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Identification and Analysis of Genes Present in Leptospira interrogans serovar lai but Absent in L. biflexa serovar monvalerio

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Acta Biochimica et Biophysica Sinica 2004年第12期36卷 832-839页

作者： Ping HE, Xiang-Yan ZHANG, Xiao-Kui GUO*, Bao-Yu HU, Xiao-Tian HUANG, Yang YANG, and Guo-Ping ZHAO1,2* Department of Microbiology and Parasitology, Shanghai Second Medical University, Shanghai 200025, China 1 research center of Biotechnology, Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China 2Chinese National Human genome center at Shanghai, Zhangjiang High Tech Park, Shanghai 201203, China Department of Microbiology and Parasitology Shanghai Second Medical UniversityShanghai 200025 China research center of Biotechnology Institutes for Biological Sciences Chinese Academy of SciencesShanghai 200031 China Chinese National Human genome center at ShanghaiZhangjiang High Tech Park Shanghai 201203 China

Genes present in virulent bacterial strains but absent in avirulent close relatives can be of great biologic and clinical interest. This project aimed to identify strain specific DNA sequences of Leptospira interrogans serovar lai, which is absent in the saprophytic L. biflexa serovar monvalerio, via suppression subtractive hybridization with the former as the tester while the latter as the driver. The mixture of PCR amplified DNA fragments from two subtractive hybridization experiments were cloned into pMD18-T vector and the positive clones were identified by dot blotting against the chromosome DNA of the two strains individually. After DNA sequencing and analysis, the distribution of these genomic fragment sequences in a panel of pathogenic and nonpathogenic leptospires was investigated employing dot blot analysis. Among the 188 positive clones randomly chosen, 24 contained the tester strain specific genomic regions, of which, 5 were non-coding fragments while the others contained 23 distinct protein coding sequences. Besides 9 genes encoding functional proteins, 12 genes encode unknown proteins and the rest two genes encode proteins with recognizable domain structures, one for a putative leucine-rich repeats (LRR) family protein while the other as an outer-membrane protein. Our experiment results indicated that suppression subtractive hybridiza- tion is effective for screening specific DNA sequences between two leptospiral strains, and some of these sequences might be responsible for virulence determination. Further analysis of these DNA sequences will provide important information on the pathogenesis of Leptospira.

关键词： Leptospira interrogans serovar lai suppression subtractive hybridization (SSH) specific genes

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Leader-following flocking for unmanned aerial vehicle swarm with distributed topology control

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Science China(Information Sciences) 2020年第4期63卷 140-153页

作者： Chao LIU Meng WANG Qian ZENG Wei HUANGFU Beijing Advanced Innovation center for Materials genome Engineering School of Computer and Communication Engineering University of Science and Technology Beijing

To address the flocking issues of an unmanned aerial vehicle(UAV) swarm operating at a leaderfollower mode, distributed control protocols comprising both kinetic controller and topology control algorithm must be implemented. For flocking the UAV swarm, a distributed control-input method is required for both maintaining a relatively steady state between neighboring vehicles(including velocity matching and distance maintenance) and avoiding vehicle-to-vehicle collision. Furthermore, the stability of control protocols should be analyzed using the potential energy function. In particular, a distributed β-angle test(BAT) rule in the proposed topology-control issue may allow each UAV to determine its neighboring set by exploiting the locally sensed information, thereby significantly reducing the communication overhead of the entire *** addition, node-degree bound is derived to demonstrate the feasibility of the proposed algorithm, in which the optimal value in terms of convergence is analyzed. The flocking of the flying ad-hoc network(FANET)can be achieved in a self-organizing way without the use of an external control center via the distributed control protocols. Ultimately, the proposed analysis is verified by numerical results.

关键词： flying ad hoc networks flocking leader-follower topology control neighbor selection

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Electronic Structure and Stability of Lead-free Hybrid Halide Perovskites:A Density Functional Theory Study

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Journal of Shanghai Jiaotong university(Science) 2018年第1期23卷 202-208页

作者：邬嘉义戚文罗哲刘科朱虹 University of Michigan-Shanghai Jiao Tong University Joint Institute National Engineering research center of Light Alloys Materials genome Initiative center Shanghai Jiao Tong UniversityShanghai 200240China

The most commonly used and studied hybrid halide perovskite is ABX_3, where A usually stands for CH_3NH_3, B for Pb, and X for I. A lead-free perovskite with high stability and ideal electronic band structure would be of essence, especially considering the toxicity of lead. In this work, we have considered 11 metal elements for the B site and three halide elements(Cl, Br, and I) including various combinations among the three halides for the X site. A total number of 99 hybrid perovskites are studied to understand how the crystal structure, band gap and stability can be tuned by the chemistry modification, i.e., the replacement of toxic element, Pb in the original MAPbX_3, with non-toxic metal elements. We find that the favorable substitutes for Pb in MAPbI_3 are Ge and Sn.

关键词： hybrid halide perovskites band gap phase stability density functional theory(DFT)

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Significant influence of trace Li on the mechanical properties, corrosion behavior, and antibacterial properties of biodegradable Zn–4Cu alloys

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Journal of Materials Science & Technology 2023年第20期151卷 245-257页

作者： Shiyu Huang Heng Liu Yanjing Su Lijie Qiao Yu Yan Beijing Advanced Innovation center for Materials genome Engineering Corrosion and Protection CenterInstitute for Advanced Materials and TechnologyUniversity of Science and TechnologyBeijing 100083China

In this work,trace Li was introduced to strengthen Zn–4Cu *** results indicated that trace amounts of Li contributed to a significant increase in strength,resulting in an acceptable loss of elongation at ***,Li in the form of LiZn_(4) led to more intensive galvanic corrosion,which accelerated the early corrosion *** release of a large amount of Zn^(2+),caused by the addition of Li,affected the phase composition of the main Zn-containing corrosion ***,the inhibition effect of the alloy on Staphylococcus aureus(***)was enhanced by the addition of 0.02 wt.%Li.

关键词： Microalloying Zn-Cu alloy LiZn_(4)/Zn pairs Biodegradable mechanism SKPFM

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Genomic and epigenomic heterogeneity in molecularsubtypes of gastric cancer

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World Journal of Gastroenterology 2016年第3期22卷 1190-1201页

作者： Byungho Lim Jong-Hwan Kim Mirang Kim Seon-Young Kim genome Structure research center Korea Research Institute of Bioscience and BiotechnologyDaejeon 305-806South Korea Department of Functional Genomics University of Science and TechnologyDaejeon 305-350South Korea Epigenome research center Korea Research Institute of Bioscience and BiotechnologyDaejeon 305-806South Korea

Gastric cancer is a complex disease that is affected by multiple genetic and environmental factors. For the precise diagnosis and effective treatment of gastric cancer, the heterogeneity of the disease must be simplified; one way to achieve this is by dividing the disease into subgroups. Toward this effort, recent advances in high-throughput sequencing technology have revealed four molecular subtypes of gastric cancer, which are classified as Epstein-Barr viruspositive, microsatellite instability, genomically stable, and chromosomal instability subtypes. We anticipate that this molecular subtyping will help to extend our knowledge for basic research purposes and will be valuable for clinical use. Here, we review the genomic and epigenomic heterogeneity of the four molecular subtypes of gastric cancer. We also describe a mutational meta-analysis and a reanalysis of DNA methylation that were performed using previously reported gastric cancer datasets.

关键词： DNA methylation Gastric cancer Molecularsubtype Mutation Next-generation sequencing

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Relationship between elements migration ofα-AlFeMnSi phase and micro-galvanic corrosion sensitivity of Al-Zn-Mg alloy

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International Journal of Minerals,Metallurgy and Materials 2023年第1期30卷 112-121页

作者： Min Ao Yucheng Ji Pan Yi Ni Li Li Wang Kui Xiao Chaofang Dong Beijing Advanced Innovation center for Materials genome Engineering Institute for Advanced Materials and TechnologyUniversity of Science and Technology BeijingBeijing 100083China China Electric Power research Institute Beijing 100192China

First principles calculations and scanning Kelvin probe force microscopy(SKPFM)were used to investigate the effect of elements migration ofα-AlFeMnSi phase on micro-galvanic corrosion behavior of Al-Zn-Mg *** simulation results showed that the average work function difference between theα-AlFeMnSi phase and Al matrix decreased from 0.232 to 0.065 eV due to the synchronous migration of elements ***,as the elements Fe-Si migration during the extrusion process,the average Volta potential difference detected by SKPFM between theα-AlFeMnSi phase and Al matrix dropped down to 432.383 mV from 648.370 ***,the elements migration reduced the micro-galvanic corrosion sensitivity of Al-Zn-Mg *** reach the calculated low micro-galvanic tendency betweenα-AlFeMnSi phase and Al matrix,the diffusion of Mn should be promoted during extruding process.

关键词： Al-Zn-Mg alloy corrosion behavior α-AlFeMnSi phase first principles calculations

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Transcriptional regulation in the development and dysfunction of neocortical projection neurons

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Neural Regeneration research 2024年第2期19卷 246-254页

作者： Ningxin Wang Rong Wan Ke Tang Precise genome Engineering center School of Life SciencesGuangzhou UniversityGuangzhouGuangdong ProvinceChina

Glutamatergic projection neurons generate sophisticated excitatory circuits to integrate and transmit information among different cortical areas,and between the neocortex and other regions of the brain and spinal *** development of cortical projection neurons is regulated by certain essential events such as neural fate determination,proliferation,specification,differentiation,migration,survival,axonogenesis,and *** processes are precisely regulated in a tempo-spatial manner by intrinsic factors,extrinsic signals,and neural *** generation of correct subtypes and precise connections of projection neurons is imperative not only to support the basic cortical functions(such as sensory information integration,motor coordination,and cognition)but also to prevent the onset and progression of neurodevelopmental disorders(such as intellectual disability,autism spectrum disorders,anxiety,and depression).This review mainly focuses on the recent progress of transcriptional regulations on the development and diversity of neocortical projection neurons and the clinical relevance of the failure of transcriptional modulations.

关键词： autism spectrum disorders cognition differentiation excitatory circuits intellectual disability neocortex neurodevelopmental disorders projection neuron specification transcriptional regulation

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PHASE TRANSITION IN SEQUENCE UNIQUE RECONSTRUCTION

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Journal of Systems Science & Complexity 2007年第1期20卷 18-29页

作者： Li XIA Chan ZHOU Theoretical Life Science research center Fudan University Shanghai 200433 China James D. Waston Institute of genome Sciences Zhejiang University Hangzhou 310008 China.

In this paper, sequence unique reconstruction refers to the property that a sequence is uniquely reconstructable from all its K-tuples. We propose and study the phase transition behavior of the probability P（K） of unique reconstruction with regard to tuple size K in random sequences （iid model）. Based on Monte Carlo experiments, artificial proteins generated from lid model exhibit a phase transition when P（K） abruptly jumps from a low value phase （e.g. 〈 0.1） to a high value phase （e.g. 〉 0.9）. With a generalization to any alphabet, we prove that for a random sequence of length L, as L is large enough, P（K） undergoes a sharp phase transition when p ≤ 0.1015 where p = P （two random letters match）. Besides, formulas are derived to estimate the transition points, which may be of practical use in sequencing DNA by hybridization. Concluded from our study, most proteins do not deviate greatly from random sequences in the sense of sequence unique reconstruction, while there are some ＂stubborn＂ proteins which only become uniquely reconstructable at a very large K and probably have biological implications.

关键词： Phase transition probability protein sequence SBH unique reconstruction

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MicroRNAs as potential biomarkers for gastric cancer

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World Journal of Gastroenterology 2014年第34期20卷 12007-12017页

作者： Han-Shao Liu Hua-Sheng Xiao National Engineering research center for Biochip at Shanghai Shanghai-MOST Key Laboratory for Disease and Health Genomics Chinese National Human Genome Center at Shanghai Advanced Institute of Translational Medicine Tongji University

Gastric cancer is the fourth most common cancer in the world and the second leading cause of cancer-related death. More than 80% of diagnoses occur at the middle to late stage of the disease, highlighting an urgent need for novel biomarkers detectable at earlier stages. Recently, aberrantly expressed microRNAs (miRNAs) have received a great deal of attention as potential sensitive and accurate biomarkers for cancer diagnosis and prognosis. This review summarizes the current knowledge about potential miRNA biomarkers for gastric cancer that have been reported in the publicly available literature between 2008 and 2013. Available evidence indicates that aberrantly expressed miRNAs in gastric cancer correlate with tumorigenesis, tumor proliferation, distant metastasis and invasion. Furthermore, tissue and cancer types can be classified using miRNA expression profiles and next-generation sequencing. As miRNAs in plasma/serum are well protected from RNases, they remain stable under harsh conditions. Thus, potential functions of these circulating miRNAs can be deduced and may implicate their diagnostic value in cancer detection. Circulating miRNAs, as well as tissue miRNAs, may allow for the detection of gastric cancer at an early stage, prediction of prognosis, and monitoring of recurrence and/or lymph node metastasis. Taken together, the data suggest that the participation of miRNAs in biomarker development will enhance the sensitivity and specificity of diagnostic and prognostic tests for gastric cancer. (C) 2014 Baishideng Publishing Group Inc. All rights reserved.

关键词： MicroRNAs Gastric cancer Biomarker Clinical application

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The complexity of G-protein coupled receptor-ligand interactions

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Science China Chemistry 2013年第10期56卷 1344-1350页

作者： WANG Ting genome center University of California 451 East Health Science DriveDavis CA 95616 USA

The G-protein coupled receptors(GPCRs)play fundamental roles in the human biololgy and drug *** function as signalling molecules that transduce extracellular signals into *** signalling transduction is generally triggered by interacting with ligands,including photons,ions,small organic compounds,peptides,proteins and *** this review,we focus on interactions with diffusible ligands such as hormones and *** discuss three aspects of the complexity of the GPCR-ligand interactions:functional selectivity of ligands,receptor subtype selectivity of ligands and orphan GPCRs.

关键词： G-protein coupled receptors (GPCR) ligand interaction functional selectivity receptor subtype

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