Landscape of transcription in human cells.

Eukaryotic cells make many types of primary and processed RNAs that are found either in specific subcellular compartments or throughout the cells. A complete catalogue of these RNAs is not yet available and their characteristic subcellular localizations are also poorly understood. Because RNA represents the direct output of the genetic information encoded by genomes and a significant proportion of a cell's regulatory capabilities are focused on its synthesis, processing, transport, modification and translation, the generation of such a catalogue is crucial for understanding genome function. Here we report evidence that three-quarters of the human genome is capable of being transcribed, as well as observations about the range and levels of expression, localization, processing fates, regulatory regions and modifications of almost all currently annotated and thousands of previously unannotated RNAs. These observations, taken together, prompt a redefinition of the concept of a gene.

'sît ich die nôt an mir weiz'. Zur narrativen Konfiguration des lyrischen 'paradoxe amoureux' im "Mauritius von Craûn"

Der am ehesten um 1200 entstandene ,Mauritius von Craûn' gilt als Forschungsproblem. Als gemeinsamen Nenner der kontroversen Zugänge zum Text konstatiert der Aufsatz das Bemühen um eine Verbindung der rätselhaften Erzählung mit einem durch die historische Distanz verlorenen oder verwischten Sinnzusammenhang über einen textexternen missing link. Demgegenüber wird ein themen- und handlungsanalytischer Zugriff vorgeschlagen: Thema der Erzählung ist die im 12. Jahrhundert vorrangig in der Lyrik entwickelte strukturelle Figur der Hohen Minne, die ihre Ästhetik aus einem Paradox gewinnt: Die Möglichkeitsbedingung dieser in beständigem Werben bestehenden Liebe, die niemals erfüllt werden darf, ist ihre Unmöglichkeit. Seine ideelle Füllung erhält das Modell durch eine darin vernetzte Ordnung höfischer Werte wie stæte, triuwe, milte oder mâze. Diese Werte, so die These, ,,erzählt" die Handlung des ,Mauritius': Hier wird nicht nur der Versuch unternommen, lyrische Struktur in narrative Struktur zu verwandeln, sondern auch der, eine ins lyrische Modell eingebettete Ordnung ethischen Wissens zu narrativieren. Einzelne Figurenhandlungen erscheinen aus dieser Perspektive weniger als Bestandteile eines inhaltlichen Entwurfs mit dem Anspruch übergreifender Stimmmigkeit und dem Fluchtpunkt eines Deutungsangebots, sondern als Ausdruck verschieden graduierter Negierungen oder Positivierungen eines bestimmtes Wertes. Hierfür sprechen auch die konstanten Über- oder Unterzeichnungen der Figurenhandlungen, die als markantestes Merkmal der narrativen Faktur des Textes beschrieben werden. Die Mikroanalyse einer einzelnen Szene zeigt ferner, wie die Dichotomie von Statik und Dynamik, die schon dem lyrischen Entwurf der Hohen Minne eingeschrieben ist und die durch die Narrativierung des lyrischen Konzepts im ,Mauritius' zunehmend virulent wird, in Sequenzen aufeinanderfolgender Doppelungen von Bewegung und Zustand auserzählt wird. Insgesamt lässt sich der ,Mauritius' als Erprobung von Verfahren verstehen, eine idealisierte höfische Welt in Analogie zum lyrischen Modus auch im narrativen Modus zu literarisieren: als ein Stück Erzählkasuistik.

Rahmenmodell vs. Geschäftsmodelle. Werkstattbericht zur Governance und zur Profilierung von aFuE an den schweizerischen Fachhochschulen

Die in den 1990er Jahren geschaffenen Fachhochschulen der Schweiz sind verpflichtet, in allen angebotenen Fachbereichen "anwendungsorientierte Forschung und Entwicklung" (aFuE) zu betreiben. Sowohl die Fachhochschulen wie auch die Fachbereiche sind allerdings sehr heterogen. Dieser Werkstattbericht zeigt auf, wie die Fachhochschulen das gesetzlich für alle gültige Rahmenmodell in zwei typologisch unterschiedlichen Geschäftsmodellen umsetzen: In einem am ökonomischen Markt ausgerichteten Modell A und in einem am Wissenschaftssystem und an ,,gesellschaftlichen Problemfeldern" ausgerichteten Modell B. Die beiden Typen stehen in einem Spannungsverhältnis zueinander, sind aber zugleich auch mit ähnlichen Problemen konfrontiert.

EGASP: the human ENCODE Genome Annotation Assessment Project.

BACKGROUND: We present the results of EGASP, a community experiment to assess the state-of-the-art in genome annotation within the ENCODE regions, which span 1% of the human genome sequence. The experiment had two major goals: the assessment of the accuracy of computational methods to predict protein coding genes; and the overall assessment of the completeness of the current human genome annotations as represented in the ENCODE regions. For the computational prediction assessment, eighteen groups contributed gene predictions. We evaluated these submissions against each other based on a 'reference set' of annotations generated as part of the GENCODE project. These annotations were not available to the prediction groups prior to the submission deadline, so that their predictions were blind and an external advisory committee could perform a fair assessment. RESULTS: The best methods had at least one gene transcript correctly predicted for close to 70% of the annotated genes. Nevertheless, the multiple transcript accuracy, taking into account alternative splicing, reached only approximately 40% to 50% accuracy. At the coding nucleotide level, the best programs reached an accuracy of 90% in both sensitivity and specificity. Programs relying on mRNA and protein sequences were the most accurate in reproducing the manually curated annotations. Experimental validation shows that only a very small percentage (3.2%) of the selected 221 computationally predicted exons outside of the existing annotation could be verified. CONCLUSION: This is the first such experiment in human DNA, and we have followed the standards established in a similar experiment, GASP1, in Drosophila melanogaster. We believe the results presented here contribute to the value of ongoing large-scale annotation projects and should guide further experimental methods when being scaled up to the entire human genome sequence.

Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions.

This report presents systematic empirical annotation of transcript products from 399 annotated protein-coding loci across the 1% of the human genome targeted by the Encyclopedia of DNA elements (ENCODE) pilot project using a combination of 5' rapid amplification of cDNA ends (RACE) and high-density resolution tiling arrays. We identified previously unannotated and often tissue- or cell-line-specific transcribed fragments (RACEfrags), both 5' distal to the annotated 5' terminus and internal to the annotated gene bounds for the vast majority (81.5%) of the tested genes. Half of the distal RACEfrags span large segments of genomic sequences away from the main portion of the coding transcript and often overlap with the upstream-annotated gene(s). Notably, at least 20% of the resultant novel transcripts have changes in their open reading frames (ORFs), most of them fusing ORFs of adjacent transcripts. A significant fraction of distal RACEfrags show expression levels comparable to those of known exons of the same locus, suggesting that they are not part of very minority splice forms. These results have significant implications concerning (1) our current understanding of the architecture of protein-coding genes; (2) our views on locations of regulatory regions in the genome; and (3) the interpretation of sequence polymorphisms mapping to regions hitherto considered to be "noncoding," ultimately relating to the identification of disease-related sequence alterations.

INTERVALO HÍDRICO ÓTIMO EM SOLO CONSTRUÍDO APÓS MINERAÇÃO DE CARVÃO EM DIFERENTES LIMITES CRÍTICOS DE RESISTÊNCIA À PENETRAÇÃO E UMIDADE

Na quantificação do intervalo hídrico ótimo (IHO), são utilizados diferentes limites críticos de resistência à penetração (RP) e umidade na capacidade de campo (θCC). Para solos agrícolas, esses valores estão sendo documentados na literatura. Entretanto, para solos construídos após mineração de carvão, constata-se grande lacuna de informações. O objetivo deste trabalho foi quantificar a faixa de variação do intervalo hídrico ótimo de um solo construído sob diferentes plantas de cobertura na área de mineração de carvão de Candiota, sul do Brasil, considerando diferentes limites críticos de umidade do solo na capacidade de campo e de resistência à penetração. Foram avaliadas no experimento, em blocos casualizados com quatro repetições, as seguintes plantas de cobertura: Hemártria (Hemarthria altissima (Poir.) Stapf & C. E. Hubbard), tratamento 1 (T1); Pensacola (Paspalum notatum Flüggé), tratamento 2 (T2); Grama Tifton (Cynodon dactilon (L.) Pers.), tratamento 3 (T3); Controle (Urochloa brizantha (Hochst.) Stapf), tratamento 4 (T4); e sem plantas de cobertura, tratamento 5 (T5). Para determinar o IHO, foram utilizados diferentes valores críticos de θCC referentes às tensões de 0,006; 0,01; e 0,033 MPa e RP de 1,5; 2,0; 2,5; e 3,0 MPa, mantendo-se sempre constante a umidade do solo no ponto de murcha permanente (θPMP) como sendo igual ao valor retido na tensão de 1,5 MPa e a umidade do solo em que a porosidade de aeração (PA) é de 10 %. A faixa de variação do IHO foi maior no solo construído cultivado com Urochloa brizantha; e a menor com Pensacola, independentemente dos limites críticos de θCC e de RP. Os limites críticos de θCC e de RP utilizados na definição do IHO originaram diferentes valores de densidade critica (Dsc) para o solo construído sob diferentes plantas de cobertura. Os menores e maiores valores de Dsc foram obtidos quando utilizados como limites críticos na definição do IHO, o θCC = 0,033 MPa e a RP = 3 MPa. O solo construído cultivado com Urochloa brizantha e Hemártria apresentou valor de Ds muito próximo ao de Dsc.

EGASP: the human ENCODE Genome Annotation Assessment Project

Background: Non-long terminal repeat (non-LTR) retrotransposons have contributed to shaping the structure and function of genomes. In silico and experimental approaches have been used to identify the non-LTR elements of the urochordate Ciona intestinalis. Knowledge of the types and abundance of non-LTR elements in urochordates is a key step in understanding their contribution to the structure and function of vertebrate genomes. Results: Consensus elements phylogenetically related to the I, LINE1, LINE2, LOA and R2 elements of the 14 eukaryotic non-LTR clades are described from C. intestinalis. The ascidian elements showed conservation of both the reverse transcriptase coding sequence and the overall structural organization seen in each clade. The apurinic/apyrimidinic endonuclease and nucleic-acid-binding domains encoded upstream of the reverse transcriptase, and the RNase H and the restriction enzyme-like endonuclease motifs encoded downstream of the reverse transcriptase were identified in the corresponding Ciona families. Conclusions: The genome of C. intestinalis harbors representatives of at least five clades of non-LTR retrotransposons. The copy number per haploid genome of each element is low, less than 100, far below the values reported for vertebrate counterparts but within the range for protostomes. Genomic and sequence analysis shows that the ascidian non-LTR elements are unmethylated and flanked by genomic segments with a gene density lower than average for the genome. The analysis provides valuable data for understanding the evolution of early chordate genomes and enlarges the view on the distribution of the non-LTR retrotransposons in eukaryotes.

Naître et grandir au sein de la triade : le développement de l'alliance familiale

INTRODUCTION : L'alliance familiale : une jonction entre les approches développementale, familiale et systémique / Nicolas Pavez, France Frascarolo-Moutinot et Hervé Tissot - LA TRIADE PARENTS-BEBE : THEORIE ET EVALUATION DES INTERACTIONS : Le modèle de l'alliance familiale et le Jeu Trilogique de Lausanne (LTP) / Nicolas Favez - Observation des interactions triadiques en périnatalité : le Jeu du Change / Jérôme Rime et Werner Stadlmayr - Observation des interactions dans les familles avec plusieurs enfants : le Jeu du Pique-Nique / France Frascarolo-Moutinot et Nicolas Favez - L'observation du coparentage dans les familles biparentales : influence du contexte et de l'âge de l'enfant / Regina Kuersten-Hogan et James P. McHale - LE DEVELOPPEMENT NORMATIF DE LA GROSSESSE A L'ECOLE : La capacité triangulaire du bébé : une illustration à l'aide de deux cas contrastés / Elisabeth Fivaz-Depeursinge et Nicolas Favez - L'alliance coparentale prénatale comme prédicteur des perceptions du coparentage au post-partum / Sarah J. Schappe-Sullivan, Claire M. Kamp Dush et Daniel J. Bower - L'évolution de l'alliance familiale et son impact sur l'enfant à l'âge de 5 ans : une étude longitudinale en Suisse / Nicolas Favez, France Frascarolo-Moutinot et Chloé Lavanchy Scaiola - L'évolution de l'alliance familiale et son impact sur l'enfant à l'âge de 4 ans : une étude longitudinale en Italie / Alessandra Simonelli, Mara Bighin et Francesca De Palo - LA THÉRAPIE AVEC LES TRIADES : Alliance familiale dans les troubles fonctionnels et du comportement du nourrisson : évaluation avant et après une intervention thérapeutique. Une étude exploratoire / Marie-Joëlle Hervé... et al. - Le Jeu Trilogique de Lausanne (LTP) en clinique : application dans le contexte d'interventions de soutien à la relation parents-enfants / Silvia Mazzoni et Anna Lubrano Lavadera - Les comportements relationnels de l'enfant comme porte d'entrée pour intervenir sur le système familial / Chloé Lavanchy Scaiola et Kaija Puura - Le Reflective Family Play : un traitement de la famille entière centré sur l'attachement et le système familial / Diane Philipp et Christie Hayos - APPLICATIONS SPECIFIQUES : Le coparentage comme construit universel caractérisant diverses formes familiales : avancées et perspectives / James McHale et Rahael Kurrien - Les alliances coparentales dans les familles lesboparentales / Salvatore D'Amore, Alessandra Simonelli et Marina Miscioscia - Alliance familiale entre père, mère et leur bébé conçu par fécondation in vitro / Joëlle Darwiche... et al. - CONCLUSION : Le bébé dans la triade précoce / Nicolas Pavez, France Frascarolo-Moutinot et Hervé Tissot