Life Sciences Commons^™

The Use Of Membrane Filtration To Increase Native Whey Protein In Infant Formula, And Effects On Bioaccessibility And Bioactivity, Yihong Chen

Theses

Breastfeeding is recognised as the gold standard for feeding newborns and infants. However, infants who cannot be breast-fed or for whom breast milk is not available, can be fed with bovine infant milk formula (IMF) as a substitute. Researchers and producers of IMF strive to continually improve or “humanise” the composition and functionality of IMF. During production of IMF it must undergo several heat treatment steps, e.g. heat-sterilisation or spray-drying, in order to provide a safe product to the infant. These heat treatments denature the globular whey proteins in IMF. In contrast, breast milk is by its nature unheated, so …

Nutrient Intakes, Compliance With Recommendations And Key Sources In Women Of Child-Bearing Age (18-50 Y) In Ireland, Abigail O' Mahony

Theses

Women’s pre-conceptional health (including nutritional status) is important for both the health of the individual themselves and also for the lifelong health of any occurring offspring. However, it has been estimated that up to 50% of pregnancies are unplanned, thus optimal nutritional status is important for all women of child-bearing age (WCBA) not just those with pregnancy intentions. Despite the accumulation of evidence of the importance of nutritional status at this life-stage, nutrient recommendations for WCBA for the most part don’t differ from recommendations for other population groups. The notable exception to this is that all WCBA are recommended to …

Investigating Optimal Lipid:Protein Profiles For Infant Milk Formula, Valentina Ivanova

Theses

From the early twentieth century onward, much research has focused on improving infant milk formula (IMF). During the development of IMF, breast milk is commonly considered as the reference and IMF manufacturers are thriving to mimic the composition and/or to match the functionality of breast milk as closely as possible. A variety of bioactive ingredients, found in human breast milk, have been isolated and investigated for their potential functionality and utilised in the production of IMF. This study evaluated the current knowledge on compositional differences between human breast milk and IMF, and recent advances and developments in IMF production. Following …

Exploring The Metabolic Capabilities And Biotransformation Potential Of Environmental Lactococcus Strains, Desirée Román Naranjo

Theses

The aim of this thesis is to characterize environmental Lactococcus strains to identify different and diverse metabolic capabilities that could be applied to microbial biotransformation, defined as the conversion of a cheap/waste substrate into a value-added product. Due to the increased amounts of food processing waste generated worldwide and the impact of climate change, new sustainable approaches are necessary to contribute to waste valorization and the circular bioeconomy. We ask to what extent and in what ways environment isolated Lactococcus strains could contribute to food biotransformation by metabolizing a different range of substrates. We do so to further understand and …

Identification And Creation Of Novel Bacteriocins With Potential Food And Clinical Applications, David Lynch

Theses

Bacteriocins represent a heterogeneous group of small, ribosomal-synthesized, potent antibacterial peptides produced by bacteria, capable of inhibiting bacteria both closely related or indeed those from other genera than the producer. In addition to their role as food preservatives, bacteriocins have potent activity against medically significant pathogens and are considered attractive alternatives to antibiotics, due to their inherent heat stability, potency at nanomolar scale, resistance to proteases and low levels of acquired resistance in commercial applications. The aim of this thesis was to identify, purify and bioengineer novel bacteriocins from Staphylococcus and Lactic Acid Bacteria (LAB), with a view to expanding …

Isolation And Characterisation Of Soil-Derived Bacteria With Antimicrobial Activity Against Antibiotic Resistant Pathogens, Ellen Twomey

Theses

Bacteriocins are a diverse range of ribosomally synthesized bioactive peptides, recognised predominantly for their potent antimicrobial activity against other strains closely related to the producer. The focus of this thesis was to explore this activity and examine the potential of bacteriocins to inhibit the growth of clinically relevant pathogens. Although evidence exists in the literature to suggest that bacteriocins could be applied in a similar fashion to conventional antibiotics, to date they are only utilised as preservative in food to prevent the growth of foodborne illness causing organisms. Isolating and screening bacterial strains in order to identify bacteriocin producers has …

Genetic Selection For Improved Production Efficiency In The Mature Dairy Herd, Maeve Williams

Theses

Improving dairy cow production efficiency is highly desirable because of its well-documented impact on profitability and sustainability. Long-term gains in dairy cow production efficiency have already been delivered through genetic selection. Nonetheless, achieving further improvements in production efficiency could cement the economic and environmental efficiency of the dairy industry, globally. To date, several components contributing to production efficiency have been overlooked, with many studies focusing on dairy cow production efficiency over short periods rather than lifetime efficiency. Therefore, the objectives of this thesis were to quantify the genetic variance components of complementary dairy cow efficiency metrics; including dry matter intake, …

Development Of Phage Therapy Strategies Against Gram-Positive Bacterial Pathogens, Sara Arroyo Moreno

Theses

Bacterial resistance to conventional antibiotics has become an urgent healthcare issue worldwide. In this light, a renewed interest has emerged for therapy with bacteriophages (phages), which are viruses that can specifically infect bacteria. These viruses encode different proteins that degrade specific bonds within the bacterial cell wall, both to inject their genomic material into the bacterial cells and to release the viral progeny: virion-associated hydrolases and endolysins, respectively. Elimination of Gram-positive pathogens with recombinant versions of phage enzymes represents a promising alternative to classical antibiotics. In this thesis, different phage therapy strategies involving either whole phages or the use of …

A Study On Plant-Derived Small Proteins And Peptides With Antiyeast Activity And Preliminary Investigations In Food Materials, Giulia Mignone

Theses

The discovery of novel antimicrobial molecules would benefit considerably different biotechnological fields, including medicine, agriculture and the food industry, on which this thesis work focuses. Specifically, here are presented fundamental studies on plant-derived antimicrobial proteins for the reduction of food spoilage caused by yeast microorganisms. Small proteins and peptides from the plant innate immune system possess several characteristics which could make them ideal candidates for a novel and natural antispoilage agent. The first Chapter reviews proteins families associated with the plant innate immune system that exhibit antiyeast activity and low molecular weight (<30 kDa), focusing on their structure and antiyeast mode of action. Chapter 2 investigates two peptides, Pn-AMP1 and Pn-AMP2 belonging to the hevein-type peptides family; peptides were synthetically generated using their native amino acid sequence. Synthetic Pn-AMP1 showed fast action activity against common food spoilage yeasts, it resulted potentially safe for consumption, and it was successfully incorporated in UHT milk and Fanta Orange, where it contained the growth of Kluyveromyces lactis and Zygosaccharomyces bailii, respectively. A different family of antimicrobial plant proteins (2S albumins) was studied in Chapters 3, 4, 5 and 6. Chapter 3 describes the selective extraction of an antiyeast protein (labelled WMS1 in this thesis work) of ~14 kDa from white mustard (Brassica hirta) seeds. The protein was purified in a relatively high yield, using a simple protocol that included only one chromatographic method step. In Chapter 4, bioinformatics tools and wet-lab techniques are used to study the structure and classify the antiyeast protein. The WMS1 antiyeast protein was identified as an isoform of the Napin protein Allergen Sin a 1 belonging to the 2S albumins family, characterised by high structural stability which donates to the protein resistance heat treatment and proteolytic degradation. Chapter 5 describes the antimicrobial spectrum of WMS1 , its antiyeast mechanism of action and its validity as preservative agent. Although WMS1 resulted potentially safe for consumption and inhibited the growth of Z. bailii in several beverage systems, its biotechnological potential is limited by its allergic properties. In Chapter 6, the protein WMS1 was cloned in a pET28a-MBP vector and expressed in an E. coli BL21 system. Interestedly, recombinant WMS1 and native WMS1 showed similar activity against the yeast Z. bailii. Thesis abstract 2 Chapter 7 includes a protocol for the rational design of ultra-short antimicrobial peptides. Since ultra-short antimicrobial sequences can be found within the sequence of any larger protein, the protocol was applied using WMS1 primary sequence, and seven ultra-short SinA-AMPs were chemically generated. Among the various SinA-AMPs, the peptide labelled SinA-pepIII had in vitro activity against several common yeast spoilage strains via membrane permeabilisation and it could be employed as a food preservative as it was pH- and heat- stable, potentially safe in terms of human consumption and it prevented the growth of Z. bailii in cranberry juice. The results obtained in this work offer new perspectives in the research for novel and clean-label food preservatives to fight the food waste phenomenon.

Elucidation Of Novel And Established Campylobacter Species With Clinical And Agricultural Significance Through Phenotypic, Genotypic, And Taxonomic Investigation, Caoimhe Lynch

Theses

Campylobacter spp. are well-established human, veterinary and economic pathogens, with a broad host range spanning from terrestrial and marine mammalian, avian and reptilian hosts. The scope of the study includes novel and notorious species within the genus, with reference to zoonotic agents Campylobacter jejuni and Campylobacter coli - the leading cause of human bacterial gastroenteritis in the EU and Ireland, Campylobacter fetus that represents the most common campylobacter causing bacteraemia and two novel species isolated from pigs not described in the literature previously. C. jejuni and C. coli isolates (n = 350) recovered from broiler caecal and neck skin samples, …

Aims: Action Against Infirmity And Malnutrition In Seniors, Maeve Lorraine Mary O'Connell

Theses

Aim: The primary aim of this thesis was to investigate the relationship between nutrition and frailty in Irish older adults. The nutritional status, dietary quality and perceived barriers/motivators to nutrition were also examined, and a frailty intervention protocol was designed. Methods: Cross-sectional study in Irish community-dwelling adults aged ≥65 years. Nutritional status, dietary intake, functional mobility and food choice motivators/healthy eating barriers were assessed using the Mini Nutritional Assessment – Short Form (MNA-SF), a food frequency questionnaire (FFQ), the Timed Up and Go (TUG) test and a custom designed 2-item questionnaire, respectively. Frailty was defined as three or more of …

Genetic Selection For Improved Efficiency And Profitability In Beef Cattle, David Kelly

Theses

Despite the importance of feed intake and efficiency in beef production, there are still gaps in our knowledge on optimal production efficiency traits and breeding strategies for improved feed, production and economic efficiency. The objectives of this thesis were to redefine production efficiency in growing cattle by exploiting carcass information and to validate current beef breeding goals for improving efficiency, and to investigate the relationships of feeding behaviour with performance, feed efficiency, and carcass merit. Feed intake and liveweight data were available on up to 6,088 cattle, of which 3,146 had carcass data, 4,672 had ultrasound data and 1,548 had …

Optimising The Carcass Merit Of Irish Beef Cattle Using Genetic And Non-Genetic Information At The Animal And Herd Level, David Kenny

Theses

Failure of beef carcasses to achieve desirable carcass specifications represent inefficiencies within the supply chain, namely greater carcass processing costs and the inability of the resulting primal cuts to conform to high-value market specifications. Analysis of a representative sample of prime Irish beef cattle conducted in this thesis determined that 59% of cattle fail to achieve the desired carcass specifications of the supply chain at slaughter. The objective of this thesis was to use readily available information to define strategies that could help to reduce this statistic. Firstly, the likelihood of Irish beef carcasses achieving the desired carcass specifications was …

Novel Molecular Approaches To Diagnostic And Epidemiological Analyses Of Cryptosporidiumspp.Implicated In Clinical Infection, Jennifer K. O'Leary

Theses

Cryptosporidium remains an underestimated, yet highly prevalent, parasitic agent of gastrointestinal illness worldwide. In clinical settings, diagnosis has previously relied on microscopic techniques. However, enteric parasite targeting molecular tools, such as real-time PCR panels, have superseded microscopy in recent years. This body of work examines the nature, implications and opportunities of this paradigm shift. This thesis is divided into seven chapters that consist of a literature review chapter, five experimental chapters focusing on the molecular diagnosis and epidemiological analysis of Cryptosporidium spp., and a final summary chapter. Chapter I provides the contextual narrative and supportive reasoning behind the research undertaken …

Predicting, Monitoring And Controlling The Growth Of Listeria In Complex Food Matrices, Laura Mary Nyhan

Theses

Listeria monocytogenes is a foodborne pathogen which is a significant challenge in food production, particularly for ready-to-eat (RTE) products. Incidence of Listeria in RTE foods can be reduced by the application of intelligent combinations of preservative factors or hurdles, while data quantifying the efficacy of hurdle combinations can be exploited and used in the area of predictive microbiology. Traditional culture-based techniques, such as viable plate counts, are commonly used to monitor the growth/survival of microorganisms in foods, however these methods are tedious, time-consuming and due to their destructive nature, are associated with low reproducibility and high variability. Therefore, rapid, non-invasive …

Elucidation Of Multi-Origin Inula Helenium L. For Antimicrobial Activity And Heavy Metal Profiling As An Exemplar For The Use And Regulation Of Plants As Antibiotics., Ciara Ruth Kenny

Theses

An impending post-antibiotic era looms, thus new sources of therapeutic chemical entities are crucial to sustain effective antimicrobial chemotherapy worldwide. Plant natural products are a source of accessible, structurally diverse compounds that provide therapeutic potential. The pharmacological applications of plants in medicine can be guided by the attestation of traditional use or the application of this knowledge to uncover new leads in the drug discovery process. The range of modified in vitro methods commonly used to investigate preclinical antimicrobial efficacy of plant-derived natural products, and the associated limitations and challenges in the provision of new antimicrobial drugs from plants is …

The Role Of Software Engineering In Bioinformatics, Brendan Sean Lawlor

Theses

This thesis proposes that by applying state-of-the-art software engineering tools, techniques and frameworks to currently recognised challenges in bioinformatics, improved outcomes can be attained in that field. It begins by decomposing software engineering into two categories, namely process and architecture, and choosing two key challenges in the practice of bioinformatics: reproducibility and scalability. The body of the thesis is an exploration of the intersection between these two software engineering categories and these two bioinformatics challenges. The question is asked: Can best practices in professional software engineering be applied to address key issues in the bioinformatics domain, creating positive outcomes? And …

Defining The Potential Of Gene Therapy With Bone Morphogenetic Proteins As A Novel Therapeutic Approach In Parkinson’S Disease, Susan Rebecca Goulding

Theses

Parkinson’s disease is a neurodegenerative disorder, characterised by the progressive degeneration of midbrain dopaminergic neurons, and the intracellular aggregation of the α-synuclein protein in neurons throughout the nervous system. These changes result in the characteristic motor impairments in Parkinson’s disease. Current treatments are solely symptomatic and therefore there is an unmet clinical need to develop new disease-modifying therapies that can alter disease progression. For over 25 years, one proposed experimental therapy has focused on the delivery of proteins called neurotrophic factors to the brain to prevent dopaminergic neuron degeneration. However, to date, clinical trials using the most well-known neurotrophic factors …

Investigating The Antioxidant, Immunomodulatory And Anti-Obesogenic Propertiesof Novel Bsg-Derived Extracts And Their Potential As Ingredients In Functional Foods For Older Adults, Suzanne O Brien

Theses

Brewer’s Spent Grain (BSG) represents a substantial waste product of the brewing industry, with 39 million tonnes generated globally every year. To date the primary use of BSG is as animal feed but there is significant interest in identifying alternative uses for this agro-industry by-product. BSG is rich in protein and fibre and is known to contain health-promoting bioactive compounds, thus one application would be in the area of functional foods. People are living longer and as the older adult population continues to increase globally so too is the prevalence of age-related chronic conditions. Diet plays an essential role in …

Predicting Carcass Cut Yields In Cattle From Digitalimages Using Artificial Intelligence, Darragh Matthews

Theses

Beef carcass classification in Europe is predicated on the EUROP grid for both fatness and conformation. Although this system performs well for grouping visually similar carcasses, it cannot be used to accurately predict meat yields from these groups, especially when considered on an individual cut level. Deep Learning (DL) has proven to be a successful tool for many image classification problems but has yet to be fully proven in a regression scenario using carcass images. Here we have trained DL models to predict carcass cut yields and compared predictions to more standard machine learning (ML) methods. Three approaches were undertaken …

Optimisation Of Grass Measurement Technologies Through Field Experimentation And Numerical Simulation Methods, Darren Joseph Murphy

Theses

Maximising pasture utilisation through optimal grassland management is vital in terms of ensuring the economic sustainability and mitigating the environmental impact of both Irish and global pasture-based livestock production. Frequent and accurate measurement of grass quantity and quality is one of the main methods of maximising grass production and utilisation on pasture-based farms. The most prominent grass measurement tool used on Irish pasture is the rising plate meter (RPM), however, there are a range of issues with this method including operator bias, precision and difficulties in accounting for spatial variation. Currently, there is no definitive protocol for grass measurement which …

The Use Of Mycobacteriophages As A Novel Therapeutic Option To Control And Treat Johne's Disease, Gillian Catherine Crowley

Theses

The incidences of Johne’s disease (JD) in farms worldwide have increased significantly over the last 80 years. The increase in JD is owing to the lack of diagnostic tests available and the long incubation period of the disease causing pathogen, Mycobacterium avium paratuberculosis (MAP). In addition, treatment of JD with antibiotics has proven difficult due to the emergence of antibiotic resistance MAP strains and the presence of the thick lipid rich mycobacterial cell wall. An alternative diagnostic and treatment method for JD involves the use of mycobacteriophages. As part of this research, individual mycobacteriophages (TM4) and a mycobacteriophage cocktail (LE1 …

Investigating The Synergistic Bioactive Effects Of Fruit, Vegetable And Protein Combinations In A Market-Ready Food Product For Young Adults, Jessica Eivers

Theses

Diets high in fruits and vegetables (FV), are widely recommended for their health-promoting properties. A low intake of FV among young adults, is associated with the risk of developing chronic diseases such as cardiovascular disease (CVD), hypertension, osteoporosis, obesity, type 2 diabetes, dental caries, hypercholesterolemia and certain cancers in later life. According to the World Health Organisation (WHO), despite an increasing awareness of the health benefits of FV, consumption by young adult’s remains below the recommended intake of 400g per day. This project aims to develop innovative, FV products for young adults with demonstrated bioactivity and high nutrient density. Initially, …

Group B Streptococcus: Molecular Epidemiology, Pathogenic Profiling And Control Strategies, Katherine Mary Hayes

Theses

Group B Streptococcus (GBS) are frequent colonisers of the gastrointestinal tract of healthy adults with worldwide rates of 18% colonisation; however, they are also opportunistic pathogens capable of causing invasive disease, particularly in neonates and adults with underlying conditions. Indeed, GBS is the leading cause of invasive neonatal disease worldwide with a global incidence of 0.49 per 1000 live births and GBS disease in adults is increasing globally, with estimated rates of 10.9 cases per 100,000 people. While GBS remain largely susceptible to penicillin, there have been reports of reduced beta-lactam susceptibility in certain countries and resistance to other antibiotic …

Modelling And Simulation Of Renewable Technologies For Economic And Environmental Analysis And Optimization Of Dairy Farms, Michael Christopher Breen

Theses

The aim of this thesis was to develop a dairy optimisation platform to optimise investments in dairy farm technology and changes to on-farm management practices and electricity tariffs, in order to maximise profitability and minimise environmental impacts. Increased dairy herd sizes and milk production levels in Ireland as well as changing regulations concerning emissions, renewable penetration and energy efficiency have necessitated a means of financial decision support for farmers. Therefore this body of work focused on the creation of a comprehensive method for optimising dairy farm technology selection, management practices and electricity tariffs. The measures which could be implemented on …

Isolation, Identification And Characterisation Of Enterococcus Faecalis Isolates For The Generation Of Multifuctional Bioactive Peptides From Milk, Kenneth Patrick Graham

Theses

Enterococci are lactic acid bacteria (LAB) that have the paradoxical position of possessing biochemical properties of technological importance, but are also considered as opportunistic pathogens capable of causing infection in immunocompromised patients. However, they have a long history of safe use in foods and have been evaluated in several studies for their role as starter, adjunct, probiotic and protective cultures. They show higher proteolytic activities than other LAB and have demonstrated the ability to produce bioactive peptides during the fermentation of milk. The aim of this project was to identify proteolytic Enterococcus faecalis isolates capable of generating health-promoting bioactive peptides …

Crystallographic Studies On Host-Interacting Proteins Of Phage K Virion, Antonio Pichel Beleiro

Theses

Phage K is a lytic bacteriophage that infects a broad range of staphylococci, including some methicillin-resistant Staphylococcus aureus strains. Phage K attaches to its host via a baseplate. The contracted conformation of the baseplate contains a fiber and two receptorbinding proteins responsible for the interaction with the host. The native conformation of the baseplate also includes a tail central spike that shears off after contraction. The aim of the thesis is the structural characterization of phage K receptor-binding proteins and tail central spike. Experimentally, the thesis relies on crystallographic methods, which encompass: production of suitable sample, crystallization, diffraction, and data …

The Occurrence Of Listeria Monocytogenes In The Mushroom Production Chain And The Use Of Bacteriophage For Its Control, Vincenzo Pennone

Theses

In Agaricus bisporus production, the occurrence of L. monocytogenes is still poorly understood. A number of studies have shown the presence of L. monocytogenes in the mushroom processing environment, suggesting its source from raw materials storage areas (Viswanath et al, 2013; Murugesan et al, 2015). In this study, 10 mushroom producers and three raw material (compost and casing) producers participated in two surveys on the occurrence of L. monocytogenes in the most high-risk areas of the production environment. In the first survey, floors, drains, platforms, crates, raw materials and mushrooms were tested for L. monocytogenes presence and the results were …

Crystallographic Structure Determination Of Bacteriophage-Encoded Enzymes That Specifically Target Pathogenic Bacteria, Marta Sanz Gaitero

Theses

Antibiotic resistance is becoming a serious public health concern. Infections that some decades ago could be treated with antibiotics now sometimes do not respond to traditional treatment, causing higher mortality and economic losses. An alternative to the use of antibiotics are bacteria's natural predators, bacteriophages (or phages), and specifically their lytic enzymes. These proteins are produced by phages to degrade bacterial peptidoglycan to inject their genetic material into the bacteria (virion-associated peptidoglycan hydrolases) or to release their progeny once the infection is finished (endolysins). They can be applied exogenously to lyse Gram-positive bacteria or be genetically engineered to lyse Gram-negative …

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 …