Optimisation of tennis string production from bovine intestine : a thesis presented in partial fulfilment of the requirements for the degree of Master in Technology at Massey University, Palmerston North, New Zealand

The collagen and elastin content of the beef thread samples ranged from between 47-70% and 1.2-2.5% respectively. Amino acid analysis showed that the collagen present was probably collagen Type I while the non-collagenous proteins predominantly were globulins with a small amount of albumins. Putative "strong" and "weak" batches of threads could not be differentiated on the basis of collagen content or mechanical properties such as ductility, ultimate tensile strength or Young's modulus. Treatment of "strong" or "weak" threads with three different processes, sodium carbonate, sodium carbonate/EDTA and sodium hydroxide, gave no significant differences in products The sodium carbonate/EDTA process can remove 31.9% of non-collagenous proteins over the three stages of the process. The shrinkage temperature and ductility were lowered while the ultimate tensile strength. Young's modulus and diameter are increased by the processing. Threads given three successive trypsin treatments had 47.4% (2% trypsin) and 36.2% (0.6% trypsin) of non-collagenous proteins had removed. Properties of the treated threads from this treatment gave similar trends to threads from the sodium carbonate/EDTA process except that enzyme treatment resulted smaller thread diameters. Moreover, when the treated threads from the second and third high concentration trypsin treatments were heated, they stretched rather than shrank. This phenomenon was unexpected and apparently has not been previously reported in the literature. On subjecting threads which had had three successive trypsin treatments to the sodium carbonate/EDTA process, the stretch temperature phenomenon was abolished and the normal shrinkage temperature property of collagen was restored. However, the shrinkage temperature of the thread from the integrated trypsin -sodium carbonate/EDTA process was significantly lower than that from the sodium carbonate/EDTA process alone. This integrated process does not affect the tensile strength properties, but the diameter of the treated threads using the higher trypsin rate is significantly smaller than the starting materials. However, threads from the integrated process using lower trypsin seemed to show a trend toward smaller diameters but this observation could not be shown to be statistically significant. It is suggested that two trypsin treatments integrated into a sodium carbonate/EDTA process could be an optimum process provided the smaller diameter trend of wet thread can translate into smaller diameter in dry string

How Philosophy of Mind Needs Philosophy of Chemistry

By the 1960s many (perhaps most) philosophers had adopted ‘physicalism’ ─ the view that physical causes fully account for mental activities. However, controversy persists about what count as ‘physical causes’. ‘Reductive’ physicalists recognize only microphysical (elementary-particle-level) causality. Many (perhaps most) physicalists are ‘non-reductive’ ─ they hold that entities considered by other (‘special’) sciences have causal powers. Philosophy of chemistry can help resolve main issues in philosophy of mind in three ways: developing an extended mereology applicable to chemical combination, testing whether ‘singularities’ prevent reduction of chemistry to microphysics, and demonstrating ‘downward causation’ in complex networks of chemical reactions

How Philosophy of Mind Needs Philosophy of Chemistry

By the 1960s many (perhaps most) philosophers had adopted ‘physicalism’ ─ the view that physical causes fully account for mental activities. However, controversy persists about what count as ‘physical causes’. ‘Reductive’ physicalists recognize only microphysical (elementary-particle-level) causality. Many (perhaps most) physicalists are ‘non-reductive’ ─ they hold that entities considered by other (‘special’) sciences have causal powers. Philosophy of chemistry can help resolve main issues in philosophy of mind in three ways: developing an extended mereology applicable to chemical combination, testing whether ‘singularities’ prevent reduction of chemistry to microphysics, and demonstrating ‘downward causation’ in complex networks of chemical reactions

Immunoglobulin motions and antigen binding effects examined by elastic network models

Immunoglobulin motions are evaluated using Normal Mode Analysis with Elastic Network Models. By employing this approach, we learn about the important motions of the protein, for the domain motions and other internal motions, and see strong evidence of the dominance of the low frequency normal modes. We particularly investigate the CDR motions. The CDR loops tend to move with their attached domains. By finding internal distance changes, we determine which parts of the structure undergo more rigid body like motions and which parts encounter larger internal distance changes. It turns out that Fab undergoes a large extent of changes in its internal distances and the Fc part moves more rigidly. We also investigate the effects of sugar and antigen binding on the IgG structures. The antigen binding effect is highly significant in the CDR regions, since antigen binding seems to enhance the motions in this region, while the sugar effects are more localized to the Fc region. By performing Principal Component Analysis on the numerous available Fab structures, we gather information about motions apparent in this ensemble of conformations, the correspondence of Principal Components to the Normal Modes of the Elastic Network Models, the residue fluctuations in the first few Principal Components and other important information about Immunoglobulin Dynamics

Immunoglobulin Structure Exhibits Control over CDR Motion

Motions of the IgG structure are evaluated using normal mode analysis of an elastic network model to detect hinges, the dominance of low frequency modes, and the most important internal motions. One question we seek to answer is whether or not IgG hinge motions facilitate antigen binding. We also evaluate the protein crystal and packing effects on the experimental temperature factors and disorder predictions. We find that the effects of the protein environment on the crystallographic temperature factors may be misleading for evaluating specific functional motions of IgG. The extent of motion of the antigen binding domains is computed to show their large spatial sampling. We conclude that the IgG structure is specifically designed to facilitate large excursions of the antigen binding domains. Normal modes are shown as capable of com- putationally evaluating the hinge motions and the spatial sampling by the structure. The antigen binding loops and the major hinge appear to behave similarly to the rest of the structure when we consider the dominance of the low frequency modes and the extent of internal motion. The full IgG structure has a lower spectral dimension than individual Fab domains, pointing to more efficient information transfer through the antibody than through each domain. This supports the claim that the IgG structure is specifically constructed to facilitate antigen binding by coupling motion of the antigen binding loops with the large scale hinge motions

How Philosophy of Mind Needs Philosophy of Chemistry

By the 1960s many (perhaps most) philosophers had adopted ‘physicalism’ ─ the view that physical causes fully account for mental activities. However, controversy persists about what count as ‘physical causes’. ‘Reductive’ physicalists recognize only microphysical (elementary-particle-level) causality. Many (perhaps most) physicalists are ‘non-reductive’ ─ they hold that entities considered by other (‘special’) sciences have causal powers. Philosophy of chemistry can help resolve main issues in philosophy of mind in three ways: developing an extended mereology applicable to chemical combination, testing whether ‘singularities’ prevent reduction of chemistry to microphysics, and demonstrating ‘downward causation’ in complex networks of chemical reactions

How Philosophy of Mind Needs Philosophy of Chemistry

By the 1960s many (perhaps most) philosophers had adopted ‘physicalism’ ─ the view that physical causes fully account for mental activities. However, controversy persists about what count as ‘physical causes’. ‘Reductive’ physicalists recognize only microphysical (elementary-particle-level) causality. Many (perhaps most) physicalists are ‘non-reductive’ ─ they hold that entities considered by other (‘special’) sciences have causal powers. Philosophy of chemistry can help resolve main issues in philosophy of mind in three ways: developing an extended mereology applicable to chemical combination, testing whether ‘singularities’ prevent reduction of chemistry to microphysics, and demonstrating ‘downward causation’ in complex networks of chemical reactions

A Balanced Secondary Structure Predictor

Secondary structure (SS) refers to the local spatial organization of the polypeptide backbone atoms of a protein. Accurate prediction of SS is a vital clue to resolve the 3D structure of protein. SS has three different components- helix (H), beta (E) and coil (C). Most SS predictors are imbalanced as their accuracy in predicting helix and coil are high, however significantly low in the beta. The objective of this thesis is to develop a balanced SS predictor which achieves good accuracies in all three SS components. We proposed a novel approach to solve this problem by combining a genetic algorithm (GA) with a support vector machine. We prepared two test datasets (CB471 and N295) to compare the performance of our predictors with SPINE X. Overall accuracy of our predictor was 76.4% and 77.2% respectively on CB471 and N295 datasets, while SPINE X gave 76.5% overall accuracy on both test datasets