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Journal of Environmental Sciences 2024年第1期135卷 274-284页

作者： Zewen Wu Luan Zhang hao lin Shungui Zhou Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation College of Resources and EnvironmentFujian Agriculture and Forestry UniversityFuzhou 350002China School of Environmental Science and Engineering Hubei Key Laboratory of Mine Environmental Pollution Control and RemediationHubei Polytechnic UniversityHuangshi 435003China Fujian Provincial Key Laboratory of Eco-Industrial Green Technology Wuyi UniversityWuyishan 354300China

This study explored the combined effects of Bacillus subtilis inoculation with biochar on the evolution of bacterial communities,antibiotic resistance genes(ARGs),and mobile genetic elements(MGEs)during the composting of chicken manure.The results showed that B.subtilis inoculation combined with biochar increased bacterial abundance and diversity as well as prolonged the compost thermophilic period.Promoted organic matter biodegradation and facilitated the organic waste compost humification process,reduced the proliferation of ARGs by altering the bacterial composition.Firmicutes and Actinobacteriota were the main resistant bacteria related to ARGs and MGEs.The decrease in ARGs and MGEs was associated with the reduction in the abundance of related host bacteria.Compost inoculation with B.subtilis and the addition of biochar could promote nutrient transformation,reduce the increase in ARGs and MGEs,and increase the abundance of beneficial soil taxa.

关键词： Antibiotic resistance gene Bacillus subtilis Bacterial community Biochar Composting

Harnessing innate immune pathways for therapeutic advancement in cancer

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Signal Transduction and Targeted Therapy 2024年第4期9卷 1506-1564页

作者： Ankang Hu Li Sun hao lin Yuheng Liao Hui Yang Ying Mao Department of Neurosurgery Huashan HospitalFudan UniversityShanghaiP.R.China Institute for Translational Brain Research Shanghai Medical CollegeFudan University ShanghaiPR.China National Center for Neurological Disorders Huashan HospitalShanghai Medical CollegeFudan UniversityShanghaiP.R.China Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration Shanghai Clinical Medical Center of NeurosurgeryNeurosurgical Institute of Fudan UniversityHuashan HospitalShanghai Medical CollegeFudan UniversityShanghaiP.R.China State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science and MOE Frontiers Center for Brain Science Institutes of Brain ScienceShanghai Medical CollegeFudan UniversityShanghaiP.R.China Shanghai Key Laboratory of Medical Epigenetics International Co-laboratory of Medical Epigenetics and Metabolism(Ministry of Science and Technology)and Key Laboratory of Metabolism and Molecular Medicine(Ministry of Education)and Molecular and Cell Biology LabInstitutes of Biomedical SciencesShanghai Medical College of Fudan UniversityShanghaiP.R.China

The innate immune pathway is receiving increasing attention in cancer therapy.This pathway is ubiquitous across various cell types,not only in innate immune cells but also in adaptive immune cells,tumor cells,and stromal cells.Agonists targeting the innate immune pathway have shown profound changes in the tumor microenvironment(TME)and improved tumor prognosis in preclinical studies.However,to date,the clinical success of drugs targeting the innate immune pathway remains limited.Interestingly,recent studies have shown that activation of the innate immune pathway can paradoxically promote tumor progression.The uncertainty surrounding the therapeutic effectiveness of targeted drugs for the innate immune pathway is a critical issue that needs immediate investigation.In this review,we observe that the role of the innate immune pathway demonstrates heterogeneity,linked to the tumor development stage,pathway status,and specific cell types.We propose that within the TME,the innate immune pathway exhibits multidimensional diversity.This diversity is fundamentally rooted in cellular heterogeneity and is manifested as a variety of signaling networks.The pro-tumor effect of innate immune pathway activation essentially reflects the suppression of classical pathways and the activation of potential pro-tumor alternative pathways.Refining our understanding of the tumor's innate immune pathway network and employing appropriate targeting strategies can enhance our ability to harness the anti-tumor potential of the innate immune pathway and ultimately bridge the gap from preclinical to clinicalapplication.

关键词： drugs therapeutic innate

Cryptic divergences and repeated hybridizations within the endangered “living fossil” dove tree(Davidia involucrata) revealed by whole genome resequencing

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Plant Diversity 2024年第2期46卷 169-180页

作者： Yumeng Ren Lushui Zhang Xuchen Yang hao lin Yupeng Sang Landi Feng Jianquan Liu Minghui Kang Key Laboratory of Bio-resource and Eco-environment of Ministry of Education College of Life SciencesSichuan UniversityChengdu 610065China State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystem College of EcologyLanzhou UniversityLanzhou 730000China Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design Guangzhou Key Laboratory of Crop Gene EditingInnovative Center of Molecular Genetics and EvolutionSchool of Life SciencesGuangzhou UniversityGuangzhou 510006China

The identification and understanding of cryptic intraspecific evolutionary units(lineages) are crucial for planning effective conservation strategies aimed at preserving genetic diversity in endangered species.However, the factors driving the evolution and maintenance of these intraspecific lineages in most endangered species remain poorly understood. In this study, we conducted resequencing of 77 individuals from 22 natural populations of Davidia involucrata, a “living fossil” dove tree endemic to central and southwest China. Our analysis revealed the presence of three distinct local lineages within this endangered species, which emerged approximately 3.09 and 0.32 million years ago. These divergence events align well with the geographic and climatic oscillations that occurred across the distributional range.Additionally, we observed frequent hybridization events between the three lineages, resulting in the formation of hybrid populations in their adjacent as well as disjunct regions. These hybridizations likely arose from climate-driven population expansion and/or long-distance gene flow. Furthermore, we identified numerous environment-correlated gene variants across the total and many other genes that exhibited signals of positive evolution during the maintenance of two major local lineages. Our findings shed light on the highly dynamic evolution underlying the remarkably similar phenotype of this endangered species. Importantly, these results not only provide guidance for the development of conservation plans but also enhance our understanding of evolutionary past for this and other endangered species with similar histories.

关键词： Davidia involucrata Cryptic lineage Hybridization Population genomics Positive evolution

Patient satisfaction and follow-up adherence to glaucoma case management clinic in China

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International Journal of Ophthalmology(English edition) 2024年第1期17卷 73-81页

作者： hao lin Hu-Jie Lu Wen-Zhe Zhou Shu-Shu Zuo Yan-Yan Chen Shao-Dan Zhang National Clinical Research Center for Ocular Diseases Eye HospitalWenzhou Medical UniversityWenzhou 325027Zhejiang ProvinceChina School of Ophthalmology and Optometry Biomedical EngineeringWenzhou Medical UniversityWenzhou 325027Zhejiang ProvinceChina

AIM:To assess glaucoma patient satisfaction and follow-up adherence in case management and identify associated predictors to improve healthcare quality and patient outcomes.METHODS:In this cross-sectional study,a total of 119 patients completed a Patient Satisfaction Questionnaire-18 and a sociodemographic questionnaire.Clinical data was obtained from the case management system.Follow-up adherence was defined as completing each follow-up within±30d of the scheduled time set by ophthalmologists during the study period.RESULTS:Average satisfaction scored 78.65±7,with an average of 4.39±0.58 across the seven dimensions.Age negatively correlated with satisfaction(P=0.008),whilst patients with follow-up duration of 2 or more years reported higher satisfaction(P=0.045).Multivariate logistics regression analysis revealed that longer follow-up durations were associated with lower follow-up adherence(OR=0.97,95%CI,0.95-1.00,P=0.044).Additionally,patients with suspected glaucoma(OR=2.72,95%CI,1.03-7.20,P=0.044)and those with an annual income over 100000 Chinese yuan demonstrated higher adherence(OR=5.57,95%CI,1.00-30.89,P=0.049).CONCLUSION:The case management model proves effective for glaucoma patients,with positive adherence rates.The implementation of this model can be optimized in the future based on the identified factors and extended to glaucoma patients in more hospitals.

关键词： glaucoma patient satisfaction follow-up adherence case management

TCP-1,a novel peptide to diagnose early colon cancer

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Chinese Chemical Letters 2024年第3期35卷 226-233页

作者： Hang Yu Baoying Wen Min Huang Ru Feng Libin Pan Manyi Xu hao lin lin Cong Sen Zhang Yan Li Chi-Hin Cho Chongjing Zhang Xiaoguang Chen Yan Wang State Key Laboratory of Bioactive Substances and Functions of Natural Medicines Institute of Materia MedicaChinese Academy of Medical SciencesBeijing 100050China School of Biomedical Sciences Faculty of MedicineThe Chinese University of Hong KongHong KongChina

A nine cyclic peptide(TCP-1)showed excellent specificity for colon cancer.TCP-1 binds with human tumor tissues at early stages and mice tumor with diameters of 1-4 mm,suggesting that TCP-1 may be used for early diagnosis of colon cancer.The mechanism of the targeted binding of TCP-1 to colon cancer was also studied using immunoprecipitation,LC-MS and bioinformatics.After screening and identifying of the possible binding target proteins of TCP-1,keratin,typeⅡcytoskeletal 5 was speculated to be the specific binding target protein of TCP-1 in human tumor tissue.Pharmacokinetics studies were conducted to investigate the target-mediated drug disposition of the new tumor-specific peptide by LC-MS/MS.The tissue distribution study showed that TCP-1 was found only in colon tumors(the target site)in tumor mice did not bind to any other tissues.Conjugating TCP-1 to tumor markedly increased its removal rate from blood circulation but mildly extended its staying time in vivo.In tumor mice,a lower AUC of TCP-1(reduced by almost 35%)and 2-fold higher clearance were found compared to that of normal mice.The proposed metabolic pathway of TCP-1 in the kidney was also determined using LC-MS^(n)-IT-TOF.The high specificity and low toxicity of the peptide may be caused by its extremely tight binding to the targets.Potential applications for future clinical use,including MRI and PET/CT were also explored,and this research may promote the development of colon cancer diagnostic technology research and provide new ideas and technical routes for tumor diagnostic technology.

关键词： Colon cancer TCP-1 Peptide Cytokeratin 5 Pharmacokinetics/pharmacodynamics(PK/PD)

Development of a single transcript CRISPR/Cas9 toolkit for efficient genome editing in autotetraploid alfalfa

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The Crop Journal 2024年第3期12卷 788-795页

作者： Haixia Zhao Siyi Zhao Yingping Cao Xiping Jiang Lijuan Zhao Zhimeng Li Mengqi Wang Ruijuan Yang Chuanen Zhou Zhaoming Wang Feng Yuan Dongmei Ma hao lin Wenwen Liu Chunxiang Fu CAS Key Laboratory of Biofuels Shandong Provincial Key Laboratory of Energy GeneticsQingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdao 266101ShandongChina Shandong Energy Institute Qingdao 266101ShandongChina Qingdao New Energy Shandong Laboratory Qingdao 266101ShandongChina University of Chinese Academy of Sciences Beijing 100049China The Key Laboratory of Plant Development and Environmental Adaptation Biology Ministry of EducationSchool of Life SciencesShandong UniversityQingdao 266101ShandongChina Key Laboratory of Forage Breeding and Seed Production of Inner Mongolia Inner Mongolia M-Grass Ecology and Environment(Group)Co.Ltd.Hohhot 010016Inner MongoliaChina School of Ecology Environment Ningxia UniversityYinchuan 750021NingxiaChina Biotechnology Research Institute Chinese Academy of Agricultural SciencesBeijing 100081China

Alfalfa(Medicago sativa.L.)is a globally significant autotetraploid legume forage crop.However,despite its importance,establishing efficient gene editing systems for cultivated alfalfa remains a formidable challenge.In this study,we pioneered the development of a highly effective ultrasonic-assisted leaf disc transformation system for Gongnong 1 alfalfa,a variety widely cultivated in Northeast China.Subsequently,we created a single transcript CRISPR/Cas9(CRISPR_2.0)toolkit,incorporating multiplex gRNAs,designed for gene editing in Gongnong 1.Both Cas9 and gRNA scaffolds were under the control of the Arabidopsis ubiquitin-10 promoter,a widely employed polymeraseⅡconstitutive promoter known for strong transgene expression in dicots.To assess the toolkit’s efficiency,we targeted PALM1,a gene associated with a recognizable multifoliate phenotype.Utilizing the CRISPR_2.0 toolkit,we directed PALM1 editing at two sites in the wild-type Gongnong 1.Results indicated a 35.1%occurrence of editing events all in target 2 alleles,while no mutations were detected at target 1 in the transgenic-positive lines.To explore more efficient sgRNAs,we developed a rapid,reliable screening system based on Agrobacterium rhizogenes-mediated hairy root transformation,incorporating the visible reporter MtLAP1.This screening system demonstrated that most purple visible hairy roots underwent gene editing.Notably,sgRNA3,with an 83.0%editing efficiency,was selected using the visible hairy root system.As anticipated,tetra-allelic homozygous palm1 mutations exhibited a clear multifoliate phenotype.These palm1 lines demonstrated an average crude protein yield increase of 21.5%compared to trifoliolate alfalfa.Our findings highlight the modified CRISPR_2.0 system as a highly efficient and robust gene editing tool for autotetraploid alfalfa.

关键词： Alfalfa Gene editing CRISPR_2.0 toolkit Hairy root system Tetra-allelic homozygous mutants

Correction:Co-expression of GR79 EPSPS and GAT generates high glyphosate-resistant alfalfa with low glyphosate residues

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aBIOTECH 2024年第1期5卷 116-116页

作者： Yingying Meng Wenwen Zhang Zhaoming Wang Feng Yuan Sandui Guo hao lin Lifang Niu Biotechnology Research Institute Chinese Academy of Agricultural SciencesBeijing 100081China Inner Mongolia Pratacultural Technology Innovation Center Co. LtdHohhot 010010China National Center of Pratacultural Technology Innovation(Under Preparation) Hohhot 010010China

Correction:aBIOTECH[2023]4:352-358 https://***/10.1007/s42994-023-00119-3 In the Acknowledgements section of this article the funding number incorrectly given as SQ2022YF F1000033 and should have been 2022YFF1003204.

关键词： residues funding F1000

Evaluation of genetic response of mesenchymal stem cells to nanosecond pulsed electric fields by whole transcriptome sequencing

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World Journal of Stem Cells 2024年第3期16卷 305-323页

作者： Jian-Jing lin Tong Ning Shi-Cheng Jia Ke-Jia Li Yong-Can Huang Qiang Liu Jian-hao lin Xin-Tao Zhang Department of Sports Medicine and Rehabilitation Peking University Shenzhen HospitalShenzhen 518036Guangdong ProvinceChina Institute of Medical Science The Second HospitalCheeloo College of MedicineShandong UniversityJinan 250033Shandong ProvinceChina Department of Biomedical Engineering Institute of Future TechnologyPeking UniversityBeijing 100871China Shenzhen Engineering Laboratory of Orthopaedic Regenerative Technologies Peking University Shenzhen HospitalShenzhen 518036Guangdong ProvinceChina Arthritis Clinical and Research Center Peking University People’s HospitalBeijing 100044China

BACKGROUND Mesenchymal stem cells(MSCs)modulated by various exogenous signals have been applied extensively in regenerative medicine research.Notably,nanosecond pulsed electric fields(nsPEFs),characterized by short duration and high strength,significantly influence cell phenotypes and regulate MSCs differentiation via multiple pathways.Consequently,we used transcriptomics to study changes in messenger RNA(mRNA),long noncoding RNA(lncRNA),microRNA(miRNA),and circular RNA expression during nsPEFs application.AIM To explore gene expression profiles and potential transcriptional regulatory mechanisms in MSCs pretreated with nsPEFs.METHODS The impact of nsPEFs on the MSCs transcriptome was investigated through whole transcriptome sequencing.MSCs were pretreated with 5-pulse nsPEFs(100 ns at 10 kV/cm,1 Hz),followed by total RNA isolation.Each transcript was normalized by fragments per kilobase per million.Fold change and difference significance were applied to screen the differentially expressed genes(DEGs).Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses were performed to elucidate gene functions,complemented by quantitative polymerase chain reaction verification.RESULTS In total,263 DEGs were discovered,with 92 upregulated and 171 downregulated.DEGs were predominantly enriched in epithelial cell proliferation,osteoblast differentiation,mesenchymal cell differentiation,nuclear division,and wound healing.Regarding cellular components,DEGs are primarily involved in condensed chromosome,chromosomal region,actin cytoskeleton,and kinetochore.From aspect of molecular functions,DEGs are mainly involved in glycosaminoglycan binding,integrin binding,nuclear steroid receptor activity,cytoskeletal motor activity,and steroid binding.Quantitative real-time polymerase chain reaction confirmed targeted transcript regulation.CONCLUSION Our systematic investigation of the wide-ranging transcriptional pattern modulated by nsPEFs revealed the differential expression of 263 mRNAs,2 miRNAs,and 65 lncRNAs.Our study demons

关键词： Nanosecond pulsed electric fields Whole transcriptome sequencing Mesenchymal stem cells Genetic response Stem cell engineering

On Fixed-Parameter Solvability of the Minimax Path Location Problem

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Communications on Applied Mathematics and Computation 2023年第4期5卷 1644-1654页

作者： hao lin Cheng He School of Science Henan University of TechnologyZhengzhou450001HenanChina

The minimax path location problem is to find a path P in a graph G such that the maximum distance d_(G)(v,P)from every vertex v∈V(G)to the path P is minimized.It is a well-known NP-hard problem in network optimization.This paper studies the fixed-parameter solvability,that is,for a given graph G and an integer k,to decide whether there exists a path P in G such that max v∈V(G)d_(G)(v,P)≤k.If the answer is affirmative,then graph G is called k-path-eccentric.We show that this decision problem is NP-complete even for k=1.On the other hand,we characterize the family of 1-path-eccentric graphs,including the traceable,interval,split,permutation graphs and others.Furthermore,some polynomially solvable special graphs are discussed.

关键词： Discrete location Path location Fixed-parameter solvability Graph characterization Polynomial-time algorithm

Classification of congenital cataracts based on multidimensional phenotypes and its association with visual outcomes

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International Journal of Ophthalmology(English edition) 2024年第3期17卷 473-479页

作者： Yuan Tan Ying-Shi Zou Ying-lin Yu Le-Yi Hu Ting Zhang Hui Chen ling Jin Duo-Ru lin Yi-Zhi Liu hao-Tian lin Zhen-Zhen Liu State Key Laboratory of Ophthalmology Zhongshan Ophthalmic CenterSun Yat-sen UniversityGuangdong Provincial Key Laboratory of Ophthalmology and Visual ScienceGuangdong Provincial Clinical Research Center for Ocular DiseasesGuangzhou 510060Guangdong ProvinceChina

●AIM:To establish a classification for congenital cataracts that can facilitate individualized treatment and help identify individuals with a high likelihood of different visual outcomes.●METHODS:Consecutive patients diagnosed with congenital cataracts and undergoing surgery between January 2005 and November 2021 were recruited.Data on visual outcomes and the phenotypic characteristics of ocular biometry and the anterior and posterior segments were extracted from the patients’medical records.A hierarchical cluster analysis was performed.The main outcome measure was the identification of distinct clusters of eyes with congenital cataracts.●RESULTS:A total of 164 children(299 eyes)were divided into two clusters based on their ocular features.Cluster 1(96 eyes)had a shorter axial length(mean±SD,19.44±1.68 mm),a low prevalence of macular abnormalities(1.04%),and no retinal abnormalities or posterior cataracts.Cluster 2(203 eyes)had a greater axial length(mean±SD,20.42±2.10 mm)and a higher prevalence of macular abnormalities(8.37%),retinal abnormalities(98.52%),and posterior cataracts(4.93%).Compared with the eyes in Cluster 2(57.14%),those in Cluster 1(71.88%)had a 2.2 times higher chance of good best-corrected visual acuity[<0.7 logMAR;OR(95%CI),2.20(1.25–3.81);P=0.006].●CONCLUSION:This retrospective study categorizes congenital cataracts into two distinct clusters,each associated with a different likelihood of visual outcomes.This innovative classification may enable the personalization and prioritization of early interventions for patients who may gain the greatest benefit,thereby making strides toward precision medicine in the field of congenital cataracts.

关键词： classification congenital cataract phenotype visual acuity cluster analysis