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

Statistical analysis of transcriptome data.

<p>(A) SOTA clustering of the different genes using Log2(TPM). T, TM-1; A, CSIL-35431; B, CSIL-31010; C, CSIL-31134; D, CSIL-35368. 15, 15 DPA; 20, 20 DPA; 25, 25 DPA. (B) Distribution of functions of genes in different clusters. Yellow square indicated group 3, green square indicated group 4 and blue square indicated group 5. X-axis indicated different enriched process and Y-axis indicated number of hit-found genes in these processes.</p

Transcriptomic Analysis of Fiber Strength in Upland Cotton Chromosome Introgression Lines Carrying Different <i>Gossypium barbadense</i> Chromosomal Segments

<div><p>Fiber strength is the key trait that determines fiber quality in cotton, and it is closely related to secondary cell wall synthesis. To understand the mechanism underlying fiber strength, we compared fiber transcriptomes from different <i>G. barbadense</i> chromosome introgression lines (CSILs) that had higher fiber strengths than their recipient, <i>G. hirsutum</i> acc. TM-1. A total of 18,288 differentially expressed genes (DEGs) were detected between CSIL-35431 and CSIL-31010, two CSILs with stronger fiber and TM-1 during secondary cell wall synthesis. Functional classification and enrichment analysis revealed that these DEGs were enriched for secondary cell wall biogenesis, glucuronoxylan biosynthesis, cellulose biosynthesis, sugar-mediated signaling pathways, and fatty acid biosynthesis. Pathway analysis showed that these DEGs participated in starch and sucrose metabolism (328 genes), glycolysis/gluconeogenesis (122 genes), phenylpropanoid biosynthesis (101 genes), and oxidative phosphorylation (87 genes), etc. Moreover, the expression of MYB- and NAC-type transcription factor genes were also dramatically different between the CSILs and TM-1. Being different to those of CSIL-31134, CSIL-35431 and CSIL-31010, there were many genes for fatty acid degradation and biosynthesis, and also for carbohydrate metabolism that were down-regulated in CSIL-35368. Metabolic pathway analysis in the CSILs showed that different pathways were changed, and some changes at the same developmental stage in some pathways. Our results extended our understanding that carbonhydrate metabolic pathway and secondary cell wall biosynthesis can affect the fiber strength and suggested more genes and/or pathways be related to complex fiber strength formation process.</p></div

Quantitative RT–PCR validation of tag-mapped genes in TM-1.

<p>These genes have been reported before, including 3 CesA genes (A,B,C) (homologous with AtCESA4, AtCESA7, AtCESA8, respectively), xyloglucan endotransglucosylase (D), beta -galactosidase (E), glycosyl hydrolase 9B7 (F), xylan alpha-glucuronosyltransferase 1, GUX1 (G), xylan alpha-glucuronosyltransferase 2, GUX2 (H).</p

Metabolism analysis of DEGs in CSILs during the secondary cell wall biosynthesis stage.

<p>(A) Motabolism overview in four CSILs at 20 DPA. (B) Secondary motabolism analysis in three CSILs at 15 DPA, 20 DPA and 25 DPA. 1, cell wall protein; 2, cell wall pectin esterases; 3, cell wall modification; 4, cell wall cellulose synthesis; 5, cell wall degradation/pectate lyases; 6, lipid metabolism/FA synthesis; 7, lipid degradation; 8, flavonoids; 9, phenylpropanoids/lignin biosynthesis. Blue square, down-regulated genes; Red square, up-regulated genes.</p

Statistical of DEGs between CSILs and TM-1 at 15, 20 and 25 DPA.

<p>(A) Up-regulated and down-regulated genes in different comparison. Red bar, up-regulated genes compared to TM-1; green bar, stand for down-regulated genes compared to TM-1, Blue square, total DEGs. CSILs included CSIL-35431, CSIL-3010, CSIL-31134, CSIL-35368 and TM-1. 15, 15DPA; 20, 20DPA; 25, 25DPA. (B) Common and special DEGs at 15 DPA, 20 DPA and 25 DPA.</p

Enrichment analysis of gene ontologies from 15 to 25 DPA.

<p>G1–G6 according to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0094642#pone-0094642-g003" target="_blank">Figure 3</a>.</p

Heat map analysis of the expression of DEGs between CSILs and TM-1.

<p>A, B and T indicated CSIL-35431, CSIL-31010 and TM-1, respectively. 15, 15DPA; 20, 20DPA; 25, 25DPA. Red color indicated up-regulated genes and green color indicated down-regulated genes. N = number of DEGs in different group.</p

Carbohydrate pathways that are differentially regulated during the secondary cell wall synthesis stage.

<p>(A) Carbohydrate pathways. Genes up-regulated in CSIL-315431 and CSIL-31010 were selected to do heat map. ABAB indicated DEGs in CSIL-35431 at 15 DPA, CSIL-35431 at 20DPA, CSIL-3010 at 15DPA and CSIL-31010 at 20DPA, from left to right. Every square stand for one gene and every line stand for the same gene. Genes with red color expressed higher in CSILs than TM-1 and gray color stand for no difference. β-D-Fru, β-D-Fructose; α-D-Glu-1p, α-D-Glucose-1-phosphate; β-D-Fru-6p, β-D-Fructose-6-phosphate. (B) Quantitative RT–PCR validation of four CesA genes in CSILs and TM-1, Gorai.004G057400.1, Gorai.009G009700.1 and Gorai.011G037900.1 homologous with <i>AtCESA4</i>, <i>AtCESA7</i> and <i>AtCESA8</i>, respectively.</p

Analysis of common and common upregulated DEGs among three stronger fiber CSILs.

<p>(A, B, C, D) Common and common upregulated DEGs among three stronger fiber CSILs at 15 and 20 DPA. Common_up, common regulated DEGs. (B) Functional enrichment analysis of these DEGs using mapman software (Summary statistic type, wlcoxon). Colors from blue to red indicated that functions were enriched more significantly with smaller p-values.</p