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Conservation genomics provides insights into genetic resilience and adaptation of the endangered Chinese hazelnut, Corylus chinensis

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Plant Diversity 2024年第3期46卷 294-308页

作者： Zhen Yang Lisong liang Weibo Xiang lujun Wang Qinghua Ma Zhaoshan Wang Key Laboratory of Tree Breeding and Cultivation National Forestry and Grassland AdministrationResearch Institute of ForestryChinese Academy of ForestryBeijing 100091China National Engineering Research Center of Eco-Environment Protection for Yangtze River Economic Belt China Three Gorges CorporationBeijing 100083China Rare Plants Research Institute of Yangtze River China Three Gorges CorporationYichang 443133China Research Institute of Economic Forest Cultivation and Processing Anhui Academy of ForestryHefei 230031China

Global climate change has increased concerns regarding biodiversity loss.However,many key conservation issues still required further research,including demographic history,deleterious mutation load,adaptive evolution,and putative introgression.Here we generated the first chromosome-level genome of the endangered Chinese hazelnut,Corylus chinensis,and compared the genomic signatures with its sympatric widespread C.kwechowensis-C yunnanensis complex.We found large genome rearrangements across all Corylus species and identified species-specific expanded gene families that may be involved in adaptation.Population genomics revealed that both C.chinensis and the C.kwechowensis-C.yunnanensis complex had diverged into two genetic lineages,forming a consistent pattern of southwestern-northern differentiation.Population size of the narrow southwestern lineages of both species have decreased continuously since the late Miocene,whereas the widespread northern lineages have remained stable(C.chinensis) or have even recovered from population bottlenecks(C.kwechowensis-C.yunnanensis complex) during the Quaternary.Compared with C.kwechowensis-C. yunnanensis complex,C.chinensis showed significantly lower genomic diversity and higher inbreeding level.However,C.chinensis carried significantly fewer deleterious mutations than C.kwechowensis-C. yunnanensis complex,as more effective purging selection reduced the accumulation of homozygous variants.We also detected signals of positive selection and adaptive introgression in different lineages,which facilitated the accumulation of favorable variants and formation of local adaptation.Hence,both types of selection and exogenous introgression could have mitigated inbreeding and facilitated survival and persistence of C.chinensis.Overall,our study provides critical insights into lineage differentiation,local adaptation,and the potential for future recovery of endangered trees.

关键词： Conservation genomics Demographic history Inbreeding Genetic load Runs of homozygosity Local adaptation

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Simultaneous capture of ISG15 conjugating and deconjugating enzymes using a semi-synthetic ISG15-Dha probe

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Science China Chemistry 2023年第3期66卷 837-844页

作者： Chuntong Li Tian Wang lujun liang Guochao Chu Jiachen Zhang Wei He Lei Liu Jinghong Li Department of Chemistry Key Laboratory of Bioorganic Phosphorus Chemistry&Chemical BiologyCenter for Synthetic and Systems BiologyState Key Laboratory of Chemical Oncogenomics(Shenzhen)Tsinghua UniversityBeijing 100084China School of Pharmaceutical Sciences Tsinghua UniversityBeijing 100084China Center for BioAnalytical Chemistry Hefei National Laboratory of Physical Science at MicroscaleUniversity of Science and Technology of ChinaHefei 230026China

ISG15 is a ubiquitin-like(Ubl) protein attached to substrate proteins by ISG15 conjugating enzymes whose dysregulation is implicated in a multitude of disease processes, but the probing of these enzymes remains to be accomplished. Here, we describe the development of a new activity-based probe ISG15-Dha(dehydroalanine) through protein semi-synthesis. In vitro crosslinking and cell lysate proteomic profiling experiments showed that this probe can sequentially capture ISG15 conjugating enzymes including E1 enzyme UBA7, E2 enzyme UBE2L6, E3 enzyme HERC5, the previously known ISG15 deconjugating enzyme(USP18), as well as some other enzymes(USP5 and USP14) which we additionally confirmed to impart deISGylation activity. Collectively, ISG15-Dha provides a new tool that can simultaneously capture ISG15 conjugating and deconjugating enzymes for biochemical or pharmacological studies.

关键词： ISG15-Dha probe semi-synthesis activity based probe proteomics ISGylation

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Semi-synthesis of disulfide-linked branched tri-ubiquitin mimics

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Science China Chemistry 2018年第4期61卷 412-417页

作者： Yanyan Si lujun liang Shan Tang Yunkun Qi Yong Huang Lei Liu Key Laboratory of Chemical Genomics School of Chemical Biology and BiotechnologyPeking UniversityShenzhen Graduate School Department of Chemistry Tsinghua University

Ubiquitin(Ub) chain isopeptide bond mimics are useful molecules for biochemical and biophysical studies. Herein, we report the semi-synthesis of the disulfide-linked K11/K48-branched tri-Ub(Ub_3^(11/48)(S-S)), the first example of an isopeptide mimic for the branched Ub chains,which have recently emerged as an interesting category of Ub modifications. Our strategy comprised the El-dependent synthesis of the Ub conjugate of aminoethanethiol, followed by disulfide formation with Ub(K11 C, K48 C). The structure of the synthetic isopeptide bond mimics was verified by the crystal structure of Ub_3^(11/48)(S-S). Deubiquitination and pulldown assays indicated that the synthetic Ub_3^(11/48)(S-S) could be hydrolyzed by linkage-specific deubiquitinases(K11-specific Cezanne and K48-specific OTUB1), and recognized by proteasomal ubiquitin receptor S5 a.

关键词：二硫化物半合成模仿连接分叉结构验证生物化学生物物理

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Inactivity of YGL082W in vitro due to impairment of conformational change in the catalytic center loop

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Science China Chemistry 2020年第2期63卷 237-243页

作者： Lining Lu Yu Guo Tian Wang lujun liang Suwen Zhao Feng Wang Lei Liu Tsinghua-Peking Center for Life Sciences Key Laboratory of Bioorganic Phosphorus Chemistry&Chemical Biology(Ministry of Education)Center for Synthetic and Systems BiologyState Key Laboratory of Chemical Oncogenomics(Shenzhen)Department of ChemistryTsinghua UniversityBeijing 100084China School of Life Science Beijing Institute of TechnologyBeijing 100081China iHuman Institute School of Life Science and TechnologyShanghaiTech UniversityShanghai 201210China

MINDY-1 is a recently discovered new family of deubiquitinating enzymes(DUB),but one of its yeast homologs,YGL082 W,does not show any DUB activity in vitro.Sequence alignment shows that YGL082 W possesses the correct catalytic triad,and yet did not catalyze either the hydrolysis of di-ubiquitin,crosslinking with C-terminally propargylated ubiquitin,or hydrolysis of ubiquitin-7-amino-4-methylcoumarin.After obtaining a crystal structure of the catalytic domain of YGL082 W,we identified an interesting difference between the catalytic center loop of YGL082 W and that of its human homolog MINDY-1.Because the conformation of the catalytic center loop was previously reported to be important for the deubiquitination activity of MINDY-1,we hypothesized that Glu27(instead of the corresponding Pro136 in MINDY-1) of the catalytic center loop of YGL082 W may impair the conformational change and account for the lack of activity.This hypothesis was supported by homology modeling and molecular dynamics simulations,which showed that the Pro-to-Glu mutation(P136 E mutation for MINDY-1) creates a hydrogen bond that inhibits the conformation change of the catalytic center loop of MINDY-1.Further experiments through site-directed mutation validated this hypothesis,showing that the P27 E mutation caused MIY1(a homologous active DUB from yeast) to lose activity.

关键词： deubiquitinating enzymes(DUB) enzymology X-ray crystal structure molecular dynamics

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超大型海水冷却塔塔群飘滴及盐沉积数值模拟研究

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核科学与工程 2024年第1期44卷 91-97页

作者：梁梓琦朱晴杨杰李陆军中广核工程有限公司广东深圳518100 中国水利水电科学研究院北京1000381

针对核电项目大型海水冷却塔,采用三维数值模型,结合厂址气象数据、冷却塔设计参数、总图布置以及周围环境特征,研究了超大型自然通风海水冷却塔在建筑物、环境风相互作用下的冷却塔飘滴扩散迁移特征和盐沉积量。结果表明,当环境风向与... 详细信息

针对核电项目大型海水冷却塔,采用三维数值模型,结合厂址气象数据、冷却塔设计参数、总图布置以及周围环境特征,研究了超大型自然通风海水冷却塔在建筑物、环境风相互作用下的冷却塔飘滴扩散迁移特征和盐沉积量。结果表明,当环境风向与塔排平行时,出口热空气相互叠加形成一股气流,有利于减少飘滴和盐沉积对环境的影响,粒径大于550μm的飘滴不能从高位冷却塔出口逸出,6台核电机组正常运行工况时,盐沉积量一般不会对植物造成严重损坏。

关键词：飘滴盐沉积海水冷却塔塔群数值模拟

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皖北平欧杂种榛优势品种坚果性状评价

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西北植物学报 2024年第4期44卷 644-653页

作者：王陆军孙璟周米生梁丽松马庆华安徽省林业科学研究院合肥230031 宿州市夹沟国有林场安徽宿州234102 国家林业和草原局林木培育重点实验室中国林业科学研究院林业研究所北京100091

【目的】平欧杂种榛是中国野生平榛和欧洲榛种间杂交获得的新种质,具有抗寒、丰产和适应性强等特点。对皖北地区平欧杂种榛优势品种坚果进行性状评价,明确品种加工适宜性,可为平欧杂种榛选择与推广提供科学依据。【方法】依据适应性和... 详细信息

【目的】平欧杂种榛是中国野生平榛和欧洲榛种间杂交获得的新种质,具有抗寒、丰产和适应性强等特点。对皖北地区平欧杂种榛优势品种坚果进行性状评价,明确品种加工适宜性,可为平欧杂种榛选择与推广提供科学依据。【方法】依据适应性和丰产性等指标,在皖北地区筛选出9个平欧杂种榛优势品种坚果,从烤制、仁用、油用、鲜食等不同加工利用角度进行分析评价。【结果】(1)皖北地区9个优势品种单粒坚果质量为2.54~4.40 g,三径(纵径、横径、侧径)均值为18.99~21.49 mm,形状指数为0.67~1.02,单粒榛仁质量为1.00~1.66 g,果壳厚度为1.53~2.41 mm,出仁率为34.36%~47.01%,榛仁脂肪含量为50.50~58.00 g/(100 g),蛋白质含量为21.10~25.10 g/(100 g),可溶性糖含量为4.08%~4.94%。(2)油脂中鉴定出8种脂肪酸成分,其中油酸含量最高,为81.21%~88.53%,不饱和脂肪酸含量为92.19%~94.61%。榛仁中钾、磷、钙和镁含量较为丰富。(3)9个优势品种单株坚果产量为1.52~2.20 kg,单株脂肪产量为330.50~503.47 g,单株蛋白质产量为141.68~224.40 g。【结论】根据不同榛果加工方式,皖北9个优势品种中‘辽榛3号’最适作为带壳烤制品种;‘辽榛3号’、‘达维’和‘辽榛4号’最适作为仁用加工品种,‘辽榛4号’可作为油用加工品种;‘辽榛1号’可作为功能性蛋白饮料加工品种;‘达维’和‘辽榛9号’可作为高钙类加工品种;‘达维’、‘辽榛3号’、‘平欧545号’是较为适宜的鲜食品种。

关键词：平欧杂种榛优势品种经济性状矿质成分脂肪酸营养物质

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经典名方养胃汤的关键信息考证

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中国实验方剂学杂志 2024年第12期30卷 147-157页

作者：梁绿圆曹佳蕾王艺萍耿萌萌朱路君魏文希魏炳琦史文丽马丙祥河南中医药大学第一附属医院儿科医院郑州450099 河南中医药大学儿科医学院郑州450046 郑州世卓医药科技有限公司郑州450000 河南中医药大学中医学院郑州450046

《证治准绳》记载的养胃汤善治外感风寒、内伤生冷及疟疾等,现已被收录于2018年国家中医药管理局公布的《古代经典名方目录(第一批)》。采用文献学研究方法,通过系统整理相关古籍文献及现代文献发现《证治准绳》养胃汤类方众多,与《证... 详细信息

《证治准绳》记载的养胃汤善治外感风寒、内伤生冷及疟疾等,现已被收录于2018年国家中医药管理局公布的《古代经典名方目录(第一批)》。采用文献学研究方法,通过系统整理相关古籍文献及现代文献发现《证治准绳》养胃汤类方众多,与《证治准绳》养胃汤交织衍化且临床应用广泛,为厘清其历史沿革和衍化脉络,对养胃汤及其类方的历史源流进行梳理,并对方义组成、药物基原、炮制方法、功效主治等关键信息进行考证分析。该研究共获取《证治准绳》养胃汤数据896条,经筛选纳入26条有效数据,涉及中医古籍17部,另纳入《证治准绳》养胃汤类方有效数据29条,涉及23部古籍供脉络梳理。考证发现,养胃汤最早可追溯至宋代《太平惠民和剂局方》所载之“人参养胃汤”,并沿用至今,后世医家在此基础上进行加减应用,因而流传版本较多。经对比分析,历代《证治准绳》养胃汤方剂组成较为统一,其药物基原和炮制方法基本清晰,建议“清半夏、厚朴(姜汁炒)、苍术(米泔水制)各37.3 g,橘红27.98 g,藿香叶、草果、茯苓、人参各18.65 g,炙甘草9.33 g。上述药物粉碎为粗粒,每服14.92 g,以水450 mL,生姜7 g,乌梅2 g,煎至270 mL,热服”。《证治准绳》养胃汤具有温中解表,燥湿除疟之效,主治病证广泛,如外感风寒、内伤生冷等脾胃不和之症及各类疟疾。现代临床未见有《证治准绳》所载养胃汤相关报道,故需加大对该方的挖掘和应用。

关键词：经典名方养胃汤考证《证治准绳》关键信息香砂养胃汤藿香养胃汤

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一种基于功能虚拟化的计量架构

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城市燃气 2024年第1期 25-28,29,30页

作者：龙祥均张陆军王帅梁睿赵艺重庆市智能燃气计量仪表企业工程技术研究中心重庆前卫表业有限公司

基于物联网技术的公用能源计量设施的快速智能化发展[1],人们对计量终端的功能需求、业务需求、智能化需求越来越多,终端的控制软件变得愈加复杂,成本和功耗亦在显著增加,可靠性、稳定性和可维护性的保证变得困难。经营企业在付出了高... 详细信息

基于物联网技术的公用能源计量设施的快速智能化发展[1],人们对计量终端的功能需求、业务需求、智能化需求越来越多,终端的控制软件变得愈加复杂,成本和功耗亦在显著增加,可靠性、稳定性和可维护性的保证变得困难。经营企业在付出了高昂的投资代价后,建成的计量终端在生命周期内却不具备业务功能升级或演进的能力,是一个潜在的巨大损失,这对技术和应用的迭代发展无疑也是非常不利的。于计量终端提供商而言,这些数量巨大的物联网设备,在投入运行后即成为了一个巨大的成本黑洞,维护代价高。为了解决现有计量架构下计量业务功能无法升级或演进的难题,基于云计算、功能虚拟化技术,本文提出了一种新的计量架构,即基于计量功能虚拟化的SDM架构。通过协议栈和网络架构的优化,将能很好解决上述问题。

关键词：云计算能源计量网络架构智能化发展物联网技术功能升级协议栈生命周期

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Population genomics reveals demographic history and selection signatures of hazelnut (Corylus)

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Horticulture Research 2023年第5期10卷 247-259页

作者： Zhen Yang Wenxu Ma lujun Wang Xiaohong Yang Tiantian Zhao Lisong liang Guixi Wang Qinghua Ma Key Laboratory of Tree Breeding and Cultivation National Forestry and Grassland AdministrationResearch Institute of ForestryChinese Academy of ForestryBeijing100091China Forest Botany and Tree Physiology University of GoettingenGoettingen37077Germany Research Institute of Economic Forest Cultivation and Processing Anhui Academy of ForestryHefei230031China Research Institute of Walnut Guizhou Academy of ForestryGuiyang550005China

Hazelnut(Corylus spp.)is known as one of the four famous tree nuts in the world due to its pleasant taste and nutritional benefits.However,hazelnut promotion worldwide is increasingly challenged by global climate change,limiting its production to a few regions.Focusing on the eurytopic Section Phyllochlamys,we conducted whole-genome resequencing of 125 diverse accessions from five geo-ecological zones in Eurasia to elucidate the genomic basis of adaptation and improvement.Population structure inference outlined five distinct genetic lineages corresponding to climate conditions and breeding background,and highlighted the differentiation between European and Asian lineages.Demographic dynamics and ecological niche modeling revealed that Pleistocene climatic oscillations dominantly shaped the extant genetic patterns,and multiple environmental factors have contributed to the lineage divergence.Whole-genome scans identified 279,111,and 164 selective sweeps that underlie local adaptation in Corylus heterophylla,Corylus kweichowensis,and Corylus yunnanensis,respectively.Relevant positively selected genes were mainly involved in regulating signaling pathways,growth and development,and stress resistance.The improvement signatures of hybrid hazelnut were concentrated in 312 and 316 selected genes,when compared to C.heterophylla and Corylus avellana,respectively,including those that regulate protein polymerization,photosynthesis,and response to water deprivation.Among these loci,22 candidate genes were highly associated with the regulation of biological quality.Our study provides insights into evolutionary processes and the molecular basis of how sibling species adapt to contrasting environments,and offers valuable resources for future climate-resilient breeding.

关键词： breeding Population signature

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新型硫酸盐还原菌的分离鉴定及其对六价铬污染物的原位修复效果

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环境工程 2024年第2期42卷 192-198页

作者：韩建均柴陆军王国金张瑜秦康佳周曼梁雪杰郝俊鹏王慧清华苏州环境创新研究院江苏苏州215010 北京本农科技发展有限公司北京100176 中国建筑材料工业地质勘查中心山东总队济南250100 清华大学北京100091

利用微生物将六价铬[Cr(Ⅵ)]还原为三价铬[Cr(Ⅲ)]是一种具有前景的铬污染土壤修复方法。从新型的分离和分子生物学鉴定着手,通过含铬溶液和铬污染土壤试验探讨了菌株对Cr(Ⅵ)的修复效果。结果表明:分离得到能够还原Cr(Ⅵ)的硫酸盐还原... 详细信息

利用微生物将六价铬[Cr(Ⅵ)]还原为三价铬[Cr(Ⅲ)]是一种具有前景的铬污染土壤修复方法。从新型的分离和分子生物学鉴定着手,通过含铬溶液和铬污染土壤试验探讨了菌株对Cr(Ⅵ)的修复效果。结果表明:分离得到能够还原Cr(Ⅵ)的硫酸盐还原菌S-7,其16S rDNA全长序列与Desulfovibrio desulfuricans DSM 642T存在98.89%相似度,属于新型脱硫弧菌种,命名为Desulfovibrio desulfuricans S-7。D.desulfuricans S-7生长繁殖的最适合生长温度为30℃,最适合pH值是7.0,耐NaCl浓度范围为0~10%。D.desulfuricans S-7修复铬溶液的结果表明:对25 mg/L的Cr(Ⅵ)去除率为79.74%,在100 mg/L的Cr(Ⅵ)条件下D.desulfuricans S-7的生长繁殖受到抑制。Cr(Ⅵ)污染土壤实验的结果表明:土壤中Cr(Ⅵ)含量50.0 mg/kg降到3.1 mg/kg,去除率达到93.8%,修复后的土地质量符合GB 36600—2018一类建设用地的标准。研究表明:D.desulfuricans S-7能够高效地原位修复厌氧环境下Cr(Ⅵ)污染土壤,为原位修复深层Cr(Ⅵ)污染土壤提供一种新的替代方案。

关键词：硫酸盐还原菌 Desulfovibrio desulfuricans 六价铬污染土壤原位修复

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