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OcBSA:An NGS-based bulk segregant analysis tool for outcross populations

Molecular Plant 2024年第4期17卷 648-657页

作者： Lingkui Zhang Yanfeng Duan Zewei Zhang Lei Zhang Shumin Chen Chengcheng Cai Shaoguang Duan Kang Zhang Guangcun Li Feng Cheng State Key laboratory of Vegetable Biobreeding Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural AffairsKey Laboratory of Biology and Genetic Improvement of Tuber and Root Crop of Ministry of Agriculture and Rural AffairsSino-Dutch Joint Laboratory of Horticultural GenomicsInstitute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijing 100081China

Constructing inbred lines for self-incompatible species and species with long generation times is challenging,making the use of F1 outcross/segregating populations the main strategy for genetic studies of such ***,there is a lack of dedicated algorithms/tools for rapid quantitative trait locus(QTL)mapping using the F1 *** this end,we have designed and developed an algorithm/tool called OcBSA specifically for QTL mapping of F1 *** transforms the four-haplotype inheritance problem from the two heterozygous diploid parents of the F1 population into the two-haplotype inheritance problem common in current genetic studies by removing the two haplotypes from the heterozygous parent that do not contribute to phenotype segregation in the F1 *** of OcBSA on 1800 simulated F1 populations demonstrated its advantages over other currently available tools in terms of sensitivity and *** addition,the broad applicability of OcBSA was validated by QTL mapping using seven reported F1 populations of apple,pear,peach,citrus,grape,tea,and *** also used OcBSA to map the QTL for flower color in a newly constructed F1 population of potato generated in this *** OcBSA mapping result was verified by the insertion or deletion markers to be consistent with a previously reported locus harboring the ANTHOCYANIN 2 gene,which regulates potato flower *** together,these results highlight the power and broad utility of OcBSA for QTL mapping using F1 populations and thus a great potential for functional gene mining in outcrossing *** ease of use,we have developed both Windows and Linux versions of OcBSA,which are freely available at:https://***/Bioinformaticslab/OcBSA.

关键词： outcross BSA self-incompatible F1 population QTL mapping potato

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Transcriptomic and pathological profiling of a new congenic mouse model with Lepr mutation:Evaluating susceptibility to the development of obesity and NAFLD

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Genes & Diseases 2024年第3期11卷 34-38页

作者： MJ Mahesh Kumar Shailendra Arindkar Masum Saini Perumal Nagarajan National Institute of Immunology New Delhi 100067India Center for Cellular and Molecular biology Hyderabad 500007India Regional Center for biotechnology Faridabad 121001India

Non-alcoholic fatty liver disease(NAFLD)and type 2 diabetes mellitus(T2DM)are two disease conditions for which obesity is a risk factor.^(1)Due to the close relationship between the three pathologies,researchers frequently use the same mouse models to identify the underlying processes of obesity,NAFLD,and *** instance,leptin(Lep)-null(ob/ob)and leptin receptor(Lepr)-deficient(db/db)mice spontaneously develop NAFLD and show different phenotypes of extreme obesity and diabetes,respectively.

关键词： obesity NAFLD Lep

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Profiles of the Headspace Volatile Organic and Essential Oil Compounds from the Tunisian Cardaria draba (L.) Desv. and Its Leaf and Stem Epidermal Micromorphology

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Phyton-International Journal of Experimental Botany 2024年第4期93卷 725-744页

作者： Wissal Saadellaoui Samiha Kahlaoui Kheiria Hcini Abir Haddada Noomene Sleimi Roberta Ascrizzi Guido Flamini Fethia Harzallah-Skhiri Sondes Stambouli-Essassi laboratory of Biodiversity Biotechnology and Climate Change(LR11-ES09)Faculty of Sciences of TunisUniversity of Tunis El ManarTunis1060Tunisia laboratory RME-Resources Materials and EcosystemsFaculty of Sciences of BizerteUniversity of CarthageJarzounaBizerte7021Tunisia Dipartimento di Farmacia Universitàdi PisaVia Bonanno 33Pisa56126Italy laboratory of Bioresources:Integrative biology and Valorization(LR14-ES06) High Institute of Biotechnology of MonastirUniversity of MonastirMonastir5000Tunisia

In this work, we investigated aroma volatiles emanated by dry roots, stems, leaves, flowers, and fruits of Cardariadraba (L.) Desv. growing wild in Tunisia and its aerial part essential oils (EOs) composition. A total of 37 volatileorganic compounds (96.7%–98.9%) were identified;4 esters, 4 alcohols, 7 hydrocarbons, 12 aldehydes, 5 ketones,1 lactone, 1 organosulfur compound, 2 organonitrogen compounds, and 1 acid. The hydrocarbons form the maingroup, representing 49.5%–84.6% of the total detected volatiles. The main constituent was 2,2,4,6,6-pentamethylheptane(44.5%–76.2%) reaching the highest relative percentages. Forty-two compounds were determined in thetwo fractions of EOs, representing 98.8% and 97.2% of the total oil composition, respectively. The principal componentswere hexadecanoic acid (34.6%), 6-methyl-5-hepten-2-one (18.3%), decanal (15.0%), 6,10,14-trimethyl-2-pentadecanone (13.2%), and n-pentacosane (13%). Micromorphological details of the leaf and stem epidermisusing light microscopy revealed polygonal cells with sinuous walls in the adaxial and abaxial leaf surfaces andnearly rectangular and long ones with linear and thick walls for the stem epidermis. The stomata complexes wereanisocytic in the leaf epidermis and mainly anisocytic and rarely paracytic in the stem epidermis. Non-glandulartrichomes were unbranched and long with an acute apex or short with a convex apex. The glandular ones wereidentified for the first time in this species. They were short-stalked with a large secretory head. The highest stomatalindex (17.02%) was recorded in the abaxial leaf surface. The identification of headspace volatiles and essentialoil compounds can be used to characterize this species, and the various epidermis micromorphologicalfeatures are very useful for biosystematics taxonomic studies within Brassicaceae.

关键词： Cardaria draba aroma profile essential oils epidermis trichomes

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Characteristics of gut microbiota determine effects of specific probiotics strains in patients with functional constipation

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Chinese Medical Journal 2024年第1期137卷 120-122页

作者： Haohao Zhang Lijuan Sun Zhixin Zhao Yao Zhou Yuyao Liu Nannan Zhang Junya Yan Shibo Wang Renlong Li Jing Zhang Xueying Wang Wenjiao Li Yan Pan Meixia Wang Bing Luo Mengbin Li Zhihong Sun Yongxiang Zhao Yongzhan Nie State Key laboratory of Targeting Oncology National Center for International Research of Bio-targeting TheranosticsGuangxi Key Laboratory of Bio-targeting TheranosticsCollaborative Innovation Center for Targeting Tumor Diagnosis and TherapyGuangxi Talent Highland of Bio-targeting TheranosticsGuangxi Medical UniversityNanningGuangxi 530021China State Key laboratory of Holistic Integrative Management of Gastrointestinal Cancers and National Clinical Research Center for Digestive Diseases Xijing Hospital of Digestive DiseasesFourth Military Medical UniversityXi’anShaanxi 710032China Key laboratory of Resource biology and biotechnology in Western China Ministry of EducationSchool of MedicineNorthwest UniversityXi’anShaanxi 710000China Key laboratory of Dairy biotechnology and Engineering Ministry of EducationKey Laboratory of Dairy Products ProcessingMinistry of Agriculture and Rural AffairsInner Mongolia Key Laboratory of Dairy Biotechnology and EngineeringInner Mongolia Agricultural UniversityHohhotInner Mongolia 010018China

To the Editor:Probiotics are a promising treatment modality for functional constipation(FC);however,the factors affecting individual responses to probiotics remain *** evidence has identified that there is a strong relationship among the gut microbiota and constipation and related gut-brain axis.[1]The gut microbiota may modulate the gut functions via gut metabolites or trigger the release of gut hormones,such as peptide YY,gastric inhibitory polypeptide,and 5-hydroxytryptamine.[2]In turn,gut hormones affect gut secretion,motility,and sensation through their receptors located on epithelial,enteric,and smooth muscle cells.[2]Based on these findings,exogenous probiotics have been used in patients with constipation;however,few have produced consistent results.[3]In this study,we investigated the efficacy and safety of several specific probiotics strains for constipation,and also examined the potential reasons for the individualized effects of probiotics,which may facilitate interventional decisionmaking for FC patients.

关键词： constipation patients sensation

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Unique anti-angiogenic effects,pharmacological targets and therapeutic mechanisms of Chinese herbal medicines for endometriosis

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Genes & Diseases 2024年第5期11卷 63-65页

作者： Bo Liang Rui Dong Sze Wan Hung Yiran Li Yuezhen Lin Ling Wu Tao Zhang Gene Chi Wai Man Hui Xu Jacqueline Pui Wah Chung Chi Chiu Wang Guangdong Provincial Key laboratory of marine biotechnology Institute of Marine SciencesShantou UniversityShantouGuangdong 515063China Department of Obstetrics and Gynaecology The Chinese University of Hong KongHong Kong SARChina Reproduction and Development laboratory Li Ka Shing Institute of Health SciencesThe Chinese University of Hong KongHong Kong SARChina School of Biomedical Sciences The Chinese University of Hong KongHong Kong SARChina Chinese University of Hong Kong-Sichuan University Joint laboratory in Reproductive Medicine The Chinese University of Hong KongHong Kong SARChina

Endometriosis is a common and benign angiogenesisdependent gynecological disorder,which refers to the proliferation and growth of endometrium-like tissues with neovasculature formation outside of the uterus.1 Available medical treatments for endometriosis containing hormonal and non-hormonal treatments had been limited for longterm usage by their side effects.2 Ideal medical treatment for endometriosis with efficacy to relieve symptoms and suppress endometriotic lesion growth and minimal side effects has been longing for decades.3 Angiogenesis is a promising therapeutic target for endometriosis.

关键词： therapeutic endometriosis herbal

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Highly sensitive nanozyme strip:An effective tool for forensic material evidence identification

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Nano Research 2024年第3期17卷 1785-1791页

作者： Juanji Hong Zhanjun Guo Dihan Duan Yi Zhang Xin Chen Yongjiu Li Zheng Tu Lei Feng Lei Chen Xiyun Yan Lizeng Gao Minmin Liang Demin Duan Experimental Center of Advanced Materials School of Materials Science&EngineeringBeijing Institute of TechnologyBeijing 100081China College of Bioscience and biotechnology Shenyang Agricultural UniversityShenyang 110866China Chongqing kangjuquanhong biology science and technology Co. ltdChongqing 400026China Key laboratory of Forensic Genetics Institute of Forensic ScienceMinistry of Public SecurityBeijing 100038China CAS Engineering laboratory for Nanozyme Key Laboratory of BiomacromoleculesInstitute of BiophysicsChinese Academic of ScienceBeijing 100101China

During criminal case investigations,blood evidence tracing is critical for criminal ***,the blood stains are often cleaned or covered up after the crime,resulting in trace residue and difficult ***,a highly sensitive and specific method for the rapid detection of human blood stains remains *** solve this problem,we established a nanozyme-based strip for rapid detection of blood evidence with high sensitivity and *** construct reliable nanozyme strips,we synthesized CoFe_(2)O_(4) nanozymes with high peroxidase-like activity by scaling up to gram level,which can be supplied for six million tests,and conjugated antibody as a detection probe in nanozyme *** developed CoFe_(2)O_(4) nanozyme strip can detect human hemoglobin(HGB)at a concentration as low as 1 ng/mL,which is 100 times lower than the commercially available colloidal gold strips(100 ng/mL).Moreover,this CoFe_(2)O_(4) nanozyme strip showed high generality on 12 substrates and high specificity to human HGB among 13 animal blood ***,we applied the developed CoFe_(2)O_(4) nanozyme strip to successfully detect blood stains in three real cases,where the current commercial colloidal gold strip failed to *** results suggest that the CoFe_(2)O_(4) nanozyme strip can be used as an effective on-scene detection method for human blood stains,and can further be used as a long-term preserved material evidence for traceability inquiry.

关键词： CoFe_(2)O_(4)nanozyme nanozyme strip peroxidase-like activity human hemoglobin blood evidence

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The piRNA size matters

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National Science Review 2024年第2期11卷 96-98页

作者： Jingwen Liu Falong Lu State Key laboratory of Molecular Developmental biology Institute of Genetics and Developmental Biology Chinese Academy of Sciences University of Chinese Academy of Sciences

Small RNAs, including small interfering RNAs(siRNAs), microRNAs(miRNAs) and PIWI-interacting RNAs(piRNAs), serve as pivotal agents in the post-transcriptional regulation of gene expression [1–3]. Among these,piRNAs t... 详细信息

关键词： PIWI

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A novel flow electrode capacitive deionization device with spindle-shaped desalting chamber

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Frontiers of Environmental Science & Engineering 2024年第4期18卷 1-4页

作者： Yunke Li Junjun Ma Chenxu Yang Jianrui Niu Yonghuan Bian Ruicheng Chen Puming Zhang Jing Zhang Chun Liu College of Environmental Science and Engineering Hebei University of Science and TechnologyShijiazhuang 050018China Pollution Prevention biotechnology laboratory of Hebei Province Shijiazhuang 050018China

Flow-electrode capacitive deionization(FCDI)is an innovative technology in which an intermediate chamber plays an important role in the desalination ***,relatively few studies have been conducted on the structures of these intermediate *** this study,we propose a novel flow-electrode capacitive deionization device with a spindle-shaped inlet chamber(S-FCDI).The desalination rate of the S-FCDI under optimal operating conditions was 36%higher than that of the FCDI device with a conventional rectangular chamber(R-FCDI).The spindle-shaped chamber transferred 1.2μmol more ions than the rectangular chamber,based on energy per ***,we performed a detailed analysis of different inlet chamber shapes using computational fluid dynamics *** concluded that S-FCDI has a relatively low flow resistance and almost no stagnation *** provides unique insights into the development of intermediate *** study may contribute to the improvement of the desalination performance in industrial applications of FCDI.

关键词： Spindle-shaped chamber Desalination performance Flow electrode capacitive deionization

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Selective extinction and habitat nestedness are the main drivers of lizard nestedness in the Zhoushan Archipelago

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Current Zoology 2024年第2期70卷 244-252页

作者： Minchu Zhang Chaonan Tang Qing Zhang Chengxiu Zhan Chuanwu Chen Yanping Wang laboratory of Island Biogeography and Conservation biology College of Life SciencesNanjing Normal UniversityNanjing 210023China

Nested subset pattern(nestedness)is an important part of the theoretical framework of island biogeography and community ***,most previous studies often used nestedness metrics or randomization algorithms that are vulnerable to type I *** this study,we inves-tigated the nestedness of lizard assemblages on 37 islands in the Zhoushan Archipelago,*** used the line-transect method to survey species occurrence,abundance,and habitat types of lizards on 37 islands during 2 breeding seasons in 2021 and *** applied the nested metric WNODF and the conservative rc null model to control for type I error and quantify the significance of *** rank cor relations were used to evaluate the role of 4 habitat variables(island area,2 isolation indices,and habitat diversity)and 4 ecological traits(body size,geographic range size,clutch size,and minimum area requirement)in generating *** results of WNODF analyses showed that lizard assemblages were significantly *** habitat-by-site matrix estimated by the program NODF was also significantly nested,support-ing the habitat nestedness *** nestedness of lizard assemblages were significantly correlated with island area,habitat *** size,and minimum area ***,our results suggest that selective extinction and habitat nestedness were the main drivers of lizard nestedness in our *** contrast,the nestedness of lizard assemblages was not due to passive sampling or selective *** maximize the number of species preserved,our results indicate that we should protect both large islands with diverse habitats and species with largearea requirement and clutch size.

关键词： clutch size habitat nestedness lizards minimum area requirement nestedness selective extinction WNODF Zhoushan Archipelago.

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Gapless Genome Assembly of ZH8015 and Preliminary Multi-Omics Analysis to Investigate ZH8015's Responses Against Brown Planthopper Infestation

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Rice science 2024年第3期31卷 317-327,I0042-I0045页

作者： LI Dian DUAN Wenjing LIU Qun’en WU Weixun ZHAN Xiaodeng SUN Lianping ZHANG Yingxin CHENG Shihua State Key laboratory of Rice biology and Breeding China National Rice Research InstituteHangzhou 310006China

Accurate genomic information is essential for advancing genetic breeding research in specific rice *** study presented a gapless genome assembly of the indica rice cultivar Zhonghui 8015(ZH8015)using Pac Bio HiFi,Hi-C,and ONT(Oxford Nanopore Technologies)ultra-long sequencing technologies,annotating 43037 gene ***,utilizing this genome along with transcriptomic and metabolomic techniques,we explored ZH8015's response to brown planthopper(BPH)*** transcriptomic sampling indicated significant changes in gene expression levels around 48 h after BPH *** analysis revealed particularly significant alterations in genes related to reactive oxygen species scavenging and cell wall *** results demonstrated marked increases in levels of several monosaccharides,which are components of the cell wall and dramatic changes in flavonoid *** association analysis identified differentially expressed genes associated with key metabolites,shedding light on ZH8015's response to BPH *** summary,this study constructed a reliable genome sequence resource for ZH8015,and the preliminary multi-omics results will guide future insect-resistant breeding research.

关键词： brown planthopper gapless genome genome assembly multi-omics Nilaparvata lugens rice

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