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KaKs_Calculator 3.0:Calculating Selective Pressure on Coding and Non-coding Sequences

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Genomics, Proteomics & Bioinformatics 2022年第3期20卷 536-540页

作者： zhang zhang National Genomics Data Center Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China China National Center for Bioinformation Beijing 100101China University of Chinese Academy of Sciences Beijing 100049China

KaKs_Calculator 3.0 is an updated toolkit that is capable of calculating selective pressure on both coding and non-coding sequences.Similar to the nonsynonymous/synonymous substitution rate ratio for coding sequences,selection on non-coding sequences can be quantified as the ratio of non-coding nucleotide substitution rate to synonymous substitution rate of adjacent coding sequences.As testified on empirical data,KaKs_Calculator 3.0 shows effectiveness to detect the strength and mode of selection operated on molecular sequences,accordingly demonstrating its great potential to achieve genome-wide scan of natural selection on diverse sequences and identification of potentially functional elements at a whole-genome scale.The package of KaKs_Calculator 3.0 is freely available for academic use only at https://***/biocode/tools/BT000001.

关键词： KaKs_Calculator Selective pressure Substitution Coding Non-coding

SARS-CoV-2 variants,immune escape,and countermeasures

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Frontiers of Medicine 2022年第2期16卷 196-207页

作者： Yi zhang Haocheng zhang Wenhong zhang Department of Infectious Diseases National Medical Center for Infectious DiseasesShanghai Key Laboratory of Infectious Diseases and Biosafety Emergency ResponseHuashan HospitalFudan UniversityShanghai 200040China State Key Laboratory of Genetic Engineering and Institute of Biostatistics School of Life SciencesFudan UniversityShanghai 200040China

Coronavirus disease 2019(COVID-19)has become a global pandemic disease.SARS-CoV-2 variants have aroused great concern and are expected to continue spreading.Although many countries have promoted rollout vaccination,the immune barrier has not yet been fully established,indicating that populations remain susceptible to infection.In this review,we summarize the literature on variants of concern and focus on the changes in their transmissibility,pathogenicity,and resistance to the immunity constructed by current vaccines.Furthermore,we analyzed relationships between variants and breakthrough infections,as well as the paradigm of new variants in countries with high vaccination rates.Terminating transmission,continuing to strengthen variant surveillance,and combining nonpharmaceutical intervention measures and vaccines are necessary to control these variants.

关键词： SARS-CoV-2 COVID-19 vaccine immune escape breakthrough prevention

Mitogen-activated protein kinase cascades in plant signaling

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Journal of Integrative Plant Biology 2022年第2期64卷 301-341页

作者： Mengmeng zhang Shuqun zhang The Key Laboratory of Plant Immunity College of Plant ProtectionNanjing Agricultural UniversityNanjing210095 China Division of Biochemistry University of MissouriColumbiaMO65211 USA

Mitogen-activated protein kinase(MAPK)cascades are key signaling modules downstream of receptors/sensors that perceive either endogenously produced stimuli such as peptide ligands and damage-associated molecular patterns(DAMPs)or exogenously originated stimuli such as pathogen/microbe-associated molecular patterns(P/MAMPs),pathogen-derived effectors,and environmental factors.In this review,we provide a historic view of plant MAPK research and summarize recent advances in the establishment of MAPK cascades as essential components in plant immunity,response to environmental stresses,and normal growth and development.Each tier of the MAPK cascades is encoded by a small gene family,and multi ple members can function redundantly in an MAPK cascade.Yet,they carry out a diverse array of biological functions in plants.How the signaling specificity is achieved has become an interesting topic of MAPK research.Future investigations into the molecular mechanism(s)underlying the regulation of MAPK activation including the activation kinetics and magnitude in response to a stimulus,the spatiotemporal expression patterns of all the components in the signaling pathway,and functional characterization of novel MAPK substrates are central to our understanding of MAPK functions and signaling specificity in plants.

关键词： abiotic stress ligand-receptor interaction mitogenactivated protein kinase MAPK substrate plant growth and development plant hormone plant immunity receptor-like protein kinase signal transduction

Seismic fragility analysis of clay-pile-pier systems considering the optimization of ground motion intensity measures

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Earthquake Engineering and Engineering Vibration 2023年第4期22卷 965-977页

作者： zhang Panpan zhang Lei zhang Zhen School of Civil Engineering and Architecture Wuhan University of TechnologyWuhan 430070China

The performance of clay-pile-pier system under earthquake shaking was comprehensively examined via three-dimensional finite element analyses,in which the complex stress-strain relationships of a clay and piled pier system were depicted by a hyperbolic-hysteretic and an equivalent elastoplastic model,respectively.One hundred twenty ground motions with varying peak accelerations were considered,along with the variations in bridge superstructure mass and pile flexural rigidity.Comprehensive comparison studies suggested that peak pile-cap acceleration and peak pile-cap velocity are the optimal ground motion intensity measures for seismic responses of the pier and the pile,respectively.Furthermore,based on two optimal ground motion intensity measures and using curvature ductility to quantify different damage states,seismic fragility analyses were performed.The pier generally had no evident damage except when the bridge girder mass was equal to 960 t,which seemed to be comparatively insensitive to the varying pile flexural rigidity.In comparison,the pile was found to be more vulnerable to seismic damage and its failure probabilities tended to clearly reduce with the increment of pile flexural rigidity,while the influence of the bridge girder mass was relatively minor.

关键词： clay-pile-pier system seismic fragility analysis ground motion intensity measures damage probability

Occupancy-aided ventilation for airborne infection risk control:Continuously or intermittently reduced occupancies?

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Building Simulation 2023年第5期16卷 733-747页

作者： Sheng zhang Dun Niu zhang Lin School of Human Settlements and Civil Engineering Xi’an Jiaotong UniversityXi’anChina Division of Building Science and Technology City University of Hong KongChina

Ventilation is an important engineering measure to control the airborne infection risk of acute respiratory diseases,e.g.,Corona Virus Disease 2019(COVID-19).Occupancy-aided ventilation methods can effectively improve the airborne infection risk control performance with a sacrifice of decreasing working productivity because of the reduced occupancy.This study evaluates the effectiveness of two occupancy-aided ventilation methods,i.e.,the continuously reduced occupancy method and the intermittently reduced occupancy method.The continuously reduced occupancy method is determined by the steady equation of the mass conservation law of the indoor contaminant,and the intermittently reduced occupancy method is determined by a genetic algorithm-based optimization.A two-scenarios-based evaluation framework is developed,i.e.,one with targeted airborne infection risk control performance(indicated by the mean rebreathed fraction)and the other with targeted working productivity(indicated by the accumulated occupancy).The results show that the improvement in the airborne infection risk control performance linearly and quadratically increases with the reduction in the working productivity for the continuously reduced occupancy method and the intermittently reduced occupancy method respectively.At a given targeted airborne infection risk control performance,the intermittently reduced occupancy method outperforms the continuously reduced occupancy method by improving the working productivity by up to 92%.At a given targeted working productivity,the intermittently reduced occupancy method outperforms the continuously reduced occupancy method by improving the airborne infection risk control performance by up to 38%.

关键词： occupancy-aided ventilation continuously reduced occupancy intermittently reduced occupancy airborne infection risk rebreathed fraction working productivity

RNA therapeutics:updates and future potential

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Science China(Life Sciences) 2023年第1期66卷 12-30页

作者： Caroline zhang Biliang zhang State Key Laboratory of Respiratory Disease Guangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhou 510530China Guangzhou RiboBio Co. LtdGuangzhou 510663China Argorna Pharmaceuticals Co. Guangzhou 510530China

Recent advancements in the production,modification,and cellular delivery of RNA molecules facilitated the expansion of RNAbased therapeutics.The increasing understanding of RNA biology initiated a corresponding growth in RNA therapeutics.In this review,the general concepts of five classes of RNA-based therapeutics,including RNA interference-based therapies,antisense oligonucleotides,small activating RNA therapies,circular RNA therapies,and messenger RNA-based therapeutics,will be discussed.Moreover,we also provide an overview of RNA-based therapeutics that have already received regulatory approval or are currently being evaluated in clinical trials,along with challenges faced by these technologies.RNA-based drugs demonstrated positive clinical trial results and have the ability to address previously“undruggable”targets,which delivers great promise as a disruptive therapeutic technology to fulfill its full clinical potentiality.

关键词： RNA RNA therapeutics mRNA vaccine RNAi

Host plant traits play a crucial role in shaping the composition of epiphytic microbiota in the arid desert,Northwest China

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Journal of Arid Land 2024年第5期16卷 699-724页

作者： zhang Jun zhang Yuanming zhang Qi State Key Laboratory of Desert and Oasis Ecology Key Laboratory of Ecological Safety and Sustainable Development in Arid LandsXinjiang Institute of Ecology and GeographyChinese Academy of SciencesUrumqi 830011China Xinjiang Key Laboratory of Biodiversity Conservation and Application in Arid Lands Xinjiang Institute of Ecology and GeographyChinese Academy of SciencesUrumqi 830011China Xinjiang Field Scientific Observation Research Station of Tianshan Wild Fruit Forest Ecosystem Yili Botanical GardenXinjiang Institute of Ecology and GeographyChinese Academy of SciencesUrumqi 830011China College of Life Sciences Shihezi UniversityShihezi 832003China

Phyllosphere microorganisms are a crucial component of environmental microorganisms,highly influenced by host characteristics,and play a significant role in plant health and productivity.Nonetheless,the impact of host characteristics on shaping phyllosphere microbial communities of plants with different life forms remains ambiguous.Utilizing high-throughput sequencing technology,this study analyzed the diversity and community composition of phyllosphere epiphytic microorganisms(e.g.,bacteria and fungi)of various plant life forms in the hinterland of the Gurbantunggut Desert,Northwest China.Functional annotation of prokaryotic taxa(FAPROTAX)and fungi function guild(FUNGuild)were employed to assess the ecological functions of microorganisms and to investigate the role of stochastic and deterministic processes in shaping phyllosphere microbial communities.Result showed a diverse array of phyllosphere epiphytic microorganisms in the desert plants,with Proteobacteria,Cyanobacteria,and Actinobacteriota dominating bacterial community,while Ascomycota and Basidiomycota were prevalent in fungal community.Comparison across different plant life forms highlighted distinct microbial communities,indicating strong filtering effects by plant characteristics.FAPROTAX prediction identified intracellular parasites(accounting for 27.44%of bacterial community abundance),chemoheterotrophy(10.12%),and phototrophy(17.41%)as the main functions of epiphytic bacteria on leaves of different life form plants.FUNGuild prediction indicated that phyllosphere epiphytic fungi primarily served as Saprotrophs(81.77%),Pathotrophs(17.41%),and Symbiotrophs(0.82%).Co-occurrence network analysis demonstrated a predominance of positive correlations among different microbial taxa.Raup-Crick dissimilarity index analysis revealed that deterministic processes predominantly influenced phyllosphere bacterial and fungal community assembly.Variance partitioning analysis and random forest modeling suggested that plant leaf functional traits significantly impacted

关键词： phyllosphere epiphytic bacteria phyllosphere epiphytic fungi community structure community diversity functional diversity plant life form plant functional traits

Reversing free-electron transfer of sulfide cocatalyst for exceptional photocatalytic H_(2)evolution

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Journal of Materials Science & Technology 2024年第4期171卷 147-149页

作者： Yanfeng zhang Zhenyi zhang National Experimental Chemistry Teaching Center Hebei Key Laboratory of Inorganic Nano-materialsCollege of Chemistry and Materials ScienceHebei Normal UniversityShijiazhuang 050024China Key Laboratory of New Energy and Rare Earth Resource Utilization of State Ethnic Affairs Commission Key Laboratory of Photosensitive Materials and Devices of Liaoning ProvinceSchool of Physics and Materials EngineeringDalian Minzu UniversityDalian 116600China

Recently,Yu and co-workers deeply explore the potential impact of free electron transfer between co-catalysts and photocatalyst carriers on H_(2)evolution efficiency of active sites over MoS_(2+x).They pro-pose an electron-reversal tactics to evade the unexpected electron transfer and synchronously regulate the above transfer in a beneficial orientation for weakening hydrogen adsorption on S sites.Herein,this highlight not only discusses and summarizes the essences of electron reversal and the optimized H ad-sorption/desorption mechanism,but also emphasizes the significance of femtosecond transient absorp-tion spectroscopy(fs-TAS)and in-situ irradiated X-ray photoelectron spectroscopy(ISI-XPS)for revealing charge transfer dynamics and processes.We anticipate that this highlight can disseminate a new per-spective on the roles of photocatalyst carriers in improving cocatalytic H_(2)-production kinetics.

关键词： Photocatalysis Cocatalyst Electron reversal Antibonding-orbital occupancy S–H bonds

N-doped graphene quantum dot-decorated N-TiO2/P-doped porous hollow g-C_(3)N_(4) nanotube composite photocatalysts for antibiotic photodegradation and H2 production

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International Journal of Minerals,Metallurgy and Materials 2024年第1期31卷 165-178页

作者： Jingshu Yuan Yao zhang Xiaoyan zhang Junjie zhang Shen’gen zhang Institute for Advanced Materials and Technology University of Science and Technology BeijingBeijing 100083China Xi’an Fanyi University Xi’an 710105China Shunde Graduate School of University of Science and Technology Beijing Foshan 528399China State Key Laboratory of Lunar and Planetary Sciences Macao University of Science and TechnologyMacao SAR 820000China

Exclusive responsiveness to ultraviolet light (~3.2 eV) and high photogenerated charge recombination rate are the two primary drawbacks of pure TiO_(2). We combined N-doped graphene quantum dots (N-GQDs), morphology regulation, and heterojunction construction strategies to synthesize N-GQD/N-doped TiO_(2)/P-doped porous hollow g-C_(3)N_(4) nanotube (PCN) composite photocatalysts (denoted as G-TPCN). The optimal sample (G-TPCN doped with 0.1wt% N-GQD, denoted as 0.1% G-TPCN) exhibits significantly enhanced photoabsorption, which is attributed to the change in bandgap caused by elemental doping (P and N), the improved light-harvesting resulting from the tube structure, and the upconversion effect of N-GQDs. In addition, the internal charge separation and transfer capability of0.1% G-TPCN are dramatically boosted, and its carrier concentration is 3.7, 2.3, and 1.9 times that of N-TiO_(2), PCN, and N-TiO_(2)/PCN(TPCN-1), respectively. This phenomenon is attributed to the formation of Z-scheme heterojunction between N-TiO_(2) and PCNs, the excellent electron conduction ability of N-GQDs, and the short transfer distance caused by the porous nanotube structure. Compared with those of N-TiO_(2), PCNs, and TPCN-1, the H2 production activity of 0.1%G-TPCN under visible light is enhanced by 12.4, 2.3, and 1.4times, respectively, and its ciprofloxacin (CIP) degradation rate is increased by 7.9, 5.7, and 2.9 times, respectively. The optimized performance benefits from excellent photoresponsiveness and improved carrier separation and migration efficiencies. Finally, the photocatalytic mechanism of 0.1% G-TPCN and five possible degradation pathways of CIP are proposed. This study clarifies the mechanism of multiple modification strategies to synergistically improve the photocatalytic performance of 0.1% G-TPCN and provides a potential strategy for rationally designing novel photocatalysts for environmental remediation and solar energy conversion.

关键词： N-doped TiO_(2) N-doped graphene quantum dots P-doped g-C_(3)N_(4) porous hollow nanotube heterojunction photocatalysis