on the gastrointestinal tract,” More explained Professor gastrointestinal tract,” explained Professor programme and application Taylor.

“Our pre-clinical trial dataprocess can noware Taylor.

“Ouron: pre-clinical trial data can now available inform the next phase Sigmoid Pharma product inform the next phase Sigmoid Pharma http://bioinfo-casl.ucd.ie/cib.

The product development pipeline”. development deadline forpipeline”. the 2011/2012 academic In addition to March the product that is currently in year is 18th 2011.

In addition to the product that is currently in phase II clinical studies, Sigmoid Pharma isis phase II clinical studies, Sigmoid Pharma developing aa LEDDS™-enabled LEDDS™-enabled formulation formulation of of developing the hydroxylase hydroxylase inhibitor inhibitor the dimethyloxaloylglycine (DMOG) (DMOG) to to bring bring about about dimethyloxaloylglycine effective, safe safe and and targeted targeted delivery delivery of of this this effective, potential therapeutic therapeutic agent. agent. potential

Ribbon representation of human hepatitis B virus core protein (HBc) dimers as found within recombinant capsids

Under Under normal normal conditions, conditions, the the gastrointestinal gastrointestinal

Conway collaboratorresearch scoops Irish Times Innovation Award Proteomics underpinning across diverse disciplines tract is lined with cellsNP thatsurface block the results in both academic outputs and the studies Bioinformatic analysis HIV progression The study detailed 44 proteins recovered of screening of the bycontents the Bioinformatic analysis of of HIV progression studies of the gutmay fromimpact leaking on intocell-particle the intestine. In an application research toward clinical product in exudatesoffrom muscle tissue.

There corona

Irish UCD biopharmaceutical development The Conway Mass Spectrometry company, Sigmoid Pharma recently scooped Resource (MSR) instrumentation and the overall are Innovation the Year at expertise being of utilised in award a diverse the inaugural Irish Times All-Island range of projects that aim to identify Meta-analysis by UCD researchers by Innovation Awards.

The life-scienceled SME, proteins and their modifications Meta-analysis byProfessor UCD researchers led byhas Conway Fellow, Denisbiology Shields founded

by UCD pharmacology graduate, implicated in fundamental inDr Conway Fellow, Professor Denis has determined that is no clear Shields evidence Ivan Coulter, hasthere actively collaborated with health and disease.

determined thatdefective there is viral noCormac clear evidence that particular sequences Conway Fellow, Professor Taylorin that particular defective sequences in the HIV-1 nefgranted gene ora certain regions of the since being Science Foundation Two recent examples ofviral publications the HIV-1 nef orhighlight certain regions the protein play significant role in disease Ireland industry research partnership award involving theagene MSR the factof protein play a significant role in disease progression. in 2004. that proteomics as a core technology progression. platform is underpinning research across The Irish Times awardcan recognises the stellar HIV-infected patients be categorised on scientific from agriculture toin innovative performance Sigmoid Pharma the basis ofdisciplines the number ofbe years it takes for HIV-infected patients canof categorised on nanotechnology. their application of research and development. them to progress to AIDS. Some patients the basis of the number of years it takes for The company developed two counts new drug maintain stablehas CD4 lymphocyte and them to progress to AIDS. Some patients Currently, major challenge for after the technologies, LEDDS™ and SmPill™, which not do not gostable ona to develop AIDS even more maintain CD4 lymphocyte counts and swine industry is to improve the water only enhance the solubility andeven permeability of thannot 10go years ofdevelop infection. do on to AIDS after more holding capacity (WHC) pork and the drug but can deliver it tooftargeted locations than 10 years of infection.

Scientists areincidence curious as why these longreduce the oftomeat withthe poor in the gastrointestinal tract, including term, non-are progressor (LTNP) patients do not appearance, textureas and reduced shelf colon.

Scientists curious to awhy these longdevelop AIDS. This may reflect differences in life. term, non- progressor (LTNP) patients do not The Sigmoid collaboration is the host, viralPharma-Taylor genetics or environmental develop AIDS. This may reflect differences in facilitating development ofbea exploited new factors thatthe could potentially Dr Giuliano Elia, MSR Director workedfor the host, viral geneticsfororthe environmental therapeutic approach treatment the treatment of the disease. with collaborators in Teagasc Food of factors that could potentially be exploited inflammatory bowel disease by bringing Research Centre and NUI (IBD) Galway to for Studies inthe model organisms have shown the treatment of the disease. together research methodology thethat identify potential biomarkers forofthe infection withwith nef-deficient virus shows an Taylor group the proprietary early prediction of meat quality in an Studies in model organisms have attenuated course of infection andshown some that liquid/emulsion drug delivery system, industrial setting. infection with nef-deficient virus shows an LEDDS®, developed by Sigmoid Pharma. attenuated course of infection and some Commenting on the award, Professor Taylor said, “We are delighted for Dr Coulter and his team and indeed it reflects well on our

development indigenous companies.” were severalwith significant associations between the protein fragment band Commenting on thehave Taylor collaboration, studies inthat humans shown thatWHC non Dr volumes can have be related to or studiessaid, in humans shown that non Coulter “Theassociated collaboration the Taylor progression was withwith gross post mortem degradation.

progression wasnef associated gross laboratory demonstrates potential deletions inclearly the gene. withthe that can beinrealised deletions the nef through gene. focused AHowever, number of peptides from the heat of the research in development the area to applicationmuch of basic research.

The shock protein (HSP) family involved However, much of the research in area to date has been based on observational or case of a smart economy will depend onthe like-minded instudies protecting cells from stress were date hasrather beenpartners basedrigorous, on observational or case than systematic collaborative identifying opportunities identified.

HSP interact with damaged studies rather than rigorous, systematic scientific evaluation.

This work by doctoral and realising basic and applied research proteins an effort to restore function. candidate Ravindra Pushker set out tothrough scientific in evaluation.

This work by doctoral synergies.

This collaboration, initiated The team Ravindra believe that HSP70 may have in a supplement, substantially larger candidate Pushkerhighlights set outsample tothe set adetermine SFI research potential as a biomarker for moderate to if any association exists between disease determine in innovative a substantially larger sample set potential that indigenous companies good WHC. progression particular amino acid if any association existscan between disease working with and academia realise.” differences orand deletions within the acid nef gene. progression particular amino Working with Professor Kenneth Dawson, Taylor’s collaboration with Sigmoid Pharma has differences or deletions within the nef gene.of On a perfor patient basis, Interactions there was no excess Centre Bio-Nano (CBNI), certainly been successful by these metrics with LTNP patients one there orin more nefof the werewith involved awas project three co-authored publications todefective date intotwo of On aMSR per patient basis, no excess sequences when compared tojournals progressors. initiate a framework study ofthe the the highest ranking scientific in LTNP patients with onefor or the more defective nef protein corona surrounding nanoparticles WhileGastroenterology the high frequency amino acidof the field, andofProceeding sequences when compared to progressors. in biological replacement atmedia. particular residues is indicative National Academy of Sciences, as well While the high frequency of amino acidas the of rapid evolvement, permutation testing generation of at proprietary replacement particularinnovative residues isproducts indicative showed that residues withprotein morejobs. replacements This durable, stabilising coating and the creation of high-skilled of rapid evolvement, permutation testing than expected were not significant. on the bare surface ofstatistically nanoparticle showed residues withinthought more replacements More thanthat 15,000 people Ireland and (NP) monomers is now to be a The researchers conclude that current data than expected were not statistically significant. millions of people worldwide arenanoscale living with the primary defining element of providesinnoIBD evidence that individual residues symptoms today. Current therapeutic objects biological media.

The extent The researchers conclude that current data options for this chronic debilitating disease are provides nowith evidence thatoften individual very limited surgery being residues the only viable option. The Sigmoid product, currently in a phase II clinical study, uniquely enables oral delivery of a powerful drug without

IBD patient, this barrier is broken and the interactions. contents of the gut leak out into surrounding of HIVThe nef arecompositionally critical in determining the rate areas. research team in UCDdifferent Conway used Taking two of disease HIV nef are critical in Professor determining the rate of progression.

Denis ananoparticles, model of IBD and, by applyingand a new class polystyrene silica, in of of disease progression.

Professor Denis Shields believes that searches for modifiers drugs known as hydroxylase inhibitors, were of different plasma concentrations, protein Shields believes that searches forthe modifiers progression rates should now that focus on other able to almost completely reverse adsorption studies showed the hardof progression rates should now focus on other host andcan viral factors.

“Systematic evaluation symptoms of evolve the disease. corona quite significantly in host andquantities viral factors.

“Systematic evaluation of large of data by bioinformatics different plasma concentrations.

“When applied these new drugs to our IBD of large quantities of data bioinformatics can bewe just as important inby refuting model, was thinking that itas can findings bethe justgut as important ininto refuting hypotheses that aretricked current in the literature, The have implications for was deprived ofcurrent oxygen.in This activated ithypotheses isbeing in discovering patterns”, hevivo said. thatdesign areunknown the literature, as experimental and in vitro – in protective pathways,unknown which in patterns”, turn prevented it is in discovering he said. extrapolations given thethrough varyingScience protein This research was funded the death of the cells that line the concentrations infunded each type of College study.

Foundation Ireland and University This research was through Science gastrointestinal tract,” explained Professor Dublin.

Taylor.

“Our pre-clinical trial data can now Foundation Ireland and University College Reference : Physical-Chemical AspectsSigmoid of ProteinPharma Corona: product inform Dublin.the next phase Relevance to inpipeline”.

Vitro and in Vivo Biological Impacts development of Nanoparticles. Marco P. Monopoli, Dorota

In addition to the product that is currently in Walczyk,Abigail Campbell,Giuliano Elia,Iseult Lynch, Reference: Baldelli Bombelli, and Kenneth A. Dawson.

Francesca phase II clinical studies, Sigmoid Pharma is Meta-analysis to test the association of HIV-1 nef amino J.Reference: Am. Chem.aSoc. 2011 In press dx.doi.org/10.1021/ developing LEDDS™-enabled formulation of acid differences and deletions with disease progression. ja107583h Meta-analysis to test the association HIV-1C.nef amino the hydroxylase inhibitor Ravindra Pushker, Jean-Marc Jacquē,ofDenis Shields. acid differences andApr deletions with disease progression.

Journal of Virology, 2010 p3644-3653 dimethyloxaloylglycine (DMOG) to bring about Centrifugal drip is an accessible sourceDenis for protein Ravindra Pushker, Jean-Marc Jacquē, Shields. effective, safe and targeted delivery ofC.this Journal ofof Virology, Apr 2010 p3644-3653 capacity. indicators pork ageing and water-holding potential agent.

Alessio Di therapeutic Luca, Anne Maria Mullen, Giuliano Elia, Grace Davey, Ruth M. Hamill. Meat Science 2010 doi:10.1016/j.meatsci.2010.12.033

Conway Fellow, Dr Breandan Kennedy Irish biopharmaceutical development and his team, in collaboration company, Sigmoid Pharma recently scooped with scientists in theofUniversity of at the overall Innovation the Year award Washington, Seattle, identified the inaugural Irish Timeshave All-Island aInnovation transcriptional that isSME, Awards. regulator The life-science sufficient enhance the initiation ofDr founded by to UCD pharmacology graduate, photoreceptor gene expression.

Ivan Coulter, has specific actively collaborated with

Success in EU FP7 call Success in EU FP7 call Conway Fellow, Professor Cormac Taylor

total cone-based resultscolour in bothblindness academicand outputs and the blindness applicationin ofzebrafish. research toward clinical product development with indigenous companies.”

The team identified photoreceptor Commentingelement on the Taylor collaboration, Dr regulatory 1 (PRE-1), a 41 base Coulter said, “The collaboration the eye Taylor pair sequence that specificallywith binds laboratory clearly It demonstrates the of potential nuclear protein. has a number unique that can be realised through focused characteristics when compared to other disease (CKD) and improve patient treatment, application of basic research.

The development cis-regulators of photoreceptor expression.

Conway researchers led by Dr. Tara Photoreceptors areathe sensory neurons since being granted Science Foundation of a smart economy will ontreatment, like-minded McMorrow and Professor Michael have with particular focus on depend CKD arising from that capture images of the world disease (CKD) and improve patient Conway researchers led by Dr. TaraRyan Ireland industry research partnership award collaborative opportunities diabetes and partners hypertension. multiaround Although theMichael two types of haveas successfully secured €485,500 inRyan funding Commenting on theonidentifying recent publication McMorrow Professor with particular focus CKDThe arising from in 2004.us.and and realising basic applied research photoreceptor appear structurally similar disciplinary consortium has 25 part of an overall award to the Systems of this research inand BMC Developmental diabetes and research hypertension.

The multisuccessfully secured €485,500 inthe funding as The Irish Times award recognises stellar13:12 May 2010.qxd:Layout 1are copy 07/05/2010 Page Dr 3This synergies. collaboration, initiated through grossly, they functionally distinct with Biology, Breandan Kennedy said, “It partners (16 universities, 9 industry partners) Biology towards Novel Chronic Kidney disciplinary research consortium has 25 part of an overall awardoftoSigmoid the Systems innovative performance Pharma in a SFI research supplement, highlights the cone photoreceptors enabling colour vision partners is only by deciphering the molecular from 15 countries and the project is due to run Disease Diagnosis and Treatment (SysKid) (16 universities, 9 industry partners) Biology towards Novel Chronic Kidney their application of research and development. potential that innovative indigenous companies and rodsDiagnosis adapted to function inUnion low light. mechanisms responsible for development for five from 15 years. countries and the project is due to run consortium under the FP7 Disease andEuropean Treatment (SysKid) The company has developed two new drug working with academia can complex realise.” systems and functionality in such for five years. consortium under the European Unionwhich FP7 not programme. technologies, LEDDS™ and SmPill™, The morphological and functional that wecollaboration can hopeteam, towith engineer appropriate The UCD Conway including postdoctoral Taylor’s Sigmoid Pharma has programme. only enhance the solubility and permeability of development of photoreceptors depends gene expression responses inand the future”.

The UCD Conway team, including postdoctoral researchers Dr. Craig Slattery Dr. Natalia Syskid (www.SysKid.eu) was established to certainly been successful by these metrics with the drug but can deliver it to targeted locations on regulated gene transcription butkidney very researchers Craig Dr. Natalia Syskid (www.SysKid.eu) was established to Martin, will Dr. utilise cellSlattery cultureand and animal further our understanding chronic three co-authored publications to date in two of in the gastrointestinal tract,ofincluding the few cis-regulatory elements have been Science Foundation Ireland funded this Martin, will utilise culture journals and animal further the highest rankingcell scientific in the colon. our understanding of chronic kidney identified to date. research.

The Kennedyand group hope toof the field, Gastroenterology Proceeding further study to identify The Sigmoid Pharma-Taylor collaboration is Nationalexpand Academythis of Sciences, as well as the Using a zebrafish model, this elements with PRE-1 to regulate facilitating the development of a study new focused generation acting of proprietary innovative products on expression in the cone transducin gene cone-specific expression. therapeutic approach for the treatment of and the creation of high-skilled jobs.

(T αC), whichbowel is required colour vision. inflammatory diseasefor (IBD) by bringing Mutations this gene in humansofcause More than 15,000 people in Ireland and together thein research methodology the

Reference tract is lined with cells that block the contents PRE-1, a cis element sufficient to enhance cone- and of the gut from leaking into the intestine. In an rod- specific expression in differentiating zebrafish IBD patient, this barrier is broken and the photoreceptors.

Maria E. Morrissey, Sara Shelton, contents of the gutJames leakB.out intoand surrounding Susan E. Brockerhoff, Hurley Breandán areas.

The BMC research team in Biology UCD Conway N. Kennedy.

Developmental 2011, 11:3used adoi:10.1186/1471-213X-11-3 model of IBD and, by applying a new class of drugs known as hydroxylase inhibitors, were able to almost completely reverse the models to identify processes involved in early symptoms of the disease.

CKD progression and investigate novel models to identify processes involved in early “When we applied these new to our strategies for preventing anddrugs slowing the IBD CKD progression and investigate novel model, thefor gutof was thinking it progression the tricked disease.

These studies strategies preventing andinto slowing thethatwill was being deprived of oxygen.

This activated be integrated clinical and epidemiological progression of with the disease.

These studies will protective pathways, which in epidemiological turn prevented studies across theclinical consortium using systems be integrated with and the death of thethe cells thatinline the biology methodologies order to develop studies across consortium using systemsnew gastrointestinal tract,”and explained diagnostic strategies treatment options to biology methodologies in order toProfessor develop new Taylor. pre-clinical data can now to diagnostic strategies andtrial treatment options prevent“Our CKD development.

Email inform the phase Sigmoid Pharma prevent CKDnext development. tara.mcmorrow@ucd.ie forEmail details of a product PhD development pipeline”. for details of a PhD tara.mcmorrow@ucd.ie position currently available. position currently available.that is currently in In addition to the product Highlighted for mention by BMC Developmental phase II clinical studies, Sigmoid Pharma is Biology. Confocal micrographs of retinal sections from developing a embryos LEDDS™-enabled 5 dpf zebrafish injected withformulation the (3x PRE- of the hydroxylase 1)-1.2 kb ZOP-EGFPinhibitor construct shows co-localisation dimethyloxaloylglycine (DMOG) to bring shows about with a marker for rod photoreceptors.

Staining enhanced green protein EGFP of (green), effective, safe fluorescent and targeted delivery this rod photoreceptors (4C12; red) and nuclei (DAPI; blue) potential therapeutic agent.

EUROCarbDB, a research infrastructure design EUROCarbDB, a research infrastructure design study funded by the EU 6th Framework study funded by the EU 6th Framework Programme. Prospective users can access the Programme. Prospective users can access the GlycoExtractortool toolon on GlycoExtractor http://glycobase.nibrt.ie:8080/DemoGlycoExtra http://glycobase.nibrt.ie:8080/DemoGlycoExtra ctor/mainPage. ctor/mainPage. tract is linedseem with that cells that block the contents “It would cigarette smoke

GlycoExtractor advances advances glycan glycan data data manipulation manipulation GlycoExtractor

cells, tissues and fluids.

Glycomics needs the proprietary supporting framework millions of people worldwide are living with the Taylor group withthe the cells, tissues and fluids.

Glycomics needs supporting framework of extensive, well-curated databases and symptoms IBD today. Current therapeutic liquid/emulsion drug delivery system, and of extensive, well-curated databases Commercial packages that support HPLC flexible analytical tools.

Currently, this field Commercial packages support HPLC options for this chronicthat debilitating disease are LEDDS®, developed

by Sigmoid Pharma. flexible analytical tools.

Currently, this field instruments cannotfacilitate facilitate the extraction instruments the extraction ofof very limited cannot with surgery often being the only of study lacks the established, of study lacks the established, large quantities of data.

In an effort toalleviate alleviate Commenting on and the award, Professor Taylor large quantities of data.

In an effort to viable option.

The Sigmoid product, currently comprehensive centralised data comprehensive and centralised data and his this bottleneck within high-throughput said, “We arestandards delighted for Dr Coulter this within high-throughput in a bottleneck phase II clinical study, uniquely enables collections, and information collections, standards and information UCD researchers in the obesity responses with the production team and indeed it reflects well on our results in projects, both academic outputs and the Irish biopharmaceutical development glycomic projects, theearly NIBRT team have glycomic the NIBRT team have oral delivery of a powerful drug without reporting protocols that exist within reporting protocols that exist within partnership.

A key driver of successful application of research toward clinical product company, Sigmoid Pharmagroup recently scooped developed a web-based tool that interfaces immunology research led by of potent cytokines.

Many studies developed a web-based tool that interfaces causing systemic side-effects. genomicsand andproteomics. proteomics. genomics scientific research inProfessor 2010 is meaningful development with indigenous companies.” the overall Innovation of the Year award at withthe the Waters chromatography software Conway Fellow, Donal have already shown that iNKT cells are with Waters chromatography software Under normal conditions, the gastrointestinal interaction ofDr academia with industry that the inaugural Irish Times All-Island package and automate theexport export Researchers, Dr Natalia Artemenko and Dr O’Shea have demonstrated for the defective inimprove certain cancers.

Researchers, Natalia Artemenko and Dr package totoimprove automate the Commenting on the and Taylor collaboration, Dr Innovation Awards.

Thethe life-science SME, of data to various file formats for subsequent Matthew Campbell from the National Institute Matthew Campbell from National of data to various file formats for subsequent first time that cigarette smokeInstitute extract Coulter said, “The collaboration with the Taylor founded

by UCD Research pharmacology graduate, Dr of Bioprocessing Research Training (NIBRT) analysis.

The modular architecture thetool tool of Bioprocessing &&Training (NIBRT) analysis.

The modular architecture the (CSE) has a specific effect on a minor This study compared the number and laboratory clearly demonstrates theofof potential Ivan has actively collaborated with led by Conway Fellow, Professor Pauline Rudd also the ofofdata from led byCoulter, Conway Fellow, Professor Pauline Rudd alsofacilitates facilitates themanipulation manipulation data from subset of immune cells and this may function of iNKT cells in a group of that can be realised through focused Conway Fellow,an Professor Cormac Taylor have developed open access, web-based other management systems. have developed open access, web-based otherdata dataindividuals management systems. application of basic research.

The development contribute to an the role of cigarette healthy who smoke 20 since being granted a Science Foundation interface that facilitates extraction, querying interface that facilitates extraction, querying of a smart economy will depend ontoto like-minded smoke in the development of cancer. cigarettes each day to those in nonThe NIBRT team are now working integrate Ireland industry research07/05/2010 partnership award The NIBRT team are now working integrate May 2010.qxd:Layout 1 copy 13:12 Page 3 and sharing of HPLC-glycan data generated in and sharing of HPLC-glycan data generated in collaborative partners identifying opportunities smoking individuals of the same age GlycoExtractor with the EUROCarbDB in 2004.

GlycoExtractor with the EUROCarbDB high throughput processes. high throughput processes. and realising basic and applied research framework Carginogens cigarette smokethe can lead group. frameworktotoprovide provideaacomprehensive comprehensivehighhighThe Irish Timesinaward recognises stellar synergies. This collaboration, initiated through Glycosylation isisby the most common throughput HPLC analysis directly toperformance lung cancer haveand been Glycosylation the most common and throughput HPLCdata data analysis platform for Meta-analysis UCD researchers led by in studies in humans have shownplatform that nonfor innovative ofand Sigmoid Pharma a SFI research supplement, highlights the the and annotation ofofwith experimental structurally diverse post-translational implicated in several other malignancies.

The recently published findings showed Conway Fellow, Professor Denis Shields has progression was associated gross thestorage storage and annotation experimental structurally diverse post-translational their application of research and development. potential that innovative indigenous companies data. integration ofofnext generation modification of proteins.

More than half ofofall determined there issmokers no clear evidence deletions in the cell nef gene.

In addition, cigarette have reduced iNKT numbers in cigarette data.The Thewith integration nextrealise.” generation modification of proteins.

More than half all The companythat has developed two new drug working academia can bioinformatic tools will further gene products have been shown totype thatincreased particular defective viral sequences an susceptibility to II innot smokers and also significant defects gene productsLEDDS™ have been shown tobe bewhich bioinformatic tools will furtherthe the technologies, and SmPill™, However, much of the research in the area to glycosylated.

With many specific glycans development of unifiedwith approaches for the HIV-1 nef gene or and certain regions ofor the Taylor’s collaboration Sigmoid Pharma has only enhance the solubility and permeability glycosylated.

With many specific glycans or of development of unified approaches foror case diabetes, infections autoimmune in the ability of iNKT cells to produce date has been based on observational glycoforms showing potential as cancer handling large scale glycomics data initiatives protein a significant role in disease certainly been successful bypatient these metrics with disease (CKD) and improve treatment, Conway researchers leditbyto Dr. Tara the drugplay but can deliver targeted locations glycoforms showing potential as cancer handling large scale glycomics data initiatives disorders such as rheumatoid arthritis. cytokines and kill target cells. studies rather than rigorous, systematic biomarkers, thereProfessor is an increasing need to with applications inpublications biomarker discovery progression. three co-authored to date in two of McMorrow and Michael Ryan with focus on CKD arising from in the gastrointestinal including thetohave biomarkers, there is antract, increasing need withparticular applications in biomarker scientific evaluation.

This work discovery by doctoral develop high throughput, highly sensitive and the highest ranking scientific journals in the colon. diabetes and hypertension.

The multisuccessfully secured €485,500 in cells funding as This research was partially supported by develop high throughput, highly sensitive and Invariant natural killer T (iNKT) Commenting on the work, postdoctoral HIV-infected patients can be categorised on candidate Ravindra Pushker set out to robust strategies that detail the glycome of This research was partially supported field, Gastroenterology and Proceeding of the disciplinary research consortium has 25by part of an overall award tothat the Systems robust strategies that detail the glycome are immune regulators play an of researcher and first author on this the basis of the number of years it takes for determine in a substantially larger sample set The Sigmoid Pharma-Taylor collaboration is National (16 Academy of Sciences, as well as the partners universities, 9 industry partners) Biology towards Novel Chronic Kidney them to progress AIDS. Some patients if any association exists between important role intomounting publication, Dr Andrew Hogandisease said, facilitating the development of aanti-tumour new generation of proprietary innovative products from 15 countries and the project due to run Disease (SysKid) maintainDiagnosis stable CD4and lymphocyte counts progression and particular amino isacid therapeutic approach forTreatment the treatment ofand andfive theyears. creation of high-skilled jobs. for consortium thedisease European Union FP7 do not go onunder to develop AIDS(IBD) even after more differences or deletions within the nef gene. inflammatory bowel by bringing programme. than 10 years of infection.

More than 15,000team, people in Ireland and together the research methodology of the The including On aUCD per Conway patient basis, there was postdoctoral no excess of millions of people worldwide are living with the Taylor group with the proprietary researchers Dr. Craig Slattery and Dr. Natalia Syskid (www.SysKid.eu) was established to Scientists are curious as to why these longLTNP patients with one or more defective nef symptoms IBD today. Current therapeutic liquid/emulsion drug delivery system,kidney Martin, will to utilise cella culture and animal further our understanding of chronic term,research nonprogressor (LTNP) patientsDrdo not sequences when compared to progressors. most likely die as result of the raised New led by Conway Fellow options for this chronic debilitating disease are LEDDS®, developed by Sigmoid Pharma. develop AIDS. Thisby may reflect differences While the high frequency of amino glucose levels seen Breandán Kennedy indicates that treatment mostlimited likely to die asinadiabetes. result the acid raised New research led Conway Fellow Dr in very with surgery oftenofbeing the results in both outputs the only Irish biopharmaceutical The Irish Drug Delivery Network Welcoming the announcement, the host, viral genetics ordevelopment environmental replacement atacademic particular residuesand isProfessor indicative Commenting on the award, Professor Taylor of diabetic blindness should look at glucose levels seen in diabetes.

Breandán Kennedy indicates that treatment viable option.

The Sigmoid product, currently application of research toward clinical product company, Sigmoid Pharma recently scooped Dr Kennedy and his team found that new blood (IDDN), a strategic research cluster David Brayden, IDDN Director and factors thatare could potentially exploited for of rapid evolvement, permutation testing said, “We delighted for Drbe Coulter his protecting the neurons responsible forand colour of diabetic blindness should look at in a phaseFellow, II clinical study, uniquely enables development with indigenous companies.” the overall Innovation of the Year award at funded by Science Foundation Ireland, Conway said, “We look forward vessels and the neuronal cell death in diabetic the treatment of the disease. showed that residues with more replacements Dr Kennedy and his team found that new blood team and indeed it reflects well on our vision in thethe eye andTimes notresponsible just targeting protecting neurons for the colour oralworking delivery with of a powerful drugNorchi, without the inaugural Irish All-Island has announced that itofwill collaborate to DrTaylor Terence retinopathy arise independently than expected were not statistically significant. vessels andcan the neuronal cell death of in each diabetic partnership.

Aeye keyis driver successful blood vessels as currently the practice.

Commenting on the collaboration, Dr causing systemic side-effects. vision in the and not just targeting the Studies in model organisms have shown that Innovation Awards.

TheArch life-science SME, with Boston-based CEO Arch Therapeutics to help optimise other.

Insaid, addition, they identified that cone retinopathy can independently of each scientific research 2010 is Therapeutics meaningful Coulter “Thearise collaboration with the Taylor blood vessels aspharmacology isin currently thegraduate, practice. infection with nef-deficient virus shows an Dr The polymer researchers conclude that current data founded by UCD to optimise the development of novel the formulation process and photoreceptor neurons, those involved in Nearly 2.5 million people worldwide arethat blind Under normal conditions, the gastrointestinal interaction of academia with industry other.

In addition, they identified that cone cells, tissues and fluids.

Glycomics needs the supporting framework laboratory clearly demonstrates the potential provides no evidence that individual residues attenuated course of infection and some Ivan Coulter, has actively collaborated with products for surgery characterise the material atinvolved all are stages colour vision and used inthose daylight, most due to diabetic retinopathy.

Thistrauma. secondary of extensive, well-curated databases and photoreceptor neurons, in of Nearly 2.5 million people and worldwide are blind that can be realised through focused Conway Fellow, Professor Cormac Taylor the synthetic process forsupport this product.

Commercial packages that HPLC affected by the high glucose levels. complication of diabetes thethis growth flexible analytical tools.activates Currently, field colour vision and used in daylight, are most due to diabetic retinopathy.

This secondary application of basic research.

The development since being granted a Science Our aim is to ensure a reproducible instruments cannot facilitate the extraction of Arch Therapeutics has developed a clear of new leaky vessels in theFoundation eye and is of study lacksblood the established, of a research smartbyeconomy will depend on like-minded affected high glucose levels. complication of diabetes activates the growth The team made observations Irelandthat industry research award process for the effective application the large quantities of data.

Intheir an effort toofalleviate liquid forms acentralised barrier when topically responsible for the death ofpartnership photoreceptors, comprehensive and data collaborative partners identifying opportunities of new leaky blood vessels in the eye and is using a novel zebrafish model of diabetes, in 2004. product in surgery. ” this bottleneck within high-throughput applied to a wound.

The barrier promptly the neurons that send visual messages to our The research team made their observations collections, standards andofinformation and realising basic and applied research responsible for the death photoreceptors, which resembles the stages ofhave diabetic glycomic projects, theearly NIBRT stops bleeding and seals brain.

The Irish Times award recognises the The stellar using a novel zebrafish modelteam of diabetes, reporting protocols that existleaking. within synergies.

This collaboration, initiated through the neurons that send visual messages to our retinopathy inweb-based humans.

Ittool is an exciting material has no effect on the coagulation IDDN scientists are based in four developed a that interfaces innovativeand performance of Sigmoid Pharma in resembles thegroup early who stages of hope diabetic genomics proteomics. awhich SFI research supplement, highlights the to development for the now Until now, it was unclear if the changes to brain. process and is biocompatible.

The academic centres; UCD, RCSI and with the Waters chromatography software their application of research and development. retinopathy humans.

It isTCD, an exciting potential thatininnovative indigenous companies further extend their research and establish a vessels and neurons occurred independently of underlying technology platform was UCC. This project will involve Prof.

David package to improve and automate the hope export Researchers, Drhas Natalia Artemenko and Dr The company developed two new drug development for the group who now Until now, it was unclear if the changes to working with academia can realise.”

Meta-analysis by UCD researchers led by studies in humans have shown that nonandto model of late stage diabetic disease. one otherCampbell and which typethe of National retinal neuron is licensed from the Massachusetts Brayden, Dr Marc Devocelle (RCSI) of data to various file formats for subsequent Matthew from Institute technologies, LEDDS™ and Denis SmPill™, whichhas not further extend their researchwith and gross establish a vessels occurred independently of Conwayand Fellow, Professor Shields progression was associated Institute ofneurons Technology. postdoctoral scientists based at analysis.

The modular architecture ofCentre the tool of Bioprocessing Research & Training (NIBRT) Taylor’s with Sigmoid only enhance the solubility permeability model ofcollaboration late stage diabetic disease.Pharma has one other and which type ofand retinal neuron isof determined that there is no clear evidence deletions in the nef gene. led by Conway Fellow, Professor Pauline Rudd also facilitates manipulation of data from certainly been the successful by these metrics with the drug but can deliver it to targeted locations that particular defective viral sequences in other data management systems. have developed an open access, web-based three co-authored toindate in two However, much ofpublications the research the area to of in gastrointestinal including thethe HIV-1 nef gene or tract, certain regionsthe of the interface that facilitates extraction, querying the highest ranking scientific journals inorthe date has been based on observational case colon. protein play a significant role in disease The NIBRT team are now working to integrate and sharing of HPLC-glycan data generated in field, Gastroenterology and Proceeding of the

Conwayofcollaborator scoopson Irish Times Innovation Specific effect cigarette smoke innate immune cellsAward Reference Reference of themultiple gut fromnegative leaking into the intestine.

In an has effects onhigh innate web-basedinterface interfacefor for GlycoExtractor: AAweb-based high the GlycoExtractor: IBD patient, this barrier isimportant broken data and immune cells that processing HPLC-Glycan throughput processing ofofare HPLC-Glycan data in throughput contents of the gutMatthew leakand out into surrounding NataliaV.V.Artemenko, Artemenko, Matthew Campbell, andPauline Pauline P.P.Campbell, and Natalia tumour surveillance protection areas.

The research teamResearch, in UCD 2010, Conway used M.Rudd Rudd Journal Proteome Research, 2010,9 9(4), (4), M. Journal ofofProteome pppp against infection.

In addition to increasing 2037–2041 a2037–2041 model of IBD and, by applying a new class of your risk of developing cancer, it appears drugs known as hydroxylase inhibitors, were thattosmoking also impairs yourthe body’s able almost completely reverse ability to fight the disease effectively”. symptoms of the disease.

Bioinformatic analysis of HIV progression studies This research was funded through a Sanofi

Success in EU FP7 call

“When applied these new drugs IBD AventisweNewman scholarship totoDrour Hogan. model, the gut was tricked into thinking that it was being deprived of oxygen. This activated of HIV nef are critical in determining the rate Reference protective pathways, which in turn prevented of disease progression.A. Corrigan, Professor Denis Andrew.

E. Hogan, the death of theMichelle. cells that line the Vincent O’Reilly, Shields believes thatJean searches forDerek. modifiers Gadintshware Gaoatswe, O’Connell, G. of gastrointestinal tract,” explained Professor Doherty, Lydia Lynch, O’Shea, smoke progression ratesDonal should nowCigarette focus on other Taylor. “Our pre-clinical trial data can now alters natural killer“Systematic T cell function and may hostinvariant and viral factors. evaluation inform the next phase Sigmoid Pharma product inhibit anti-tumour responses, Clinical Immunology of large of data byinvolved bioinformatics models toquantities identify processes in early development pipeline”.

(2011), doi:10.1016/j.clim.2011.01.011 can progression be just as important in refuting CKD and investigate novel NIBRT researchers Dr Matthew Campbell and Dr Natalia hypotheses that current inisthe literature, In addition todeveloped theDrare product that currently in as strategies for preventing and slowing the NIBRT researchers Matthew Campbell and Dr Natalia Artemenko who GlycoExtractor it is inIIdiscovering unknown patterns”, phase clinical studies, Sigmoid Pharma issaid.

Artemenko who GlycoExtractor progression ofdeveloped the disease.

These studieshewill developing formulation of be integrateda LEDDS™-enabled with clinical and epidemiological This research was funded through Science the hydroxylase inhibitor studies across the consortium using systems Foundation Ireland and University College dimethyloxaloylglycine (DMOG) todevelop bring about biology methodologies in order to new Dublin. effective, safe and targeted delivery options of this to diagnostic strategies and treatment potentialCKD therapeutic agent.Email prevent development. tara.mcmorrow@ucd.ie for details of a PhD position currently available.

Commenting on the research, Dr Kennedy

Zebrafish model insights into diabetic blindness Zebrafish model gives gives insightsscoops into diabetic blindness Conway collaborator Irish Times Innovation Award IDDN announce new industrial partnership with Arch Therapeutics Reference:

Commenting on the research, DrHIV-1 Kennedy said, “By establishing athat robust model for early Meta-analysis to test the association of nef amino tract is lined with block the contents for Synthesis & cells Chemical Biology (UCD) and late stage diabetic retinopathy, we would said, “By establishing ainto robust model forInearly acid differences and deletions withthe disease progression. of the gut from leaking intestine. an and the Peptide Synthesis Laboratory Ravindra Pushker, Jean-Marcretinopathy, Jacquē, Deniswe C. Shields. hope to better understand the progression of andpatient, late stage diabetic IBD this barrier broken and thewould (RCSI).

Abina Crean (UCC) will Journal ofDr Virology, Apr 2010isp3644-3653 the disease andgut pave theout way forprogression identifying hope to of better understand the of contents the leak into surrounding work to optimise certain aspects of new drug forteam its successful treatment”. the manufacturing disease and pave the forConway identifying areas.

Thetargets research inway UCD used the process and look at apeptide model of IBD and,forby a new class of new drug targets itsapplying successful treatment”. secondary structure.

The research was funded through Science EUROCarbDB, a research infrastructure design drugs known as hydroxylase inhibitors, were Foundation Ireland and Health Research study funded by thefunded EU the 6ththrough Framework The research was Science able almost completely reverse the ArchtoTherapeutics was users co-founded Programme.

Prospective can Research access the Board.

Foundation Ireland and the Health symptoms the disease. by a groupofof Irish-Americans in GlycoExtractor tool on Board.

Massachusetts, USA and named after http://glycobase.nibrt.ie:8080/DemoGlycoExtra “When we applied these new drugs to our IBD the iconic Spanish Arch in Galway.

Reference: ctor/mainPage. model, the gut was tricked into thinking that it Predominant cone photoreceptor dysfunction in a was being deprived of oxygen.

This activated Reference Reference: hyperglycaemic Amodel of non-proliferative diabetic web-based interface for high GlycoExtractor: protective pathways, which in turn prevented Predominant cone photoreceptor dysfunction in a retinopathy.

Yolanda Alvarez, Jenneth Chen, Alison processing of HPLC-Glycan throughput the deathNore of the cells lineO’Connor, thedata diabetic hyperglycaemic model ofthat non-proliferative Reynolds, Waghorne, JohnP. J.Campbell, Breandan Natalia V. Artemenko, Matthew and Pauline gastrointestinal tract,” explained Professor of HIV nef are critical in determining the rate retinopathy.

Yolanda Alvarez, Jenneth Chen, Alison Kennedy.

Disease Models & Mechanisms (2010) M. Rudd Journal of Proteome Research, 2010, 9 (4), pp Taylor.

“Our pre-clinical trial data can now of diseaseNore progression.

Professor Denis Reynolds, Waghorne, John J. O’Connor, Breandan 2037–2041 inform the next phase Sigmoid Pharma Kennedy.

Disease Models & Mechanisms (2010)product Shields believes that searches for modifiers of development progression pipeline”. rates should now focus on other host and viral factors. “Systematic evaluation In addition to the product that is currently in of large quantities of data by bioinformatics phase II clinical studies, Sigmoid Pharma is

GlycoExtractor advances glycan data manipulation

Bioinformatic analysis of HIV progression studies