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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

A repertoire of intronic lariat RNAs reveals tissue-specific regulation and target mimicry potential in plants

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Science China(Life Sciences) 2024年第6期67卷 1280-1291页

作者： Yong Zhang Xiaotuo Zhang qi tang Lei Li Ting Jiang Yixiao Fang Hong Zhang Jixian Zhai Guodong Ren Binglian Zheng State Key Laboratory of Genetic Engineering Institute of Plant BiologySchool of Life SciencesFudan UniversityShanghai 200438China Department of Biology School of Life SciencesSouthern University of Science and TechnologyShenzhen 518055China

Lariat RNA is concomitantly produced by excised intron during RNA splicing,which is usually debranched by DBR1,an RNA debranching ***,increasing evidence showed that some lariat RNA could escape *** is known about how and why these lariat RNAs could be *** comparing the atlas of lariat RNAs between the non-dividing cell(mature pollen)and three actively dividing tissues(young shoot apex,young seeds,and young roots),we identified hundreds to thousands of lariat RNA naturally retained in each tissue,and the incidence of lariat RNA retention is much less in shoot apex while much more in *** lariat RNAs derived from the same intron or different lariat RNAs from the same pre-m RNA could be retained in one tissue while degraded in the other *** deciphering lariat RNA sequences,we identified an AG-rich(RAAAAVAAAR)motif and a UC-rich(UCUCUYUCUC)motif for pollen-specific and the other three tissues-retained lariat RNAs,*** of the pollen-specific AG-rich motif indeed enhanced lariat RNA retention in ***,hundreds of lariat RNAs harbored mi RNA binding sites,and dual-luciferase reporter assay showed that these natural lariat RNAs had the potential to protect expression of mi RNA target ***,our results uncover that selective retention of lariat RNA is an actively regulatory process,and provide new insights into understanding how lariat RNA metabolism may impact mi RNA activity.

关键词： intron turnover lariat RNA miRNA RNA splicing DBR1

Staphylococcus aureus and biofilms:transmission, threats, and promising strategies in animal husbandry

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Journal of Animal Science and Biotechnology 2024年第4期15卷 1408-1423页

作者： Mengda Song qi tang Yakun Ding Peng Tan Yucheng Zhang Tao Wang Chenlong Zhou Shenrui Xu Mengwei Lyu Yueyu Bai Xi Ma State Key Laboratory of Animal Nutrition and Feeding College of Animal Science and TechnologyChina Agricultural UniversityBeijing 100193China Key Laboratory of Innovative Utilization of Local Cattle and Sheep Germplasm Resources(Co‑Construction by Ministry and Province) Ministry of Agriculture and Rural AffairsSchool of Agricultural SciencesZhengzhou UniversityZhengzhou 450001China

Staphylococcus aureus(S. aureus) is a common pathogenic bacterium in animal husbandry that can cause diseases such as mastitis, skin infections, arthritis, and other ailments. The formation of biofilms threatens and exacerbates S. aureus infection by allowing the bacteria to adhere to pathological areas and livestock product surfaces, thus triggering animal health crises and safety issues with livestock products. To solve this problem, in this review, we provide a brief overview of the harm caused by S. aureus and its biofilms on livestock and animal byproducts(meat and dairy products). We also describe the ways in which S. aureus spreads in animals and the threats it poses to the livestock industry. The processes and molecular mechanisms involved in biofilm formation are then explained. Finally, we discuss strategies for the removal and eradication of S. aureus and biofilms in animal husbandry, including the use of antimicrobial peptides, plant extracts, nanoparticles, phages, and antibodies. These strategies to reduce the spread of S. aureus in animal husbandry help maintain livestock health and improve productivity to ensure the ecologically sustainable development of animal husbandry and the safety of livestock products.

关键词： Animal husbandry Biofilm Mastitis Mitigation strategies Staphylococcus aureus

Calcium/calcimimetic via calcium-sensing receptor ameliorates cholera toxin-induced secretory diarrhea in mice

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World Journal of Gastroenterology 2024年第3期30卷 268-279页

作者： Lie-qi tang Johnathan Fraebel Shi Jin Steven P Winesett Jane Harrell Wen-Han Chang Sam Xianjun Cheng Department of Pediatrics University of FloridaGainesvilleFL 32610United States College of Medicine University of FloridaGainesvilleFL 32610United States Applied Physiology and Kinesiology University of FloridaGainesvilleFL 32610United States Brain Rehabilitation Research Center Malcom Randall VA Medical CenterGainesvilleFL 32610United States Department of Medicine Endocrine Research UnitVeterans Affairs Medical CenterUniversity of CaliforniaSan FranciscoSan FranciscoCA 94121United States Department of Pediatric Gastroenterology Hepatologyand NutritionUniversity of Florida Shands Children’s HospitalGainesvilleFL 32608United States

BACKGROUND Enterotoxins produce diarrhea through direct epithelial action and indirectly by activating the enteric nervous ***-sensing receptor(CaSR)inhibits both *** latter has been well documented in vitro but not in *** hypothesis to be tested was that activating CaSR inhibits diarrhea in *** To determine whether CaSR agonists ameliorate secretory diarrhea evoked by cholera toxin(CTX)in *** CTX was given orally to C57BL/6 mice to induce *** and calci-mimetic R568 were used to activate *** maximize their local intestinal actions,calcium was administered luminally via oral rehydration solution(ORS),whereas R568 was applied serosally using an intraperitoneal *** verify that their actions resulted from the intestine,effects were also examined on Cre-lox intestine-specific CaSR *** outcome was measured biochemically by monitoring changes in fecal Cl-or clinically by assessing stool consistency and weight *** CTX induced secretory diarrhea,as evidenced by increases in fecal Cl-,stool consistency,and weight loss following CTX exposure,but did not alter CaSR,neither in content nor in ***,calcium and R568 were each able to ameliorate diarrhea when applied to diseased *** CaSR involvement is suggested by gene knockout experiments where the anti-diarrheal actions of R568 were lost in intestinal epithelial CaSR knockouts(villinCre/Casrflox/flox)and neuronal CaSR knockouts(nestinCre/Casrflox/flox).CONCLUSION Treatment of acute secretory diarrheas remains a global *** advances in diarrhea research,few have been made in the realm of diarrhea *** therapy has remained the standard of care,although it does not halt the losses of intestinal fluid and ions caused by *** is no cost-effective therapeutic for *** and other studies suggest that adding calcium to ORS or using calcimimetics to activate intestinal CaSR might

关键词： Cholera Enteric nervous system Secretory diarrhea Oral rehydration solution Calcium-sensing receptor Gene knockout

农业大灾保险与粮食安全——基于农业大灾保险试点的准自然实验

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农业技术经济 2024年第4期 4-17页

作者：黄少安唐琦山东大学经济研究院济南250199

本文以农业大灾保险试点作为准自然实验,首先基于特征事实进行理论分析,提出研究假说:农业大灾保险试点显著提高粮食产量,且存在区域异质性。然后基于2013—2019年山东省县域面板数据,采用渐进双重差分法实证分析试点对粮食产量的影响,... 详细信息

本文以农业大灾保险试点作为准自然实验,首先基于特征事实进行理论分析,提出研究假说:农业大灾保险试点显著提高粮食产量,且存在区域异质性。然后基于2013—2019年山东省县域面板数据,采用渐进双重差分法实证分析试点对粮食产量的影响,而且进一步识别和验证试点政策在提高粮食产量时,通过促进农业规模化经营程度发挥了中介效应,通过影响农户投保积极性发挥了调节效应。本文认为应继续提高粮食作物保险保障水平,加快农业保险向收入险转变。同时,要持续提升农业规模化经营水平,培养农民保险意识,发挥农业保险在保障粮食安全等方面的积极作用。

关键词：农业大灾保险试点粮食产量规模经营渐进双重差分法

Phage-displayed heptapeptide sequence conjugation significantly improves the specific targeting ability of antimicrobial peptides against Staphylococcus aureus

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mLife 2024年第2期3卷 251-268页

作者： Tao Wang Peng Tan qi tang Chenlong Zhou Yakun Ding Shenrui Xu Mengda Song Huiyang Fu Yucheng Zhang Xiaohui Zhang Yueyu Bai Zhihong Sun Xi Ma State Key Laboratory of Animal Nutrition and Feeding College of Animal Science and TechnologyChina Agricultural UniversityBeijingChina Luoyang Key Laboratory of Animal Genetic and Breeding College of Animal ScienceHenan University of Science and TechnologyLuoyangChina Key Laboratory of Innovative Utilization of Indigenous Cattle and Sheep Germplasm Resources(Co‐construction by Ministry and Province) Ministry of Agriculture and Rural AffairsZhengzhou UniversityZhengzhouChina Animal Health Supervision in Henan Province ZhengzhouChina Laboratory for Bio‐Feed and Molecular Nutrition Department of Animal Science and TechnologySouthwest UniversityChongqingChina

Broad-spectrum antibacterial drugs often lack specificity,leading to indiscriminate bactericidal activity,which can disrupt the normal microbial balance of the host flora and cause unnecessary cytotoxicity during systemic *** this study,we constructed a specifically targeted antimicrobial peptide against Staphylococcus aureus by introducing a phage-displayed peptide onto a broad-spectrum antimicrobial peptide and explored its structure–function relationship through one-factor ***2 obtained by screening based on the selectivity index and the targeting index showed specific killing ability against ***,SFK2 showed excellent biocompatibility in mice and piglet,and demonstrated significant therapeutic efficacy against *** *** conclusion,our screening of phage-derived heptapeptides effectively enhances the specific bactericidal ability of the antimicrobial peptides against ***,providing a theoretical basis for developing targeted antimicrobial peptides.

关键词： antimicrobial peptides membrane disruption mechanism microbial infection phage display technology Staphylococcus aureus

先进优质生产要素赋能新质生产力的实践路径研究

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浙江工商大学学报 2024年第4期 98-110页

作者：唐琦张辉北京大学医学人文学院北京100191 北京大学经济与人类发展研究中心北京100871 北京大学经济学院北京100871

生产要素的质效提升和结合方式变化是新质生产力的重要特质,其创新性配置和顺畅流动能够高效赋能新质生产力的培育和发展。优质生产要素的先进性体现为要素对产业发展带动作用的创新式突破,优质性体现为要素之间结合方式的颠覆性发展及... 详细信息

生产要素的质效提升和结合方式变化是新质生产力的重要特质,其创新性配置和顺畅流动能够高效赋能新质生产力的培育和发展。优质生产要素的先进性体现为要素对产业发展带动作用的创新式突破,优质性体现为要素之间结合方式的颠覆性发展及要素生产效率的大幅提高。当前,为创新生产要素配置方式,应采取建设高标准生产要素市场、探索生产要素结合新方式、协同现代化产业体系建设的措施;为推动先进优质生产要素顺畅流动,应深化经济体制、科技体制改革,打通束缚发展的堵点卡点,用好两个市场两种资源。通过优化生产要素配置、发挥新型要素的纽带作用、推动科技成果加快转化,能够有效促进全要素生产率的大幅提升。

关键词：先进优质生产要素新质生产力实践路径全要素生产率

Plasmonic Ag nanoparticles decorated MIL-101(Fe) for enhanced photocatalytic degradation of bisphenol A with peroxymonosulfate under visible-light irradiation

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Chinese Chemical Letters 2024年第1期35卷 418-423页

作者： Yan Gong Yu Ding qi tang Fei Lian Chun Bai Ruiyi Xie Haijiao Xie Xu Zhao School of Energy and Environmental Engineering Hebei University of TechnologyTianjin 300401China Hangzhou Yanqu Information Technology Co. Ltd.Hangzhou 310003China Key Laboratory of Drinking Water Science and Technology Research Center for Eco-Environmental SciencesChinese Academy of SciencesBeijing 100085China Collapse

Photocatalytic activation of peroxymonosulfate (PMS) has garnered a lot of interest in the field of wastewater treatment. Herein, a plasmonic Ag nanoparticles decorated MIL-101(Fe) hybrid was synthesized through a photodeposition process. Upon light irradiation, the Ag/MIL-101(Fe) exhibit reinforced photocatalytic activities for elimination of bisphenol A (BPA) with PMS. The optimized 2.0% Ag/MIL-101(Fe) composite presented the highest photocatalytic activity with kinetic constant k of 0.102 min-1, which was about 10-fold of the pristine MIL-101(Fe). Loading of plasmonic Ag into MIL-101(Fe) boosts photoinduced carrier separation and accelerates PMS activation to generate strong oxidative radicals. Photoelectrochemical tests and multiple spectroscopic studies confirmed the promoted charge carrier separation and transfer capability of Ag/MIL-101(Fe). Combining the results of radical trapping experiments and electron spin resonance (ESR), the formed SO4·-, ·OH, ·O2- and 1O2 had a significant role in the photocatalytic process. According to intermediate study, the degradation pathway was studied, and the possible mechanism was proposed.

关键词： Photocatalysis MOF Peroxymonosulfate Plasmonic Ag BPA

“想象的学科”代替“学科的想象”?——论计算档案学的“来路”与“归途”

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档案学研究 2024年第3期 28-36页

作者：唐启于英香上海大学文化遗产与信息管理学院上海200444

计算档案学是诞生于大数据背景下的一种数据密集型档案学术研究范式,是档案治理在微观领域的技术工具,是计算科学、数据科学、档案学三者交叉形成的学术领域。分析并研究计算档案学的产生原因与发展前途,分析其与传统档案学及相关学科... 详细信息

计算档案学是诞生于大数据背景下的一种数据密集型档案学术研究范式,是档案治理在微观领域的技术工具,是计算科学、数据科学、档案学三者交叉形成的学术领域。分析并研究计算档案学的产生原因与发展前途,分析其与传统档案学及相关学科的矛盾,可以为计算档案学的总体发展指明方向。科学研究的范式转型是计算档案学概念产生的根本原因、内在原因、必然原因;自然科学的“内卷化”和档案学科的体量小是计算档案学概念产生的直接原因、外在原因、偶然原因。计算档案学重在分析数据,这与传统档案学的研究对象存在矛盾;且基于数据分析的计算档案学与其他学科的边界难以划定。从制度、数据、算法角度对计算档案学进行宏观调整,要首先解决数据隐私与伦理问题;要对档案数据的质量与结构进行完善,使档案数据变为档案大数据;要解决信息双层不对称下学者信息不对称和算法黑箱的问题,使计算档案学真正成为赋能档案治理,并最终服务国家治理的技术工具。

关键词：计算档案学档案治理国家治理数字人文