ex-vivo-culture-chick-cerebellar-slices-spatially-targeted

<em>Ex Vivo</em> Culture of Chick Cerebellar Slices and Spatially Targeted Electroporation of Granule Cell Precursors

The cerebellar external granule layer (EGL) is the site of the largest transit amplification in the developing brain, and an excellent model for studying ...

Queen Mary, University of London

Tribolium castaneum is a member of the most species-rich eukaryotic order, a powerful model organism for the study of generalized insect development, and an important pest of stored agricultural products. We describe its genome sequence here. This omnivorous beetle has evolved the ability to interact with a diverse chemical environment, as shown by large expansions in odorant and gustatory receptors, as well as P450 and other detoxification enzymes. Development in Tribolium is more representative of other insects than is Drosophila, a fact reflected in gene content and function. For example, Tribolium has retained more ancestral genes involved in cell-cell communication than Drosophila, some being expressed in the growth zone crucial for axial elongation in short-germ development. Systemic RNA interference in T. castaneum functions differently from that in Caenorhabditis elegans, but nevertheless offers similar power for the elucidation of gene function and identification of targets for selective insect control.

The genome of the model beetle and pest Tribolium castaneum.

&#x8D64;&#x62DF;&#x8C37;&#x76D7;&#x662F;&#x5E7F;&#x4E49;&#x7684;&#x6606;&#x866B;&#x53D1;&#x5C55;&#x7814;&#x7A76;&#x4E0E;&#x5B58;&#x50A8;&#x519C;&#x4EA7;&#x54C1;&#x91CD;&#x8981;&#x5BB3;&#x866B;&#x529F;&#x80FD;&#x5F3A;&#x5927;&#x7684;&#x6A21;&#x578B;&#x751F;&#x7269;&#x7269;&#x79CD;&#x6700;&#x4E30;&#x5BCC;&#x771F;&#x6838;&#x79E9;&#x5E8F;&#x7684;&#x6210;&#x5458;&#x3002;&#x6211;&#x4EEC;&#x63CF;&#x8FF0;&#x4E86;&#x5176;&#x57FA;&#x56E0;&#x7EC4;&#x5E8F;&#x5217;&#x5728;&#x8FD9;&#x91CC;&#x3002;&#x8FD9;&#x79CD;&#x6742;&#x98DF;&#x6027;&#x7684;&#x7532;&#x866B;&#x5DF2;&#x6F14;&#x53D8;&#x4E0E;&#x5404;&#x79CD;&#x4E0D;&#x540C;&#x7684;&#x5316;&#x5B66;&#x73AF;&#x5883;&#x8FDB;&#x884C;&#x4EA4;&#x4E92;&#x7684;&#x80FD;&#x529B;&#xFF0C;&#x5982;&#x56FE;&#x6240;&#x793A;&#x7684;&#x6C14;&#x5473;&#x548C;&#x5473;&#x89C9;&#x53D7;&#x4F53;&#xFF0C;&#x4EE5;&#x53CA; p450 &#x6C27;&#x5316;&#x5927;&#x6269;&#x4EA7;&#x548C;&#x5176;&#x4ED6;&#x89E3;&#x6BD2;&#x9176;&#x3002;&#x8D64;&#x62DF;&#x8C37;&#x53D1;&#x5C55;&#x662F;&#x66F4;&#x80FD;&#x4EE3;&#x8868;&#x5176;&#x4ED6;&#x6606;&#x866B;&#x6BD4;&#x679C;&#x8747;&#xFF0C;&#x8FD9;&#x53CD;&#x6620;&#x5728;&#x57FA;&#x56E0;&#x5185;&#x5BB9;&#x548C;&#x529F;&#x80FD;&#x3002;&#x4F8B;&#x5982;&#xFF0C;&#x8D64;&#x62DF;&#x8C37;&#x4FDD;&#x7559;&#x4E86;&#x66F4;&#x591A;&#x7956;&#x5148;&#x7684;&#x9057;&#x4F20;&#x57FA;&#x56E0;&#x6240;&#x6D89;&#x53CA;&#x7684;&#x5355;&#x5143;&#x683C;&#x901A;&#x4FE1;&#x6BD4;&#x679C;&#x8747;&#xFF0C;&#x4E00;&#x4E9B;&#x8868;&#x793A;&#x77ED;&#x80DA;&#x53D1;&#x80B2;&#x4E2D;&#x7684;&#x8F74;&#x5411;&#x4F38;&#x957F;&#x7684;&#x5173;&#x952E;&#x589E;&#x957F;&#x533A;&#x57DF;&#x4E2D;&#x3002;T.&#x76D7;&#x7CFB;&#x7EDF;&#x6027; RNA &#x5E72;&#x6270;&#x4EE5;&#x4E0D;&#x540C;&#x7684;&#x65B9;&#x5F0F;&#xFF0C;&#x4ECE;&#x6746;&#x7EBF;&#x866B;&#x4E2D;&#x7684;&#x51FD;&#x6570;&#xFF0C;&#x4F46;&#x4E0D;&#x8FC7;&#x63D0;&#x4F9B;&#x4E86;&#x7C7B;&#x4F3C;&#x7684;&#x6743;&#x529B;&#xFF0C;&#x4E3A;&#x6F84;&#x6E05;&#x8FD9;&#x79CD;&#x57FA;&#x56E0;&#x529F;&#x80FD;&#x548C;&#x9009;&#x62E9;&#x6027;&#x7684;&#x6606;&#x866B;&#x63A7;&#x5236;&#x76EE;&#x6807;&#x7684;&#x6807;&#x8BC6;&#x3002;

&#x6A21;&#x578B;&#x7532;&#x58F3;&#x866B;&#x548C;&#x5BB3;&#x866B;&#x8D64;&#x62DF;&#x8C37;&#x76D7;&#x7684;&#x57FA;&#x56E0;&#x7EC4;&#x3002;

Tribolium castaneum est membre de l&#39;ordre de plus riche en esp&egrave;ces eucaryote, un organisme mod&egrave;le puissant pour l&#39;&eacute;tude du d&eacute;veloppement g&eacute;n&eacute;ralis&eacute; des insectes et un important ravageur des produits agricoles stock&eacute;s. Nous d&eacute;crivons ici sa s&eacute;quence de g&eacute;nome. Cet insecte omnivore a &eacute;volu&eacute; de la capacit&eacute; d&#39;interagir avec un environnement chimique diversifi&eacute;, comme en t&eacute;moignent les grandes expansions dans odorant et r&eacute;cepteurs gustatifs, comme P450 et d&#39;autres enzymes de d&eacute;toxification. D&eacute;veloppement de Tribolium est plus repr&eacute;sentatif des autres insectes qu&#39;est la drosophile, un fait refl&eacute;t&eacute; par le contenu de g&egrave;ne et de la fonction. Par exemple, Tribolium a conserv&eacute; les plus ancestrales de g&egrave;nes impliqu&eacute;s dans la communication de cellule-cellule que la drosophile, certains s&#39;exprime dans la zone de croissance cruciale pour une &eacute;longation axiale dans le d&eacute;veloppement de germe court. L&#39;interf&eacute;rence ARN syst&eacute;mique chez T. castaneum fonctionne diff&eacute;remment de celle chez Caenorhabditis elegans, mais propose n&eacute;anmoins une puissance semblable pour l&#39;&eacute;lucidation de la fonction du g&egrave;ne et l&#39;identification de cibles pour la lutte contre les insectes s&eacute;lective.

Le g&eacute;nome de la mod&egrave;le beetle et pest Tribolium castaneum.

Tribolium Castaneum ist Mitglied der meisten artenreichen eukaryotischen Ordnung, leistungsstarke Modellorganismus f&uuml;r die Studie des generalisierten Insekt Entwicklung und einen wichtigen Sch&auml;dling gespeicherte landwirtschaftlicher Erzeugnisse. Wir beschreiben hier die Genom-Sequenz. Diese Allesfresser K&auml;fer hat die F&auml;higkeit zur Interaktion mit einer vielf&auml;ltigen chemischen Umgebung entwickelt, wie gro&szlig;e Erweiterungen in Odoriermittel sowie gustatorisches Rezeptoren und P450 und andere Entgiftung Enzyme gezeigt. Entwicklung in Tribolium ist mehr Vertreter der anderen Insekten als Drosophila, ist eine Tatsache spiegelt sich in gen-Inhalt und Funktion. Beispielsweise hat Tribolium weitere Vorfahren Selbstmordprogramm Zell-Zell-Kommunikation als Drosophila, einige ausgedr&uuml;ckt im Bereich Wachstum entscheidend f&uuml;r axialen Dehnung in kurz-Keim Entwicklung beibehalten. Systemische RNA-Interferenz in T. Castaneum funktioniert anders aus, die in Caenorhabditis Elegans, aber dennoch bietet &auml;hnliche Kraft f&uuml;r die Aufkl&auml;rung der Genfunktion und Identifikation von Zielen f&uuml;r die selektive Insektenbek&auml;mpfung.

Das Genom von der Modell-K&auml;fer und Pest Tribolium Castaneum.

Tribolium castaneum &egrave; un membro dell&#39;ordine negli eucarioti pi&ugrave; ricche di specie, un organismo potente modello per lo studio dello sviluppo dell&#39;insetto generalizzato e un parassita importante dei prodotti agricoli immagazzinati. Descriviamo qui la sequenza del genoma. Questo coleottero onnivoro ha evoluto la capacit&agrave; di interagire con un ambiente chimico vario, come dimostrato dalle grandi espansioni nel odorant e recettori gustativi, nonch&eacute; P450 e altri enzimi di disintossicazione. Sviluppo in Tribolium &egrave; pi&ugrave; rappresentativo di altri insetti che &egrave; Drosophila, un fatto riflette nel gene contenuto e funzione. Ad esempio, Tribolium ha mantenuto pi&ugrave; ancestrali geni coinvolti nella comunicazione cellula-cellula di drosofila, alcuni espressi nella zona di crescita fondamentale per allungamento assiale in germe di breve sviluppo. Sistemica RNA interference in T. Tribolium funziona in modo diverso da quello in Caenorhabditis elegans, ma tuttavia offre potenza simile per la delucidazione di funzione del gene e l&#39;identificazione di obiettivi di controllo selettivo degli insetti.

Il genoma di Tribolium castaneum da modello beetle e pest.

&#x30B3;&#x30AF;&#x30CC;&#x30B9;&#x30C8;&#x30E2;&#x30C9;&#x30AD;&#x6700;&#x3082;&#x7A2E;&#x8C4A;&#x5BCC;&#x306A;&#x771F;&#x6838;&#x751F;&#x7269;&#x9806;&#x5E8F;&#x3001;&#x30B9;&#x30C8;&#x30A2;&#x30C9;&#x306E;&#x8FB2;&#x7523;&#x7269;&#x306E;&#x91CD;&#x8981;&#x306A;&#x5BB3;&#x866B;&#x3068;&#x4E00;&#x822C;&#x5316;&#x3055;&#x308C;&#x305F;&#x6606;&#x866B;&#x306E;&#x958B;&#x767A;&#x306E;&#x7814;&#x7A76;&#x306E;&#x5F37;&#x529B;&#x306A;&#x30E2;&#x30C7;&#x30EB;&#x751F;&#x7269;&#x306E;&#x30E1;&#x30F3;&#x30D0;&#x30FC;&#x3067;&#x3059;&#x3002;&#x3053;&#x3053;&#x306B;&#x305D;&#x306E;&#x30B2;&#x30CE;&#x30E0; &#x30B7;&#x30FC;&#x30B1;&#x30F3;&#x30B9;&#x3092;&#x8A18;&#x8FF0;&#x3057;&#x307E;&#x3059;&#x3002;&#x3053;&#x306E;&#x96D1;&#x98DF;&#x6027;&#x7532;&#x866B;&#x306F;&#x591A;&#x69D8;&#x306A;&#x5316;&#x5B66;&#x74B0;&#x5883;&#x3068;&#x5BFE;&#x8A71;&#x3059;&#x308B;&#x80FD;&#x529B;&#x306F;&#x3001;&#x55C5;&#x899A;&#x3068;&#x5473;&#x899A;&#x306E;&#x53D7;&#x5BB9;&#x4F53;&#x3068;&#x3057;&#x3066; P450 &#x306E;&#x5927;&#x898F;&#x6A21;&#x306A;&#x5C55;&#x958B;&#x3068;&#x4ED6;&#x306E;&#x89E3;&#x6BD2;&#x306E;&#x9175;&#x7D20;&#x306B;&#x3088;&#x3063;&#x3066;&#x793A;&#x3059;&#x3088;&#x3046;&#x306B;&#x9032;&#x5316;&#x3057;&#x3066;&#x3044;&#x307E;&#x3059;&#x3002;&#x30B3;&#x30AF;&#x30CC;&#x30B9;&#x30C8;&#x30E2;&#x30C9;&#x30AD;&#x306E;&#x958B;&#x767A;&#x306F;&#x3001;&#x30B7;&#x30E7;&#x30A6;&#x30B8;&#x30E7;&#x30A6;&#x30D0;&#x30A8;&#x3001;&#x907A;&#x4F1D;&#x5B50;&#x306E;&#x5185;&#x5BB9;&#x3068;&#x6A5F;&#x80FD;&#x306F;&#x3001;&#x4E8B;&#x5B9F;&#x3092;&#x53CD;&#x6620;&#x3088;&#x308A;&#x3082;&#x4ED6;&#x306E;&#x6606;&#x866B;&#x306E;&#x3088;&#x308A;&#x4EE3;&#x8868;&#x7684;&#x3067;&#x3059;&#x3002;&#x305F;&#x3068;&#x3048;&#x3070;&#x3001;&#x30B3;&#x30AF;&#x30CC;&#x30B9;&#x30C8;&#x30E2;&#x30C9;&#x30AD;&#x3044;&#x304F;&#x3064;&#x304B;&#x6210;&#x9577;&#x30BE;&#x30FC;&#x30F3;&#x306E;&#x77ED;&#x3044;&#x80DA;&#x306E;&#x958B;&#x767A;&#x8EF8;&#x306E;&#x4F38;&#x9577;&#x306E;&#x305F;&#x3081;&#x306E;&#x91CD;&#x8981;&#x3067;&#x8868;&#x660E;&#x3055;&#x308C;&#x3066;&#x3044;&#x308B;&#x30B7;&#x30E7;&#x30A6;&#x30B8;&#x30E7;&#x30A6;&#x30D0;&#x30A8;&#x3088;&#x308A;&#x7D30;&#x80DE;&#x30B3;&#x30DF;&#x30E5;&#x30CB;&#x30B1;&#x30FC;&#x30B7;&#x30E7;&#x30F3;&#x306B;&#x95A2;&#x308F;&#x308B;&#x3088;&#x308A;&#x7956;&#x5148;&#x907A;&#x4F1D;&#x5B50;&#x3092;&#x4FDD;&#x6301;&#x3057;&#x3066;&#x3044;&#x307E;&#x3059;&#x3002;T. &#x30B3;&#x30AF;&#x30CC;&#x30B9;&#x30C8;&#x30E2;&#x30C9;&#x30AD;&#x306E;&#x5168;&#x8EAB;&#x306E; RNA &#x5E72;&#x6E09;&#x304B;&#x3089;&#x7DDA;&#x866B;&#x306E;&#x7570;&#x306A;&#x308B;&#x95A2;&#x6570;&#x304C;&#x305D;&#x308C;&#x306B;&#x3082;&#x304B;&#x304B;&#x308F;&#x3089;&#x305A;&#x907A;&#x4F1D;&#x5B50;&#x306E;&#x6A5F;&#x80FD;&#x89E3;&#x660E;&#x3068;&#x9078;&#x629E;&#x7684;&#x6606;&#x866B;&#x5236;&#x5FA1;&#x30BF;&#x30FC;&#x30B2;&#x30C3;&#x30C8;&#x306E;&#x540C;&#x5B9A;&#x306E;&#x305F;&#x3081;&#x306E;&#x540C;&#x69D8;&#x306E;&#x30D1;&#x30EF;&#x30FC;&#x3092;&#x63D0;&#x4F9B;&#x3057;&#x307E;&#x3059;&#x3002;

&#x30E2;&#x30C7;&#x30EB; &#x30AB;&#x30D6;&#x30C8;&#x30E0;&#x30B7;&#x3068;&#x5BB3;&#x866B;&#x30B3;&#x30AF;&#x30CC;&#x30B9;&#x30C8;&#x30E2;&#x30C9;&#x30AD;&#x306E;&#x30B2;&#x30CE;&#x30E0;&#x3002;

Tribolium castaneum&#xB294; &#xAC00;&#xC7A5; &#xD48D;&#xBD80;&#xD55C; &#xC885; &#xC9C4; &#xD575; &#xC21C;&#xC11C;, &#xC77C;&#xBC18;&#xC801;&#xC778;&#xB41C; &#xACE4;&#xCDA9; &#xAC1C;&#xBC1C; &#xC5F0;&#xAD6C; &#xBC0F; &#xC800;&#xC7A5;&#xB41C; &#xB18D;&#xC0B0;&#xBB3C;&#xC758; &#xC911;&#xC694; &#xD574;&#xCDA9;&#xC5D0; &#xB300; &#xD55C; &#xAC15;&#xB825;&#xD55C; &#xBAA8;&#xB378; &#xC720;&#xAE30; &#xCCB4; &#xC704;&#xC6D0;. &#xC6B0;&#xB9AC; &#xC5EC;&#xAE30;&#xC758; &#xAC8C;&#xB188; &#xC2DC;&#xD000;&#xC2A4;&#xB97C; &#xC124;&#xBA85;&#xD569;&#xB2C8;&#xB2E4;. &#xC774; &#xC7A1; &#xC2DD; &#xBE44;&#xD2C0; odorant &#xBBF8;&#xAC01; &#xC218;&#xC6A9; &#xCCB4; &#xBFD0;&#xB9CC; &#xC544;&#xB2C8;&#xB77C; P450 &#xB300;&#xD615; &#xD655;&#xC7A5;&#xACFC; &#xB2E4;&#xB978; &#xD574;&#xB3C5; &#xD6A8;&#xC18C;&#xC5D0; &#xC758;&#xD574; &#xD45C;&#xC2DC; &#xB41C; &#xAC83; &#xCC98;&#xB7FC; &#xB2E4;&#xC591; &#xD55C; &#xD654;&#xD559;&#xC801; &#xD658;&#xACBD;&#xACFC; &#xC0C1;&#xD638; &#xC791;&#xC6A9;&#xD560; &#xC218; &#xC788;&#xAC8C;&#xB97C; &#xC9C4;&#xD654; &#xD558;&#xACE0;&#xC788;&#xB2E4;. Tribolium&#xC5D0;&#xC11C; &#xAC1C;&#xBC1C;&#xC740; &#xCD08;&#xD30C;&#xB9AC;, &#xC0AC;&#xC2E4; &#xC9C4; &#xCF58;&#xD150;&#xCE20; &#xBC0F; &#xAE30;&#xB2A5;&#xC5D0; &#xBC18;&#xC601; &#xBCF4;&#xB2E4; &#xB354; &#xB9CE;&#xC740; &#xB2E4;&#xB978; &#xACE4;&#xCDA9;&#xC744; &#xB300;&#xD45C; &#xD558;&#xB294;. &#xC608;&#xB97C; &#xB4E4;&#xC5B4;, Tribolium&#xB294; &#xC9E7;&#xC740; &#xC138;&#xADE0; &#xAC1C;&#xBC1C;&#xC5D0;&#xC11C; &#xCD95; &#xC5F0;&#xC2E0; &#xC728;&#xC5D0; &#xB300; &#xD55C; &#xC911;&#xC694; &#xD55C; &#xC131;&#xC7A5; &#xC601;&#xC5ED;&#xC5D0; &#xD45C;&#xC2DC; &#xB418; &#xACE0; &#xC77C;&#xBD80;&#xB294; &#xCD08;&#xD30C;&#xB9AC; &#xBCF4;&#xB2E4; &#xC140; &#xD1B5;&#xC2E0;&#xC5D0; &#xAD00;&#xB828; &#xB41C; &#xB354; &#xB9CE;&#xC740; &#xC870;&#xC0C1;&#xC758; &#xC720;&#xC804;&#xC790;&#xB97C; &#xC720;&#xC9C0; &#xD588;&#xB2E4;. T. castaneum&#xC5D0; &#xB300; &#xD55C; &#xC870;&#xC9C1;&#xC758; RNA &#xAC04;&#xC12D; Caenorhabditis elegans&#xC5D0; &#xADF8;&#xC5D0;&#xC11C; &#xB2E4;&#xB974;&#xAC8C; &#xC791;&#xB3D9; &#xD558;&#xC9C0;&#xB9CC; &#xADF8;&#xB7FC;&#xC5D0;&#xB3C4; &#xBD88;&#xAD6C; &#xD558; &#xACE0; &#xC720;&#xC804;&#xC790; &#xAE30;&#xB2A5;&#xC758; &#xD574;&#xBA85; &#xBC0F; &#xC120;&#xD0DD;&#xC801; &#xACE4;&#xCDA9; &#xC81C;&#xC5B4; &#xB300;&#xC0C1;&#xC758; &#xC2DD;&#xBCC4;&#xC5D0; &#xB300; &#xD55C; &#xBE44;&#xC2B7;&#xD55C; &#xD30C;&#xC6CC;&#xB97C; &#xC81C;&#xACF5; &#xD569;&#xB2C8;&#xB2E4;.

&#xBAA8;&#xB378; &#xBC8C;&#xB808; &#xBC0F; &#xD574;&#xCDA9; Tribolium castaneum&#xC758; &#xAC8C;&#xB188;.

Tribolium castaneum es miembro de la orden de eucariota m&aacute;s ricos en especies, un organismo poderoso modelo para el estudio de insectos generalizados del desarrollo y una plaga importante de productos agr&iacute;colas almacenados. Describimos aqu&iacute; su secuencia de genoma. Este escarabajo omn&iacute;voro ha evolucionado la capacidad de interactuar con un entorno diverso de la qu&iacute;mico, como se muestra por grandes expansiones en olfativa y gustativos receptores, as&iacute; como P450 y otras enzimas de desintoxicaci&oacute;n. Desarrollo en Tribolium es m&aacute;s representativo de otros insectos que es Drosophila, un hecho que se refleja en gen contenido y funci&oacute;n. Por ejemplo, Tribolium ha conservado m&aacute;s ancestrales genes implicados en la comunicaci&oacute;n de la c&eacute;lula de Drosophila, algunos se expresa en la zona de crecimiento crucial para el alargamiento axial en desarrollo corto-germen. ARN de interferencia sist&eacute;mica en T. castaneum funciona diferentemente de eso en Caenorhabditis elegans, pero sin embargo ofrece una potencia similar para la aclaraci&oacute;n de funciones de los genes y la identificaci&oacute;n de dianas para control de insectos selectiva.

El genoma de la modelo escarabajo y plagas Tribolium castaneum.

Comparison of whole genome sequences of representative animals enables reconstruction of the ancestral bilaterian genome: the starting point from which most extant animal lineages evolved. The Hox gene cluster patterns the anterior-posterior axis of bilaterians. Here we show that this cluster was embedded within a larger homeobox gene cluster, the Super-Hox cluster, in the ancestral bilaterian. This Super-Hox cluster contained at least eight genes alongside the core Hox genes ('EuHox' genes).

The urbilaterian Super-Hox cluster.

Cephalochordates, urochordates, and vertebrates evolved from a common ancestor over 520 million years ago. To improve our understanding of chordate evolution and the origin of vertebrates, we intensively searched for particular genes, gene families, and conserved noncoding elements in the sequenced genome of the cephalochordate Branchiostoma floridae, commonly called amphioxus or lancelets. Special attention was given to homeobox genes, opsin genes, genes involved in neural crest development, nuclear receptor genes, genes encoding components of the endocrine and immune systems, and conserved cis-regulatory enhancers. The amphioxus genome contains a basic set of chordate genes involved in development and cell signaling, including a fifteenth Hox gene. This set includes many genes that were co-opted in vertebrates for new roles in neural crest development and adaptive immunity. However, where amphioxus has a single gene, vertebrates often have two, three, or four paralogs derived from two whole-genome duplication events. In addition, several transcriptional enhancers are conserved between amphioxus and vertebrates--a very wide phylogenetic distance. In contrast, urochordate genomes have lost many genes, including a diversity of homeobox families and genes involved in steroid hormone function. The amphioxus genome also exhibits derived features, including duplications of opsins and genes proposed to function in innate immunity and endocrine systems. Our results indicate that the amphioxus genome is elemental to an understanding of the biology and evolution of nonchordate deuterostomes, invertebrate chordates, and vertebrates.

The amphioxus genome illuminates vertebrate origins and cephalochordate biology.

Lancelets ('amphioxus') are the modern survivors of an ancient chordate lineage, with a fossil record dating back to the Cambrian period. Here we describe the structure and gene content of the highly polymorphic approximately 520-megabase genome of the Florida lancelet Branchiostoma floridae, and analyse it in the context of chordate evolution. Whole-genome comparisons illuminate the murky relationships among the three chordate groups (tunicates, lancelets and vertebrates), and allow not only reconstruction of the gene complement of the last common chordate ancestor but also partial reconstruction of its genomic organization, as well as a description of two genome-wide duplications and subsequent reorganizations in the vertebrate lineage. These genome-scale events shaped the vertebrate genome and provided additional genetic variation for exploitation during vertebrate evolution.

The amphioxus genome and the evolution of the chordate karyotype.

The homeobox genes comprise a large and diverse gene superfamily, many of which encode transcription factors with pivotal roles in the embryonic development of animals. We searched the assembled draft genome sequence of an amphioxus, Branchiostoma floridae, for genes possessing homeobox sequences. Phylogenetic analysis was used to divide these into gene families and classes. The 133 amphioxus homeobox genes comprise 60 ANTP class genes, 29 PRD genes (excluding Pon and Pax1/9), nine TALE genes, seven POU genes, seven LIM genes, five ZF genes, four CUT genes, four HNF genes, three SINE genes, one CERS gene, one PROS gene, and three unclassified genes. Ten of the 11 homeobox gene classes are less diverse in amphioxus than humans, as a result of gene duplication on the vertebrate lineage. Amphioxus possesses at least one member for all of the 96 homeobox gene families inferred to be present in the common ancestor of chordates, including representatives of the Msxlx, Bari, Abox, Nk7, Ro, and Repo gene families that have been lost from tunicates and vertebrates. We find duplication of several homeobox genes in the cephalochordate lineage (Mnx, Evx, Emx, Vent, Nk1, Nedx, Uncx, Lhx2/9, Hmbox, Pou3, and Irx) and several divergent genes that probably originated by extensive sequence divergence (Hx, Ankx, Lcx, Acut, Atale, Azfh, Ahbx, Muxa, Muxb, Aprd1-6, and Ahnf). The analysis reveals not only the repertoire of amphioxus homeobox genes but also gives insight into the evolution of chordate homeobox genes.

Comprehensive survey and classification of homeobox genes in the genome of amphioxus, Branchiostoma floridae.

The homeobox genes are a large and diverse group of genes, many of which play important roles in the embryonic development of animals. Comparative study of homeobox genes, both within and between species, requires an evolutionary-based classification. HomeoDB was designed and implemented as a manually curated database to collect and present homeobox genes in an evolutionarily structured way, allowing genes, gene families and gene classes to be compared between species more readily than was possible previously. In its first release, HomeoDB includes all homeobox genes from human, amphioxus (Branchiostoma floridae) and fruitfly (Drosophila melanogaster); additional species can be added. HomeoDB is freely accessible at (http://homeodb.cbi.pku.edu.cn).

HomeoDB: a database of homeobox gene diversity.

Homeobox genes encode a large superclass of transcription factors with widespread roles in animal development. Within chordates there are over 100 homeobox genes in the invertebrate cephalochordate amphioxus and over 200 in humans. Set against this general trend of increasing gene number in vertebrate evolution, some ancient homeobox genes that were present in the last common ancestor of chordates have been lost from vertebrates. Here, we describe the embryonic expression of four amphioxus descendants of these genes--AmphiNedxa, AmphiNedxb, AmphiMsxlx and AmphiNKx7. All four genes are expressed with a striking asymmetry about the left-right axis in the pharyngeal region of neurula embryos, mirroring the pronounced asymmetry of amphioxus embryogenesis. AmphiMsxlx and AmphiNKx7 are also transiently expressed in an anterior neural tube region destined to become the cerebral vesicle. These findings suggest significant rewiring of developmental gene regulatory networks occurred during chordate evolution, coincident with homeobox gene loss. We propose that loss of otherwise widely conserved genes is possible when these genes function in a confined role in development that is subsequently lost or significantly modified during evolution. In the case of these homeobox genes, we propose that this has occurred in relation to the evolution of the chordate pharynx and brain.

Ancient homeobox gene loss and the evolution of chordate brain and pharynx development: deductions from amphioxus gene expression.

The cerebellum sits at the rostral end of the vertebrate hindbrain and is responsible for sensory and motor integration. Owing to its relatively simple architecture, it is one of the most powerful model systems for studying brain evolution and development. Over the last decade, the combination of molecular fate mapping techniques in the mouse and experimental studies, both in vitro and in vivo, in mouse and chick have significantly advanced our understanding of cerebellar neurogenesis in space and time. In amniotes, the most numerous cell type in the cerebellum, and indeed the brain, is the cerebellar granule neurons, and these are born from a transient secondary proliferative zone, the external granule layer (EGL), where proliferation is driven by sonic hedgehog signalling and causes cerebellar foliation. Recent studies in zebrafish and sharks have shown that while the molecular mechanisms of neurogenesis appear conserved across vertebrates, the EGL as a site of shh-driven transit amplification is not, and is therefore implicated as a key amniote innovation that facilitated the evolution of the elaborate foliated cerebella found in birds and mammals. Ellucidating the molecular mechanisms underlying the origin of the EGL in evolution could have significant impacts on our understanding of the molecular details of cerebellar development.

Can clues from evolution unlock the molecular development of the cerebellum?

The roof plate is a signalling centre positioned at the dorsal midline of the central nervous system and generates dorsalising morphogenic signals along the length of the neuraxis. Within cranial ventricles, the roof plate gives rise to choroid plexus, which regulates the internal environment of the developing and adult brain and spinal cord via the secretion of cerebrospinal fluid. Using the fourth ventricle as our model, we show that the organiser properties of the roof plate are determined by its boundaries with the adjacent neuroepithelium. Through a combination of in ovo transplantation, co-culture and electroporation techniques in chick embryos between embryonic days 3 and 6, we demonstrate that organiser properties are maintained by interactions between the non-neural roof plate and the neural rhombic lip. At the molecular level, this interaction is mediated by Delta-Notch signalling and upregulation of the chick homologue of Hes1: chairy2. Gain- and loss-of-function approaches reveal that cdelta1 is both necessary and sufficient for organiser function. Our results also demonstrate that while chairy2 is specifically required for the maintenance of the organiser, its ectopic expression is not sufficient to recapitulate organiser properties. Expression of atonal1 in the rhombic lip adjacent at the roof plate boundary is acutely dependent on both boundary cell interactions and Delta-Notch signalling. Correspondingly, the roof plate boundary organiser also signals to the roof plate itself to specify the expression of early choroid plexus markers. Thus, the roof plate boundary organiser signals bi-directionally to acutely coordinate the development of adjacent neural and non-neural tissues.

The roof plate boundary is a bi-directional organiser of dorsal neural tube and choroid plexus development.

Old before their time: the ancient origins of the neural crest.

The cerebellum represents one of the most morphologically variable structures in the vertebrate brain. To shed light on its evolutionary history, we have examined the molecular anatomy and proliferation of the developing cerebellum of the North American paddlefish, Polyodon spathula. Absence of an external proliferative cerebellar layer and the restriction of Atonal1 expression to the rhombic lip and valvular primordium demonstrate that transit amplification in a cerebellar external germinal layer, a prominent feature of amniote cerebellum development, is absent in paddlefish. Furthermore, expression of Sonic hedgehog, which drives secondary proliferation in the mouse cerebellum, is absent from the paddlefish cerebellum. These data are consistent with what has been observed in zebrafish and suggest that the transit amplification seen in the amniote cerebellum was either lost very early in the ray-finned fish lineage or evolved in the lobe-finned fish lineage. We also suggest that the Atoh1-positive proliferative valvular primordium may represent a synapomorphy (shared derived character) of ray-finned fishes. The topology of valvular primordium development in paddlefish differs significantly from that of zebrafish and correlates with the adult cerebellar form. The distribution of proliferative granule cell precursors in different vertebrate taxa is thus the likely determining factor in cerebellar morphological diversity.

The evolution of the vertebrate cerebellum: absence of a proliferative external granule layer in a non-teleost ray-finned fish.

The cerebellum has evolved elaborate foliation in the amniote lineage as a consequence of extensive Atoh1-mediated transit amplification in an external germinal layer (EGL) comprising granule cell precursors. To explore the evolutionary origin of this layer, we have examined the molecular geography of cerebellar development throughout the life cycle of Xenopus laevis. At metamorphic stages Xenopus displays a superficial granule cell layer that is not proliferative and expresses both Atoh1 and NeuroD1, a marker of postmitotic cerebellar granule cells. Premature misexpression of NeuroD1 in chick partially recapitulates the amphibian condition by suppressing transit amplification. However, unlike in the amphibian, granule cells fail to enter the EGL. Furthermore, misexpression of NeuroD1 once the EGL is established both triggers radial migration and downregulates Atoh1. These results show that the evolution of transit amplification in the EGL required adaptation of NeuroD1, both in the timing of its expression and in its regulatory function, with respect to Atoh1.

Transit amplification in the amniote cerebellum evolved via a heterochronic shift in NeuroD1 expression.

Segmentation is a feature of the body plans of a number of diverse animal groupings, including the annelids, arthropods and chordates. However, it has been unclear whether or not these different manifestations of segmentation are independently derived or have a common origin. Central to this issue is whether or not there are common developmental mechanisms that establish segmentation and the evolutionary origins of these processes. A fruitful way to address this issue is to consider how segmentation in vertebrates is directed. During vertebrate development three different segmental systems are established: the somites, the rhombomeres and the pharyngeal arches. In each an iteration of parts along the long axis is established. However, it is clear that the formation of the somites, rhombomeres or pharyngeal arches have little in common, and as such there is no single segmentation process. These different segmental systems also have distinct evolutionary histories, thus highlighting the fact that segmentation can and does evolve independently at multiple points. We conclude that the term segmentation indicates nothing more than a morphological description and that it implies no mechanistic similarity. Thus it is probable that segmentation has arisen repeatedly during animal evolution.

What can vertebrates tell us about segmentation?

Faculty cuts: University managers misled by metrics.

The cerebellum is a pre-eminent model for the study of neurogenesis and circuit assembly. Increasing interest in the cerebellum as a participant in higher cognitive processes and as a locus for a range of disorders and diseases make this simple yet elusive structure an important model in a number of fields. In recent years, our understanding of some of the more familiar aspects of cerebellar growth, such as its territorial allocation and the origin of its various cell types, has undergone major recalibration. Furthermore, owing to its stereotyped circuitry across a range of species, insights from a variety of species have contributed to an increasingly rich picture of how this system develops. Here, we review these recent advances and explore three distinct aspects of cerebellar development - allocation of the cerebellar anlage, the significance of transit amplification and the generation of neuronal diversity - each defined by distinct regulatory mechanisms and each with special significance for health and disease.

Development of the cerebellum: simple steps to make a 'little brain'.

Ray-finned fishes (Actinopterygii) are the dominant vertebrate group today (+30 000 species, predominantly teleosts), with great morphological diversity, including their dentitions. How dental morphological variation evolved is best addressed by considering a range of taxa across actinopterygian phylogeny; here we examine the dentition of Polyodon spathula (American paddlefish), assigned to the basal group Acipenseriformes. Although teeth are present and functional in young individuals of Polyodon, they are completely absent in adults. Our current understanding of developmental genes operating in the dentition is primarily restricted to teleosts; we show that shh and bmp4, as highly conserved epithelial and mesenchymal genes for gnathostome tooth development, are similarly expressed at Polyodon tooth loci, thus extending this conserved developmental pattern within the Actinopterygii. These genes map spatio-temporal tooth initiation in Polyodon larvae and provide new data in both oral and pharyngeal tooth sites. Variation in cellular intensity of shh maps timing of tooth morphogenesis, revealing a second odontogenic wave as alternate sites within tooth rows, a dental pattern also present in more derived actinopterygians. Developmental timing for each tooth field in Polyodon follows a gradient, from rostral to caudal and ventral to dorsal, repeated during subsequent loss of teeth. The transitory Polyodon dentition is modified by cessation of tooth addition and loss. As such, Polyodon represents a basal actinopterygian model for the evolution of developmental novelty: initial conservation, followed by tooth loss, accommodating the adult trophic modification to filter-feeding.

Article	Year
The genome of the model beetle and pest Tribolium castaneum. Nature\| PubMed ID: 18362917	2008
The urbilaterian Super-Hox cluster. Trends in genetics : TIG\| PubMed ID: 18472178	2008
The amphioxus genome illuminates vertebrate origins and cephalochordate biology. Genome research\| PubMed ID: 18562680	2008
The amphioxus genome and the evolution of the chordate karyotype. Nature\| PubMed ID: 18563158	2008
Comprehensive survey and classification of homeobox genes in the genome of amphioxus, Branchiostoma floridae. Development genes and evolution\| PubMed ID: 18797923	2008
HomeoDB: a database of homeobox gene diversity. Evolution & development\| PubMed ID: 18803769	2008
Ancient homeobox gene loss and the evolution of chordate brain and pharynx development: deductions from amphioxus gene expression. Proceedings. Biological sciences / The Royal Society\| PubMed ID: 20554554	2010
Can clues from evolution unlock the molecular development of the cerebellum? Molecular neurobiology\| PubMed ID: 21174175	2011
The roof plate boundary is a bi-directional organiser of dorsal neural tube and choroid plexus development. Development (Cambridge, England)\| PubMed ID: 23052907	2012
Old before their time: the ancient origins of the neural crest. Pigment cell & melanoma research\| PubMed ID: 23490033	2013
The evolution of the vertebrate cerebellum: absence of a proliferative external granule layer in a non-teleost ray-finned fish. Evolution & development\| PubMed ID: 24617988	2014
Transit amplification in the amniote cerebellum evolved via a heterochronic shift in NeuroD1 expression. Development (Cambridge, England)\| PubMed ID: 25005474	2014
What can vertebrates tell us about segmentation? EvoDevo\| PubMed ID: 25009737	2014
Faculty cuts: University managers misled by metrics. Nature\| PubMed ID: 25079545	2014
Development of the cerebellum: simple steps to make a 'little brain'. Development (Cambridge, England)\| PubMed ID: 25336734	2014
Making teeth to order: conserved genes reveal an ancient molecular pattern in paddlefish (Actinopterygii). Proceedings. Biological sciences / The Royal Society\| PubMed ID: 25788604	2015

Thomas Butts

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