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PAMPHLET:PAM Prediction HomoLogous-Enhancement Toolkit for precise PAM prediction in CRISPR-Cas systems

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Journal of Genetics and Genomics 2025年第2期52卷 258-268页

作者： chen Qi Xuechun shen Baitao Li Chuan Liu Lei Huang Hongxia Lan Donglong chen Yuan Jiang Dan Wang Guangdong Provincial Key Laboratory of Interdisciplinary Research and Application for Data Science BNU-HKBU United International CollegeZhuhaiGuangdong 519087China School of Biology and Biological Engineering South China University of TechnologyGuangzhouGuangdong 510006China BGI Research HangzhouZhejiang 310030China BGI Research ShenzhenGuangdong 518083China College of Life Sciences University of Chinese Academy of SciencesBeijing 100049China Laboratory of Integrative Biomedicine Department of BiologyFaculty of ScienceUniversity of CopenhagenCopenhagenDenmark Qingdao-Europe Advanced Institute for Life Sciences BGI ResearchQingdaoShandong 266555China School of Life Science Hangzhou Institute for Advanced StudyUniversity of Chinese Academy of SciencesHangzhouZhejiang 310024China STOmics Americas Ltd. 2904 Orchard PkwySan Jose CA 95134USA

CRISPR-Cas technology has revolutionized our ability to understand and engineer organisms,evolving from a singular Cas9 model to a diverse CRISPR toolbox.A critical bottleneck in developing new Cas proteins is identifying protospacer adjacent motif(PAM)*** to the limitations of experimental methods,bioinformatics approaches have become ***,existing PAM prediction programs are limited by the small number of spacers in CRISPR-Cas systems,resulting in low *** address this,we develop PAMPHLET,a pipeline that uses homology searches to identify additional spacers,significantly increasing the number of spacers up to *** is validated on 20 CRISPR-Cas systems and successfully predicts PAM sequences for 18 *** predictions are further validated using the DocMF platform,which characterizes protein-DNA recognition patterns via next-generation *** high consistency between PAMPHLET predictions and DocMF results for Cas proteins demonstrates the potential of PAMPHLET to enhance PAM sequence prediction accuracy,expedite the discovery process,and accelerate the development of CRISPR tools.

关键词： CRISPR-Cas Protospacer adjacentmotif Genome editing PAM prediction Computational framework

Super-high bed sintering for iron ores:variation and optimization of bed resistance

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Journal of Iron and Steel Research International 2025年第1期32卷 40-51页

作者： Liang-ping Xu Lin Xiong Hui-bo Liu Xi-duan Yang Ai-xiang Mao Pei-dun chen Guang-hui Li School of Minerals Processing and Bioengineering Central South UniversityChangsha410083HunanChina Central Research Institute Baosteel Group Co.Ltd.Shanghai201900China Manufacturing Management Department Guangdong Zhongnan Iron and Steel Co.Ltd.Shaoguan512123GuangdongChina Technology and Development Center Shandong Taishan Iron and Steel Group Co.Ltd.Jinan271100ShandongChina

As the bed depth increases,sintering yield increases,but the productivity *** reveal the reasons for the decrease in productivity and explore targeted solutions,the bed resistance of mixtures,wet zone,and combustion zone was analyzed in the *** results showed that the decreased porosity of mixture resulted in the increased bed resistance by 160.56%when the bed depth increased from 600 to 1000 *** improving porosity of 1%by adding loosening bars with optimized size and distribution,the bed resistance decreased,and the productivity increased by 5%.The increase in bed depth increased the thickness of the wet zone from 120 to 680 mm and the resistance from 1.56 to 8.83 *** using a three-stage intensive mixer and pre-adding water for granulation,the moisture of mixture was reduced by 0.6%,and the sintering productivity increased by 4%.Besides,the high bed resistance is mainly caused by the increase in the thickness of the combustion zone from 31.9 to 132.7 mm,and the bed resistance increased from 0.70 to 5.62 *** bed resistance of the combustion zone at 900 mm was increased by 90.51%compared to 700 *** optimization of the distribution of coke breeze,the thickness of combustion zone at the lower layer decreased from 132.7 to 106.84 mm and permeability improved significantly.

关键词： Super-high bed sintering Bed resistance Permeability Productivity Wet zone Combustion zone

Homologous CoS2 interface with directed electron transfer and strong chloridion repulsion for efficient seawater oxidation

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Science China Chemistry 2025年

作者： Yuan Tian Jiang-bo chen Jie Ying Ge Tian Yu-Xuan Xiao Yi Lu Si-Ming Wu Wei Geng Ling shen Xiao-Yu Yang State Key Laboratory of Advanced Technology for Materials Synthesis and Processing and School of Materials Science and Engineering and Shenzhen Research Institute & Laoshan Laboratory Wuhan University of Technology School of Chemical Engineering and Technology Sun Yat-Sen University National Energy Key Laboratory for New Hydrogen-Ammonia Energy Technologies Foshan Xianhu Laboratory

Seawater electrolysis is a highly promising method to produce high energy density hydrogen,especially in dry areas that have scarce freshwater ***,application of seawater electrolysis is confronted by two major problems associated with catalysts employed for the anodic oxygen evolution reaction （OER） including the competitive hypochlorite evolution reaction（HCER） and strong chloridion （Cl–） triggered *** studies aimed at overcoming these problems,a facile method has been developed to synthesize a homologous CoS2heterojunction as an OER *** to a difference in work functions at the interface and increased electron density,this material has directed electron transfer and strong chloridion repulsion properties,*** have shown that CoS2achieves low overpotentials of 289 and 322 mV at 10 mA cm-2current density in respective alkaline （1 M KOH） and alkaline simulated seawater ***,the outstanding stability of CoS2is reflected in a negligible decline in activity during promotion of the OER for 100 *** of density functional theory calculations reveal that the homologous CoS2heterojunction promotes directed electron transport for optimizing adsorption/desorption of reactive species and heightens the Cl-adsorption energy for strongly repulsing Cl-,phenomena that enhance OER performance in alkaline simulated seawater.

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Polymer microbottle with flexible tunability for ultrasensitive ultrasound sensing

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Science China(Physics,Mechanics & Astronomy) 2025年第3期68卷 124-130页

作者： Liaosha Kuang Jialve Sun shengnan Huangfu Tinglan chen Zijing Cai Tian Xu Xuanyi Zhang bo Ni Fangxing Zhang School of Physics and Technology Nantong UniversityNantong226019China Peking University Yangtze Delta Institute of Optoelectronics Nantong226010China State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano-optoelectronics School of PhysicsPeking UniversityBeijing100871China School of Electronic Information Engineering Shanghai DianJi UniversityShanghai201306China

Optical whispering-gallery-mode microcavities have attracted significant attention for their potential in ultrasensitive ultrasound sensing,despite always relying on expensive tunable lasers in *** this study,we integrated an electrothermal tuning function inside the microcavity,enabling fast scanning of modes by applying voltages,which helps provide real-time searching and tracking of the optimal *** device demonstrated a quality factor exceeding 10^(6)with a broad tuning range over 33 *** structure achieved high sensitivity in ultrasound detection,with a noise equivalent pressure(NEP)of 3.35 m Pa/Hz^(1/2)at 20 *** further reported the advantages of the mode thermal broadening effect for ultrasound detection,with successfully obtaining high-contrast photoacoustic *** research introduces an innovative approach for cost-effective,high-stability ultrasound detection with microcavity,showing great value for application in photoacoustic imaging.

关键词： microbottle broad tuning range ultrasound detection photoacoustic imaging

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Macrophage polarization in cardiac transplantation:Insights into immune modulation and therapeutic approaches

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BIOCELL 2025年第1期49卷 61-78页

作者： JINGWEI JIANG bo JIA CHUAN WANG chen FANG YUGUI LI GUOXING LING BAOSHI ZHENG chenG LUO Department of Cardiovascular Surgery The First Affiliated Hospital of Guangxi Medical UniversityNanning530021China The First Clinical Medical College of Guangxi Medical University Nanning530021China Department of Cardiovascular Surgery Beijing Anzhen Hospital of Capital Medical UniversityBeijing100029China

The role and regulatory mechanisms of macrophage polarization in cardiac transplantation have gained significant *** can polarize into either the M1(pro-inflammatory)or M2(anti-inflammatory)phenotype in response to environmental cues.M1 macrophages facilitate transplant rejection by releasing inflammatory mediators and activating T cells,whereas M2 macrophages support graft survival by secreting antiinflammatory factors and promoting tissue *** quality control regulation plays a crucial role in macrophage polarization,which may influence graft survival and immune *** review provides an overview of the current understanding of mitochondrial quality control-regulated macrophage polarization in cardiac transplantation,its effects on graft outcomes,and potential therapeutic strategies to modulate this process to enhance transplant success *** review was conducted by systematically analyzing recent studies and integrating findings from key research articles to synthesize a comprehensive understanding of this emerging field.

关键词： Cardiac transplantation Mitochondrial quality control Macrophage polarization immune tolerance transplant rejection

Two-dimensional lateral magnetic tunnel junction with ultrahigh tunneling magnetoresistance

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Nano Research 2025年第2期18卷 958-964页

作者： Qiu-Qiu Li Zhi-Fu Duan Wen-Wen Liu Rong Yang bo Li Ke-Qiu chen Changsha Semiconductor Technology and Application Innovation Research Institute College of Semiconductors(College of Integrated Circuits)Hunan UniversityChangsha 410082China Department of Applied Physics School of Physics and ElectronicsHunan UniversityChangsha 410082China Research Institute of Hunan University in Chongqing Chongqing 401120China shenzhen Research Institute of Hunan University Shenzhen 518063China

Giant tunneling magnetoresistance(TMR)has always been a pursuit in the research of magnetic tunnel junctions(MTJ).Two-dimensional(2D)magnetic materials have been used to construct lateral MTJ with high *** we investigated the crystal structure and magnetic property of CrSI monolayer,and found that it is a ferromagnetic semiconductor with a Curie temperature of about 180 *** CrSI monolayer with Li adsorption(Li-CrSI)show ferromagnetic half-metallic with a high Curie temperature of 300 *** we designed a lateral Li CrSI/CrSI/Li-CrSI monolayer *** TMR of the MTJs along b transport direction is 3 orders of magnitude times larger than that of the a transport direction,which should result from the different spin filtering ability along the two *** TMR of b transport direction in the MTJ is 7.67×10^(14),which is significantly higher than that of any reported lateral MTJs based on 2D *** results provide a promising avenue for designing lateral MTJs with giant TMR and high Curie temperature.

关键词： two-dimensional materials magnetic tunnel junctions CrSI monolayer tunneling magnetoresistance Li atom adsorption

Assembly and network of Rhei Radix et Rhizoma surface microbiome shaped by processing methods and sampling locations

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Chinese Herbal Medicines 2025年第1期17卷 189-199页

作者： Guangfei Wei Xiao chen Guozhuang Zhang Conglian Liang Zhaoyu Zhang bo Zhang Shilin chen Linlin Dong State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs Institute of Chinese Materia Medica China Academy of Chinese Medical Sciences School of Biomedicine Beijing City University Shandong University of Traditional Chinese Medicine School of Pharmacy Linyi University Institute of Herbgenomics Chengdu University of Traditional Chinese Medicine

Objective:Rhei Radix et Rhizoma has five types of products,namely,raw rhubarb(RR),wine rhubarb(WR),vinegar rhubarb(VR),cooked rhubarb(CR),and rhubarb charcoal(RC).However,Rhei Radix et Rhizoma is easily contaminated with fungi and mycotoxins if not harvested or processed ***,we intend to analyze how microbiome assemblies and co-occurrence patterns are influenced by sampling locations and processing ***:High-throughput sequencing and internal transcribed spacer 2(ITS2) were carried out to study the diversities(α-and β-diversity),composition(dominant taxa and potential biomarkers),and network complexitity of surface fungi on RR, WR,VR,CR,and RC collected from Gansu and Sichuan provinces,***:The phyla Ascomycota and Basidiomycota;the genera Kazachstania,Malassezia,and Asterotremella;and the species Kazachstania exigua,Asterotremella pseudolonga,and Malassezia restricta were the dominant fungi and exhibited differences in the two provinces and the five processed *** α-diversity and network complexity were strongly dependent on processing *** 1,the Shannon index,and network complexity and connectivity were highest in the CR *** α-diversity and network complexity were influenced by sampling *** 1 and network complexity and connectivity were highest in the Gansu ***:The assembly and network of the surface microbiome on Rhei Radix et Rhizoma were shaped by processing methods and sampling *** paper offers a comprehensive understanding of microorganisms,which can provide early warning for potential mycotoxins and ensure the safety of drugs and consumers.

关键词： community assembly fungi processing methods Rhei Radix et Rhizoma sampling locations

Leucine-Rich Repeat Protein Family Regulates Stress Tolerance and Development in Plants

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Rice science 2025年第1期32卷 32-43页

作者： HAO Zhiqi WANG Tingyi chen Dongdong shen Lan ZHANG Guangheng QIAN Qian ZHU Li State Key Laboratory of Rice Biology and Breeding China National Rice Research InstituteHangzhou 310006China Yazhouwan National Laboratory Sanya 572024China National Nanfan Research Institute(Sanya) Chinese Academy of Agricultural SciencesSanya 572024China

The leucine-rich repeat(LRR)protein family is involved in a variety of fundamental metabolic and signaling processes in plants,including growth and defense *** proteins can be divided into two categories:those containing LRR domains along with other structural elements,which are further subdivided into five groups,LRR receptor-like kinases,LRR receptor-like proteins,nucleotide-binding site LRR proteins,LRR-extensin proteins,and polygalacturonase-inhibiting proteins,and those containing only LRR ***,various LRR proteins are primarily involved in plant development and responses to environmental ***,the LRR protein family plays a central role in signal transduction pathways related to stress *** this review,we classify and analyze the functions of LRR proteins in *** extensive research has been conducted on the roles of LRR proteins in disease resistance signaling,these proteins also play important roles in abiotic stress *** review highlights recent advances in understanding how LRR proteins mediate responses to biotic and abiotic *** upon these insights,further exploration of the roles of LRR proteins in abiotic stress resistance may aid efforts to develop rice varieties with enhanced stress and disease tolerance.

关键词： leucine-rich repeat classification function stress tolerance plant development

维普期刊数据库

Unveiling solid-solid contact states in all-solid-state lithium batteries:An electrochemical impedance spectroscopy viewpoint

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Journal of Energy Chemistry 2025年第2期101卷 16-22页

作者： Jin-Liang Li Liang shen Zi-Ning cheng Jun-Dong Zhang Ling-Xuan Li Yu-Tong Zhang Yan-Bin Gao Chunli Guo Xiang chen chen-Zi Zhao Rui Zhang Qiang Zhang Tsinghua Center for Green Chemical Engineering Electrification Beijing Key Laboratory of Green Chemical Reaction Engineering and Technology Department of Chemical Engineering Tsinghua University College of Materials Science and Engineering Taiyuan University of Technology Advanced Research Institute of Multidisciplinary Science School of Materials Science and Engineering Beijing Institute of Technology Beijing Huairou Laboratory Institute for Carbon Neutrality Tsinghua University Shanxi Research Institute for Clean Energy Tsinghua University

All-solid-state lithium batteries（ASSLBs） are strongly considered as the next-generation energy storage devices for their high energy density and intrinsic *** solid-solid contact between lithium metal and solid electrolyte plays a vital role in the performance of working ASSLBs,which is challenging to investigate quantitatively by experimental *** work proposed a quantitative model based on the finite element method for electrochemical impedance spectroscopy simulation of different solid-solid contact states in *** the assistance of an equivalent circuit model and distribution of relaxation times,it is discovered that as the number of voids and the sharpness of cracks increase,the contact resistance Rcgrows and ultimately dominates the battery *** accurate fitting,inverse proportional relations between contact resistance Rcand（1-porosity） as well as crack angle was *** contribution affords a fresh insight into clarifying solid-solid contact states in ASSLBs.

关键词： All-solid-state lithium batteries Distribution of relaxation times Electrochemical impedance spectroscopy Equivalent circuit model Finite element method Solid-solid contacts