Life Sciences Commons^™

Polyol-Producing Lactic Acid Bacteria Isolated From Sourdough And Their Application To Reduce Sugar In A Quinoa-Based Milk Substitute, Stephanie Jeske, Emanuele Zannini, Kieran M. Lynch, Aidan Coffey, Elke K. Arendt

Department of Biological Sciences Publications

The interest for plant-based dairy substitutes is expanding rapidly and consumers are opting for nutritious and healthy dairy alternatives. The reduction of sugar using different exogenous enzymes in combination with lactic acid fermentation in a quinoa-based milk substitute was explored in this study. Different amylolytic enzymes were used to release sugar from the raw material, which were further metabolised to mannitol, due to fermentation with two heterofermentative lactic acid bacteria. Using these two biotechnological techniques enables the reduction of sugar, while also preserving some of the sweetness. Leuconostoc citreum TR116, and Lactobacillus brevis TR055 were isolated from sourdough. Both strains …

A Rapid And Sensitive System For Recovery Of Nucleic Acids From Mycobacteria Sp. On Archived Glass Slides, Balkis A. Talip, William J. Snelling, Roy D. Sleator, Colm Lowery, James S.G. Dooley

Department of Biological Sciences Publications

The field of diagnostics continues to advance rapidly with a variety of novel approaches, mainly dependent upon high technology platforms. Nonetheless much diagnosis, particularly in developing countries, still relies upon traditional methods such as microscopy. Biological material, particularly nucleic acids, on archived glass slides is a potential source of useful information both for diagnostic and epidemiological purposes. There are significant challenges faced when examining archived samples in order that an adequate amount of amplifiable DNA can be obtained. Herein, we describe a model system to detect low numbers of bacterial cells isolated from glass slides using (laser capture microscopy) LCM …

Identification And Characterisation Of Novel Phages Of Pectobacterium And Erwinia, Colin Buttimer

PhDs

Losses in crop yields due to disease need to be reduced to meet increasing global food demands associated with growth in the human population. There is a well-recognised need to develop new environmentally-friendly control strategies to combat bacterial crop diseases. There are several crop diseases for which no effective bactericidal agents are currently available, such as potato blackleg and soft rot disease caused by Pectobacterium atrosepticum and other members of soft rot Enterobacteriaceae (Czajkowski et al., 2011). Furthermore, current control measures involving the use of traditional chemicals or antibiotics are losing their efficacy due to the natural development of bacterial …

Improving Health Through Diet And Exercise In Children, Elaine Rush, Tara Coppinger

Publications

We know that nutritious foods and quality physical activity are two of the fundamental needs for normal growth and development of children. Food based dietary guidelines and physical activity recommendations have universal evidence base but the teaching of fundamental movement skills is limited without support. Given the importance of prevention of childhood obesity the distal drivers also need to be examined including poverty. Interventions trialled in carefully controlled conditions while shown to have efficacy are not effective in the real world. There is a need for more research and rigorous evaluation of interventions in combinations of settings and with innovative …

Phage Therapy And Development Of Delivery Systems For Gram-Positive Phage Endolysins, Jude Ajuebor

PhDs

This thesis focussed on Gram positive phages and their endolysins. Here, two similar kay-like staphylococcal phages B1 (vB_SauM_B1) and JA1 (vB_SauM_JA1) were isolated from a commercial therapeutic phage mix. Their host range was established on the Irish National MRSA bank, which included twenty one sequence types in addition relevant control strains. Based on this, distinct phages were identified and subjected to genome sequencing. The sequences were compared with the sequence of phage K (vB_SauM_K), which was also determined in this work. All three phages had a genome size of at least 139 kb, although some key differences were identified between …

Pectobacterium Atrosepticum Phage Vb_Patp_Cb5: A Member Of The Proposed Genus ‘Phimunavirus’, Colin Buttimer, Alan Lucid, Horst Neve, Charles M.A.P. Franz, Jim O’Mahony, Dann Turner, Rob Lavigne, Aidan Coffey

Department of Biological Sciences Publications

© 2018 by the authors. Licensee MDPI, Basel, Switzerland. Pectobacterium atrosepticum is a phytopathogen of economic importance as it is the causative agent of potato blackleg and soft rot. Here we describe the Pectobacterium phage vB_PatP_CB5 (abbreviated as CB5), which specifically infects the bacterium. The bacteriophage is characterized in detail and TEM micrographs indicate that it belongs to the Podoviridae family. CB5 shares significant pairwise nucleotide identity (≥80%) with P. atrosepticum phages 'M1, Peat1, and PP90 and also shares common genome organization. Phylograms constructed using conserved proteins and whole-genome comparison-based amino acid sequences show that these phages form a distinct …

Silk Route To The Acceptance And Re-Implementation Of Bacteriophage Therapy—Part Ii, Wilbert Sybesma, Christine Rohde, Pavol Bardy, Jean Paul Pirnay, Ian Cooper, Jonathan Caplin, Nina Chanishvili, Aidan Coffey, Daniel De Vos, Amber Hartman Scholz, Shawna Mccallin, Hilke Marie Püschner, Roman Pantucek, Rustam Aminov, Jiří Doškař, D. İpek Kurtböke

Department of Biological Sciences Publications

© 2018 by the authors. Licensee MDPI, Basel, Switzerland. This perspective paper follows up on earlier communications on bacteriophage therapy that we wrote as a multidisciplinary and intercontinental expert-panel when we first met at a bacteriophage conference hosted by the Eliava Institute in Tbilisi, Georgia in 2015. In the context of a society that is confronted with an ever-increasing number of antibiotic-resistant bacteria, we build on the previously made recommendations and specifically address how the Nagoya Protocol might impact the further development of bacteriophage therapy. By reviewing a number of recently conducted case studies with bacteriophages involving patients with bacterial …

Novel N4-Like Bacteriophages Of Pectobacterium Atrosepticum, Colin Buttimer, Hanne Hendrix, Alan Lucid, Horst Neve, Jean Paul Noben, Charles Franz, Jim O’Mahony, Rob Lavigne, Aidan Coffey

Department of Biological Sciences Publications

© 2018 by the authors. Licensee MDPI, Basel, Switzerland. Pectobacterium atrosepticum is an economically important phytopathogen that is responsible for potato blackleg and soft rot, and for which current control strategies are limited. In this study, stem samples of potato crops exhibiting blackleg were taken from three farms in Co. Cork, Ireland, and they were found to be infected with P. atrosepticum. Three closely related bacteriophages (phages) that are specific to this phytopathogen were isolated and characterized, namely vB_PatP_CB1, vB_PatP_CB3, and vB_PatP_CB4 (abbreviated as CB1, CB3, and CB4). Both CB1 and CB3 were determined to infect 12 strains and CB4 …

Inhibition Of Listeria Monocytogenes By Human Gut Bacteria, Patrycja Sylvia Olesky

Masters

Listeria monocytogenes is a foodborne pathogen, which continues to be problematic to the food industry due to its ability survive within food products and persist within food processing environments. The growing trend towards natural food preservatives and antimicrobial agents increases the need for the development of novel, natural anti-Listeria agents. Evidence presented in the literature suggests that the human gut microbiota is a reservoir of novel antimicrobial agents. It was therefore hypothesized that novel anti-Listeria agents are produced by human gut-derived bacteria. The objective of this study was to isolate and characterize gut bacteria with anti-Listeria monocytogenes activity. A total …

Comparison Of Staphylococcus Phage K With Close Phage Relatives Commonly Employed In Phage Therapeutics, Jude Ajuebor, Colin Buttimer, Sara Arroyo-Moreno, Nina Chanishvili, Emma M. Gabriel, Jim O'Mahony, Olivia Mcauliffe, Horst Neve, Charles Franz, Aidan Coffey

Department of Biological Sciences Publications

The increase in antibiotic resistance in pathogenic bacteria is a public health danger requiring alternative treatment options, and this has led to renewed interest in phage therapy. In this respect, we describe the distinct host ranges of Staphylococcus phage K, and two other K-like phages against 23 isolates, including 21 methicillin-resistant S. aureus (MRSA) representative sequence types representing the Irish National MRSA Reference Laboratory collection. The two K-like phages were isolated from the Fersisi therapeutic phage mix from the Tbilisi Eliava Institute, and were designated B1 (vB_SauM_B1) and JA1 (vB_SauM_JA1). The sequence relatedness of B1 and JA1 to phage K …

Selection Of Potential Therapeutic Bacteriophages That Lyse A Ctx-M-15 Extended Spectrum Β-Lactamase Producing Salmonella Enterica Serovar Typhi Strain From The Democratic Republic Of The Congo, Elene Kakabadze, Khatuna Makalatia, Nino Grdzelishvili, Nata Bakuradze, Marina Goderdzishvili, Ia Kusradze, Marie France Phoba, Octavie Lunguya, Cédric Lood, Rob Lavigne, Jan Jacobs, Stijn Deborggraeve, Tessa De Block, Sandra Van Puyvelde, David Lee, Aidan Coffey, Anahit Sedrakyan, Patrick Soentjens, Daniel De Vos, Jean Paul Pirnay, Nina Chanishvili

Department of Biological Sciences Publications

© 2018 by the authors. Licensee MDPI, Basel, Switzerland. Recently, a Salmonella Typhi isolate producing CTX-M-15 extended spectrum β-lactamase (ESBL) and with decreased ciprofloxacin susceptibility was isolated in the Democratic Republic of the Congo. We have selected bacteriophages that show strong lytic activity against this isolate and have potential for phage-based treatment of S. Typhi, and Salmonella in general.

Daily And Seasonal Trends Of Electricity And Water Use On Pasture-Based Automatic Milking Dairy Farms, John Shortall, Bernadette O'Brien, Roy D. Sleator, J. Upton

Department of Biological Sciences Publications

The objective of this study was to identify the major electricity and water-consuming components of a pasture-based automatic milking (AM) system and to establish the daily and seasonal consumption trends. Electricity and water meters were installed on 7 seasonal calving pasture-based AM farms across Ireland. Electricity-consuming processes and equipment that were metered for consumption included milk cooling components, air compressors, AM unit(s), auxiliary water heaters, water pumps, lights, sockets, automatic manure scrapers, and so on. On-farm direct water-consuming processes and equipment were metered and included AM unit(s), auxiliary water heaters, tubular coolers, wash-down water pumps, livestock drinking water supply, and …

The Effect Of Dairy Cow Breed On Milk Production, Cow Traffic And Milking Characteristics In A Pasture-Based Automatic Milking System, John Shortall, Cathriona Foley, Roy D. Sleator, Bernadette O'Brien

Dept. of Biological Sciences Preprints

Despite the increasing frequency of integrated automatic milking (AM) and pasture-based systems, there is limited knowledge available on the suitability of different dairy cow breeds to these systems. Thus, the objective of this experiment was to establish the performance of three breeds in a pasture-based AM system with respect to milk production, cow traffic and milking characteristics. The breeds examined were Holstein Friesian (HF), Jersey x HF (JEX) and Norwegian Red x HF (NRX), all of which have been previously identified as being compatible with conventional milking pasture-based systems. The experiment was conducted in mid-lactation and variables measured included milking …

The Extent To Which Strategic Talent Management Is Understood, And Properly Utilised, In The Life Science Sector In Ireland, Jennifer O'Brien

Theses

In 2017, Ireland was named the best country in the world for attracting high-value foreign direct investment for the sixth year in a row and is home to the top ten global Life Science organisations. The Life Science industry in Ireland depends on a consistent pipeline of talent to realise the growth incentivised by this investment and as the war for talent rages, there is unrelenting pressure on these organisations to attract, manage, develop, engage and retain highly skilled STEM talent. The talent focus, consequently, has to become more strategic.

This thesis focuses on the extent to which Strategic Talent …

Development Of Multi-Class Analytical Methods For Agrochemical Contaminants, Sarah Tuck

Theses

In this project, cost-effective multi-class analytical methods were developed to detect a range of antiparasitic, feed additive and pesticide substances in foodstuffs of animal origin. These substances have the potential to enter the food chain through their occurrence as residues either through the animals themselves or other routes e.g. contamination. To ensure the continued safety of food destined for human consumption regulatory control limits have been established for permitted levels of these residues in foods of animal origin. Despite these controls the continued monitoring of foodstuffs is necessary to ensure these limits are not breached and that substances are not …

Predicting Energy And Water Consumption On Dairy Farms Through Statistical Analysis And Machine-Learning Methods, Philip Shine

Theses

With the abolishment of milking quotas across all European Union member states in April 2015, dairy farmers must adjust their farming practises to minimise milk production costs to adequately prepare for potential periods of reduced revenue. Milk production is an intense energy and water consuming process. Coupled with challenging European greenhouse gas reduction targets and legislation regarding the prevention of groundwater pollution and deterioration, increasing the production of milk in Ireland must be met with the sustainable consumption of on-farm energy and direct water resources, to ensure the future monetary and environmental sustainability of Ireland’s dairy industry. Thus, this body …

Optimisation Of Ion Exchange Chromatography Purification Protocols For A Staphylococcal Peptidoglycan Degrading Hydrolase Enzyme, Fiona Maher

Theses

Bacteriophage (phage) are the most abundant biological entities on earth and were first discovered by d’Herelle in 1917. They are found wherever their hosts live and, like all viruses they do not have the ability to make their own protein. Therefore, in order to reproduce, phage must invade and infect bacterial cells. This project focused on the optimisation of Ion Exchange Chromatography purification protocols for a staphylococcal peptidoglycan degrading hydrolase enzyme (CHAPk). The project objective was to obtain the greatest yield of enzyme from the growth of the E.coU XL 1-Blue expression system into which the vector pQE60 was previously …

A Mixed Methods Sequential Explanatory Study Of Male Farmers' Health Beliefs, Attitudes And Practices In Rural Kerry, Chrystal O'Brien

Theses

Aim/Background: Beliefs and attitudes about health directly and indirectly influence concomitant behaviours, practices and health outcomes. In Ireland, male farmers are experiencing a disproportionate burden of ill health in preventable lifestyle diseases, yet there is a lack of behavioural research in relation to male farmers and their health. Therefore, the purpose of this study was to examine the health beliefs, attitudes and practices of male farmers in rural Kerry, and to explore healthcare professionals' insights of male farmers' health beliefs, attitudes and practices.

Methodology: The study adopted a mixed methods design. Phase one of the study involved structured interviews with …

The Use Of Machine Learning To Detect Suckling In Pre-Weaned Calves, Sukumar Katamreddy

Theses

The weaning of cattle is a process which is known to be labour intensive and to have stressful effects on both cow and calf Common methods used in the weaning process include the temporary removal of a mother from the calf and manual observation and intervention. Early and speedy weaning is known to have a number of benefits, including health benefits for both cow and calf, additional weight gains for the calves as well as reduced labour and feed requirements. The process known as Two-Stage Weaning is recognised to be an effective low-stress approach to weaning in which the calf …

Marine Bioactives From Saccharina Latissima, Orlaith O'Connell

Masters

Due to rapid global urbanization and therefore increased adoption of a 'Westernized' lifestyle, including decreased physical activity and increased consumption of highly processed and refined foods with a high sugar, fat and salt content, prevalence of gastrointestinal disorders are on the rise. Inflammatory bowel disease (IBD) in particular is closely associated with this type of lifestyle. IBD is a term used to describe chronic inflammatory conditions which affects all or parts of the gastrointestinal tract. It includes conditions such as Crohn's Disease, which affects all the gastrointestinal tract and Ulcerative Colitis which mainly affects the colan. Due to the role …