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Genomic consequences of population decline in critically endangered pangolins and their demographic histories

National Science Review 2020年第4期7卷 798-814页

作者： Jing-Yang Hu Zi-Qian Hao Laurent Frantz Shi-Fang Wu Wu Chen Yun-Fang Jiang Hong Wu Wei-Min Kuang Haipeng Li Ya-Ping Zhang Li Yu State Key laboratory for Conservation and Utilization of Bio-Resource in Yunnan School of Life Sciences Yunnan University State Key laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming College of Life Science University of Chinese Academy of Sciences CAS Key laboratory of Computational Biology CAS-MPG Partner Institute for Computational Biology Shanghai Institute of Nutrition and Health Chinese Academy of Sciences University of Chinese Academy of Sciences School of Biological and Chemical Sciences Queen Mary University of London The Palaeogenomics and Bio-Archaeology Research Network Department of Archaeology University of Oxford Guangzhou Zoo Lushui Management and Conservation Branch of Gaoligong Mountain National Nature Reserve Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences

Pangolins are among the most critically endangered animals due to heavy poaching and worldwide trafficking. However, their demographic histories and the genomic consequences of their recent population declines remain unknown. We generated high-quality de novo reference genomes for critically endangered Malayan(Manis javanica, MJ) and Chinese(M. pentadactyla, MP) pangolins and re-sequencing population genomic data from 74 MJs and 23 MPs. We recovered the population identities of illegally traded pangolins and previously unrecognized genetic populations that should be protected as evolutionarily distinct conservation units. Demographic reconstruction suggested environmental changes have resulted in a population size fluctuation of pangolins. Additionally, recent population size declines due to human activities have resulted in an increase in inbreeding and genetic load. Deleterious mutations were enriched in genes related to cancer/diseases and cholesterol homeostasis, which may have increased their susceptibility to diseases and decreased their survival potential to adapt to environmental changes and high-cholesterol diets. This comprehensive study provides not only high-quality pangolin reference genomes, but also valuable information concerning the driving factors of long-term population size fluctuations and the genomic impact of recent population size declines due to human activities, which is essential for pangolin conservation management and global action planning.

关键词： pangolins population genomics population declines genetic diversity inbreeding genetic load demographic history

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Decoding altitude-activated regulatory mechanisms occurring during apple peel ripening

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Horticulture Research 2020年第1期7卷 1149-1160页

作者： Evangelos Karagiannis Michail Michailidis Georgia Tanou Federico Scossa Eirini Sarrou George Stamatakis Martina Samiotaki Stefan Martens Alisdair R.Fernie Athanassios Molassiotis laboratory of Pomology Department of AgricultureAristotle University of Thessaloniki54124 ThessalonikiGreece Institute of Soil and Water Resources ELGO-DEMETERThermiThessaloniki 57001Greece Max-Planck-Institute of Molecular Plant Physiology Am Müehlenberg 1.Potsdam-Golm 14476Germany Council for Agricultural Research and Economics Research Center for Genomics and BioinformaticsVia Ardeatina 54600178 RomeItaly Institute of Plant Breeding and Genetic Resources ELGO-DEMETERThermiThessaloniki 57001Greece Biomedical Sciences Research Center“Alexander Fleming” Vari 16672Greece Fondazione Edmund Mach Centro Ricerca e InnovazioneDepartment of Food Quality and NutritionVia E.Mach138010 San Michele all’AdigeTNItaly

Apple(Malus domestica Borkh)is an important fruit crop cultivated in a broad range of environmental *** fruit ripening is a physiological process,whose molecular regulatory network response to different environments is still not sufficiently investigated and this is particularly true of the peel *** this study,the influence of environmental conditions associated with low(20 m)and high(750 m)altitude on peel tissue ripening was assessed by physiological measurements combined with metabolomic and proteomic analyses during apple fruit development and *** apple fruit ripening was itself not affected by the different environmental conditions,several key color parameters,such as redness and color index,were notably induced by high *** with this observation,increased levels of anthocyanin and other phenolic compounds,including cyanidin-3-O-galactoside,quercetin-3-O-rhamnoside,quercetin-3-O-rutinoside,and chlorogenic acid were identified in the peel of apple grown at high ***,the high-altitude environment was characterized by elevated abundance of various carbohydrates(e.g.,arabinose,xylose,and sucrose)but decreased levels of glutamic acid and several related proteins,such as glycine hydroxymethyltransferase and glutamate–glyoxylate *** processes affected by high altitude were the TCA cycle,the synthesis of oxidative/defense enzymes,and the accumulation of photosynthetic *** the obtained data we were able to construct a metabolite-protein network depicting the impact of altitude on peel *** combined analyses presented here provide new insights into physiological processes linking apple peel ripening with the prevailing environmental conditions.

关键词： altitude network prevailing

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How to disentangle microbially functional complexity: an insight from the network analysis of C, N, P and S cycling genes

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Science Bulletin 2019年第16期64卷 1129-1131页

作者： Bang-Xiao Zheng Yi Zhao Qing-Fang Bi Guo-Wei Zhou Hong-Jie Wang Xiu-Li Hao Kai Ding Key laboratory of Urban Environment and Health Institute of Urban EnvironmentChinese Academy of SciencesXiamen 361021China Faculty of Biological and Environmental Sciences Ecosystems and Environment Research ProgrammeUniversity of HelsinkiNiemenkatu 73FI-15140 LahtiFinland Section for Microbial Ecology and Biotechnology Department of Plant and Environmental SciencesUniversity of CopenhagenThorvaldsenvej 40DK-1871 Frederiksberg CDenmark Key laboratory of Subtropical Soil Science and Plant nutrition of Zhejiang Province College of Environmental&Resource SciencesZhejiang UniversityHangzhou 310058China Department of Microbiology and Ecosystem Science Research Network'Chemistry Meets Microbiology’University of ViennaVienna A-1090Austria State Key Lab of Urban and Regional Ecology Research Center for Eco-Environmental SciencesChinese Academy of SciencesBeijing 100085China Microbial Ecophysiology Group Faculty of Biology/ChemistryUniversity of BremenD-28359 BremenGermany Institute for Environmental genomics University of OklahomaNormanOK 73019USA State Key laboratory of Agricultural Microbiology Huazhong Agricultural UniversityWuhan 430070China Key laboratory of Arable Land Conservation(Middle and Lower Reaches of Yangtze River) Ministry of AgricultureCollege of Resources and EnvironmentHuazhong Agricultural UniversityWuhan 430070China

A complete ecosystem is also a complex network in which multifarious species interact with each other to achieve system-level functions, such as nutrient biogeochemistry (1)Microbial community is commonly considered as the primary driving force of ecosystem nutrient mobilization and metabolism, especially carbon (C), nitrogen (N), phosphorus (P), sulfur (S) and methane coupling process (2)The rise of metagenomics and high-throughput array (e.g. PhyloChip, GeoChip, etc.

关键词： net P and S cycling genes an insight from the network analysis of C How to disentangle microbially functional complexity

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Hemoglobin A1c Levels and Aortic Arterial Stiffness:The Cardiometabolic Risk in Chinese(CRC) Study

Hemoglobin A1c Levels and Aortic Arterial Stiffness:The Card...

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中华医学会第十二次全国内分泌学学术会议

作者： Jun Liang Na Zhou Fei Teng Caiyan Zou Manqing Yang YingXue Huaidong Song Lu Qi Department of Endocrinology the Central Hospital of Xuzhou Xuzhou Clinical School of Xuzhou Medical College Affiliated Hospital of Southeast University Department of nutrition Harvard School of Public HealthBostonMassachusettsUnited States of America Ruijin Hospital State Key Laboratory of Medical GenomicsMolecular Medical GenomicsMolecular Medical CenterShanghai Institute of EndocrinologyShanghai Jiao Tong University School of Medicine Channing laboratory Department of MedicineBrigham and Women's Hospital and Harvard Medical SchoolBostonMassachusettsUnited States of America

Objective The American Diabetes Association(ADA) recently published new clinical guidelines in which hemoglobin A1c(HbA1c) was recommended as a diagnostic test for *** recent studies associated HbAlc with arterial stiffness measured by cf-fasting glucose and 2-hour oral glucose tolerance test(2 h OGTT).We also assessed the modification effects of age,sex,obesity and blood pressure on the based health examination survey for 6,431 individuals(18-93 y) who were randomly selected from residents living in the urban area

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Cloning and Characterization of Eukaryotic Translation Initiation Factor 4E (eIF4E) Gene Family in Ipomoea batatas L. (Lam) for Understanding Hexaploid Sweetpotato-Virus Interactions

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American Journal of Molecular Biology 2022年第4期12卷 203-244页

作者： Adrianne P. A. Brown Marceline Egnin Foaziatu Bukari Osagie Idehen Inocent Ritte Desmond Mortley Gregory Bernard Deloris Alexander Conrad Bonsi Plant Biotech and genomics Research Lab Department of Agriculture and Environmental Sciences College of Agriculture Environment and Nutrition Sciences (CAES) Tuskegee University Tuskegee USA Integrative Biosciences PhD Program Tuskegee University Tuskegee USA Heliae Development LLC Gilbert USA

Characterization of genes related to sweetpotato viral disease resistance is critical for understanding plant-pathogen interactions, especially with feathery mottle virus infection. For example, genes encoding eukaryotic translation initiation factor (eIF)4E, its isoforms, eIF(iso)4E, and the cap-binding protein (CBP) in plants, have been implicated in viral infections aside from their importance in protein synthesis. Full-length cDNA encoding these putative eIF targets from susceptible/resistant and unknown hexaploid sweetpotato (Ipomoea batatas L. Lam) were amplified based on primers designed from the diploid wild-type relative Ipomoea trifida consensus sequences, and designated IbeIF4E, IbeIF(iso)4E and IbCBP. Comparative analyses following direct-sequencing of PCR-amplified cDNAs versus the cloned cDNA sequences identified multiple homeoalleles: one to four IbeIF4E, two to three IbeIF(iso)4E, and two IbCBP within all cultivars tested. Open reading frames were in the length of 696 bp IbeIF4E, 606 bp IbeIF(iso)4E, and 675 bp IbCBP. The encoded single polypeptide lengths were 232, 202, and 225 amino acids for IbeIF4E, IbeIF(iso)4E, and IbCBP, with a calculated protein molecular mass of 26 kDa, 22.8 kDa, and 25.8 kDa, while their theoretical isoelectric points were 5.1, 5.57, and 6.6, respectively. Although the homeoalleles had similar sequence lengths, single nucleotide polymorphisms and multi-allelic variations were detected within the coding sequences. The multi-sequence alignment performed revealed a 66.9% - 96.7% sequence similarity between the predicted amino acid sequences obtained from the homeoalleles and closely related species. Furthermore, phylogenetic analysis revealed ancestral relationships between the eIF4E homeoalleles and other species. The outcome herein on the eIF4E superfamily and its correlation in sequence variations suggest opportunities to decipher the role of eIF4E in hexaploid sweetpotato feathery mottle virus infection.

关键词： Ipomoea batatas Eukaryotic Translation Initiation Factors eIF4E CBP eIF(iso)4E Sweetpotato Viral Diseases

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Back to Science in Searching for SARS-CoV-2 Origins

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China CDC weekly 2023年第14期5卷 315-317页

作者： William J Liu Wenwen Lei Xiaozhou He Peipei Liu Qihui Wang Zhiqiang Wu Yun Tan Shuhui Song Gary Wong Jian Lu Jingkun Jiang Qiang Wei Mingkun Li Juncai Ma Xiaozhong Peng Yixue Li Baoxu Huang Yigang Tong Jun Han Guizhen Wu NHC Key laboratory of Biosafety National Institute for Viral Disease Control and PreventionChinese Center for Disease Control and PreventionBeijingChina CAS Key laboratory of Pathogen Microbiology and Immunology Institute of MicrobiologyChinese Academy of SciencesBeijingChina NHC Key laboratory of Systems Biology of Pathogens Institute of Pathogen BiologyChinese Academy of Medical Sciences&Peking Union Medical CollegeBeijingChina Shanghai Institute of Hematology State Key Laboratory of Medical GenomicsNational Research Center for Translational MedicineRuijin Hospital Affiliated to Shanghai Jiao Tong University School of MedicineShanghaiChina Beijing Institute of genomics Chinese Academy of Sciencesand China National Center for BioinformationBeijingChina laboratory of Molecular Virology and Immunology Institut Pasteur of ShanghaiChinese Academy of SciencesShanghaiChina State Key laboratory of Protein and Plant Gene Research Center for BioinformaticsSchool of Life SciencesPeking UniversityBeijingChina School of Environment Tsinghua UniversityBeijingChina National Pathogen Resource Center Chinese Center for Disease Control and Prevention(China CDC)BeijingChina Microbial Resource and Big Data Center Chinese National Microbiology Data Center(NMDC)Institute of MicrobiologyChinese Academy of SciencesBeijingChina State Key laboratory of Medical Molecular Biology Department of Molecular Biology and BiochemistryInstitute of Basic Medical SciencesMedical Primate Research CenterNeuroscience CenterChinese Academy of Medical SciencesSchool of Basic MedicinePeking Union Medical CollegeBeijingChina School of Life Science and Technology ShanghaiTech UniversityShanghaiChina Bio-Med Big Data Center Key Laboratory of Computational BiologyCAS-MPG Partner Institute for Computational BiologyShanghai Institute of Nutrition and HealthUniversity of Chinese Academy of SciencesChinese Academy of SciencesShanghaiChina China Animal Health and Epidemiology Center Qingdao CityShandong ProvinceChi

In recent decades,emerging and re-emerging human-infecting pathogens have been represented as huge threats to public health and have become a global concern(1).After outbreaks of two coronaviruses(CoVs),severe acute respiratory syndrome coronavirus(SARS-CoV)and Middle East respiratory syndrome coronavirus(MERS-CoV),severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)became the first-known pandemic hastening CoV with tremendous wrecking to the world(2).The origin tracing of these emerging pathogens is of great significance in infectious disease prevention and control(3–4).The origin of SARS-CoV-2 remains elusive after the more than 3-year pandemic,though scientists around the world are making great *** the experience of studying many other infectious pathogens,origin tracing is systematic and time-consuming *** supposed origins of many infectious pathogens are still in debate,including SARS-CoV and human immunodeficiency virus,etc(5).

关键词： prevention respiratory acute

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Early osmotic adjustment responses in drought-resistant and drought-sensitive oilseed rape

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Journal of Integrative Plant Biology 2014年第8期56卷 797-809页

作者： Sarah Hatzig L.Irina Zaharia Suzanne Abrams Marie Hohmann Laurie Legoahec Alain Bouchereau Nathalie Nesi Rod J.Snowdon Department of Plant Breeding IFZ Research Centre for Biosystems Land Use and Nutrition Justus Liebig University National Research Council of Canada Aquatic and Crop Resource Development Department of Chemistry University of Saskatchewan UMR 1349 INRA-AgroCampus Ouest-Université de Rennes 1 Joint Laboratory for Genetics Environment and Plant Protection (IGEPP) Bat.301 BP 35327 35653 Le Rheu Cedex France

The impact of osmotic stress on growth, physiolo- gy, and metabolism of winter oilseed rape （Brassica napus L.） was investigated by detailed analysis of biomass traits, hormone metabolites and osmolytes in two genetically unrelated drought-tolerant genotypes and two unrelated drought-sensitive genotypes. Seedlings were grown in vitro under controlled conditions and osmotic stress was simulated by applying a gradual treatment with polyethylene glycol （PEG 6ooo）, followed by hypo-osmotic treatment of variants used for metabolite determination. The results provide a basis for the identification of reliable selection criteria for drought resistance in oilseed rape. The in vitro cultivation system established during this study enabled effective discrimination of early osmotic stress responses between drought-resistant and -susceptible oilseed rape genotypes that also show large differences in relative seed yield under drought conditions in the field. Clear physiological and metabolic differences wereobserved between the drought-resistant and drought-sensitive genotypes, suggesting that osmotic adjustment is a key component of drought response in oilseed rape. Unexpected- ly, however, the drought-resistant genotypes did not show typical hormonal adjustment and osmolyte accumulation, suggesting that they possess alternative physiological mech- anisms enabling avoidance of stress symptoms.

关键词： Abscisic acid Brassica napus drought hormones metabolites

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Effects of starvation and hormones on DNA synthesis in silk gland cells of the silkworm, Bombyx mori

Effects of starvation and hormones on DNA synthesis in silk ...

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第十二届家（柞）蚕遗传育种暨良种繁育学术研讨会

作者： Yao-Feng Li Xiang-Yun Chen Chun-Dong Zhang Xiao-Fang Tang La Wang Tai-Hang Liu Min-Hui Pan Cheng Lu State Key laboratory of Silkworm Genome Biology Southwest University Department of Biochemistry and Molecular Biology Chongqing Medical University Key laboratory for Sericulture Functional genomics and Biotechnology of Agricultural Ministry Southwest University

Silk gland cells of silkworm larvae undergo multiple cycles of endomitosis for the synthesis of silk proteins during the spinning phase. In this paper, we analyzed the endomitotic DNA synthesis of silk gland cells during larval development, and found that it was a periodic fluctuation, increasing during the vigorous feeding phase and being gradually inhibited in the next molting phase. That means it might be activated by a self-regulating process after molting. The expression levels of cyclin E, cdt1 and pcna were consistent with these developmental changes. Moreover, we further examined whether these changes in endomitotic DNA synthesis resulted from feeding or hormonal stimulation. The results showed that DNA synthesis could be inhibited by starvation and re-activated by re-feeding, and therefore appears to be dependent on nutrition. DNA synthesis was suppressed by in vivo treatment with 20-hydroxyecdysone（20E）. However, there was no effect on DNA synthesis by in vitro 20E treatment or by either in vivo or in vitro juvenile hormone treatment. The levels of Akt and 4E-BP phosphorylation in the silk glands were also reduced by starvation and in vivo treatment with 20E. These results indicate that the activation of endomitotic DNA synthesis during the inter molt stages is related to feeding and DNA synthesis is inhibited indirectly by 20E.

关键词： Bombyx mori DNA synthesis endomitosis silk gland star va tion 20-hydrox yecdysone

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A genome-wide association study of facial morphology identifies novel genetic loci in Han Chinese

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Journal of Genetics and genomics 2021年第3期48卷 198-207页

作者： Yin Huang Dan Li Lu Qiao Yu Liu Qianqian Peng Sijie Wu Manfei Zhang Yajun Yang Jingze Tan Shuhua Xu Li Jin Sijia Wang Kun Tang Stefan Grunewald Chinese Academy of Sciences Key laboratory of Computational Biology CAS-MPG Partner Institute for Computational BiologyShanghai Institute of Nutrition and HealthShanghai Institutes for Biological SciencesUniversity of Chinese Academy of SciencesCASShanghai 200031China DeepBlue Technology(Shanghai)Co. LtdShanghai 200336China State Key laboratory of Genetic Engineering and Ministry of Education Key laboratory of Contemporary Anthropology School of Life SciencesFudan UniversityShanghai 200433China Fudan-Taizhou Institute of Health Sciences Taizhou 225300China Collaborative Innovation Center of Genetics and Development Shanghai 200438China f Center for Excellence in Animal Evolution and Genetics Chinese Academy of SciencesKunmingYunnan 650223China School of Life Science and Technology ShanghaiTech UniversityShanghai 201210China

The human face is a heritable surface with many complex sensory *** recent years,many genetic loci associated with facial features have been reported in different populations,yet there is a lack of studies on the Han Chinese ***,we report a genome-wide association study of 3D normal human faces of 2,659 Han Chinese with autosegment phenotypes of facial *** identify singlenucleotide polymorphisms(SNPs)encompassing four genomic regions showing significant associations with different facial regions,including SNPs in DENND1 B associated with the chin,SNPs among PISRT1 associated with eyes,SNPs between DCHS2 and SFRP2 associated with the nose,and SNPs in VPS13 B associated with the *** replicate 24 SNPs from previously reported genetic loci in different populations,whose candidate genes are DCHS2,SUPT3 H,HOXD1,SOX9,PAX3,and *** results provide a more comprehensive understanding of the genetic basis of variation in human facial morphology.

关键词： Genome-wide association study Facial morphology Automatic phenotyping Visualization

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Aminoflavone upregulates putative tumor suppressor miR-125b-2-3p to inhibit luminal A breast cancer stem cell-like properties

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Precision Clinical Medicine 2022年第2期5卷 72-86页

作者： Nicole Mavingire Petreena Campbell Tiantian Liu Jonathan Wooten Salma Khan Xin Chen Jason Matthews Charles Wang Eileen Brantley Department of Basic Sciences Loma Linda University School of MedicineLoma LindaCA 92350USA Center for genomics Loma Linda University School of MedicineLoma LindaCA 92350USA Center for Health Disparities and Molecular Medicine Loma Linda University School of MedicineLoma LindaCA 92350USA Department of nutrition University of OsloOslo 0372Norway Department of Pharmacology and Toxicology University of TorontoTorontoOntario M5S 1A8Canada Frederick National laboratory for Cancer Research PO Box BBldg.432Room 232 FrederickMD 21702-1201USA

Metastatic breast cancer is incurable and often due to breast cancer stem cell(CSC)-mediated *** previously determined that the aryl hydrocarbon receptor(AhR)agonist aminoflavone(AF)inhibits the expression of the CSC biomarkerα6-integrin(ITGA6)to disrupt the formation of luminal(hormone receptor-positive)mammospheres(3D breast cancer spheroids).In this study,we performed miRNA-sequencing analysis of luminal A MCF-7 mammospheres treated with AF to gain further insight into the mechanism of AF-mediated anti-cancer and anti-breast CSC *** significantly induced the expression of>70 microRNAs(miRNAs)including miR125b-2–3p,a predicted stemness gene ***-mediated miR125b-2–3p induction was validated in MCF-7 mammospheres and ***125b-2–3p levels were low in breast cancer tissues irrespective of subtype compared to normal breast *** miR125b-2–3p levels were low in MCF-7 cells,they were much lower in AHR100 cells(MCF-7 cells made unresponsive to AhR agonists).The miR125b-2–3p mimic decreased,while the antagomiR125b-2–3p increased the expression of stemness genes ITGA6 and SOX2 in MCF-7 *** MCF-7 mammospheres,the miR125b-2–3p mimic decreased only ITGA6 expression although the antagomiR125b-2–3p increased ITGA6,SOX2 and MYC ***125b-2–3p reversed AF-mediated suppression of *** miR125b-2–3p mimic decreased proliferation,migration,and mammosphere formation while the antagomiR125b-2–3p increased proliferation and mammosphere formation in MCF-7 *** miR125b-2–3p mimic also inhibited proliferation,mammosphere formation,and migration in AHR100 *** induced AhR-and miR125b2-3p-dependent anti-proliferation,anti-migration,and mammosphere disruption in MCF-7 *** findings suggest that miR125b-2–3p is a tumor suppressor and AF upregulates miR125b-2–3p to disrupt mammospheres via mechanisms that rely at least partially on AhR in luminal A breast cancer cells.

关键词： breast cancer cancer stem cells therapeutic targeting miR125b-2-3p aminoflavone aryl hydrocarbon receptor mammospheres

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