Phylogeography and hybrid swarms: history of brackish water bivalve diversity in North European marginal seas

This study addressed the large-scale molecular zoogeography in two brackish water bivalve molluscs, Macoma balthica and Cerastoderma glaucum, and genetic signatures of the postglacial colonization of Northern Europe by them. The traditional view poses that M. balthica in the Baltic, White and Barents seas (i.e. marginal seas) represent direct postglacial descendants of the adjacent Northeast Atlantic populations, but this has recently been challenged by observations of close genetic affinities between these marginal populations and those of the Northeast Pacific. The primary aim of the thesis was to verify, quantify and characterize the Pacific genetic contribution across North European populations of M. balthica and to resolve the phylogeographic histories of the two bivalve taxa in range-wide studies using information from mitochondrial DNA (mtDNA) and nuclear allozyme polymorphisms. The presence of recent Pacific genetic influence in M. balthica of the Baltic, White and Barents seas, along with an Atlantic element, was confirmed by mtDNA sequence data. On a broader temporal and geographical scale, altogether four independent trans-Arctic invasions of Macoma from the Pacific since the Miocene seem to have been involved in generating the current North Atlantic lineage diversity. The latest trans-Arctic invasion that affected the current Baltic, White and Barents Sea populations probably took place in the early post-glacial. The nuclear genetic compositions of these marginal sea populations are intermediate between those of pure Pacific and Atlantic subspecies. In the marginal sea populations of mixed ancestry (Barents, White and Northern Baltic seas), the Pacific and Atlantic components are now randomly associated in the genomes of individual clams, which indicates both pervasive historical interbreeding between the previously long-isolated lineages (subspecies), and current isolation of these populations from the adjacent pure Atlantic populations. These mixed populations can be characterized as self-supporting hybrid swarms, and they arguably represent the most extensive marine animal hybrid swarms so far documented. Each of the three swarms still has a distinct genetic composition, and the relative Pacific contributions vary from 30 to 90 % in local populations. This diversity highlights the potential of introgressive hybridization to rapidly give rise to new evolutionarily and ecologically significant units in the marine realm. In the south of the Danish straits and in the Southern Baltic Sea, a broad genetic transition zone links the pure North Sea subspecies M. balthica rubra to the inner Baltic hybrid swarm, which has about 60 % of Pacific contribution in its genome. This transition zone has no regular smooth clinal structure, but its populations show strong genotypic disequilibria typical of a hybrid zone maintained by the interplay of selection and gene flow by dispersing pelagic larvae. The structure of the genetic transition is partly in line with features of Baltic water circulation and salinity stratification, with greater penetration of Atlantic genes on the Baltic south coast and in deeper water populations. In all, the scenarios of historical isolation and secondary contact that arise from the phylogeographic studies of both Macoma and Cerastoderma shed light to the more general but enigmatic patterns seen in marine phylogeography, where deep genetic breaks are often seen in species with high dispersal potential.

Characterization of genomic diversity in extraintestinal pathogenic Escherichia coli (ExPEC) and development of a diagnostic DNA microarray for the differentiation of ExPEC isolates causing urinary tract infections

Extraintestinal pathogenic Escherichia coli (ExPEC) represent a diverse group of strains of E. coli, which infect extraintestinal sites, such as the urinary tract, the bloodstream, the meninges, the peritoneal cavity, and the lungs. Urinary tract infections (UTIs) caused by uropathogenic E. coli (UPEC), the major subgroup of ExPEC, are among the most prevalent microbial diseases world wide and a substantial burden for public health care systems. UTIs are responsible for serious morbidity and mortality in the elderly, in young children, and in immune-compromised and hospitalized patients. ExPEC strains are different, both from genetic and clinical perspectives, from commensal E. coli strains belonging to the normal intestinal flora and from intestinal pathogenic E. coli strains causing diarrhea. ExPEC strains are characterized by a broad range of alternate virulence factors, such as adhesins, toxins, and iron accumulation systems. Unlike diarrheagenic E. coli, whose distinctive virulence determinants evoke characteristic diarrheagenic symptoms and signs, ExPEC strains are exceedingly heterogeneous and are known to possess no specific virulence factors or a set of factors, which are obligatory for the infection of a certain extraintestinal site (e. g. the urinary tract). The ExPEC genomes are highly diverse mosaic structures in permanent flux. These strains have obtained a significant amount of DNA (predictably up to 25% of the genomes) through acquisition of foreign DNA from diverse related or non-related donor species by lateral transfer of mobile genetic elements, including pathogenicity islands (PAIs), plasmids, phages, transposons, and insertion elements. The ability of ExPEC strains to cause disease is mainly derived from this horizontally acquired gene pool; the extragenous DNA facilitates rapid adaptation of the pathogen to changing conditions and hence the extent of the spectrum of sites that can be infected. However, neither the amount of unique DNA in different ExPEC strains (or UPEC strains) nor the mechanisms lying behind the observed genomic mobility are known. Due to this extreme heterogeneity of the UPEC and ExPEC populations in general, the routine surveillance of ExPEC is exceedingly difficult. In this project, we presented a novel virulence gene algorithm (VGA) for the estimation of the extraintestinal virulence potential (VP, pathogenicity risk) of clinically relevant ExPECs and fecal E. coli isolates. The VGA was based on a DNA microarray specific for the ExPEC phenotype (ExPEC pathoarray). This array contained 77 DNA probes homologous with known (e.g. adhesion factors, iron accumulation systems, and toxins) and putative (e.g. genes predictably involved in adhesion, iron uptake, or in metabolic functions) ExPEC virulence determinants. In total, 25 of DNA probes homologous with known virulence factors and 36 of DNA probes representing putative extraintestinal virulence determinants were found at significantly higher frequency in virulent ExPEC isolates than in commensal E. coli strains. We showed that the ExPEC pathoarray and the VGA could be readily used for the differentiation of highly virulent ExPECs both from less virulent ExPEC clones and from commensal E. coli strains as well. Implementing the VGA in a group of unknown ExPECs (n=53) and fecal E. coli isolates (n=37), 83% of strains were correctly identified as extraintestinal virulent or commensal E. coli. Conversely, 15% of clinical ExPECs and 19% of fecal E. coli strains failed to raster into their respective pathogenic and non-pathogenic groups. Clinical data and virulence gene profiles of these strains warranted the estimated VPs; UPEC strains with atypically low risk-ratios were largely isolated from patients with certain medical history, including diabetes mellitus or catheterization, or from elderly patients. In addition, fecal E. coli strains with VPs characteristic for ExPEC were shown to represent the diagnostically important fraction of resident strains of the gut flora with a high potential of causing extraintestinal infections. Interestingly, a large fraction of DNA probes associated with the ExPEC phenotype corresponded to novel DNA sequences without any known function in UTIs and thus represented new genetic markers for the extraintestinal virulence. These DNA probes included unknown DNA sequences originating from the genomic subtractions of four clinical ExPEC isolates as well as from five novel cosmid sequences identified in the UPEC strains HE300 and JS299. The characterized cosmid sequences (pJS332, pJS448, pJS666, pJS700, and pJS706) revealed complex modular DNA structures with known and unknown DNA fragments arranged in a puzzle-like manner and integrated into the common E. coli genomic backbone. Furthermore, cosmid pJS332 of the UPEC strain HE300, which carried a chromosomal virulence gene cluster (iroBCDEN) encoding the salmochelin siderophore system, was shown to be part of a transmissible plasmid of Salmonella enterica. Taken together, the results of this project pointed towards the assumptions that first, (i) homologous recombination, even within coding genes, contributes to the observed mosaicism of ExPEC genomes and secondly, (ii) besides en block transfer of large DNA regions (e.g. chromosomal PAIs) also rearrangements of small DNA modules provide a means of genomic plasticity. The data presented in this project supplemented previous whole genome sequencing projects of E. coli and indicated that each E. coli genome displays a unique assemblage of individual mosaic structures, which enable these strains to successfully colonize and infect different anatomical sites.

Diversity in the Early Years: Intercultural Learning and Teaching

"New global contexts are presenting new challenges and new possibilities for young children and those around them. Climate change, armed conflict and poverty combine with new frontiers of discovery in science and technology to create a paradoxical picture of both threat and opportunity for our world and our children. On the one hand, children are experiencing unprecedented patterns of disparity and inequity; yet, on the other hand, they have seemingly limitless possibilities to engage with new technologies and social processes. Seismic shifts such as these are inviting new questions about the conditions that young children need to learn and thrive. Diversity in the Early Years: Intercultural Learning and Teaching explores significant aspects of working with children and adults from diverse backgrounds. It is a valuable resource for teaching early childhood pre-service teachers to raise awareness about issues of diversity - whether diversity of culture, language, education and/or gender - and for helping them to develop their own pedagogical approaches to working with diverse populations."--Publisher website

Regulation of GABAergic neuron identity and diversity in the developing midbrain

Gamma-aminobutyric acid (GABA) is the most abundant inhibitory neurotransmitter in the vertebrate brain. In the midbrain, GABAergic neurons contribute to the regulation of locomotion, nociception, defensive behaviours, fear and anxiety, as well as sensing reward and addiction. Despite the clinical relevance of this group of neurons, the mechanisms regulating their development are largely unknown. In addition, their migration and connectivity patterns are poorly characterized. This study focuses on the molecular mechanisms specifying the GABAergic fate, and the developmental origins of midbrain GABAergic neurons. First, we have characterized the function of a zink-finger transcription factor Gata2. Using a tissue-specific mutagenesis in mouse midbrain and anteror hindbrain, we showed that Gata2 is a crucial determinant of the GABAergic fate in midbrain. In the absence of Gata2, no GABAergic neurons are produced from the otherwise competent midbrain neuroepithelium. Instead, the Gata2-mutant cells acquire a glutamatergic neuron phenotype. Ectopic expression of Gata2 was also sufficient to induce GABAergic in chicken midbrain. Second, we have analyzed the midbrain phenotype of mice mutant for a proneural gene Ascl1, and described the variable and region-dependent requirements for Ascl1 in the midbrain GABAergic neurogenesis. These studies also have implications on the origin of distinct anatomical and functional GABAergic subpopulations in midbrain. Third, we have identified unique developmental properties of GABAergic neurons that are associated with the midbrain dopaminergic nuclei, the substantia nigra pars reticulata (SNpr) and ventral tegmental area (VTA). Namely, the genetic regulation of GABAergic fate in these cells is distinct from the rest of midbrain. In accordance to this phenomenon, our detailed fate-mapping analyses indicated that the SNpr-VTA GABAergic neurons are generated outside midbrain, in the neuroepithelium of anterior hindbrain.

Phylogenetics, taxon delimitation and phylogenetic diversity

Throughout the history of Linnean taxonomy, species have been described with varying degrees of justification. Many descriptions have been based on only a few ambiguous morphological characters. Moreover, species have been considered natural, well-defined units whereas higher taxa have been treated as disparate, non-existent creations. In the present thesis a few such cases were studied in detail. Often the species-level descriptions were based on only a few specimens and the variation previously thought to be interspecific was found to be intraspecific. In some cases morphological characters were sufficient to resolve the evolutionary relationships between the taxa, but generally more resolution was gained by the addition of molecular evidence. However, both morphological and molecular data were found to be deceptive in some cases. The DNA sequences of morphologically similar specimens were found to differ distinctly in some cases, whereas in other closely related species the morphology of specimens with identical DNA sequences differed substantially. This study counsels caution when evolutionary relationships are being studied utilizing only one source of evidence or a very limited number of characters (e.g. barcoding). Moreover, it emphasizes the importance of high quality data as well as the utilization of proper methods when making scientific inferences. Properly conducted analyses produce robust results that can be utilized in numerous interesting ways. The present thesis considered two such extensions of systematics. A novel hypothesis on the origin of bioluminescence in Elateriformia beetles is presented, tying it to the development of the clicking mechanism in the ancestors of these animals. An entirely different type of extension of systematics is the proposed high value of the white sand forests in maintaining the diversity of beetles in the Peruvian Amazon. White sand forests are under growing pressure from human activities that lead to deforestation. They were found to harbor an extremely diverse beetle fauna and many taxa were specialists living only in this unique habitat. In comparison to the predominant clay soil forests, considerably more elateroid beetles belonging to all studied taxonomic levels (species, genus, tribus, and subfamily) were collected in white sand forests. This evolutionary diversity is hypothesized to be due to a combination of factors: (1) the forest structure, which favors the fungus-plant interactions important for the elateroid beetles, (2) the old age of the forest type favoring survival of many evolutionary lineages and (3) the widespread distribution and fragmentation of the forests in the Miocene, favoring speciation.

Imagination for inclusion: Shared understandings across diverse contexts of educational practice

This chapter explores inclusive education as a social imaginary; that is, a common understanding that has become a global perspective. We trace the roots of inclusive education in early movements for social justice and the development of special education and note that these two domains continue to be seen in the ongoing tensions within the practice of inclusive education. We conclude that although much has been achieved in opening up greater opportunities for all children and young people to participate in and engage with education, there is still much work to be done. Creative imagining, discursive dialogue, and courageous actions in breaking down barriers in schools and communities will strengthen the local and global social imaginary of inclusive education, thus affording even greater opportunities for all children and young people regardless of any categorisation that may have been applied to their differences.

Ma Ma Ma Mad

Ma Ma Ma Mad is an autobiographical work, written and performed by Singaporean-Australian theatre maker Merlynn Tong. This production, presented at the Brisbane Powerhouse in December 2015, was a multi-genre work incorporating aspects of Butoh, physical theatre, cabaret and contemporary monologue. More than an experiment in mixed performative forms, however, this particular production was also an exercise in inter-cultural collaboration as well as gender in (and of) performance. Heavily influenced by the creator's experiences growing up in urban Southeast Asia, the director's specialisation in contemporary Australian theatre and experience telling uniquely Australian stories worked to manipulate the form in an endeavour to succinctly speak to local audiences, without pandering to entrenched stereotypes or diluting the underlying Chinese-Singaporean themes. The success of this production was also somewhat of a personal challenge for the creatives, after being told by some of Brisbane's most influential theatre venues and festivals that they would rather not support the work because a) it was a one woman show, and b) it was a one woman show about an Asian woman; and therefore would not sell well. One very influential local producer even said that he already had a one-woman show about an Asian person programmed, so he couldn't possibly program another. Operating in such a biased and out-of-touch artistic environment was seen as an easy challenge for the artists involved, which resulted in a highly successful and critically acclaimed sell-out run of Ma Ma Ma Mad, followed by offers to tour the work nationally and internationally. As such, this production also stands as a practical example of the ingrained and patriarchal structures of the Australian arts scene, and how art can work to break down the very barriers that it has helped to construct through a lack of vision and diversity amongst its leaders.

Low ML-Decoding Complexity, Large Coding Gain, Full-Rate, Full-Diversity STBCs for 2 x 2 and 4 x 2 MIMO Systems

This paper deals with low maximum-likelihood (ML)-decoding complexity, full-rate and full-diversity space-time block codes (STBCs), which also offer large coding gain, for the 2 transmit antenna, 2 receive antenna (2 x 2) and the 4 transmit antenna, 2 receive antenna (4 x 2) MIMO systems. Presently, the best known STBC for the 2 2 system is the Golden code and that for the 4 x 2 system is the DjABBA code. Following the approach by Biglieri, Hong, and Viterbo, a new STBC is presented in this paper for the 2 x 2 system. This code matches the Golden code in performance and ML-decoding complexity for square QAM constellations while it has lower ML-decoding complexity with the same performance for non-rectangular QAM constellations. This code is also shown to be information-lossless and diversity-multiplexing gain (DMG) tradeoff optimal. This design procedure is then extended to the 4 x 2 system and a code, which outperforms the DjABBA code for QAM constellations with lower ML-decoding complexity, is presented. So far, the Golden code has been reported to have an ML-decoding complexity of the order of for square QAM of size. In this paper, a scheme that reduces its ML-decoding complexity to M-2 root M is presented.

Functional diversity of human protein kinase splice variants marks significant expansion of human kinome

Background: Protein kinases are involved in diverse spectrum of cellular processes. Availability of draft version of the human genomic data in the year 2001 enabled recognition of repertoire of protein kinases. However, over the years the human genomic data is being refined and the current release of human genomic data has helped us to recognize a larger repertoire of over 900 human protein kinases represented mainly by splice variants. Results: Many of these identified protein kinases are alternatively spliced products. Interestingly, some of the human kinase splice variants appear to be significantly diverged in terms of their functional properties as represented by incorporation or absence of one or more domains. Many sets of protein kinase splice variants have substantially different domain organization and in a few sets of splice variants kinase domains belong to different subfamilies of kinases suggesting potential participation in different signal transduction pathways. Conclusions: Addition or deletion of a domain between splice variants of multi-domain kinases appears to be a means of generating differences in the functional features of otherwise similar kinases. It is intriguing that marked sequence diversity within the catalytic regions of some of the splice variant kinases result in kinases belonging to different subfamilies. These human kinase splice variants with different functions might contribute to diversity of eukaryotic cellular signaling.

Characterization of DNA Strand Transfer Promoted by Mycobacterium smegmatis RecA Reveals Functional Diversity with Mycobacterium tuberculosis RecA†

The RecA-like proteins constitute a group of DNA strand transfer proteins ubiquitous in eubacteria, eukarya, and archaea. However, the functional relationship among RecA proteins is poorly understood. For instance, Mycobacterium tuberculosis RecA is synthesized as a large precursor, which undergoes an unusual protein-splicing reaction to generate an active form. Whereas the precursor was inactive, the active form promoted DNA strand transfer less efficiently compared to EcRecA. Furthermore, gene disruption studies have indicated that the frequencies of allele exchange are relatively lower in Mycobacterium tuberculosis compared to Mycobacterium smegmatis. The mechanistic basis and the factors that contribute to differences in allele exchange remain to be understood. Here, we show that the extent of DNA strand transfer promoted by the M. smegmatis RecA in vitro differs significantly from that of M. tuberculosis RecA. Importantly, M. smegmatis RecA by itself was unable to promote strand transfer, but cognate or noncognate SSBs rendered it efficient even when added prior to RecA. In the presence of SSB, MsRecA or MtRecA catalyzed strand transfer between ssDNA and varying lengths of linear duplex DNA with distinctly different pH profiles. The factors that were able to suppress the formation of DNA networks greatly stimulated strand transfer reactions promoted by MsRecA or MtRecA. Although the rate and pH profiles of dATP hydrolysis catalyzed by MtRecA and MsRecA were similar, only MsRecA was able to couple dATP hydrolysis to DNA strand transfer. Together, these results provide insights into the functional diversity in DNA strand transfer promoted by RecA proteins of pathogenic and nonpathogenic species of mycobacteria.

Diversity and degrees of freedom of cooperative wireless networks

Two key parameters in the outage characterization of a wireless fading network are the diversity and the degrees of freedom (DOF). These two quantities represent the two endpoints of the diversity multiplexing gain tradeoff, In this paper, we present max-flow min-cut type theorems for computing both the diversity and the DOF of arbitrary single-source single-sink networks with nodes possessing multiple antennas. We also show that an amplify-and-forward protocol is sufficient to achieve the same. The DOF characterization is obtained using a conversion to a deterministic wireless network for which the capacity was recently found. This conversion is operational in the sense that a capacity-achieving scheme for the deterministic network can be converted into a DOF-achieving scheme for the fading network. We also show that the diversity result easily extends to multisource multi-sink networks whereas the DOF result extends to a single-source multi-cast network. Along the way, we prove that the zero error capacity of the deterministic network is the same as its c-error capacity.

The inclusion of geography in TIMSS: Can consensus be reached?

An initial call by the editors of International Research in Geographical and Environmental Education (IRGEE) prompted a study about the inclusion of geography in the Trends in International Mathematics and Science Study (TIMSS) tests. This study found that the geography education community were overwhelmingly in favour of such a move, believing that the information collected would be valuable in enhancing learning outcomes through its impact on research, policy and teaching practice (Lane & Bourke, 2016). However, a number of questions about the development and implementation of this assessment were posed. This paper addresses two of these questions: (1) What is the global geographical education community’s views about Grades 4 and 8 as target year levels for the assessment?; and, (2) What types of knowledge and cognitive dimensions would they like to see assessed? Based on these findings, the overarching key question that requires further discussion is: Can there be some degree of consensus in terms of what should be assessed and how the test should be implemented?

Inclusive values: Exploring the perspectives of pre-service teachers

Since the turn of the century there has been an increasing focus on inclusive education in Australian schools, and growing interest in understanding how the values of pre-service teachers impact on their willingness to implement inclusive principles in their future classrooms. The current qualitative study explored the values and views toward diversity and inclusion of pre-service teachers at one university in Queensland, Australia. Results showed that first and fourth year pre-service teachers held similar ideas about the values that teachers should have, and showed congruence between their own personal values and teacher values. Fourth year students who had undertaken an inclusive education minor placed greater emphasis on the importance of inclusion, and felt more confident about supporting this diversity in their future classrooms, than those fourth years who had not undertaken this minor. The findings from this study will inform future planning in preparing teachers for inclusive work in schools.