An Amino Acid Substitution Matrix for Protein Conformation Identification

Amino acid substitution matrices play an essential role in protein sequence alignment, a fundamental task in bioinformatics. Most widely used matrices, such as PAM matrices derived from homologous sequences and BLOSUM matrices derived from aligned segments of PROSITE, did not integrate conformation information in their construction. There are a few structure-based matrices, which are derived from limited data of structure alignment. Using databases PDB_SELECT and DSSP, we create a database of sequence-conformation blocks which explicitly represent sequence-structure relationship. Members in a block are identical in conformation and are highly similar in sequence. From this block database, we derive a conformation-specific amino acid substitution matrix CBSM60. The matrix shows an improved performance in conformational segment search and homolog detection.

Effect of oxygen substitution by halide ions on structure, thermal stability and upconversion fluorescence in Er3(+)/Yb3(+)-codoped germanium-bismuth glasses

For the first time. effect of halide ions (F-, Cl-, Br-, and I-) introduction on structure, thermal stability, and upconversion fluorescence in Er3+/Yb3+-codoped oxide-halide germanium-bismuth glasses has been systematically investigated. The results show that halide ions modified germanium-bismuth glasses have lower maximum phonon energy and phonon density, worse thermal stability. longer measured lifetimes of I-4(l1/2) level, and stronger upconversion emission than germanium-bismuth glass. All these results indicate that halide ions play an important role in the formation of glass network, and have an important influence on the upconversion luminescence. The possible upconversion mechanisms of Er3+ ion are also evaluated. © 2005 Elsevier Ltd. All rights reserved.

Effects of chloride substitution on the chemical and physical properties and the crystallization behavior in heavy metal fluoride glasses

Effect of the substitutions of chloride for fluoride on the chemical and physical properties and the crystallization behavior in heavy metal fluoride glasses has been investigated. The characteristic temperature of the glass does not changed obviously when the fluoride was taken place by chloride. Compared with samples of being free of ErF3, the doping samples are more inclined to be surface crystallization. Optical basicity in the glass system increases with increasing the negative charge provided by the chloride atoms and the absorption peak red shifted is observed in absorption spectra. XRD measurements show that not a single crystalline phase appears in the heated glass samples, which indicate the substitutions of chloride for fluoride with a variety of crystalline precipitation trends. (c) 2007 Elsevier B.V All rights reserved.

Mapping chromosomal homologies between humans and two langurs (Semnopithecus francoisi and S-Phayrei) by chromosome painting

Chromosomal homologies were established between human and two Chinese langurs (Semnopithecus francoisi, 2n=44, and S. phayrei, 2n=44) by chromosome painting with chromosome-specific DNA probes of all human chromosomes except the Y. Both langur species showed identical hybridization patterns in addition to similar G-banding patterns. In total, 23 human chromosome-specific probes detected 30 homologous chromosome segments in a haploid langur genome. Except for human chromosomes 1, 2, 6, 16 and 19 probes, which each gave signals on two non-homologous langur chromosomes respectively, all other probes each hybridized to a single chromosome. The results indicate a high degree of conservation of chromosomal synteny between human and these two Chinese langurs. The human chromosome 2 probe painted the entire euchromatic regions of langur chromosomes 14 and 19. Human chromosome 1 probe hybridized to three regions on langur autosomes, one region on langur chromosome 4 and two regions on langur chromosome 5. Human 19 probe hybridized on the same pattern to one region on chromosome 4 and to two regions on langur chromosome 5, where it alternated with the human chromosome 1 probe. Human 6 and 16 probes both hybridized to one region on each of the two langur autosomes 15 and 18. Only two langur chromosomes (12 and 21) were each labelled by probes specific for two whole human chromosomes (14 and 15 and 21 and 22 respectively). Comparison of the hybridization patterns of human painting probes on these two langurs with the data on other Old World primates suggests that reciprocal and Robertsonian translocations as will as inversions could have occurred since the divergance of human and the langurs from a common ancestor. This comparison also indicates that Asian colobines are karyotypically more closely related to each other that to African colobines.

Comparative molecular cytogenetic studies in the order Carnivora: mapping chromosomal rearrangements onto the phylogenetic tree

We have made a set of chromosome-specific painting probes for the American mink by degenerate oligonucleotide primed-PCR (DOP-PCR) amplification of flow-sorted chromosomes. The painting probes were used to delimit homologous chromosomal segments among human, red fox, dog, cat and eight species of the family Mustelidae, including the European mink, steppe and forest polecats, least weasel, mountain weasel, Japanese sable, striped polecat, and badger. Based on the results of chromosome painting and G-banding, comparative maps between these species have been established. The integrated map demonstrates a high level of karyotype conservation among mustelid species. Comparative analysis of the conserved chromosomal segments among mustelids and outgroup species revealed 18 putative ancestral autosomal segments that probably represent the ancestral chromosomes, or chromosome arms, in the karyotype of the most recent ancestor of the family Mustelidae. The proposed 2n = 38 ancestral Mustelidae karyotype appears to have been retained in some modern mustelids, e.g., Martes, Lutra, ktonyx, and Vormela. The derivation of the mustelid karyotypes from the putative ancestral state resulted from centric fusions, fissions, the addition of heterochromatic arms, and occasional pericentric inversions. Our results confirm many of the evolutionary conclusions suggested by other data and strengthen the topology of the carnivore phylogenetic tree through the inclusion of genome-wide chromosome rearrangements. Copyright (C) 2002 S. KargerAG, Basel.

Chromosomal mechanisms underlying the karyotype evolution of the oriental voles (Muridae, Eothenomys)

We have investigated the karyotype relationships of two oriental voles, i.e. the Yulong vole (Eothenomys proditor, 2n = 32) and the large oriental vole (Eothenomys miletus, 2n = 56) as well as the Clarke's vole (Microtus clarkei, 2n = 52), by a combined a

Chromosomal rearrangements underlying karyotype differences between Chinese pangolin (Manis pentadactyla) and Malayan pangolin (Manis javanica) revealed by chromosome painting

The Chinese pangolin (Manis pentadactyla), a representative species of the order Pholidota, has been enlisted in the mammalian whole-genome sequencing project mainly because of its phylogenetic importance. Previous studies showed that the diploid number o

Construction, characterization and chromosomal mapping of bacterial artificial chromosome (BAC) library of Yunnan snub-nosed monkey (Rhinopithecus bieti)

We constructed a high redundancy bacterial artificial chromosome library of a seriously endangered Old World Monkey, the Yunnan snub-nosed monkey (Rhinopithecus bieti) from China. This library contains a total of 136 320 BAC clones. The average insert size of BAC clones was estimated to be 148 kb. The percentage of small inserts (50-100 kb) is 2.74%, and only 2.67% non-recombinant clones were observed. Assuming a similar genome size with closely related primate species, the Yunnan snub-nosed monkey BAC library has at least six times the genome coverage. By end sequencing of randomly selected BAC clones, we generated 201 sequence tags for the library. A total of 139 end-sequenced BAC clones were mapped onto the chromosomes of Yunnan snub-nosed monkey by fluorescence in-situ hybridization, demonstrating a high degree of synteny conservation between humans and Yunnan snub-nosed monkeys. Blast search against human genome showed a good correlation between the number of hit clones and the size of the chromosomes, an indication of unbiased chromosomal distribution of the BAC library. This library and the mapped BAC clones will serve as a valuable resource in comparative genomics studies and large-scale genome sequencing of nonhuman primates. The DNA sequence data reported in this paper were deposited in GenBank and assigned the accession number CG891489-CG891703.