The aim of this study was to determine how daily yield records might be used to improve the genetic evaluation of dairy cattle, which is currently based on 305-day yield predicted from monthly test day records. Daily milk yield records of 488 first lactation Holstein Friesian cows were obtained from one UK herd and summarised into weekly averages. Weekly fat, protein and lactose content records, from the same herd, were also obtained and each multiplied by test day yield to estimate fat, protein and lactose yields. Analysis of variance indicated that residual standard deviation (RSD) for each trait was lower when season of production was included in the model instead of the season of calving. The difference in RSD was more for fat and protein yields than the other traits. Lactation stage and season were the most important environmental factors affecting daily milk yield and composition while calving age had a small but significant (P<0.05) effect. Pregnancy accounted for 1.4 to 1.7% of the variation in yield traits but less than 0.4% of the variation in content traits. Its effects varied with gestation stage causing daily milk yield to decline by 3kg in the 8<SUP>th</SUP> month of gestation. A significant interaction between lactation and gestation stage was observed which suggested that the negative effect of pregnancy was higher in mid than late stages of lactation. Standard models of the lactation curve studied accounted for a substantial proportion of the variation in daily milk yields of typical lactations, which made up about half of the lactations studied. The other half was made up of atypical lactations such as highly persistent animals with almost flat curves whose lactation could not be adequately modelled with the standard curve functions. A regression spline model was derived which was as good as the best 3 parameter model and more flexible. These results indicate that models which make rigid assumptions about the shape of the lactation curve may not be very effective in accounting for the effect of lactation stage on daily yields. Yields of the same trait at different stages of lactation were positively correlated throughout but the correlation between yield and content traits was negative. Average correlation between milk yield and adjacent weeks was 0.93 declining to 0.61 between yields 41 weeks apart. Daily milk yields in mid and late stages of lactation were more highly correlated with 305-day yield than yields in early lactation. Covariance functions, using orthogonal polynomials up to the order of 4, were used to model genetic and permanent environmental covariances in a restricted maximum likelihood (REML) random regression (RR) model. Genetic parameters and breeding values were estimated for yield in every week of lactation. There were compared with estimates from a multivariate model, which considered yield at different stages as different traits, and a repeatability model without random regressions.

Regional cheeses in Europe, including red smear cheeses, are part of the cultural heritage of their source region and an important, traditional industry. However, the incidence of Listeria, including Listeria monocytogenes, has been relatively high, and despite extensive upgrading of hygiene in the production of these cheeses across Europe it has not decreased. The anti-listerial activity of the complex microbial surface flora has been seen as protective in their production, and the use of defined microbial inocula, or the manipulation of the surface microflora, as tools in the fight against contamination by Listeria. However, the microbial flora, bacteria and yeast, especially bacteria, on different red smear cheeses have been poorly defined and identified. The surface microflora needs to be properly identified to enable the selection of strains which generate the colour, aroma and organoleptic qualities of specific cheeses and to screen for anti-listerial activity – identifying the bacterial flora was the subject of this study. In this project 1424 isolates from 5 European red smear cheeses were dereplicated by rep-PCR and representatives of the rep-PCR clusters sent for comparison with reference strains at the Belgium Coordinated Collections of Microorganisms (BCCM) Laboratorium voor Microbiologie, Universiteit Gent (LMG) culture collection, Ghent. The 16S rRNA genes of unidentified strains were sequenced and novel strains subjected to a full polyphasic taxonomic identification. Four novel species were described Agrococcus casei, Mycetocola reblochoni, Brevibacterium superficiens and Leucobacter lepicola. The remaining diversity of isolates, as identified using molecular fingerprints (rep-PCR, this thesis, and Box PCR, Ghent) and 16S rDNA sequencing from 3 stages of ripening for each of 5 cheeses gave a comparative overview of the bacteria and their variation, across cheeses and with stage of ripening. Although many of the strains recovered were identified to known species, the molecular characterisation showed extensive sub-specific variation. This was exemplified by the isolation of Brevibacterium linens. Although a commercial strain of B. linens was typically inoculated with the initial smear wash and B. linens was isolated from many cheese surface samples, the strains isolated were not the same as the strains used for inoculation. Common species of Brevibacterium, Corynebacterium and Microbacterium were isolated from multiple cheeses. vi Following the introduction of molecular ecological techniques it has become clear that isolation techniques give a biased view of community composition (Tabacchioni et al., 2000), often missing dominant members of the community and isolating rapid growing but numerically insignificant strains. Therefore denaturing gradient gel electrophoresis (DGGE) was applied to DNA extracted and amplified from 15 duplicate samples of the surface microflora, from 3 stages of ripening and from 5 cheeses. Extensive optimisations of procedures for the DGGE method in terms of DNA extraction procedures to the use of GC clamped primers were developed on Tilsit. The DNA extraction method was optimised and a nested PCR approach, using actinobacterial specific primers for the 16S gene, was utilised to generate DGGE profiles for all five smear cheeses at early, middle and late ripening stages. Selected bands were excised and sequenced. A combined approach of cloning with DGGE, with Tilsit and Livarot cheeses, gave similar results showing the robustness of the method. The molecular analysis revealed different complex patterns of bands for each cheese, and changes with ripening stage. However, part of the complexity was probably due to single strand DNA leading to multiple sequences present in single bands and multiple bands from the same sequence. Excision of bands, re-amplification and re-analysis generated multiple single sequence bands that could be sequenced. Most of the species revealed by molecular analysis using DGGE and sequencing were similar to recognised species of Brevibacterium, Corynebacterium and Microbacterium though not always assigned to the same species as the isolates from the same cheese sample. Some unexpected species were detected such as Citrococcus and Propionibacterium. The project provided a comprehensive overview of the actinobacterial flora present on five red smear cheeses and provides the source information for the future study of anti-listerial properties and to develop defined inocula. However, the example of Brevibacterium linens and the extensive sub-specific variation detected may indicate that commercially developed inocula may still be outcompeted by natural flora.

This thesis is an investigation into the production of exopolysaccharides (EPS) produced by strains of Lactobacillus delbrueckii ssp. bulgaricus and Lactococcus lactis ssp. cremoris. These are used in the dairy industry for the production of yoghurt and fermented drinks products. For many years EPS producing lactic acid bacteria have been used by the dairy industry as a thickening agent in the production of yoghurt. However, this EPS producing trait is unstable and is readily lost which can cause an alteration in the texture of the final product. It was found that all the strains of Lb. delbrueclcii ssp. bulgaricus and Le. /aetis ssp. eremoris produced quantities of EPS that could be used for further analysis. They were found to be in the molecular weight range of 6.6 x 1 06g /mol to 1.26 x 1011 glmol and were composed of different quantities of glucose, galactose and rhamnose. Temperature, carbon source and shaking all affected the quantities of EPS produced by all strains of Le. laetis ssp. eremoris. The firmness and viscosity of fermented milks produced by strains of Lb. delbrueckii ssp. bulgaricus were higher than those produced by strains of Le. laetis ssp. cremoris indicating that firmness and viscosity are not solely related to the levels of EPS production. A 40kb plasmid was found in all strains of Le. /aetis ssp. cremoris that could potentially contain the genes for EPS production. The plasmid could not be removed using elevated temperature or with the addition of acriflavin. Fourier transform infrared spectroscopy (FTIR) showed that it was possible to differentiate different strains based on their spectra and that differences were found in the protein and EPS regions of the spectra. It was also established that the age of culture, whether the growth medium was liquid or solid and the carbon source of the growth media had an effect on the FTIR spectra produced and the ability to differentiate between strains. There is further potential to develop this technique to provide a quick and easy method of identifying strains of lactic acid bacteria and monitor their EPS producing ability.

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The aim of this study was to first evaluate the benefits of including Jersey milk into Holstein-Friesian milk on the Cheddar cheese making process and secondly, using the data gathered, identify the effects and relative importance of a wide range of milk components on milk coagulation properties and the cheese making process. Blending Jersey and Holstein-Friesian milk led to quadratic trends on the size of casein micelle and fat globule and on coagulation properties. However this was not found to affect the cheese making process. Including Jersey milk was found, on a pilot scale, to increase cheese yield (up to + 35 %) but it did not affect cheese quality, which was defined as compliance with the legal requirements of cheese composition, cheese texture, colour and grading scores. Profitability increased linearly with the inclusion of Jersey milk (up to 11.18 p£ L-1 of milk). The commercial trials supported the pilot plant findings, demonstrating that including Jersey milk increased cheese yield without having a negative impact on cheese quality, despite the inherent challenges of scaling up such a process commercially. The successful use of a large array of milk components to model the cheese making process challenged the commonly accepted view that fat, protein and casein content and protein to fat ratio are the main contributors to the cheese making process as other components such as the size of casein micelle and fat globule were found to also play a key role with small casein micelle and large fat globule reducing coagulation time, improving curd firmness, fat recovery and influencing cheese moisture and fat content. The findings of this thesis indicated that milk suitability for Cheddar making could be improved by the inclusion of Jersey milk and that more compositional factors need to be taken into account when judging milk suitability.

This thesis has investigated the fouling and cleaning behaviour of dairy fluids in a pilot scale plate heat exchanger (PHE). Commissioning of the pilot scale PHE showed that accurate and repeatable data was obtainable. The fouling and cleaning behaviour of two types of dairy fluid, whey protein concentrate (WPC) and WPC with minerals added (WPC m ), were investigated and compared to that of milk. The model fluid, WPC m , was developed by adding calcium and phosphorus salts to WPC to the same levels found in milk. Comparison of WPC m and WPC fouling behaviour revealed two differences: (i) fouling rate declined for WPC m relative to WPC, (ii) deposit distribution in the PHE changed to resemble milk behaviour. Addition of calcium and phosphorus salts also resulted in a decline in the pH of the WPC solution from 7.01 to 5.57. Decline in pH could explain the reduction of the extent of fouling. Addition of calcium ions could be responsible for deposition earlier on in the PHE at lower temperatures due to increased aggregation. Distribution of deposit across sections of the PHE and the type of deposit produced had important influences on the cleaning behaviour. For the first time observations of changes in overall heat transfer coefficient (U) and pressure drop (AP) across different sections of the PHE were made during cleaning. The former indicated surface cleanliness and the latter indicated complete removal of deposit from the system. Differences were noted when cleaning WPC and WPC m deposits. WPC deposit was removed from PHE surfaces as a whole very quickly. Although WPC m deposit was also removed from PHE surfaces quickly, it took considerably longer for the cleaning fluid containing the deposit to be removed from the PHE. This was indicated by secondary pressure peaks observed in all PHE sections for WPC m only. Cleaning end-points occurred successively in each section of the PHE: the pasteuriser cleaned first, then the intermediate and finally the UHT section. Distribution of deposit in the PHE was critical in its final removal and thus WPC m was most appropriate as a milk simulant. Removal may depend on: (a) mass transfer of the cleaning chemical into the deposit to dissolve or break it up, (b) shear on the deposit from the fluid, or (c) formation of a fluid of high viscosity which is difficult to remove, for example close to the surface of the deposit. Thermal recovery was an incomplete measure of cleaning: pressure drop measured the removal both of surface-bound deposit and of the fluid which has dissolved the deposit. Cleaning times and cleaning rates were assessed for the pasteuriser section and the PHE as a whole. They were defined as the time taken for AP and U to recover to a percentage of their clean values. The effects of varying the three process variables, concentration, flowrate and temperature of cleaning chemical (single-stage cleaner, LQ32), were assessed for their effects on cleaning behaviour individually. In general, an optimum chemical concentration of 0.7wt% with respect to NaOH and cleaning temperature of 80-85°C was found, increasing flowrate increased cleaning rate and decreased cleaning times. This work was extended by the development of empirical relationships to account for interactive effects of these process variables using Response Surface Methodology. Heat transfer measurements were better correlated than pressure drops. Flowrate emerged as the most important factor in cleaning. The experiments showed that the chemistry of cleaning can be less important than the engineering and that the key step is the removal of the deposit from the exchanger.

No description available.