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Marine Life Science & Technology 2024年第1期6卷 1-14页

作者： Meiru Liu Yue Song Suyu Zhang Lili Yu Zengbao Yuan Hengjia Yang Mengqi Zhang Zhuocheng Zhou inge seim Shanshan Liu Guangyi Fan Huanming Yang College of Life Sciences University of Chinese Academy of SciencesBeijing 100049China BGI-Qingdao BGI-ShenzhenQingdao 266555China BGI-Shenzhen Shenzhen 518083China Professional Committee of Native Aquatic Organisms and Water Ecosystem of China Fisheries Association Beijing 100125China Integrative Biology Laboratory College of Life SciencesNanjing Normal UniversityNanjing 210023China State Key Laboratory of Agricultural Genomics BGI-ShenzhenShenzhen 518083China

The electric catfish(Malapterurus electricus),belonging to the family Malapteruridae,order Siluriformes(Actinopterygii:Ostariophysi),is one of the six branches that has independently evolved electrical organs.We assembled a 796.75 Mb M.electricus genome and anchored 88.72%sequences into 28 chromosomes.Gene family analysis revealed 295 expanded gene families that were enriched on functions related to glutamate receptors.Convergent evolutionary analyses of electric organs among different lineage of electric fishes further revealed that the coding gene of rho guanine nucleotide exchange factor 4-like(arhgef4),which is associated with G-protein coupled receptor(GPCR)signaling pathway,underwent adaptive parallel evolution.Gene identification suggests visual degradation in catfishes,and an important role for taste in environmental adaptation.Our findings fill in the genomic data for a branch of electric fish and provide a relevant genetic basis for the adaptive evolution of Siluriformes.

关键词： Electric fish Karyotype analysis Convergent evolution Environmental adaptation Historical effective population size

Evolutionary impacts of purine metabolism genes on mammalian oxidative stress adaptation

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Zoological Research 2022年第2期43卷 241-254页

作者： Ran Tian Chen Yang Si-Min Chai Han Guo inge seim Guang Yang Jiangsu Key Laboratory for Biodiversity and Biotechnology College of Life SciencesNanjing Normal UniversityNanjingJiangsu 210023China Integrative Biology Laboratory College of Life SciencesNanjing Normal UniversityNanjingJiangsu 210023China School of Biology and Environmental Science Queensland University of TechnologyBrisbaneQueensland 4001Australia

Many mammals risk damage from oxidative stress stemming from frequent dives(i.e., cycles of ischemia/reperfusion and hypoxia/reoxygenation),high altitude and subterranean environments, or powered flight. Purine metabolism is an essential response to oxidative stress, and an imbalance between purine salvage and de novo biosynthesis pathways can generate damaging reactive oxygen species(ROS). Here, we examined the evolution of 117 purine metabolism-related genes to explore the accompanying molecular mechanisms of enhanced purine metabolism in mammals under high oxidative stress. We found that positively selected genes,convergent changes, and nonparallel amino acid substitutions are possibly associated with adaptation to oxidative stress in mammals. In particular, the evolution of convergent genes with c AMP and c GMP regulation roles may protect mammals from oxidative damage. Additionally, 32 genes were identified as under positive selection in cetaceans, including key purine salvage enzymes(i.e., HPRT1), suggesting improved re-utilization of non-recyclable purines avoid hypoxanthine accumulation and reduce oxidative stress. Most intriguingly, we found that six unique substitutions in cetacean xanthine dehydrogenase(XDH), an enzyme that regulates the generation of the ROS precursor xanthine oxidase(XO) during ischemic/hypoxic conditions, show enhanced enzyme activity and thermal stability and diminished XO conversion activity. These functional adaptations are likely beneficial for cetaceans by reducing radical oxygen species production during diving. In summary, our findings offer insights into the molecular and functional evolution of purine metabolism genes in mammalian oxidative stress adaptations.

关键词： Evolution Mammals Cetaceans Purine metabolism Oxidative stress

High-quality chromosome-level genome assembly of the melon-headed whale(Peponocephala electra)

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Zoological Research 2022年第6期43卷 931-934页

作者： Zhen-Peng Yu Xing Liu Biao Zhang Lei Shan inge seim Guang Yang Shi-Xia Xu Jiangsu Key Laboratory for Biodiversity and Biotechnology College of Life SciencesNanjing Normal UniversityNanjingJiangsu 210023China

DEAR EDITOR,The melon-headed whale(Peponocephala electra),a small toothed whale in the Delphinidae family,inhabits tropical and subtropical oceans.It is an attractive model species for studying secondary aquatic adaptation and evolution.Here,we successfully assembled a high-quality chromosome-level genome of P.electra using Pac Bio and Hi-C sequencing technologies.

关键词： evolution subtropical tropical

Oxidative stress drives divergent evolution of the glutathione peroxidase(GPX)gene family in mammals

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Integrative Zoology 2021年第5期16卷 696-711页

作者： Ran TIAN Yuepan GENG Ying YANG inge seim Guang YANG Jiangsu Key Laboratory for Biodiversity and Biotechnology College of Life SciencesNanjing Normal UniversityNanjingJiangsuChina Integrative Biology Laboratory College of Life SciencesNanjing Normal UniversityNanjingJiangsuChina School of Biology and Environmental Science Queensland University of TechnologyBrisbaneQueenslandAustralia

The molecular basis for adaptations to extreme environments can now be understood by interrogating the everincreasing number of sequenced genomes.Mammals such as cetaceans,bats,and highland species can protect themselves from oxidative stress,a disruption in the balance of reactive oxygen species,which results in oxidative injury and cell damage.Here,we consider the evolution of the glutathione peroxidase(GPX)family of antioxidant enzymes by interrogating publicly available genome data from 70 mammalian species from all major clades.We identified 8 GPX subclasses ubiquitous to all mammalian groups.Mammalian GPX gene families resolved into the GPX4/7/8 and GPX1/2/3/5/6 groups and are characterized by several instances of gene duplication and loss,indicating a dynamic process of gene birth and death in mammals.Seven of the eight GPX subfamilies(all but GPX7)were under positive selection,with the residues under selection located at or close to active sites or at the dimer interface.We also reveal evidence of a correlation between ecological niches(e.***.high oxidative stress)and the divergent selection and gene copy number of GPX subclasses.Notably,a convergent expansion of GPX1 was observed in several independent lineages of mammals under oxidative stress and may be important for avoiding oxidative damage.Collectively,this study suggests that the GPX gene family has shaped the adaption of mammals to stressful environments.

关键词： adaptive evolution gene family glutathione peroxidase mammals oxidative stress

Comparative analyses of aging-related genes in long-lived mammals provide insights into natural longevity

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The Innovation 2021年第2期2卷 31-39页

作者： Zhenpeng Yu inge seim Mengxin Yin Ran Tian Di Sun Wenhua Ren Guang Yang Shixia Xu Jiangsu Key Laboratory for Biodiversity and Biotechnology College of Life SciencesNanjing Normal UniversityNanjing 210023China Integrative Biology Laboratory College of Life SciencesNanjing Normal UniversityNanjing 210023China School of Biology and Environmental Science Faculty of Science and EngineeringQueensland University of TechnologyBrisbaneQLDAustralia

Extreme longevity has evolved multiple times during the evolution of mammals,yet its underlying molecular mechanisms remain largely underexplored.Here,we compared the evolution of 115 aging-related genes in 11 long-lived species and 25 mammals with non-increased lifespan(control group)in the hopes of better understanding the common molecular mechanisms behind longevity.We identified 16 unique positively selected genes and 23 rapidly evolving genes in long-lived species,which included nine genes involved in regulating lifespan through the insulin/IGF-1 signaling(IIS)pathway and 11 genes highly enriched in immune-response-related pathways,suggesting that the IIS pathway and immune response play a particularly important role in exceptional mammalian longevity.Interestingly,11 genes related to cancer progression,including four positively selected genes and seven genes with convergent amino acid changes,were shared by two or more long-lived lineages,indicating that long-lived mammals might have evolved convergent or similar mechanisms of cancer resistance that extended their lifespan.This suggestion was further corroborated by our identifi-cation of 12 robust candidates for longevity-related genes closely related to cancer.

关键词： mammals longevity positive selection IIS pathway immune response cancer resistance

Circulating microRNA expression and nonalcoholic fatty liver disease in adolescents with severe obesity

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World Journal of Gastroenterology 2024年第4期30卷 332-345页

作者： Yi-Jie Li Brittney O Baumert Nikos Stratakis Jesse A Goodrich Hao-Tian Wu Jing-Xuan He Yin-Qi Zhao Max T Aung Hong-Xu Wang Sandrah P Eckel Douglas I Walker Damaskini Valvi Michele A La Merrill Justin R Ryder Thomas H inge Todd Jenkins Stephanie Sisley Rohit Kohli Stavra A Xanthakos Andrea A Baccarelli Rob McConnell David V Conti Lida Chatzi Department of Population and Public Health Sciences Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCA 90032United States Barcelona Institute of Global Health Barcelona Institute of Global HealthBarcelona 08036Spain Department of Environmental Health Sciences Mailman School of Public HealthColumbia UniversityNew YorkNY 10032United States Gangarosa Department of Environmental Health Rollins School of Public HealthEmory UniversityAtlantaGA 30329United States Department of Environmental Medicine and Public Health Icahn School of Medicine at Mount SinaiNew YorkNY 10029United States Department of Environmental Toxicology University of CaliforniaDavisCA 95616United States Department of Surgery Lurie Children’s Hospital of ChicagoChicagoIL 60611United States Northwestern University Feinberg School of Medicine Northwestern UniversityChicagoIL 60611United States Division of Biostatistics and Epidemiology Cincinnati Children's Hospital Medical CenterCincinnatiOH 45229United States Department of Pediatrics University of Cincinnati College of MedicineCincinnatiOH 45229United States Department of Pediatrics Children’s Nutrition Research Center USDA/ARSBaylor College of MedicineHoustonTX 77030United States Department of Gastroenterology Children’s Hospital Los AngelesLos AngelesCA 90027United States Division of Gastroenterology Hepatology and NutritionCincinnati Children's Hospital Medical CenterCincinnatiOH 45229United States

BACKGROUND Nonalcoholic fatty liver disease(NAFLD)is one of the most common chronic liver diseases in children and adolescents.NAFLD ranges in severity from isolated hepatic steatosis to nonalcoholic steatohepatitis(NASH),wherein hepatocellular inflammation and/or fibrosis coexist with steatosis.Circulating microRNA(miRNA)levels have been suggested to be altered in NAFLD,but the extent to which miRNA are related to NAFLD features remains unknown.This analysis tested the hypothesis that plasma miRNAs are significantly associated with histological features of NAFLD in adolescents.AIM To investigate the relationship between plasma miRNA expression and NAFLD features among adolescents with NAFLD.METHODS This study included 81 adolescents diagnosed with NAFLD and 54 adolescents without NAFLD from the Teen-Longitudinal Assessment of Bariatric Surgery study.Intra-operative core liver biopsies were collected from participants and used to characterize histological features of NAFLD.Plasma samples were collected during surgery for miRNA profiling.A total of 843 plasma miRNAs were profiled using the HTG EdgeSeq platform.We examined associations of plasma miRNAs and NAFLD features using logistic regression after adjusting for age,sex,race,and other key covariates.ingenuity Pathways Analysis was used to identify biological functions of miRNAs that were associated with multiple histological features of NAFLD.RESULTS We identified 16 upregulated plasma miRNAs,including miR-193a-5p and miR-193b-5p,and 22 downregulated plasma miRNAs,including miR-1282 and miR-6734-5p,in adolescents with NAFLD.Moreover,52,16,15,and 9 plasma miRNAs were associated with NASH,fibrosis,ballooning degeneration,and lobular inflammation,respectively.Collectively,16 miRNAs were associated with two or more histological features of NAFLD.Among those miRNAs,miR-411-5p was downregulated in NASH,ballooning,and fibrosis,while miR-122-5p,miR-1343-5p,miR-193a-5p,miR-193b-5p,and miR-7845-5p were consistently and positively associated with all histological features

关键词： MicroRNA Nonalcoholic fatty liver disease Non-alcoholic steatohepatitis Liver fibrosis Lobular inflammation Ballooning degeneration

大尺度转录组分析揭示哺乳动物寿命演化的遗传和选择压力特征

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大尺度转录组分析揭示哺乳动物寿命演化的遗传和选择压力特征

Self-Reported Social Status among Rural Residents:A Case in the Outskirts of the Beijing-Tianjin-Hebei Metropolitan Region

第十六届全国野生动物生态与资源保护学术研讨会

作者：刘伟强朱平芬李萌李子豪俞阳刘高鸣杜娟王潇杨婧田然 inge seim Alaattin Kaya 李明洲李明 Vadim N Gladyshev 周旭明中国科学院动物研究所动物生态与保护生物学重点实验室中国科学院大学中国科学技术大学生命科学与医学部南京师范大学生命科学学院 School of Biology and Environmental Science Queensland University of Technology Department of Biology Virginia Commonwealth University 四川农业大学动物科技学院动物遗传育种研究中心 Division of Genetics Department of MedicineBrigham and Women's HospitalHarvard Medical School

哺乳动物的寿命差异很大,最短和最长的物种之间的差异超过100倍。这种自然差异可能会揭示决定长寿的进化力量和分子特征。为了探究基因表达的变化与寿命的关系,本研究对103种哺乳动物的肝、肾和脑组织进行了比较转录组学分析。结果发现... 详细信息

哺乳动物的寿命差异很大,最短和最长的物种之间的差异超过100倍。这种自然差异可能会揭示决定长寿的进化力量和分子特征。为了探究基因表达的变化与寿命的关系,本研究对103种哺乳动物的肝、肾和脑组织进行了比较转录组学分析。结果发现,仅有很少的基因在所分析的三个器官中表现出共同的长寿表达模式。然而,与转录和翻译保真度相关的途径与哺乳动物的寿命相关,例如无义介导的衰变和真核细胞的翻译延伸等。另外,本研究对不同基因分类的比较分析发现,与寿命相关的基因富集在必需基因和在哺乳动物分化之前的‘Old’基因中。这表明细胞中具有必需功能的基因的表达变化对物种的寿命控制和演化比较重要。对选择压力的分析发现,与长寿相关基因随寿命变化的方向关联的选择强度在不同器官之间是不一致的。此外,蛋氨酸限制相关基因的表达与寿命相关,并且在长寿哺乳动物中处于强化选择之下,这表明自然选择和人工干预使用了一种共同的策略来控制寿命。我们的结果表明,通过基因表达来调节寿命是通过多基因微效性和间接的自然选择来驱动的。

关键词：哺乳动物比较转录组寿命自然选择

来源： cnki会议评论

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Social Sciences in China 2023年第3期44卷 181-202页

作者： Geir inge Orderud Gu Jintu Luo Jing Norwegian Institute of Urban and Regional Research Oslo Metropolitan University Department of Sociology Hohai University Institute of Chinese Borderland Research Chinese Academy of Social Sciences

China has in recent decades undergone profound changes and continues to do so—changes that are transforming the social fabric,motivating studies on how self-reported social status is changing in different parts of China.Applying a realist approach,the study emanates from theories on self-reported social status underlining the role of reference-groups,adding insights from the work of Pierre Bourdieu by introducing the terminology of habitus and types of capital.Furthermore,the study adds a spatial scale,thereby contributing to theoretical development.Hence the empirical study asked villagers to provide self-reported social status at village,county and national levels.The statistical analyses include objective and subjective conditions,representing economic,cultural,social,and symbolic capital,as well as other factors.The results confirm the relevance of the reference-group theory,with self-reported social status decreasing from village to national level.Based on multivariate analyses,the study identifies two segments of habitus at the village level,one at the county level and one at the national level,facilitating high scores on self-reported social status.These habitus segments underline the importance of incorporating spatial scale as a theoretical dimension.In doing so,the study reveals that a habitus segment including cultural capital of farming competence is important at village and county levels but is replaced at the national level by a segment including the social capital of instruction sources related to farming and not wanting to move.Furthermore,a habitus segment revolving around the economic capital of jobs outside farming,younger generations,and wanting to move is active at the village level.In addition to revealing reference-group differences this habitus segment also indicates that large-scale,national transitional forces are at work,facilitating new drivers for self-reported social status locally.

关键词： self-reported social status reference-group theory peri-urban region rural communities farming

A physically active lifestyle is related to a lower level of skin autofluorescence in a large population with chronic-disease(LifeLines cohort)

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Journal of Sport and Health Science 2022年第2期11卷 260-265页

作者： Saskia Corine van de Zande Jeroen Klaas de Vries inge van den Akker-Scheek Johannes Zwerver Andries Jan Smit Department of Internal Medicine Division of Vascular MedicineUniversity of GroningenUniversity Medical Center GroningenGroningen9700 RBthe Netherlands Department of Internal Medicine Antonius Hospital SneekSneek8601 ZKthe Netherlands Department of Orthopaedics University of GroningenUniversity Medical Center GroningenGroningen9700 RBthe Netherlands Center for Human Movement Sciences University of GroningenUniversity Medical Center GroningenGroningen9700 RBthe Netherlands Sports Valley Gelderse Vallei HospitalEde6716 RPthe Netherlands

Background:Physical activity(PA)has substantial health benefits and is important in combatting chronic diseases,which have been associated with elevated levels of advanced glycation endproducts(AGEs).AGEs play a role in the aging process,and an association between PA and AGEs has been reported.We aimed to investigate the relationship between PA and AGE accumulation in a general population and in a population with chronic diseases.Methods:This large cross-sectional population study used data from adult participants in the LifeLines project,with participant information drawn from the LifeLines database as well data from patients with diabetes mellitus or renal and/or cardiovascular diseases.Tissue AGE accumulation was assessed non-invasively by skin-autofluorescence(SAF)using an AGE reader(DiagnOptics Technologies BV,Groningen,the Netherlands).PA was assessed using the short questionnaire to assess health-enhancing physical activity(SQUASH).Multivariate linear regression analyses were adjusted for age,body mass index,sex,and smoking status.Results:Data from 63,452 participants(general population n=59,177,chronic disease n=4275)were analyzed.The general population was significantly younger(43.58±11.77 years,mean±SD)and had significantly lower SAF(1.90±0.42 arbitrary units(AU))compared to the population with chronic disease(age:55.51±12.07 years;SAF:2.27±0.51 AU).In the group with chronic disease,more hours of moderate to vigorous physical activities per week were associated with lower SAF(β=-0.002,95%confidence interval(95%CI):-0.002 to-0.001).For the general population,there was no association between hours of moderate to vigorous activity and SAF(β=3.2×10^(-5),95%CI:0.000-0.001,p=0.742).However,there was an association in the general population between total hours of PA per week and SAF(β=4.2×10^(-4),95%CI:0.000-0.001,p<0.001),but this association was not found in the chronic disease population(β=-3.2×10^(-4),95%CI:-0.001 to 0.000,p=0.347).Conclusion:Our study demonstrates that an inverse relationship exists betwe

关键词： Advanced glycation endproducts Chronic disease population General population Physical activity Skin autofluorescence

Ghrelin's second life:From appetite stimulator to glucose regulator

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World Journal of Gastroenterology 2012年第25期18卷 3183-3195页

作者： Pieter-Jan Verhulst inge Depoortere Translational Research Center for Gastrointestinal Disorders Catholic University of Leuven3000 LeuvenBelgium

Ghrelin,a 28 amino acid peptide hormone produced by the stomach,was the first orexigenic hormone to be discovered from the periphery.The octanoyl modification at Ser3,mediated by ghrelin O-acyltransferase(GOAT),is essential for ghrelin's biological activity.Ghrelin stimulates food intake through binding to its receptor(GRLN-R) on neurons in the arcuate nucleus of the hypothalamus.Ghrelin is widely expressed throughout the body;accordingly,it is implicated in several other physiological functions,which include growth hormone release,gastric emptying,and body weight regulation.Ghrelin and GRLN-R expression are also found in the pancreas,suggesting a local physiological role.Accordingly,several recent studies now point towards an important role for ghrelin and its receptor in the regulation of blood glucose homeostasis,which is the main focus of this review.Several mechanisms of this regulation by ghrelin have been proposed,and one possibility is through the regulation of insulin secretion.Despite some controversy,most studies suggest that ghrelin exerts an inhibitory effect on insulin secretion,resulting in increased circulating glucose levels.Ghrelin may thus be a diabetogenic factor.Obesity-related type2 diabetes has become an increasingly important health problem,almost reaching epidemic proportions in the world;therefore,antagonists of the ghrelin-GOAT signaling pathway,which will tackle both energy-and glucose homeostasis,may be considered as promising new therapies for this disease.

关键词： Ghrelin 血糖食欲生长素释放肽 ghrelin 调节剂胰岛素分泌 2型糖尿病