MEI Kodierung der frühesten Notation in linienlosen Neumen

Das Optical Neume Recognition Project (ONRP) hat die digitale Kodierung von musikalischen Notationszeichen aus dem Jahr um 1000 zum Ziel – ein ambitioniertes Vorhaben, das die Projektmitglieder veranlasste, verschiedenste methodische Ansätze zu evaluieren. Die Optical Music Recognition-Software soll eine linienlose Notation aus einem der ältesten erhaltenen Quellen mit Notationszeichen, dem Antiphonar Hartker aus der Benediktinerabtei St. Gallen (Schweiz), welches heute in zwei Bänden in der Stiftsbibliothek in St. Gallen aufbewahrt wird, erfassen. Aufgrund der handgeschriebenen, linienlosen Notation stellt dieser Gregorianische Gesang den Forscher vor viele Herausforderungen. Das Werk umfasst über 300 verschiedene Neumenzeichen und ihre Notation, die mit Hilfe der Music Encoding Initiative (MEI) erfasst und beschrieben werden sollen. Der folgende Artikel beschreibt den Prozess der Adaptierung, um die MEI auf die Notation von Neumen ohne Notenlinien anzuwenden. Beschrieben werden Eigenschaften der Neumennotation, um zu verdeutlichen, wo die Herausforderungen dieser Arbeit liegen sowie die Funktionsweise des Classifiers, einer Art digitalen Neumenwörterbuchs

Genome-Wide Transcriptome Profiling Revealed Cotton Fuzz Fiber Development Having a Similar Molecular Model as <i>Arabidopsis</i> Trichome

<div><p>The cotton fiber, as a single-celled trichome, is a biological model system for studying cell differentiation and elongation. However, the complexity of gene expression and regulation in the fiber complicates genetic research. In this study, we investigated the genome-wide transcriptome profiling in Texas Marker-1 (TM-1) and five naked seed or fuzzless mutants (three dominant and two recessive) during the fuzz initial development stage. More than three million clean tags were generated from each sample representing the expression data for 27,325 genes, which account for 72.8% of the annotated <i>Gossypium raimondii</i> primary transcript genes. Thousands of differentially expressed genes (DEGs) were identified between TM-1 and the mutants. Based on functional enrichment analysis, the DEGs downregulated in the mutants were enriched in protein synthesis-related genes and transcription factors, while DEGs upregulated in the mutants were enriched in DNA/chromatin structure-related genes and transcription factors. Pathway analysis showed that ATP synthesis, and sugar and lipid metabolism-related pathways play important roles in fuzz initial development. Also, we identified a large number of transcription factors such as MYB, bHLH, HB, WRKY, AP2/EREBP, bZIP and C2H2 zinc finger families that were differently expressed between TM-1 and the mutants, and were also related to trichome development in <i>Arabidopsis</i>.</p></div

Dynamic progression of common differentially expressed genes in the recessive mutants.

<p>(a) Unsupervised hierarchical clustering of 6,693 common differentially expressed genes in the recessive mutants. Common DEGs were clustered into six groups and the number of genes of each group was listed at right. Red region, genes upregulated in the mutants; green region, genes downregulated in the mutants. A, TM-1; C, XZ142FLM; F, n₂NSM; 1, +1 DPA; 2, +3 DPA; 3, +5 DPA. (b) Functional category distribution of common DEGs in the recessive mutants. (c) Functional category enrichment of common differentially expressed genes in the recessive mutants.</p

Dynamics of transcription factor expression profiles in various dominant mutants.

<p>(a) Unsupervised hierarchical clustering of 355 transcription factor genes included in the 4,358 common DEGs in the dominant mutants. Four groups were generated and the number of each group was in parentheses. Red region, genes upregulated in the mutants; green region, genes downregulated in the mutants. A, TM-1; B, SL1-7-1FLM; D, MD17FLM; E, N₁NSM; 1, +1 DPA; 2, +3 DPA; 3, +5 DPA. (b) Representative functions and genes showing expression gradients. (c) Distribution of transcription factor families among G1, G2, G3 and G4.</p

Model for the action of GL1-activating trichome development in <i>Arabidopsis thaliana</i> and fuzz development in <i>Gossypium hirsutum</i>.

<p>a: Model for the action of <i>GL1</i>-activating trichome development in <i>Arabidopsis thaliana.</i> b: Model for the action of <i>GL1</i>-activating fuzz development in <i>Gossypium hirsutum</i> A: TM-1, B: SL1-7-1FLM, C: XZ142FLM, D: MD17FLM, E: N₁NSM, F: n₂NSM, 1: +1 DPA, 2: +3 DPA, 3: +5 DPA. Light red/green bars indicate cotton fiber gene expression in the upper/lower group.</p

Dynamics of transcription factor accumulation profiles in various dominant/recessive mutants.

<p>(a) Unsupervised hierarchical clustering of 153 transcription factor genes included in the 1,932 common DEGs in the recessive mutants. Four groups were generated and the number of each group was in parentheses. Red region, genes upregulated in the mutants; green region, genes downregulated in the mutants. A, TM-1; B, SL1-7-1FLM; C, XZ142FLM; D, MD17FLM; E, N₁NSM; F, n₂NSM; 1, +1 DPA; 2, +3 DPA; 3, +5 DPA. (b) Representative functions and genes showing expression gradients. (c) Distribution of transcription factor families among G1, G2, G3 and G4.</p

Data_Sheet_3_Visible gland constantly traces virus-induced gene silencing in cotton.DOCX

A virus-induced gene silencing (VIGS) system was established to induce endogenous target gene silencing by post-transcriptional gene silencing (PTGS), which is a powerful tool for gene function analysis in plants. Compared with stable transgenic plant via Agrobacterium-mediated gene transformation, phenotypes after gene knockdown can be obtained rapidly, effectively, and high-throughput through VIGS system. This approach has been successfully applied to explore unknown gene functions involved in plant growth and development, physiological metabolism, and biotic and abiotic stresses in various plants. In this system, GhCLA1 was used as a general control, however, silencing of this gene leads to leaf albino, wilting, and plant death ultimately. As such, it cannot indicate the efficiency of target gene silencing throughout the whole plant growth period. To address this question, in this study, we developed a novel marker gene, Gossypium PIGMENT GLAND FORMATION GENE (GoPGF), as the control to trace the efficiency of gene silencing in the infected tissues. GoPGF has been proved a key gene in gland forming. Suppression of GoPGF does not affect the normal growth and development of cotton. The number of gland altered related to the expression level of GoPGF gene. So it is a good marker that be used to trace the whole growth stages of plant. Moreover, we further developed a method of friction inoculation to enhance and extend the efficiency of VIGS, which facilitates the analysis of gene function in both the vegetative stage and reproductive stage. This improved VIGS technology will be a powerful tool for the rapid functional identification of unknown genes in genomes.</p

Conserved miRNA families expression in cotton.

<p>FoRPM, reads per million. Fold, fold change of TM-1L-A/TM-1L-B.</p

Cotton fiber morphology in the wild-type line and the mutant lines.

<p>a: wild line: TM-1; b: recessive naked-seed mutant: n₂NSM; c: dominant naked-seed mutant: N₁NSM; d: fuzzless-lintless mutants: SL1-7-1FLM (with <i>N₁</i> gene), XZ142FLM (with <i>n₂</i> gene), MD17FLM (with <i>N₁</i> and <i>n₂</i>). Matured seed were separated from the opened bolls on the cotton plant. Ginned seeds (right) and matured seeds (left) showed on linted-fuzzy and linted-fuzzless panel.</p

Dynamic progression of common differentially expressed genes in the dominant/recessive mutants.

<p>(a) Hierarchical clustering of the 1,932 common DEGs in five mutants. Common DEGs were clustered into five groups and the number of genes of each group was listed at right. Red region, genes upregulated in the mutants; green region, genes downregulated in the mutants. A, TM-1; B, SL1-7-1FLM; C, XZ142FLM; D, MD17FLM; E, N₁NSM; F, n₂NSM; 1, +1 DPA; 2, +3 DPA; 3, +5 DPA. (b) Functional distribution of common DEGs in the dominant/recessive mutants. (c) Functional category enrichment of common DEGs in the dominant/recessive mutants.</p