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Transfer learning enhanced graph neural network for aldehyde oxidase metabolism prediction and its experimental application

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Acta Pharmaceutica Sinica B 2024年第2期14卷 623-634页

作者： Jiacheng Xiong Rongrong Cui Zhaojun Li Wei Zhang Runze Zhang Zunyun Fu Xiaohong Liu Zhenghao Li Kaixian Chen Mingyue Zheng Drug Discovery and Design Center State Key Laboratory of Drug ResearchShanghai Institute of Materia MedicaChinese Academy of SciencesShanghai 201203China University of Chinese Academy of Sciences Beijing 100049China College of Computer and Information engineering Dezhou UniversityDezhou 253023China AI department Suzhou Alphama Biotechnology Co.Ltd.Suzhou 215000China Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and TechnologyShanghaiTech UniversityShanghai 200031China State Key Laboratory of Pharmaceutical biotechnology Nanjing UniversityNanjing 210023China

Aldehyde oxidase(AOX)is a molybdoenzyme that is primarily expressed in the liver and is involved in the metabolism of drugs and other ***-mediated metabolism can result in unexpected outcomes,such as the production of toxic metabolites and high metabolic clearance,which can lead to the clinical failure of novel therapeutic *** models can assist medicinal chemists in rapidly evaluating the AOX metabolic risk of compounds during the early phases of drug discovery and provide valuable clues for manipulating AOX-mediated metabolism *** this study,we developed a novel graph neural network called AOMP for predicting AOX-mediated *** integrated the tasks of metabolic substrate/non-substrate classification and metabolic site prediction,while utilizing transfer learning from 13C nuclear magnetic resonance data to enhance its performance on both *** significantly outperformed the benchmark methods in both cross-validation and external *** AOMP,we systematically assessed the AOX-mediated metabolism of common fragments in kinase inhibitors and successfully identified four new scaffolds with AOX metabolism liability,which were validated through in vitro ***,for the convenience of the community,we established the first online service for AOX metabolism prediction based on AOMP,which is freely available at https://***.

关键词： Drugmetabolism Aldehyde oxidase Transferlearning Graph neural network Kinase inhibitor

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Genome-wide identification and expression profiling of photosystem II(PsbX)gene family in upland cotton(Gossypium hirsutum L.)

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Journal of Cotton Research 2024年第1期7卷 1-14页

作者： RAZA Irum PARVEEN Abida AHMAD Adeel HU Daowu PAN Zhaoe ALI Imran DU Xiongming Institute of Cotton Research Chinese Academy of Agricultural SciencesNational Key Laboratory of Cotton Bio-Breeding and Integrated UtilizationAnyangHenan 455000China department of biotechnology and Genetic engineering Kohat University of Science and TechnologyKohatPakistan department of Botany Kohat University of Science and TechnologyKohatPakistan.

Background Photosystem II(PSII)constitutes an intricate assembly of protein pigments,featuring extrinsic and intrinsic polypeptides within the photosynthetic *** low-molecular-weight transmembrane protein PsbX has been identified in PSII,which is associated with the oxygen-evolving *** expression of PsbX gene protein is regulated by ***’s central role involves the regulation of PSII,facilitating the binding of quinone molecules to the Qb(PsbA)site,and it additionally plays a crucial role in optimizing the efficiency of *** these insights,a comprehensive understanding of the PsbX gene’s functions has remained *** In this study,we identified ten PsbX genes in Gossypium hirsutum *** phylogenetic analysis results showed that 40 genes from nine species were classified into one *** resulting sequence logos exhibited substantial conservation across the N and C terminals at multiple sites among all Gossypium ***,the ortholo-gous/paralogous,Ka/Ks ratio revealed that cotton PsbX genes subjected to positive as well as purifying selection pressure might lead to limited divergence,which resulted in the whole genome and segmental *** expression patterns of GhPsbX genes exhibited variations across specific tissues,as indicated by the ***,the expression of GhPsbX genes could potentially be regulated in response to salt,intense light,and drought ***,GhPsbX genes may play a significant role in the modulation of photosynthesis under adverse abiotic *** We examined the structure and function of PsbX gene family very first by using comparative genom-ics and systems biology approaches in *** seems that PsbX gene family plays a vital role during the growth and development of cotton under stress ***,the results of this study provide basic information to unveil the molecular and physiological function of PsbX genes of cotton plan

关键词： Photosystem Phylogenetic Synteny RNA seq Gene expression Orthologous

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A review of ultrafast laser micro/nano fabrication:Material processing,surface/interface controlling,and devices fabrication

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Nano Research 2024年第7期17卷 6212-6230页

作者： Heng Guo Jiawang Xie Guangzhi He Dezhi Zhu Ming Qiao Jianfeng Yan Jiachen Yu Jiaqun Li Yuzhi Zhao Ma Luo Haoze Han State Key Laboratory of Tribology in Advanced Equipment Department of Mechanical EngineeringTsinghua UniversityBeijing 100084China

Ultrafast laser processing technology has offered a wide range of opportunities in micro/nano fabrication and other fields such as nanotechnology,biotechnology,energy science,and photonics due to its controllable processing precision,diverse processing capabilities,and broad material *** processing abilities and applications of the ultrafast laser still need more *** the field of material processing,controlling the atomic scale structure in nanomaterials is *** effects exist in ultrafast laser surface/interface processing,making it difficult to modulate the nanostructure and properties of the surface/interface as *** the ultrafast laser fabrication of micro functional devices,the processing ability needs to be ***,we review the research progress of ultrafast laser micro/nano fabrication in the areas of material processing,surface/interface controlling,and micro functional devices *** useful ultrafast laser processing methods and applications in these areas are *** various processing effects and abilities,the ultrafast laser processing technology has demonstrated application values in multiple fields from science to industry.

关键词： ultrafast laser micro/nano fabrication material processing surface/interface controlling devices fabrication

Diet and monensin influence the temporal dynamics of the rumen microbiome in stocker and finishing cattle

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Journal of Animal Science and biotechnology 2024年第2期15卷 733-748页

作者： Jianmin Chai Caleb P.Weiss Paul A.Beck Wei Zhao Ying Li Jiangchao Zhao Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding College of Life Science and EngineeringFoshan UniversityFoshanChina Division of Agriculture Department of Animal ScienceUniversity of ArkansasFayettevilleARUSA department of Animal and Food Sciences Oklahoma State UniversityStillwaterOKUSA Institute of Feed Research of Chinese Academy of Agricultural Sciences Key Laboratory of Feed Biotechnology of the Ministry of Agriculture and Rural AffairsBeijing 100193China

Background Stocker cattle diet and management influence beef cattle performance during the finishing stage,but knowledge of the dynamics of the rumen microbiome associated with the host are lacking.A longitudinal study was conducted to determine how the feeding strategy from the stocker to the finishing stages of production affects the temporal dynamics of rumen *** the stocker phase,either dry hay or wheat pasture were provided,and three levels of monensin were *** calves were then transported to a feedlot and received similar finishing diets with or without *** microbial samples were collected on d 0,28,85 during the stocker stage(S0,S28 and S85)and d 0,14,28,56,30 d before slaughter and the end of the trial during the finishing stage(F0,F14,F28,F56,Pre-Ba,and Final).The V4 region of the bacterial 16S rRNA gene of 263 rumen samples was *** Higher alpha diversity,including the number of observed bacterial features and the Shannon index,was observed in the stocker phase compared to the finishing *** bacterial amplicon sequence variants(ASVs)differentiating different sampling time points were *** treatments during the stocker stage temporally impact the dynamics of rumen *** example,shared bacteria,including Bacteroidales(ASV19)and Streptococcus infantarius(ASV94),were significantly higher in hay rumen on S28,S85,and F0,while Bacteroidaceae(ASV11)and Limivicinus(ASV15)were more abundant in *** affected rumen microbial composition at a specific *** to feedlot significantly influenced microbiome structure and diversity in hay-fed *** taxa associated with body weight were classified,and core microbiotas interacted with each other during the *** In summary,the temporal dynamics of the rumen microbiome in cattle at the stocker and finishing stage are influenced by multiple factors of the feeding *** at the stocker phase may t

关键词： Beef cattle Diet Feedlot phase Monensin Next-generation sequencing Rumen microbiota Stocker

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Recent advances and applications of single atom catalysts based electrochemical sensors

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Nano Research 2024年第4期17卷 2994-3013页

作者： Mingyue Wang Mingfu Ye Jieyue Wang Yong Xu Zhendong Wang Xinyue Tong Xinya Han Kui Zhang Wenhai Wang Konglin Wu Xianwen Wei Institute of Clean Energy and Advanced Nanocatalysis(iClean) School of Chemistry and Chemical EngineeringAnhui University of TechnologyMaanshan 243002China School of Materials Science and engineering Anhui University of TechnologyMaanshan 243002China Anhui International Research Center of Energy materials green manufacturing and biotechnology School of Chemistry and Chemical EngineeringAnhui University of TechnologyMaanshan 243002China Carbon Cycle and Emission Control Research Center Low-Carbon Research InstituteAnhui University of TechnologyMaanshan 243002China

Single atom catalysts(SACs)have attracted considerable attention due to their unique structures and excellent catalytic performance,especially in the area of catalysis science and energy conversion and *** recent years,SACs have emerged as a new type of sensing material for constructing electrochemical sensors(ECSs),presenting excellent sensitivity,selectivity,and ***,we review the recent advances of SACs in electrochemical sensing and discuss the status quo of current SAC-based ***,the fundamentals of SAC-based ECSs are outlined,including the involved central metal atoms and various supports of SACs in this field,the detection mechanisms,and improving strategies of SAC-based ***,the important applications of SAC-based ECSs are listed and classified,covering the detection of reactive oxygen and nitrogen species,environmental pollutants,disease biomarkers,and ***,based on abundant reported cases,the current conundrums of SAC-based ECSs are summarized,and the prediction of their future developing trends is also put forward.

关键词： single atom catalysts(SACs) electrochemical sensors(ECSs) reactive oxygen and nitrogen species environmental pollutants disease biomarkers pharmaceuticals

Dental-derived stem cells in tissue engineering:the role of biomaterials and host response

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Regenerative Biomaterials 2024年第1期3卷 17-26页

作者： Weihao Yuan Luiza de Almeida Queiroz Ferreira Bo Yu Sahar Ansari Alireza Moshaverinia Weintraub Center for Reconstructive biotechnology Section of ProsthodonticsSchool of DentistryUniversity of CaliforniaLos AngelesLos AngelesCA 90095USA department of Restorative Dentistry School of DentistryUniversidade Federal de Minas GeraisBelo HorizonteMinas GeraisBrazil Section of Restorative Dentistry School of DentistryUniversity of CaliforniaLos AngelesLos AngelesCA 90095USA department of Bioengineering Henry Samueli School of Engineering and Applied SciencesUniversity of CaliforniaLos AngelesLos AngelesCA 90095USA

Dental-derived stem cells(DSCs)are attractive cell sources due to their easy access,superior growth capacity and low *** can respond to multiple extracellular matrix signals,which provide biophysical and biochemical cues to regulate the fate of residing ***,the direct transplantation of DSCs suffers from poor proliferation and differentiation toward functional cells and low survival rates due to local ***,elegant advances in the design of novel biomaterials have been made to give promise to the use of biomimetic biomaterials to regulate various cell behaviors,including proliferation,differentiation and *** could be tailored with multiple functionalities,e.g.,*** is an emerging need to summarize recent advances in engineered biomaterials-mediated delivery and therapy of DSCs and their potential ***,we outlined the design of biomaterials for supporting DSCs and the host response to the transplantation.

关键词： dental-derived stem cells biomaterials host response tissue engineering

Inkjet-Printing Controlled Phase Evolution Boosts the Efficiency of Hole Transport Material Free and Carbon-Based CsPbBr3 Perovskite Solar Cells Exceeding 9%

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Energy & Environmental Materials 2024年第2期7卷 213-224页

作者： Lihua Zhang Shi Chen Jie Zeng Zhengyan Jiang Qian Ai Xianfu Zhang Bihua Hu Xingzhu Wang Shihe Yang Baomin Xu department of Materials Science and engineering and Shenzhen engineering Research and Development Center for Flexible Solar Cells Southern University of Science and Technology department of Chemistry The Hong Kong University of Science and Technology Henan Key Laboratory of Photovoltaic Materials Henan University Guangdong Key Lab of Nano-Micro Material Research School of Chemical Biology and Biotechnology Shenzhen Graduate School Peking University Key University Laboratory of Highly Efficient Utilization of Solar Energy and Sustainable Development of Guangdong Southern University of Science and Technology Guangdong-Hong Kong-Macao Joint Laboratory for Photonic-Thermal-Electrical Energy Materials and Devices Southern University of Science and Technology

Hole transport material free carbon-based all-inorganic CsPbBr3perovskite solar cells（PSCs） are promising for commercialization due to its low-cost,high open-circuit voltage(Voc) and superior *** to the different solubility of PbBr2and CsBr in conventional solvents,CsPbBr3films are mainly obtained by multi-step spin-coating through the phase evolution from PbBr2to CsPb2Br5and then to *** scalable fabrication of highquality CsPbBr3films has been rarely ***,an inkjet-printing method is developed to prepare high-quality *** formation of long-range crystalline CsPb2Br5phase can effectively improve phase purity and promote regular crystal stacking of ***,the inkjetprinted CsPbBr3C-PSCs realized PCEs up to 9.09%,8.59% and 7.81% with active areas of 0.09,0.25,and 1 cm2,respectively,demonstrating the upscaling potential of our fabrication method and *** high performance is mainly ascribed to the high purity,strong crystal orientation,reduced surface roughness and lower trap states density of the as-printed *** work provides insights into the relationship between the phase evolution mechanisms and crystal growth dynamics of cesium lead bromide halide films.

关键词： all-inorganic perovskite solar cells CsPbBr3 inkjet-printing phase evolution

Ce6 nanoassemblies:Molecular mechanism and strategies for combinational anticancer therapy Special Collection:Aggregation-Induced Processes and Functions

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Aggregate

Aggregate 2024年第1期5卷 130-147页

作者： Yuwei Liu Shuting Xu Qingyang Lyu Yi Huang Weiping Wang State Key Laboratory of Pharmaceutical biotechnology The University of Hong KongHong KongChina department of Pharmacology and Pharmacy Li Ka Shing Faculty of MedicineThe University of Hong KongHong KongChina Laboratory of Molecular engineering and Nanomedicine Dr.Li Dak-Sum Research CentreThe University of Hong KongHong KongChina

Nowadays,cancer has become the leading cause of death worldwide,driving the need for effective therapeutics to improve patient *** therapy(PDT)has been widely applied as an antitumor modality,owing to its minimal invasiveness,localized tumor damage,and high safety ***,its efficacy is limited by poor stability of photosensitizers,inadequate tumor accumulation,and a complex tumor *** overcome these challenges,extensive endeavors have been made to explore the co-assembly of the widely used photosensitizer chlorin e6(Ce6)with various functional small molecules to enhance pharmacodynamic *** review provides a comprehensive overview of current studies on Ce6-based nanoparticles for effective PDT and precise delivery of functional *** self-assembly mechanism will be discussed in detail,with a focus on potential strategies for combinational therapy with PDT.

关键词： cancer treatment carrier-free chlorin e6(Ce6) light nanomedicine photodynamic therapy(PDT) selfassembly

Overlap in oncogenic and pro-inflammatory pathways associated with areca nut and nicotine exposure

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Cancer Pathogenesis and Therapy 2024年第3期2卷 187-194页

作者： Krati Garg Anuj Kumar Vidisha Kizhakkethil Pramod Kumar Shalini Singh department of Biochemical engineering and biotechnology Indian Institute of Technology(IIT)DelhiDelhi 110016India Division of Molecular Biology ICMR-National Institute of Cancer Prevention and Research(ICMR-NICPR)Indian Council of Medical ResearchNoidaUttar Pradesh 201301India department of biotechnology Vellore Institute of Technology(VIT)VelloreTamil Nadu 632024India ICMR-National Institute of Cancer Prevention&Research(ICMR-NICPR) Indian Council of Medical ResearchNoidaUttar Pradesh 201301India

Background:Betel nut/areca nut/Areca catechu is one of the most commonly used psychoactive substance,and is also a major preventable cause of *** other psychoactive substances,such as nicotine,the mechanisms underlying addiction to areca nuts and related oncogenesis remain *** reports suggest a possible overlap in the mechanisms of action of nicotine and areca nuts in the human ***,this study aimed to investigate the interactome of human proteins associated with areca nut exposure and the intricate similarities and differences in the effects of the two psychoactive substances on ***:A list of proteins associated with areca nut use was obtained from the available literature using terms from Medical Subject Headings(MeSH).Protein-protein interaction(PPI)networks and functional enrichment were *** results obtained for both psychoactive substances were ***:Given the limited number of common proteins(36/226,16%)in the two sets,a substantial overlap(612/1176 nodes,52%)was observed in the PPI networks,as well as in Gene *** nuts mainly affect signaling pathways through three hub proteins(alpha serine/threonine-protein kinase,tumor protein 53,and interleukin-6),which are common to both psychoactive substances,as well as two unique hub proteins(epidermal growth factor receptor and master regulator of cell cycle entry and proliferative metabolism).Areca nut-related proteins are associated with unique pathways,such as extracellular matrix organization,lipid storage,and metabolism,which are not found in nicotine-associated ***:Areca nuts affect regulatory mechanisms,leading to systemic toxicity and *** nuts also affect unique pathways that can be studied as potential markers of exposure,as well as targets for anticancer therapeutic agents.

关键词： Cancer Areca nut Nicotine Interactome Cell signaling