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Dr. Ursula Mary Bond

Fellow Emeritus (Microbiology)
      
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Dr. Ursula Mary Bond

Fellow Emeritus (Microbiology)

 ubond@tcd.ie

 


Dr. Ursula Bond, a Fellow of Trinity College Dublin, graduated from TCD with a degree in Biochemistry and was awarded a PhD in Molecular Biology by Washington University, St Louis, Missouri. As a PhD student, Dr. Bond was awarded the Carl F. and Gerty T. Cori prize for research excellence in Biochemistry. She conducted post-doctoral research at Yale University as an Anna Fuller Fellow before returning to Trinity College Dublin, taking up an academic role in the Department of Microbiology. A world leader in the genetics of industrial yeasts, Dr. Bond has published seminal papers in the fields of yeast genetics and molecular biology. Key areas of research include the (i) Composition, Structure and Evolution of the genomes of the Lager Yeasts, Saccharomyces pastorianus, (ii) adaptive evolution and synthetic biology approaches to expand the metabolic and physiological capacities of industrial yeasts and (iii) fundamental molecular biological questions on the molecular mechanisms of RNA biogenesis in yeasts. During her tenure at Trinity, Dr. Bond has been awarded 21 research grants, and was the lead PI on 19, with research funding of 15.67 million euro. She currently leads an International consortium of academic and industrial scientists studying the genetics of flavour production in industrial yeasts in a project funded by the EU Horizon 2020 programme.
  Cancer Biology   Cell cycle regulation in yeasts   Gene Expression in yeasts   Genetic Engineering   Genetics   Genome structures in brewery yeasts   Molecular Biology   Molecular Genetics   Molecular markers and recognition   mRNA metabolism   Nuclei acids, polynucleotides, protein synthesis   Tumour markers
Project Title
 Aromagenesis
From
01/05/2017
To
30/11/2021
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
Programme
European Training Network
Project Type
Research and Training
Person Months
48
Project Title
 Natural peptides to enhance food quality and safety
From
01/04/2014
To
30/09/2018
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
Programme
FIRM
Project Type
Applied research
Person Months
48
Project 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
From
1/10/2012
To
1/04/2014
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
Programme
FIRM Plus
Project Type
Research and Development
Project Title
 Bioengineering bespoke yeast strains to convert biomass to biofuel.
From
To
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
Programme
TIDA
Project Title
 Antimicrobial peptide preventing beer spoilage wit neutraceutic potential
From
01/10/06
To
30/09/09
Summary
Funding Agency
Department of Agriculture and Food
Programme
Food Institutional Research Measure
Project Type
Research

Page 1 of 2
Details Date From Date To
Member of the American Association for the Advancement of Science
Member of the American Society of Microbiologists
Member of the RNA Society
Member Society for General Microbiology
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), 2022, Notes: [cited By 0], Journal Article, PUBLISHED  TARA - Full Text  DOI
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, p535-547 , Notes: [cited By 0], Journal Article, PUBLISHED  DOI
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), 2021, Notes: [cited By 1], Journal Article, PUBLISHED  TARA - Full Text  DOI
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), 2021, Notes: [cited By 9], Journal Article, PUBLISHED  TARA - Full Text  DOI
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, p5437-5452 , Notes: [cited By 1], Journal Article, PUBLISHED  TARA - Full Text  DOI
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 - 1586, Journal Article, PUBLISHED  TARA - Full Text  URL
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, p425-437 , Notes: [cited By 1], Journal Article, PUBLISHED  DOI
Monerawela, C and U. Bond, The hybrid genomes of Saccharomyces pastorianus-a current perspective, YEAST, 35, (1), 2018, p39-50 , Review Article, PUBLISHED  TARA - Full Text  DOI
Chandre Monerawela and Ursula Bond, Brewing up a storm: The genomes of lager yeasts and how they evolved, Biotechnology Advances, 2017, p1-8 , Notes: [pii: S0734-9750(17)30021-6.], Journal Article, PUBLISHED  DOI  URL
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 - 12, Notes: [ https://doi.org/10.1093/femsyr/fox047], Journal Article, PUBLISHED  URL
  

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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, 2015, Conference Paper, PUBLISHED
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, 2007, Conference Paper, PUBLISHED
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, 1999, Conference Paper, PUBLISHED
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, PUBLISHED
Agell, N., Bond. U and S.J Schlesinger , Proteolytic processing of polyubiquitin, polyubiquitin J. Cell Biology , 105, 1987, Conference Paper, PUBLISHED
Thomas, G.H., Siegfried, E., Bond. U, and S. Elgin. , Hypersensitivity sites in Hsp26 Promoter, Genetics, 113, (1), 1986, Conference Paper, PUBLISHED
Siegfried, E., Bond, U., Elgin, SCR., Supercoil-dependent s1-nuclease sensitive sites in the drosophila locus-67B199 , Journal of Cell Biology., 4, 1986, Conference Paper, PUBLISHED
James T C, Maack C C, Bond U, et al , Vitellogenin coding sequences in insects are conserved , Journal of Cellular Biochemistry , 6, 1982, Conference Paper, PUBLISHED

  


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