Computational Methods for Locating and Analyzing Conserved Gene Regulatory DNA Elements

This thesis presents methods for locating and analyzing cis-regulatory DNA elements involved with the regulation of gene expression in multicellular organisms. The regulation of gene expression is carried out by the combined effort of several transcription factor proteins collectively binding the DNA on the cis-regulatory elements. Only sparse knowledge of the 'genetic code' of these elements exists today. An automatic tool for discovery of putative cis-regulatory elements could help their experimental analysis, which would result in a more detailed view of the cis-regulatory element structure and function. We have developed a computational model for the evolutionary conservation of cis-regulatory elements. The elements are modeled as evolutionarily conserved clusters of sequence-specific transcription factor binding sites. We give an efficient dynamic programming algorithm that locates the putative cis-regulatory elements and scores them according to the conservation model. A notable proportion of the high-scoring DNA sequences show transcriptional enhancer activity in transgenic mouse embryos. The conservation model includes four parameters whose optimal values are estimated with simulated annealing. With good parameter values the model discriminates well between the DNA sequences with evolutionarily conserved cis-regulatory elements and the DNA sequences that have evolved neutrally. In further inquiry, the set of highest scoring putative cis-regulatory elements were found to be sensitive to small variations in the parameter values. The statistical significance of the putative cis-regulatory elements is estimated with the Two Component Extreme Value Distribution. The p-values grade the conservation of the cis-regulatory elements above the neutral expectation. The parameter values for the distribution are estimated by simulating the neutral DNA evolution. The conservation of the transcription factor binding sites can be used in the upstream analysis of regulatory interactions. This approach may provide mechanistic insight to the transcription level data from, e.g., microarray experiments. Here we give a method to predict shared transcriptional regulators for a set of co-expressed genes. The EEL (Enhancer Element Locator) software implements the method for locating putative cis-regulatory elements. The software facilitates both interactive use and distributed batch processing. We have used it to analyze the non-coding regions around all human genes with respect to the orthologous regions in various other species including mouse. The data from these genome-wide analyzes is stored in a relational database which is used in the publicly available web services for upstream analysis and visualization of the putative cis-regulatory elements in the human genome.

SorGSD: a sorghum genome SNP database

Sorghum (Sorghum bicolor) is one of the most important cereal crops globally and a potential energy plant for biofuel production. In order to explore genetic gain for a range of important quantitative traits, such as drought and heat tolerance, grain yield, stem sugar accumulation, and biomass production, via the use of molecular breeding and genomic selection strategies, knowledge of the available genetic variation and the underlying sequence polymorphisms, is required.

The complete validated mitochondrial genome of the black marlin Istiompax indica (Cuvier, 1832)

Two complete mitochondrial genomes of the black marlin Istiompax indica were assembled from approximately 3.5 and 2.5 million reads produced by Ion Torrent next generation sequencing. The complete genomes were 16,531 bp and 16,532 bp in length consisting of 2 rRNA, 13 protein-coding genes, 22tRNA and 2 coding regions. They demonstrated a similar A + T base (52.6%) to other teleosts. Intraspecific sequence variation was 99.5% for three I. indica mitogenomes and 99.7% for X. gladius. A lower value (85%) was found for the I. platypterus mitogenomes from genbank and accredited to inadvertent inclusion of gene regions from a con-familial species in one record, highlighting the need for cautious downstream use of genbank data. © 2014 Informa UK Ltd.

Drafting the Kensington Pride Mango Genome

The mango industry in Australia is worth in excess of $150 million annually with the Kensington Pride (KP) cultivar capturing 60% of the domestic market. Valued by consumers for desirable taste and colour characteristics, KP has been used extensively as a parent in the Department of Agriculture and Fisheries’ (Queensland, Australia) mango breeding program with over 400 hybrid trees sharing KP as the male parent. In order to gain a better understanding of Australia’s most significant mango variety, Horticulture Innovation Australia had led an international collaboration between the Queensland Department of Agriculture and Fisheries (Australia), the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT, India) and the Beijing Genomics Institute (China) to sequence the KP genome. Preliminary de novo assembly of illumina short read sequence data suggests that the KP genome is highly heterozygous and has an estimated genome size of 407 Mb. As refinements and additional sequence data are added to the assembly, a more complete picture of the mango genome will be elucidated.

Two Complete Genome Sequences of Phasey Bean Mild Yellows Virus, a Novel Member of the Luteoviridae from Australia

We present here the complete genome sequences of a novel polerovirus from Trifolium subterraneum (subterranean clover) and Cicer arietinum (chickpea) and compare these to a partial viral genome sequence obtained from Macroptilium lathyroides (phasey bean). We propose the name phasey bean mild yellows virus for this novel polerovirus.

The first genome sequence of a metatherian herpesvirus: Macropodid herpesvirus 1

While many placental herpesvirus genomes have been fully sequenced, the complete genome of a marsupial herpesvirus has not been described. Here we present the first genome sequence of a metatherian herpesvirus, Macropodid herpesvirus 1 (MaHV-1).

From Francovich to Köbler and beyond : The evolution of a State liability regime for the EC

The aim of this paper is to present the evolution of the Francovich doctrine within the European legal order. The first part deals with the gradual development of the ECJ's case law on State liability in damages for breach of EC law. Starting from the seminal Francovich and Brasserie du Pêcheur, the clarification of the criteria set by the Court is attempted with reference to subsequent case law, whereas issues concerning the extent and form of the compensation owned are also mentioned. The second part concerns one of the more recent developments in the field, namely State liability for breaches of Community law attributed to national judiciary. The Court's ruling in Köbler is examined in connection with two other recent judgments, namely Commission v. Italy of 2003 and Kühne & Heitz, as an attempt of the ECJ to reframe its relationships with national supreme courts and appropriate for itself the position of the Supreme Court in the European legal order. The implications on State liability claims by the ruling in Commission v. France of 1997 constitute the theme of the third part, where it is submitted that Member States can also be held liable for disregard of Community law by private individuals within their respected territories. To this extent, Schmidberger is viewed as a manifestation of this opinion, with fundamental rights acquiring a new dimension, being invoked by the States, contra the individuals as a shield to liability claims. Finally, the third part examines the relationship between the Francovich doctrine and the principle of legal certainty and concludes that the solutions employed by the ECJ have been both predictable and acceptable by the national legal orders. Keywords: State liability, damages, Francovich, Köbler, Schmidberger

Evolution of Social Behavior Through Interpopulation Selection

Under certain special conditions natural selection can be effective at the level of local populations, or demes. Such interpopulation selection will favor genotypes that reduce the probability of extinction of their parent population even at the cost of a lowered inclusive fitness. Such genotypes may be characterized by altruistic traits only in a viscous population, i.e., in a population in which neighbors tend to be closely related. In a non-viscous population the interpopulation selection will instead favor spiteful traits when the populations are susceptible to extinction through the overutilization of the habitat, and cooperative traits when it is the newly established populations that are in the greatest danger of extinction.

Elite Bargaining and the Evolution of Centre-Periphery Relations in Post-Soviet Russia : A Comparative Analysis

This work is concerned with presenting a modified theoretical approach to the study of centre-periphery relations in the Russian Federation. In the widely accepted scientific discourse, the Russian federal system under the Yeltsin Administration (1991-2000) was asymmetrical; largely owing to the varying amount of structural autonomy distributed among the federation s 89 constituent units. While providing an improved understanding as to which political and socio-economic structures contributed to federal asymmetry, it is felt that associated large N-studies have underemphasised the role played by actor agency in re-shaping Russian federal institutions. It is the main task of this thesis to reintroduce /re-emphasise the importance of actor agency as a major contributing element of institutional change in the Russian federal system. By focusing on the strategic agency of regional elites simultaneously within regional and federal contexts, the thesis adopts the position that political, ethnic and socio-economic structural factors alone cannot fully determine the extent to which regional leaders were successful in their pursuit of economic and political pay-offs from the institutionally weakened federal centre. Furthermore, this work hypothesises that under conditions of federal institutional uncertainty, it is the ability of regional leaders to simultaneously interpret various mutable structural conditions then translate them into plausible strategies which accounts for the regions ability to extract variable amounts of economic and political pay-offs from the Russian federal system. The thesis finds that while the hypothesis is accurate in its theoretical assumptions, several key conclusions provide paths for further inquiry posed by the initial research question. First, without reliable information or stable institutions to guide their actions, both regional and federal elites were forced into ad-hoc decision-making in order to maintain their core strategic focus: political survival. Second, instead of attributing asymmetry to either actor agency or structural factors exclusively, the empirical data shows that both agency and structures interact symbiotically in the strategic formulation process, thus accounting for the sub-optimal nature of several of the actions taken in the adopted cases. Third, as actor agency and structural factors mutate over time, so, too do the perceived payoffs from elite competition. In the case of the Russian federal system, the stronger the federal centre became, the less likely it was that regional leaders could extract the high degree of economic and political pay-offs that they clamoured for earlier in the Yeltsin period. Finally, traditional approaches to the study of federal systems which focus on institutions as measures of federalism are not fully applicable in the Russian case precisely because the institutions themselves were a secondary point of contention between competing elites. Institutional equilibriums between the regions and Moscow were struck only when highly personalised elite preferences were satisfied. Therefore the Russian federal system is the product of short-term, institutional solutions suited to elite survival strategies developed under conditions of economic, political and social uncertainty.

Phylogenetic analysis of human Chlamydia pneumoniae strains reveals a distinct Australian indigenous clade that predates European exploration of the continent

Background The obligate intracellular bacterium Chlamydia pneumoniae is a common respiratory pathogen, which has been found in a range of hosts including humans, marsupials and amphibians. Whole genome comparisons of human C. pneumoniae have previously highlighted a highly conserved nucleotide sequence, with minor but key polymorphisms and additional coding capacity when human and animal strains are compared. Results In this study, we sequenced three Australian human C. pneumoniae strains, two of which were isolated from patients in remote indigenous communities, and compared them to all available C. pneumoniae genomes. Our study demonstrated a phylogenetically distinct human C. pneumoniae clade containing the two indigenous Australian strains, with estimates that the most recent common ancestor of these strains predates the arrival of European settlers to Australia. We describe several polymorphisms characteristic to these strains, some of which are similar in sequence to animal C. pneumoniae strains, as well as evidence to suggest that several recombination events have shaped these distinct strains. Conclusions Our study reveals a greater sequence diversity amongst both human and animal C. pneumoniae strains, and suggests that a wider range of strains may be circulating in the human population than current sampling indicates.

Kinetics of hydrogen evolution on a stainless steel electrode

The kinetic parameters for the hydrogen evolution reaction on a stainless steel substrate have been obtained from a study of the steady-state polarization curves as well as the galvanostatic transients. The high Tafel slope obtained in the steady-state polarization measurements was ascribed to the presence of an oxide film present on the surface of the stainless steel electrode.

Evolution of Grain-Boundary Microstructure and Texture in Interstitial-Free Steel Processed by Equal-Channel Angular Extrusion

The equal-channel angular extrusion (ECAE) of Ti-bearing interstitial-free (IF) steel was performed following two different routes, up to four passes, at a temperature of 300 degrees C. The ECAE led to a grain refinement to submicron size. After the second pass, the grain size attained saturation thereafter. The microstructural analysis indicated the presence of coincident-site lattice (CSL) boundaries in significant fraction, in addition to a high volume fraction of high-angle random boundaries and some low-angle boundaries after the deformation. Among the special boundaries, Sigma 3 and Sigma 13 were the most prominent ones and their fraction depended on the processing route followed. A deviation in the misorientation angle distribution from the Mackenzie distribution was noticed. The crystallographic texture after the first pass resembled that of simple shear, with the {112}, {110}, and {123} aligned to the macroscopic shear plane.

Human genetic variation in the Baltic Sea region: Features of population history and natural selection

In this thesis, the genetic variation of human populations from the Baltic Sea region was studied in order to elucidate population history as well as evolutionary adaptation in this region. The study provided novel understanding of how the complex population level processes of migration, genetic drift, and natural selection have shaped genetic variation in North European populations. Results from genome-wide, mitochondrial DNA and Y-chromosomal analyses suggested that the genetic background of the populations of the Baltic Sea region lies predominantly in Continental Europe, which is consistent with earlier studies and archaeological evidence. The late settlement of Fennoscandia after the Ice Age and the subsequent small population size have led to pronounced genetic drift, especially in Finland and Karelia but also in Sweden, evident especially in genome-wide and Y-chromosomal analyses. Consequently, these populations show striking genetic differentiation, as opposed to much more homogeneous pattern of variation in Central European populations. Additionally, the eastern side of the Baltic Sea was observed to have experienced eastern influence in the genome-wide data as well as in mitochondrial DNA and Y-chromosomal variation – consistent with linguistic connections. However, Slavic influence in the Baltic Sea populations appears minor on genetic level. While the genetic diversity of the Finnish population overall was low, genome-wide and Y-chromosomal results showed pronounced regional differences. The genetic distance between Western and Eastern Finland was larger than for many geographically distant population pairs, and provinces also showed genetic differences. This is probably mainly due to the late settlement of Eastern Finland and local isolation, although differences in ancestral migration waves may contribute to this, too. In contrast, mitochondrial DNA and Y-chromosomal analyses of the contemporary Swedish population revealed a much less pronounced population structure and a fusion of the traces of ancient admixture, genetic drift, and recent immigration. Genome-wide datasets also provide a resource for studying the adaptive evolution of human populations. This study revealed tens of loci with strong signs of recent positive selection in Northern Europe. These results provide interesting targets for future research on evolutionary adaptation, and may be important for understanding the background of disease-causing variants in human populations.

Social evolution - Has nature ever rewound the tape?

Social insects such as ants, bees, wasps and termites exhibit extreme forms of altruism where some individuals remain sterile and assist other individuals in reproduction. Hamilton's inclusive fitness theory provides a powerful framework for investigating the evolution of such altruism. Using the paper wasp Ropalidia marginata, we have quantified and delineated the role of ecological, physiological, genetic and demographic factors in social evolution. An interesting feature of the models we have developed is their symmetry so that either altruism or selfishness can evolve, depending on the numerical values of various parameters. This suggests that selfish/solitary behaviour must occasionally re-emerge even from the eusocial state, It is useful to contemplate expected intermediate states during such potential reversals. We can perhaps envisage three successive steps in such a hypothetical process: i) workers revolt against the hegemony of the queen and challenge her status as the sole reproductive, ii) workers stop producing queens and one or more of them function as egg layers (functional queen/s) capable of producing both haploid as well as diploid offspring and iii) social evolution reverses completely so that a eusocial species becomes solitary, at least facultatively. It appears that the third step, namely transition from eusociality to the solitary state, is rare and has been restricted to transitions from the primitively eusocial state only. The absence of transitions from the highly eusocial state to the solitary state may be attributed to a number of 'preventing mechanisms' such as (a) queen control of workers (b) loss of spermathecae and ability to mate (c) morphological specialization (d) caste polyethism and (e) homeostasis, which must each make the transition difficult and, taken together, perhaps very difficult. However, the discovery of a transition from the highly eusocial to the solitary state can hardly he ruled out, given that little or no effort has gone into its detection. In this paper I discuss social evolution and its possible reversal and cite potential examples of stages in the transition from the social to the solitary.