Xuying Nan

Analysis of similarity/dissimilarity of protein sequences

On the basis of a selected pair of physicochemical properties of amino acids, we introduce a dynamic 2D graphical representation of protein sequences. Then, we introduce and compare two numerical characterizations of protein graphs as descriptors to analyze the nine ND5 proteins. The approach is simple, convenient, and fast. Proteins 2008.

Similarity/dissimilarity studies of protein sequences based on a new 2D graphical representation

A (two‐dimensional) 2D graphical representation of protein sequences based on six physicochemical properties of amino acids is outlined. The numerical characterization of protein graphs is given as descriptors of protein sequences. It is not only useful for comparative study of proteins but also for encoding innate information about the structure of proteins. The coefficient of determination is proposed as a new similarity/dissimilarity measure. Finally, a simple example is taken to highlight the behavior of the new similarity/dissimilarity measure on protein sequences taken from the ND6 (NADH dehydrogenase subunit 6) proteins for eight different species. The results demonstrate the approach is convenient, fast, and efficient.

The graphical representation of protein sequences based on the physicochemical properties and its applications

Based on the chaos game representation, a 2D graphical representation of protein sequences was introduced in which the 20 amino acids are rearranged in a cyclic order according to their physicochemical properties. The Euclidean distances between the corresponding amino acids from the 2‐D graphical representations are computed to find matching (or conserved) fragments of amino acids between the two proteins. Again, the cumulative distance of the 2D‐graphical representations is defined to compare the similarity of protein. And, the examination of the similarity among sequences of the ND5 proteins of nine species shows the utility of our approach.

A class of 2D graphical representations of RNA secondary structures and the analysis of similarity based on them

Based on the concepts of cell and system of graphical representation, a class of 2D graphical representations of RNA secondary structures are given in terms of classifications of bases of nucleic acids. The representations can completely avoid loss of information associated with crossing and overlapping of the corresponding curve. As an application, we make quantitative comparisons for a set of RNA secondary structures at the 3′‐terminus of different viruses based on the graphical representations. The examination of similarities/dissimilarities illustrates the utility of the approach.

Analysis of similarity/dissimilarity of DNA sequences based on a class of 2D graphical representation

On the basis of a class of 2D graphical representations of DNA sequences, sensitivity analysis has been performed, showing the high‐capability of the proposed representations to take into account small modifications of the DNA sequences. And sensitivity analysis also indicates that the absolute differences of the leading eigenvalues of the L/L matrices associated with DNA increase with the increase of the number of the base mutations. Besides, we conclude that the similarity analysis method based on the correlation angles can better eliminate the effects of the lengths of DNA sequences if compared with the method using the Euclidean distances. As application, the examination of similarities/dissimilarities among the coding sequences of the first exon of β‐globin gene of different species has been performed by our method, and the reasonable results verify the validity of our method.

Comparative transcriptome analysis of the different tissues between the cultivated and wild tomato

Although domesticated tomato is cultivated by wild tomato, there are a lot of differences between cultivated tomato and wild tomato, such as shape, physiological function and life history. Many studies show that wild tomato has better salt resistance and drought resistance. In addition to, domesticated tomato’s fruit is bigger and has more nutritious than wild tomato. The different features are closely related to differentially expressed genes. We identified 126 up-regulated differentially expressed genes and 87 down-regulated differentially expressed genes in cultivated tomato and wild tomato by RNA-Seq. These differentially expressed genes may be associated with salt resistance, drought resistance and fruit nutrition. These differentially expressed genes also further highlight the large-scale reconstruction between wild and cultivated species. In this paper, we mainly study GO enrichment analysis and pathway analysis of the differentially expressed genes. After GO and pathway enrichment analysis, a set of significantly enriched GO annotations and pathways were identified for the differentially expressed genes. What’s more, we also identified long non-coding RNAs and mRNAs in the two species and analyzed its essential features. In addition to, we construct a co-expression network of long non-coding RNAs and mRNAs, and annotate mRNAs associated with long non-coding RNAs as target genes, and speculate the regulation function of long non-coding RNAs. In total, our results reveal the effects of artificial and natural selection on tomato’s transcript, providing scientific basis for tomato’s research in the future.

Photoinitiating characteristic of erythrosine B derivatives and its application on pigmented visible photo-curing ink of textile digital printing

Eight visible photoinitiators composed of a series of erythrosine B derivatives with different structures, combined with ethyl-4-dimethylaminobenzoate and diphenyliodonium hexafluorophosphate, were evaluated for their photoinitiating characteristic and the tensile properties of photo-curing films initiated by them, to acquire the relationship between structure and performance. The visible photoinitiator was the key component for the pigmented visible photo-curing ink of textile digital printing. So, based on the experimental results, the preferred photoinitiator was incorporated into three pigmented photo-curing inks (red, yellow and blue) to perform textile digital jet printing. After photo-curing under visible light irradiation, the printed fabric samples showed excellent dry–wet rubbing fastness, and possessed a consistent hue with the samples initiated by the photoinitiator containing camphorquinone.

A 3-D Graphical Method Applied to The Similarities of Protein Sequences

Based on the selected chemical and physical properties of amino acids, a dynamic 3-D graphical representation of protein sequences is outlined. We introduce the numerical characterization of protein graphs as descriptors to analyze and compare the nine ND5 proteins, and the results consist with the known fact of evolution. The graph of protein sequences have good visibility, the approach is simple, convenient, and fast.

Different photoinitiating ability and photobleaching efficiency of erythrosine B derivatives in radical/cationic photopolymerization

A series of erythrosine B derivatives with a linked coinitiator on different position, combined with iodonium salt and/or tertiary amine were used to initiate free radical/cationic photopolymerization. Their photoinitiating ability and photobleaching behaviors were investigated and compared with those of the systems containing separated counterparts. The polymerization results showed that compared to the systems containing separated counterparts, the systems containing derivatives with a linked coinitiator on carboxyl group exhibited higher photoinitiating ability in radical photopolymerization, but had poorer one in cationic polymerization. Simultaneously, in free radical/cationic polymerizations, these linked derivatives could be photobleached more efficiently than the separated one, due to fast intramolecular reaction, which was especially significant for the industrial application. Besides, it was found that the investigated systems were photobleached more efficiently in cationic photopolymerization than in radical one. These results will provide useful information for designing effective photoinitiators for different polymerization.

A sequence-segmented method applied to the similarity analysis of proteins

A 2-D graphical representation of protein sequences based on two classifications of amino acids is outlined. The method of dividing a long sequence into k segments (SSM) is introduced, so protein graph is divided into k segments, geometrical center of the points for all protein curve segment is given as descriptors of protein sequences. It is not only useful for comparative study of proteins, but also for encoding innate information about the structure of proteins. Finally, a simple example is taken to highlight the behavior of the new descriptor on protein sequences taken from the 12 baculoviruse proteins.