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Improved genome annotation of Brassica oleracea highlights the importance of alternative splicing

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Horticultural Plant Journal 2024年第4期10卷 961-970页

作者： Yinqing Yang Lei Zhang Qi Tang Lingkui Zhang Xing Li shumin chen Kang Zhang Ying Li Xilin Hou Feng cheng State Key Laboratory of Crop Genetics and Germplasm Enhancement College of HorticultureNanjing Agricultural UniversityNanjing 210095China State Key Laboratory of Vegetable Biobreeding Institute of Vegetables and FlowersChinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural AffairsSino-Dutch Joint Laboratory of Horticultural GenomicsBeijing 100081China

Brassica oleracea has been developed into many important crops,including cabbage,kale,cauliflower,broccoli and so *** genome and gene annotation of cabbage(cultivar JZS),a representative morphotype of ***,has been widely used as a common reference in biological *** its genome assembly has been updated twice,the current gene annotation still lacks information on untranslated regions(UTRs)and alternative splicing(AS).Here,we constructed a high-quality gene annotation(JZSv3)using a full-length transcriptome acquired by nanopore sequencing,yielding a total of 59452 genes and 75684 ***,we re-analyzed the previously reported transcriptome data related to the development of different tissues and cold response using JZSv3 as a reference,and found that 3843 out of 11908 differentially expressed genes(DEGs)underwent AS during the development of different tissues and 309 out of 903 cold-related genes underwent AS in response to cold ***,we also identified many AS genes,including BolLHCB5 and BolHSP70,that displayed distinct expression patterns within variant transcripts of the same gene,highlighting the importance of JZSv3 as a pivotal reference for AS ***,JZSv3 provides a valuable resource for exploring gene function,especially for obtaining a deeper understanding of AS regulation mechanisms.

关键词： Brassica oleracea Oxford nanopore technologies Gene annotation Alternative splicing

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

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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

Acupuncture with different frequencies for tobacco dependence: a randomized controlled trial

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Journal of Traditional Chinese Medicine 2024年

作者： chen shumin LIU Zhenyu JI Jia WANG Yingying YANG Jinsheng CHANG Jin LI Zhihua Institute of Acupuncture and Moxibustion， China Academy of Chinese Medical Sciences Institute of Basic Theory for Chinese Medicine， China Academy of Chinese Medical Sciences

OBJECTIVE: To observe the effect of different acupuncture frequencies on the abstinence rate which could be used as a reference for optimizing acupuncture cessation ***: From July 2018 to June 2022， a total of 220 smokers were recruited based on inclusion criteria and randomly divided into the high-frequency acupuncture group (HF group， n = 110): 5 times a week from the 1st to the 4th week， from weeks 5 to 8， three times a week and the low-frequency acupuncture group (LF group， n = 110): 3 times a week from the 1st to the 4th week， from weeks 5 to 8， twice a week， then treated for 8 weeks and follow-up at 1 month in ***: In total， 162 subjects completed the whole study with a drop-out rate of 20.45%. The expiratory CO point abstinence rate was HF group 53/110 (48.18%) vs LF group 41/110 (37.27%) in Week 8 (P = 0.102) and HF group 46/110 (41.82%) vs LF group 45/110 (40.91%) in Week 12 (P = 0.891) and the HF acupuncture and LF acupuncture were nearly equal in the 8-week abstinence rate. In addition， both HF and LF acupuncture significantly reduced Fagerstr?m test for nicotine dependence scale (FTND) scores (P < 0.05)， Minnesota nicotine withdrawal scale (MNWS) scores (P < 0.05)， and Brief Questionnaire of Smoking Urges scale (QSU-Brief) scores (P < 0.05)， but HF acupuncture showed some superiority over LF acupuncture in relieving patients' smoking cravings (P < 0.05).Conclusions: The study initially showed that both high-frequency acupuncture and low-frequency acupuncture treatment were safe and effective on smoking cessation for 8 weeks， but high-frequency acupuncture was advantageous in reducing smoking cravings. More accurate acupuncture frequency needs to be validated through larger clinical studies to optimize acupuncture smoking cessation programs.

关键词：

“治脑调神”刺法治疗神志病探析及其临床应用

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中华中医药杂志 2024年第5期39卷 2630-2632页

作者：陈淑敏王莹莹中国中医科学院针灸研究所北京100700 中国中医科学院国医大师程莘农传承工作室北京100700

中国中医科学院国医大师程莘农传承工作室在程院士“一窍开百窍法”治疗脑病的学术观点基础上,结合“凡刺之法,先必本于神”和现代医学“身心疾病模式”,提出“主穴在脑、配穴在心”整体调理的“治脑调神”刺法,在神志病治疗中效果较佳... 详细信息

中国中医科学院国医大师程莘农传承工作室在程院士“一窍开百窍法”治疗脑病的学术观点基础上,结合“凡刺之法,先必本于神”和现代医学“身心疾病模式”,提出“主穴在脑、配穴在心”整体调理的“治脑调神”刺法,在神志病治疗中效果较佳。文章通过分析“治脑调神”刺法治疗神志病的理论内涵及临床应用特色,提出组穴上安脑神为主,调心神为要;针法上强调得气以调神;情绪不良者加以背俞穴快针,以调五脏;日久不愈者重用奇经穴,以交会经气;并指出临床可拓宽调治脑神法的运用思路,以丰富针刺调神法治疗,提高临床疗效。

关键词：程莘农治脑调神神志病临证经验

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信息不对称下新产品研发的合同设计

系统科学与数学 2024年第6期44卷 1675-1688页

作者：陈丹梅李仲飞陈树敏上海应用技术大学理学院上海201418 南方科技大学商学院深圳518055 广东工业大学管理学院广州510520

假设企业研发一种新产品,其研发成功的时间具有不确定性.文章运用实物期权方法和委托代理理论,分析信息不对称下新产品研发的合同设计问题,得到了最优合同的显式解.在此基础上,文章进一步分析了信息不对称对委托人价值、新产品研发的退... 详细信息

假设企业研发一种新产品,其研发成功的时间具有不确定性.文章运用实物期权方法和委托代理理论,分析信息不对称下新产品研发的合同设计问题,得到了最优合同的显式解.在此基础上,文章进一步分析了信息不对称对委托人价值、新产品研发的退出时机的影响.研究结果表明,信息不对称减少了委托人的价值,使得高成本的新产品的研发退出时机提前;新产品研发成功的平均时间越短,委托人的价值越大.

关键词：信息不对称实物期权委托代理最优择时

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犬心脏二尖瓣退行性疾病研究进展

中国畜牧兽医 2024年第7期51卷 3215-3223页

作者：陈淑敏曾丽薇陈宇刘萌萌海南大学热带农林学院(农业农村学院、乡村振兴学院) 海口570228

黏液瘤样二尖瓣疾病(myxomatous mitral valve disease,MMVD)又称为退行性二尖瓣疾病,是瓣膜发生退行性病变的结果。该病是犬最常见心脏病之一,会导致其发生二尖瓣反流(mitral regurgitation,MR)和左侧充血性心力衰竭(congestive heart ... 详细信息

黏液瘤样二尖瓣疾病(myxomatous mitral valve disease,MMVD)又称为退行性二尖瓣疾病,是瓣膜发生退行性病变的结果。该病是犬最常见心脏病之一,会导致其发生二尖瓣反流(mitral regurgitation,MR)和左侧充血性心力衰竭(congestive heart failure,CHF)等严重后果。MMVD发病率随年龄增长而增加,在某些品种犬中具有高遗传特性。MMVD的病理变化主要是二尖瓣的增厚、脱垂和腱索的伸长甚至断裂。该病的发病机制尚不完全清晰,目前已有的研究分别从组织细胞层面、遗传学和蛋白质组学及信号通路等方面取得了一定的研究结果。从组织细胞层面研究发现,在犬等物种上证实,MMVD与瓣膜间质细胞(valve interstitial cells,VICs)的活化及细胞外基质(extracellular matrix,ECM)中胶原和蛋白聚糖的沉积相关。从遗传学和蛋白质组学层面研究发现,miRNAs可能参与了MMVD的遗传调控,血液循环中的miRNAs有望成为MMVD患犬CHF的生物标志物。从分子信号通路层面研究发现,MMVD与许多信号通路息息相关,其中研究较多的5-羟色胺(5-hydroxytryptamine,5-HT)和转化生长因子β(transforming growth factor-β,TGF-β)通路在VICs的活化中具有重要作用,同时其还受二尖瓣在心脏收缩和舒张时所受的牵拉和血液冲刷的机械应力影响,两条通路相互影响,促使MMVD的发生和发展。笔者就犬MMVD流行病学特征、病理变化、临床症状、诊断分期、治疗手段和疾病相关机制的研究进展做一综述。

关键词：黏液瘤样二尖瓣疾病二尖瓣瓣膜间质细胞 5-羟色胺转化生长因子β

雪峰弧形构造带中段沅陵—桃江地区金矿成矿规律及找矿方向

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地质论评 2024年第S1期70卷 104-106页

作者：娄元林曾昊廖驾陈澍民陈坤汪斯毓杨桃中国地质调查局长沙自然资源综合调查中心长沙410600 中国地质科学院矿产资源研究所北京100037 中国地质大学(北京) 北京100083 中国地质调查局海口海洋地质调查中心海口571127 常德职业技术学院湖南常德415000

沅陵—桃江地区位于雪峰弧形构造带中段,属江南造山带西南段,该带金矿资源潜力巨大,约90%以上的金矿床成带状横贯湘中分布,被誉为湖南的“金腰带”。该区金矿成矿地质条件优越,矿床类型众多,迄今为止陆续发现了沃溪、沈家垭、符竹溪、... 详细信息

沅陵—桃江地区位于雪峰弧形构造带中段,属江南造山带西南段,该带金矿资源潜力巨大,约90%以上的金矿床成带状横贯湘中分布,被誉为湖南的“金腰带”。该区金矿成矿地质条件优越,矿床类型众多,迄今为止陆续发现了沃溪、沈家垭、符竹溪、王家冲、板溪、陈家村、天明等二十余处金锑矿床(黄建中等,2020;柏道远等,2021)。

关键词：金矿成矿规律找矿方向沅陵—桃江地区雪峰弧形构造带湖南

Subaquatic volcanic eruptions in continental facies and their influence on high quality source rocks shown by the volcanic rocks of a faulted depression in Northeast China

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Science China Earth Sciences 2013年第12期56卷 1926-1933页

作者： SHAN XuanLong LI JiYan chen shumin RAN QingChang chen GuiBiao LIU Chao College of Earth Sciences Jilin University Exploration and Development Research Institute Daqing Oil field Co. Ltd.

This paper reports the analysis on cores and rock slices, data on seismic and logging activities, characteristics of core samples, and the paleogeographic background of the Yingcheng Formation of the Xujiaweizi faulted depression in the Songliao Basin. The results show that some of the volcanic rocks were formed during subaquatic eruptions. These subaqueous volcanic rocks are further characterized by the interbedded black mudstone and tuffite, the presence of double-layer perlite enclosing aphyric or sparsely phyric rhyolite, the presence of a bentonite layer, and the coefficient of oxidation （Fe203/FeO）. The types of rocks are volcanic breccia, lava breccias, perlite, rhyolite, tuff and sedimentary tuff. The subaquatic eruptions are distributed mainly in Wangjiatun, Shengping, Xuxi, Xuzhong, and Xudong. The XS-I area is the most typical. The organic abundance of over- burden mud rocks within the volcanic rocks of the Yingcheng Formation indicates that these rocks represent high-quality source rocks. The analysis also shows that continental subaquatic volcanic eruptions provide a rich supply of minerals and en- ergies for the lake basin and increase the organic matter content in the water. Moreover, the water differentiation provides a good reducing environment for the conservation of organic matter, and is beneficial for the formation of high-quality source rocks. Finally, we propose a hypothesis to describe the mode of subaquatic eruptions and the formation of high-quality source rocks.

关键词： subaquatic volcanic rocks in continental facies recognition marks high-quality source rocks Yingcheng Formation Xujiaweizi faulted depression

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Satellite Observations of Reflectivity Maxima above the Freezing Level Induced by Terrain

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Advances in Atmospheric Sciences 2021年第4期38卷 627-640页

作者： Aoqi ZHANG Weibiao LI shumin chen Yilun chen Yunfei FU Guangdong Province Key Laboratory for Climate Change and Natural Disaster Studies School of Atmospheric SciencesSun Yat-sen UniversityGuangzhou 510275China Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai) Zhuhai 519082China School of Earth and Space Sciences University of Science and Technology of ChinaHefei 230026China

Previous studies have recognized reflectivity maxima above the freezing level(RMAF) within stratiform precipitation over mountain slopes, however, quantitative studies are limited due to the lack of adequate identification criteria. Here, we establish an identification method for RMAF precipitation and apply it to the Tropical Rainfall Measuring Mission(TRMM) Precipitation Radar(PR) observations. Using the TRMM 2A25 product from 1998 to 2013, we show that the RMAF structure in reflectivity profiles can be effectively identified. RMAF exists not only in stratiform precipitation but also in convective precipitation. RMAF frequency is positively correlated with elevation, which is thought to be caused by enhanced updrafts in the middle layers of stratiform precipitation, or in the low to middle layers of convective precipitation over mountains. The average RMAF heights in stratiform and convective precipitation were 1.35 and 2.01 km above the freezing level, respectively, which is lower than previous results. In addition, our results indicate that the RMAF structure increased the echo top height and enhanced precipitation processes above the RMAF height, but it suppressed the downward propagation of ice particles and the near-surface rain rate. Future studies of orographic precipitation should take into account the impact of the RMAF structure and its relevant dynamic triggers.

关键词： orographic precipitation reflectivity maxima above the freezing level precipitation structure TRMM PR