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Haplotype-based phylogenetic analysis and population genomics uncover the origin and domestication of sweetpotato

molecular Plant 2024年第2期17卷 277-296页

作者： Mengxiao Yan Ming Li Yunze Wang Xinyi Wang M-Hossein Moeinzadeh Dora G.Quispe-Huamanquispe Weijuan Fan Yijie Fang Yuqin Wang Haozhen Nie Zhangying Wang Aiko Tanaka Bettina Heider Jan F.Kreuze Godelieve Gheysen Hongxia Wang Martin Vingron Ralph Bock Jun Yang Shanghai key laboratory of Plant Functional Genomics and Resources Shanghai Chenshan Botanical GardenShanghai 201602China College of Life Sciences Chongqing Normal UniversityChongqing 401331China Biotechnology and Nuclear Technology Research Institute Sichuan Academy of Agricultural SciencesChengdu 610061China College of Life Sciences Shanghai Normal UniversityShanghai 200234China department of Computational molecular Biology Max Planck Institute for Molecular GeneticsIhnestraBe 63-7314195 BerlinGermany department of Biotechnology Ghent University9000 GhentBelgium Guangdong Provincial key laboratory of Crops Genetics and Improvement Crop Research InstituteGuangdong Academy of Agricultural SciencesGuangzhou 510640China Graduate School of Bioagricultural Sciences Nagoya UniversityChikusaNagoya 464-8601Japan international Potato Center(CIP) LimaPeru CAS Center for Excellence of molecular Plant Sciences Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghai 200233China Max-Planck-Institut fur Molekulare Pflanzenphysiologie Am Muhlenberg 114476 Potsdam-GolmGermany

The hexaploid sweetpotato(lpomoea batatas)is one of the most important root crops worldwide.However,its genetic origin remains controversial,and its domestication history remains unknown.In this study,we used a range of genetic evidence and a newly developed haplotype-based phylogenetic analysis to identify two probable progenitors of sweetpotato.The diploid progenitor was likely closely related to lpomoea ae-quatoriensis and contributed the B,subgenome,IbT-DNA2,and the lineage 1 type of chloroplast genome to sweetpotato.The tetraploid progenitor of sweetpotato was most likely l.batatas 4x,which donated the B2 subgenome,IbT-DNA1,and the lineage 2 type of chloroplast genome.Sweetpotato most likely originated from reciprocal crosses between the diploid and tetraploid progenitors,followed by a subsequent whole-genome duplication.In addition,we detected biased gene exchanges between the subgenomes;the rate of B,to B2 subgenome conversions was nearly three times higher than that of B2 to B subgenome conver-sions.Our analyses revealed that genes involved in storage root formation,maintenance of genome stabil-ity,biotic resistance,sugar transport,and potassium uptake were selected during the speciation and domestication of sweetpotato.This study sheds light on the evolution of sweetpotato and paves the way forimprovementofthiscrop.

关键词： sweetpotato origin gene conversion domestication IbT-DNA HPA

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Dual neovascular targets of vascular endothelial growth factor receptors and platelet-derived growth factor receptor ameliorate thioacetamide induced liver fibrosis in rats

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Portal Hypertension & Cirrhosis 2024年第1期3卷 1-13页

作者： Bin Xiong Yaowei Bai Jiacheng Liu Tongqiang Li Yingliang Wang Chen Zhou department of Interventional Radiology The First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouGuangdongChina department of Radiology Union HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubeiChina Hubei Province key laboratory of molecular imaging WuhanHubeiChina

Aims:Neovascularization plays a crucial role in liver fibrosis(LF),and blocking vascular endothelial growth factor receptors(VEGFR)has been shown to improve fibrosis.The aim of our study was to investigate the role of dual neovascularization targets,VEGFR,and platelet-derived growth factor receptor(PDGFR),in ameliorating fibrosis.Methods:In vitro,we observed the effects of apatinib(APA)(a VEGFR inhibitor)and donafenib(DON)(a VEGFR and PDGFR inhibitor)on the activation,proliferation,and apoptosis of hepatic stellate cells(HSCs)from rats and humans.In vivo,we established a thioacetamide(TAA)-induced liver fibrosis rat model to explore the antifibrosis effect of APA and DON.We used the method of random table to randomly divide the rats into 4 groups.We detected the expression of angiogenesis-related proteins using Western blot and immunohistochemistry.Results:APA and DON inhibited the proliferation and activation of HSCs,promoted apoptosis of HSCs,and arrested the S phase of the cell cycle in vitro.We also found that DON had a stronger inhibitory effect on HSCs.In vivo,APA and DON ameliorated liver fibrosis,reduced collagen deposition andα-SMA expression in rats,and DON had a stronger improvement effect.APA and DON downregulated the expression of VEGFR2 while inhibiting the phosphorylation of Akt and ERK1/2.DON can act through both VEGF and PDGF pathways,whereas APA can only act through the VEGF pathway.Conclusion:Antiangiogenesis is a promising approach for the treatment of fibrosis.Compared with a single-target drug(APA),the dual-target drug(DON)can achieve better therapeutic effects.

关键词： antiangiogenesis apatinib donafenib fibrosis

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Analysis of large datasets for identifying molecular targets in intestinal polyps and metabolic disorders

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BIOCELL 2024年第3期48卷 415-429页

作者： SHAN OU YUN XU QINGLAN LIU TIANWEN YANG WEI CHEN XIU YUAN XIN ZUO PENG SHI JIE YAO department of Gastroenterology The First Affiliated Hospital of Chongqing Medical and Pharmaceutical CollegeChongqingChina

Background:The interrelation between intestinal polyps,metabolic syndrome(MetS),and colorectal cancer(CRC)is a critical area of study.This research focuses on pinpointing potential molecular targets to understand the link between intestinal polyp formation,metabolic irregularities,and CRC progression.Methods:We examined clinical samples from patients with intestinal polyps coexisting with MetS and compared them with samples from patients with standard intestinal polyps.Transcriptome sequencing and public database analysis were employed to identify significant pathways and genes.These targets were then validated through immunohistochemistry(IHC).Following the RNA interference of key target expression,a series of experiments,including the cell counting kit-8 assay,colony formation,wound healing,and Transwell assays,were conducted.Results:Comparative analysis revealed 75 up-regulated and 61 down-regulated differentially expressed genes(DEGs)in the MetS polyp group vs.the control.Kyoto encyclopedia of genes and genomes(KEGG)pathway enrichment suggested these DEGs were primarily associated with cell cycle and mitosis.Integration with comparative toxicogenomics database(CTD)and the cancer genome atlas(TCGA)databases highlighted 44 key CRC-related genes.Protein interaction networks indicated connections of purkinje cell protein 4(PCP4),olfactomedin 1(OLFM1),fibronectin 1(FN1),and transforming growth factor beta 3(TGF-β3)with the mitogen-activated protein kinase(MAPK)pathway.Tumor correlation studies suggested higher risk associations with FN1,PCP4,and TGF-β3,while OLFM1 was identified as a lower risk gene.Immunohistochemical analysis revealed a decrease in OLFM1 in MetS-associated intestinal polyps.Upon interference with OLFM1 in polyp epithelial cells,there was a significant enhancement in cell proliferation,colony formation,and cell migration and invasion capabilities.Conclusion:Our study highlights a significant decrease in OLFM1 expression in MetS-associated intestinal polyps.And,this reduction in OLFM1 is associate

关键词： Colorectal cancer Metabolic syndrome Intestinal polyp OLFM1 Exosome

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基于基态和激发态之间跃迁过程的DBTTF-TCNB共晶的光热转换机制

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Science China Materials 2024年第1期67卷 242-250页

作者：付思姚何旦张小涛 key laboratory of Organic Integrated Circuits Ministry of Education&Tianjin Key Laboratory of Molecular Optoelectronic SciencesDepartment of ChemistrySchool of ScienceTianjin UniversityTianjin 300072China key laboratory of Organic Integrated Circuits Ministry of Education&Tianjin Key Laboratory of Molecular Optoelectronic SciencesDepartment of ChemistryInstitute of Molecular Aggregation ScienceTianjin UniversityTianjin 300072China College of Chemistry and Chemical Engineering Central South UniversityChangsha 410083China

有机共晶,由于其光热转换性质,为光热成像、生物应用和海水淡化等诸多领域带来了希望和活力.然而,有机共晶的光热转换机制尤其缺少详细且深入的理论研究.本研究使用含时密度泛函理论方法探索了激发和去激发过程,并解释了DBTTF-TCNB共晶... 详细信息

有机共晶,由于其光热转换性质,为光热成像、生物应用和海水淡化等诸多领域带来了希望和活力.然而,有机共晶的光热转换机制尤其缺少详细且深入的理论研究.本研究使用含时密度泛函理论方法探索了激发和去激发过程,并解释了DBTTF-TCNB共晶比其组分单晶具有更高光热转换效率的原因.结果显示,高激发态的高占比促进了非辐射跃迁的发生.基于DBTTF-TCNB共晶中给电子基团和吸电子基团间的电荷转移结果,我们发现给体和受体之间吸引电子的竞争可能会促进光热转换,且给电子基团在共晶结构中也十分重要.这些结果可为光热转换共晶的设计提供理论指导.轨道贡献和电子密度差进一步证明了我们的结论.因此,本研究从量子化学的角度给光热共晶在创新领域的应用提供了理论依据.

关键词：光热转换含时密度泛函理论激发过程生物应用吸电子基团非辐射跃迁高激发态共晶结构

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Ankylosing spondylitis coexisting with Clonorchis sinensis infection: A case report

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World Journal of Clinical Cases 2024年第5期12卷 1018-1024页

作者： Tian-Xin Yi Wei Liu Wen-Fei Leng Xiao-Chuan Wang Liang Luo department of Rheumatology Traditional Chinese Medicine Hospital Dianjiang ChongqingChongqing 408300China department of Orthopaedic Traditional Chinese Medicine Hospital Dianjiang ChongqingChongqing 408300China department of Chinese Medicine The People's Hospital of Yubei District of Chongqing CityChongqing 401120China

BACKGROUND Ankylosing spondylitis(AS)is a chronic immune-mediated inflammatory disease.The prevailing theory links AS onset to infections in susceptible individuals.Furthermore,infections may impair the immune responses.Numerous studies have investigated links between AS and various infections-bacterial,viral,fungal,and other microorganism infections.However,limited attention has been given to the association between AS and Clonorchis sinensis(C.sinensis)infection.CASE SUMMARY A 27-year-old male with a 10-yr history of AS presented to our hospital with inflammatory lower back pain as the primary manifestation.Ten years ago,the patient had achieved a stable condition after treatment with biological agents.However,he experienced a recurrence of lumbosacral pain with an unexplained cause 10 d before hospital admission.A lumbosacral magnetic resonance imaging(MRI)scan revealed bone marrow edema in the left sacroiliac joint,and laboratory indicators were elevated.Moreover,the presence of C.sinensis eggs was detected in the stool.The patient was prescribed praziquantel,resulting in the disap-pearance of C.sinensis eggs in subsequent routine stool tests and relief from lumbosacral pain.A follow-up MRI scan performed after 4 months revealed a reduction in bone marrow edema around the left sacroiliac joint.CONCLUSION C.sinensis infections could potentially trigger the exacerbation of AS.Clinicians should pay attention to investigating the presence of infections.INTRODUCTION Ankylosing spondylitis(AS)is a chronic inflammatory and rheumatic disease resulting from an imbalance between innate and acquired immune responses[1].While it can affect any part of the spine,its primary symptoms are persistent back pain and stiffness in the lower back and pelvis.The prevalence of AS per 10000 individuals is 23.8 in Europe,31.9 in North America,16.7 in Asia,10.2 in Latin America,and 7.4 in Africa[2].Infections commonly occur in the first 3 months and may act as potential triggers for the first symptoms of AS,often manifesting as gastro

关键词： Ankylosing spondylitis Clonorchis sinensis Parasites Infection Case report

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A review on electrocatalytic CO_(2) conversion via C-C and C-N coupling

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Carbon Energy 2024年第2期6卷 167-194页

作者： Zhuangzhi Zhang Sijun Li Zheng Zhang Zhou Chen Hua Wang Xianguang Meng Wenquan Cui Xiwei Qi Jiacheng Wang Hebei Provincial laboratory of Inorganic Nonmetallic Materials College of Materials Science and EngineeringNorth China University of Science and TechnologyTangshanChina key laboratory of Luminescence Analysis and molecular Sensing Ministry of EducationCollege of Chemistry and Chemical EngineeringSouthwest UniversityChongqingChina State key laboratory of New Textile Materials and Advanced Processing Technologies Hubei Key Laboratory of Biomass Fibers and Eco-Dyeing and FinishingCollege of Chemistry and Chemical EngineeringWuhan Textile UniversityWuhanChina College of Materials Xiamen UniversityXiamenChina Hebei Iron and Steel laboratory TangshanChina Hebei key laboratory for Environment Photocatalytic and Electrocatalytic Materials College of Chemical EngineeringNorth China University of Science and TechnologyTangshanChina College of Metallurgy and Energy North China University of Science and TechnologyTangshanChina State key laboratory of High Performance Ceramics and Superfine Microstructure Shanghai Institute of CeramicsChinese Academy of SciencesShanghaiChina Institute of Electrochemistry School of Materials Science and EngineeringTaizhou UniversityTaizhouChina

Electrochemical C-C and C-N coupling reactions with the conversion of abundant and inexpensive small molecules,such as CO_(2) and nitrogencontaining species,are considered a promising route for increasing the value of CO_(2) reduction products.The development of high-performance catalysts is the key to the both electrocatalytic reactions.In this review,we present a systematic summary of the reaction systems for electrocatalytic CO_(2) reduction,along with the coupling mechanisms of C-C and C-N bonds over outstanding electrocatalytic materials recently developed.The key intermediate species and reaction pathways related to the coupling as well as the catalyst-structure relationship will be also discussed,aiming to provide insights and guidance for designing efficient CO_(2) reduction systems.

关键词： C-C coupling C-N coupling CO_(2) conversion electrocatalysis urea synthesis

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What benefit can be obtained from magnetic resonance imaging diagnosis with artificial intelligence in prostate cancer compared with clinical assessments?

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Military Medical Research 2024年第2期11卷 268-286页

作者： Li-Tao Zhao Zhen-Yu Liu Wan-Fang Xie Li-Zhi Shao Jian Lu Jie Tian Jian-Gang Liu School of Engineering Medicine Beihang UniversityBeijing 100191China School of Biological Science and Medical Engineering Beihang UniversityBeijing 100191China CAS key laboratory of molecular imaging Institute of AutomationBeijing 100190China University of Chinese Academy of Sciences Beijing 100080China department of Urology Peking University Third HospitalPeking UniversityBeijing 100191China key laboratory of Big Data‑Based Precision Medicine(Beihang University) Ministry of Industry and Information Technology of the People's Republic of ChinaBeijing 100191China Beijing Engineering Research Center of Cardiovascular Wisdom Diagnosis and Treatment Beijing 100029China

The present study aimed to explore the potential of artificial intelligence(AI)methodology based on magnetic resonance(MR)images to aid in the management of prostate cancer(PCa).To this end,we reviewed and summarized the studies comparing the diagnostic and predictive performance for PCa between AI and common clinical assessment methods based on MR images and/or clinical characteristics,thereby investigating whether AI methods are generally superior to common clinical assessment methods for the diagnosis and prediction fields of PCa.First,we found that,in the included studies of the present study,AI methods were generally equal to or better than the clinical assessment methods for the risk assessment of PCa,such as risk stratification of prostate lesions and the prediction of therapeutic outcomes or PCa progression.In particular,for the diagnosis of clinically significant PCa,the AI methods achieved a higher summary receiver operator characteristic curve(SROC-AUC)than that of the clinical assessment methods(0.87 vs.0.82).For the prediction of adverse pathology,the AI methods also achieved a higher SROC-AUC than that of the clinical assessment methods(0.86 vs.0.75).Second,as revealed by the radiomics quality score(RQS),the studies included in the present study presented a relatively high total average RQS of 15.2(11.0–20.0).Further,the scores of the individual RQS elements implied that the AI models in these studies were constructed with relatively perfect and standard radiomics processes,but the exact generalizability and clinical practicality of the AI models should be further validated using higher levels of evidence,such as prospective studies and open-testing datasets.

关键词： Clinically significant prostate cancer Adverse pathology Radiomics quality score Artificial intelligence Magnetic resonance imaging

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Two-color emissive AIEgens with anti-Kasha property for dual-organelle imaging and phototherapy

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Science China Chemistry 2024年第5期67卷 1740-1752页

作者： Pu Chen Guogang Shan Qingli Nie Yuting Yan Pengfei Zhang Zujin Zhao Hai-Tao Feng Ben Zhong Tang AIE Research Center Shaanxi Key Laboratory of PhytochemistryCollege of Chemistry and Chemical EngineeringBaoji University of Arts and SciencesBaoji 721013China Institute of Functional Material Chemistry and National&Local United Engineering Lab for Power Battery Faculty of ChemistryNortheast Normal UniversityChangchun 130024China College of Chemistry&Materials Science Northwest UniversityXi’an 710127China Guangdong key laboratory of Nanomedicine CAS-HK Joint Lab of BiomaterialsCAS Key Laboratory of Biomedical Imaging Science and SystemShenzhen Engineering Laboratory of Nanomedicine and NanoformulationsCAS Key Lab for Health InformaticsShenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhen 518055China State key laboratory of Luminescent Materials and Devices Key Laboratory of Luminescence from Molecular Aggregates of Guangdong ProvinceSouth China University of TechnologyGuangzhou 510640China School of Science and Engineering Shenzhen Institute of Aggregate Science and TechnologyThe Chinese University of Hong KongShenzhen(CUHK-Shenzhen)Shenzhen 518172China

Despite the rapid development of probes for targeting single organelle, the construction of robust dual-organelle targeting probes with multicolor emission was rarely reported. Herein, two dual-emissive aggregation-induced emission luminogens(AIEgens)with donor-π-acceptor structures were designed and synthesized, namely QT-1 and QF-2. Both two AIEgens exhibited excitation wavelength-dependence defying the Kasha's rule, and could stain lipid droplets(LDs) and mitochondria in blue and red fluorescence, respectively. Moreover, thanks to the near-infrared emission and abundant reactive oxygen species(ROS) generation efficiency of QT-1, it was chosen as a photodynamic therapy agent to selectively kill cancer cells from normal cells. Upon light irradiation, an obvious decrease of mitochondrial membrane potential(MMP) and serious change of mitochondrial shape in cells were observed, which corresponded to the efficient inhibition of tumor growth in vivo. This work afforded a promising strategy for the construction of multicolor emission by tuning anti-Kasha behaviors and expanding their application in dualorganelle targeting-based phototheranostics.

关键词： aggregation-induced emission anti-Kasha luminescence fluorescent probe bioimaging photodynamic therapy

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RSPSSL:A novel high-fidelity Raman spectral preprocessing scheme to enhance biomedical applications and chemical resolution visualization

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Light(Science & Applications) 2024年第2期13卷 366-386页

作者： Jiaqi Hu Gina Jinna Chen Chenlong Xue Pei Liang Yanqun Xiang Chuanlun Zhang Xiaokeng Chi Guoying Liu Yanfang Ye Dongyu Cui De Zhang Xiaojun yu Hong Dang Wen Zhang Junfan Chen Quan Tang Penglai Guo Ho-Pui Ho Yuchao Li Longqing Cong Perry Ping Shum State key laboratory of Optical Fiber and Cable Manufacture Technology Guangdong Key Laboratory of Integrated Optoelectronics IntellisenseDepartment of EEESouthern University of Science and TechnologyShenzhen 518055China College of Optical and Electronic Technology China Jiliang UniversityHangzhou 310018China department of Nasopharyngeal Carcinoma Sun Yat-sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyGuangzhou 510060China department of Ocean Science and Engineering Southern University of Science and TechnologyShenzhen 518055China department of Nephrology Chaozhou People’s HospitalChaozhou 521011China Clinical Research Design Division Sun Yatsen Memorial HospitalGuangzhouGuangdong 510120China School of Automation Northwestern Polytechnical UniversityXi’anShaanxi 710072China department of Biomedical Engineering The Chinese University of Hong KongHong KongChina Guangdong Provincial key laboratory of Nanophotonic Manipulation Institute of NanophotonicsJinan UniversityGuangzhou 511443China

Raman spectroscopy has tremendous potential for material analysis with its molecular fingerprinting capability in many branches of science and technology.It is also an emerging omics technique for metabolic profiling to shape precision medicine.However,precisely attributing vibration peaks coupled with specific environmental,instrumental,and specimen noise is problematic.Intelligent Raman spectral preprocessing to remove statistical bias noise and sample-related errors should provide a powerful tool for valuable information extraction.Here,we propose a novel Raman spectral preprocessing scheme based on self-supervised learning(RSPSSL)with high capacity and spectral fidelity.It can preprocess arbitrary Raman spectra without further training at a speed of~1900 spectra per second without human interference.The experimental data preprocessing trial demonstrated its excellent capacity and signal fidelity with an 88%reduction in root mean square error and a 60%reduction in infinite norm(L__(∞))compared to established techniques.With this advantage,it remarkably enhanced various biomedical applications with a 400%accuracy elevation(ΔAUC)in cancer diagnosis,an average 38%(few-shot)and 242%accuracy improvement in paraquat concentration prediction,and unsealed the chemical resolution of biomedical hyperspectral images,especially in the spectral fingerprint region.It precisely preprocessed various Raman spectra from different spectroscopy devices,laboratories,and diverse applications.This scheme will enable biomedical mechanism screening with the label-free volumetric molecular imaging tool on organism and disease metabolomics profiling with a scenario of high throughput,cross-device,various analyte complexity,and diverse applications.

关键词： spectral scheme resolution

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PACS gene family-related neurological diseases: limited genotypes and diverse phenotypes

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World Journal of Pediatrics 2024年第1期20卷 82-91页

作者： Han Zhang Kai Gao Shuang Wang Yue-Hua Zhang Zhi-Xian Yang Ye Wu Yu-Wu Jiang department of Pediatrics Peking University First Hospital.No.1 Xi'an Men StreetWest DistrictBeijing 100034China Bejing key laboratory of molecular Diagnosis and Study on Pediatric Genetic Diseases BeijingChina Children Epilepsy Center Peking University First HospitalBeijingChina key laboratory for Neuroscience Ministry of Education/National Health and Family Planning CommissionPeking UniversityBeijingChina Center of Epilepsy Beijing Institute for Brain DisordersBeijingChina

Background The PACS gene family has been demonstrated to be related to intracellular vesicular trafficking.The phenotypic manifestations caused by the pathogenic variants of PACS include epilepsy,intellectual disability/developmental delay,and malformations,such as facial abnormalities.Methods We identified seven new cases with pathogenic or likely pathogenic PACS variants using next-generation sequencing.Detailed information obtained from these patients was analyzed along with that obtained from previously reported patients.Results With the inclusion of the newly diagnosed cases in this study,103 cases with PACS gene family-related neurological diseases were reported,of which 43 were PACS2-related cases and the remaining were PACSI-related cases.Most patients had seizures,which have been reported to be effectively controlled by several types of anti-seizure medications(ASMs).The most efficacious and frequently prescribed ASMs included sodium valproate(43.3%,13/30),oxcarbazepine/carbamazepine(26.7%,8/30),and levetiracetam(20%,6/30).Almost all patients had intellectual disability/developmental delay.The most common pathogenic missense variants were PACSI p.Arg203Trp and PACS2 p.Glu209Lys.In addition,we report a patient carrying a likely pathogenic copy number variation(CNV)(de novo heterozygous deletion of chr14:105821380-106107443,286 kilobase,destroyed part of the furin-binding region domain and the protein structure after it)with more severe and refractory late-onset epilepsy.Conclusions The clinical phenotypes of the different PACS heterozygous missense variants were similar.The pathogenic variant sites of PACSI and PACS2 were quite limited but located in different regions.A CNV destroying part of the PACS2 gene might also be pathogenic.These findings may provide an important clue for further functional studies on the pathogenic mechanism of neurological disorders related to the PACS gene family.

关键词： Developmental delay Epilepsy Intellectual disability PACSI PACS2

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