A fundamental goal in cellular signaling is to understand allosteric communication, the process by which sig-nals originating at one site in a protein propagate reliably to affect distant functional sites. The general...A fundamental goal in cellular signaling is to understand allosteric communication, the process by which sig-nals originating at one site in a protein propagate reliably to affect distant functional sites. The general principles of protein structure that underlie this process remain unknown. Statistical coupling analysis （SCA） is a statistical technique that uses evolutionary data of a protein family to measure correlation between distant functional sites and suggests allosteric communication. In proteins, very distant and small interactions between collections of amino acids provide the communication which can be important for signaling process. In this paper, we present the SCA of protein alignment of the esterase family （pfam ID： PF00756） containing the sequence of antigen 85C secreted by Mycobacterium tuberculosis to identify a subset of interacting residues. Clustering analysis of the pairwise correlation highlighted seven important residue positions in the esterase family alignments. These resi-dues were then mapped on the crystal structure of antigen 85C （PDB ID： 1DQZ）. The mapping revealed corre-lation between 3 distant residues （Asp38, Leu123 and Met125） and suggests allosteric communication between them. This information can be used for a new drug against this fatal disease.展开更多
In 2009, an emerging citrus viral disease caused by Citrus chlorotic dwarf-associated virus(CCDaV) was discovered in Yunnan Province of China. However, the occurrence and spread of CCDaV in other citrus-growing provin...In 2009, an emerging citrus viral disease caused by Citrus chlorotic dwarf-associated virus(CCDaV) was discovered in Yunnan Province of China. However, the occurrence and spread of CCDaV in other citrus-growing provinces in China is unknown to date. To better understand the distribution and molecular diversity of CCDaV in China, a total of 1 772 citrus samples were collected from 11 major citrus-growing provinces and were tested for CCDaV by PCR. Among these, 134 citrus samples from Guangxi, Yunnan and Guangdong were tested positive for CCDaV, demonstrating that the occurrence and spread of CCDaV are increasing in China. The complete genome sequences of 17 CCDaV isolates from different provinces and hosts were sequenced. Comparisons of the whole-genome sequences of the 17 CCDaV isolates as well as the 15 isolates available in GenBank revealed that the sequence identity was about 99–100%, showing that the CCDaV isolates were highly conserved. Phylogenetic studies showed that the 32 CCDaV isolates belonged to four different groups based on geographical origins and host species, and that CCDaV isolates from China and Turkey were clustered into different groups. The results provide important information for clarifying the distribution and genetic diversity of CCDaV in China.展开更多
In the last ten years, high-performance and massively parallel computing technology comes into a high speed developing phase and is used in all fields. The cluster computer systems are also being widely used for their...In the last ten years, high-performance and massively parallel computing technology comes into a high speed developing phase and is used in all fields. The cluster computer systems are also being widely used for their low cost and high performance. In bioinformatics research, solving a problem with computer usually takes hours even days. To speed up research, high-performance cluster computers are considered to be a good platform. Moving into the new MPP (massively parallel processing) system, the original algorithm should be parallelized in a proper way. In this paper, a new parallelizing method of useful sequence alignment algorithm (Smith-Waterman) is designed based on its optimizing algorithm already exists. The result is gratifying.展开更多
Total-Routhian-Surface calculations have been performed to investigate the deformation and alignment properties of the No isotopes. It is found that normal deformed and superdeformed states in these nuclei can coexist...Total-Routhian-Surface calculations have been performed to investigate the deformation and alignment properties of the No isotopes. It is found that normal deformed and superdeformed states in these nuclei can coexist at low excitation energies. In neutron-deficient No isotopes, the superdeformed shapes can even become the ground states. Moreover, we plotted the kinematic moments of inertia of the No isotopes, which follow very nicely available experimental data. It is noted that, as the rotational frequency increases, alignments develop at hω = 0.2- 0.3 MeV. Our calculations show that the occupation of the νj15/2 orbital plays an important role in the alignments of the No isotopes.展开更多
A new liquid crystalline polyacetylene containing a phenyl benzoate mesogen (5) is synthesized,whose mesomorphic properties are found to be easily 'tunab1e' by simple mechanical perturbation. Thepolymerization...A new liquid crystalline polyacetylene containing a phenyl benzoate mesogen (5) is synthesized,whose mesomorphic properties are found to be easily 'tunab1e' by simple mechanical perturbation. Thepolymerization of 10- [ 4 - (4' -methoxyphenoxycarbonyl )phenoxycarbonyl] - 1 -decyne (4 ) in itiated by theWCl_6-Ph_4Sn/dioxane complex yields polymer 5 with a M_w of 28400. The molecular structure of 5 ischaracterized by NMR, IR, and UV spectroscopy and its liquid crystalline behavior is investigated by DSC,POM, and XRD analysis. Upon mechanical perturbation, 5 exhibits unusual agitation-induced high-strengthdisclinations, shear-induced inversion walls, and solidification-induced banded textures. Such phenomenahave been observed in the main-chain liquid crystalline polymers with rigid backbones, but have seldom beenreported for the side-chain liquid crystalline polymers with flexible backbones, suggesting that the rigidpolyacetylene backbone of 5 plays a constructive role in inducing the novel molecular alignments.展开更多
The Xuhuai fold thrust belt(XHTB)is a curved structure in the southeastern margin of the North China Craton(NCC)that has attracted great attentions due to its tectonic and petrological characteristics.However,few geop...The Xuhuai fold thrust belt(XHTB)is a curved structure in the southeastern margin of the North China Craton(NCC)that has attracted great attentions due to its tectonic and petrological characteristics.However,few geophysical studies have focused on the deep structure of this belt.In this study,we carry out a systematic demonstration of the main geophysical features that characterize the XHTB and surrounding areas.The results reveal small negative gravity and magnetic anomalies,thin crust and lithosphere,lower shear velocity and shallower earthquake epicenters relative to other areas of the NCC,collectively indicating a lithospheric-scale rheological anomaly at this belt.The magnetic alignments show a trend similar to that of geological units in southeastern NCC and adjacent areas,although they differ from the SKS-splitting fast polarization directions,except in the Qinling-Dabie orogen where a vertical coherent deformation of the crust and mantle may be involved there.Based on the geophysical data,we propose a detachment-controlled model,which was caused by the different detachment depth/strength,for the formation of XHTB to explain its arcuate shape as well as the magnetic alignments,thus providing new insight into the deep processes of southeastern NCC.展开更多
The recent explosion of biological data and the concomitant proliferation of distributed databases make it challenging for biologists and bioinformaticians to discover the best data resources for their needs, and the ...The recent explosion of biological data and the concomitant proliferation of distributed databases make it challenging for biologists and bioinformaticians to discover the best data resources for their needs, and the most efficient way to access and use them For the biologist, running bioinformatics analyses involve a time-consuming management of data and tools. Users need support to organize their work, retrieve parameters and reproduce their analyses. They also need to be able to combine their analytic tools using a safe data flow software mechanism. Finally we have designed a system, Bioinfo-Portal, to provide a flexible and usable web environment for defining and running bioinformatics analyses. It embeds simple yet powerful data management features that allow the user to reproduce analyses and to combine tools using an adobe flex tool. Bioinfo-Portal can also act as a front end to provide a unified view of already-existing collections of bioinformatics resources. Users can analyze genomic and proteomic data by using the tools that has been integrated in the portal （tools for alignments, dotplots, motif detection, domain analysis, profile searching and tertiary structure prediction）. The sequences that user obtained from portal＇s nucleotide and protein databases are easily analyzed by the portal tools on the same interface in no time. User can also take benefit from the animations.展开更多
文摘A fundamental goal in cellular signaling is to understand allosteric communication, the process by which sig-nals originating at one site in a protein propagate reliably to affect distant functional sites. The general principles of protein structure that underlie this process remain unknown. Statistical coupling analysis （SCA） is a statistical technique that uses evolutionary data of a protein family to measure correlation between distant functional sites and suggests allosteric communication. In proteins, very distant and small interactions between collections of amino acids provide the communication which can be important for signaling process. In this paper, we present the SCA of protein alignment of the esterase family （pfam ID： PF00756） containing the sequence of antigen 85C secreted by Mycobacterium tuberculosis to identify a subset of interacting residues. Clustering analysis of the pairwise correlation highlighted seven important residue positions in the esterase family alignments. These resi-dues were then mapped on the crystal structure of antigen 85C （PDB ID： 1DQZ）. The mapping revealed corre-lation between 3 distant residues （Asp38, Leu123 and Met125） and suggests allosteric communication between them. This information can be used for a new drug against this fatal disease.
基金supported by the National Key R&D Program of China(2019YFD1001800)the China Agriculture Research System,Overseas Expertise Introduction Project for Discipline Innovation(B18044)+2 种基金the China Agriculture Research System of MOF and MARA(CARS-26-05B)the Natural Science Foundation of Chongqing,China(cstc2019jcyj-msxmX0557)the Guangxi Natural Science Foundation,China(2018GXNSFBA050027)。
文摘In 2009, an emerging citrus viral disease caused by Citrus chlorotic dwarf-associated virus(CCDaV) was discovered in Yunnan Province of China. However, the occurrence and spread of CCDaV in other citrus-growing provinces in China is unknown to date. To better understand the distribution and molecular diversity of CCDaV in China, a total of 1 772 citrus samples were collected from 11 major citrus-growing provinces and were tested for CCDaV by PCR. Among these, 134 citrus samples from Guangxi, Yunnan and Guangdong were tested positive for CCDaV, demonstrating that the occurrence and spread of CCDaV are increasing in China. The complete genome sequences of 17 CCDaV isolates from different provinces and hosts were sequenced. Comparisons of the whole-genome sequences of the 17 CCDaV isolates as well as the 15 isolates available in GenBank revealed that the sequence identity was about 99–100%, showing that the CCDaV isolates were highly conserved. Phylogenetic studies showed that the 32 CCDaV isolates belonged to four different groups based on geographical origins and host species, and that CCDaV isolates from China and Turkey were clustered into different groups. The results provide important information for clarifying the distribution and genetic diversity of CCDaV in China.
文摘In the last ten years, high-performance and massively parallel computing technology comes into a high speed developing phase and is used in all fields. The cluster computer systems are also being widely used for their low cost and high performance. In bioinformatics research, solving a problem with computer usually takes hours even days. To speed up research, high-performance cluster computers are considered to be a good platform. Moving into the new MPP (massively parallel processing) system, the original algorithm should be parallelized in a proper way. In this paper, a new parallelizing method of useful sequence alignment algorithm (Smith-Waterman) is designed based on its optimizing algorithm already exists. The result is gratifying.
基金Supported by National Natural Science Foundation of China (10735010, 10525520)Chinese Major State Basic Research Development Program (2007CB815000)
文摘Total-Routhian-Surface calculations have been performed to investigate the deformation and alignment properties of the No isotopes. It is found that normal deformed and superdeformed states in these nuclei can coexist at low excitation energies. In neutron-deficient No isotopes, the superdeformed shapes can even become the ground states. Moreover, we plotted the kinematic moments of inertia of the No isotopes, which follow very nicely available experimental data. It is noted that, as the rotational frequency increases, alignments develop at hω = 0.2- 0.3 MeV. Our calculations show that the occupation of the νj15/2 orbital plays an important role in the alignments of the No isotopes.
基金This project was in part supported by the Hong Kong Research Grants Council(HKUST597/95P&6149/97P)
文摘A new liquid crystalline polyacetylene containing a phenyl benzoate mesogen (5) is synthesized,whose mesomorphic properties are found to be easily 'tunab1e' by simple mechanical perturbation. Thepolymerization of 10- [ 4 - (4' -methoxyphenoxycarbonyl )phenoxycarbonyl] - 1 -decyne (4 ) in itiated by theWCl_6-Ph_4Sn/dioxane complex yields polymer 5 with a M_w of 28400. The molecular structure of 5 ischaracterized by NMR, IR, and UV spectroscopy and its liquid crystalline behavior is investigated by DSC,POM, and XRD analysis. Upon mechanical perturbation, 5 exhibits unusual agitation-induced high-strengthdisclinations, shear-induced inversion walls, and solidification-induced banded textures. Such phenomenahave been observed in the main-chain liquid crystalline polymers with rigid backbones, but have seldom beenreported for the side-chain liquid crystalline polymers with flexible backbones, suggesting that the rigidpolyacetylene backbone of 5 plays a constructive role in inducing the novel molecular alignments.
基金supported by the National Key R&D Program of China(No.2016YFC0600402)the National Natural Science Foundation of China(Nos.41874106,42021002)+1 种基金the Youth Innovation Promotion Association of CAS(No.YIPA2018385)the project from Guangdong Province(No.2019QN01H101)。
文摘The Xuhuai fold thrust belt(XHTB)is a curved structure in the southeastern margin of the North China Craton(NCC)that has attracted great attentions due to its tectonic and petrological characteristics.However,few geophysical studies have focused on the deep structure of this belt.In this study,we carry out a systematic demonstration of the main geophysical features that characterize the XHTB and surrounding areas.The results reveal small negative gravity and magnetic anomalies,thin crust and lithosphere,lower shear velocity and shallower earthquake epicenters relative to other areas of the NCC,collectively indicating a lithospheric-scale rheological anomaly at this belt.The magnetic alignments show a trend similar to that of geological units in southeastern NCC and adjacent areas,although they differ from the SKS-splitting fast polarization directions,except in the Qinling-Dabie orogen where a vertical coherent deformation of the crust and mantle may be involved there.Based on the geophysical data,we propose a detachment-controlled model,which was caused by the different detachment depth/strength,for the formation of XHTB to explain its arcuate shape as well as the magnetic alignments,thus providing new insight into the deep processes of southeastern NCC.
文摘The recent explosion of biological data and the concomitant proliferation of distributed databases make it challenging for biologists and bioinformaticians to discover the best data resources for their needs, and the most efficient way to access and use them For the biologist, running bioinformatics analyses involve a time-consuming management of data and tools. Users need support to organize their work, retrieve parameters and reproduce their analyses. They also need to be able to combine their analytic tools using a safe data flow software mechanism. Finally we have designed a system, Bioinfo-Portal, to provide a flexible and usable web environment for defining and running bioinformatics analyses. It embeds simple yet powerful data management features that allow the user to reproduce analyses and to combine tools using an adobe flex tool. Bioinfo-Portal can also act as a front end to provide a unified view of already-existing collections of bioinformatics resources. Users can analyze genomic and proteomic data by using the tools that has been integrated in the portal （tools for alignments, dotplots, motif detection, domain analysis, profile searching and tertiary structure prediction）. The sequences that user obtained from portal＇s nucleotide and protein databases are easily analyzed by the portal tools on the same interface in no time. User can also take benefit from the animations.
