Genomic structure and expression of Jmjd6 and evolutionary analysis in the context of related JmjC domain containing proteins

<p>Abstract</p> <p>Background</p> <p>The <it>jumonji C (JmjC) domain containing gene 6 </it>(<it>Jmjd6</it>, previously known as phosphatidylserine receptor) has misleadingly been annotated to encode a transmembrane receptor for the engulfment of apoptotic cells. Given the importance of JmjC domain containing proteins in controlling a wide range of diverse biological functions, we undertook a comparative genomic analysis to gain further insights in <it>Jmjd6 </it>gene organisation, evolution, and protein function.</p> <p>Results</p> <p>We describe here a semiautomated computational pipeline to identify and annotate JmjC domain containing proteins. Using a sequence segment N-terminal of the Jmjd6 JmjC domain as query for a reciprocal BLAST search, we identified homologous sequences in 62 species across all major phyla. Retrieved <it>Jmjd6 </it>sequences were used to phylogenetically analyse corresponding loci and their genomic neighbourhood. This analysis let to the identification and characterisation of a bi-directional transcriptional unit compromising the <it>Jmjd6 </it>and <it>1110005A03Rik </it>genes and to the recognition of a new, before overseen <it>Jmjd6 </it>exon in mammals. Using expression studies, two novel <it>Jmjd6 </it>splice variants were identified and validated <it>in vivo</it>. Analysis of the <it>Jmjd6 </it>neighbouring gene <it>1110005A03Rik </it>revealed an incident deletion of this gene in two out of three earlier reported <it>Jmjd6 </it>knockout mice, which might affect previously described conflicting phenotypes. To determine potentially important residues for <it>Jmjd6 </it>function a structural model of the Jmjd6 protein was calculated based on sequence conservation. This approach identified a conserved double-stranded β^-helix (DSBH) fold and a HxDx_nH facial triad as structural motifs. Moreover, our systematic annotation in nine species identified 313 DSBH fold-containing proteins that split into 25 highly conserved subgroups.</p> <p>Conclusion</p> <p>We give further evidence that <it>Jmjd6 </it>most likely has a function as a nonheme-Fe(II)-2-oxoglutarate-dependent dioxygenase as previously suggested. Further, we provide novel insights into the evolution of Jmjd6 and other related members of the superfamily of JmjC domain containing proteins. Finally, we discuss possibilities of the involvement of <it>Jmjd6 </it>and <it>1110005A03Rik </it>in an antagonistic biochemical pathway.</p

Artificial neural network surrogate modeling for uncertainty quantification and structural optimization of reinforced concrete structures

Optimization approaches are important to design sustainable structures. In structural mechanics, different design objectives can be defined, for example, to minimize the required construction material or to maximize the structural durability. In this paper, the durability of a reinforced concrete (RC) structure is assessed by advanced finite element (FE) models to simulate the cracking behavior and the chloride transport process. The corrosion initiation time is used as durability measure to be maximized within an optimization approach, where the concrete cover is defined as design variable. The variability of structural loads and material parameters and unavoidable construction imprecision leads to a probabilistic reliability and durability assessment, where aleatory as well as epistemic uncertainties are quantified by random variables, intervals and probability-boxes. The FE simulation models cannot directly be applied to structural analyses and optimizations with polymorphic uncertain parameters and design variables because of the high computational demand of the multi-loop algorithm (Monte Carlo simulation, interval analysis, global optimization). In this paper, a new surrogate modeling strategy is presented, where artificial neural networks are trained sequentially to speed-up the coupled mechanical and transport simulation FE models. The new approach is applied to the uncertainty quantification and the structural durability optimization of a RC structure

Genomic structure and expression of Jmjd6 and evolutionary analysis in the context of related JmjC domain containing proteins

<p>Abstract</p> <p>Background</p> <p>The <it>jumonji C (JmjC) domain containing gene 6 </it>(<it>Jmjd6</it>, previously known as phosphatidylserine receptor) has misleadingly been annotated to encode a transmembrane receptor for the engulfment of apoptotic cells. Given the importance of JmjC domain containing proteins in controlling a wide range of diverse biological functions, we undertook a comparative genomic analysis to gain further insights in <it>Jmjd6 </it>gene organisation, evolution, and protein function.</p> <p>Results</p> <p>We describe here a semiautomated computational pipeline to identify and annotate JmjC domain containing proteins. Using a sequence segment N-terminal of the Jmjd6 JmjC domain as query for a reciprocal BLAST search, we identified homologous sequences in 62 species across all major phyla. Retrieved <it>Jmjd6 </it>sequences were used to phylogenetically analyse corresponding loci and their genomic neighbourhood. This analysis let to the identification and characterisation of a bi-directional transcriptional unit compromising the <it>Jmjd6 </it>and <it>1110005A03Rik </it>genes and to the recognition of a new, before overseen <it>Jmjd6 </it>exon in mammals. Using expression studies, two novel <it>Jmjd6 </it>splice variants were identified and validated <it>in vivo</it>. Analysis of the <it>Jmjd6 </it>neighbouring gene <it>1110005A03Rik </it>revealed an incident deletion of this gene in two out of three earlier reported <it>Jmjd6 </it>knockout mice, which might affect previously described conflicting phenotypes. To determine potentially important residues for <it>Jmjd6 </it>function a structural model of the Jmjd6 protein was calculated based on sequence conservation. This approach identified a conserved double-stranded β^-helix (DSBH) fold and a HxDx_nH facial triad as structural motifs. Moreover, our systematic annotation in nine species identified 313 DSBH fold-containing proteins that split into 25 highly conserved subgroups.</p> <p>Conclusion</p> <p>We give further evidence that <it>Jmjd6 </it>most likely has a function as a nonheme-Fe(II)-2-oxoglutarate-dependent dioxygenase as previously suggested. Further, we provide novel insights into the evolution of Jmjd6 and other related members of the superfamily of JmjC domain containing proteins. Finally, we discuss possibilities of the involvement of <it>Jmjd6 </it>and <it>1110005A03Rik </it>in an antagonistic biochemical pathway.</p

Konjunktiv II-Variation im urbanen Sprachgebrauch in Österreich

The city as a social structure has a distinct relationship with its inhabitants. It creates a socio-pragmatic environment that produces communicative characteristics in the form of usage patterns that go hand in hand with conventionalised practices (cf. Gal 1987) and are dependent on everyday-life contextual aspects. Accordingly, research of urban varieties is ideally based on language data that is as authentic as possible and includes socio-demographic and diatopic aspects. Following this idea, the study presented examines the subjunctive II in urban Austria by analysing free conversations in formal and informal contexts (interviews and conversations among friends), and correlating the results with spatial and social parameters. The data used was collected in Vienna and Graz, the two largest cities in Austria, as well as in their respective surrounding areas and was grouped by gender, age and place of residence. The subjunctive II is realised in synthetic as well as periphrastic forms (cf. Merkle 1993: 69–73.; Donhauser 1992; Glauninger 2008). In rural Austria speakers use the entire range of variants (cf. Ziegler/Glantschnig 2013; Breuer/Wittibschlager 2020), while urban speakers exhibit a much narrower range, as we show in our analysis. Striking features in the use of variants can be seen above all in the form of contrasting modes of construction, i.&nbsp;e. synthetic vs. periphrastic realisation. The study reveals that there are hardly any differences between the two urban centres and only minor differences between a city and its surrounding area. However, the inclusion of social parameters provides a more differentiated picture: Here, higher relative frequencies of synthetic forms are found among male and older speakers compared to female and younger speakers. Thus, a preference for more conservative forms among the former contrasts with a preference for more modern (analytical) variants among the latter

Bairisch-österreichische Dialektliteratur vor 1800

Literatur in und mit Dialekt war auch vor 1800 ein wesentlicher, prägender Bestandteil der Elite-, Alltags- und Komplementärkultur im bairisch-österreichischen Sprachraum. Christian Neuhuber, Stefanie Edler, Elisabeth Zehetner präsentieren erstmals die wichtigsten Ausdrucksformen, Arbeiten und Autoren, kontextualisieren die bislang überwiegend nicht edierten Werke aus einer Vielzahl an Archiven und Bibliotheken und stellen sie in aktuelle kulturwissenschaftliche Forschungszusammenhänge.Literatur in und mit Dialekt war auch vor 1800 ein wesentlicher, prägender Bestandteil der Elite-, Alltags- und Komplementärkultur im bairisch-österreichischen Sprachraum. Christian Neuhuber, Stefanie Edler, Elisabeth Zehetner präsentieren erstmals die wichtigsten Ausdrucksformen, Arbeiten und Autoren, kontextualisieren die bislang überwiegend nicht edierten Werke aus einer Vielzahl an Archiven und Bibliotheken und stellen sie in aktuelle kulturwissenschaftliche Forschungszusammenhänge

Bairisch-österreichische Dialektliteratur vor 1800

Literatur in und mit Dialekt war auch vor 1800 ein wesentlicher, prägender Bestandteil der Elite-, Alltags- und Komplementärkultur im bairisch-österreichischen Sprachraum. Christian Neuhuber, Stefanie Edler, Elisabeth Zehetner präsentieren erstmals die wichtigsten Ausdrucksformen, Arbeiten und Autoren, kontextualisieren die bislang überwiegend nicht edierten Werke aus einer Vielzahl an Archiven und Bibliotheken und stellen sie in aktuelle kulturwissenschaftliche Forschungszusammenhänge.Literatur in und mit Dialekt war auch vor 1800 ein wesentlicher, prägender Bestandteil der Elite-, Alltags- und Komplementärkultur im bairisch-österreichischen Sprachraum. Christian Neuhuber, Stefanie Edler, Elisabeth Zehetner präsentieren erstmals die wichtigsten Ausdrucksformen, Arbeiten und Autoren, kontextualisieren die bislang überwiegend nicht edierten Werke aus einer Vielzahl an Archiven und Bibliotheken und stellen sie in aktuelle kulturwissenschaftliche Forschungszusammenhänge

Bairisch-österreichische Dialektliteratur vor 1800

These days, it is commonly forgotten that Bavarian-Austrian dialect art flourished in elite culture and even more in popular counterculture before 1800. The book makes the amazing variety of forms and modes of operation visible again. In eight chapters, the most important, predominantly unedited texts and their authors are presented, contextualized, and related to current research fields using an interdisciplinary approach

Genomic structure and expression of and evolutionary analysis in the context of related JmjC domain containing proteins-7

of 25 identified DSBH fold containing protein subgroups as indicated with protein family names on the right side. Scale bar represents the relative phylogenetic distance as determined with PHYLIP. Bootstrap values are shown for values <p><b>Copyright information:</b></p><p>Taken from "Genomic structure and expression of and evolutionary analysis in the context of related JmjC domain containing proteins"</p><p>http://www.biomedcentral.com/1471-2164/9/293</p><p>BMC Genomics 2008;9():293-293.</p><p>Published online 18 Jun 2008</p><p>PMCID:PMC2453528.</p><p></p