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A Key to Genome Maze in 3D

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Genomics, Proteomics & Bioinformatics 2016年第1期14卷 4-6页

作者： Zhihua Zhang CAS Key Laboratory of Genome Sciences and Information Beijing Institute of Genomics Chinese Academy of Sciences

How a genome with linear length over meters is compacted into the micrometer-sized nucleus of higher eukaryotic cells, and how this compaction affects and is affected by the genome functionalities have puzzled biologists for decades. There are mainly two classes of technologies that are dedicated to the probing of genome spatial organization. Image-based analyses of three-dimensional （3D） fluorescence in situ hybridization （FISH） [1] have been widely used in genome spatial research. This technology family has contributed to many early land- mark discoveries of 3D genome （e.g., finding that chromo- somes occupy distinct non-overlapping territories in interphase [2]）, and continues to assist biologists in zooming into the genome spatial structure [3]. The other technology family is 3D genome mapping, which takes advantage of the next-generation sequencing （NGS） technology to sample the proximity ligated genome fragments [4,5] as chromatin interac- tions. Chromatin interaction analysis by paired-end tag sequencing （ChIA-PET） and high-throughput chromosome conformation capture （Hi-C） are two representative technolo- gies in this class [4,5]. ChIA-PET detects chromatin interac- tions mediated by specific protein factors, thus it is more specific and has higher resolution in comparison to Hi-C, which captures all chromatin contacts comprehensively. Since the introduction of ChIA-PET and Hi-C seven years ago [6,7], more detailed spatial genome architectures have been revealed,such as topologically associated domains （TAD） [8] and clus- tered gene promoters for transcription [9]. However, both Hi-C and ChlA-PET technologies face challenges including data noise stemming from complicated experimental protocols, exponential explosion in the sequencing depth required for higher resolution analysis, and large starting cell numbers. Some endeavors have been made to address one or some of such challenges. For instance, DNase I or micrococcal nucle- ase have been used to substitute restriction enzymes for chro- matin fragmentati

关键词： CTCF A Key to Genome Maze in 3D

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Nitrogen-Use Divergence Between Indica and Japonica Rice: Variation at Nitrate Assimilation

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Molecular Plant 2020年第1期13卷 6-7页

作者： Zhihua Zhang Chengcai Chu State Key Laboratory of Plant Genomics Institute of Genetics and Developmental BiologyInnovative Academy of Seed DesignChinese Academy of SciencesBeijingChina

Nitrogen (N) is the most abundant mineral element in plants and often constitutes a major limiting factor in agricultural practice. The application of N fertilizer has greatly enhanced the global crop production, but the accompanying economic and environmental costs are becoming unaffordable. Rice is the staple food for more than half of world population;therefore, understanding the molecular mechanisms regulating N uptake and utilization and thereby developing the strategies to improve the N use efficiency (NUE) in rice have become urgently needed.

关键词： thereby becoming limiting

Delta.EPI:a probabilistic voting-based enhancer-promoter interaction prediction platform

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Journal of Genetics and Genomics 2023年第7期50卷 519-527页

作者： Yuyang zhang Haoyu Wang Jing Liu Junlin Li Qing zhang Bixia Tang Zhihua Zhang CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of Sciencesand China National Center for BioinformationBeijing 100101China College of Life Sciences University of Chinese Academy of SciencesBeijing 100049China School of Artificial Intelligence University of Chinese Academy of SciencesBeijing 100049China

Enhancer promoter interaction(EPI)involves most of gene transcriptional regulation in the high eukaryotes.Predicting the EPIs from given genomic loci or DNA sequences is not a trivial task.The benchmarking work so far for EPI predictors is more or less empirical and lacks quantitative model-based comparisons,posing challenges for molecular biologists to obtain reliable EPI predictions.Here,we present an EPI prediction platform,namely Delta.EPI.Based on a statistic model of the data integration,Delta.EPI is capable of comprehensively assessing the predictions from four state-of-the-art EPI predictors.Equipped with a userfriendly interface and visualization platform,Delta.EPI presents the sorted results with the confidence of EPI relevance,which may guide the molecular biologists who lack the pre-knowledge of the algorithms of EPI prediction.Last,we showcase the utility of Delta.EPI with a case study.Delta.EPI provides a powerful tool to fuel the gene regulation and 3D genome studies by ease-to-access EPI predictions.Delta.EPI can be freely accessed at https://***/deltaEPI/.

关键词： Enhancer-promoter interaction Hi-C Prediction Benchmark Web server

Kinetics and mechanism of propylene hydro-oxidation to acrolein on Au catalysts

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Nano Research 2024年第1期17卷 354-363页

作者： Wei Du Zhihua Zhang Nan Song Xuezhi Duan Xinggui Zhou State Key Laboratory of Chemical Engineering School of Chemical EngineeringEast China University of Science and TechnologyShanghai 200237China

Propylene epoxidation by H_(2)and O_(2)to propylene oxide(PO)over the Au-Ti bifunctional catalysts,as an ideal reaction for PO production,has attracted great interest.Revealing the mechanism of acrolein formation is of great importance for understanding the mechanism of molecular oxygen activation and the formation of hydroperoxo species on the Au sites.Here,we investigate the reaction mechanism of propylene oxidation to acrolein on the Au/uncalcined TS-1(Au/TS-1-B)catalyst through a combination of multiple characterization,H_(2)/D_(2)exchange,kinetics experiment,and modeling.The Ti sites are found to be non-essential to acrolein formation.Moreover,the acrolein formation on the Au/TS-1-B catalyst is confirmed to be promoted by H_(2)through hydroperoxo species formation,which includes two main steps:propylene dehydrogenation to*C_(3)H_(5)with the aid of*OOH species,and*C_(3)H_(5)oxidation by*OOH to acrolein.The latter step is determined to be the rate-determining step because the corresponding kinetics model gives the best description for experimental results.This work not only provides kinetics insights for the propylene hydro-oxidation to acrolein on the Au-Ti bifunctional catalysts,but also facilitates the rational design of Au catalysts with high activity and selectivity in the direct propylene epoxidation with H_(2)and O_(2).

关键词： kinetics mechanism gold acrolein hydro-oxidation

Lighting Up Neural Circuits by Viral Tracing

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Neuroscience Bulletin 2022年第11期38卷 1383-1396页

作者： Liyao Qiu Bin zhang zhihua Gao Department of Neurobiology and Department of Neurology of the Second Affiliated Hospital NHC and CAMS Key Laboratory of Medical NeurobiologyZhejiang University School of MedicineHangzhou 310058China The MOE Frontier Science Center for Brain Research and Brain-Machine Integration School of Brain Science and Brain MedicineZhejiang UniversityHangzhou 310058China

Neurons are highly interwoven to form intricate neural circuits that underlie the diverse functions of the brain.Dissecting the anatomical organization of neural circuits is key to deciphering how the brain processes information,produces thoughts,and instructs behaviors.Over the past decades,recombinant viral vectors have become the most commonly used tracing tools to define circuit architecture.In this review,we introduce the current categories of viral tools and their proper application in circuit tracing.We further discuss some advances in viral tracing strategy and prospective innovations of viral tools for future study.

关键词： Viral tracing Neural circuit Anterograde Retrograde Transsynaptic

Kinetics and mechanistic insights into the active sites of Au catalysts for selective propylene oxidation

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Nano Research 2023年第5期16卷 6220-6227页

作者： Qianhong Wang Zhihua Zhang Keng Sang Wenyao Chen Gang Qian Jing zhang Xinggui Zhou Xuezhi Duan State Key Laboratory of Chemical Engineering School of Chemical EngineeringEast China University of Science and TechnologyShanghai 200237China

Identification of the catalytically active sites emerges as the prerequisite for an atomic-level comprehensive understanding and further rational design of highly efficient catalysts.Here,we demonstrate a kinetics strategy to identify the active sites of Au catalyst for the disentanglement of geometric and electronic effects on the selective oxidation of propylene to acrolein.Both the Ti-containing titanium-silicalite-1(TS-1)and Ti-free silicalite-1(S-1)were employed as supports to immobilize Au catalysts,which were investigated by a combination of multiple characterization,kinetics analysis,crystal structure modelling.The Au(111)sites are identified as the main active site for acrolein formation,while their electronic effects are highly relevant to the presence or absence of Ti.Moreover,propylene epoxide(PO)formation mainly involves the co-participation of Au and Ti sites,the proximity between Au and Ti sites is found to have less influences on PO formation in a certain distance.In comparison,acrolein is very likely to generate over Au(111)sites via the hydrogen-assisted O_(2) activation to oxygenated species for its oxidizing propylene.The insights gained here could guide the design and preparation of Au catalysts for selective propylene oxidation.

关键词： propylene oxidation Au catalysts active site geometric and electronic effects Au-Ti proximity

AutoBPS-BIM:A toolkit to transfer BIM to BEM for load calculation and chiller design optimization

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Building Simulation 2023年第7期16卷 1287-1298页

作者： zhihua Chen zhang Deng Adrian Chong Yixing Chen College of Civil Engineering Hunan UniversityChangshaHunan 410082China Key Laboratory of Building Safety and Energy Efficiency(Hunan University) Ministry of EducationChina Department of Building National University of Singapore4 Architecture Drive117566Singapore

This study developed a rapid building modeling tool,AutoBPS-BIM,to transfer the building information model(BIM)to the building energy model(BEM)for load calculation and chiller design optimization.An eight-storey office building in Beijing,33.2 m high,67.2 m long and 50.4 m wide,was selected as a case study building.First,a module was developed to transfer BIM in IFC format into BEM in EnergyPlus.Variable air volume systems were selected for the air system,while water-cooled chillers and boilers were used for the central plant.The EnergyPlus model calculated the heating and cooling loads for each space as well as the energy consumption of the central plant.Moreover,a chiller optimization module was developed to select the optimal chiller design for minimizing energy consumption while maintaining thermal comfort.Fifteen available chillers were included,with capacities ranging from 471 kW to 1329 kW.The results showed that the cooling loads of the spaces ranged from 33 to 100 W/m^(2) with a median of 45 W/m^(2),and the heating load ranged from 37 to 70 W/m^(2) with a median of 52 W/m^(2).The central plant’s total cooling load under variable air volume systems was 1400 kW.Compared with the static load calculation method,the dynamic method reduced 33%of the chiller design capacity.When two chillers were used,different chiller combinations’annual cooling energy consumption ranged from 10.41 to 11.88,averaging 11.12 kWh/m^(2).The lowest energy consumption was 10.41 kWh/m^(2) when two chillers with 538 kW and 1076 kW each were selected.Selecting the proper chiller number with different capacities was critical to achieving lower energy consumption,which achieved 12.6%cooling system energy consumption reduction for the case study building.This study demonstrated that AutoBPS-BIM has a large potential in modeling BEM and optimizing chiller design.

关键词： BIM building energy model EnergyPlus chiller design optimization AutoBPS-BIM

Generalized degradation reliability model considering phase transition

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Journal of Systems Engineering and Electronics 2022年第3期33卷 748-758页

作者： zhang Ao WANG zhihua WU Qiong LIU Chengrui School of Aeronautic Science and Engineering Beihang UniversityBeijing 100191China Institute of Spacecraft System Engineering China Academy of Space TechnologyBeijing 100094China Beijing Institute of Control Engineering Beijing 100094China

Aiming to evaluate the reliability of phase-transition degrading systems,a generalized stochastic degradation model with phase transition is constructed,and the corresponding analytical reliability function is formulated under the concept of the first hitting time.The phase-varying stochastic property and the phase-varying nonlinearity are considered simultaneously in the proposed model.To capture the phase-varying stochastic pro-perty,a Wiener process is adopted to model the non-monotonous degradation phase,while a Gamma process is utilized to model the monotonous one.In addition,the phase-varying non-linearity is captured by different transformed time scale functions.To facilitate the practical application of the proposed model,identification of phase model type and estimation of model parameters are discussed,and the initial guesses for parameters optimization are also given.Based on the constructed model,two simulation studies are carried out to verify the analytical reliability function and analyze the influence of model misspecification.Finally,a practical case study is conducted for illustration.

关键词： degradation phase transition reliability stochastic process nonlinearity

Archetype identification and urban building energy modeling for city-scale buildings based on GIS datasets

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Building Simulation 2022年第9期15卷 1547-1559页

作者： zhang Deng Yixing Chen Jingjing Yang zhihua Chen College of Civil Engineering Hunan UniversityChangsha 410082China Key Laboratory of Building Safety and Energy Efficiency of Ministry of Education Hunan UniversityChangsha 410082China

Urban building energy modeling has become an efficient way to understand urban building energy use and explore energy conservation and emission reduction potential.This paper introduced a method to identify archetype buildings and generate urban building energy models for city-scale buildings where public building information was unavailable.A case study was conducted for 68,966 buildings in Changsha city,China.First,clustering and random forest methods were used to determine the building type of each building footprint based on different GIS datasets.Then,the convolutional neural network was employed to infer the year built of commercial buildings based on historical satellite images from multiple years.The year built of residential buildings was collected from the housing website.Moreover,twenty-two building types and three vintages were selected as archetype buildings to represent 59,332 buildings,covering 87.4%of the total floor area.Ruby scripts leveraging on OpenStudio-Standards were developed to generate building energy models for the archetype buildings.Finally,monthly and annual electricity and natural gas energy use were simulated for the blocks and the entire city by EnergyPlus.The total electricity and natural gas use for the 59,332 buildings was 13,864 GWh and 23.6×10^(6) GJ.Three energy conservation measures were evaluated to demonstrate urban energy saving potential.The proposed methods can be easily applied to other cities in China.

关键词： urban building energy modeling building type year built-archetype building EnergyPlus