Studies on factors relating to the development of defects in commercial cheese

Defects in commercial cheese result in a downgrading of the final cheese and a consequential economic loss to the cheese producer. Developments of defects in cheese are often not fully understood and therefore not controllable by the producer. This research investigated the underlying factors in the development of split and secondary fermentation defect and of pinking defects in commercial Irish cheeses. Split defect in Swiss-type cheese is a common defect associated with eye formation and manifests as slits and cracks visible in the cut cheese loaf (Reinbold, 1972; Daly et al., 2010). No consensus exists as to the definitive causes of the defect and possible factors which may contribute to the defect were reviewed. Models were derived to describe the relationship between moisture, pH, and salt levels and the distance from sample location to the closest external block surface during cheese ripening. Significant gradients within the cheese blocks were observed for all measured parameters in cheeses at 7 day post/after manufacture. No significant pH gradient was found within the blocks on exit from hot-room ripening and at three months post exit from the hot-room. Moisture content reached equilibrium within the blocks between exit from hot-room and 3 months after exit from hot-room while salt and salt-to-moisture levels had not reached equilibrium within the cheese blocks even at three months after exit from hot-room ripening. A characterisation of Swiss-type cheeses produced from a seasonal milk supply was undertaken. Cheeses were sampled on two days per month of the production year, at three different times during the manufacturing day, at internal and external regions of the cheese block and at four ripening time points (7 days post manufacture, post hot-room, 14 days post hot-room and 3 months in a cold room after exit from hot-room). Compositional, biochemical and microbial indices were determined, and the results were analysed as a splitplot with a factorial arrangement of treatments (season, time of day, area) on the main plot and ripening time on the sub-plot. Season (and interactions) had a significant effect on pH and salt-in-moisture levels (SM), mean viable counts of L. helveticus, propionic acid and non-starter lactic acid bacteria, levels of primary and secondary proteolysis and cheese firmness. Levels of proteolysis increased significantly during hot-room ripening but also during cold room storage, signifying continued development of cheese ripening during cold storage (> 8°C). Rheological parameters (e.g. springiness and cohesiveness) were significantly affected by interactions between ripening and location within cheese blocks. Time of day of manufacture significantly affected mean cheese calcium levels at 7 days post manufacture and mean levels of arginine and mean viable counts of NSLAB. Cheeses produced during the middle of the production day had the best grading scores and were more consistent compared to cheeses produced early or late during day of manufacture. Cheeses with low levels of S/M and low values of resilience were associated with poor grades at 7 days post manufacture. Chesses which had high elastic index values and low values of springiness in the external areas after exit from hot-room ripening also obtained good commercial grades. Development of a pink colour defect is an intermittent defect in ripened cheese which may or may not contain an added colourant, e.g., annatto. Factors associated with the defect were reviewed. Attempts at extraction and identification of the pink discolouration were unsuccessful. The pink colour partitioned with the water insoluble protein fraction. No significant difference was observed between ripened control and defect cheese for oxygen levels and redox potential or for the results of elemental analysis. A possible relationship between starter activity and defect development was established in cheeses with added coulourant, as lower levels of residual galactose and lactose were observed in defective cheese compared to control cheese free of the defect. Swiss-type cheese without added colourant had significantly higher levels of arginine and significantly lower lactate levels. Flow cell cytometry indicated that levels of bacterial cell viability and metabolic state differed between control and defect cheeses (without added colourant). Pyrosequencing analysis of cheese samples with and without the defect detected the previously unreported bacteria in cheese, Deinococcus thermus (a potential carotenoid producer). Defective Swiss-type cheeses had elevated levels of Deinococcus thermus compared to control cheeses, however the direct cause of pink was not linked to this bacterium alone. Overall, research was undertaken on underlying factors associated with the development of specific defects in commercial cheese, but also characterised the dynamic changes in key microbial and physicochemical parameters during cheese ripening and storage. This will enable the development of processing technologies to enable seasonal manipulation of manufacture protocols to minimise compositional and biochemical variability and to reduce and inhibit the occurrence of specific quality defects.

Computational modeling of defects in nanoscale device materials

This PhD thesis concerns the computational modeling of the electronic and atomic structure of point defects in technologically relevant materials. Identifying the atomistic origin of defects observed in the electrical characteristics of electronic devices has been a long-term goal of first-principles methods. First principles simulations are performed in this thesis, consisting of density functional theory (DFT) supplemented with many body perturbation theory (MBPT) methods, of native defects in bulk and slab models of In0.53Ga0.47As. The latter consist of (100) - oriented surfaces passivated with A12O3. Our results indicate that the experimentally extracted midgap interface state density (Dit) peaks are not the result of defects directly at the semiconductor/oxide interface, but originate from defects in a more bulk-like chemical environment. This conclusion is reached by considering the energy of charge transition levels for defects at the interface as a function of distance from the oxide. Our work provides insight into the types of defects responsible for the observed departure from ideal electrical behaviour in III-V metal-oxidesemiconductor (MOS) capacitors. In addition, the formation energetics and electron scattering properties of point defects in carbon nanotubes (CNTs) are studied using DFT in conjunction with Green’s function based techniques. The latter are applied to evaluate the low-temperature, low-bias Landauer conductance spectrum from which mesoscopic transport properties such as the elastic mean free path and localization length of technologically relevant CNT sizes can be estimated from computationally tractable CNT models. Our calculations show that at CNT diameters pertinent to interconnect applications, the 555777 divacancy defect results in increased scattering and hence higher electrical resistance for electron transport near the Fermi level.

Investigation of electrically active defects at the interface of high-k dielectrics and compound semiconductors

As silicon based devices in integrated circuits reach the fundamental limits of dimensional scaling there is growing research interest in the use of high electron mobility channel materials, such as indium gallium arsenide (InGaAs), in conjunction with high dielectric constant (high-k) gate oxides, for Metal-Oxide-Semiconductor Field Effect Transistor (MOSFET) based devices. The motivation for employing high mobility channel materials is to reduce power dissipation in integrated circuits while also providing improved performance. One of the primary challenges to date in the field of III-V semiconductors has been the observation of high levels of defect densities at the high-k/III-V interface, which prevents surface inversion of the semiconductor. The work presented in this PhD thesis details the characterization of MOS devices incorporating high-k dielectrics on III-V semiconductors. The analysis examines the effect of modifying the semiconductor bandgap in MOS structures incorporating InxGa1-xAs (x: 0, 0.15. 0.3, 0.53) layers, the optimization of device passivation procedures designed to reduce interface defect densities, and analysis of such electrically active interface defect states for the high-k/InGaAs system. Devices are characterized primarily through capacitance-voltage (CV) and conductance-voltage (GV) measurements of MOS structures both as a function of frequency and temperature. In particular, the density of electrically active interface states was reduced to the level which allowed the observation of true surface inversion behavior in the In0.53Ga0.47As MOS system. This was achieved by developing an optimized (NH4)2S passivation, minimized air exposure, and atomic layer deposition of an Al2O3 gate oxide. An extraction of activation energies allows discrimination of the mechanisms responsible for the inversion response. Finally a new approach is described to determine the minority carrier generation lifetime and the oxide capacitance in MOS structures. The method is demonstrated for an In0.53Ga0.47As system, but is generally applicable to any MOS structure exhibiting a minority carrier response in inversion.

The application of next generation sequencing to profile microbe related cheese quality defects

High throughput next generation sequencing, together with advanced molecular methods, has considerably enhanced the field of food microbiology. By overcoming biases associated with culture dependant approaches, it has become possible to achieve novel insights into the nature of food-borne microbial communities. In this thesis, several different sequencing-based approaches were applied with a view to better understanding microbe associated quality defects in cheese. Initially, a literature review provides an overview of microbe-associated cheese quality defects as well as molecular methods for profiling complex microbial communities. Following this, 16S rRNA sequencing revealed temporal and spatial differences in microbial composition due to the time during the production day that specific commercial cheeses were manufactured. A novel Ion PGM sequencing approach, focusing on decarboxylase genes rather than 16S rRNA genes, was then successfully employed to profile the biogenic amine producing cohort of a series of artisanal cheeses. Investigations into the phenomenon of cheese pinking formed the basis of a joint 16S rRNA and whole genome shotgun sequencing approach, leading to the identification of Thermus species and, more specifically, the pathway involved in production of lycopene, a red coloured carotenoid. Finally, using a more traditional approach, the effect of addition of a facultatively heterofermentative Lactobacillus (Lactobacillus casei) to a Swiss-type cheese, in which starter activity was compromised, was investigated from the perspective of its ability to promote gas defects and irregular eye formation. X-ray computed tomography was used to visualise, using a non-destructive method, the consequences of the undesirable gas formation that resulted. Ultimately this thesis has demonstrated that the application of molecular techniques, such as next generation sequencing, can provide a detailed insight into defect-causing microbial populations present and thereby may underpin approaches to optimise the quality and consistency of a wide variety of cheeses.