a-murine-model-stent-implantation-carotid-artery-for-study

A Murine Model of Stent Implantation in the Carotid Artery for the Study of Restenosis

Despite  the considerable progress made in the stent development in the last decades,  cardiovascular diseases remain the main cause of death in western ...

RWTH Aachen University

The origin of many of the defining features of animal body plans, such as symmetry, nervous system, and the mesoderm, remains shrouded in mystery because of major uncertainty regarding the emergence order of the early branching taxa: the sponge groups, ctenophores, placozoans, cnidarians, and bilaterians. The "phylogenomic" approach [1] has recently provided a robust picture for intrabilaterian relationships [2, 3] but not yet for more early branching metazoan clades. We have assembled a comprehensive 128 gene data set including newly generated sequence data from ctenophores, cnidarians, and all four main sponge groups. The resulting phylogeny yields two significant conclusions reviving old views that have been challenged in the molecular era: (1) that the sponges (Porifera) are monophyletic and not paraphyletic as repeatedly proposed [4-9], thus undermining the idea that ancestral metazoans had a sponge-like body plan; (2) that the most likely position for the ctenophores is together with the cnidarians in a "coelenterate" clade. The Porifera and the Placozoa branch basally with respect to a moderately supported "eumetazoan" clade containing the three taxa with nervous system and muscle cells (Cnidaria, Ctenophora, and Bilateria). This new phylogeny provides a stimulating framework for exploring the important changes that shaped the body plans of the early diverging phyla.

Phylogenomics revives traditional views on deep animal relationships.

L&#39;origine de bon nombre des caract&eacute;ristiques d&eacute;terminantes des plans du corps animal, telles que la sym&eacute;trie du syst&egrave;me nerveux et le m&eacute;soderme, reste envelopp&eacute;e de myst&egrave;re en raison de l&#39;incertitude importante concernant l&#39;ordre d&#39;apparition des taxons ramifications pr&eacute;coces : les groupes de l&#39;&eacute;ponge, ct&eacute;nophores, placozoans, cnidaires et bilat&eacute;raux. L&#39;approche &laquo; phylogenomic &raquo; [1] a r&eacute;cemment fourni une image solide pour des relations d&#39;intrabilaterian [2, 3], mais pas encore pour plusieurs clades de m&eacute;tazoaires ramifications pr&eacute;coces. Nous avons r&eacute;uni un ensemble de donn&eacute;es 128 g&egrave;ne complet y compris les donn&eacute;es nouvellement g&eacute;n&eacute;r&eacute;e s&eacute;quence de chacun des quatre groupes principaux d&#39;&eacute;ponge, cnidaires et ct&eacute;nophores. La phylog&eacute;nie qui en r&eacute;sulte conduit &agrave; deux conclusions importantes, renouant avec des vues anciennes qui ont &eacute;t&eacute; contest&eacute;es dans l&#39;&egrave;re mol&eacute;culaire: (1) que les &eacute;ponges (Porifera) sont monophyl&eacute;tiques et pas paraphyl&eacute;tique propos&eacute; &agrave; maintes reprises [4-9], qui ont nui &agrave; l&#39;id&eacute;e que les m&eacute;tazoaires ancestrales avaient un plan de corps spongieux ; (2) que le plus probable pour les ct&eacute;nophores se situe avec les cnidaires dans un clade &quot;coelent&eacute;r&eacute;&quot;. Les porif&egrave;res et la branche Placozoa &agrave; la base en ce qui concerne un clade mod&eacute;r&eacute;ment pris en charge &quot;eumetazoan&quot; contenant trois taxons avec le syst&egrave;me nerveux et des cellules musculaires (cnidaires, Ctenophora et Bilateria). Cette nouvelle phylog&eacute;nie fournit un cadre stimulant pour d&eacute;couvrir les changements importants qui ont fa&ccedil;onn&eacute; les plans de corps des d&eacute;but phylums divergentes.

Phylog&eacute;nomique renoue avec des points de vue traditionnels sur les relations profondes animales.

L&#39;origine di molte delle caratteristiche di definizione dei piani di corpo animale, come la simmetria, sistema nervoso e il mesoderma, resta avvolta nel mistero a causa della maggiore incertezza per quanto riguarda l&#39;ordine di comparsa dei primi ramificazione taxa: gruppi di spugna, ctenofori, placozoans, cnidari e bilaterians. L&#39;approccio &quot;phylogenomic&quot; [1] ha recentemente fornito una robusta foto per relazioni intrabilaterian [2, 3] ma non ancora per pi&ugrave; precoce ramificazione metazoi clades. Abbiamo montato un completo set di dati di 128 gene compresi i dati di sequenza appena generato da tutti i quattro gruppi principali di spugna, cnidari e Ctenofori. La filogenia risultante produce due conclusioni significative rivivere vecchie viste che sono state contestate in epoca molecolare: (1) che le spugne (Poriferi) sono monofiletici e non parafiletico come pi&ugrave; volte proposto [4-9], minando cos&igrave; l&#39;idea che metazoi ancestrali avevano un piano corpo spugnoso; (2) che &egrave; la posizione pi&ugrave; probabile per i Ctenofori insieme i cnidari in un clade &quot;coelenterate&quot;. I Poriferi e il ramo Placozoa le rispetto un clade moderatamente supportati &quot;eumetazoan&quot; contenente i tre taxa con sistema nervoso e le cellule muscolari (cnidari Ctenophora e Bilateria). Questo nuovo phylogeny fornisce un quadro stimolante per esplorare i cambiamenti importanti che hanno plasmato i piani del corpo dei primi phyla divergenti.

Phylogenomics ravviva tradizionali viste sui rapporti profondi degli animali.

In the absence of whole genome sequences for many organisms, the use of expressed sequence tags (EST) offers an affordable approach for researchers conducting phylogenetic analyses to gain insight about the evolutionary history of organisms. Reliable alignments for phylogenomic analyses are based on orthologous gene sequences from different taxa. So far, researchers have not sufficiently tackled the problem of the completely automated construction of such datasets. Existing software tools are either semi-automated, covering only part of the necessary data processing, or implemented as a pipeline, requiring the installation and configuration of a cascade of external tools, which may be time-consuming and hard to manage. To simplify data set construction for phylogenomic studies, we set up a web server that uses our recently developed OrthoSelect approach. To the best of our knowledge, our web server is the first web-based EST analysis pipeline that allows the detection of orthologous gene sequences in EST libraries and outputs orthologous gene alignments. Additionally, OrthoSelect provides the user with an extensive results section that lists and visualizes all important results, such as annotations, data matrices for each gene/taxon and orthologous gene alignments. The web server is available at http://orthoselect.gobics.de.

OrthoSelect: a web server for selecting orthologous gene alignments from EST sequences.

En l&#39;absence de s&eacute;quences du g&eacute;nome pour de nombreux organismes, l&#39;utilisation des &eacute;tiquettes de s&eacute;quences exprim&eacute;es (EST) offre une approche abordable pour les chercheurs qui effectuent des analyses phylog&eacute;n&eacute;tiques avoir un aper&ccedil;u sur l&#39;histoire &eacute;volutive des organismes. Alignements fiables pour analyses phylogenomic reposent sur des s&eacute;quences de g&egrave;nes orthologues de taxons diff&eacute;rents. Jusqu&#39;&agrave; pr&eacute;sent, les chercheurs n&#39;ont pas suffisamment r&eacute;solu le probl&egrave;me de la construction compl&egrave;tement automatis&eacute;e de ces ensembles de donn&eacute;es. Les outils logiciels existants sont soit semi-automatique, qui couvre une partie seulement du traitement n&eacute;cessaire, ou mis en &oelig;uvre comme un pipeline, n&eacute;cessitant l&#39;installation et la configuration d&#39;une cascade d&#39;outils externes, ce qui peut &ecirc;tre long et difficile &agrave; g&eacute;rer. Pour simplifier la construction de jeu de donn&eacute;es pour les &eacute;tudes de phylogenomic, nous avons mis en place un serveur web qui utilise notre approche OrthoSelect r&eacute;cemment d&eacute;velopp&eacute;. Au meilleur de nos connaissances, notre serveur web est le premier sur le web EST analyse pipeline qui permet la d&eacute;tection des orthologues des s&eacute;quences de g&egrave;nes dans les biblioth&egrave;ques de l&#39;EST et les sorties des alignements de g&egrave;nes orthologues. En outre, OrthoSelect fournit &agrave; l&#39;utilisateur avec une section de vastes r&eacute;sultats qui r&eacute;pertorie et visualise tous les r&eacute;sultats importants, tels que les annotations, les matrices de donn&eacute;es pour chaque g&egrave;ne/taxon et orthologues des alignements de g&egrave;ne. Le serveur web est disponible &agrave; http://orthoselect.gobics.de.

OrthoSelect : un serveur web pour la s&eacute;lection des alignements de g&egrave;nes orthologues de s&eacute;quences EST.

In assenza di sequenze di genoma intero per molti organismi, l&#39;uso dei tag espressa di sequenza (EST) offre un approccio conveniente per i ricercatori di condurre analisi filogenetiche comprendere la storia evolutiva degli organismi. Allineamenti affidabili per analisi phylogenomic sono basati su sequenze di geni orthologous da diversi taxa. Finora, i ricercatori non hanno sufficientemente affrontato il problema della costruzione completamente automatizzato di tali set di dati. Strumenti software esistenti sono o semi-automatico, che copre solo parte dell&#39;elaborazione dei dati necessario, o implementato come una pipeline, che richiedono l&#39;installazione e la configurazione di una cascata di strumenti esterni, che pu&ograve; essere un&#39;operazione lunga e difficile da gestire. Per semplificare la costruzione di set di dati per studi di phylogenomic, impostiamo un server web che utilizza il nostro approccio OrthoSelect recentemente sviluppato. Al meglio delle nostre conoscenze, il nostro server web &egrave; il prima web-based EST analisi pipeline che permette la rilevazione di orthologous sequenze geniche nelle librerie di EST e uscite orthologous allineamenti gene. Inoltre, OrthoSelect fornisce all&#39;utente una sezione ricca di risultati che elenca e Visualizza tutti i risultati importanti, come le annotazioni, matrici di dati per ogni gene/taxon e orthologous allineamenti di gene. Il server web &egrave; disponibile presso http://orthoselect.gobics.de.

OrthoSelect: un server web per la selezione degli allineamenti di gene orthologous da sequenze EST.

Les &eacute;tudes phylog&eacute;n&eacute;tiques &agrave; l&#39;aide d&#39;&eacute;tiquettes de s&eacute;quences exprim&eacute;es (EST) deviennent une approche standard pour r&eacute;pondre aux questions &eacute;volutives. Ces &eacute;tudes se fondent habituellement sur des ensembles de s&eacute;quences de EST nouvellement g&eacute;n&eacute;r&eacute;s non annot&eacute;es et sujette aux erreurs provenant de diff&eacute;rentes esp&egrave;ces. Une premi&egrave;re &eacute;tape cruciale dans la reconstruction de la phylog&eacute;nie EST bas&eacute; sur est d&#39;identifier les groupes de s&eacute;quences orthologues. De ces ensembles de donn&eacute;es, les g&egrave;nes cibles appropri&eacute;s sont s&eacute;lectionn&eacute;s et s&eacute;quences redondantes sont &eacute;limin&eacute;s afin d&#39;obtenir des ensembles appropri&eacute;s de s&eacute;quence comme donn&eacute;es d&#39;entr&eacute;e pour le logiciel de l&#39;arbre-reconstruction. &Eacute;lectrog&egrave;nes manuellement ces donn&eacute;es peut &ecirc;tre tr&egrave;s chronophage. Ainsi, les outils logiciels sont n&eacute;cessaires qu&#39;effectuer ces &eacute;tapes automatiquement.

OrthoSelect : un protocole de s&eacute;lection des groupes orthologues dans phylog&eacute;nomique.

Studi filogenetici utilizzando tag espressa di sequenza (EST) stanno diventando un approccio standard per rispondere alle domande evolutive. Tali studi sono di solito basati su grandi insiemi di sequenze di EST appena generate, non annotate ed errore-prone da diverse specie. Un primo passo fondamentale nella ricostruzione della filogenesi EST-base &egrave; quello di identificare gruppi di sequenze orthologous. Da questi insiemi di dati, vengono selezionati geni bersaglio appropriato e sequenze ridondanti vengono eliminati per ottenere adatto sequenza imposta come dati di input per software albero-ricostruzione. Elettrogeni manualmente tali dati pu&ograve; richiedere molto tempo. Cos&igrave;, sono necessari strumenti software che effettuano questi passi automaticamente.

OrthoSelect: un protocollo per la selezione di gruppi di orthologous in phylogenomics.

Phylogenetic studies using expressed sequence tags (EST) are becoming a standard approach to answer evolutionary questions. Such studies are usually based on large sets of newly generated, unannotated, and error-prone EST sequences from different species. A first crucial step in EST-based phylogeny reconstruction is to identify groups of orthologous sequences. From these data sets, appropriate target genes are selected, and redundant sequences are eliminated to obtain suitable sequence sets as input data for tree-reconstruction software. Generating such data sets manually can be very time consuming. Thus, software tools are needed that carry out these steps automatically.

OrthoSelect: a protocol for selecting orthologous groups in phylogenomics.

SUMMARY: Assessment of phylogenetic diversity is a key element to the analysis of microbial communities. Tools are needed to handle next-generation sequencing data and to cope with the computational complexity of large-scale studies. Here, we present Treephyler, a tool for fast taxonomic profiling of metagenomes. Treephyler was evaluated on real metagenome to assess its performance in comparison to previous approaches for taxonomic profiling. Results indicate that Treephyler is in terms of speed and accuracy prepared for next-generation sequencing techniques and large-scale analysis. AVAILABILITY: Treephyler is implemented in Perl; it is portable to all platforms and applicable to both nucleotide and protein input data. Treephyler is freely available for download at http://www.gobics.de/fabian/treephyler.php.

Treephyler: fast taxonomic profiling of metagenomes.

R&eacute;sum&eacute; : &Eacute;valuation de la diversit&eacute; phylog&eacute;n&eacute;tique est un &eacute;l&eacute;ment cl&eacute; pour l&#39;analyse des communaut&eacute;s microbiennes. Outils sont n&eacute;cessaires pour g&eacute;rer les donn&eacute;es de s&eacute;quen&ccedil;age de prochaine g&eacute;n&eacute;ration et pour faire face &agrave; la complexit&eacute; des &eacute;tudes &agrave; grande &eacute;chelle. Nous pr&eacute;sentons ici, Treephyler, un outil de profilage rapide taxonomique des m&eacute;tag&eacute;nomes. Treephyler a &eacute;t&eacute; &eacute;valu&eacute; sur le m&eacute;tag&eacute;nome r&eacute;el pour &eacute;valuer sa performance par rapport aux approches pr&eacute;c&eacute;dentes pour le profilage taxonomique. Les r&eacute;sultats indiquent que la Treephyler est en termes de rapidit&eacute; et de pr&eacute;cision &eacute;tabli pour les techniques de s&eacute;quen&ccedil;age de la g&eacute;n&eacute;ration et l&#39;analyse &agrave; grande &eacute;chelle. Disponibilit&eacute; : Treephyler est impl&eacute;ment&eacute; en Perl ; Il est portable pour toutes les plates-formes et applicables aux donn&eacute;es d&#39;entr&eacute;e nucl&eacute;otides et prot&eacute;ine. Treephyler est disponible gratuitement en t&eacute;l&eacute;chargement sur http://www.gobics.de/fabian/treephyler.php.

Treephyler : rapide profilage taxonomique des m&eacute;tag&eacute;nomes.

Sommario: Valutazione della diversit&agrave; filogenetica &egrave; un elemento chiave per l&#39;analisi di comunit&agrave; microbiche. Gli strumenti sono necessari per gestire dati di sequenziamento di nuova generazione e di affrontare la complessit&agrave; computazionale di studi su larga scala. Presentiamo qui, Treephyler, uno strumento per l&#39;analisi veloce tassonomica della metagenomica. Treephyler &egrave; stata valutata su metagenome reale per valutare le prestazioni rispetto ai precedenti approcci per l&#39;analisi tassonomica. I risultati indicano che il Treephyler sia in termini di velocit&agrave; e precisione preparato per tecniche di sequenziamento di nuova generazione e analisi su larga scala. DISPONIBILIT&Agrave;: Treephyler &egrave; implementato in Perl; &egrave; applicabile ai dati di input della proteina e nucleotidi e portatili per tutte le piattaforme. Treephyler &egrave; liberamente disponibile per il download presso http://www.gobics.de/fabian/treephyler.php.

Treephyler: veloce analisi tassonomica della metagenomica.

Existing coalescent models and phylogenetic tools based on them are not designed for studying the genealogy of sequences like those of HIV, since in HIV recombinants with multiple cross-over points between the parental strains frequently arise. Hence, ambiguous cases in the classification of HIV sequences into subtypes and circulating recombinant forms (CRFs) have been treated with ad hoc methods in lack of tools based on a comprehensive coalescent model accounting for complex recombination patterns.

HIV classification using the coalescent theory.

Les mod&egrave;les existants de coalescence et outils phylog&eacute;n&eacute;tiques bas&eacute;s sur eux ne sont pas con&ccedil;us pour l&#39;&eacute;tude de la g&eacute;n&eacute;alogie des s&eacute;quences comme ceux du VIH, car en mati&egrave;re de VIH recombinants avec plusieurs points de cross-over entre les souches parentales fr&eacute;quemment se posent. Ainsi, les cas ambigus dans la classification du VIH s&eacute;quences en sous-types et formes recombinantes circulantes (ERC) ont &eacute;t&eacute; trait&eacute;s avec des m&eacute;thodes ad hoc en manque d&#39;outils bas&eacute;s sur une comptabilit&eacute; compl&egrave;te mod&egrave;le coalescent pour des mod&egrave;les complexes de recombinaison.

Classification du VIH &agrave; l&#39;aide de la th&eacute;orie de coalescence.

Modelli coalescenti esistenti e filogenetici strumenti basati su di essi non sono progettati per studiare la genealogia di sequenze come quelle dell&#39;HIV, poich&eacute; in HIV ricombinanti con pi&ugrave; punti di cross-over tra i ceppi parentali frequentemente sorgono. Quindi, sequenze di casi ambigui nella classificazione dell&#39;HIV in sottotipi e forme recombinant di circolazione (CRF) sono stati trattati con metodi ad hoc in mancanza di strumenti basati su una contabilit&agrave; completa modello coalescente per modelli complessi di ricombinazione.

Classificazione dell&#39;HIV usando la teoria coalescente.

&#x4F53;&#x5916;&#x819C;&#x6C27;&#x5408; (&#x6A21;&#x5F0F;) &#x662F;&#x51E0;&#x4E2A;&#x80BA;&#x548C;&#x5FC3;&#x810F;&#x75BE;&#x75C5; &#xFF08;&#x5982;&#x6025;&#x6027;&#x547C;&#x5438;&#x7A98;&#x8FEB;&#x7EFC;&#x5408;&#x5F81;&#x3001; &#x5148;&#x5929;&#x6027;&#x5FC3;&#x8870;&#x3001; &#x5FC3;&#x808C;&#x75C5;) &#x7684;&#x65B0;&#x751F;&#x513F;&#x548C;&#x513F;&#x79D1;&#x533B;&#x5B66;&#x9886;&#x57DF;&#x7684;&#x516C;&#x8BA4;&#x6CBB;&#x7597;&#x3002;&#x5F53;&#x524D;&#x6A21;&#x5F0F;&#x7CFB;&#x7EDF;&#x901A;&#x5E38;&#x7531;&#x4E3B;&#x5200;&#x548C;&#x5355;&#x72EC;&#x7684; nonpulsatile &#x8840;&#x6CF5;&#x7EC4;&#x6210;&#x3002;&#x80BA;&#x4E0E;&#x7EFC;&#x5408;&#x640F;&#x52A8;&#x8840;&#x6CF5;&#x7684;&#x5C0F;&#x5A74;&#x513F;&#x6A21;&#x5F0F;&#x5F00;&#x53D1;&#x7684;&#x548C;&#x8FD9;&#x79CD;&#x65B0;&#x578B;&#x7684;&#x6982;&#x5FF5;&#x5173;&#x4E8E;&#x529F;&#x80FD;&#x548C;&#x6C14;&#x4F53;&#x4EA4;&#x6362;&#x7387;&#x8FDB;&#x884C;&#x4E86;&#x6D4B;&#x8BD5;&#x3002;&#x9A71;&#x52A8;&#x7684;&#x7A7A;&#x6C14;&#x538B;&#x529B;&#x8109;&#x52A8;&#x7845;&#x80F6;&#x7BA1; (STs) &#x5E76;&#x5C06;&#x5176;&#x653E;&#x7F6E;&#x5728;&#x5706;&#x67F1;&#x7EA4;&#x7EF4;&#x675F;&#x7684;&#x6C27;&#x5408;&#x5668;&#x7528;&#x4F5C;&#x6CF5;&#x6A21;&#x5757;&#x5185;&#x3002;&#x8FD9;&#x9879;&#x7814;&#x7A76;&#x7684;&#x7ED3;&#x679C;&#x786E;&#x8BA4;&#x62BD;&#x8840;&#x6DB2;&#x4E0E; STs &#x662F;&#x672A;&#x6765;&#x53EF;&#x884C;&#x7684;&#x9009;&#x62E9;&#x3002;&#x6C27;&#x7684;&#x6700;&#x5927;&#x5929;&#x7136;&#x6C14;&#x6C47;&#x7387;&#x662F; 48mL/min/L(blood) &#x7EA6; 300 &#x6BEB;&#x5347;/&#x5206;&#x949F;&#x672A;&#x6765;&#x8BBE;&#x8BA1;&#x6B65;&#x9AA4;&#x7684;&#x4E2D;&#x578B;&#x8840;&#x6DB2;&#x6D41;&#x52A8;&#x901F;&#x5EA6;&#x786E;&#x5B9A;&#x4E86;&#x4F18;&#x5316;&#x901A;&#x8FC7;&#x7EA4;&#x7EF4;&#x675F;&#xFF0C;&#x4EE5;&#x5B9E;&#x73B0;&#x66F4;&#x9AD8;&#x7684;&#x6C14;&#x4F53;&#x4EA4;&#x6362;&#x7387;&#x7684;&#x6D41;&#x573A;&#x3002;&#x7B2C;&#x4E00;&#xFF0C;&#x4E2D;&#x7A7A;&#x7EA4;&#x7EF4;&#x675F;&#x7684;&#x5806;&#x79EF;&#x5BC6;&#x5EA6;&#x4F4E;&#x4E8E;&#x5546;&#x4E1A;&#x6C27;&#x5408;&#x5668;&#x7531;&#x4E8E;&#x624B;&#x5DE5;&#x5236;&#x9020;&#x3002;&#x901A;&#x8FC7;&#x589E;&#x52A0;&#x6B64;&#x5305;&#x88C5;&#x5BC6;&#x5EA6;&#xFF0C;&#x6C14;&#x4F53;&#x4EA4;&#x6362;&#x7387;&#x4F1A;&#x76F8;&#x5E94;&#x589E;&#x52A0;&#x3002;&#x7B2C;&#x4E8C;&#xFF0C;&#x66F4;&#x5747;&#x5300;&#x7684;&#x8840;&#x6D41;&#x91CF;&#x7684;&#x5206;&#x5E03;&#x677F;&#x53EF;&#x4EE5;&#x653E;&#x5165;&#x53E3;&#x548C;&#x51FA;&#x53E3;&#x5904;&#x7684;&#x80BA;&#x3002;&#x7B2C;&#x4E09;&#xFF0C;&#x53EF;&#x4EE5;&#x5355;&#x72EC;&#x653E;&#x7F6E;&#x4E2D;&#x7A7A;&#x7EA4;&#x7EF4;&#x819C;&#xFF0C;&#x786E;&#x4FDD;&#x76F8;&#x7B49;&#x5468;&#x56F4;&#x4E2D;&#x7A7A;&#x7EA4;&#x7EF4;&#x4E4B;&#x95F4;&#x7684;&#x8DDD;&#x79BB;&#x3002;

&#x6D41;&#x7684;&#x63CF;&#x8FF0;&#x4E0E;&#x7EFC;&#x5408;&#x640F;&#x52A8;&#x6CF5;&#x4F18;&#x5316;&#x5F0F;&#x6C27;&#x5408;&#x5668;&#x3002;

Extracorporeal membrane oxygenation (ECMO) is a well-established therapy for several lung and heart diseases in the field of neonatal and pediatric medicine (e.g., acute respiratory distress syndrome, congenital heart failure, cardiomyopathy). Current ECMO systems are typically composed of an oxygenator and a separate nonpulsatile blood pump. An oxygenator with an integrated pulsatile blood pump for small infant ECMO was developed, and this novel concept was tested regarding functionality and gas exchange rate. Pulsating silicone tubes (STs) were driven by air pressure and placed inside the cylindrical fiber bundle of an oxygenator to be used as a pump module. The findings of this study confirm that pumping blood with STs is a viable option for the future. The maximum gas exchange rate for oxygen is 48mL/min/L(blood) at a medium blood flow rate of about 300mL/min. Future design steps were identified to optimize the flow field through the fiber bundle to achieve a higher gas exchange rate. First, the packing density of the hollow-fiber bundle was lower than commercial oxygenators due to the manual manufacturing. By increasing this packing density, the gas exchange rate would increase accordingly. Second, distribution plates for a more uniform blood flow can be placed at the inlet and outlet of the oxygenator. Third, the hollow-fiber membranes can be individually placed to ensure equal distances between the surrounding hollow fibers.

Description of a flow optimized oxygenator with integrated pulsatile pump.

Oxyg&eacute;nation extracorporelle (ECMO) est une th&eacute;rapie bien &eacute;tablie pour plusieurs de poumon et de maladies cardiaques dans le domaine de la m&eacute;decine n&eacute;onatale et p&eacute;diatrique (syndrome de d&eacute;tresse respiratoire, une insuffisance cardiaque cong&eacute;nitale, cardiomyopathie). Les syst&egrave;mes actuels d&#39;ECMO sont g&eacute;n&eacute;ralement compos&eacute;es d&#39;un oxyg&eacute;nateur et une pompe sanguine pulsative distinct. Un oxyg&eacute;nateur avec une pompe &agrave; sang pulsatile int&eacute;gr&eacute;e pour petit enfant ECMO a &eacute;t&eacute; d&eacute;velopp&eacute;, et ce concept novateur a &eacute;t&eacute; test&eacute; en ce qui concerne les taux de change de fonctionnalit&eacute; et de gaz. Tubes de silicone pulsatoire (STs) ont &eacute;t&eacute; pilot&eacute;es par pression d&#39;air et plac&eacute;s &agrave; l&#39;int&eacute;rieur du faisceau de fibres cylindriques d&#39;un oxyg&eacute;nateur pour &ecirc;tre utilis&eacute; comme un module de la pompe. Les r&eacute;sultats de cette &eacute;tude confirment que pomper le sang avec STs est une option viable pour l&#39;avenir. Le taux de change de gaz maximale d&#39;oxyg&egrave;ne est 48mL/min/L(blood) &agrave; un d&eacute;bit sanguin moyen d&#39;environ 300 mL/min. &eacute;tapes de conception Future ont &eacute;t&eacute; identifi&eacute;es afin d&#39;optimiser le champ d&#39;&eacute;coulement &agrave; travers le faisceau de fibres pour atteindre un taux de change de gaz plus &eacute;lev&eacute;. Tout d&#39;abord, la densit&eacute; du faisceau de fibres creuses &eacute;tait plus faible que les oxyg&eacute;nateurs commerciales en raison de la fabrication manuelle. En augmentant cette densit&eacute;, le taux de change du gaz augmenterait en cons&eacute;quence. Deuxi&egrave;mement, les plaques de distribution pour une circulation sanguine plus uniforme peuvent &ecirc;tre plac&eacute;s &agrave; l&#39;entr&eacute;e et la sortie de l&#39;oxyg&eacute;nateur. Troisi&egrave;mement, les membranes &agrave; fibres creuses peuvent &ecirc;tre test&eacute;es individuellement afin d&#39;assurer des distances &eacute;gales entre les fibres creuses environnantes.

Description d&#39;un flux optimis&eacute; oxyg&eacute;nateur avec int&eacute;gr&eacute; pompe pulsatile.

Extrakorporale Membranoxygenierung (ECMO) ist eine etablierte Therapie f&uuml;r mehrere Lungen- und Herzkrankheiten in den Neugeborenen und P&auml;diatrische Medizin (z.B. Schweres Akutes Atemnotsyndrom, angeborene Herzinsuffizienz, Kardiomyopathie). Aktuelle ECMO-Systeme bestehen in der Regel aus einer Oxygenator und einer separaten nonpulsatile Blutpumpe. Ein Oxygenator mit einer integrierten pulsierender Blutpumpe f&uuml;r kleine Kind ECMO entwickelt wurde, und dieses neuartige Konzept bez&uuml;glich Funktionalit&auml;t und Gas-Wechselkurses getestet wurde. Pulsierende Silikon Schl&auml;uche (STs) wurden von Luftdruck und Platzierung innerhalb der zylindrischen Faserb&uuml;ndel der ein Oxygenator als Pumpenmodul verwendet werden. Die Ergebnisse dieser Studie best&auml;tigen, dass Pumpen Blut mit STs eine praktikable Option f&uuml;r die Zukunft. Der maximale Gas-Wechselkurs f&uuml;r Sauerstoff ist 48mL/min/L(blood) mit einer mittlere Blut-Durchfluss von ca. 300 mL/min. Zukunft Entwurfsschritte wurden identifiziert, um das Str&ouml;mungsfeld durch die Faserb&uuml;ndel, einen h&ouml;heren Wechselkurs von Gas zu erreichen zu optimieren. Erstens war die Packungsdichte der Mulde-Faserb&uuml;ndel niedriger als kommerzielle Oxygenatoren aufgrund der manuellen Fertigung. Durch diese Packungsdichte erh&ouml;hen, w&uuml;rde der Gas-Wechselkurs entsprechend erh&ouml;hen. Zweitens k&ouml;nnen Verteilung Platten f&uuml;r eine einheitlichere Blutfluss an der Einlass- und der der Oxygenator platziert werden. Drittens k&ouml;nnen die Mulde-Faser-Membranen einzeln platziert werden, um im gleichen Abstand zwischen den umliegenden Hohlfasern zu gew&auml;hrleisten.

Beschreibung eines Volumenstromes optimiert Oxygenator mit integrierter pulsierender Pumpe.

Ossigenazione extracorporea (ECMO) &egrave; una terapia consolidata per diversi al polmone e malattie di cuore nel campo della medicina neonatale e pediatrica (ad es., sindrome da distress respiratorio, congenita insufficienza cardiaca, cardiomiopatia). Attuali sistemi ECMO sono in genere composte da un ossigenatore e una pompa separata nonpulsatile sangue. &Egrave; stato sviluppato un ossigenatore con pompa integrata sangue pulsatile per piccolo neonato ECMO, e questo nuovo concetto &egrave; stato testato per quanto riguarda il tasso di cambio di gas e di funzionalit&agrave;. Tubi in silicone palpitazione (STs) erano spinti dalla pressione dell&#39;aria e collocati all&#39;interno del fascio di fibre cilindriche di un ossigenatore per essere utilizzato come modulo pompa. I risultati di questo studio confermano che pompare sangue con STs &egrave; una valida opzione per il futuro. Il tasso di cambio del gas di massima per l&#39;ossigeno &egrave; 48mL/min/L(blood) ad una velocit&agrave; di flusso di sangue medio di circa 300 mL/min passi design futuro sono stati identificati per ottimizzare il campo di flusso attraverso il fascio di fibre ottiche per raggiungere un pi&ugrave; alto tasso di cambio gas. In primo luogo, la densit&agrave; di intasamento del fascio cavi-fibra era inferiore ossigenatori commerciale grazie alla lavorazione manuale. Aumentando questa densit&agrave; di intasamento, il tasso di cambio gas aumenterebbe di conseguenza. In secondo luogo, piastre di distribuzione per un pi&ugrave; uniforme del flusso sanguigno possono essere collocati all&#39;entrata e all&#39;uscita dell&#39;ossigenatore. In terzo luogo, le membrane a fibra cava possono essere posizionate individualmente per garantire distanze uguali tra le fibre cave circostanti.

Descrizione di un flusso ottimizzato ossigenatore con integrato pompa pulsatile.

&#x4F53;&#x5916;&#x819C; (ecmo) &#x306F;&#x3044;&#x304F;&#x3064;&#x304B;&#x306E;&#x80BA;&#x3084;&#x5FC3;&#x81D3;&#x75BE;&#x60A3; &#xFF08;&#x4F8B;&#x3048;&#x3070;&#x3001;&#x6025;&#x6027;&#x547C;&#x5438;&#x7AAE;&#x8FEB;&#x75C7;&#x5019;&#x7FA4;, &#x5148;&#x5929;&#x6027;&#x5FC3;&#x4E0D;&#x5168;&#x3001;&#x5FC3;&#x7B4B;&#x75C7;&#xFF09; &#x65B0;&#x751F;&#x5150;&#x30FB;&#x5C0F;&#x5150;&#x533B;&#x5B66;&#x306E;&#x5206;&#x91CE;&#x3067;&#x5B9A;&#x8A55;&#x306E;&#x3042;&#x308B;&#x7642;&#x6CD5;&#x3067;&#x3059;&#x3002;&#x73FE;&#x5728; ECMO &#x30B7;&#x30B9;&#x30C6;&#x30E0;&#x306F;&#x3001;&#x901A;&#x5E38;&#x3001;&#x4EBA;&#x5DE5;&#x80BA;&#x3068;&#x5225;&#x3005; &#x306E;&#x5B9A;&#x5E38;&#x6D41;&#x8840;&#x6DB2;&#x30DD;&#x30F3;&#x30D7;&#x306E;&#x3067;&#x69CB;&#x6210;&#x3055;&#x308C;&#x307E;&#x3059;&#x3002;&#x5C0F;&#x3055;&#x3044;&#x4E73;&#x5150; ECMO &#x306E;&#x7D71;&#x5408;&#x62CD;&#x52D5;&#x8840;&#x6DB2;&#x30DD;&#x30F3;&#x30D7;&#x3068;&#x4EBA;&#x5DE5;&#x80BA;&#x3092;&#x958B;&#x767A;&#x3057;&#x3001;&#x3053;&#x306E;&#x65AC;&#x65B0;&#x306A;&#x30B3;&#x30F3;&#x30BB;&#x30D7;&#x30C8;&#x6A5F;&#x80FD;&#x3068;&#x30AC;&#x30B9;&#x306E;&#x4EA4;&#x63DB;&#x7387;&#x306B;&#x95A2;&#x3059;&#x308B;&#x30C6;&#x30B9;&#x30C8;&#x3055;&#x308C;&#x307E;&#x3057;&#x305F;&#x3002;&#x8108;&#x52D5;&#x306E;&#x30B7;&#x30EA;&#x30B3;&#x30FC;&#x30F3; &#x30C1;&#x30E5;&#x30FC;&#x30D6; (STs) &#x7A7A;&#x6C17;&#x5727;&#x306B;&#x3088;&#x308B;&#x99C6;&#x52D5;&#x3057;&#x3001;&#x30DD;&#x30F3;&#x30D7; &#x30E2;&#x30B8;&#x30E5;&#x30FC;&#x30EB;&#x3068;&#x3057;&#x3066;&#x4F7F;&#x7528;&#x3059;&#x308B;&#x306B;&#x306F;&#x3001;&#x4EBA;&#x5DE5;&#x7E4A;&#x7DAD;&#x5186;&#x7B52;&#x30D0;&#x30F3;&#x30C9;&#x30EB;&#x5185;&#x306B;&#x914D;&#x7F6E;&#x3002;&#x672C;&#x7814;&#x7A76;&#x306E;&#x7D50;&#x679C;&#x306F;&#x3001;STs &#x3068;&#x8840;&#x6DB2;&#x3092;&#x30DD;&#x30F3;&#x30D4;&#x30F3;&#x30B0;&#x3001;&#x5C06;&#x6765;&#x306E;&#x305F;&#x3081;&#x306E;&#x73FE;&#x5B9F;&#x7684;&#x306A;&#x9078;&#x629E;&#x80A2;&#x3067;&#x3042;&#x308B;&#x3053;&#x3068;&#x3092;&#x78BA;&#x8A8D;&#x3057;&#x307E;&#x3059;&#x3002;&#x9178;&#x7D20;&#x306E;&#x6700;&#x5927;&#x30AC;&#x30B9;&#x4EA4;&#x63DB;&#x901F;&#x5EA6;&#x306F;&#x3001;48mL/min/L(blood) &#x7D04; 300 mL/&#x5206;&#x306E;&#x672A;&#x6765;&#x306E;&#x8A2D;&#x8A08;&#x306E;&#x624B;&#x9806;&#x306E;&#x4E2D;&#x306E;&#x8840;&#x6D41;&#x91CF;&#x3067;&#x6D41;&#x308C;&#x5834;&#x3092;&#x901A;&#x3058;&#x3066;&#x9AD8;&#x3044;&#x30AC;&#x30B9;&#x4EA4;&#x63DB;&#x901F;&#x5EA6;&#x3092;&#x9054;&#x6210;&#x3059;&#x308B;&#x305F;&#x3081;&#x306B;&#x7E4A;&#x7DAD;&#x675F;&#x3092;&#x6700;&#x9069;&#x5316;&#x3059;&#x308B;&#x305F;&#x3081;&#x306B;&#x8B58;&#x5225;&#x3055;&#x308C;&#x305F;&#x3067;&#x3059;&#x3002;&#x307E;&#x305A;&#x3001;&#x4E2D;&#x7A7A;&#x30D5;&#x30A1;&#x30A4;&#x30D0;&#x30FC; &#x30FB; &#x30D0;&#x30F3;&#x30C9;&#x30EB;&#x306E;&#x5145;&#x586B;&#x5BC6;&#x5EA6;&#x306F;&#x624B;&#x52D5;&#x306E;&#x88FD;&#x9020;&#x696D;&#x306B;&#x3088;&#x308B;&#x5546;&#x696D;&#x4EBA;&#x5DE5;&#x80BA;&#x3088;&#x308A;&#x4F4E;&#x3044;&#x3060;&#x3063;&#x305F;&#x3002;&#x3053;&#x306E;&#x30D1;&#x30C3;&#x30AD;&#x30F3;&#x30B0;&#x5BC6;&#x5EA6;&#x306E;&#x5897;&#x52A0;&#x306B;&#x3088;&#x308A;&#x3001;&#x30AC;&#x30B9;&#x4EA4;&#x63DB;&#x901F;&#x5EA6;&#x3092;&#x9069;&#x5B9C;&#x5897;&#x3084;&#x3059;&#x3067;&#x3057;&#x3087;&#x3046;&#x3002;&#x7B2C;&#x4E8C;&#x3088;&#x308A;&#x5747;&#x4E00;&#x306A;&#x8840;&#x6D41;&#x5206;&#x5E03;&#x30D7;&#x30EC;&#x30FC;&#x30C8;&#x3001;&#x5165;&#x53E3;&#x3068;&#x51FA;&#x53E3;&#x3001;&#x4EBA;&#x5DE5;&#x3067;&#x914D;&#x7F6E;&#x3067;&#x304D;&#x307E;&#x3059;&#x3002;&#x7B2C;&#x4E09;&#x306B;&#x3001;&#x4E2D;&#x7A7A;&#x7CF8;&#x819C;&#x5468;&#x56F2;&#x306E;&#x4E2D;&#x7A7A;&#x30D5;&#x30A1;&#x30A4;&#x30D0;&#x30FC;&#x9593;&#x306E;&#x7B49;&#x3057;&#x3044;&#x8DDD;&#x96E2;&#x3092;&#x78BA;&#x4FDD;&#x3059;&#x308B;&#x305F;&#x3081;&#x306B;&#x500B;&#x5225;&#x306B;&#x914D;&#x7F6E;&#x3067;&#x304D;&#x307E;&#x3059;&#x3002;

&#x8AAC;&#x660E;&#x6D41;&#x306E;&#x4EBA;&#x5DE5;&#x80BA;&#x7D71;&#x5408;&#x306E;&#x62CD;&#x52D5;&#x6D41;&#x30DD;&#x30F3;&#x30D7;&#x3092;&#x6700;&#x9069;&#x5316;&#x3057;&#x307E;&#x3057;&#x305F;&#x3002;

&#xACFC;&#xD559;&#xAE30;&#xC220;&#xCC98; &#xB9C9; &#xC0B0;&#xC18C; (ECMO)&#xC740; &#xC5EC;&#xB7EC; &#xAC00;&#xC9C0; &#xD3D0; &#xBC0F; &#xC2EC;&#xC7A5; &#xC9C8;&#xD658; (&#xAE09;&#xC131; &#xD638;&#xD761; &#xACE4;&#xB780; &#xC99D;&#xD6C4;&#xAD70;, &#xC120; &#xCC9C; &#xC131; &#xC2EC;&#xC7A5; &#xB9C8;&#xBE44;, &#xC2EC;&#xC7A5; &#xADFC;&#xC721; &#xBCD1; &#xC99D;) &#xC2E0;&#xC0DD;&#xC544; &#xBC0F; &#xC18C;&#xC544;&#xACFC; &#xC758;&#xD559; &#xBD84;&#xC57C;&#xC5D0;&#xC11C; &#xC798; &#xC124;&#xB9BD; &#xCE58;&#xB8CC;. &#xD604;&#xC7AC; ECMO &#xC2DC;&#xC2A4;&#xD15C;&#xC740; oxygenator&#xC640; &#xBCC4;&#xB3C4; nonpulsatile &#xD608;&#xC561; &#xD38C;&#xD504;&#xB97C; &#xC77C;&#xBC18;&#xC801;&#xC73C;&#xB85C; &#xAD6C;&#xC131; &#xB429;&#xB2C8;&#xB2E4;. &#xC791;&#xC740; &#xC720;&#xC544; ECMO &#xD1B5;&#xD569;&#xB41C; &#xD0C0;&#xC545;&#xAE30; &#xD608;&#xC561; &#xD38C;&#xD504; oxygenator &#xAC1C;&#xBC1C;&#xACFC;&#xC774; &#xC18C;&#xC124; &#xAC1C;&#xB150; &#xAE30;&#xB2A5; &#xBC0F; &#xAC00;&#xC2A4; &#xD658;&#xC728;&#xC5D0; &#xAD00;&#xD55C; &#xD14C;&#xC2A4;&#xD2B8;&#xB97C; &#xD588;&#xB2E4;. Pulsating &#xC2E4;&#xB9AC;&#xCF58; &#xD29C;&#xBE0C; (STs) &#xACF5;&#xAE30; &#xC555;&#xB825;&#xC5D0; &#xC758;&#xD574; &#xC8FC;&#xB3C4; &#xB418;&#xC5C8;&#xACE0; &#xD38C;&#xD504; &#xBAA8;&#xB4C8;&#xB85C; &#xC0AC;&#xC6A9;&#xD560; oxygenator &#xC6D0;&#xD1B5;&#xD615; &#xC12C;&#xC720; &#xB2E4;&#xBC1C;&#xC5D0; &#xBC30;&#xCE58;. &#xC774; &#xC5F0;&#xAD6C;&#xC758; &#xACB0;&#xACFC; Sts&#xC640; &#xD608;&#xC561; &#xD38C;&#xD551; &#xBBF8;&#xB798;&#xC5D0; &#xB300; &#xD55C; &#xAC00;&#xB2A5;&#xD55C; &#xC635;&#xC158; &#xC778;&#xC9C0; &#xD655;&#xC778; &#xD569;&#xB2C8;&#xB2E4;. &#xC0B0;&#xC18C;&#xC758; &#xCD5C;&#xB300; &#xAC00;&#xC2A4; &#xD658;&#xC728;&#xC740; &#xC911;&#xAC04; &#xD608;&#xC561; &#xC720;&#xB7C9;&#xC758; &#xC57D; 300 mL/&#xBD84; &#xBBF8;&#xB798; &#xB514;&#xC790;&#xC778; &#xB2E8;&#xACC4;&#xC5D0;&#xC11C; 48mL/min/L(blood) &#xB192;&#xC740; &#xAC00;&#xC2A4; &#xAD50;&#xD658; &#xC728;&#xC744; &#xB2EC;&#xC131; &#xD558;&#xAE30; &#xC704;&#xD574; &#xC12C;&#xC720; &#xBC88;&#xB4E4;&#xC744; &#xD1B5;&#xD574; &#xD750;&#xB984; &#xD544;&#xB4DC; &#xCD5C;&#xC801;&#xD654;&#xB97C; &#xBC1C;&#xACAC; &#xD588;&#xB2E4;. &#xCCAB;&#xC9F8;, &#xC18D;&#xC774; &#xBE48; &#xC12C;&#xC720; &#xB2E4;&#xBC1C;&#xC758; &#xD328;&#xD0B9; &#xBC00;&#xB3C4; &#xC218;&#xB3D9; &#xC81C;&#xC870; &#xB54C;&#xBB38; &#xC0C1;&#xC5C5; oxygenators &#xBCF4;&#xB2E4; &#xB0AE;&#xC740;. &#xC774; &#xD328;&#xD0B9; &#xBC00;&#xB3C4; &#xC99D;&#xAC00; &#xC2DC;&#xCF1C; &#xAC00;&#xC2A4; &#xD658;&#xC728;&#xC5D0; &#xB530;&#xB77C; &#xC99D;&#xAC00;&#xD560; &#xAC83;&#xC785;&#xB2C8;&#xB2E4;. &#xB458;&#xC9F8;, &#xC720;&#xD1B5; &#xD310; &#xB354; &#xADE0;&#xC77C; &#xD55C; &#xD608;&#xC561;&#xC758; &#xD750;&#xB984;&#xC5D0; &#xB300; &#xD55C; &#xC785;&#xAD6C;&#xC640; &#xCD9C;&#xAD6C;&#xB294; oxygenator&#xC758;&#xC5D0; &#xBC30;&#xCE58;&#xD560; &#xC218; &#xC788;&#xC2B5;&#xB2C8;&#xB2E4;. &#xC14B;&#xC9F8;, &#xC18D;&#xC774; &#xBE48; &#xC12C;&#xC720; &#xC138;&#xD3EC; &#xB9C9; &#xC8FC;&#xBCC0; &#xC18D;&#xC774; &#xBE48; &#xC12C;&#xC720; &#xC0AC;&#xC774;&#xC758; &#xB3D9;&#xB4F1;&#xD55C; &#xAC70;&#xB9AC;&#xB97C; &#xBCF4;&#xC7A5; &#xD558;&#xAE30; &#xC704;&#xD574; &#xAC1C;&#xBCC4;&#xC801;&#xC73C;&#xB85C; &#xBC30;&#xCE58;&#xD560; &#xC218; &#xC788;&#xC2B5;&#xB2C8;&#xB2E4;.

&#xC124;&#xBA85; &#xD750;&#xB984;&#xC758; &#xD1B5;&#xD569; &#xD0C0;&#xC545;&#xAE30; &#xD38C;&#xD504; oxygenator&#xB97C; &#xCD5C;&#xC801;&#xD654;.

La oxigenaci&oacute;n por membrana extracorp&oacute;rea (ECMO) es una terapia establecida para varios de pulm&oacute;n y enfermedades card&iacute;acas en el campo de la medicina neonatal y pedi&aacute;trico (p. ej., s&iacute;ndrome de dificultad respiratoria agudo, la insuficiencia card&iacute;aca cong&eacute;nita, cardiomiopat&iacute;a). Los sistemas actuales de oxigenaci&oacute;n por membrana extracorp&oacute;rea se componen t&iacute;picamente de un oxigenador y una bomba de sangre nonpulsatile separado. Un oxigenador con una bomba de sangre puls&aacute;til integrado para ni&ntilde;o peque&ntilde;o ECMO fue desarrollado, y este concepto fue probado en cuanto a funcionalidad y gas de tipo de cambio. Tubos de silicona pulsante (STs) fueron impulsados por la presi&oacute;n de aire y dentro el fibrado cil&iacute;ndrico de un oxigenador para ser utilizado como un m&oacute;dulo de la bomba. Los hallazgos de este estudio confirman que bombear sangre con STs es una opci&oacute;n viable para el futuro. La tasa de cambio m&aacute;ximo de gas ox&iacute;geno es 48mL/min/L(blood) con un caudal medio de sangre de unos 300 mL/min medidas de dise&ntilde;o de futuro se identificaron para optimizar el campo de flujo a trav&eacute;s del haz de fibra para lograr una tasa de cambio de gas. En primer lugar, la densidad de la fibra hueca paquete fue menor de oxigenadores comerciales debido a la fabricaci&oacute;n manual. Al aumentar esta densidad, el tipo de cambio de gas aumentar&iacute;a en consecuencia. En segundo lugar, las placas de distribuci&oacute;n para un flujo m&aacute;s uniforme de la sangre pueden colocarse en la entrada y salida del oxigenador. En tercer lugar, las membranas de fibra hueca pueden colocarse individualmente para asegurar iguales distancias entre las fibras huecas circundantes.

Descripci&oacute;n de un flujo hab&iacute;a optimizado oxigenador con bomba puls&aacute;til integrada.

Orthology is one of the most important tools available to modern biology, as it allows making inferences from easily studied model systems to much less tractable systems of interest, such as ourselves. This becomes important not least in the study of genetic diseases. We here review work on the orthology of disease-associated genes and also present an updated version of the InParanoid-based disease orthology database and web site OrthoDisease, with 14-fold increased species coverage since the previous version. Using this resource, we survey the taxonomic distribution of orthologs of human genes involved in different disease categories. The hypothesis that paralogs can mask the effect of deleterious mutations predicts that known heritable disease genes should have fewer close paralogs. We found large-scale support for this hypothesis as significantly fewer duplications were observed for disease genes in the OrthoDisease ortholog groups.

OrthoDisease: tracking disease gene orthologs across 100 species.

Niveau est l&#39;un des outils plus importants pour la biologie moderne, car elle permet de faire des inf&eacute;rences de facilement a &eacute;tudi&eacute; les syst&egrave;mes mod&egrave;les aux syst&egrave;mes tractable beaucoup moins d&#39;int&eacute;r&ecirc;t, tels que nous. Cela devient important surtout dans l&#39;&eacute;tude des maladies g&eacute;n&eacute;tiques. Nous passons ici en revue les travaux sur le niveau des g&egrave;nes associ&eacute;s &agrave; la maladie et aussi pr&eacute;senter une version actualis&eacute;e de la base de donn&eacute;es de niveau de maladies InParanoid et web site OrthoDisease, avec une couverture de 14 fois esp&egrave;ces accrue depuis la version pr&eacute;c&eacute;dente. L&#39;utilisation de cette ressource, nous sondons la distribution taxonomique des orthologues de g&egrave;nes humains impliqu&eacute;s dans les cat&eacute;gories de maladies diff&eacute;rentes. L&#39;hypoth&egrave;se que paralogues peut masquer l&#39;effet de mutations d&eacute;l&eacute;t&egrave;res pr&eacute;dit que les g&egrave;nes de maladies h&eacute;r&eacute;ditaires connues devraient avoir moins paralogues &eacute;troites. Nous avons trouv&eacute; appui &agrave; grande &eacute;chelle pour cette hypoth&egrave;se car on a observ&eacute; une moins duplications de g&egrave;nes de la maladie dans les groupes d&#39;orthologue de OrthoDisease.

OrthoDisease : suivi maladie g&egrave;nes orthologues chez toutes les esp&egrave;ces de 100.

Orthology &egrave; uno dei pi&ugrave; importanti strumenti disponibili per la biologia moderna, in quanto permette di fare inferenze da facilmente studiato sistemi modello per sistemi molto meno trattabili di interesse, come noi stessi. Questo diventa importante non meno importante nello studio delle malattie genetiche. Abbiamo qui rassegna lavoro su orthology di geni associati a malattie e presente anche una versione aggiornata del database orthology malattia basati su InParanoid e web site OrthoDisease, con copertura 14-fold specie maggiore rispetto alla versione precedente. Utilizzando questa risorsa, sondaggio sulla distribuzione tassonomica di orthologs dei geni umani coinvolti nelle categorie differenti di malattia. L&#39;ipotesi che paralogs pu&ograve; mascherare l&#39;effetto di mutazioni dannose predice che geni malattia ereditaria nota dovrebbero avere meno paralogs stretta. Abbiamo trovato grande sostegno per questa ipotesi come significativamente meno duplicazioni sono stati osservati per geni malattia nei gruppi ortholog OrthoDisease.

OrthoDisease: tracking orthologs gene malattia attraverso 100 specie.

Analyzing the functional potential of newly sequenced genomes and metagenomes has become a common task in biomedical and biological research. With the advent of high-throughput sequencing technologies comparative metagenomics opens the way to elucidate the genetically determined similarities and differences of complex microbial communities. We developed the web server 'CoMet' (http://comet.gobics.de), which provides an easy-to-use comparative metagenomics platform that is well-suitable for the analysis of large collections of metagenomic short read data. CoMet combines the ORF finding and subsequent assignment of protein sequences to Pfam domain families with a comparative statistical analysis. Besides comprehensive tabular data files, the CoMet server also provides visually interpretable output in terms of hierarchical clustering and multi-dimensional scaling plots and thus allows a quick overview of a given set of metagenomic samples.

CoMet--a web server for comparative functional profiling of metagenomes.

Analyser la faisabilit&eacute; fonctionnelle des g&eacute;nomes nouvellement s&eacute;quenc&eacute;es et m&eacute;tag&eacute;nomes est devenu une t&acirc;che courante dans la recherche biom&eacute;dicale et biologique. Avec l&#39;av&egrave;nement des technologies de s&eacute;quen&ccedil;age haut d&eacute;bit m&eacute;tag&eacute;nomique comparative ouvre la voie &agrave; &eacute;lucider les similitudes g&eacute;n&eacute;tiquement d&eacute;termin&eacute;es et les diff&eacute;rences des communaut&eacute;s microbiennes complexes. Nous avons d&eacute;velopp&eacute; le serveur web &laquo; Com&egrave;te &raquo; (http://comet.gobics.de), qui fournit une plate-forme de m&eacute;tag&eacute;nomique comparative facile &agrave; utiliser qui est bien adapt&eacute;e pour l&#39;analyse des grandes collections de m&eacute;tag&eacute;nomique court lire les donn&eacute;es. Com&egrave;te combine la constatation de l&#39;ORF et cession subs&eacute;quente de s&eacute;quences de prot&eacute;ines aux familles de domaine Pfam avec une analyse statistique comparative. Outre les fichiers de donn&eacute;es tabulaires complet, le serveur CoMet fournit &eacute;galement sortie visuellement interpr&eacute;table en termes de regroupement hi&eacute;rarchique et multi-dimensional scaling parcelles et permet ainsi un aper&ccedil;u rapide d&#39;un ensemble donn&eacute; de m&eacute;tag&eacute;nomique &eacute;chantillons.

Com&egrave;te--un serveur web pour le profilage fonctionnelle comparative des m&eacute;tag&eacute;nomes.

Analizzando il potenziale funzionale dei genomi sequenziati appena e metagenomica &egrave; diventata un&#39;attivit&agrave; comune nella ricerca biologica e biomedica. Con l&#39;avvento delle tecnologie high-throughput sequencing metagenomica comparativa apre la strada a delucidare i geneticamente determinate somiglianze e le differenze delle comunit&agrave; microbiche complesse. Abbiamo sviluppato il server web &#39;Cometa&#39; (http://comet.gobics.de), che fornisce una piattaforma easy-to-use metagenomica comparativa che &egrave; ben adatta per l&#39;analisi di grandi raccolte di breve metagenomica leggere i dati. Cometa combina la constatazione ORF e successiva assegnazione delle sequenze della proteina per le famiglie di dominio Pfam con un&#39;analisi statistica comparata. Oltre ai file di dati tabellari completi, server cometa fornisce anche visivamente interpretabile output in termini di clustering gerarchico e scaling multidimensionale trame e permette quindi una rapida panoramica di un determinato insieme di campioni metagenomica.

Cometa - un server web per l&#39;analisi funzionale comparativa della metagenomica.

There is a great need for standards in the orthology field. Users must contend with different ortholog data representations from each provider, and the providers themselves must independently gather and parse the input sequence data. These burdensome and redundant procedures make data comparison and integration difficult. We have designed two XML-based formats, SeqXML and OrthoXML, to solve these problems. SeqXML is a lightweight format for sequence records-the input for orthology prediction. It stores the same sequence and metadata as typical FASTA format records, but overcomes common problems such as unstructured metadata in the header and erroneous sequence content. XML provides validation to prevent data integrity problems that are frequent in FASTA files. The range of applications for SeqXML is broad and not limited to ortholog prediction. We provide read/write functions for BioJava, BioPerl, and Biopython. OrthoXML was designed to represent ortholog assignments from any source in a consistent and structured way, yet cater to specific needs such as scoring schemes or meta-information. A unified format is particularly valuable for ortholog consumers that want to integrate data from numerous resources, e.g. for gene annotation projects. Reference proteomes for 61 organisms are already available in SeqXML, and 10 orthology databases have signed on to OrthoXML. Adoption by the entire field would substantially facilitate exchange and quality control of sequence and orthology information.

Letter to the editor: SeqXML and OrthoXML: standards for sequence and orthology information.

Il y a un grand besoin de normes dans le domaine de niveau. Les utilisateurs doivent composer avec orthologue diff&eacute;rentes repr&eacute;sentations de donn&eacute;es de chaque fournisseur, et les fournisseurs eux-m&ecirc;mes doivent ind&eacute;pendamment recueillir et analyser les donn&eacute;es de la s&eacute;quence d&#39;entr&eacute;e. Ces proc&eacute;dures lourdes et redondantes difficile int&eacute;gration et comparaison de donn&eacute;es. Nous avons con&ccedil;u deux formats bas&eacute;s sur XML, SeqXML et OrthoXML, pour r&eacute;soudre ces probl&egrave;mes. SeqXML est un format l&eacute;ger pour l&#39;entr&eacute;e de documents-la s&eacute;quence pour la pr&eacute;diction du niveau. Il stocke la m&ecirc;me s&eacute;quence et les m&eacute;tadonn&eacute;es dans les documents de format FASTA typiques, mais surmonte les probl&egrave;mes communs tels que des m&eacute;tadonn&eacute;es structur&eacute;es dans l&#39;en-t&ecirc;te et le contenu de la s&eacute;quence erron&eacute;e. XML fournit la validation pour &eacute;viter les probl&egrave;mes d&#39;int&eacute;grit&eacute; des donn&eacute;es qui sont fr&eacute;quentes dans les fichiers FASTA. La gamme d&#39;applications pour SeqXML est large et non limit&eacute; &agrave; orthologue pr&eacute;diction. Nous fournissons des fonctions de lecture/&eacute;criture pour BioJava et BioPerl Biopython. OrthoXML a &eacute;t&eacute; con&ccedil;u pour repr&eacute;senter les affectations orthologue de toute source de mani&egrave;re coh&eacute;rente et structur&eacute;e, mais r&eacute;pondent &agrave; des besoins sp&eacute;cifiques tels que les syst&egrave;mes de notation ou meta-informations. Un format unifi&eacute; est particuli&egrave;rement utile pour les consommateurs orthologue qui veulent int&eacute;grer des donn&eacute;es provenant de nombreuses ressources, par exemple pour les projets d&#39;annotation de g&egrave;ne. R&eacute;f&eacute;rence proteomes pour 61 organismes sont d&eacute;j&agrave; disponibles dans SeqXML, et 10 bases de donn&eacute;es de niveau de sont joindre &agrave; OrthoXML. Adoption par l&#39;ensemble du champ faciliterait consid&eacute;rablement &eacute;change et contr&ocirc;le de la qualit&eacute; de la s&eacute;quence et le niveau d&#39;informations.

Lettre &agrave; l&#39;&eacute;diteur : SeqXML et OrthoXML : normes pour les informations de s&eacute;quence et de niveau.

C&#39;&egrave; un grande bisogno di norme nel campo orthology. Utenti devono vedersela con ortholog diverse rappresentazioni di dati da ogni provider e i fornitori stessi indipendentemente devono raccogliere e analizzare i dati della sequenza di input. Queste procedure ridondanti e gravose fare integrazione e confronto di dati difficili. Abbiamo progettato i due formati basati su XML, SeqXML e OrthoXML, per risolvere questi problemi. SeqXML &egrave; un leggero formato input record, la sequenza per orthology previsione. Esso memorizza la stessa sequenza e metadati come record di formato FASTA tipico, ma supera i problemi comuni come metadati non strutturati nell&#39;intestazione e contenuto sequenza errata. XML fornisce la convalida per evitare problemi di integrit&agrave; dei dati che sono frequenti nei file FASTA. La gamma di applicazioni per SeqXML &egrave; ampio e non limitato alla previsione ortholog. Forniamo le funzioni di lettura/scrittura per BioJava e BioPerl Biopython. OrthoXML &egrave; stato progettato per rappresentare ortholog assegnazioni da qualsiasi fonte in modo coerenza e strutturato, ma per esigenze specifiche quali schemi di punteggi o meta-informazioni. Un formato unificato &egrave; particolarmente prezioso per i consumatori ortholog che desidera integrare dati provenienti da numerose risorse, ad esempio per i progetti di annotazione genica. Riferimento ai proteomi per 61 organismi sono gi&agrave; disponibili in SeqXML, e 10 orthology database hanno firmato a OrthoXML. Adozione da parte dell&#39;intero campo sostanzialmente facilitare scambio e controllo di qualit&agrave; della sequenza e orthology informazioni.

Lettera all&#39;editore: SeqXML e OrthoXML: standard per la sequenza e orthology informazioni.

Percutaneous transluminal angioplasty with stent implantation is used to dilate arteries narrowed by atherosclerotic plaques and to revascularize coronary arteries occluded by atherothrombosis in myocardial infarction. Commonly applied drug-eluting stents release antiproliferative or anti-inflammatory agents to reduce the incidence of in-stent stenosis. However, these stents may still lead to in-stent stenosis; they also show increased rates of late stent thrombosis, an obstacle to optimal revascularization possibly related to endothelial recovery. Here, we examined the contribution of neutrophils and neutrophilic granule proteins to arterial healing after injury. We found that neutrophil-borne cathelicidin (mouse CRAMP, human LL-37) promoted reendothelization and thereby limited neointima formation after stent implantation. We then translated these findings to an animal model using a neutrophil-instructing, biofunctionalized, miniaturized Nitinol stent coated with LL-37. This stent reduced in-stent stenosis in a mouse model of atherosclerosis, suggesting that LL-37 may promote vascular healing after interventional therapy.

Neutrophil-derived cathelicidin protects from neointimal hyperplasia.

L&#39;angioplastie transluminale percutan&eacute;e avec implantation de stents sert &agrave; dilater les art&egrave;res r&eacute;tr&eacute;cies par des plaques d&#39;ath&eacute;roscl&eacute;rose et &agrave; recanalisent des art&egrave;res coronaires occlus par ath&eacute;rothrombose dans l&#39;infarctus du myocarde. Couramment appliqu&eacute;es des stents &agrave; &eacute;lution m&eacute;dicamenteuse lib&eacute;rer des agents antiprolif&eacute;ratifs ou anti-inflammatoire pour r&eacute;duire l&#39;incidence de la st&eacute;nose intrastent. Cependant, ces stents peut induire encore intrastent st&eacute;nose ; ils montrent &eacute;galement une augmentation des taux de retard thrombose de stent, un obstacle &agrave; la revascularisation optimale &eacute;ventuellement li&eacute;es &agrave; la r&eacute;cup&eacute;ration endoth&eacute;liale. Ici, nous avons examin&eacute; la contribution des neutrophiles et des prot&eacute;ines de neutrophiles granule &agrave; art&eacute;riel de gu&eacute;rison apr&egrave;s une blessure. Nous avons trouv&eacute; que cath&eacute;licidine transmises par les neutrophiles (souris CRAMPE, humain LL-37) promu reendothelization et formation n&eacute;ointima ainsi limit&eacute;e apr&egrave;s implantation de stents. Nous avons ensuite traduit ces r&eacute;sultats d&#39;un mod&egrave;le animal en utilisant un neutrophile-instruire, la biofunctionalized, miniaturis&eacute; stent Nitinol recouvert de LL-37. Cette endoproth&egrave;se r&eacute;duit intrastent st&eacute;nose dans un mod&egrave;le murin de l&#39;ath&eacute;roscl&eacute;rose, ce qui sugg&egrave;re que LL-37 peut favoriser la cicatrisation vasculaire apr&egrave;s traitement interventionnel.

D&eacute;riv&eacute; de neutrophile cath&eacute;licidine prot&egrave;ge contre l&#39;hyperplasie n&eacute;ointimale.

Angioplastica transluminale percutanea con impianto di stent viene utilizzato per dilatare le arterie ridotte da placche aterosclerotiche e revascularize arterie coronarie occluse da ATEROTROMBOSI nell&#39;infarto miocardico. Comunemente applicato stent medicati rilasciare agenti antiproliferativi o anti-infiammatori per ridurre l&#39;incidenza di stenosi in-stent. Tuttavia, questi stent pu&ograve; ancora portare a stenosi di stent; essi mostrano anche tassi di aumentati del tardo trombosi dello stent, un ostacolo all&#39;ottima rivascolarizzazione possibilmente correlate al ripristino endoteliale. Qui, abbiamo esaminato il contributo di neutrofili e proteine neutrofila granulo alla guarigione arteriosa dopo l&#39;infortunio. Abbiamo trovato che cathelicidin neutrofili-borne (mouse CRAMPO, LL umano-37) promosso reendothelization e formazione di neointima quindi limitato dopo l&#39;impianto dello stent. Poi abbiamo tradotto questi risultati in un modello animale utilizzando un neutrofili-istruire, biofunctionalized, miniaturizzato stent in Nitinol rivestiti con LL-37. Questo stent ridotto in-stent stenosi in un modello murino di aterosclerosi, suggerendo che LL-37 pu&ograve; favorire la guarigione vascolare dopo terapia interventistica.

Neutrofili derivata cathelicidin protegge da iperplasia neointimale.

Percutaneous stenting of occluded peripheral vessels is a well-established technique in clinical practice. Unfortunately, the patency rates of small-caliber vessels after stenting remain unsatisfactory. The aim of the BioStent concept is to overcome in-stent restenosis by excluding the diseased vessel segment entirely from the blood stream, in addition to providing an intact endothelial cell layer.

The BioStent: novel concept for a viable stent structure.

Pose d&#39;un stent percutan&eacute;e des vaisseaux p&eacute;riph&eacute;riques occlus est une technique bien &eacute;tablie en pratique clinique. Malheureusement, le taux de perm&eacute;abilit&eacute; des vaisseaux de petit calibre apr&egrave;s pose d&#39;un stent reste insatisfaisante. Le concept de BioStent vise &agrave; surmonter la rest&eacute;nose intrastent en excluant le tron&ccedil;on de malades navire enti&egrave;rement &agrave; partir de la circulation sanguine, en plus de fournir une couche de cellules endoth&eacute;liales intactes.

Le BioStent : concept novateur pour une structure viable stent.

Stenting percutaneo dei vasi periferici occlusi &egrave; una tecnica ben consolidata nella pratica clinica. Purtroppo, il tasso di perviet&agrave; dei vasi di piccolo calibro dopo stenting rimane insoddisfacente. Lo scopo del concetto di BioStent &egrave; quello di superare la ristenosi in-stent escludendo il segmento di vaso malato interamente dal flusso sanguigno, oltre a fornire uno strato di cellule endoteliali intatte.

BioStent: nuovo concetto per una struttura valida dello stent.

Current stent system efficacy for the treatment of coronary artery disease is hampered by in-stent restenosis (ISR) rates of up to 20% in certain high-risk settings and by the risk of stent thrombosis, which is characterized by a high mortality rate. In theory, biodegradable vascular devices exhibit crucial advantages. Most absorbable implant materials are based on poly-L-lactic acid (PLLA) owing to its mechanical properties; however, PLLA might induce an inflammatory reaction in the vessel wall. Evaluation of biodegradable implant efficacy includes a long-term examination of tissue response; therefore, a simple in vivo tool for thorough biocompatibility and biodegradation evaluation would facilitate future stent system development. Rats have been used for the study of in vivo degradation processes, and stent implantation into the abdominal aorta of rats is a proven model for stent evaluation. Here, we report the transformation of the porcine double-stent animal model into the high-throughput rat abdominal aorta model. As genetic manipulation of rats was introduced recently, this novel method presents a powerful tool for future in vivo biodegradable candidate stent biocompatibility and biodegradation characterization in a reliable simple model of coronary ISR.

Introduction of a high-throughput double-stent animal model for the evaluation of biodegradable vascular stents.

Efficacit&eacute; du syst&egrave;me actuel des stent pour le traitement de la maladie coronarienne est entrav&eacute;e par des taux de rest&eacute;nose (ISR)-stent de jusqu&#39;&agrave; 20 % dans certains milieux &agrave; risque &eacute;lev&eacute; et par le risque de thrombose de stent, qui se caract&eacute;rise par un taux &eacute;lev&eacute; de mortalit&eacute;. En th&eacute;orie, les dispositifs vasculaires biod&eacute;gradables pi&egrave;ce avantages cruciaux. Plupart des mat&eacute;riaux implant r&eacute;sorbable reposent sur l&#39;acide L-polylactique (PLLA) en raison de ses propri&eacute;t&eacute;s m&eacute;caniques ; Cependant, PLLA peut induire une r&eacute;action inflammatoire dans la paroi des vaisseaux. &Eacute;valuation de l&#39;efficacit&eacute; de l&#39;implant biod&eacute;gradable comprend un examen &agrave; long terme de r&eacute;action tissulaire ; donc, un outil simple et in vivo pour la biocompatibilit&eacute; approfondie et l&#39;&eacute;valuation de la biod&eacute;gradation faciliterait le d&eacute;veloppement du syst&egrave;me futur de stent. Des rats ont &eacute;t&eacute; utilis&eacute;s pour l&#39;&eacute;tude des processus de d&eacute;gradation in vivo, et l&#39;implantation de stents dans l&#39;aorte abdominale des rats est un mod&egrave;le &eacute;prouv&eacute; pour l&#39;&eacute;valuation de l&#39;endoproth&egrave;se. Nous rapportons ici, la transformation du mod&egrave;le animal porcine double-stent dans le mod&egrave;le d&#39;aorte abdominale haut d&eacute;bit chez le rat. Comme la manipulation g&eacute;n&eacute;tique des rats a &eacute;t&eacute; introduite r&eacute;cemment, cette nouvelle m&eacute;thode pr&eacute;sente un outil puissant pour le futur candidat biod&eacute;gradable in vivo caract&eacute;risation de biocompatibilit&eacute; et de biod&eacute;gradation de stent dans un mod&egrave;le fiable et simple de coronaire EIS.

Introduction d&#39;un mod&egrave;le animal de l&#39;endoproth&egrave;se double haut d&eacute;bit pour l&#39;&eacute;valuation des endoproth&egrave;ses vasculaires biod&eacute;gradables.

Attuale efficacia del sistema di stent per il trattamento della malattia coronarica &egrave; ostacolata da in-stent restenosi (ISR) tariffe fino al 20% in determinate impostazioni ad alto rischio e il rischio di trombosi dello stent, che sono caratterizzata da un elevato tasso di mortalit&agrave;. In teoria, biodegradabile vascolari periferiche presentano vantaggi decisivi. La maggior parte dei materiali riassorbibili impianto sono basati su acido L-polilattico (PLLA) a causa delle sue propriet&agrave; meccaniche; Tuttavia, PLLA potrebbe indurre una reazione infiammatoria nella parete del vaso. Valutazione dell&#39;efficacia dell&#39;impianto biodegradabile comprende un esame a lungo termine della risposta dei tessuti; Pertanto, un semplice strumento in vivo per la valutazione di biodegradazione e biocompatibilit&agrave; approfondita faciliterebbe lo sviluppo del sistema di stent futuri. Ratti sono stati utilizzati per lo studio dei processi di degradazione in vivo, e l&#39;impianto di stent in aorta addominale di ratti &egrave; un modello collaudato per la valutazione dello stent. Riportiamo la trasformazione del modello animale suina double-stent nel modello high-throughput ratto aorta addominale. Come la manipolazione genetica di ratti &egrave; stato introdotto di recente, questo nuovo metodo presenta un potente strumento per il futuro candidato biodegradabile in vivo stent biocompatibilit&agrave; e biodegradabilit&agrave; caratterizzazione in un modello semplice affidabile di ISR. coronarica

Introduzione di un modello animale di alto-rendimento double-stent per la valutazione di stent vascolari biodegradabile.

Molecular phylogenetic analyses have produced a plethora of controversial hypotheses regarding the patterns of diversification of non-bilaterian animals. To unravel the causes for the patterns of extreme inconsistencies at the base of the metazoan tree of life, we constructed a novel supermatrix containing 122 genes, enriched with non-bilaterian taxa. Comparative analyses of this supermatrix and its two non-overlapping multi-gene partitions (including ribosomal and non-ribosomal genes) revealed conflicting phylogenetic signals. We show that the levels of saturation and long branch attraction artifacts in the two partitions correlate with gene sampling. The ribosomal gene partition exhibits significantly lower saturation levels than the non-ribosomal one. Additional systematic errors derive from significant variations in amino acid substitution patterns among the metazoan lineages that violate the stationarity assumption of evolutionary models frequently used to reconstruct phylogenies. By modifying gene sampling and the taxonomic composition of the outgroup, we were able to construct three different yet well-supported phylogenies. These results show that the accuracy of phylogenetic inference may be substantially improved by selecting genes that evolve slowly across the Metazoa and applying more realistic substitution models. Additional sequence-independent genomic markers are also necessary to assess the validity of the phylogenetic hypotheses.

Deep metazoan phylogeny: when different genes tell different stories.

Les analyses phylog&eacute;n&eacute;tiques mol&eacute;culaires ont produit une multitude d&#39;hypoth&egrave;ses controvers&eacute;es sur les patrons de diversification d&#39;animaux non-forment. Pour d&eacute;m&ecirc;ler les causes pour les patrons des incoh&eacute;rences extr&ecirc;mes &agrave; la base de l&#39;arbre de vie m&eacute;tazoaire, nous avons construit un roman supermatrix contenant 122 g&egrave;nes, enrichis de taxons non-forment. Des analyses comparatives de cette supermatrix et ses deux partitions multig&eacute;niques non-cumul (y compris les g&egrave;nes ribosomiques et non ribosomales) ont r&eacute;v&eacute;l&eacute; des signaux contradictoires phylog&eacute;n&eacute;tiques. Nous montrons que les niveaux de saturation et long branch artefacts d&#39;attraction dans les deux partitions sont en corr&eacute;lation avec &eacute;chantillonnage de g&egrave;ne. La partition de g&egrave;ne ribosomal expose les niveaux de saturation significativement plus faibles que celle non ribosomale. Erreurs syst&eacute;matiques suppl&eacute;mentaires d&eacute;coulent des variations importantes dans les mod&egrave;les de substitution d&#39;acide amin&eacute; parmi les lign&eacute;es m&eacute;tazoaires qui violent l&#39;hypoth&egrave;se de stationnarit&eacute; des mod&egrave;les &eacute;volutifs, fr&eacute;quemment utilis&eacute; pour reconstruire les phylog&eacute;nies. En modifiant le g&egrave;ne pr&eacute;l&egrave;vement d&#39;&eacute;chantillons et de la composition taxonomique de l&#39;exogroupe, nous avons pu construire trois phylog&eacute;nies diff&eacute;rentes mais bien soutenus. Ces r&eacute;sultats montrent que l&#39;exactitude de l&#39;inf&eacute;rence phylog&eacute;n&eacute;tique peut &ecirc;tre consid&eacute;rablement am&eacute;lior&eacute; par s&eacute;lection de g&egrave;nes qui &eacute;voluent lentement &agrave; travers des m&eacute;tazoaires et en appliquant des mod&egrave;les plus r&eacute;alistes de substitution. Marqueurs g&eacute;nomiques additionnels de s&eacute;quences ind&eacute;pendantes sont &eacute;galement n&eacute;cessaires pour &eacute;valuer la validit&eacute; des hypoth&egrave;ses phylog&eacute;n&eacute;tiques.

Phylog&eacute;nie profond m&eacute;tazoaire : quand diff&eacute;rents g&egrave;nes racontent des histoires diff&eacute;rentes.

Analisi filogenetiche molecolari hanno prodotto una pletora di controverse ipotesi per quanto riguarda i modelli di diversificazione di spriggina non animali. Per svelare le cause per i modelli di estreme incongruenze alla base dell&#39;albero della vita metazoi, abbiamo costruito un romanzo supermatrice contenente 122 geni, arricchiti con non-Spriggina taxa. Analisi comparative di questo supermatrice e i suoi due partizioni non sovrapposte multi-gene (ribosomiale e non-ribosomal geni compresi) ha rivelato segnali contrastanti filogenetiche. Ci mostrano che i livelli di saturazione e long branch artefatti di attrazione in due partizioni correlano con campionamento di gene. La partizione di gene ribosomiale presenta livelli di saturazione significativamente inferiori rispetto a quella non-ribosomal. Ulteriori errori sistematici derivano da variazioni significative nel pattern di sostituzione dell&#39;amminoacido tra i lignaggi metazoi che violano l&#39;ipotesi di stazionariet&agrave; dei modelli evolutivi frequentemente utilizzata per ricostruire la filogenesi. Modificando il campionamento di gene e la composizione tassonomica dell&#39;outgroup, siamo stati in grado di costruire tre differenti ma ben supportati filogenesi. Questi risultati mostrano che l&#39;accuratezza dell&#39;inferenza filogenetica pu&ograve; essere migliorato sostanzialmente selezione di geni che si evolvono lentamente attraverso il Metazoa e applicando modelli pi&ugrave; realistici di sostituzione. Supplementare indipendente dalla sequenza genomiche marcatori sono anche necessarie per valutare la validit&agrave; delle ipotesi filogenetiche.

Filogenesi profondo metazoi: Quando diversi geni raccontano storie diverse.

An accurate inference of orthologs is essential in many research fields such as comparative genomics, molecular evolution, and genome annotation. Existing methods for genome-scale orthology inference are mostly based on all-versus-all similarity searches that scale quadratically with the number of species. This limits their application to the increasing number of available large-scale datasets. Here, we present Hieranoid, a new orthology inference method using a hierarchical approach. Hieranoid performs pairwise orthology analysis using InParanoid at each node in a guide tree as it progresses from its leaves to the root. This concept reduces the total runtime complexity from a quadratic to a linear function of the number of species. The tree hierarchy provides a natural structure in multi-species ortholog groups, and the aggregation of multiple sequences allows for multiple alignment similarity searching techniques, which can yield more accurate ortholog groups. Using the recently published orthobench benchmark, Hieranoid showed the overall best performance. Our progressive approach presents a new way to infer orthologs that combines efficient graph-based methodology with aspects of compute-intensive tree-based methods. The linear scaling with the number of species is a major advantage for large-scale applications and makes Hieranoid well suited to cope with vast amounts of sequenced genomes in the future. Hieranoid is an open source and can be downloaded at Hieranoid.sbc.su.se.

Hieranoid: Hierarchical Orthology Inference.

Une conclusion exacte des orthologues est essentielle dans de nombreux domaines de recherche tels que la g&eacute;nomique comparative, &eacute;volution mol&eacute;culaire et annotation du g&eacute;nome. Les m&eacute;thodes existantes pour l&#39;inf&eacute;rence de niveau &agrave; l&#39;&eacute;chelle du g&eacute;nome sont principalement bas&eacute;s sur des recherches de similarit&eacute; de tout-contre-tout cela l&#39;&eacute;chelle quadratiquement avec le nombre d&#39;esp&egrave;ces. Ce qui limite leur application &agrave; la multiplication des jeux de donn&eacute;es disponibles &agrave; grande &eacute;chelle. Nous pr&eacute;sentons ici les Hieranoid, une nouvelle m&eacute;thode d&#39;inf&eacute;rence niveau &agrave; l&#39;aide d&#39;une approche hi&eacute;rarchique. Hieranoid effectue une analyse de niveau par paires &agrave; l&#39;aide de InParanoid &agrave; chaque n&oelig;ud dans une arborescence de guide lorsqu&#39;il passe de ses feuilles &agrave; la racine. Ce concept r&eacute;duit la complexit&eacute; de la duree totale d&#39;un quadratique &agrave; une fonction lin&eacute;aire du nombre d&#39;esp&egrave;ces. La hi&eacute;rarchie d&#39;arborescence fournit une structure naturelle en groupes plurisp&eacute;cifiques orthologue, et l&#39;agr&eacute;gation de multiples s&eacute;quences permet plusieurs similitude alignement, la recherche de techniques, qui peuvent produire des groupes orthologue plus pr&eacute;cis. &Agrave; l&#39;aide de la r&eacute;f&eacute;rence orthobench publi&eacute; r&eacute;cemment, Hieranoid a montr&eacute; le meilleur rendement. Notre approche progressive pr&eacute;sente une nouvelle fa&ccedil;on d&#39;inf&eacute;rer des orthologues qui allie m&eacute;thodologie efficace ax&eacute;e sur le graphique des aspects des m&eacute;thodes de calcul intensif bas&eacute; sur l&#39;arborescence. La mise &agrave; l&#39;&eacute;chelle lin&eacute;aire avec le nombre d&#39;esp&egrave;ces est un atout majeur pour les applications &agrave; grande &eacute;chelle et fait Hieranoid bien adapt&eacute; pour faire face aux &eacute;normes quantit&eacute;s de g&eacute;nomes s&eacute;quenc&eacute;s &agrave; l&#39;avenir. Hieranoid est un logiciel libre et peut &ecirc;tre t&eacute;l&eacute;charg&eacute; &agrave; Hieranoid.sbc.su.se.

Hieranoid : Inf&eacute;rence de niveau hi&eacute;rarchique.

Un&#39;inferenza accurata di orthologs &egrave; essenziale in molti campi di ricerca quali la genomica comparativa, evoluzione molecolare e annotazione del genoma. Metodi esistenti per inferenza orthology genoma-scala principalmente sono basati su ricerche di somiglianza di tutti-contro-tutti che scala quadraticamente con il numero di specie. Questo limita la loro applicazione per il crescente numero di DataSet disponibile su larga scala. Presentiamo qui, Hieranoid, un nuovo metodo di inferenza orthology utilizzando un approccio gerarchico. Hieranoid esegue analisi pairwise orthology utilizzando InParanoid in ogni nodo in un albero di guida mentre progredisce dalle sue foglie alla radice. Questo concetto riduce la complessit&agrave; totale runtime da un quadratica di una funzione lineare del numero di specie. La gerarchia della struttura fornisce una struttura naturale in gruppi ortholog multispecie, e consente l&#39;aggregazione di sequenze multiple per somiglianza di allineamento pi&ugrave; tecniche, che possono produrre pi&ugrave; accurate ortholog gruppi di ricerca. Utilizzando il benchmark recentemente pubblicato orthobench, Hieranoid ha mostrato le prestazioni complessivamente migliori. Il nostro approccio progressivo presenta un nuovo modo di dedurre orthologs che combina efficiente metodologia basata su grafico con aspetti dei metodi basati su albero complesse. La scala lineare con il numero di specie &egrave; un grande vantaggio per applicazioni su larga scala e rende Hieranoid adatto per far fronte a grandi quantit&agrave; di genomi sequenziati in futuro. Hieranoid &egrave; un open source e pu&ograve; essere scaricato da Hieranoid.sbc.su.se.

Article	Year
Phylogenomics revives traditional views on deep animal relationships. Current biology : CB\| PubMed ID: 19345102	2009
OrthoSelect: a web server for selecting orthologous gene alignments from EST sequences. Nucleic acids research\| PubMed ID: 19491309	2009
OrthoSelect: a protocol for selecting orthologous groups in phylogenomics. BMC bioinformatics\| PubMed ID: 19607672	2009
Treephyler: fast taxonomic profiling of metagenomes. Bioinformatics (Oxford, England)\| PubMed ID: 20172941	2010
HIV classification using the coalescent theory. Bioinformatics (Oxford, England)\| PubMed ID: 20400454	2010
Description of a flow optimized oxygenator with integrated pulsatile pump. Artificial organs\| PubMed ID: 21092033	2010
OrthoDisease: tracking disease gene orthologs across 100 species. Briefings in bioinformatics\| PubMed ID: 21565935	2011
CoMet--a web server for comparative functional profiling of metagenomes. Nucleic acids research\| PubMed ID: 21622656	2011
Letter to the editor: SeqXML and OrthoXML: standards for sequence and orthology information. Briefings in bioinformatics\| PubMed ID: 21666252	2011
Neutrophil-derived cathelicidin protects from neointimal hyperplasia. Science translational medicine\| PubMed ID: 21974936	2011
The BioStent: novel concept for a viable stent structure. Tissue engineering. Part A\| PubMed ID: 22519682	2012
Introduction of a high-throughput double-stent animal model for the evaluation of biodegradable vascular stents. Journal of biomedical materials research. Part B, Applied biomaterials\| PubMed ID: 22997102	2012
Deep metazoan phylogeny: when different genes tell different stories. Molecular phylogenetics and evolution\| PubMed ID: 23353073	2013
Hieranoid: Hierarchical Orthology Inference. Journal of molecular biology\| PubMed ID: 23485417	2013

Fabian Schreiber

Biography

JoVE Journal Publications

Other Publications