The South American Plasmodium falciparum var gene repertoire is limited, highly shared and possibly lacks several antigenic types

The Plasmodium falciparum var gene family encodes large variant antigens, which are important virulence factors, and also targets of the humoral host response. The frequently observed mild outcomes of falciparum malaria in many places of the Amazon area prompted us to ask whether a globally restricted variant (var) gene repertoire is present in currently circulating and older isolates of this area. By exhaustive analysis of var gene tags from 89 isolates and clones taken during many years from all over the Brazilian Amazon, we estimate that there are probably no more than 350-430 distinct sequence types, less than for any similar sized area studied so far. Detailed analysis of the var tags from genetically distinct clones obtained from single isolates revealed restricted and redundant repertoires suggesting either a low incidence of infective bites or restricted variant gene diversity in inoculated parasites. Additionally, we found a structuring of var gene repertoires observed as a higher pairwise typing sharing in isolates from the same microregion compared to isolates from different regions. Fine analysis of translated var tags revealed that certain Distinct Sequence Identifiers (DSIDs) were differently represented in Brazilian/South American isolates when compared to datasets from other continents. By global alignment of worldwide var DBL alpha sequences and sorting in groups with more than 76% identity, 125 clusters were formed and more than half of all genes were found in nine clusters with 50 or more sequences. While Brazilian/South American sequences were represented only in 64 groups, African sequences were found in the majority of clusters. DSID type 1 related sequences accumulated almost completely in one single cluster, indicating that limited recombination occurs in these specific var gene types. These data demonstrate the so far highest pairwise type sharing values for the var gene family in isolates from all over an entire subcontinent. The apparent lack of specific sequences types suggests that the P. falciparum transmission dynamics in the whole Amazon are probably different from any other endemic region studied and possibly interfere with the parasite`s ability to efficiently diversify its variant gene repertoires. (C) 2010 Elsevier B.V. All rights reserved.

At Sunny Bay: building students` repertoire of literacy practices through process drama

This collection of resources provides classroom examples and case studies, offers a platform of ideas for teachers to investigate new ways of building the literacy development of their students.

Song sharing and repertoire size in the sedge warbler, Acrocephalus schoenobaenus: changes within and between years

The complex song of the male sedge warbler functions mainly in sexual attraction and the evolution of repertoire size is driven primarily by female choice. As male song ceases upon pairing, male–male singing interactions are relatively brief and have not been studied to our knowledge. This study shows that young males in their first breeding season shared significantly more syllables with their nearest neighbour than with their fathers or more distant males. Moreover, daily recordings revealed that rapid learning and modification of syllable repertoires occurred, resulting in a progressive increase in sharing within just a few days. This does not lead to a gradual increase in repertoire size as some syllables are dropped and new ones are acquired. This turnover process allows males to share syllables with their neighbours, whilst repertoire size, known to be important in female choice, remains relatively constant in any one year. Individual males were followed for several years and also showed considerable syllable turnover between years. However, in this case, repertoire size was found to increase between years, the largest increase occurring between the first and second years. We obtained a significant positive correlation between repertoire size and age, suggesting that females choosing males with larger repertoires may gain indirect (genetic) benefits for their offspring, such as good genes for viability. Whilst these results reveal a more flexible picture of repertoire turnover than previously suspected, the relative stability of repertoire size within a season and the increase with age suggests that repertoire size remains a likely target for sexual selection by female choice.

Exploring the possibilities of an expanded practice repertoire in child protection

Summary: This article discusses research that explored an alternative to proceduralized child protection practice informed by the risk paradigm, by expanding the repertoire available to practitioners through combining features of the risk paradigm with social constructionism. This approach incorporates three dimensions: theories of knowledge and power, related professional roles, and practice skills. In this article, we discuss and critically evaluate only the first dimension: theories of knowledge and power. Through dialogue facilitated by semi-structured questions, we explored practitioners' perspectives about the relevance and appropriateness of the alternative approach for practice.

Findings: The practitioners' participation and feedback offer insights into complex connections between `theory' and `practice' with the practitioner as a positioned subject and mediator of practical meanings of formal concepts.

Applications: 1) Recognition of each practitioner's interpretation of formal concepts and how they are applied in actual practice, even within shared organizational contexts. 2) The importance of dialogue to expand the range of possibilities that maintain openness to ongoing learning. 3) The value of theoretical pluralism that may offer greater opportunities for professional discretion, rather than single self-contained approaches that may constrain effective and ethical practice.

Tracking phenotypically and functionally distinct T cell subsets via T cell repertoire diversity

Antigen-specific T cell receptors (TCRs) recognise complexes of immunogenic peptides (p) and major histocompatibility complex (MHC) glycoproteins. Responding T cell populations show profiles of preferred usage (or bias) toward one or few TCRβ chains. Such skewing is also observed, though less commonly, in TCRα chain usage. The extent and character of clonal diversity within individual, antigen-specific T cell sets can be established by sequence analysis of the TCRVβ and/or TCRVα CDR3 loops. The present review provides examples of such TCR repertoires in prominent responses to acute and persistent viruses. The determining role of structural constraints and antigen dose is discussed, as is the way that functionally and phenotypically distinct populations can be defined at the clonal level. In addition, clonal dissection of “high” versus “low” avidity, or “central” versus “effector” memory sets provides insights into how these antigen specific T cell responses are generated and maintained. As TCR diversity potentially influences both the protective capacity of CD8+ T cells and the subversion of immune control that leads to viral escape, analysing the spectrum of TCR selection and maintenance has implications for improving the functional efficacy of T cell responsiveness and effector function.

Teaching in the iWorld: developing a repertoire of pedagogical discourse around the usage of touch screen devices in early years classrooms

 Touch-screen devices have been enthusiastically adopted by schools across Australia and Canada. Their ease of use means that they are accessible by very young children, and these children often have free access to these devices in their home, however the devices tend to be ‘domesticated’ in the school context (O’Mara and Laidlaw, 2011). In the short period of their availability, a plethora of educational applications have been developed for these devices. This paper addresses emergent themes from our 2011-2013 Canadian/Australian project, Literacy learning in playful spaces: using multi-modal strategies to develop narrative with young learners, funded by the Canadian Social Sciences and Humanities Research Council (Insight Development Grant). In our analysis of the discourse around the introduction of portable touch screen devices into school literacy classes (published texts, teacher interviews, classroom observations), we noted that much of the public discourse is slanted towards the idea of “teacher-proofing” the curriculum. Initially the teachers we have been working with saw the apps themselves as complete, as doing all the work and the discourse around the devices was around what apps are “best”, and “is there an app for that?” It was only with more experience and time that teachers were able to harness the range of affordances of the devices—their capacity for recording audio, video, pictures etc., and start to categorise the apps themselves. In this paper we suggest ways in which current literacy models might be used to develop a repertoire of pedagogical discourse around these devices, providing language and framings for teachers to think about how these new tools might best be used to enhance literacy teaching and learning. O’Mara, J. & Laidlaw, L. (2011). Living in the iWorld: Two literacy researchers reflect on the changing texts and literacy practices of childhood. English Teaching: Practice and Critique 10 (4): 149-159. Available: http://edlinked.soe.waikato.ac.nz/research/journal/view.php?article=true&id=754&p=1

Behavioral Repertoire of Basal Fungus-Growing Ant Sexuals (Hymenoptera: Formicidae) in the Parental Nest

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Acoustic repertoire and calling behavior of Scinax fuscomarginatus (Anura, Hylidae)

Vocalizations are important in anuran communication, especially during the breeding season. Calling affects spatial organization of males at breeding sites, promotes attraction of new individuals to the chorus, and attracts mature females for reproduction. We describe four distinct vocalizations (advertisement calls, sporadic calls, and two types of aggressive calls) emitted by adult males of Scinax fuscomarginatus. With the exception of the advertisement call, the remaining descriptions are novel. We also describe calling sites, calling season, and nightly calling activity. Fieldwork was made in a fragment of Cerrado (Estação Ecológica de Itirapina), Municipalities of Itirapina and Brotas, State of São Paulo, southeastern Brazil. At this ecological station, S. fuscomarginatus exhibits a complex acoustic repertoire, social interactions and a prolonged reproductive pattern similar to observations of congeneric species at other localities. Copyright 2005 Society for the Study of Amphibians and Reptiles.

Calling activity and vocal repertoire of hypsiboas prasinus (Anura, Hylidae), a treefrog from the Atlantic Forest of Brazil

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

The anuran calling repertoire in the light of social context

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Repertoire, Genealogy and Genomic Organization of Cruzipain and Homologous Genes in Trypanosoma cruzi, T. cruzi-Like and Other Trypanosome Species

Trypanosoma cruzi, the agent of Chagas disease, is a complex of genetically diverse isolates highly phylogenetically related to T. cruzi-like species, Trypanosoma cruzi marinkellei and Trypanosoma dionisii, all sharing morphology of blood and culture forms and development within cells. However, they differ in hosts, vectors and pathogenicity: T. cruzi is a human pathogen infective to virtually all mammals whilst the other two species are non-pathogenic and bat restricted. Previous studies suggest that variations in expression levels and genetic diversity of cruzipain, the major isoform of cathepsin L-like (CATL) enzymes of T. cruzi, correlate with levels of cellular invasion, differentiation, virulence and pathogenicity of distinct strains. In this study, we compared 80 sequences of genes encoding cruzipain from 25 T. cruzi isolates representative of all discrete typing units (DTUs TcI-TcVI) and the new genotype Tcbat and 10 sequences of homologous genes from other species. The catalytic domain repertoires diverged according to DTUs and trypanosome species. Relatively homogeneous sequences are found within and among isolates of the same DTU except TcV and TcVI, which displayed sequences unique or identical to those of TcII and TcIII, supporting their origin from the hybridization between these two DTUs. In network genealogies, sequences from T. cruzi clustered tightly together and closer to T. c. marinkellei than to T. dionisii and largely differed from homologues of T. rangeli and T. b. brucei. Here, analysis of isolates representative of the overall biological and genetic diversity of T. cruzi and closest T. cruzi-like species evidenced DTU- and species-specific polymorphisms corroborating phylogenetic relationships inferred with other genes. Comparison of both phylogenetically close and distant trypanosomes is valuable to understand host-parasite interactions, virulence and pathogenicity. Our findings corroborate cruzipain as valuable target for drugs, vaccine, diagnostic and genotyping approaches.

Das Globingen-Repertoire von Amphibien und Teleostiern

Im Rahmen der vorliegenden Dissertation wurde die molekulare Evolution von Globinen in Amphibien und Teleostiern untersucht und Analysen zur Genexpression ausgewählter Globine durchgeführt. Die bisher besonders für die neueren Mitglieder der Superfamilie der Globine – Neuroglobin und Cytoglobin – schwerpunktmäßig in Mammaliern erbrachten Daten sollten durch die Analyse in Amphibien und Teleostiern auf ihre generelle Gültigkeit für Vertebraten überprüft werden. Die Analysen zur Genexpression wurden sowohl in silico, basierend auf genomischen wie EST-Daten, als auch experimentell durch qualitative und quantitative RT-PCR-Nachweise durchgeführt. Die mRNA-Lokalisation wurde durch in situ-Hybridisierungen an Gewebeschnitten beziehungsweise durch Whole mount in situ-Hybridisierung an ganzen Embryonen detektiert. In einem ersten Teil der Arbeit wurde das Globin-Repertoire von Xenopus tropicalis umfassend analysiert. Die Expressionsanalyse der gefundenen Globine umfasste nicht nur adulte Tiere, sonder erstmals auch detailliert die Entwicklungsstadien eines Vertebraten. Dabei wurde festgestellt, dass die vorwiegend neuronale Expression des streng konservierten Neuroglobins ein generelles Charakteristikum aller Tetrapoden ist und bereits in der frühembryonalen Entwicklung auftritt. Auch für das als Einzelkopie im Amphibiengenom vertretene Cytoglobin konnte eine strenge Sequenzkonservierung gezeigt werden. Das Expressionsmuster des Amphibien-Cytoglobins stimmte mit dem aus Mammaliern bekannten überein und zeigte konservierte Charakteristika dieses Globins bei Tetrapoden auf. Die Analyse des Xenopus-Genoms ergab zudem, dass Krallenfrösche nicht über Myoglobin verfügen. Genomische Vergleiche syntäner Genregionen ließen auf Rearrangements in diesem Genombereich im Verlauf der Evolution schließen, in deren Folge das Myoglobingen in den Krallenfröschen deletiert wurde. Die Hämoglobine wurden in Xenopus tropicalis erstmals in einem Amphibium umfassend analysiert. Die Gene zeigten demnach eine geclusterte Anordnung: der tropische Krallenfrosch verfügte über je ein funktionelles α- bzw. β-adultes und sieben bzw. vier α- bzw. β-larvale Hämoglobine, die während der Entwicklung bzw. in adulten Tieren charakteristisch exprimiert wurden. Die Analyse der Hämoglobine hinsichtlich ihrer Lage in einem Cluster, ihrer phylogenetischen Relation zueinander und nicht zuletzt ihres Expressionsmusters ließen Rückschlüsse auf ihre Evolution zu. Zusätzlich zu diesen bereits bekannten Globinen konnte im Rahmen dieser Dissertation das Globingen-Repertoirs von Xenopus um zwei weitere, bisher unbekannte Globine erweitert werden. Diese wurden entsprechend ihrer bisher unbekannten Funktion als GlobinX und GlobinY bezeichnet. Während GlobinY bisher ausschließlich in Amphibien nachgewiesen werden konnte, wurde GlobinX zudem in Teleostiern detektiert und repräsentiert damit ein auf Anamnia beschränktes Globin. Die rekombinante Proteinexpression von Neuroglobin, Cytoglobin, GlobinX und GlobinY des tropischen Krallenfrosches zeigte ein hexakoordiniertes Bindungsschema dieser Globine in ihrem Deoxy-Zustand. In einem zweiten Teil dieser Dissertation wurden Neuroglobin und Cytoglobin in Teleostiern untersucht und die Analyse für diese zwei Gene somit über die Tetrapoden hinaus auf den gesamten Stammbaum der Vertebraten ausgedehnt. Dabei wurde deutlich, dass die vorwiegend neuronale Expression des seit 420 Millionen Jahren streng konservierten Neuroglobins ein generelles Merkmal dieses Globins in allen Vertebraten ist. Der in Amphibien und Teleostiern erbrachte und mit Ergebnissen in Mammaliern übereinstimmende Nachweis von Neuroglobin in neuronalen Geweben mit einem hohen Stoffwechsel lässt derzeit eine Funktion dieses Globins im Sauerstoffmetabolimus als wahrscheinlich erscheinen. Ob Neuroglobin dabei als kurzzeitiger Sauerstoffspeicher, O2-Transoprter oder aber in der Detoxifikation reaktiver Sauerstoff- bzw. Stickstoffspezies agiert, bleibt zu untersuchen. Für Cytoglobin konnte eine offenbar alle Teleostier betreffende Genduplikation nachgewiesen werden. Phylogenetische Analysen zeigen die Monophylie der Vertebraten-Cytoglobine. Der Vergleich der paralogen Cytoglobine der Teleostier mit dem syntänen Genombereich des humanen Cytoglobins zeigte die wahrscheinliche Entstehung der Fisch-Cytoglobine durch eine Genomduplikation in einem Vorfahren aller Teleostier vor etwa 300-450 Millionen Jahren. Die paralogen Cytoglobine zeigten in Danio rerio und Tetraodon nigroviridis differierende, charakteristische Expressionsmuster, die mit der Theorie der Subfunktionalisierung von Genen in Folge eines Duplikationsereignisses kompatibel sind. Die Analyse zeigte, dass Cygb-1 prädominant in Gehirn und Herz exprimiert wurde, Cygb-2 hingegen bevorzugt in Gehirn und Auge. Dies bestätigte indirekt die Hypothese, nach der das Cytoglobin der Mammalier zwei unterschiedliche Funktionen in differenten Geweben wahrnimmt. Die rekombinante Expression von Cygb-1 des Zebrabärblings zeigte zudem, das auch dieses Globin in seiner Deoxy-Form über ein hexakoordiniertes Bindungsschema verfügt.