Multiscale analysis of protein functions and stochastic modelling of gene transcriptional regulatory networks

Genomic and proteomic analyses have attracted a great deal of interests in biological research in recent years. Many methods have been applied to discover useful information contained in the enormous databases of genomic sequences and amino acid sequences. The results of these investigations inspire further research in biological fields in return. These biological sequences, which may be considered as multiscale sequences, have some specific features which need further efforts to characterise using more refined methods. This project aims to study some of these biological challenges with multiscale analysis methods and stochastic modelling approach. The first part of the thesis aims to cluster some unknown proteins, and classify their families as well as their structural classes. A development in proteomic analysis is concerned with the determination of protein functions. The first step in this development is to classify proteins and predict their families. This motives us to study some unknown proteins from specific families, and to cluster them into families and structural classes. We select a large number of proteins from the same families or superfamilies, and link them to simulate some unknown large proteins from these families. We use multifractal analysis and the wavelet method to capture the characteristics of these linked proteins. The simulation results show that the method is valid for the classification of large proteins. The second part of the thesis aims to explore the relationship of proteins based on a layered comparison with their components. Many methods are based on homology of proteins because the resemblance at the protein sequence level normally indicates the similarity of functions and structures. However, some proteins may have similar functions with low sequential identity. We consider protein sequences at detail level to investigate the problem of comparison of proteins. The comparison is based on the empirical mode decomposition (EMD), and protein sequences are detected with the intrinsic mode functions. A measure of similarity is introduced with a new cross-correlation formula. The similarity results show that the EMD is useful for detection of functional relationships of proteins. The third part of the thesis aims to investigate the transcriptional regulatory network of yeast cell cycle via stochastic differential equations. As the investigation of genome-wide gene expressions has become a focus in genomic analysis, researchers have tried to understand the mechanisms of the yeast genome for many years. How cells control gene expressions still needs further investigation. We use a stochastic differential equation to model the expression profile of a target gene. We modify the model with a Gaussian membership function. For each target gene, a transcriptional rate is obtained, and the estimated transcriptional rate is also calculated with the information from five possible transcriptional regulators. Some regulators of these target genes are verified with the related references. With these results, we construct a transcriptional regulatory network for the genes from the yeast Saccharomyces cerevisiae. The construction of transcriptional regulatory network is useful for detecting more mechanisms of the yeast cell cycle.

Thermal decomposition of hydrotalcite with hexacyanoferrite(II) and hexacyanoferrate(III) anions in the interlayer : a controlled rate thermal analysis study

The mechanism for the decomposition of hydrotalcite remains unsolved. Controlled rate thermal analysis enables this decomposition pathway to be explored. The thermal decomposition of hydrotalcites with hexacyanoferrite(II) and hexacyanoferrate(III) in the interlayer has been studied using controlled rate thermal analysis technology. X-ray diffraction shows the hydrotalcites studied have a d(003) spacing of 11.1 and 10.9 Å which compares with a d-spacing of 7.9 and 7.98 Å for the hydrotalcite with carbonate or sulphate in the interlayer. Calculations based upon CRTA measurements show that 7 moles of water is lost, proving the formula of hexacyanoferrite(II) intercalated hydrotalcite is Mg6Al2(OH)16[Fe(CN)6]0.5 .7 H2O and for the hexacyanoferrate(III) intercalated hydrotalcite is Mg6Al2(OH)16[Fe(CN)6]0.66 * 9 H2O. Dehydroxylation combined with CN unit loss occurs in three steps between a) 310 and 367°C b) 367 and 390°C and c) between 390 and 428°C for both the hexacyanoferrite(II) and hexacyanoferrate(III) intercalated hydrotalcite.

Being Grateful : Does it Bring Us Closer? Gratitude, Attachment and Intimacy in Romantic Relationships

To date, little is known about the function of gratitude in romantic relationships. Being grateful has been demonstrated to provide a number of positive benefits for individuals; however, few studies have explored how grateful experiences may be beneficial in enhancing romantic relationships. This study explored the extent to which adult attachment moderates the relationship between dispositional gratitude and the experience of intimacy within romantic relationships. A greater disposition toward gratitude was expected to result in more frequent experiences of gratitude. It was also anticipated that experiences of gratitude would be associated with feelings of closeness. Participants (n = 156) were required to be currently in a relationship of at least six months duration and completed a series of questionnaires assessing dispositional gratitude, attachment and emotional intimacy. Moderation analysis revealed that although a positive, weak correlation existed between dispositional gratitude and intimacy, attachment did not moderate this association. It was concluded that further investigation of the experience of gratitude is necessary to understand the function of gratitude in romantic relationships. Methods focusing on specific experiences of gratitude in romantic relationships, and the associated feelings of closeness experienced by each partner, may yield more conclusive findings and may provide support for therapeutic approaches focused on enhancing closeness between couples by increasing experiences of gratitude.

Being grateful : does it bring us closer? Gratitude, attachment and intimacy in romantic relationships

This study proposed that levels of dispositional gratitude influence experiences of intimacy within romantic relationships and that this influence is moderated by relationship attachment. Gratitude, in this study, was described as feelings of appreciation associated with the perception that one had been the focus of another’s intentionally beneficial actions. A greater disposition toward gratitude was expected to result in more frequent experiences of gratitude. It was also anticipated that experiences of gratitude would be associated with feelings of closeness toward the one responsible for the beneficial act. Participants (n=156) ranged in age from 18 – 70 and, although required to be currently in a relationship of at least six months’ duration, each was studied as an individual. Participants included both males and females, in same-sex or other-sex relationships, and completed a series of questionnaires assessing dispositional gratitude, attachment and emotional intimacy. Moderation analysis was conducted using hierarchical regression and revealed that although a positive, weak correlation exists between gratitude and intimacy, attachment did not moderate that association. However, the measures used did not elicit sufficiently divergent responses. Thus neither complete exploration of the proposed association between gratitude and intimacy, nor of the moderation of that association by attachment were possible. In conclusion, further investigation of experiences of gratitude, particularly in relation to enhancing feelings of closeness, is necessary to understand the function of gratitude in romantic relationships. Methods focusing on specific experiences of gratitude in romantic relationships and the associated feelings of closeness experienced by each partner may yield more conclusive findings. In addition, such findings may provide support for therapeutic approaches focused on enhancing closeness between couples by increasing experiences of gratitude.

Hall-petch relationship and strain rate sensitivity of nanocrystalline Mg - 5wt% A1 alloy

This study investigated the grain size dependence of mechanical properties and deformation mechanisms of microcrystalline (mc) and nanocrystalline (nc: grain size below 100 nm) Mg-5wt% Al alloys. The Hall-Petch relationship was investigated by both instrumented indentation tests and compression tests. The test results from the indentation tests and compression tests match well with each other. The breakdown of Hall-Petch relationship and the elevated strain rate sensitivity (SRS) of present Mg-5wt% Al alloys when the grain size was reduced below 58nm indicated the more significant role of GB mediated mechanisms in plastic deformation process. However, the relatively smaller SRS values compared to GB sliding and coble creep process suggested the plastic deformation in the current study is still dislocation mediated mechanism dominant.

Characteristics of utility cyclists in Queensland, Australia : an examination of the associations between individual, social and environmental factors and utility cycling

Background: Initiatives to promote utility cycling in countries like Australia and the US, which have low rates of utility cycling, may be more effective if they first target recreational cyclists. This study aimed to describe patterns of utility cycling and examine its correlates, among cyclists in Queensland, Australia. Methods: An online survey was administered to adult members of a state-based cycling community and advocacy group (n=1813). The survey asked about demographic characteristics and cycling behavior, motivators and constraints. Utility cycling patterns were described, and logistic regression modeling was used to examine associations between utility cycling and other variables. Results: Forty-seven percent of respondents reported utility cycling: most did so to commute (86%). Most journeys (83%) were >5 km. Being male, younger, employed full-time, or university-educated increased the likelihood of utility cycling (p<0.05). Perceiving cycling to be a cheap or a convenient form of transport were associated with utility cycling (p<0.05). Conclusions: The moderate rate of utility cycling among recreational cyclists highlights a potential to promote utility cycling among this group. To increase utility cycling, strategies should target female and older recreational cyclists and focus on making cycling a cheap and convenient mode of transport.

Multiple evolutionary rate classes in animal genome evolution

The proportion of functional sequence in the human genome is currently a subject of debate. The most widely accepted figure is that approximately 5% is under purifying selection. In Drosophila, estimates are an order of magnitude higher, though this corresponds to a similar quantity of sequence. These estimates depend on the difference between the distribution of genomewide evolutionary rates and that observed in a subset of sequences presumed to be neutrally evolving. Motivated by the widening gap between these estimates and experimental evidence of genome function, especially in mammals, we developed a sensitive technique for evaluating such distributions and found that they are much more complex than previously apparent. We found strong evidence for at least nine well-resolved evolutionary rate classes in an alignment of four Drosophila species and at least seven classes in an alignment of four mammals, including human. We also identified at least three rate classes in human ancestral repeats. By positing that the largest of these ancestral repeat classes is neutrally evolving, we estimate that the proportion of nonneutrally evolving sequence is 30% of human ancestral repeats and 45% of the aligned portion of the genome. However, we also question whether any of the classes represent neutrally evolving sequences and argue that a plausible alternative is that they reflect variable structure-function constraints operating throughout the genomes of complex organisms.

Diversification and value-at-risk

A pervasive and puzzling feature of banks’ Value-at-Risk (VaR) is its abnormally high level, which leads to excessive regulatory capital. A possible explanation for the tendency of commercial banks to overstate their VaR is that they incompletely account for the diversification effect among broad risk categories (e.g., equity, interest rate, commodity, credit spread, and foreign exchange). By underestimating the diversification effect, bank’s proprietary VaR models produce overly prudent market risk assessments. In this paper, we examine empirically the validity of this hypothesis using actual VaR data from major US commercial banks. In contrast to the VaR diversification hypothesis, we find that US banks show no sign of systematic underestimation of the diversification effect. In particular, diversification effects used by banks is very close to (and quite often larger than) our empirical diversification estimates. A direct implication of this finding is that individual VaRs for each broad risk category, just like aggregate VaRs, are biased risk assessments.

The contribution of maize cropping in the Midwest USA to global warming: A regional estimate

Agricultural soils emit about 50% of the global flux of N2O attributable to human influence, mostly in response to nitrogen fertilizer use. Recent evidence that the relationship between N2O fluxes and N-fertilizer additions to cereal maize are non-linear provides an opportunity to estimate regional N2O fluxes based on estimates of N application rates rather than as a simple percentage of N inputs as used by the Intergovernmental Panel on Climate Change (IPCC). We combined a simple empirical model of N2O production with the SOCRATES soil carbon dynamics model to estimate N2O and other sources of Global Warming Potential (GWP) from cereal maize across 19,000 cropland polygons in the North Central Region (NCR) of the US over the period 1964–2005. Results indicate that the loading of greenhouse gases to the atmosphere from cereal maize production in the NCR was 1.7 Gt CO2e, with an average 268 t CO2e produced per tonne of grain. From 1970 until 2005, GHG emissions per unit product declined on average by 2.8 t CO2e ha−1 annum−1, coinciding with a stabilisation in N application rate and consistent increases in grain yield from the mid-1970’s. Nitrous oxide production from N fertilizer inputs represented 59% of these emissions, soil C decline (0–30 cm) represented 11% of total emissions, with the remaining 30% (517 Mt) from the combustion of fuel associated with farm operations. Of the 126 Mt of N fertilizer applied to cereal maize from 1964 to 2005, we estimate that 2.2 Mt N was emitted as N2O when using a non-linear response model, equivalent to 1.75% of the applied N.