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Modeling the relationship between gene expression and mutational signature

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Quantitative Biology 2023年第1期11卷 31-43页

作者： limin jiang Hui Yu Yan Guo Department of Internal Medicine Comprehensive Cancer CenterUniversity of New Mexico AlbuquerqueNM 87109USA

Background:Mutational signatures computed from somatic mutations,allow an in-depth understanding of tumorigenesis and may illuminate early prevention *** studies have shown the regulation effects between somatic mutation and gene expression ***:We hypothesized that there are potential associations between mutational signature and gene *** capitalized upon RNA-seq data to model 49 established mutational signatures in 33 cancer *** accuracy and area under the curve were used as performance measures in five-fold ***:A total of 475 models using unconstrained genes,and 112 models using protein-coding genes were selected for future inference *** independent gene expression dataset on lung cancer smoking status was used for validation which achieved over 80%for both accuracy and area under the ***:These results demonstrate that the associations between gene expression and somatic mutations can translate into the associations between gene expression and mutational signatures.

关键词： mutational signature gene expression support vector machine random forest extreme gradient boost

CHANNEL ERROR CORRECTION FOR WIDEBAND SAR-A JOINT MULTIPLE SUBPULSES PROCESSING METHOD

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Journal of Electronics(China) 2011年第1期28卷 134-140页

作者： Chen Shuxuan jiang limin Xiang Maosheng National Key Lab of Microwave Imaging Technology Institute of Electronics Chinese Academy of Sciences Beijing 100190 China Graduate School of Chinese Academy of Sciences Beijing 100190 China

A novel method,referred to as joint multiple subpulses processing,is developed to calibrate the nonideal transfer function of radio frequency front-end and I/Q imbalance in quadrature modulate/demodulate systems simultaneously,which frequently occur in wideband Synthetic Aperture Radar(SAR) *** on the time-frequency relation of the chirp signal and the analyses of the channel errors in wideband SAR,joint multiple subpulses processing method is adopted to separate the image frequency component due to the I/Q channel ***,the complete description of the channel error is acquired for building the correction function,which is used to correct the radar raw echo in frequency *** validity and capability of this method are demonstrated by the experiments of the channel error correction on the high resolution SAR system with the effective bandwidth of 500 MHz.

关键词： Wideband Synthetic Aperture Radar(SAR) Channel error Joint multiple subpulses processing Weighted least squares Correction function

Future evolution of automated demand response system in smart grid for low-carbon economy

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Journal of Modern Power Systems and Clean Energy 2015年第1期3卷 72-81页

作者： Huaguang YAN Bin LI Songsong CHEN Ming ZHONG Dezhi LI limin jiang Guixiong HE China Electric Power Research Institute Beijing 100192China School of Electric and Electronic Engineering North China Electric Power UniversityBeijing 102206China

Smart grid construction is an important carrier and an effective way to promote the development of lowcarbon *** response(DR)is commonly regarded as an important core technology in smart grid field,and it reflects the flexible and interactive features of the core business in smart *** is the developing direction of automated demand response(ADR)technology,and its main features are the standardization of information exchange,together with the intelligence of decision-making and the automation of *** technology can improve the efficiency of the whole power system and enhance the ability to accept new energy *** paper analyzes the role of demand response in improving efficiency and low-carbon energy saving power *** automated demand response system architecture is investigated,and the ADR roadmap of commercial/industrial and residential customer is *** key technologies for ADR system are analyzed,including demand response strategy,information exchanging model,measurement and verification techniques,and multi-agent scheduling *** ensure the interoperability between the grid side and the user side,the ADR business in smart grid user interface standards is concluded to support further demand side management project.

关键词： Demand response Information model System architecture Load shifting

Morphological and molecular examination of the ciliate family Lagynusidae(Protista,Ciliophora,Prostomatea)with descriptions of two new genera and two new species from China

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Marine Life Science & Technology 2023年第2期5卷 178-195页

作者： limin jiang Congcong Wang Saleh A.Al-Farraj Hunter N.Hines Xiaozhong Hu College of Fisheries and Key Laboratory of MaricultureMinistry of EducationOcean University of ChinaQingdao 266003China Institute of Evolution and Marine Biodiversity Ocean University of ChinaQingdao 266003China Department of Zoology College of ScienceKing Saud UniversityRiyadh 11451Saudi Arabia Harbor Branch Oceanographic Institute Florida Atlantic UniversityFort PierceFL 34982USA

Ciliates in the class Prostomatea play an important role in the global microbial loop due to their signifcant abundances and broad feeding strategies at the foundation of food *** their importance in ecosystems,the taxonomy and systematics of this group of ciliates has long been poorly understood,with this being especially true for members of the family *** we examine four lagynusids collected from sandy beaches in China,using silver-staining and 18S rRNA gene sequencing *** investigations revealed two new genera and two new species and provided details for two little known forms:Penardella marina ***.,***.,Apolagynus cucumis(as reported by Penard.Études sur les infusoires d’eau *** and Cie,Genève,1922)***.,***.,Lagynus minutus ***.,and Lagynus elegans(Engelmann in Z Wiss Zool 11:347-393,1862)Quennerstedt(Acta Univ Lund 4:1-48,1867).Penardella *** be morphologically distinguished by having more than three dikinetidal perioral *** *** from the closely related genus Lagynus in the absence of a conspicuous neck-like *** ciliature of Apolagynus cucumis is revealed here for the frst time,which demonstrates the classifcation of this species within ***,Apolagynus binucleatus(jiang et al.,2021)*** established according to the new *** results of our phylogenetic analyses based on the 18S rRNA gene support the establishment of two new genera and indicate that Lagynusidae is monophyletic,which further strengthens its valid taxonomic status.

关键词： Ciliate Morphology New genus New species Phylogeny 18S rRNA gene

Dynamics of synthetic yeast chromosome evolution shaped by hierarchical chromatin organization

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National Science Review 2023年第5期10卷 240-250页

作者： Sijie Zhou Yi Wu Yu Zhao Zhen Zhang limin jiang Lin Liu Yan Zhang Jijun Tang Ying-Jin Yuan Frontiers Science Center for Synthetic Biology (Ministry of Education) Tianjin University Key Laboratory of Systems Bioengineering(Ministry of Education) School of Chemical Engineering and TechnologyTianjin University Institute for Systems Genetics NYU Langone Health School of Computer Science and Technology College of Intelligence and ComputingTianjin University Epigenetic Group Frasergen Bioinformatics Co.Ltd. Department of Computer Science University of South Carolina

Synthetic genome evolution provides a dynamic approach for systematically and straightforwardly exploring evolutionary *** Chromosome Rearrangement and Modification by LoxP-mediated Evolution(SCRaMbLE) is an evolutionary system intrinsic to the synthetic yeast genome that can rapidly drive structural ***,we detect over 260 000 rearrangement events after the SCRaMbLEing of a yeast strain harboring 5.5 synthetic yeast chromosomes(synⅡ,synⅢ,synⅤ,circular synⅥ,synⅨR and synⅩ).Remarkably,we find that the rearrangement events exhibit a specific landscape of *** further reveal that the landscape is shaped by the combined effects of chromatin accessibili and spatial contact *** rearrangements tend to occur in 3D spatially proximal and chromatin-accessible *** enormous numbers of rearrangements mediated by SCRaMbLE provide a driving force to potentiate directed genome evolution,and the investigation of the rearrangement landscape offers mechanistic insights into the dynamics of genome evolution.

关键词： synthetic biology genome rearrangement hierarchical chromatin organization synthetic yeast genome SCRaMbLE Saccharomyces cerevisiae

Comprehensive cross cancer analyses reveal mutational signature cancer specificity

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Quantitative Biology 2024年第3期12卷 245-254页

作者： Rui Xin limin jiang Hui Yu Fengyao Yan Jijun Tang Yan Guo Department of Computer Science University of South CarolinaColumbiaSouth CarolinaUSA Department of Public Health and Sciences Sylvester Comprehensive Cancer CenterUniversity of MiamiMiamiFloridaUSA

Mutational signatures refer to distinct patterns of DNA mutations that occur in a specific context or under certain *** is a powerful tool to describe cancer *** conducted a study to show cancer heterogeneity and cancer specificity from the aspect of mutational signatures through collinearity analysis and machine learning *** thorough training and independent validation,our results show that while the majority of the mutational signatures are distinct,similarities between certain mutational signature pairs can be observed through both mutation patterns and mutational signature *** observation can potentially assist to determine the etiology of yet elusive mutational *** analysis using machine learning approaches demonstrated moderate mutational signature cancer *** cancer among all cancer types demonstrated the strongest mutational signature specificity.

关键词： cancer specificity collinearity analysis DNA mutational signatures machine learning

The Dof transcription factor COG1 acts as a key regulator of plant biomass by promoting photosynthesis and starch accumulation

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Molecular Plant 2023年第11期16卷 1759-1772页

作者： Zhuoyun Wei Haoyong Zhang Meng Fang Shuyuan Lin Mingsong Zhu Yuxiu Li limin jiang Tianliang Cui Yanwei Cui Hong Kui Liang Peng Xiaoping Gou Jia Li Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations School of Life SciencesLanzhou UniversityLanzhou 730000China Gansu Key Laboratory of Gene Editing for Breeding School of Life SciencesLanzhou UniversityLanzhou 730000China Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution School of Life SciencesLanzhou UniversityLanzhou 730000China Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design School of Life SciencesGuangzhou UniversityGuangzhou 510006China

Photosynthetic efficiency is the primary determinant of crop yield,including vegetative biomass and grain *** of key transcription factors known to directly control photosynthetic machinery can be an effective strategy to improve photosynthetic *** this study,we identified an Arabidopsis gain-of-function mutant,cogwheel1-3D,that shows a significantly enlarged rosette and increased biomass compared with wild-type *** of COG1,a Dof transcription factor,recapitulated the phenotype of cogwheel1-3D,whereas knocking out COG1 and its six paralogs resulted in a reduced rosette size and decreased *** and quantitative reverse transcription polymerase chain reaction analyses demonstrated that COG1 and its paralogs were required for light-induced expression of genes involved in *** chromatin immunoprecipitation and electrophoretic mobility shift assays indicated that COG1 can directly bind to the promoter regions of multiple genes encoding light-harvesting antenna ***,biochemical,and microscopy analyses revealed that COG1 enhances photosynthetic capacity and starch accumulation in Arabidopsis rosette ***,combined results of bioinformatic,genetic,and molecular experiments suggested that the functions of COG1 in increasing biomass are conserved in different plant *** results collectively demonstrated that COG1 acts as a key regulator of plant biomass by promoting photosynthesis and starch *** COG1 to optimize photosynthetic capacity would create new strategies for future crop yield improvement.

关键词： COG1 Dof transcription factor LHCA LHCB photosynthetic genes biomass

Anti-enrofloxacin Antibody Production by Using Enrofloxacin-screened HSA as an Immunogen

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Journal of Ocean University of China 2005年第3期4卷 262-266页

作者： LIU Chune LIN Hong CAO limin jiang Jie Aquatic Products Safety Laboratory Ocean University of China Qingdao 266003 P.R. China

A two-step zero-length cross-linking procedure using active esters was successfully adopted for conjugating en-rofloxacin (EF) to human serum albumin (HSA). The derived conjugate was characterized by UV spectrum and then usedfor immunization of BALB/C mice. In enzyme-linked immunosorbent assay (ELISA) and competitive inhibition ELISA ex-periments, the derived antiserum exhibited high antibody titer (greater than 1: 250 000) as well as varied cross-reactivity(from 97.8% to 161.7%) to three analogs of EF belonging to fluoroquinolones family. But over the concentration rangestudied, no significant cross-reactivity was observed to other group of antibiotics (chloramphenicol, oxytetracycline, sul-phamethoxazole and nysfungin). It was confirmed that the synthesized immunogen was highly antigenic and elicited specificantibody responses in BALB/C mice against EF.

关键词： enrofloxacin immunogen enzyme-linked immunosorbent assay human serum albumin

时事热点中的地理学——利用时事热点进行高中地理研拓课程的开发与实施

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地理教学 2019年第21期 37-41页

作者：蒋黎敏上海市市北中学

时事热点材料是来源于实际生活中有一定影响力的即时事件和现象,是丰富的地理教学资源。在地理教学中,时事热点材料的开发利用具有较高的价值和意义。本文按照《普通高中地理课程标准(2017年版)》的理念和要求,将利用时事热点开展地理... 详细信息

时事热点材料是来源于实际生活中有一定影响力的即时事件和现象,是丰富的地理教学资源。在地理教学中,时事热点材料的开发利用具有较高的价值和意义。本文按照《普通高中地理课程标准(2017年版)》的理念和要求,将利用时事热点开展地理教学的过程进行了课程化。"时事热点中的地理学"是一门利用时事热点开展的高中地理校本研拓课程,是高中地理基础型课程的延伸和拓展。本文从课程性质、目标、内容、教学及评价等多个方面描述了课程开发的完整过程,通过具体教学案例说明了课程实施的方法和意义。

关键词：时事热点地理教学研拓课程课程开发