Dr. Ursula Mary Bond

• Ursula Bond, Tharappel C. James, Joanne Kavanagh, 'Preventing spoilage in alcohol fermentations ', US, US 13/482,223, 2013, Ursula Bond, James Tharappel C, Joanne KavanaghPatent, 2013, URL
• Ursula Bond, Christina SIEBKE, Tharappel JAMES, 'BIOMARKERS FOR BREAST TUMOURS FROM Hsp70-ASSOCIATED PEPTIDES', World Intellectual Property Organisation, WO2013037714 A1, 2013, The Provost, Fellows, Foundation Scholars, And The Other Members Of Board, Of The College Of The Holy And Undivided Trinity Of Queen Elizabeth, Near DublinPatent, 2013, URL
• Christina Siebke, Identification of novel peptides using phage display with the potential for the use in breast cancer therapy, Trinity College Dublin, 2011Thesis, 2011
• Beggs, Suzanne, Identification of factors involved in 3' end processing and transcription termination of histone mRNAs, Trinity College Dublin, 2011Thesis, 2011
• Fitzpatrick, J, Biomass to Biofuel: toward the bioengineering of Saccharomyces species for cellulosoe degradation, Trinity College dublin, 2011Thesis, 2011
• Kavanagh, Joanne, Antimicrobial Peptide Preventing Beer Spoliage, Trinity College Dublin, 2012Thesis, 2012
• Kricka, William, Biomass to biofuel: The engineering of Saccharomyces species for the co-fermentation of cellulose and xylose, Trinity College Dublin, 2014Thesis, 2014
• Lall, P., Lindsay, A.J., Hanscom, S., (...), McCaffrey, M.W., Khan, A.R., Structure-function analyses of the interactions between Rab11 and Rab14 small GTPases with their shared effector Rab coupling protein (RCP), Journal of Biological Chemistry, 290, (30), 2015, 18817-18832Journal Article, 2015, DOI , TARA - Full Text
• C. O'Fagain, U. Bond, B.A. Orsi, and T.J. Mantle, The slow kinetic transients of Arylsulphatase A., Biochem. J., 201, 1982, p345 - 352Journal Article, 1982
• T.C. James, U.M. Bond, C.A. Maack, S.W. Applebaum, and J.R. Tata, Construction and partial characterization of a recombinant DNA probe for locust vitellogenin messenger RNA, Biochem. J., 205, 1982, p521 - 528Journal Article, 1982
• T.C. James, U.M. Bond, C.A. Maack, S.W. Applebaum, and J.R. Tata, Evolutionary conservation of vitellogenin genes, DNA, 1, 1982, p345 - 353Journal Article, 1982
• T.C. James, C.A. Maack, U.M. Bond, J.C. Champion and J.R. Tata, Xenopus egg coat proteins. II. Characterization of messenger RNAs of the oviduct and cloning of estradiol inducible sequences, Comp. Biochem. Physiol., 80, 1985, p89 - 97Journal Article, 1985
• U. Bond and M.J. Schlesinger, Ubiquitin is a heat shock protein in chicken embryo fibroblasts, Mol. Cell. Biol., 5, 1985, p949 - 956Journal Article, 1985
• U. Bond and M.J. Schlesinger, The chicken ubiquitin gene contains a heat shock promoter and expresses an unstable mRNA in heat shocked cells, Mol. Cell Biol, 12, 1986, p4602 - 4610Journal Article, 1986
• E. Siegfried, G.H. Thomas, U.M. Bond and S.C.R. Elgin, Characterization of a supercoil-dependent S1 sensitive site 5' to the Drosophila melanogaster hsp 26 gene, Nuc. Acids Res., 14, 1986, p9425 - 9444Journal Article, 1986
• U. Bond and M.J. Schlesinger, Heat Shock Proteins and Development, Adv. Genetics., 24, 1987, p1 - 29Journal Article, 1987
• M.J. Schlesinger and U. Bond, Ubiquitin Genes, Oxford Surveys on Eukaryotic Genes, 4, 1987, p77 - 91Journal Article, 1987
• U. Bond, N. Agell, A.L. Haas, K. Redmen, and M.J. Schlesinger, Ubiquitin in stressed chicken embryo fibroblasts, J. Biol. Chem, 263, 1988, p2384 - 2388Journal Article, 1988
• N. Agell, U. Bond, and M.J. Schlesinger, In vitro proteolytic processing of a di-ubiquitin and a truncated di-biquitin from in vitro generated mRNAs, Proc. Natl. Acad. Sci., 85, 1988, p3693 - 3697Journal Article, 1988
• U. Bond, Heat shock but not other stress inducers leads to the disruption of a sub-set of snRNPS and inhibition of in vitro splicing in HeLa cells, EMBO J., 7, 1988, p3509 - 3518Journal Article, 1988
• M. J. Schlesinger, N. C. Collier, N. Agell and U. Bond, Molecular events in avian cells stressed by heat shock and arsenite. In Stress Induced Proteins, J. Cellular Biochemistry, 1989, p137 - 148Journal Article, 1989
• K. Parker and U. Bond, Analysis of Pre-mRNAs in heat shocked Hela cells allows identification of the upstream termination site of human polymerase I transcription, Mol. Cell. Biol., 9, 1989, p2500 - 2512Journal Article, 1989
• T. S. Nowak Jr, U. Bond and M. J. Schlesinger, Heat shock levels in brain and other tissues after hyperthermia and transient ischemia, J. Neurochem., 54, (2), 1990, p451 - 458Journal Article, 1990
• Bond, U, T. Yario, and J. A. Steitz, Multiple processing-defective mutations in a mammalian histone pre-mRNA are suppressed by compensatory changes in U7 RNA both in vivo and in vitro, Genes and Dev., 5, 1991, p1709 - 1722Journal Article, 1991
• Bond, U, T. Yario and J. A. Steitz, Analysis of the basepairing interaction between mammalian U7 and the downstream element of histone pre-mRNAs, J. Cellular Biochem, 1991, p256Journal Article, 1991
• N.P. Pandey, J. Sun, A.S. Williams, V.D. Brown, U. Bond and W. F. Marzluff, Point mutations in the stem-loop at the 3' end of mouse histone mRNA reduce expression by reducing the efficiency of 3' end formation, Mol. Cell Biol., , 14, 1994, p1709 - 1720Journal Article, 1994
• Bond, U, and T. Yario, The steady state levels and structure of the U7 snRNP are constant during the human cell cycle: lack of cell cycle regulation of histone mRNA 3' end formation, Cell. Mol. Biol. Res., 40, 1994, p27 - 34Journal Article, 1994
• Ngan,V, G. Vacano, U. Bond, and T.C. James, Characterization of a new class of transcribed repetitive DNA sequence which exists as a hybrid with HP1 mRNA; potential for site specific recombination in Drosophila melanogaster, J. Insect Mol. Biol. and Biochem., 25, 1995, p331 - 334Journal Article, 1995
• Bracken A. and U. Bond, Reassembly and protection of small nuclear ribonucleoprotein particles by heat shock proteins in yeast cells, RNA, 5, 1999, p1586 - 1596Journal Article, 1999, URL
• Brosnan, T., T. C. James, D. Donnelly and U. Bond, The stress response is repressed during fermentation in brewery strains of yeast, J. Appl. Microbiology, 88, 2000, p746 - 755Journal Article, 2000
• Bond, U. and T. C. James, Dynamic changes in small nuclear ribonucleoproteins of heat-stressed and thermotolerant HeLa cells, Int. J. Biochem. Cell. Biol., 32, 2000, p644 - 656Journal Article, 2000
• Campbell, S. and U. Bond, Bio-informatical analysis of histone 3'end processing in Saccharomycesmcerevisiae:isentification of U7-like RNAs, Biochem. Soc. Trans., 28, 2000, p41Journal Article, 2000
• Bond, U., S. Campbell and T.C. James, A model organism for genomic and postgenomic studies, IEEE: Engineering in Medicine and Biology, 20, 2001, p22 - 32Journal Article, 2001
• Campbell, S., M. li del Olmo, Beglan, P. and U. Bond, A sequence element downstream of the yeast HTB1 gene connects mRNA'3 end processing, transcription termination and cell cycle regulation of a histone gene, Mol. Cell Biol., 22, 2002, p8415 - 8425Journal Article, 2002
• T.C. James, S. Campbell, and U. Bond, Comparative Analysis of global gene expression in lager and laboratory yeast strains grown in wort, Proc. of IEEE: Challenges in Functional Genomics, 90, 2002, p1887 - 1899Journal Article, 2002
• T.C. James, S. Campbell, D. Donnelly and U. Bond, Transcription profile of a brewery yeast under fermentation conditions, Journal of Applied Microbiology., 94, 2003, p432 - 448Journal Article, 2003
• T.C. James, D. Donnelly and U. Bond, Aneuploidy and copy number breakpoints in the genome of lager yeasts mapped by microarray hybridisation, Current Genetics, 24, 2004, p360 - 370Journal Article, 2004
• Arnaiz, B., L. Madrigal, D. Doherty, T.C.James and U. Bond, Structural mimics of heat shock protein 70- associated peptides from breast tumour cells can prime T-cells to respond to tumour antigens, European Journal of Cancer, 2, 2004, p79Journal Article, 2004
• Thery T, Tharappel J.C, Kraszewska J, Beckett M, Bond U, Arendt E.K, Antifungal activity of a synthetic human β-defensin 3 and potential applications in cereal-based products, Innovative Food Science and Emerging Technologies, 38, 2016, p160 - 168Journal Article, 2016, DOI , URL
• Kraszewska J, Beckett M.C, James T.C, Bond U, Comparative analysis of the antimicrobial activities of plant defensin-like and ultrashort peptides against food-spoiling bacteria, Applied and Environmental Microbiology, 82, (14), 2016, p4288 - 4298Journal Article, 2016, DOI , URL
• Chandre Monerawela and Ursula Bond, Brewing up a storm: The genomes of lager yeasts and how they evolved, Biotechnology Advances, 2017, p1-8Journal Article, 2017, DOI , URL
• Chandre Monerawela , Brewing up a Mystery: The origins and recombination events in lager yeasts, Trinity College Dublin, 2017Thesis, 2017
• Ichimura S, Mita K, Nenol M, James T C, and Bond U. , Developmental Expression Of Ubiquitin Genes In Posterior Silk Gland Of Bombyx-Mori, Journal of Cell Biology, 111, (5), 1990, p1 - 5Journal Article, 1990
• Schlesinger M.J., Collier N and U. Bond , Events in heat-shocked avian fibroblasts, J. Cell. Biochem, 12, 1988, p1-4Journal Article, 1988
• Steitz, J. and U. Bond, Differential effects of stress on pre-messenger RNA processing in HeLa cells, J. Cell. Biochem, (12), 1988, p267 - 271Journal Article, 1988
• Canaan, R, Biogenesis of histone mRNA in the yeast Saccharomyces cerevisiae, Trinity College Dublin, 2007Thesis, 2007
• Usher, Jane, Analysis of the genomic organisation and gene expression of brewery strains of yeast, Trinity College Dublin, 2007Thesis, 2007
• Arnaiz, Blanca, Characterisation of peptide mimics to antigens chaperoned by Hsp70 in MDA-MB-231 Breast tumour cells, Trinity College Dublin, 2005Thesis, 2005
• Campbell, Susan, Characterisation of histone mRNA 3' end processing in the yeast Saccharomyces cerevisiae, Trinity College Dublin, 2001Thesis, 2001
• Bracken, Adrian, Interaction of heat shock proteins with splicing components during and after thermal stress, Trinity College Dublin, 1999Thesis, 1999
• Brosnan, M.P, Alterations in Gene Expression of Saccharomyces cerevisiae during the brewing process, Trinity College Dublin, 1998Thesis, 1998
• Monerawela, C and U. Bond, Recombination Sites on Hybrid Chromosomes in S. pastorianus share Common Sequence Motifs and define a Complex Evolutionary Relationship between Group I and II Lager Yeasts, FEMS Yeast Research, 17, (5), 2017, p1 - 12Journal Article, 2017, URL
• Monerawela, C and U. Bond, The hybrid genomes of Saccharomyces pastorianus-a current perspective, YEAST, 35, (1), 2018, p39-50Review Article, 2018, DOI , TARA - Full Text
• Langdon QK, Peris D, Baker EP, Opulente DA, Nguyen HV, Bond U, Gonçalves P, Sampaio JP, Libkind D, Hittinger CT., Fermentation innovation through complex hybridization of wild and domesticated yeasts., Nat Ecol Evol, 11, 2019, p1576 - 1586Journal Article, 2019, URL , TARA - Full Text
• Vakirlis, N. and Monerawela, C. and McManus, G. and Ribeiro, O. and McLysaght, A. and James, T. and Bond, U., Evolutionary journey and characterisation of a novel pan-gene associated with beer strains of Saccharomyces cerevisiae, Yeast, 36, (7), 2019, p425-437Journal Article, 2019, DOI , URL
• de la Cerda-Garcia Caro, R. and Hokamp, K. and Roche, F. and Thompson, G. and Timouma, S. and Delneri, D. and Bond, U., Aneuploidy influences the gene expression profiles in Saccharomyces pastorianus group I and II strains during fermentation, PLoS Genetics, 18, (4), 2022Journal Article, 2022, DOI , URL , TARA - Full Text
• Lin, C.L. and García-Caro, R.D.L.C. and Zhang, P. and Carlin, S. and Gottlieb, A. and Petersen, M.A. and Vrhovsek, U. and Bond, U., Packing a punch: Understanding how flavours are produced in lager fermentations, FEMS Yeast Research, 21, (5), 2021Journal Article, 2021, DOI , URL , TARA - Full Text
• O'Brien, C.E. and Oliveira-Pacheco, J. and Cinnéide, E.Ã". and Haase, M.A.B. and Hittinger, C.T. and Rogers, T.R. and Zaragoza, O. and Bond, U. and Butler, G., Population genomics of the pathogenic yeast Candida tropicalis identifies hybrid isolates in environmental samples, PLoS Pathogens, 17, (3), 2021Journal Article, 2021, DOI , URL , TARA - Full Text
• Timouma, S. and Balarezo-Cisneros, L.N. and Pinto, J. and De La Cerda, R. and Bond, U. and Schwartz, J.-M. and Delneri, D., Transcriptional Profile of the Industrial Hybrid Saccharomyces pastorianus Reveals Temperature-Dependent Allele Expression Bias and Preferential Orthologous Protein Assemblies, Molecular Biology and Evolution, 38, (12), 2021, p5437-5452Journal Article, 2021, DOI , URL , TARA - Full Text
• Monerawela, C. and Bond, U., Recombination sites on hybrid chromosomes in Saccharomyces pastorianus share common sequence motifs and define a complex evolutionary relationship between group I and II lager yeasts, FEMS yeast research, 17, (5), 2017Journal Article, 2017, DOI , URL
• Bond, U., Chapter 6 The Genomes of Lager Yeasts, Advances in Applied Microbiology, 69, 2009, p159-182Journal Article, 2009, DOI , URL
• Campbell, S.G. and Del Olmo, M. and Beglan, P. and Bond, U., A sequence element downstream of the yeast HTB1 gene contributes to mRNA 3′ processing and cell cycle regulation (Molecular and Cellular Biology (2002) 22, 24, (8415-8425)), Molecular and Cellular Biology, 28, (5), 2008, p1873Journal Article, 2008, DOI , URL
• Arnaiz, B. and Madrigal-Estebas, L. and Todryk, S. and James, T.C. and Doherty, D.G. and Bond, U., A novel method to identify and characterise peptide heat shock protein 70-associated antigens, Journal of Immune Based Therapies and Vaccines, 4, (2), 2006Journal Article, 2006, DOI , URL
• Campbell, S.G. and Del Olmo, M.L. and Beglan, P. and Bond, U., A sequence element downstream of the yeast HTB1 gene contributes to mRNA 3′ processing and cell cycle regulation, Molecular and Cellular Biology, 22, (24), 2002, p8415-8425Journal Article, 2002, DOI , URL
• Bond, U. and Campbell, S.G. and James, T.C., A model organism for genomic and postgenomic studies: The vast amount of genetic data available on saccharomyces cerevisiae provides important clues, IEEE Engineering in Medicine and Biology Magazine, 20, (4), 2001, p22-32Journal Article, 2001, DOI , URL
• de la Cerda Garcia-Caro, R. and Thompson, G. and Zhang, P. and Hokamp, K. and Roche, F. and Carlin, S. and Vrhovsek, U. and Bond, U., Enhanced flavour profiles through radicicol induced genomic variation in the lager yeasts, Saccharomyces pastorianus, Yeast, 39, (10), 2022, p535-547Journal Article, 2022, DOI , URL
• Principles and applications of genomics and proteomics in the analysis of industrial yeasts. in, editor(s)A. Querol , The Yeast Handbook, Heidleberg, Springer-Verlag, 2006, pp175 - 213, [A. Blomberg and U. Bond]Book Chapter, 2006
• U. Bond, Stressed Out! The effects of environmental stress on mRNA metabolism., FEMS Yeast Research, 6, 2006, p160 - 170Journal Article, 2006
• Canavan, R and U. Bond, Deletion of the nuclear exosome component RRP6 leads to continued accumulation of the histone mRNA HTB1 in S-phase of the cell cycle in Saccharomyces cerevisiae., Nucleic Acids Research, 35, (18), 2007, p6268 - 6279Journal Article, 2007, DOI , TARA - Full Text
• Tharappel, J, Usher, J, Campbell, S and Bond, U., Lager yeasts possess dynamic genomes that undergo rearrangements and gene amplification in response to stress., Current Genetics, Jan 9; [Epub], 2008, p139-152Journal Article, 2008, DOI
• Querol, A and Bond U, The complex and dynamic genomes of industrial yeasts. , FEMS Microbiol Lett. , 293, (1), 2009, p1 - 10Journal Article, 2009, DOI , TARA - Full Text
• Usher, J and Bond, U., Recombination between Homeologous Chromosomes in Lager Yeasts leads to Loss of Function of the Hybrid GPH1 Gene., Applied and Environmental Microbiology, 75, (13), 2009, p4573 - 4579Journal Article, 2009, DOI , TARA - Full Text
• The Genomes of Lager Yeasts in, editor(s)Laskin, A., Sariaslani, S. and Gadd, G. , Advances in Applied Microbiology, Academic Press, 2010, pp159 - 182, [Bond, U.]Book Chapter, 2010
• Arnaiz B, Madrigal-Estebas L, Todryk S, James TC, Doherty DG, Bond U., A Novel method to identify and characterise peptide mimotopes of heat shock protein 70-associated antigens., Journal of Immune Based Therapies and Vaccines, 4, (12), 2006, p1-12Journal Article, 2006, DOI
• Suzanne Beggs, Tharappel C. James and Ursula Bond, The PolyA tail length of yeast histone mRNAs varies during the cell cycle and is influenced by Sen1p and Rrp6p, Nucleic Acids Research, 40, (6), 2012, p2700 - 2711Journal Article, 2012, DOI , URL , TARA - Full Text
• Siebke C, James TC, Cummins R, O'Grady T, Kay E, Bond U., Phage display biopanning identifies the translation initiation and elongation factors (IF1α-3 and eIF-3) as components of Hsp70-peptide complexes in breast tumour cells., Cell Stress Chaperones, 17, (2), 2012, p145 - 156Journal Article, 2012, DOI
• James, T.C. and U, Bond, Molecular Mimics of the Tumour Antigen MUC1, PLOS One, 7, (11), 2012, p2700 - 2711Journal Article, 2012, DOI , URL , TARA - Full Text
• James TC, Gallagher L, Titze J, Bourke P, Kavanagh J, Arendt E, Bond U., In situ production of human β defensin-3 in lager yeasts provides bactericidal activity against beer-spoiling bacteria under fermentation conditions., Journal of Applied Microbiology, 116, (2 ), 2014, p368 - 379Journal Article, 2014, DOI
• Fitzpatrick, J. Kricka, W., James, T.C. and U. Bond, Expression of three Trichoderma reesei cellulase genes in Saccharomyces pastorianus for the development of a two-step process of hydrolysis and fermentation of cellulose , Journal of Applied Microbiology, epub 03/14, 2014, p96-108Journal Article, 2014, DOI
• Generation of New Genotypic and Phenotypic Features in Artificial and Natural Yeast Hybrids (2014) Pfliegler, W.P., Atanasova, L., Karanyicz, E., Sipiczki, M. Bond, U., Druzhinina,I.S., Sterflinger, K., and K. Lopandic, Generation of New Genotypic and Phenotypic Features in Artificial and Natural Yeast Hybrids, Food Technology and Biotechnology , 52, (1), 2014, p46 - 57Journal Article, 2014, TARA - Full Text
• Kricka, W., Fitzpatrick, J. and U. Bond. , Metabolic engineering of yeasts by heterologous enzyme production for degradation of cellulose and hemicellulose from biomass: a perspective, Frontiers in Microbiology, 5, 2014, p174 - 177Journal Article, 2014, DOI , TARA - Full Text
• Monerawela, C., James, T.C., Wolfe, K., and U. Bond, Loss Of Lager Specific Genes And Subtelomeric Regions Define Two Different Saccharomyces cerevisiae Lineages for Saccharomyces pastorianus Group I and II Strains., FEMS Yeast Research, 15, 2015, p1 - 11Journal Article, 2015, DOI , TARA - Full Text
• Kricka, W., Fitzpatrick, J., and U. Bond, Challenges for the Production of Bioethanol from Biomass using Recombinant Yeasts, Advances in Applied Microbiology, 92, 2015, p89 - 125Journal Article, 2015, DOI
• Kricka, W., Fitzpatrick, J., T.C. James and U. Bond, Engineering Saccharomyces pastorianus for the co-utilisation of xylose and cellulose from biomass., Microbial Cell Factories, 14, (61), 2015, p1-11Journal Article, 2015, DOI , TARA - Full Text

• Bond, U., Monerawela, C., and I. Sugre. (2015) , Impact of unique lager-specific genes on phenotypes in Saccharomyces pastorianus. , YEAST, International Congress on Yeast genetics and Molecular Biology, Levico Therme, Italy, 32, 2015Conference Paper
• U. Bond, J. Usher and T.C. James , Brewing yeasts possess dynamic genomes that undergo rearrangements and chromosome loss in response to stress., YEAST, International Congress on Yeast genetics and Molecular Biology, Serrento Italy, 2007, 24, 2007Conference Paper
• Donnelly, D., P. Brosnan, and U. Bond. , The active response to stress., A New Era of Opportunity, European Brewery Monograph , Proceedings of the European Brewery Convention Symposium, Nutfield, U.K., , 1999, 228, 1999Conference Paper
• Donnelly, D.; Brosnan, P., U. Bond , Stress responses in brewing yeasts , Journal of the Institute of Brewing , 2nd Technical Meeting of the European Brewery Convention Brewing Science Group , Edinburgh, Scotland, 1998, 105, (1), 1998, pp8-Conference Paper
• Agell, N., Bond. U and S.J Schlesinger , Proteolytic processing of polyubiquitin, polyubiquitin J. Cell Biology , 105, 1987Conference Paper
• Thomas, G.H., Siegfried, E., Bond. U, and S. Elgin. , Hypersensitivity sites in Hsp26 Promoter, Genetics, 113, (1), 1986Conference Paper
• Siegfried, E., Bond, U., Elgin, SCR., Supercoil-dependent s1-nuclease sensitive sites in the drosophila locus-67B199 , Journal of Cell Biology., 4, 1986Conference Paper
• James T C, Maack C C, Bond U, et al , Vitellogenin coding sequences in insects are conserved , Journal of Cellular Biochemistry , 6, 1982Conference Paper

Ursula Bond, Eukaryotic Gene Expression and Biotechnology Laboratory, Department of Microbiology. 1. The Genomes of Lager Yeasts My research group focuses on understanding the complex genetic make-up of yeasts used in the production of lager beer. Saccharomyces pastorinaus is a hybrid species that emerged just 500-600 years ago as a result of a fusion between of two yeast species, Saccharomyces cerevisiae and Saccharomyces eubayanus. There are two different types of lager yeast, namely Groups I and II that differ from each other in their gene content and structure. Given the importance of these yeasts in the global beer industry, we are addressing questions such as . What is the genetic composition of the genomes of lager yeasts? We discovered that the parent genomes have recombined at specific chromosomal locations to create a unique set of hybrid chromosomes. We identified a common sequence motif at the recombination epicentres, indicative of a common molecular mechanism controlling the recombination events. Recombination at these sites is induced in response to environmental stress. Thus, stresses encountered during industrial fermentations play an important role in the evolution of these yeasts. . How did this species evolve? By analysing the genomes of hundreds of yeast species, we search for the ancestral origins of the species. We discovered that the genomes of lagers yeasts contain genetic information related to modern day Ale and Stout yeasts, leading us to hypothesis that the two lager yeast types arose by sequential rounds of hybridisation firstly between S. eubayanus and an Ale yeasts and subsequently with a Stout yeasts giving rise to Group I and II lager yeasts respectively. . Unique genetic characteristics of lager yeasts. Through mining the genomes of lager yeasts, we identified several genes unique to the species. These include hybrid genes emerging as a result of the recombination between parental chromosomes as well as genes located at the tips of chromosomes have been lost in most other yeast species but preferentially retained in lager yeasts. Through analyzing the effects of the gene products on the biochemistry and physiology of the cell, we aim to decipher the complex algorithm of gene expression leading to the unique characteristics of beer produced by lager yeasts. 2. Improving yeast strains. We are interested in generating industrial yeasts with improved characteristics such as increased ethanol tolerance, improved fermentation capacity and for producing new biological products, using adaptive evolution, synthetic biology and metabolic engineering approaches. Specifically, we have developed (i) Strains of lager yeasts that can metabolise both xylose and cellulose, the major components of plant biomass, in a project aimed at using alternative environmentally sustainable energy sources for biofuel production. (ii) Lager yeasts that produce their own natural antibacterial peptides, by expressing genes encoding defensin-like peptides from plant sources. We examine how the co-expression of multiple peptides on artificial chromosomes can provide natural protection against beer-spoiling bacteria. 3. RNA Production in Yeasts. We study fundamental molecular biological questions in yeasts, specifically relating to the biogenesis RNA. Specifically, we are interested in analysing the novel alleles of XRN1 found exclusively in the lager yeasts. XRN1 encodes for a 5' to 3' exonuclease that plays a central role in the degradation of mRNAs in the cytoplasm and in controlling the steady state levels of mRNA in the cell. Lager yeasts have hybrid copies of XRN1, containing sequences from both S. cerevisiae and S. eubayanus. We are interested in understanding how the presence of the hybrid copies of XRN1 influence the RNA landscape of the lager yeast cells.

• Title

  Biomass to Biofuel: Generation of Cellulose-based Biomass-degrading strains of brewery yeasts
  Summary
  Funding Agency

  Environment Protection Agency
  Date From

  01/10/06
  Date To

  30/09/09
• Title

  Synthetic Immuno-modulatory Ppetides for Cancer Therapy
  Summary
  Funding Agency

  Enterprise Ireland
  Date From

  01/10/06
  Date To

  30/09/09
• Title

  Characterisation of the Role of messenger RNA 3' end formation and transcription termination in the cell cycle regulation of histone mRNAs
  Summary
  Funding Agency

  Science Foundation Ireland
  Date From

  01/08/06
  Date To

  30/09/09
• Title

  Natural peptides to enhance food quality and safety
  Summary

  Food spoilage through microbial contamination is a major problem in our modern food supply chain. Contamination of fresh food products by bacteria or fungi can limit shelf-life and more alarmingly, can be a major health hazard for consumers. Defensins are peptides possessing antimicrobial activity against microorganisms such as bacteria, fungi and viruses. We have previously shown the effectiveness of defensins in preventing bacterial contamination during the brewing process. The aim of the project is to expand on these findings, identifying novel defensin-like peptides that can prevent bacterial and fungal contamination during bread and dough-making processes. Two complementary approaches will be taken. First, synthetic defensin peptides, identified from animal and plant sources will be tested for antifungal and/or antibacterial activity against common bacteria and moulds that contaminate dough fermentations. The peptides will be synthetically modified to optimise antimicrobial activity. Second, yeast species used in the baking industry will be bioengineered to produce defensins in situ. In situ produced defensins and their synthetic counterparts will be evaluated to determine their effect on the shelf-life of baked good, chilled doughs. Extending our previous work, we will also examine the effects of defensins on extending the shelf-life of bottled beers and in preventing fungal contaminations during malting.
  Funding Agency

  Department of Agriculture, Food and Marine
  Date From

  01/04/2014
  Date To

  30/09/2018
• Title

  Bioengineering bespoke yeast strains to convert biomass to biofuel.
  Summary

  Biomass is an alternative source of sustainable energy as we enter the post fossil fuel era. The goal of our research is to bio-engineer bespoke yeast strains, which are capable of converting cellulosic biomass to bioethanol by melding together the fermentative capacity of yeasts with the cellulosic degradation properties of the fungus Trichoderma reesi. Such yeast strains have commercial potential through licensing to Bioethanol-producing companies, for the development of an indigenous Irish Bioethanol Industry and of benefit to breweries and distilleries for the extraction of sugars from spent grains, which currently are a waste product in both industries.
  Funding Agency

  Science Foundation Ireland
• Title

  Aromagenesis
  Summary

  Project AROMAGENESIS will bring together the expertise of researchers in both academia and industry with the strategic aim of generating new yeast strains with novel and unique sensory flavor characteristics. The project will provide training and education of the next generation of scientists in the areas of yeast fermentation processes, physiology, biochemistry, molecular biology, biotechnology, genomics and synthetic biology through a unique interdisciplinary and intersectoral project using cutting edge technology at the leading edge of food and beverage science.
  Funding Agency

  European Commission
  Date From

  01/05/2017
  Date To

  30/11/2021
• Title

  Preventing Beer Spoilage in Lager Fermentations: Optimisation of the production of the antimicrobial defensin peptides in lager strains of yeast, a natural defense against beer-spoiling bacteria
  Summary

  Beer spoilage is a major concern to every Master Brewer in the world. Contamination of brews with beer spoiling bacteria can lead to loss of entire batches of beer resulting in severe financial losses for the brewery. Product withdrawal or recall can have major implications for Brand and business. In a FIRM-funded research project, we have tested whether the naturally occurring antimicrobial agent β-defensin, which forms part of the innate immune system in humans, could be effective as a bacteriocidal agent against beer spoiling bacteria (BSMs). Having demonstrated the effectiveness of β-defensin against BSMs, we then engineered a lager yeast strain to express β-defensin and to secrete the peptide into the beer. The secreted peptide was capable of killing BSMs seeded during fermentation but not in bottled beer. This novel approach not only provides a prophylactic mechanism to prevent beer-spoilage but additionally provides added neutraceutic value to the product as the small quantities of the antimicrobial peptide remaining in the lager can enhance the natural levels of β-defensin in the oral cavity. Defensins are important in maintaining the natural balance of the normal flora of the oral cavity and to protect against bacterial infections. The purpose of the proposed research is the carry out a number of experiments to determine the optimum conditions for the production of β-defensin during and after fermentations and to determine the effective bacterial load that can be eliminated by β-defensin in contaminated fermentations. Our ultimate goal will be to prepare a patent application to protect and license the yeast strains expressing β-defensin and other subsequent modification. To achieve this, we will instigate a Road to Commercialisation strategy involving preparation of an Invention Disclosure Form, market analysis, identification and engagement with of potential industrial partners with the aim of licensing the technology to stakeholders in the Brewery Industry.
  Funding Agency

  Department of Agriculture, Food and Marine
  Date From

  1/10/2012
  Date To

  1/04/2014
• Title

  Antimicrobial peptide preventing beer spoilage wit neutraceutic potential
  Summary
  Funding Agency

  Department of Agriculture and Food
  Date From

  01/10/06
  Date To

  30/09/09

Biomass, Food Processing technologies, Industrial Biotechnology & Bioprocessing, Food products incl. Ingredients, Enzymes, by-products, functional ingredients etc., Genetics and Genomics, Microbiology, Waste to energy, Biochemistry, Molecular & Cellular Biology,

• Gerti T Cori award in Biochemistry 1984
• Fellow of Trinity College Dublin May 2007
• Anna Fuller Cancer Fellowship 1987

• Member Society for General Microbiology
• Member of the RNA Society
• Member of the American Society of Microbiologists
• Member of the American Association for the Advancement of Science