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biomarkers of aging

Science China(Life Sciences) 2023年第5期66卷 893-1066页

作者： aging biomarker consortium Hainan Bao Jiani Cao Mengting Chen Min Chen Wei Chen Xiao Chen Yanhao Chen Yu Chen Yutian Chen Zhiyang Chen Jagadish K Chhetri Yingjie Ding Junlin Feng Jun Guo Mengmeng Guo Chuting He Yujuan Jia Haiping Jiang Ying Jing Dingfeng Li Jiaming Li Jingyi Li Qinhao Liang Rui Liang Feng Liu Xiaoqian Liu Zuojun Liu Oscar Junhong Luo Jianwei Lv Jingyi Ma Kehang Mao Jiawei Nie Xinhua Qiao Xinpei Sun Xiaoqiang Tang Jianfang Wang Qiaoran Wang Siyuan Wang Xuan Wang Yaning Wang Yuhan Wang Rimo Wu Kai Xia Fu-Hui Xiao Lingyan Xu Yingying Xu Haoteng Yan Liang Yang Ruici Yang Yuanxin Yang Yilin Ying Le Zhang Weiwei Zhang Wenwan Zhang Xing Zhang Zhuo Zhang Min Zhou Rui Zhou Qingchen Zhu Zhengmao Zhu Feng Cao Zhongwei Cao Piu Chan Chang Chen Guobing Chen Hou-Zao Chen Jun Chen Weimin Ci Bi-Sen Ding Qiurong Ding Feng Gao Jing-Dong JHan Kai Huang Zhenyu Ju Qing-Peng Kong Ji Li Jian Li Xin Li Baohua Liu Feng Liu Lin Liu Qiang Liu Qiang Liu Xingguo Liu Yong Liu Xianghang Luo Shuai Ma Xinran Ma Zhiyong Mao Jing Nie Yaojin Peng Jing Qu Jie Ren Ruibao Ren Moshi Song Zhou Songyang Yi Eve Sun Yu Sun Mei Tian Shusen Wang Si Wang Xia Wang Xiaoning Wang Yan-Jiang Wang Yunfang Wang Catherine CL Wong Andy Peng Xiang Yichuan Xiao Zhengwei Xie Daichao Xu Jing Ye Rui Yue Cuntai Zhang Hongbo Zhang Liang Zhang Weiqi Zhang Yong Zhang Yun-Wu Zhang Zhuohua Zhang Tongbiao Zhao Yuzheng Zhao Dahai Zhu Weiguo Zou Gang Pei Guang-Hui Liu aging biomarker consortium(ABC) Beijing 100101China CAS Key Laboratory of Genomic and Precision Medicine Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijing 100101China State Key Laboratory of Stem Cell and Reproductive Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China Department of Dermatology Xiangya HospitalCentral South UniversityChangsha 410008China Hunan Key Laboratory of aging Biology Xiangya HospitalCentral South UniversityChangsha 410008China National Clinical Research Center for Geriatric Disorders Xiangya HospitalCentral South UniversityChangsha 410008China Clinic Center of Human Gene Research Union HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhan 430022China Hubei Clinical Research Center of Metabolic and Cardiovascular Disease Huazhong University of Science and TechnologyWuhan 430022China Hubei Key Laboratory of Metabolic Abnormalities and Vascular aging Huazhong University of Science and TechnologyWuhan 430022China Stem Cell Translational Research Center Tongji HospitalTongji University School of MedicineShanghai 200065China Department of Nuclear Medicine Daping HospitalThird Military Medical UniversityChongqing 400042China CAS Key Laboratory of Nutrition Metabolism and Food SafetyShanghai Institute of Nutrition and HealthUniversity of Chinese Academy of SciencesChinese Academy of SciencesShanghai 200031China Shanghai Key Laboratory of Maternal Fetal Medicine Clinical and Translational Research Center of Shanghai First Maternity and Infant HospitalFrontier Science Center for Stem Cell ResearchShanghai Key Laboratory of Signaling and Disease ResearchSchool of Life Sciences and TechnologyTongji UniversityShanghai 200092China The Department of Endovascular Surgery The First Affiliated Hospital of Zhengzhou UniversityZhengzhou 450052China Key Laboratory of Regenerative Medicine of Ministry of Education Institute of Ageing and Regenerative MedicineJ

aging biomarkers are a combination of biological parameters to(i)assess age-related changes,(ii)track the physiological aging process,and(iii)predict the transition into a pathological *** a broad spectrum of aging biomarkers has been developed,their potential uses and limitations remain poorly *** immediate goal of biomarkers is to help us answer the following three fundamental questions in aging research:How old are we?Why do we get old?And how can we age slower?This review aims to address this ***,we summarize our current knowledge of biomarkers developed for cellular,organ,and organismal levels of aging,comprising six pillars:physiological characteristics,medical imaging,histological features,cellular alterations,molecular changes,and secretory *** fulfill all these requisites,we propose that aging biomarkers should qualify for being specific,systemic,and clinically relevant.

关键词： aging senescence biomarker clock

Phylogenomic Mining of the Mints Reveals Multiple Mechanisms Contributing to the Evolution of Chemical Diversity in Lamiaceae

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Molecular Plant 2018年第8期11卷 1084-1096页

作者： Mint Evolutionary Genomics consortium Department of Biochemistry Purdue University West Lafayette IN 47907-2063 USA Department of Plant Biology Michigan State University East Lansing MI 48824 USA Florida Museum of Natural History University of Florida Gainesville FL 32611 USA The John Innes Centre Department of Biological Chemistry Norwich NR4 7UH UK Department of Biology University of Florida Gainesville FL 32611 USA

The evolution of chemical complexity has been a major driver of plant diversification, with novel compounds serving as key innovations. The species-rich mint family （Lamiaceae） produces an enormous variety of compounds that act as attractants and defense molecules in nature and are used widely by humans as flavor additives, fragrances, and anti-herbivory agents. To elucidate the mechanisms by which such diversity evolved, we combined leaf transcriptome data from 48 Lamiaceae species and four outgroups with a robust phylogeny and chemical analyses of three terpenoid classes （monoterpenes, sesquiterpenes, and iridoids） that share and compete for precursors. Our integrated chemical-genomic-phylogenetic approach revealed that：（1） gene family expansion rather than increased enzyme promiscuity of terpene synthases is correlated with mono- and sesquiterpene diversity; （2） differential expression of core genes within the iri- doid biosynthetic pathway is associated with iridoid presence/absence; （3） generally, production of iridoids and canonical monoterpenes appears to be inversely correlated; and （4） iridoid biosynthesis is significantly associated with expression of geraniol synthase, which diverts metabolic flux away from canonical mono- terpenes, suggesting that competition for common precursors can be a central control point in specialized metabolism. These results suggest that multiple mechanisms contributed to the evolution of chemodiversity in this economically important family.

关键词： chemodiversity evolution terpene iridoid

“Beijing Region” (3pter-D3S3397) of the Human Genome: Complete sequence and analysis

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Science China(Life Sciences) 2005年第4期48卷 311-329页

作者： The Chinese Human Genome Sequencing consortium Beijing Genomics Institute Chinese Academy of Sciences Beijing 101300 China /James D. Watson Institute of Genome Sciences Zhejiang University Hangzhou 310008 China Chinese National Human Genome Center at Shanghai (CHGC) Shanghai 201203 China Chinese National Human Genome Center Beijing (CHGB) Beijing 100176 China

The goal of the Human Genome Project (HGP) is to determine a complete and high-quality sequence of the human genome. China, as one of the six member states, takes a region between 3pter and D3S3397 of the human chromosome 3 as its share of this historic project, referred as “Beijing Region”. The complete sequence of this region comprises of 17.4 megabasepairs (Mb) with an average GC content of 42% and an average recombination rate of 2.14 cM/Mb. Within Beijing Region, 122 known and 20 novel genes are identified, as well as 42607 single nucleotide polymorphisms (SNPs). Comprehensive analyses also reveal: (i) gene density and GC-content of Beijing Region are in agreement with human cytogenetic maps, i.e. G-minus bands are GC-rich and of a high gene density, whereas G-plus bands are GC-poor and of a relatively low gene density; (ii) the average recombination rate within Beijing Region is rela-tively high compared with other regions of chromosome 3, with the highest recombination rate of 6.06 cM/Mb in the subtelomeric area; (iii) it is most likely that a large gene, associated with the mammary gland, may reside in the 1.1 Mb gene-poor area near the telomere; (iv) many dis-ease-related genes are genetically mapped to Beijing Region, including those associated with cancers and metabolic syndromes. All make Beijing Region an important target for in-depth mo-lecular investigations with a purpose of medical applications.

关键词： Human Genome Project (HGP), "Beijing Region", complete sequence, genome landscape, sequence annotation.

Biohydrometallurgy applied to exploitation of black shale resources： Overview of Bioshale FP6 European project

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中国有色金属学会会刊：英文版 2008年第6期18卷 1485-1490页

作者： P. D＇HUGUES P. SPOLAORE Bioshale consortium BRGM EPI/Eco 3 Avenue C. Guillemin 45060 Orleans Cedex 2 France

Bioshale 工程，由欧洲委员会(FP6 计划) 共同资助，在 2004 年 10 月开始了并且在 2007 年 10 月完成了。这个工程的主要目的是为黑页岩矿石的 eco 有效的利用定义创新 biotechnological 过程。黑页岩矿石包含贱、宝贵、高技术的金属... 详细信息

Bioshale 工程，由欧洲委员会(FP6 计划) 共同资助，在 2004 年 10 月开始了并且在 2007 年 10 月完成了。这个工程的主要目的是为黑页岩矿石的 eco 有效的利用定义创新 biotechnological 过程。黑页岩矿石包含贱、宝贵、高技术的金属而且有机物的高内容由常规技术的那缺陷金属恢复。三世界级黑人页岩沉积物被选择为 R&D 行动的目标。这些包括在自然条件下面存在的一沉积物(Talvivaara，芬兰) ，一个当前在过程(Lubin，波兰) 并且在采矿以后的(Mansfeld，德国) 。工作计划的主要技术方面能如下被总结：忍受金属的部件的地质的资源和选择的评估；为金属恢复要测试的生物协会的选择；对 bioprocessing 的评价发送，包括为金属恢复处理的 hydrometallurgical；包括社会、环境的影响的新过程的 techno 经济的评估。13 欧洲人获得的主要结果的概述合伙(从 8 个国家) 在这个完成的研究计划包含了在这个工作被给。

关键词：生物技术生物浸取矿石处理黑页岩

PSA density in the diagnosis of prostate cancer in the Chinese population: results from the Chinese Prostate Cancer consortium

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Asian Journal of Andrology 2021年第3期23卷 300-305页

作者： Zi-Jian Song Jin-Ke Qian Yue Yang Han-Xiao Wu Mao-Yu Wang Si-Yuan Jiang Fu-Bo Wang Wei Zhang Rui Chen Chinese Prostate Cancer consortium Department of Urology Shanghai Changhai HospitalThe Second Military Medical UniversityShanghai 200433China Department of Urology Binhai People's HospitalYancheng 224500China 不详

We performed this study to investigate the diagnostic performance of prostate-specific antigen density(PSAD)in a multicenter cohort of the Chinese Prostate Cancer *** with prostate-specific antigen(PSA)levels≥4.0 ng ml^(-1) regardless of digital rectal examination(DRE)results or PSA levels<4.0 ng ml^(-1)and abnormal DRE results were included from 18 large referral hospitals in *** diagnostic performance of PSAD and the sensitivity and specificity for the diagnosis of prostate cancer(PCa)and high-grade prostate cancer(HGPCa)at different cutoff values were evaluated.A total of 5220 patients were included in the study,and 2014(38.6%)of them were diagnosed with *** patients with PSA levels ranging from 4.0 to 10.0 ng ml^(-1),PSAD was associated with PCa and HGPCa in both univariate(odds ratio[OR]=45.15,P<0.0001 and OR=25.38,P<0.0001,respectively)and multivariate analyses(OR=52.55,P<0.0001 and OR=26.05,P<0.0001,respectively).The areas under the receiver operating characteristic curves(AUCs)of PSAD in predicting PCa and HGPCa were 0.627 and 0.630,*** the PSAD cutoff of 0.10 ng ml^(-2),we obtained a sensitivity of 88.7%for PCa,and nearly all(89.9%)HGPCa cases could be detected and biopsies could be avoided in 20.2%of the patients(359/1776 cases).Among these patients who avoided biopsies,only 30 cases had *** recommend 0.10 ng ml^(-2) as the proper cutoff value of PSAD,which will obtain a sensitivity of nearly 90%for both PCa and *** results of this study should be validated in prospective,population-based multicenter studies.

关键词： Chinese early detection of cancer prostate cancer prostate-specific antigen prostate-specific antigen density

Report on the 3rd Board Meeting of the International Human Phenome consortium

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Phenomics 2023年第1期3卷 77-82页

作者： Mei Tian Han Liu Shunling Chen Zhong Yang Weishuo Tao Shiwen Peng Huiting Che Li Jin The Secretariat of International Human Phenome consortium Human Phenome Institute Fudan UniversityShanghai 200438China International Human Phenome Institutes(Shanghai) Shanghai 200433China School of Life Sciences Fudan UniversityShanghai 200438China Shanghai Medical College Fudan UniversityShanghai 200032China

Introduction The phenome is a set of measurable traits,including the physical,chemical and biological traits of individuals and populations,that result from the complex interactions of genes,epigenetics,symbiotic microorganisms,diet and environmental exposures(Jin 2021).The aim of human phe-nomics is to precisely measure the human phenotypes and to comprehensively analyze the human *** doing so,we can systemically deconstruct the relationship among perceived phenotypes,compile phenotypic network,expand multi-dimensional and cross-scale correlations between macro and micro phenotypes,and eventually clarify the correlations among these *** the completion of the Human Genome Project,there is an urgent need for discovering the multi-level association among genes,envi-ronment and phenotypes to complement the other half of the required information for human ***,Fudan University has initiated the International Human Phenome Project in 2018,providing a new opportunity for biomedical research and leading the development of biomedicine.

关键词： Human eventually initiated

Imitating and exploring the human brain's resting and task-performing states via brain computing: scaling and architecture

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National Science Review 2024年第5期11卷 17-28页

作者： Wenlian Lu Longbin Zeng Jiexiang Wang Shitong Xiang Yang Qi Qibao Zheng Ningsheng Xu Jianfeng Feng DTB consortium Institute of Science and Technology for Brain-Inspired Intelligence Fudan University Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence(Fudan University) Ministry of Education Fudan University Shanghai Center for Mathematical Sciences Fudan University Department of Computer Science University of Warwick Zhangjiang Fudan International Innovation Center Fudan University

A computational human brain model with the voxel-wise assimilation method was established based on individual structural and functional imaging data. We found that the more similar the brain model is to the biological counterpart in both scale and architecture, the more similarity was found between the assimilated model and the biological brain both in resting states and during tasks by quantitative metrics. The hypothesis that resting state activity reflects internal body states was validated by the interoceptive circuit's capability to enhance the similarity between the simulation model and the biological brain. We identified that the removal of connections from the primary visual cortex(V1) to downstream visual pathways significantly decreased the similarity at the hippocampus between the model and its biological counterpart,despite a slight influence on the whole brain. In conclusion, the model and methodology present a solid quantitative framework for a digital twin brain for discovering the relationship between brain architecture and functions, and for digitally trying and testing diverse cognitive, medical and lesioning approaches that would otherwise be unfeasible in real subjects.

关键词： digital twin brain computational cortico-subcortical model fMRI data assimilation interoceptive circuit

Convergent adaptation of the genomes of woody plants at the land–sea interface

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National Science Review 2020年第6期7卷 978-993页

作者： Ziwen He Shaohua Xu Zhang Zhang Wuxia Guo Haomin Lyu Cairong Zhong David E.Boufford Norman C.Duke The International Mangrove consortium Suhua Shi State Key Laboratory of Biocontrol Guangdong Provincial Key Laboratory of Plant Resources Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes School of Life Sciences Sun Yat-Sen University Hainan Dongzhai Harbor National Nature Reserve Administration Harvard University Herbaria Centre for Tropical Water and Aquatic Ecosystem Research James Cook University the consortium of 26 Institutions

Sequencing multiple species that share the same ecological niche may be a new frontier for genomic *** such studies should shed light on molecular convergence, genomic-level analyses have been unsuccessful, due mainly to the absence of empirical controls. Woody plant species that colonized the global tropical coasts, collectively referred to as mangroves, are ideal for convergence studies. Here, we sequenced the genomes/transcriptomes of 16 species belonging in three major mangrove clades. To detect convergence in a large phylogeny, a CCS+ model is implemented, extending the more limited CCS method(convergence at conservative sites). Using the empirical control for reference, the CCS+ model reduces the noises drastically, thus permitting the identification of 73 convergent genes with Ptrue(probability of true convergence) > 0.9. Products of the convergent genes tend to be on the plasma membrane associated with salinity tolerance. Importantly, convergence is more often manifested at a higher level than at amino-acid(AA) sites. Relative to >50 plant species, mangroves strongly prefer 4 AAs and avoid 5 others across the genome. AA substitutions between mangrove species strongly reflect these tendencies. In conclusion, the selection of taxa, the number of species and, in particular, the empirical control are all crucial for detecting genome-wide convergence. We believe this large study of mangroves is the first successful attempt at detecting genome-wide site convergence.

关键词： convergent evolution genome mangrove adaptive evolution woody plants

Phenotypic and genotypic background underlying variations in fatty acid composition and sensory parameters in European bovine breeds

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Journal of Animal Science and Biotechnology 2014年第2期5卷 154-162页

作者： Natalia Sevane Hubert Levéziel Geoffrey R Nute Carlos Sanudo Alessio Valentini John Williams Susana Dunner the GeMQual consortium Departamento de Producción Animal Facultad de Veterinaria Universidad Complutense de Madrid Madrid Spain INRA UMR 1061 F-87000 LimogesFrance Umversité de Limoges UMR 1061 F-87000 Limoges France Division of Farm Animal Science University of Bristol Bristol BS40 5DU UK Departimento de Producción Animal y Ciencia de los Alimentos Universidad de Zaragoza 50013 Zaragoza Spain Dipartimento di Produzioni Animali Universitá della Tuscia via De Lellis 01100 Viterbo italy Parco Tecnologico Padano Via Einstein Polo Universitario 26900 Lodi Italy

Background： Consuming moderate amounts of lean red meat as part of a balanced diet valuably contributes to intakes of essential nutrients, in this study, we merged phenotypic and genotypic information to characterize the variation in lipid profile and sensory parameters and to represent the diversity among 15 cattle populations. Correlations between fat content, organoleptic characteristics and lipid profiles were also investigated. Methods： A sample of 436 largely unrelated purebred bulls belonging to 15 breeds and reared under comparable management conditions was analyzed. Phenotypic data -including fatness score, fat percentage, individual fatty acids （FA） profiles and sensory panel tests- and genotypic information from 11 polymorphisms was used. Results： The correlation coefficients between muscle total lipid measurements and absolute vs. relative amounts of polyunsaturated FA （PUFA） were in opposite directions. Increasing carcass fat leads to an increasing amount of FAs in triglycerides, but at the same time the relative amount of PUFAs is decreasing, which is in concordance with the negative correlation obtained here between the percentage of PUFA and fat measurements, as well as the weaker correlation between total phospholipids and total lipid muscle content compared with neutral lipids. Concerning organoleptic characteristics, a negative correlation between fiavour scores and the percentage of total PUFA, particularly to n-6 fraction, was found. The correlation between juiciness and texture is higher than with flavour scores. The distribution of SNPs plotted by principal components analysis （PCA） mainly reflects their known trait associations, although influenced by their specific breed allele frequencies. Conclusions： The results presented here help to understand the phenotypic and genotypic background underlying variations in FA composition and sensory parameters between breeds. The wide range of traits and breeds studied, along with the genotypic informa

关键词： Bos taurus Beef Fatty acids Omega-3 Genotype assisted selection