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Search Results: 1 - 10 of 51064 matches for " Wei Yanjie "
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A novel hierarchical clustering algorithm for gene sequences
Wei Dan,Jiang Qingshan,Wei Yanjie,Wang Shengrui
BMC Bioinformatics , 2012, DOI: 10.1186/1471-2105-13-174
Abstract: Background Clustering DNA sequences into functional groups is an important problem in bioinformatics. We propose a new alignment-free algorithm, mBKM, based on a new distance measure, DMk, for clustering gene sequences. This method transforms DNA sequences into the feature vectors which contain the occurrence, location and order relation of k-tuples in DNA sequence. Afterwards, a hierarchical procedure is applied to clustering DNA sequences based on the feature vectors. Results The proposed distance measure and clustering method are evaluated by clustering functionally related genes and by phylogenetic analysis. This method is also compared with BlastClust, CD-HIT-EST and some others. The experimental results show our method is effective in classifying DNA sequences with similar biological characteristics and in discovering the underlying relationship among the sequences. Conclusions We introduced a novel clustering algorithm which is based on a new sequence similarity measure. It is effective in classifying DNA sequences with similar biological characteristics and in discovering the relationship among the sequences.
H2 Enhances Arabidopsis Salt Tolerance by Manipulating ZAT10/12-Mediated Antioxidant Defence and Controlling Sodium Exclusion
Yanjie Xie, Yu Mao, Diwen Lai, Wei Zhang, Wenbiao Shen
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0049800
Abstract: Background The metabolism of hydrogen gas (H2) in bacteria and algae has been extensively studied for the interesting of developing H2-based fuel. Recently, H2 is recognized as a therapeutic antioxidant and activates several signalling pathways in clinical trials. However, underlying physiological roles and mechanisms of H2 in plants as well as its signalling cascade remain unknown. Methodology/Principal Findings In this report, histochemical, molecular, immunological and genetic approaches were applied to characterize the participation of H2 in enhancing Arabidopsis salt tolerance. An increase of endogenous H2 release was observed 6 hr after exposure to 150 mM NaCl. Arabidopsis pretreated with 50% H2-saturated liquid medium, mimicking the induction of endogenous H2 release when subsequently exposed to NaCl, effectively decreased salinity-induced growth inhibition. Further results showed that H2 pretreatment modulated genes/proteins of zinc-finger transcription factor ZAT10/12 and related antioxidant defence enzymes, thus significantly counteracting the NaCl-induced reactive oxygen species (ROS) overproduction and lipid peroxidation. Additionally, H2 pretreatment maintained ion homeostasis by regulating the antiporters and H+ pump responsible for Na+ exclusion (in particular) and compartmentation. Genetic evidence suggested that SOS1 and cAPX1 might be the target genes of H2 signalling. Conclusions Overall, our findings indicate that H2 acts as a novel and cytoprotective regulator in coupling ZAT10/12-mediated antioxidant defence and maintenance of ion homeostasis in the improvement of Arabidopsis salt tolerance.
Side-chain and backbone ordering in Homopolymers
Yanjie Wei,Walter Nadler,Ulrich H. E. Hansmann
Physics , 2006,
Abstract: In order to study the relation between backbone and side chain ordering in proteins, we have performed multicanonical simulations of deka-peptide chains with various side groups. Glu10, Gln10, Asp10, Asn10, and Lys10 were selected to cover a wide variety of possible interactions between the side chains of the monomers. All homopolymers undergo helix-coil transitions. We found that peptides with long side chains that are capable of hydrogen bonding, i.e. Glu10, and Gln10, exhibit a second transition at lower temperatures connected with side chain ordering. This occurs in gas phase as well as in solvent, although the character of the side chain structure is different in each case. However, in polymers with short side chains capable of hydrogen bonding, i.e. Asp10 and Asn10, side chain ordering takes place over a wide temperature range and exhibits no phase transition like character. Moreover, non-backbone hydrogen bonds show enhanced formation and fluctuations already at the helix-coil transition temperature, indicating competition between side chain and backbone hydrogen bond formation. Again, these results are qualitatively independent of the environment. Side chain ordering in Lys10, whose side groups are long and polar, also takes place over a wide temperature range and exhibits no phase transition like character in both environments. Reasons for the observed chain length threshold and consequences from these results for protein folding are discussed.
On the Average Errors of Multivariate Lagrange Interpolation  [PDF]
Zengbo Zhang, Yanjie Jiang
Journal of Applied Mathematics and Physics (JAMP) , 2013, DOI: 10.4236/jamp.2013.16001
Abstract:

In this paper, we discuss the average errors of multivariate Lagrange interpolation based on the Chebyshev nodes of the first kind. The average errors of the interpolation sequence are determined on the multivariate Wiener space.

The Average Errors for Linear Combinations of Bernstein Operators on the Wiener Space*  [PDF]
Yanjie Jiang, Ziqing Zhang
Journal of Data Analysis and Information Processing (JDAIP) , 2013, DOI: 10.4236/jdaip.2013.14009
Abstract:

In this paper, we discuss the average errors of function approximation by linear combinations of Bernstein operators. The strongly asymptotic orders for the average errors of the combinations of Bernstein operators sequence are determined on the Wiener space.

Establishment of Output Models and Constraints Analysis for Independent Wind/PV/Storage System  [PDF]
Linjing Hu, Yanjie Fu
Journal of Power and Energy Engineering (JPEE) , 2014, DOI: 10.4236/jpee.2014.29015
Abstract:

In remote areas far from the grid, wind/PV/storage generating system is relatively a good choice, whatever in resource configuration, performance or prices. For the independent hybrid power system, the output models of wind turbines, photovoltaic arrays and batteries are built in this paper, and based on the objectives of the capacity configuration optimal model, constraints used in the process of capacity configuration are analyzed. These provide convenient conditions and theoretical basis for the optimal capacity configuration of independent wind/PV/storage system.

Effects of Stratification and Hormone Treatments on Germination and Physio-Biochemical Properties of Taxus chinensis var. mairei Seed  [PDF]
Yanjie Zhang, Shunbao Lu, Handong Gao
American Journal of Plant Sciences (AJPS) , 2012, DOI: 10.4236/ajps.2012.37100
Abstract: In order to learn dormancy mechanism of Taxtts chinensis var. mairei seed, effects of stratification and hormone treatments on physiological and biochemical indexes of the seeds after stratifying for eight months were researched. The content of amylase activity and soluble sugar gradually increased at first stratification, and then to the maximum for the end of after-ripening period. With the dormancy of seed relieving, some soluble sugar of endosperm was used or consumed by respiration and that led to their content decreased. Seed soluble protein was gradually accumulated at the beginning of stratification and then the initial raw material of protein synthesis of embryo during development had been used or in part converted into carbohydrates for energy consumption, so that the soluble protein content decreased. The fat and starch content slowly decreased during stratification, which showed that the storage of material had continually carrying out catabolism and conversion, which might provide energy sources for seed germination in the stratification process. The peroxidase activity of Taxus seeds increased gradually at the beginning of stratification, and then reached maximum point during stratification for 4 months in A1 and A2. The G-6-PDH and 6-PGDH joint activity was rapidly increased to reach the maximum during stratification for 4 months in A1, which showed the pentose phosphate pathway was activated at this time. The peroxidase activity rapidly increased might also be related to respiratory metabolic pathway during stratification. In plants, acid phosphatase hydrolyze PAM metabolites, namely phosphate material was related to energy metabolism, especially to high-energy phosphate, and phosphate enzyme activity changes affected the energy metabolism. The acid phosphatase activity of Taxus seeds in different treatments has no significant changes during stratification process, but there were two maximums. Energy metabolism might get benefit from the increase of acid phosphatase activity. There were significant differences in amylase activity, peroxidase activity, soluble sugar and soluble protein content with different treatments. Effect of promoting seed germination soaked by GA before stratification was obvious, but the concentration of GA should not be too high. The high concentration of GA caused seed to rot and reduce the seed germination rate. In this study, the highest germination rate of seed was 71.8% and soaked in 200 mg·L-1 gibberellin.
An Optimal Inequality for One-Parameter Mean  [PDF]
Hongya Gao, Yanjie Zhang, Tian Wang
Journal of Applied Mathematics and Physics (JAMP) , 2013, DOI: 10.4236/jamp.2013.15006
Abstract:

In the present paper, we answer the question: for 0 < α < 1 fixed, what are the greatest value p(a) and the least

value q(a) such that the inequality.

For more information about abstract,please download the PDF file.

Instability of chromosome number and DNA methylation variation induced by hybridization and amphidiploid formation between Raphanus sativus L. and Brassica alboglabra Bailey
Xuanli Li, Weiwei Guo, Bing Wang, Xiangsong Li, Honggao Chen, Lihua Wei, Yanjie Wang, Jiangsheng Wu, Hong Long
BMC Plant Biology , 2010, DOI: 10.1186/1471-2229-10-207
Abstract: F1 plants from intergeneric hybridization between Raphanus sativus L. (2n = 18, RR) and Brassica alboglabra Bailey (2n = 18, CC) were obtained by hand crosses and subsequent embryo rescue. Random amplification of polymorphic DNA (RAPD) markers were used to identify the F1 hybrid plants. The RAPD data indicated that the hybrids produced specific bands similar to those of parents and new bands that were not present in either parent. Chromosome number variation of somatic cells from allotetraploids in the F4 to F10 generations showed that intensive genetic changes occurred in the early generations of distant hybridization, leading to the formation of mixopolyploids with different chromosome numbers. DNA methylation variation was revealed using MSAP (methylation-sensitive amplification polymorphism), which showed that cytosine methylation patterns changed markedly in the process of hybridization and amphidiploid formation. Differences in cytosine methylation levels demonstrated an epigenetic instability of the allopolyploid of Raphanobrassica between the genetically stable and unstable generations.Our results showed that chromosome instability occurred in the early generations of allopolyploidy and then the plants were reverted to largely euploidy in later generations. During this process, DNA methylation changed markedly. These results suggest that, epigenetic mechanisms play an important role in intergeneric distant hybridization, probably by maintaining a genetic balance through the modification of existing genetic materials.Hybridization between distant genera is a driver of genome evolution and new species formation. Distant hybridization generates novel variation by causing genetic recombination [1]. Allopolyploids resulting from genome doubling during hybridization events are widespread, and include 50%-70% of angiosperms (including crops such as wheat, rapeseed, tobacco and cotton) [2]. Even though allopolyploidy is recognized as important to plant evolution [3]
Formation and performances of aerobic granules in a sequencing batch reactor treating landfill leachate
序批式反应器处理垃圾渗滤液的污泥颗粒化及污染物去除性能研究

Wei Yanjie,Ji Min,Qin Feifei,Wang Fen,
魏燕杰
,季民,秦菲菲,王芬

环境工程学报 , 2010,
Abstract: 应用序批式反应器(SBR)处理垃圾渗滤液,以絮状活性污泥为接种污泥,经过37 d的运行,反应器内出现小粒径颗粒污泥。第50 d,反应器中污泥完全颗粒化。稳定运行期间,反应器内污泥的平均粒径为0.7 mm;SVI 5min一直维持在较低的水平(27~47 mL/g);MLSS基本稳定在3 700~4 500 mg/L;当COD和氨氮的平均进水浓度为2 150 mg/L和312 mg/L时,平均出水浓度分别为540 mg/L和35 mg/L,去除率分别为75%和89%。
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