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.

Threat and management strategies of potentially invasive insects in China

The Global Invasive Species Database, GISD, comprises 27 species of the most significant invasive alien insects in the world (through November, 2005), 6 of which are originally native to China, 11 are established in China, and 10 have a potential invasion

The reproductive strategies of an endemic Tibetan fish, Gymnocypris selincuoensis

The reproductive traits of Gymnocypris selincuoensis from Selincuo Lake and its tributaries were investigated in 1997 and 1998. The youngest mature male was age 7 with a standard length (SL) of 172.0 mm, and the youngest mature female was age 8 with a SL of 194.0 mm. The L(50)s Of SL and age at first maturity were respectively 250.32 mm and age 9 for males and 224.71 mm and age 8 for females. The gonadosomatic index (GSI) significantly changed with seasons for mature individuals but not for immature individuals. GSIs of mature females at stages IV and V of ovary development increased with SL and reached a maximum value at the SL range from 370 mm to 390 mm; the GSIs of mature males were negatively correlated with SL. The breeding season lasted from early April to early August. Egg size did not significantly change with SL but increased with the delay of spawning. The individual absolute fecundity varied from 1,341 to 28,002 eggs (mean 12,607+/-7,349), and the individual relative fecundity varied from 6.4 to 42.0 eggs.g(-1) (mean 25.5+/-9.7). The individual fecundity increased with total body weight; it also increased with SL for those of SL less than 370 mm. There was a rest of spawning for mature individuals.

Ultraviolet-B exposure induces photo-oxidative damage and subsequent repair strategies in a desert cyanobacterium Microcoleus vaginatus Gom.

Biological soil crusts are important in reversing desertification. Ultraviolet radiation, however, may be detrimental for the development of soil crusts. The cyanobacterium Microcoleus vaginatus can be a dominant species occurring in desert soil crusts all over the world. To investigate the physico-chemical consequences of ultraviolet-B radiation on M. vaginatus, eight parameters including the contents of chlorophyll a, reactive oxygen species, malondialdehyde and proline, as well as the activities of photosynthesis, superoxide dismutase (EC 1.15.1.1), peroxiclase (EC 1.11.1.7) and catalase (EC 1.11.1.6) were determined. As shown by the results of determinations, ultraviolet-B radiation caused decreases both in contents of chlorophyll a and in ratios of variable fluorescence over maximum fluorescence that indicate the growth and photosynthesis of M. vaginatus, besides, increases both in levels of reactive oxygen species and in contents of malondialdehyde and proline, while intensified activities of superoxide dismutase, peroxiclase and catalase reflecting the abilities of enzymatic preventive substances to oxidative stress of the treated cells. Therefore, ultraviolet-B radiation affects the growth of M. vaginatus and leads to oxidative stress in cells. Under ultraviolet-B radiation, the treated cells can improve their antioxidant abilities to alleviate oxidative injury. The change trends of reactive oxygen species, superoxide dismutase, peroxiclase and catalase are synchronous. These results suggest that a balance between the antioxidant system and the reactive oxygen species content may be one part of a complex stress response pathway in which multiple environmental factors including ultraviolet-B radiation affect the Survival of M. vaginatus. (C) 2009 Elsevier Masson SAS. All rights reserved.

Progress in the evaluation of transgenic fish for possible ecological risk and its containment strategies

Genetically improved transgenic fish possess many beneficial economic traits; however, the commercial aquaculture of transgenic fish has not been performed till date. One of the major reasons for this is the possible ecological risk associated with the escape or release of the transgenic fish. Using a growth hormone transgenic fish with rapid growth characteristics as a subject, this paper analyzes the following: the essence of the potential ecological risks posed by transgenic fish; ecological risk in the current situation due to transgenic fish via one-factor phenotypic and fitness analysis, and mathematical model deduction. Then, it expounds new ideas and the latest findings using an artificially simulated ecosystem for the evaluation of the ecological risks posed by transgenic fish. Further, the study comments on the strategies and principles of controlling these ecological risks by using a triplold approach. Based on these results, we propose that ecological risk evaluation and prevention strategies are indispensable important components and should be accompanied with breeding research in order to provide enlightments for transgenic fish breeding, evaluation of the ecological risks posed by transgenic fish, and development of containment strategies against the risks.

The reproductive strategies of an endemic Tibetan fish, Gymnocypris selincuoensis

The reproductive traits of Gymnocypris selincuoensis from Selincuo Lake and its tributaries were investigated in 1997 and 1998. The youngest mature male was age 7 with a standard length (SL) of 172.0 mm, and the youngest mature female was age 8 with a SL of 194.0 mm. The L(50)s Of SL and age at first maturity were respectively 250.32 mm and age 9 for males and 224.71 mm and age 8 for females. The gonadosomatic index (GSI) significantly changed with seasons for mature individuals but not for immature individuals. GSIs of mature females at stages IV and V of ovary development increased with SL and reached a maximum value at the SL range from 370 mm to 390 mm; the GSIs of mature males were negatively correlated with SL. The breeding season lasted from early April to early August. Egg size did not significantly change with SL but increased with the delay of spawning. The individual absolute fecundity varied from 1,341 to 28,002 eggs (mean 12,607+/-7,349), and the individual relative fecundity varied from 6.4 to 42.0 eggs.g(-1) (mean 25.5+/-9.7). The individual fecundity increased with total body weight; it also increased with SL for those of SL less than 370 mm. There was a rest of spawning for mature individuals.

Conservation strategies for endemic fish species threatened by the Three Gorges Dam

The largest damming project to date, the Three Gorges Dam has been built along the Yangtze River (China), the most species-rich river in the Palearctic region. Among 162 species of fish inhabiting the main channel of the upper Yangtze, 44 are endemic and are therefore under serious threat of global extinction from the dam. Accordingly, it is urgently necessary to develop strategies to minimize the impacts of the drastic environmental changes associated with the dam. We sought to identify potential reserves for the endemic species among the 17 tributaries in the upper Yangtze, based on presence/absence data for the 44 endemic species. Potential reserves for the endemic species were identified by characterizing the distribution patterns of endemic species with an adaptive learning algorithm called a "self-organizing map" (SOM). Using this method, we also predicted occurrence probabilities of species in potential reserves based on the distribution patterns of communities. Considering both SOM model results and actual knowledge of the biology of the considered species, our results suggested that 24 species may survive in the tributaries, 14 have an uncertain future, and 6 have a high probability of becoming extinct after dam filling.

Exciton localization due to isoelectronic substitution in ZnSTe

We have systematically investigated the optical properties of isoelectronic centers (IECs) of ZnSTe in the whole composition range from ZnS to ZnTe. In the S-rich ZnSTe photoluminescence is dominated by Te-bound excitons, while in Te-rich side, S-related bound exciton emission dominates the radiative recombination. Localization nature of IEC bound exciton emissions in both S-rich and Te-rich side ZnSTe alloys are studied in detail. (c) 2006 Elsevier B.V. All rights reserved.

Creation and suppression of point defects through a kick-out substitution process of Fe in InP

Indium antisite defect In-P-related photoluminescence has been observed in Fe-diffused semi-insulating (SI) InP. Compared to annealed undoped or Fe-predoped SI InP, there are fewer defects in SI InP obtained by long-duration, high-temperature Fe diffusion. The suppression of the formation of point defects in Fe-diffused SI InP can be explained in terms of the complete occupation by Fe at indium vacancy. The In-P defect is enhanced by the indium interstitial that is caused by the kick out of In and the substitution at the indium site of Fe in the diffusion process. Through these Fe-diffusion results, the nature of the defects in annealed undoped SI InP is better understood. (C) 2002 American Institute of Physics.