Mutation of OsCAX1a Results in Panicle Degeneration in Rice

Background: Rice is one of the most common cereal crops in China. Increasing the yield of rice has always been a primary purpose of rice breeding. However, panicle degeneration in rice, a complex characteristic regulated by many genes and commonly encountered in rice production, seriously reduces the yield. Findings: In this study, we obtained a new apical panicle degeneration mutant named ym48, which exhibits a serious degeneration rate and reduced grain yield in rice. After fine mapping, the OsCAX1a gene responsible for Ca2+ selection and transportation was identified. In the ym48 mutant of the OsCAX1a gene, a A to G substitution was noted at the 190th nucleotide, and the corresponding 64th amino acid was changed from threonine to alanine. Also, the tolerance from Ca2+ stress was damaged due to the mutation. Phylogenetics, protein sequence alignment and motif identification of CAX family members in Arabidopsis and rice indicated that this mutation site was highly conserved and might play an essential role in Ca2+ transportation. Moreover, the OsCAX1a expression pattern was analyzed in rice. qRT-PCR and GUS (β-glucuronidase) staining experiments showed that OsCAX1a was highly expressed in roots, stems and panicles and that its expression increased with panicle development. Conclusions: These results demonstrated that OsCAX1a played an essential role in the regulation of panicle development for the first time and mutation of OsCAX1a would generate the panicle degeneration in rice. This study provided a new view point to explore the mechanism of panicle development and degeneration in rice.

Financial Time Series: Market Analysis Techniques Based on Matrix Profiles †

The Matrix Profile (MP) algorithm has the potential to revolutionise many areas of data analysis. In this article, several applications to financial time series are examined. Several approaches for the identification of similar behaviour patterns (or motifs) are proposed, illustrated, and the results discussed. While the MP is primarily designed for single series analysis, it can also be applied to multi-variate financial series. It still permits the initial identification of time periods with indicatively similar behaviour across individual market sectors and indexes, together with the assessment of wider applications, such as general market behaviour in times of financial crisis. In short, the MP algorithm offers considerable potential for detailed analysis, not only in terms of motif identification in financial time series, but also in terms of exploring the nature of underlying events.

Information Transmission among Multiple Investors: A Micro Perspective Revealed by Motifs

We build the shareholderco-holding network(SCN)based on common shareholding data from 2007 to 2017.Considering the node attributes and the link weights, we reveal the basic structure and dynamic evolution of the SCN from two aspects: motif identification and motif evolution.Research on motifidentificationshows that although closed motifs have a low proportion, they are statistically significant.Further,research on the motif evolution shows that all motif structures have a higher tendency to disappear. The motifs containing financial investment company shareholders tend to disappear, while the motifs containing general corporate shareholders tend to remain unchanged during the evolution process.In short, we have developed the local motif structure of the SCN, which helps understand how information is transmitted among multiple investors.

Twins/Zwillinge: A Broader View. A Contribution to Stith Thompson’s Incomplete Motif System—A Case of the Continuation of Pseudoscientific Fallacies †

Explaining the rationale and main objectives for his motif system; Stith Thompson declared that it emulates what “the scientists have done with the worldwide phenomena of biology” (Thompson 1955, I, p. 10). In this respect; the underlying principles for motif identification and indexing are comparable to those devised by anthropologists at Yale for “categorizing” culture materials into 78 macro-units and 629 subdivisions thereof used to establish “The Human Relations Area Files” (HRAF). By comparison, 23 divisions (chapters) make up the spectrum of sociocultural materials covered in Thompson’s Motif-Index system. Thompson’s cardinal themes are divided into 1730 subdivisions permitting more specificity of identification (El-Shamy 1995, I, xiii). Historically; the disciplines of “anthropology” and of “folklore” targeted different categories of the human population; with “folklore” assigned to populations stratified into “social classes” (Dorson 1972, pp. 4–5: For details, see El-Shamy: “Folk Groups” (1997b, pp. 318–322, in: T.A Green, gen. ed. 1997c, p. 321); El-Shamy 1980, p. li; compare El-Shamy (1997a), p. 233 (“African hunter”). The limitations Thompson placed on the goals of his motif system (along with its tale-type companion) were triggered by the fact that “folklore” was; then; primarily interested in literature (prose and verse). The sociocultural milieu surrounding the creation of the literary forms occupied minor roles. Considering that a folktale is a “description of life and/or living” including all five universal culture institutions; the relevance of the contents of folktales are of primary significance for understanding the community in which they were born and maintained (El-Shamy 1995, I, p. xiii). Consequently; for the present writer; a folktale is considered a sixth (universal) culture institution. Also; because Thompson’s Motif-Index sought global coverage; many regions and national entities didn’t receive adequate attention: significant fields of human experience are missing or sketchily presented. This article offers two cases as examples of: (1) How editors of folklore publications ignore novel ideas incompatible with established trends; and (2) Samples of the spectrum of current psychosocial issues addressed in an expanded Thompson’s System (with more than 26,000 new motifs and 630 tale-types added).

Ion-Mobility Mass Spectrometry of Glycans and Glycopeptides Using Both Intact and Glycan Sequencing Approaches In Positive Ion Mode Facilitates Glycan Isomer and Glycan Motif Identification

High resolution glycan analysis has become an important part of biopharmaceutical API production and quality control. Liquid chromatography (LC) is now a well-established technique in this field but the resolution of similar isomeric glycan structures is still a challenge. Here we show that the addition of ion mobility spectroscopy (IMS) in a hyphenated LC-IMS-MS setting allows for the high resolution of N-glycan isomers during positive ion analysis. We have identified unique features in the IM chromatograms to help differentiate a range of isomeric N-glycans for both RFMS labelled glycans and glycopeptides.<br>

Ion-Mobility Mass Spectrometry of Glycans and Glycopeptides Using Both Intact and Glycan Sequencing Approaches In Positive Ion Mode Facilitates Glycan Isomer and Glycan Motif Identification

High resolution glycan analysis has become an important part of biopharmaceutical API production and quality control. Liquid chromatography (LC) is now a well-established technique in this field but the resolution of similar isomeric glycan structures is still a challenge. Here we show that the addition of ion mobility spectroscopy (IMS) in a hyphenated LC-IMS-MS setting allows for the high resolution of N-glycan isomers during positive ion analysis. We have identified unique features in the IM chromatograms to help differentiate a range of isomeric N-glycans for both RFMS labelled glycans and glycopeptides.<br>

eCAMI: simultaneous classification and motif identification for enzyme annotation

Motivation Carbohydrate-active enzymes (CAZymes) are extremely important to bioenergy, human gut microbiome, and plant pathogen researches and industries. Here we developed a new amino acid k-mer-based CAZyme classification, motif identification and genome annotation tool using a bipartite network algorithm. Using this tool, we classified 390 CAZyme families into thousands of subfamilies each with distinguishing k-mer peptides. These k-mers represented the characteristic motifs (in the form of a collection of conserved short peptides) of each subfamily, and thus were further used to annotate new genomes for CAZymes. This idea was also generalized to extract characteristic k-mer peptides for all the Swiss-Prot enzymes classified by the EC (enzyme commission) numbers and applied to enzyme EC prediction. Results This new tool was implemented as a Python package named eCAMI. Benchmark analysis of eCAMI against the state-of-the-art tools on CAZyme and enzyme EC datasets found that: (i) eCAMI has the best performance in terms of accuracy and memory use for CAZyme and enzyme EC classification and annotation; (ii) the k-mer-based tools (including PPR-Hotpep, CUPP and eCAMI) perform better than homology-based tools and deep-learning tools in enzyme EC prediction. Lastly, we confirmed that the k-mer-based tools have the unique ability to identify the characteristic k-mer peptides in the predicted enzymes. Availability and implementation https://github.com/yinlabniu/eCAMI and https://github.com/zhanglabNKU/eCAMI. Supplementary information Supplementary data are available at Bioinformatics online.