Biomethane production from food waste and organic residues

Anaerobic digestion (AD) of biodegradable waste is an environmentally and economically sustainable solution which incorporates waste treatment and energy recovery. The organic fraction of municipal solid waste (OFMSW), which comprises mostly of food waste, is highly degradable under anaerobic conditions. Biogas produced from OFMSW, when upgraded to biomethane, is recognised as one of the most sustainable renewable biofuels and can also be one of the cheapest sources of biomethane if a gate fee is associated with the substrate. OFMSW is a complex and heterogeneous material which may have widely different characteristics depending on the source of origin and collection system used. The research presented in this thesis investigates the potential energy resource from a wide range of organic waste streams through field and laboratory research on real world samples. OFMSW samples collected from a range of sources generated methane yields ranging from 75 to 160 m3 per tonne. Higher methane yields are associated with source segregated food waste from commercial catering premises as opposed to domestic sources. The inclusion of garden waste reduces the specific methane yield from household organic waste. In continuous AD trials it was found that a conventional continuously stirred tank reactor (CSTR) gave the highest specific methane yields at a moderate organic loading rate of 2 kg volatile solids (VS) m-3 digester day-1 and a hydraulic retention time of 30 days. The average specific methane yield obtained at this loading rate in continuous digestion was 560 ± 29 L CH4 kg-1 VS which exceeded the biomethane potential test result by 5%. The low carbon to nitrogen ratio (C: N <14:1) associated with canteen food waste lead to increasing concentrations of volatile fatty acids in line with high concentrations of ammonia nitrogen at higher organic loading rates. At an organic loading rate of 4 kg VS m-3day-1 the specific methane yield dropped considerably (381 L CH4 kg-1 VS), the pH rose to 8.1 and free ammonia (NH3 ) concentrations reached toxicity levels towards the end of the trial (ca. 950 mg L-1). A novel two phase AD reactor configuration consisting of a series of sequentially fed leach bed reactors connected to an upflow anaerobic sludge blanket (UASB) demonstrated a high rate of organic matter decay but resulted in lower specific methane yields (384 L CH4 kg-1 VS) than the conventional CSTR system.

Biomethane production from grass silage: laboratory assessment to maximise yields

On-farm biogas production is typically associated with forage maize as the biomass source. Digesters are designed and operated with the focus of optimising the conditions for this feedstock. Thus, such systems may not be ideally suited to the digestion of grass. Ireland has ca. 3.85 million ha of grassland. Annual excess grass, surplus to livestock requirements, could potentially fuel an anaerobic digestion industry. Biomethane associated with biomass from 1.1 % of grassland in Ireland, could potentially generate over 10 % renewable energy supply in transport. This study aims to identify and optimise technologies for the production of biomethane from grass silage. Mono-digestion of grass silage and co-digestion with slurry, as would occur on Irish farms, is investigated in laboratory trials. Grass silage was shown to have 7 times greater methane potential than dairy slurry on a fresh weight basis (107 m3 t-1 v 16 m3 t-1). However, comprehensive trace element profiles indicated that cobalt, iron and nickel are deficient in mono-digestion of grass silage at a high organic loading rate (OLR) of 4.0 kg VS m-3 d-1. The addition of a slurry co-substrate was beneficial due to its wealth of essential trace elements. To stimulate hydrolysis of high lignocellulose grass silage, particle size reduction (physical) and rumen fluid addition (biological) were investigated. In a continuous trial, digestion of grass silage of <1 cm particle size achieved a specific methane yield of 371 L CH4 kg-1 VS when coupled with rumen fluid addition. The concept of demand driven biogas was also examined in a two-phase digestion system (leaching with UASB). When demand for electricity is low it is recommended to disconnect the UASB from the system and recirculate rumen fluid to increase volatile fatty acid (VFA) and soluble chemical oxygen demand (SCOD) production whilst minimising volatile solids (VS) destruction. At times of high demand for electricity, connection of the UASB increases the destruction of volatiles and associated biogas production. The above experiments are intended to assess a range of biogas production options from grass silage with a specific focus on maximising methane yields and provide a guideline for feasible design and operation of on-farm digesters in Ireland.

Biogas production from novel substrates

Biogas production is the conversion of the organic material into methane (CH4) and carbon dioxide (CO2) under anaerobic conditions. Anaerobic digestion (AD) is widely used in continental and Scandinavian communities as both a waste treatment option and a source of renewable energy. Ireland however lags behind this European movement. Numerous feedstocks exist which could be digested and used to fuel a renewable transport fleet in Ireland. An issue exists with the variety of feedstocks; these need to be assessed and quantified to ascertain their potential resource and application to AD. From literature the ideal C:N ratio is between 25 and 30:1. Low levels of C:N (<15) can lead to problems with ammonia inhibition. Within the digester a plentiful supply of nutrients and a balanced C:N is required for stable performance. Feedstocks were sampled from a range of over 100 different substrates in Ireland including for first, second and third generation feedstocks. The C:N ranged from 81:1 (Winter Oats) to 7:1 (Silage Effluent). The BMP yields were recorded ranging from 38 ± 2.0 L CH4 kg−1 VS for pig slurry (weaning pigs) to 805 ± 57 L CH4 kg−1 VS for used cooking oil (UCO). However the selection of the best preforming feedstock in terms of C:N ratio or BMP yield alone is not sufficiently adequate. A total picture has to be created which includes C:N ratio, BMP yield, harvest yield and availability. Potential feedstocks which best meet these requirements include for Grass silage, Milk processing waste (MPW) and Saccharina latissima. MPW has a potential of meeting over 6 times the required energy for Ireland’s 2020 transport in energy targets. S. Latissima recorded a yield of over 10,000 GJ ha-1 yr-1 which out ranks traditional second generation biofuels by a factor of more than 4.

Biomethane production from macroalgae

Irish brown seaweeds have been identified as a potential bio-resource with potentially high specific methane yields. Anaerobic digestion is deemed the most feasible technology due to its commercial viability for handling such wet feedstock. However, the biomethane potential of seaweed is highly dependent on its chemical composition which can vary by species type, cultivation method, and time of harvest. This study aims to investigate and optimize the process for the production of biomethane from Irish brown seaweeds focusing on the key technology bottlenecks including for seaweed characterization, biomethane potential assessment, optimization of long-term anaerobic digestion and suitable pre-treatment technologies to enhance potential gas yields. Laminaria digitata and Ascophyllum nodosum were tested for seasonal variation. From the characterization and batch digestion of L. digitata, August was found to be the optimal month for harvest due to high organic matter content, low level of ash and ultimately highest biomethane yield. The specific methane yield of 53 m3 CH4 t-1 wwt in August was 4.5 times higher than the yield in December (12 m3 CH4 t-1 wwt), with ash content the key factor in seasonal variation. For A. nodosum, the optimal harvest month was October with polyphenol content found to be a more influential factor than ash. The gross energy yields from both species were evaluated in the range of 116-200 GJ ha-1 yr-1. Continuous digestion trials were subsequently designed for S. latissima and L. digitata to optimize the key digestion parameters. Results from mono-digestion and co-digestion with dairy slurry revealed that both seaweeds could be digested at maximum biomethane efficiency to a loading rate of 4 kg VS m-3 d-1. Accumulation of salt in the digesters was a concern for long term digestion and it was reasoned that suitable pretreatment may be required prior to digestion. Various pre-treatments were subsequently tested on L. digitata to enhance the gas yield. It was found that maceration after hot water washing yielded 25% more specific methane and up to 54% salt removal as compared to untreated L. digitata. The experiments undertaken aim to assist in providing a basic guideline for feasible design and operation of seaweed digesters in Ireland.

Ruthenibacterium lactatiformans gen. nov., sp.nov., an anaerobic, lactate-producing member of the family Ruminococcaceae isolated from human faeces

Two novel strains of Gram-stain-negative, rod-shaped, obligately anaerobic, non-spore-forming, non-motile bacteria were isolated from the faeces of healthy human subjects. The strains, designated as 585-1T and 668, were characterized by mesophilic fermentative metabolism, production of d-lactic acid, succinic acid and acetic acid as end products of d-glucose fermentation, prevalence of C18 : 1 ω9, C18 : 1 ω9 aldehyde, C16 : 0 and C16 : 1 ω7c fatty acids, presence of glycine, glutamic acid, lysine, alanine and aspartic acid in the petidoglycan peptide moiety and lack of respiratory quinones. Whole genome sequencing revealed the DNA G+C content was 56.4–56.6 mol%. The complete 16S rRNA gene sequences of the two strains shared 91.7/91.6 % similarity with Anaerofilum pentosovorans FaeT, 91.3/91.2 % with Gemmiger formicilis ATCC 27749T and 88.9/88.8 % with Faecalibacterium prausnitzii ATCC 27768T. On the basis of chemotaxonomic and genomic properties it was concluded that the strains represent a novel species in a new genus within the family Ruminococcaceae , for which the name Ruthenibacterium lactatiformans gen. nov., sp. nov. is proposed. The type strain of Ruthenibacterium lactatiformans is 585-1T (=DSM 100348T=VKM B-2901T).

Studies on equine milk and comparative studies on equine and bovine milk systems

The composition of equine milk differs considerably from that of the milk of the principal dairying species, i.e., the cow, buffalo, goat and sheep. Because equine milk resembles human milk in many respects and is claimed to have special therapeutic properties, it is becoming increasingly popular in Western Europe, where it is produced on large farms in several countries. Equine milk is considered to be highly digestible, rich in essential nutrients and to possess an optimum whey protein:casein ratio, making it very suitable as a substitute for bovine milk in paediatric dietetics. There is some scientific basis for the special nutritional and health-giving properties of equine milk but this study provides a comprehensive analysis of the composition and physico-chemical properties of equine milk which is required to fully exploit its potential in human nutrition. Quantification and distribution of the nitrogenous components and principal salts of equine milk are reported. The effects of the high concentration of ionic calcium, large casein micelles (~ 260 nm), low protein, lack of a sulphydryl group in equine β-lactoglobulin and a very low level of κ-casein on the physico-chemical properties of equine milk are reported. This thesis provides an insight into the stability of equine casein micelles to heat, ethanol, high pressure, rennet or acid. Differences in rennet- and acid-induced coagulation between equine and bovine milk are attributed not only to the low casein content of equine milk but also to differences in the mechanism by which the respective micelles are stabilized. It has been reported that β-casein plays a role in the stabilization of equine casein micelles and proteomic techniques support this view. In this study, equine κ-casein appeared to be resistant to hydrolysis by calf chymosin but equine β-casein was readily hydrolysed. Resolution of equine milk proteins by urea-PAGE showed the multi-phosphorylated isoforms of equine αs- and β-caseins and capillary zone electrophoresis showed 3 to 7 phosphorylated residues in equine β-casein. In vitro digestion of equine β-casein by pepsin and Corolase PP™ did not produce casomorphins BCM-5 or BCM-7, believed to be harmful to human health. Electron microscopy provided very clear, detailed images of equine casein micelles in their native state and when renneted or acidified. Equine milk formed flocs rather then a gel when renneted or acidified which is supported by dynamic oscillatory analysis. The results presented in this thesis will assist in the development of new products from equine milk for human consumption which will retain some of its unique compositional and health-giving properties.

Cellular and in-vitro models to assess antioxidant activities of seaweed extracts and the potential use of the extracts as ingredients

Seaweeds contain a range of antioxidant compounds such as polyphenols, carotenoids, sulphated polysaccharides and vitamins and have the potential to be used as ingredients in neutraceuticals. The antioxidant activity of crude 60% methanol extracts prepared from five Irish seaweeds, Ascophyllum nodosum, Laminaria hyperborea, Pelvetia canaliculata, Fucus vesiculosus and Fucus serratus were examined using in-vitro assays and a cell model system to determine the antioxidant activity of the extracts and their ability to protect against H2O2 and tert-BOOH-induced DNA damage and alterations in cellular antioxidant status in the human adenocarcinoma, Caco-2 cell line. To optimise the extraction of antioxidant compounds from seaweeds, an accelerated solvent extraction (ASE®) was used in combination with food grade solvents. The antioxidant activity of these extracts against H2O2 and tert-BOOH-induced DNA damage and alterations in cellular antioxidant status was also assessed. Extracts that exhibited the highest antioxidant activity, A. nodosum (100% water and 80% ethanol extracts) and F. vesiculosus (60% ethanol extract) were selected as ingredients for incorporation into fluid milk and yogurt at concentrations of 0.25% and 0.5%. The addition of the seaweed extracts to milk and yogurt did not affect the pH or shelf-life properties of the products. Seaweed addition did however significantly influence the colour properties of the milk and yogurt. Yellowness values were significantly higher in yogurts containing F. vesiculosus at both concentrations and A. nodosum (80% ethanol) at the 0.5% concentration. In milk, the F. vesiculosus (60% ethanol) and A. nodosum (80% ethanol) at both the 0.25% and the 0.5% concentrations had higher greenness and yellowness values than the milk containing A. nodosum (100% water). Sensory analysis revealed that appearance and flavour governed the overall acceptability of yogurts with the control yogurt, and yogurts containing A. nodosum (100% water) were the most preferred samples by panellists. However, in the milk trial the perception of a fishy taste was the determining factor in the negative perception of milk. The unsupplemented control and the milk containing A. nodosum (100% water) at a concentration of 0.5% were the most overall accepted milk samples by the sensory panellists. The antioxidant activity of the extracts in milk and yogurt remained stable during storage as determined by the in-vitro assays. Seaweed supplemented milk and yogurt were also subjected to an in-vitro digestion procedure which mimics the human digestive system. The milk and yogurt samples and their digestates were added to Caco-2 cells to investigate their antioxidant potential however neither the undigested or digested samples protected against H2O2-induced DNA damage in Caco-2 cells.

Investigation of polyhydroxyalkanoate production by an activated sludge microbial consortium treating artificial dairy wastewater

Petrochemical plastics/polymers are a common feature of day to day living as they occur in packaging, furniture, mobile phones, computers, construction equipment etc. However, these materials are produced from non-renewable materials and are resistant to microbial degradation in the environment. Considerable research has therefore been carried out into the production of sustainable, biodegradable polymers, amenable to microbial catabolism to CO2 and H2O. A key group of microbial polyesters, widely considered as optimal replacement polymers, are the Polyhydroxyalkaonates (PHAs). Primary research in this area has focused on using recombinant pure cultures to optimise PHA yields, however, despite considerable success, the high costs of pure culture fermentation have thus far hindered the commercial viability of PHAs thus produced. In more recent years work has begun to focus on mixed cultures for the optimisation of PHA production, with waste incorporations offering optimal production cost reductions. The scale of dairy processing in Ireland, and the high organic load wastewaters generated, represent an excellent potential substrate for bioconversion to PHAs in a mixed culture system. The current study sought to investigate the potential for such bioconversion in a laboratory scale biological system and to establish key operational and microbial characteristics of same. Two sequencing batch reactors were set up and operated along the lines of an enhanced biological phosphate removal (EBPR) system, which has PHA accumulation as a key step within repeated rounds of anaerobic/aerobic cycling. Influents to the reactors varied only in the carbon sources provided. Reactor 1 received artificial wastewater with acetate alone, which is known to be readily converted to PHA in the anaerobic step of EBPR. Reactor 2 wastewater influent contained acetate and skim milk to imitate a dairy processing effluent. Chemical monitoring of nutrient remediation within the reactors as continuously applied and EBPR consistent performances observed. Qualitative analysis of the sludge was carried out using fluorescence microscopy with Nile Blue A lipophillic stain and PHA production was confirmed in both reactors. Quantitative analysis via HPLC detection of crotonic acid derivatives revealed the fluorescence to be short chain length Polyhydroxybutyrate, with biomass dry weight accumulations of 11% and 13% being observed in reactors 1 and 2, respectively. Gas Chromatography-Mass Spectrometry for medium chain length methyl ester derivatives revealed the presence of hydroxyoctanoic, -decanoic and -dodecanoic acids in reactor 1. Similar analyses in reactor 2 revealed monomers of 3-hydroxydodecenoic and 3-hydroxytetradecanoic acids. Investigation of the microbial ecology of both reactors as conducted in an attempt to identify key species potentially contributing to reactor performance. Culture dependent investigations indicated that quite different communities were present in both reactors. Reactor 1 isolates demonstrated the following species distributions Pseudomonas (82%), Delftia acidovorans (3%), Acinetobacter sp. (5%) Aminobacter sp., (3%) Bacillus sp. (3%), Thauera sp., (3%) and Cytophaga sp. (3%). Relative species distributions among reactor 2 profiled isolates were more evenly distributed between Pseudoxanthomonas (32%), Thauera sp (24%), Acinetobacter (24%), Citrobacter sp (8%), Lactococcus lactis (5%), Lysinibacillus (5%) and Elizabethkingia (2%). In both reactors Gammaproteobacteria dominated the cultured isolates. Culture independent 16S rRNA gene analyses revealed differing profiles for both reactors. Reactor 1 clone distribution was as follows; Zooglea resiniphila (83%), Zooglea oryzae (2%), Pedobacter composti (5%), Neissericeae sp. (2%) Rhodobacter sp. (2%), Runella defluvii (3%) and Streptococcus sp. (3%). RFLP based species distribution among the reactor 2 clones was as follows; Runella defluvii (50%), Zoogloea oryzae (20%), Flavobacterium sp. (9%), Simplicispira sp. (6%), Uncultured Sphingobacteria sp. (6%), Arcicella (6%) and Leadbetterella bysophila (3%). Betaproteobacteria dominated the 16S rRNA gene clones identified in both reactors. FISH analysis with Nile Blue dual staining resolved these divergent findings, identifying the Betaproteobacteria as dominant PHA accumulators within the reactor sludges, although species/strain specific allocations could not be made. GC analysis of the sludge had indicated the presence of both medium chain length as well short chain length PHAs accumulating in both reactors. In addition the cultured isolates from the reactors had been identified previously as mcl and scl PHA producers, respectively. Characterisations of the PHA monomer profiles of the individual isolates were therefore performed to screen for potential novel scl-mcl PHAs. Nitrogen limitation driven PHA accumulation in E2 minimal media revealed a greater propensity among isoates for mcl-pHA production. HPLC analysis indicated that PHB production was not a major feature of the reactor isolates and this was supported by the low presence of scl phaC1 genes among PCR screened isolates. A high percentage distribution of phaC2 mcl-PHA synthase genes was recorded, with the majority sharing high percentage homology with class II synthases from Pseudomonas sp. The common presence of a phaC2 homologue was not reflected in the production of a common polymer. Considerable variation was noted in both the monomer composition and ratios following GC analysis. While co-polymer production could not be demonstrated, potentially novel synthase substrate specificities were noted which could be exploited further in the future.

Development of food ingredients for modulation of glycemia

Starches are a source of digestible carbohydrate and are frequently used in formulated food products in the presence of other carbohydrates, proteins and fat. This thesis explored the effect of addition of neutral (Konjac glucomannan) or charged (milk proteins) polymers on the physical characteristics and digestion kinetics of waxy maize starch. The aim was to identify mechanisms to modulate the pasting properties and subsequent susceptibility to amylolytic digestion. Addition of αs- or β-caseinate protein fractions to waxy maize starch restricted granular swelling during gelatinisation, increasing granule integrity. It was shown that, while β-caseinate can adsorb to starch granules during pasting, αscaseinate can be absorbed into maize starch granules. The resultant effect was a reduction in granule size after heating, more intact granules and a subsequent decrease in starch digestion in vitro as determined by analysis of reducing sugars. The ability of αs-caseinate to reduce the level of amylolytic digestion was confirmed through in vivo pig (Teagasc, Moorepark) and human (University of Surrey, UK) trials. The scope of the thesis extended to the development of a new automated cell for attachment to a rheometer to measure digestion kinetics of starch-protein mixtures. In conclusion, the thesis offers new approaches to modulation of the physical characteristics of unmodified starch during gelatinisation and suggests that the type of protein and/or polysaccharide used in starch-based food systems may influence the ability of the food to modulate glycemia. This is an important consideration in the design of foods with positive health benefits.

Nutraceutical and functional food bioactive peptides in beef

In recent years, the potential to positively modulate human health through dietary approaches has received considerable attention. Bioactive peptides which are released during the hydrolysis or fermentation of food proteins or following digestion may exert beneficial physiological effects in vivo. The aim of this work was to isolate, characterise and evaluate Angiotensin-І-converting enzyme (ACE-І) inhibitory, antimicrobial and antioxidant peptides from the bovine myofibrillar proteins actin and myosin. In order to generate these peptides, the myofibrillar proteins actin and myosin were hydrolysed with digestive enzymes pepsin, trypsin and α-chymotrypsin, or with the industrial thermolysin-like enzyme “Thermoase”, Amano Inc. It was found that each hydrolysate generated contained peptides which possessed ACE inhibitory, antioxidant and antimicrobial activity. The peptides responsible in part for the observed ACE inhibitory, antioxidant and antimicrobial activity of a number of hydrolysates were isolated using the method of RP-HPLC and the bioactive peptides contained within each active fraction was determined using either MALDI-TOF MS/MS or N-terminal peptide sequencing. During the course of this thesis six ACE inhibitory and five antimicrobial peptides were identified. It was determined that the reported antioxidant activity was a direct result of a number of peptides working in synergy with each other. The IC50 values of the six ACE inhibitory peptides ranged in values of 6.85 to 75.7 µM which compare favourably to values previously reported for other food derived ACE inhibitory peptides, particularly the well known milk peptides IPP and VPP, IC50 values of 5 and 9 µM respectively. All five antimicrobial peptides identified in this thesis displayed activity against Escherichia coli, Salmonella typhimurium, Staphylococcus aureus and Listeria innocua with MIC values ranging from 0.625 to10 mM. The activity of each antimicrobial peptide was strain specific. Furthermore the role and importance of charged amino acids to the activity of antimicrobial peptides was also determined. Generally the removal of charged amino acids from the sequence of antimicrobial peptides resulted in a loss of antimicrobial activity. In conclusion, this thesis revealed that a range of bioactive peptides exhibiting ACE inhibitory, antioxidant and antimicrobial activities were encrypted in bovine myofibrillar proteins that could be released using digestive and industrial enzymes. Finally enzymatic hydrolysates of muscle proteins could potentially be incorporated into functional foods; however, the potential health benefits would need to be proven in human clinical studies.

Novel ingredients from brewers' spent grain - bioactivity in cell culture model systems and bioactivity retention in fortified food products

Functional food ingredients, with scientifically proven and validated bioactive effects, present an effective means of inferring physiological health benefits to consumers to reduce the risk of certain diseases. The search for novel bioactive compounds for incorporation into functional foods is particularly active, with brewers’ spent grain (BSG, a brewing industry co-product) representing a unique source of potentially bioactive compounds. The DNA protective, antioxidant and immunomodulatory effects of phenolic extracts from both pale (P1 - P4) and black (B1 – B4) BSG were examined. Black BSG extracts significantly (P < 0.05) protected against DNA damage induced by hydrogen peroxide (H2O2) and extracts with the highest total phenolic content (TPC) protected against 3-morpholinosydnonimine hydrochloride (SIN-1)-induced oxidative DNA damage, measured by the comet assay. Cellular antioxidant activity assays were used to measured antioxidant potential in the U937 cell line. Extracts P1 – P3 and B2 - B4 demonstrated significant (P < 0.05) antioxidant activity, measured by the superoxide dismutase (SOD) activity, catalase (CAT) activity and gluatathione (GSH) content assays. Phenolic extracts P2 and P3 from pale BSG possess anti-inflammatory activity measured in concanavalin-A (conA) stimulated Jurkat T cells by an enzyme-linked immunosorbent assay (ELISA); significantly (P < 0.05) reducing production of interleukin-2 (IL-2), interleukin-4 (IL-4, P2 only), interleukin-10 (IL-10) and interferon-γ (IFN-γ). Black BSG phenolic extracts did not exhibit anti-inflammatory effects in vitro. Hydroxycinnamic acids (HA) have previously been shown to be the phenolic acids present at highest concentration in BSG; therefore the HA profile of the phenolic extracts used in this research, the original barley (before brewing) and whole BSG was characterised and quantified using high performance liquid chromatography (HPLC). The concentration of HA present in the samples was in the order of ferulic acid (FA) > p-coumaric acid (p-CA) derivatives > FA derivatives > p-CA > caffeic acid (CA) > CA derivatives. Results suggested that brewing and roasting decreased the HA content. Protein hydrolysates from BSG were also screened for their antioxidant and anti-inflammatory potential. A total of 34 BSG protein samples were tested. Initial analyses of samples A – J found the protein samples did not exert DNA protective effects (except hydrolysate H) or antioxidant effects by the comet and SOD assays, respectively. Samples D, E, F and J selectively reduced IFN-γ production (P < 0.05) in Jurkat T cells, measured using enzyme linked immunosorbent assay (ELISA). Further testing of hydrolysates K – W, including fractionated hydrolysates with molecular weight < 3, < 5 and > 5 kDa, found that higher molecular weight (> 5 kDa) and unfractionated hydrolysates demonstrate greatest anti-inflammatory effects, while fractionated hydrolysates were also shown to have antioxidant activity, by the SOD activity assay. A commercially available yogurt drink (Actimel) and snack-bar and chocolate-drink formulations were fortified with the most bioactive phenolic and protein samples – P2, B2, W, W < 3 kDa, W < 5 kDa, W > 5 kDa. All fortified foods were subjected to a simulated gastrointestinal in vitro digestion procedure and bioactivity retention in the digestates was determined using the comet and ELISA assays. Yogurt fortified with B2 digestate significantly (P < 0.05) protected against H2O2-induced DNA damage in Caco-2 cells. Greatest immunomodulatory activity was demonstrated by the snack-bar formulation, significantly (P < 0.05) reducing IFN-γ production in con-A stimulated Jurkat T cells. Hydrolysate W significantly (P < 0.05) increased the IFN-γ reducing capacity of the snack-bar. Addition of fractionated hydrolysate W < 3 kDa and W < 5 kDa to yogurt also reduced IL-2 production to a greater extent than the unfortified yogurt (P < 0.05).

Investigations into selective metabolic aspects of bifidobacteria: carbohydrate metabolism, fatty acid biosynthesis and plasmid biology

The gastrointestinal tract (GIT) is a diverse ecosystem, and is colonised by a diverse array of bacteria, of which bifidobacteria are a significant component. Bifidobacteria are Gram-positive, saccharolytic, non-motile, non-sporulating, anaerobic, Y-shaped bacteria, which possess a high GC genome content. Certain bifidobacteria possess the ability to produce conjugated linoleic acid (CLA) from linoleic acid (LA) by a biochemical pathway that is hypothesised to be achieved via a linoleic isomerase. In Chapter two of this thesis it was found that the MCRA-specifying gene is not involved in CLA production in B. breve NCFB 2258, and that this gene specifies an oleate hydratase involved in the conversion of oleic acid into 10-hydroxystearic acid. Prebiotics are defined as non-digestible food ingredients that beneficially affect the host by selectively stimulating growth and/or activity of one or a limited number of bacteria in the colon. Key to the development of such novel prebiotics is to understand which carbohydrates support growth of bifidobacteria and how such carbohydrates are metabolised. In Chapter 3 of this thesis we describe the identification and characterisation of two neighbouring gene clusters involved in the metabolism of raffinose-containing carbohydrates (plus related carbohydrate melibiose) and melezitose by Bifidobacterium breve UCC2003. The fourth chapter of this thesis describes the analysis of transcriptional regulation of the raf and mel clusters. In the final experimental chapter two putative rep genes, designated repA7017 and repB7017, are identified on the megaplasmid pBb7017 of B. breve JCM 7017, the first bifidobacterial megaplasmid to be reported. One of these, repA7017, was subjected to an in-depth characterisation. The work described in this thesis has resulted in an improved understanding of bifidobacterial fatty acid and carbohydrate metabolism, Furthermore, attempts were made to develop novel genetic tools.

A novel activation mechanism for Clostridial bacteriophage endolysins

Bacteriophage-encoded endolysins are produced at the end of the phage lytic cycle for the degradation of the host bacterial cell. Endolysins offer the potential as alternatives to antibiotics as biocontrol agents or therapeutics. The lytic mechanisms of three bacteriophage endolysins that target Clostridium species living under different conditions were investigated. For these endolysins a trigger and release mechanism is proposed for their activation. During host lysis, holin lesion formation suddenly permeabilises the membrane which exposes the cytosol-sequestered endolysins to a sudden environmental shock. This shock is suggested to trigger a conformational switch of the endolysins between two distinct dimer states. The switch between dimer states is proposed to activate a novel autocleavage mechanism that cleaves the linker connecting the N-terminal catalytic domain and the C-terminal domain to release the catalytic domain for more efficient digestion of the bacterial cell wall. Crystal structures of cleaved fragments of CD27L and CTP1L were previously obtained. In these structures cleavage occurs at the stem of the linker connected to the C-terminal domain. Despite a sequence identity of only 22% between 81 residues of the C-terminal domains of CD27L and CTP1L, they represent a novel fold that is identified in a number of different lysins. Within the crystal structures the two distinct dimerization modes are represented: the elongated head‐on dimer and the side-by‐side dimer. Introducing mutations that inhibit either of the dimerization states caused a decrease in the efficiency of both the autocleavage mechanism and the lytic activity of the endolysins. The two dimer states were validated for the full-length endolysins in solution by using right angle light scattering, small angle X‐ray scattering and cross-linking experiments. Overall, the data represents a new type of regulation governed by the C-terminal domains that is used to activate these endolysins once they enter the bacterial cell wall.

Precursor chemistry for oxide related materials

This thesis describes modelling, synthesis, spectroscopic and physical characterisation, as well as application of Magnesium, Calcium and Copper β-diketonate, β-ketoiminate, β-diiminate, Schiff base, amide and fluorenyl compounds. The selected compounds could potentially find application in materials deposition using Atomic Layer Deposition (ALD), MOCVD, CVD and Sol-Gel techniques. Quantum chemical modelling was used as a tool to perform the comprehensive and rapid study of magnesium and calcium precursor molecules in order to predict which of them would be more successful in ALD of metal oxides. Precursor chemistry plays a key role in ALD, since precursors must be volatile, thermally stable, chemisorb on the surface and react rapidly with existing surface groups. This Thesis describes one aspect of this, surface reactivity between ligands and hydroxyl groups, via a gas-phase model with energetics computed at the level of Density Functional Theory (DFT). A number of different synthetic strategies, both aerobic and anaerobic, were investigated for the synthesis of the described metal complexes. These included the use of different metal starting reagents such as, anhydrous and hydrated inorganic metal salts, metal alkyls and Grignard reagents. Some of previously unreported metal complexes of homoleptic and heteroleptic magnesium, calcium and copper β-diketonates, β-ketoiminates, β-diiminates, amides and Schiff base type were synthesised and characterised: [Mg(hfpd)2(DipPa)], [Mg(hfpd)2(MapH)2], [Mg(hf-ebp)(THF)2], [Mg(tf-Pap)Cl(THF)2], [Ca(PhNacnac)2], [Cu(tf-Pap)2], [Cu(PhNacnac)2], [Cu(hf-ebp)], [Cu(DipPa)] and [Cu(DipPa)2(4,4’-bypy)]. A comprehensive study on the thermal properties of magnesium, calcium and copper β-diketonates, β-ketoiminates, β-diiminates, Schiff base, amide and fluorenyl complexes was performed using TGA and sublimation of selected compounds. Atomic Layer Deposition of MgO using magnesium β-ketoiminate – [bis{(4-N-phenyl)-2-pentonato} magnesium] and β-diketonate - [bis(1,1,1,5,5,5-hexafluoropentane-2,4-dionato)(THF)magnesium hydrate] was performed on Si(100) substrates at 180°C and 0.2 Torr using O2 plasma.

Metabolism of host-derived carbohydrates by Bifidobacterium breve UCC2003

Bifidobacteria are Gram positive, anaerobic, typically Y-shaped bacteria which are naturally found in the digestive tract of certain mammals, birds and insects. Bifidobacterium breve strains are numerically prevalent among the gut microbiota of many healthy breast-fed infants. The prototypical B. breve strain UCC2003 has previously been shown to utilise numerous carbohydrates of plant origin. Various aspects of host-derived carbohydrate metabolism occurring in this bacterium will be described in this thesis. Chapter II describes B. breve UCC2003 utilisation of sialic acid, a nine-carbon monosaccharide, which is found in human milk oligosaccharides (HMOs) and the mucin glycoprotein. B. breve UCC2003 was also shown to cross-feed on sialic acid released from 3’ sialyllactose, a prominent HMO, by the extracellular sialidase activity of Bifidobacterium bifidum PRL2010. Chapter III reports on the transcriptional regulation of sialic acid metabolism in B. breve UCC2003 by a transcriptional repressor encoded by the nanR gene. NanR belongs to the GntR-family of transcriptional regulators and represents the first bifidobacterial member of this family to be characterised. Chapter IV investigates B. breve UCC2003 utilisation of mucin. B. breve UCC2003 was shown to be incapable of degrading mucin; however when grown in co-culture with B. bifidum PRL2010 it exhibits enhanced growth and survival properties. A number of methods were used to investigate and identify the mucin components supporting this enhanced growth/viability phenotype. Chapter V describes the characterisation of two sulfatase-encoding gene clusters from B. breve UCC2003. The transcriptional regulation of both sulfatase-encoding gene clusters was also investigated. The work presented in this thesis represents new information on the metabolism of host-derived carbohydrates in bifidobacteria, thus increasing our understanding of how these gut commensals are able to colonise and persist in the gastrointestinal tract.