201
|
Andrews C, Nettle D, Larriva M, Gillespie R, Reichert S, Brilot BO, Bedford T, Monaghan P, Spencer KA, Bateson M. A marker of biological age explains individual variation in the strength of the adult stress response. ROYAL SOCIETY OPEN SCIENCE 2017; 4:171208. [PMID: 28989794 PMCID: PMC5627134 DOI: 10.1098/rsos.171208] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 08/31/2017] [Indexed: 05/07/2023]
Abstract
The acute stress response functions to prioritize behavioural and physiological processes that maximize survival in the face of immediate threat. There is variation between individuals in the strength of the adult stress response that is of interest in both evolutionary biology and medicine. Age is an established source of this variation-stress responsiveness diminishes with increasing age in a range of species-but unexplained variation remains. Since individuals of the same chronological age may differ markedly in their pace of biological ageing, we asked whether biological age-measured here via erythrocyte telomere length-predicts variation in stress responsiveness in adult animals of the same chronological age. We studied two cohorts of European starlings in which we had previously manipulated the rate of biological ageing by experimentally altering the competition experienced by chicks in the fortnight following hatching. We predicted that individuals with greater developmental telomere attrition, and hence greater biological age, would show an attenuated corticosterone (CORT) response to an acute stressor when tested as adults. In both cohorts, we found that birds with greater developmental telomere attrition had lower peak CORT levels and a more negative change in CORT levels between 15 and 30 min following stress exposure. Our results, therefore, provide strong evidence that a measure of biological age explains individual variation in stress responsiveness: birds that were biologically older were less stress responsive. Our results provide a novel explanation for the phenomenon of developmental programming of the stress response: observed changes in stress physiology as a result of exposure to early-life adversity may reflect changes in ageing.
Collapse
Affiliation(s)
- Clare Andrews
- Centre for Behaviour and Evolution, Institute of Neuroscience and Newcastle University Institute of Ageing, Newcastle University, Newcastle upon Tyne, UK
| | - Daniel Nettle
- Centre for Behaviour and Evolution, Institute of Neuroscience and Newcastle University Institute of Ageing, Newcastle University, Newcastle upon Tyne, UK
| | - Maria Larriva
- School of Psychology and Neuroscience, University of St Andrews, St Andrews, UK
| | - Robert Gillespie
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Sophie Reichert
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, UK
| | - Ben O. Brilot
- Centre for Behaviour and Evolution, Institute of Neuroscience and Newcastle University Institute of Ageing, Newcastle University, Newcastle upon Tyne, UK
- School of Biological Sciences, Plymouth University, Plymouth, UK
| | - Thomas Bedford
- Centre for Behaviour and Evolution, Institute of Neuroscience and Newcastle University Institute of Ageing, Newcastle University, Newcastle upon Tyne, UK
| | - Pat Monaghan
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Karen A. Spencer
- School of Psychology and Neuroscience, University of St Andrews, St Andrews, UK
| | - Melissa Bateson
- Centre for Behaviour and Evolution, Institute of Neuroscience and Newcastle University Institute of Ageing, Newcastle University, Newcastle upon Tyne, UK
- Author for correspondence: Melissa Bateson e-mail:
| |
Collapse
|
202
|
Zsakai A, Sipos R, Takacs-Vellai K, Szabo A, Bodzsar EB. The relationship between reproductive and biochemical ageing at the time of the menopausal transition. Exp Gerontol 2017; 98:162-168. [PMID: 28843511 DOI: 10.1016/j.exger.2017.08.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 07/04/2017] [Accepted: 08/21/2017] [Indexed: 10/19/2022]
Abstract
The biochemical ageing status of women in the menopausal transition was studied using quantitative analysis of age- and autophagy-related gene activities (CDC42 and MAP1LC3 genes were selected as target genes). Free estradiol and progesterone levels in saliva were estimated. General linear models were used to determine the relationship between lifestyle, health status, socioeconomic factors and CDC42 and MAP1LC3 gene expression levels. Gene expression analysis revealed (1) an increasing expression of CDC42 gene after 45years in women, (2) expression level of CDC42 gene associated with menopausal status, (3) while endocrine status was found to associate with the expression of both of the studied age-related genes, (4) the "never used hormonal contraceptives" and "obese nutritional status" were the strongest factors for increased level of age-related gene expressions, and (5) changes in gene expression levels by ageing should be studied by considering not only chronological, but also biological ages. Gene expression profile of ageing has mostly been studied in model systems or human blood samples, but rarely in human saliva samples. The concordance of results between the present and former gene expression analyses, and the simplicity of saliva sample collection emphasizes the importance of saliva tissue samples in gene expression analyses especially in epidemiological surveys.
Collapse
Affiliation(s)
- Annamaria Zsakai
- Department of Biological Anthropology, Eotvos Lorand University, Pazmany P. 1/c, 1117 Budapest, Hungary.
| | - Rita Sipos
- Biomi Ltd, Szent-Gyorgyi Albert ut 4, 2100 Godollo, Hungary.
| | - Krisztina Takacs-Vellai
- Department of Biological Anthropology, Eotvos Lorand University, Pazmany P. 1/c, 1117 Budapest, Hungary
| | - Attila Szabo
- Department of Microbiology, Eotvos Lorand University, Pazmany P. 1/c, 1117 Budapest, Hungary
| | - Eva B Bodzsar
- Department of Biological Anthropology, Eotvos Lorand University, Pazmany P. 1/c, 1117 Budapest, Hungary.
| |
Collapse
|
203
|
Tang X, Shi L, Xie N, Liu Z, Qian M, Meng F, Xu Q, Zhou M, Cao X, Zhu WG, Liu B. SIRT7 antagonizes TGF-β signaling and inhibits breast cancer metastasis. Nat Commun 2017; 8:318. [PMID: 28827661 PMCID: PMC5566498 DOI: 10.1038/s41467-017-00396-9] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 06/27/2017] [Indexed: 12/15/2022] Open
Abstract
Distant metastasis is the main cause of breast cancer-related death; however, effective therapeutic strategies targeting metastasis are still scarce. This is largely attributable to the spatiotemporal intratumor heterogeneity during metastasis. Here we show that protein deacetylase SIRT7 is significantly downregulated in breast cancer lung metastases in human and mice, and predicts metastasis-free survival. SIRT7 deficiency promotes breast cancer cell metastasis, while temporal expression of Sirt7 inhibits metastasis in polyomavirus middle T antigen breast cancer model. Mechanistically, SIRT7 deacetylates and promotes SMAD4 degradation mediated by β-TrCP1, and SIRT7 deficiency activates transforming growth factor-β signaling and enhances epithelial-to-mesenchymal transition. Significantly, resveratrol activates SIRT7 deacetylase activity, inhibits breast cancer lung metastases, and increases survival. Our data highlight SIRT7 as a modulator of transforming growth factor-β signaling and suppressor of breast cancer metastasis, meanwhile providing an effective anti-metastatic therapeutic strategy.Metastatic disease is the major reason for breast cancer-related deaths; therefore, a better understanding of this process and its players is needed. Here the authors report the role of SIRT7 in inhibiting SMAD4-mediated breast cancer metastasis providing a possible therapeutic avenue.
Collapse
Affiliation(s)
- Xiaolong Tang
- Department of Biochemistry and Molecular Biology, Shenzhen University Health Science Center, Shenzhen, 518060, China
- Center for Anti-aging and Regenerative Medicine, Shenzhen University Health Science Center, Shenzhen, 518060, China
| | - Lei Shi
- Department of Biochemistry and Molecular Biology, Shenzhen University Health Science Center, Shenzhen, 518060, China
- Center for Anti-aging and Regenerative Medicine, Shenzhen University Health Science Center, Shenzhen, 518060, China
| | - Ni Xie
- Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, 518035, China
| | - Zuojun Liu
- Department of Biochemistry and Molecular Biology, Shenzhen University Health Science Center, Shenzhen, 518060, China
- Center for Anti-aging and Regenerative Medicine, Shenzhen University Health Science Center, Shenzhen, 518060, China
| | - Minxian Qian
- Department of Biochemistry and Molecular Biology, Shenzhen University Health Science Center, Shenzhen, 518060, China
- Center for Anti-aging and Regenerative Medicine, Shenzhen University Health Science Center, Shenzhen, 518060, China
| | - Fanbiao Meng
- Department of Biochemistry and Molecular Biology, Shenzhen University Health Science Center, Shenzhen, 518060, China
- Center for Anti-aging and Regenerative Medicine, Shenzhen University Health Science Center, Shenzhen, 518060, China
| | - Qingyang Xu
- Department of Biochemistry and Molecular Biology, Shenzhen University Health Science Center, Shenzhen, 518060, China
- Center for Anti-aging and Regenerative Medicine, Shenzhen University Health Science Center, Shenzhen, 518060, China
| | - Mingyan Zhou
- Department of Biochemistry and Molecular Biology, Shenzhen University Health Science Center, Shenzhen, 518060, China
- Center for Anti-aging and Regenerative Medicine, Shenzhen University Health Science Center, Shenzhen, 518060, China
| | - Xinyue Cao
- Department of Biochemistry and Molecular Biology, Shenzhen University Health Science Center, Shenzhen, 518060, China
- Center for Anti-aging and Regenerative Medicine, Shenzhen University Health Science Center, Shenzhen, 518060, China
| | - Wei-Guo Zhu
- Department of Biochemistry and Molecular Biology, Shenzhen University Health Science Center, Shenzhen, 518060, China
| | - Baohua Liu
- Department of Biochemistry and Molecular Biology, Shenzhen University Health Science Center, Shenzhen, 518060, China.
- Center for Anti-aging and Regenerative Medicine, Shenzhen University Health Science Center, Shenzhen, 518060, China.
| |
Collapse
|
204
|
Kwon Y, Natori Y, Tanokura M. New approach to generating insights for aging research based on literature mining and knowledge integration. PLoS One 2017; 12:e0183534. [PMID: 28817730 PMCID: PMC5560588 DOI: 10.1371/journal.pone.0183534] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 08/05/2017] [Indexed: 01/01/2023] Open
Abstract
The proportion of the elderly population in most countries worldwide is increasing dramatically. Therefore, social interest in the fields of health, longevity, and anti-aging has been increasing as well. However, the basic research results obtained from a reductionist approach in biology and a bioinformatic approach in genome science have limited usefulness for generating insights on future health, longevity, and anti-aging-related research on a case by case basis. We propose a new approach that uses our literature mining technique and bioinformatics, which lead to a better perspective on research trends by providing an expanded knowledge base to work from. We demonstrate that our approach provides useful information that deepens insights on future trends which differs from data obtained conventionally, and this methodology is already paving the way for a new field in aging-related research based on literature mining. One compelling example of this is how our new approach can be a useful tool in drug repositioning.
Collapse
Affiliation(s)
- Yeondae Kwon
- Laboratory of Basic Science on Healthy Longevity, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Yukikazu Natori
- Laboratory of Basic Science on Healthy Longevity, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Masaru Tanokura
- Laboratory of Basic Science on Healthy Longevity, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
- * E-mail:
| |
Collapse
|
205
|
Mechanisms underlying longevity: A genetic switch model of aging. Exp Gerontol 2017; 107:136-139. [PMID: 28797825 DOI: 10.1016/j.exger.2017.08.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 07/18/2017] [Accepted: 08/04/2017] [Indexed: 01/08/2023]
Abstract
While the questions of "What causes aging?" and "Why do we age?" and "How can we stop it?" remain unanswered, recent advances in aging research have continued to increase our understanding of the aging process. Until the last couple of decades, aging was viewed as an inevitable process of damage accumulation and not a subject for scientific pursuit. This view changed when it was demonstrated that the aging process is in fact malleable and genetically determined: mutations in single genes can have dramatic effects on longevity. Despite the rapid advancement of our knowledge about aging, the cause of aging remains unclear. In this paper, experiments demonstrating the roles of genetics and epigenetics in modulating longevity are reviewed, concluding with a new model of aging. This genetic switch model of aging proposes that aging is caused by a genetically-programmed turning off of survival and maintenance pathways after reproduction finishes leading to a progressive functional decline. If this model is correct, it may be possible to extend lifespan and healthspan by identifying the molecular pathways involved and simply turning the switch back on.
Collapse
|
206
|
de Magalhães JP, Stevens M, Thornton D. The Business of Anti-Aging Science. Trends Biotechnol 2017; 35:1062-1073. [PMID: 28778607 DOI: 10.1016/j.tibtech.2017.07.004] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 06/18/2017] [Accepted: 07/06/2017] [Indexed: 12/16/2022]
Abstract
Age-related conditions are the leading causes of death and health-care costs. Reducing the rate of aging would have enormous medical and financial benefits. Myriad genes and pathways are known to regulate aging in model organisms, fostering a new crop of anti-aging companies. Approaches range from drug discovery efforts to big-data methods and direct-to-consumer (DTC) strategies. Challenges and pitfalls of commercialization include reliance on findings from short-lived model organisms, poor biological understanding of aging, and hurdles in performing clinical trials for aging. A large number of potential aging-associated interventions and targets exist, but given the long validation times only a small fraction can be explored for clinical applications. If even one company succeeds, however, the impact will be huge.
Collapse
Affiliation(s)
- João Pedro de Magalhães
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool L7 8TX, UK; Joint first authors.
| | - Michael Stevens
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool L7 8TX, UK; Joint first authors
| | - Daniel Thornton
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool L7 8TX, UK
| |
Collapse
|
207
|
Barardo DG, Newby D, Thornton D, Ghafourian T, de Magalhães JP, Freitas AA. Machine learning for predicting lifespan-extending chemical compounds. Aging (Albany NY) 2017; 9:1721-1737. [PMID: 28783712 PMCID: PMC5559171 DOI: 10.18632/aging.101264] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 07/12/2017] [Indexed: 12/12/2022]
Abstract
Increasing age is a risk factor for many diseases; therefore developing pharmacological interventions that slow down ageing and consequently postpone the onset of many age-related diseases is highly desirable. In this work we analyse data from the DrugAge database, which contains chemical compounds and their effect on the lifespan of model organisms. Predictive models were built using the machine learning method random forests to predict whether or not a chemical compound will increase Caenorhabditis elegans' lifespan, using as features Gene Ontology (GO) terms annotated for proteins targeted by the compounds and chemical descriptors calculated from each compound's chemical structure. The model with the best predictive accuracy used both biological and chemical features, achieving a prediction accuracy of 80%. The top 20 most important GO terms include those related to mitochondrial processes, to enzymatic and immunological processes, and terms related to metabolic and transport processes. We applied our best model to predict compounds which are more likely to increase C. elegans' lifespan in the DGIdb database, where the effect of the compounds on an organism's lifespan is unknown. The top hit compounds can be broadly divided into four groups: compounds affecting mitochondria, compounds for cancer treatment, anti-inflammatories, and compounds for gonadotropin-releasing hormone therapies.
Collapse
Affiliation(s)
- Diogo G. Barardo
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, UK
| | - Danielle Newby
- Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford, UK
| | - Daniel Thornton
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, UK
| | | | - João Pedro de Magalhães
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, UK
| | | |
Collapse
|
208
|
Hoffman JM, Lyu Y, Pletcher SD, Promislow DEL. Proteomics and metabolomics in ageing research: from biomarkers to systems biology. Essays Biochem 2017; 61:379-388. [PMID: 28698311 PMCID: PMC5743054 DOI: 10.1042/ebc20160083] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 05/16/2017] [Accepted: 05/17/2017] [Indexed: 02/07/2023]
Abstract
Age is the single greatest risk factor for a wide range of diseases, and as the mean age of human populations grows steadily older, the impact of this risk factor grows as well. Laboratory studies on the basic biology of ageing have shed light on numerous genetic pathways that have strong effects on lifespan. However, we still do not know the degree to which the pathways that affect ageing in the lab also influence variation in rates of ageing and age-related disease in human populations. Similarly, despite considerable effort, we have yet to identify reliable and reproducible 'biomarkers', which are predictors of one's biological as opposed to chronological age. One challenge lies in the enormous mechanistic distance between genotype and downstream ageing phenotypes. Here, we consider the power of studying 'endophenotypes' in the context of ageing. Endophenotypes are the various molecular domains that exist at intermediate levels of organization between the genotype and phenotype. We focus our attention specifically on proteins and metabolites. Proteomic and metabolomic profiling has the potential to help identify the underlying causal mechanisms that link genotype to phenotype. We present a brief review of proteomics and metabolomics in ageing research with a focus on the potential of a systems biology and network-centric perspective in geroscience. While network analyses to study ageing utilizing proteomics and metabolomics are in their infancy, they may be the powerful model needed to discover underlying biological processes that influence natural variation in ageing, age-related disease, and longevity.
Collapse
Affiliation(s)
- Jessica M Hoffman
- Department of Biology, University of Alabama at Birmingham, 1300 University Blvd CH464, Birmingham, AL 35294, U.S.A
| | - Yang Lyu
- Department of Molecular and Integrative Physiology and Geriatrics Center, Biomedical Sciences and Research Building, University of Michigan, Ann Arbor, MI 48109, U.S.A
| | - Scott D Pletcher
- Department of Molecular and Integrative Physiology and Geriatrics Center, Biomedical Sciences and Research Building, University of Michigan, Ann Arbor, MI 48109, U.S.A
| | - Daniel E L Promislow
- Department of Pathology, University of Washington, Box 357705, 1959 NE Pacific Street, Seattle, Washington 98195, U.S.A.
- Department of Biology, University of Washington, Seattle, Washington 98195, U.S.A
| |
Collapse
|
209
|
Plourde BT, Burgess TL, Eskew EA, Roth TM, Stephenson N, Foley JE. Are disease reservoirs special? Taxonomic and life history characteristics. PLoS One 2017; 12:e0180716. [PMID: 28704402 PMCID: PMC5509157 DOI: 10.1371/journal.pone.0180716] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 06/20/2017] [Indexed: 11/18/2022] Open
Abstract
Pathogens that spill over between species cause a significant human and animal health burden. Here, we describe characteristics of animal reservoirs that are required for pathogen spillover. We assembled and analyzed a database of 330 disease systems in which a pathogen spills over from a reservoir of one or more species. Three-quarters of reservoirs included wildlife, and 84% included mammals. Further, 65% of pathogens depended on a community of reservoir hosts, rather than a single species, for persistence. Among mammals, the most frequently identified reservoir hosts were rodents, artiodactyls, and carnivores. The distribution among orders of mammalian species identified as reservoirs did not differ from that expected by chance. Among disease systems with high priority pathogens and epidemic potential, we found birds, primates, and bats to be overrepresented. We also analyzed the life history traits of mammalian reservoir hosts and compared them to mammals as a whole. Reservoir species had faster life history characteristics than mammals overall, exhibiting traits associated with greater reproductive output rather than long-term survival. Thus, we find that in many respects, reservoirs of spillover pathogens are indeed special. The described patterns provide a useful resource for studying and managing emerging infectious diseases.
Collapse
Affiliation(s)
- Benjamin T. Plourde
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, California, United States of America
- * E-mail:
| | - Tristan L. Burgess
- Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | - Evan A. Eskew
- Graduate Group in Ecology, University of California, Davis, California, United States of America
- EcoHealth Alliance, New York, New York, United States of America
| | - Tara M. Roth
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | - Nicole Stephenson
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | - Janet E. Foley
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, California, United States of America
| |
Collapse
|
210
|
Modelling the influence of host community composition in a sylvatic Trypanosoma cruzi system. Parasitology 2017; 144:1881-1889. [PMID: 28701240 DOI: 10.1017/s0031182017001287] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Species composition of wild reservoir hosts can influence the transmission and maintenance of multi-host vector borne pathogens. The 'pace of life' hypothesis proposes that the life history strategy of reservoir hosts can influence pathogen transmission of vector borne generalist pathogens. We use empirical data to parameterize a mathematical model that investigates the impacts of host life history traits on vector transmission dynamics of the vector-borne multi-host parasite Trypanosoma cruzi in habitats characterized by different degrees of deforestation and varying host community structure. The model considers susceptible and infected vector and host populations. When comparing the proportion of vectors infected with T. cruzi predicted by the model with empirical data, we found a trend of increasing vector infection as anthropogenic landscape disturbance increases for both data and model output. The model's vector infection rates were significantly lower than empirical results, but when incorporating host congenital transmission in the model, vector infection approaches field data. We conclude that intervened habitats associated with r-selected host species communities predict higher proportions of infected vectors.
Collapse
|
211
|
Dammann P. Slow aging in mammals-Lessons from African mole-rats and bats. Semin Cell Dev Biol 2017; 70:154-163. [PMID: 28698112 DOI: 10.1016/j.semcdb.2017.07.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 07/04/2017] [Accepted: 07/05/2017] [Indexed: 12/30/2022]
Abstract
Traditionally, the main mammalian models used in aging research have been mice and rats, i.e. short-lived species that obviously lack effective maintenance mechanisms to keep their soma in a functional state for prolonged periods of time. It is doubtful that life-extending mechanisms identified only in such short-lived species adequately reflect the diversity of longevity pathways that have naturally evolved in mammals, or that they have much relevance for long-lived species such as humans. Therefore, some complementary, long-lived mammalian models have been introduced to aging research in the past 15-20 years, particularly naked mole-rats (and to a lesser extent also other mole-rats) and bats. Here, I summarize and compare the most important results regarding various aspects of aging - oxidative stress, molecular homeostasis and repair, and endocrinology - that have been obtained from studies using these new mammalian models of high longevity. I argue that the inclusion of these models was an important step forward, because it drew researchers' attention to certain oversimplifications of existing aging theories and to several features that appear to be universal components of enhanced longevity in mammals. However, even among mammals with high longevity, considerable variation exists with respect to other candidate mechanisms that also must be taken into account if inadequate generalizations are to be avoided.
Collapse
Affiliation(s)
- Philip Dammann
- Central Animal Laboratory, Faculty of Medicine, University of Duisburg, Essen, Germany.
| |
Collapse
|
212
|
Bhak Y, Jeon Y, Jeon S, Chung O, Jho S, Jun J, Kim HM, Cho Y, Yoon C, Lee S, Kang JH, Lim JD, An J, Cho YS, Ryu DY, Bhak J. Myotis rufoniger genome sequence and analyses: M. rufoniger's genomic feature and the decreasing effective population size of Myotis bats. PLoS One 2017; 12:e0180418. [PMID: 28678835 PMCID: PMC5498047 DOI: 10.1371/journal.pone.0180418] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 05/23/2017] [Indexed: 12/14/2022] Open
Abstract
Myotis rufoniger is a vesper bat in the genus Myotis. Here we report the whole genome sequence and analyses of the M. rufoniger. We generated 124 Gb of short-read DNA sequences with an estimated genome size of 1.88 Gb at a sequencing depth of 66× fold. The sequences were aligned to M. brandtii bat reference genome at a mapping rate of 96.50% covering 95.71% coding sequence region at 10× coverage. The divergence time of Myotis bat family is estimated to be 11.5 million years, and the divergence time between M. rufoniger and its closest species M. davidii is estimated to be 10.4 million years. We found 1,239 function-altering M. rufoniger specific amino acid sequences from 929 genes compared to other Myotis bat and mammalian genomes. The functional enrichment test of the 929 genes detected amino acid changes in melanin associated DCT, SLC45A2, TYRP1, and OCA2 genes possibly responsible for the M. rufoniger's red fur color and a general coloration in Myotis. N6AMT1 gene, associated with arsenic resistance, showed a high degree of function alteration in M. rufoniger. We further confirmed that the M. rufoniger also has bat-specific sequences within FSHB, GHR, IGF1R, TP53, MDM2, SLC45A2, RGS7BP, RHO, OPN1SW, and CNGB3 genes that have already been published to be related to bat's reproduction, lifespan, flight, low vision, and echolocation. Additionally, our demographic history analysis found that the effective population size of Myotis clade has been consistently decreasing since ~30k years ago. M. rufoniger's effective population size was the lowest in Myotis bats, confirming its relatively low genetic diversity.
Collapse
Affiliation(s)
- Youngjune Bhak
- The Genomics Institute, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Yeonsu Jeon
- The Genomics Institute, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Sungwon Jeon
- The Genomics Institute, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Oksung Chung
- Personal Genomics Institute, Genome Research Foundation, Cheongju, Republic of Korea
- Geromics, Ulsan, Republic of Korea
| | - Sungwoong Jho
- Personal Genomics Institute, Genome Research Foundation, Cheongju, Republic of Korea
| | - JeHoon Jun
- Personal Genomics Institute, Genome Research Foundation, Cheongju, Republic of Korea
- Geromics, Ulsan, Republic of Korea
| | - Hak-Min Kim
- The Genomics Institute, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Yongsoo Cho
- The Genomics Institute, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Changhan Yoon
- The Genomics Institute, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- Department of Biomedical Science, School of Nano-Bioscience & chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Seungwoo Lee
- BK21 PLUS Program for Creative Veterinary Science Research, Research Institute for Veterinary Science, and College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Jung-Hoon Kang
- National Research Institute of Cultural Heritage, Cultural Heritage Administration, Daejeon, Republic of Korea
| | - Jong-Deock Lim
- National Research Institute of Cultural Heritage, Cultural Heritage Administration, Daejeon, Republic of Korea
| | - Junghwa An
- Animal Resources Division, National Institute of Biological Resources, Incheon, Republic of Korea
| | - Yun Sung Cho
- The Genomics Institute, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- Personal Genomics Institute, Genome Research Foundation, Cheongju, Republic of Korea
| | - Doug-Young Ryu
- BK21 PLUS Program for Creative Veterinary Science Research, Research Institute for Veterinary Science, and College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Jong Bhak
- The Genomics Institute, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- Personal Genomics Institute, Genome Research Foundation, Cheongju, Republic of Korea
- Geromics, Ulsan, Republic of Korea
| |
Collapse
|
213
|
Global priorities for conservation across multiple dimensions of mammalian diversity. Proc Natl Acad Sci U S A 2017; 114:7641-7646. [PMID: 28674013 DOI: 10.1073/pnas.1706461114] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Conservation priorities that are based on species distribution, endemism, and vulnerability may underrepresent biologically unique species as well as their functional roles and evolutionary histories. To ensure that priorities are biologically comprehensive, multiple dimensions of diversity must be considered. Further, understanding how the different dimensions relate to one another spatially is important for conservation prioritization, but the relationship remains poorly understood. Here, we use spatial conservation planning to (i) identify and compare priority regions for global mammal conservation across three key dimensions of biodiversity-taxonomic, phylogenetic, and traits-and (ii) determine the overlap of these regions with the locations of threatened species and existing protected areas. We show that priority areas for mammal conservation exhibit low overlap across the three dimensions, highlighting the need for an integrative approach for biodiversity conservation. Additionally, currently protected areas poorly represent the three dimensions of mammalian biodiversity. We identify areas of high conservation priority among and across the dimensions that should receive special attention for expanding the global protected area network. These high-priority areas, combined with areas of high priority for other taxonomic groups and with social, economic, and political considerations, provide a biological foundation for future conservation planning efforts.
Collapse
|
214
|
Tidière M, Lemaître JF, Douay G, Whipple M, Gaillard JM. High reproductive effort is associated with decreasing mortality late in life in captive ruffed lemurs. Am J Primatol 2017; 79. [DOI: 10.1002/ajp.22677] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 05/06/2017] [Accepted: 05/11/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Morgane Tidière
- Université de Lyon; Laboratoire de Biométrie et Biologie Evolutive; Villeurbanne France
| | | | | | | | - Jean-Michel Gaillard
- Université de Lyon; Laboratoire de Biométrie et Biologie Evolutive; Villeurbanne France
| |
Collapse
|
215
|
Veitschegger K. The effect of body size evolution and ecology on encephalization in cave bears and extant relatives. BMC Evol Biol 2017; 17:124. [PMID: 28583080 PMCID: PMC5460516 DOI: 10.1186/s12862-017-0976-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 05/22/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The evolution of larger brain volumes relative to body size in Mammalia is the subject of an extensive amount of research. Early on palaeontologists were interested in the brain of cave bears, Ursus spelaeus, and described its morphology and size. However, until now, it was not possible to compare the absolute or relative brain size in a phylogenetic context due to the lack of an established phylogeny, comparative material, and phylogenetic comparative methods. In recent years, many tools for comparing traits within phylogenies were developed and the phylogenetic position of cave bears was resolved based on nuclear as well as mtDNA. RESULTS Cave bears exhibit significantly lower encephalization compared to their contemporary relatives and intraspecific brain mass variation remained rather small. Encephalization was correlated with the combined dormancy-diet score. Body size evolution was a main driver in the degree of encephalization in cave bears as it increased in a much higher pace than brain size. In Ursus spelaeus, brain and body size increase over time albeit differently paced. This rate pattern is different in the highest encephalized bear species within the dataset, Ursus malayanus. The brain size in this species increased while body size heavily decreased compared to its ancestral stage. CONCLUSIONS Early on in the evolution of cave bears encephalization decreased making it one of the least encephalized bear species compared to extant and extinct members of Ursidae. The results give reason to suspect that as herbivorous animals, cave bears might have exhibited a physiological buffer strategy to survive the strong seasonality of their environment. Thus, brain size was probably affected by the negative trade-off with adipose tissue as well as diet. The decrease of relative brain size in the herbivorous Ursus spelaeus is the result of a considerable increase in body size possibly in combination with environmental conditions forcing them to rest during winters.
Collapse
Affiliation(s)
- Kristof Veitschegger
- Palaeontological Institute and Museum, University of Zurich, Karl Schmid-Strasse 4, 8006, Zürich, Switzerland.
| |
Collapse
|
216
|
Barardo D, Thornton D, Thoppil H, Walsh M, Sharifi S, Ferreira S, Anžič A, Fernandes M, Monteiro P, Grum T, Cordeiro R, De-Souza EA, Budovsky A, Araujo N, Gruber J, Petrascheck M, Fraifeld VE, Zhavoronkov A, Moskalev A, de Magalhães JP. The DrugAge database of aging-related drugs. Aging Cell 2017; 16:594-597. [PMID: 28299908 PMCID: PMC5418190 DOI: 10.1111/acel.12585] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/07/2017] [Indexed: 11/30/2022] Open
Abstract
Aging is a major worldwide medical challenge. Not surprisingly, identifying drugs and compounds that extend lifespan in model organisms is a growing research area. Here, we present DrugAge (http://genomics.senescence.info/drugs/), a curated database of lifespan‐extending drugs and compounds. At the time of writing, DrugAge contains 1316 entries featuring 418 different compounds from studies across 27 model organisms, including worms, flies, yeast and mice. Data were manually curated from 324 publications. Using drug–gene interaction data, we also performed a functional enrichment analysis of targets of lifespan‐extending drugs. Enriched terms include various functional categories related to glutathione and antioxidant activity, ion transport and metabolic processes. In addition, we found a modest but significant overlap between targets of lifespan‐extending drugs and known aging‐related genes, suggesting that some but not most aging‐related pathways have been targeted pharmacologically in longevity studies. DrugAge is freely available online for the scientific community and will be an important resource for biogerontologists.
Collapse
Affiliation(s)
- Diogo Barardo
- Integrative Genomics of Ageing Group; Institute of Ageing and Chronic Disease; University of Liverpool; Liverpool UK
| | - Daniel Thornton
- Integrative Genomics of Ageing Group; Institute of Ageing and Chronic Disease; University of Liverpool; Liverpool UK
| | - Harikrishnan Thoppil
- Integrative Genomics of Ageing Group; Institute of Ageing and Chronic Disease; University of Liverpool; Liverpool UK
- Amrita School of Biotechnology; Amrita Vishwa Vidyapeetham (Amrita University); Coimbatore India
| | - Michael Walsh
- Energy Metabolism Laboratory; Swiss Federal Institute of Technology (ETH) Zurich; Zurich Switzerland
| | - Samim Sharifi
- Integrative Genomics of Ageing Group; Institute of Ageing and Chronic Disease; University of Liverpool; Liverpool UK
| | - Susana Ferreira
- Integrative Genomics of Ageing Group; Institute of Ageing and Chronic Disease; University of Liverpool; Liverpool UK
| | - Andreja Anžič
- Integrative Genomics of Ageing Group; Institute of Ageing and Chronic Disease; University of Liverpool; Liverpool UK
| | - Maria Fernandes
- Integrative Genomics of Ageing Group; Institute of Ageing and Chronic Disease; University of Liverpool; Liverpool UK
| | - Patrick Monteiro
- Integrative Genomics of Ageing Group; Institute of Ageing and Chronic Disease; University of Liverpool; Liverpool UK
| | - Tjaša Grum
- Integrative Genomics of Ageing Group; Institute of Ageing and Chronic Disease; University of Liverpool; Liverpool UK
| | - Rui Cordeiro
- Integrative Genomics of Ageing Group; Institute of Ageing and Chronic Disease; University of Liverpool; Liverpool UK
| | | | - Arie Budovsky
- The Shraga Segal Department of Microbiology, Immunology and Genetics; Center for Multidisciplinary Research on Aging; Ben-Gurion University of the Negev; Beer Sheva Israel
- Judea Regional Research & Development Center; Carmel 90404 Israel
| | - Natali Araujo
- Integrative Genomics of Ageing Group; Institute of Ageing and Chronic Disease; University of Liverpool; Liverpool UK
| | - Jan Gruber
- Department of Science; Yale- NUS College; Singapore City 138527 Singapore
- Department of Biochemistry; Yong Loo Lin School of Medicine; National University of Singapore; Singapore City 117597 Singapore
| | - Michael Petrascheck
- Department of Chemical Physiology; The Scripps Research Institute; La Jolla CA USA
| | - Vadim E. Fraifeld
- The Shraga Segal Department of Microbiology, Immunology and Genetics; Center for Multidisciplinary Research on Aging; Ben-Gurion University of the Negev; Beer Sheva Israel
| | - Alexander Zhavoronkov
- Pharmaceutical Artificial Intelligence Research Division; Emerging Technology Centers; Insilico Medicine, Inc; Johns Hopkins University at Eastern; B301, 1101 33rd Street Baltimore MD 21218 USA
- The Biogerontology Research Foundation; Oxford UK
| | - Alexey Moskalev
- Moscow Institute of Physics and Technology; Dolgoprudny 141700 Russia
- Laboratory of Molecular Radiobiology and Gerontology; Institute of Biology of Komi Science Center of Ural Branch of Russian Academy of Sciences; Syktyvkar 167982 Russia
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences; Moscow 119991 Russia
| | - João Pedro de Magalhães
- Integrative Genomics of Ageing Group; Institute of Ageing and Chronic Disease; University of Liverpool; Liverpool UK
- The Biogerontology Research Foundation; Oxford UK
| |
Collapse
|
217
|
Ben-Avraham D, Govindaraju DR, Budagov T, Fradin D, Durda P, Liu B, Ott S, Gutman D, Sharvit L, Kaplan R, Bougnères P, Reiner A, Shuldiner AR, Cohen P, Barzilai N, Atzmon G. The GH receptor exon 3 deletion is a marker of male-specific exceptional longevity associated with increased GH sensitivity and taller stature. SCIENCE ADVANCES 2017; 3:e1602025. [PMID: 28630896 PMCID: PMC5473676 DOI: 10.1126/sciadv.1602025] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 04/26/2017] [Indexed: 05/26/2023]
Abstract
Although both growth hormone (GH) and insulin-like growth factor 1 (IGF-1) signaling were shown to regulate life span in lower organisms, the role of GH signaling in human longevity remains unclear. Because a GH receptor exon 3 deletion (d3-GHR) appears to modulate GH sensitivity in humans, we hypothesized that this polymorphism could play a role in human longevity. We report a linear increased prevalence of d3-GHR homozygosity with age in four independent cohorts of long-lived individuals: 841 participants [567 of the Longevity Genes Project (LGP) (8% increase; P = 0.01), 152 of the Old Order Amish (16% increase; P = 0.02), 61 of the Cardiovascular Health Study (14.2% increase; P = 0.14), and 61 of the French Long-Lived Study (23.5% increase; P = 0.02)]. In addition, mega analysis of males in all cohorts resulted in a significant positive trend with age (26% increase; P = 0.007), suggesting sexual dimorphism for GH action in longevity. Further, on average, LGP d3/d3 homozygotes were 1 inch taller than the wild-type (WT) allele carriers (P = 0.05) and also showed lower serum IGF-1 levels (P = 0.003). Multivariate regression analysis indicated that the presence of d3/d3 genotype adds approximately 10 years to life span. The LGP d3/d3-GHR transformed lymphocytes exhibited superior growth and extracellular signal-regulated kinase activation, to GH treatment relative to WT GHR lymphocytes (P < 0.01), indicating a GH dose response. The d3-GHR variant is a common genetic polymorphism that modulates GH responsiveness throughout the life span and positively affects male longevity.
Collapse
Affiliation(s)
- Danny Ben-Avraham
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Institute of Aging Research, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Diddahally R. Govindaraju
- Institute of Aging Research, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Temuri Budagov
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Institute of Aging Research, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Delphine Fradin
- INSERM U986, Pincus Building, Bicêtre Hospital, Paris Sud University, 94275 Le Kremlin Bicêtre, France
| | - Peter Durda
- Department of Pathology University of Vermont, 208 South Park Drive, Colchester, VT 05446, USA
| | - Bing Liu
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Sandy Ott
- University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Danielle Gutman
- Department of Human Biology, Faculty of Natural Sciences, University of Haifa, Haifa, Israel
| | - Lital Sharvit
- Department of Human Biology, Faculty of Natural Sciences, University of Haifa, Haifa, Israel
| | - Robert Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Pierre Bougnères
- INSERM U986, Pincus Building, Bicêtre Hospital, Paris Sud University, 94275 Le Kremlin Bicêtre, France
- INSERM U1169 and Department of Pediatric Endocrinology and Diabetes, Bicêtre Hospital, Pôle I3E, Paris Sud University, 94275 Le Kremlin Bicêtre, France
| | - Alex Reiner
- Department of Epidemiology, University of Washington School of Public Health, Seattle, WA 98195, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Alan R. Shuldiner
- University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Geriatrics Research and Education Clinical Center, Veterans Administration Medical Center, Baltimore, MD 20420, USA
| | - Pinchas Cohen
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Nir Barzilai
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Institute of Aging Research, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Gil Atzmon
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Institute of Aging Research, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Human Biology, Faculty of Natural Sciences, University of Haifa, Haifa, Israel
| |
Collapse
|
218
|
Convergent adaptation of cellular machineries in the evolution of large body masses and long life spans. Biogerontology 2017; 18:485-497. [PMID: 28573417 PMCID: PMC5514201 DOI: 10.1007/s10522-017-9713-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 05/22/2017] [Indexed: 02/06/2023]
Abstract
In evolutionary terms, life on the planet has taken the form of independently living cells for the majority of time. In comparison, the mammalian radiation is a relatively recent event. The common mammalian ancestor was probably small and short-lived. The “recent” acquisition of an extended longevity and large body mass of some species of mammals present on the earth today suggests the possibility that similar cellular mechanisms have been influenced by the forces of natural selection to create a convergent evolution of longevity. Many cellular mechanisms are potentially relevant for extending longevity; in this assay, we review the literature focusing primarily on two cellular features: (1) the capacity for extensive cellular proliferation of differentiated cells, while maintaining genome stability; and (2) the capacity to detect DNA damage. We have observed that longevity and body mass are both positively linked to these cellular mechanisms and then used statistical tools to evaluate their relative importance. Our analysis suggest that the capacity for extensive cellular proliferation while maintaining sufficient genome stability, correlates to species body mass while the capacity to correctly identify the presence of DNA damage seems more an attribute of long-lived species. Finally, our data are in support of the idea that a slower development, allowing for better DNA damage detection and handling, should associate with longer life span.
Collapse
|
219
|
Sahm A, Bens M, Platzer M, Cellerino A. Parallel evolution of genes controlling mitonuclear balance in short-lived annual fishes. Aging Cell 2017; 16:488-496. [PMID: 28295945 PMCID: PMC5418189 DOI: 10.1111/acel.12577] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/23/2016] [Indexed: 12/15/2022] Open
Abstract
The current molecular understanding of the aging process derives almost exclusively from the study of random or targeted single‐gene mutations in highly inbred laboratory species, mostly invertebrates. Little information is available as to the genetic mechanisms responsible for natural lifespan variation and the evolution of lifespan, especially in vertebrates. Here, we investigated the pattern of positive selection in annual (i.e., short‐lived) and nonannual (i.e., longer‐lived) African killifishes to identify a genomic substrate for evolution of annual life history (and reduced lifespan). We identified genes under positive selection in all steps of mitochondrial biogenesis: mitochondrial (mt) DNA replication, transcription from mt promoters, processing and stabilization of mt RNAs, mt translation, assembly of respiratory chain complexes, and electron transport chain. Signs of paralleled evolution (i.e., evolution in more than one branch of Nothobranchius phylogeny) are observed in four out of five steps. Moreover, some genes under positive selection in Nothobranchius are under positive selection also in long‐lived mammals such as bats and mole‐rats. Complexes of the respiratory chain are formed in a coordinates multistep process where nuclearly and mitochondrially encoded components are assembled and inserted into the inner mitochondrial membrane. The coordination of this process is named mitonuclear balance, and experimental manipulations of mitonuclear balance can increase longevity of laboratory species. Our data strongly indicate that these genes are also casually linked to evolution lifespan in vertebrates.
Collapse
Affiliation(s)
- Arne Sahm
- Leibniz Insitute on Ageing; Fritz-Lipmann Institute; Jena 07745 Germany
| | - Martin Bens
- Leibniz Insitute on Ageing; Fritz-Lipmann Institute; Jena 07745 Germany
| | - Matthias Platzer
- Leibniz Insitute on Ageing; Fritz-Lipmann Institute; Jena 07745 Germany
| | - Alessandro Cellerino
- Leibniz Insitute on Ageing; Fritz-Lipmann Institute; Jena 07745 Germany
- Bio@SNS; Scuola Normale Superiore; Pisa 56124 Italy
| |
Collapse
|
220
|
Ancell H, Pires-daSilva A. Sex-specific lifespan and its evolution in nematodes. Semin Cell Dev Biol 2017; 70:122-129. [PMID: 28554570 DOI: 10.1016/j.semcdb.2017.05.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 05/03/2017] [Accepted: 05/18/2017] [Indexed: 12/22/2022]
Abstract
Differences between sexes of the same species in lifespan and aging rate are widespread. While the proximal and evolutionary causes of aging are well researched, the factors that contribute to sex differences in these traits have been less studied. The striking diversity of nematodes provides ample opportunity to study variation in sex-specific lifespan patterns associated with shifts in life history and mating strategy. Although the plasticity of these sex differences will make it challenging to generalize from invertebrate to vertebrate systems, studies in nematodes have enabled empirical evaluation of predictions regarding the evolution of lifespan. These studies have highlighted how natural and sexual selection can generate divergent patterns of lifespan if the sexes are subject to different rates or sources of mortality, or if trade-offs between complex traits and longevity are resolved differently in each sex. Here, we integrate evidence derived mainly from nematodes that addresses the molecular and evolutionary basis of sex-specific aging and lifespan. Ultimately, we hope to generate a clearer picture of current knowledge in this area, and also highlight the limitations of our understanding.
Collapse
Affiliation(s)
- Henry Ancell
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | | |
Collapse
|
221
|
In vivo and in vitro ageing results in accumulation of de novo copy number variations in bulls. Sci Rep 2017; 7:1631. [PMID: 28487564 PMCID: PMC5431667 DOI: 10.1038/s41598-017-01793-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 04/03/2017] [Indexed: 11/24/2022] Open
Abstract
We have identified de novo copy number variations (CNVs) generated in bulls as they age. Blood samples from eight bulls were collected and SNP arrayed in a prospective design over 30 months allowing us to differentiate de novo CNVs from constant CNVs that are present throughout the sampling period. Quite remarkably, the total number of CNVs doubled over the 30-month period, as we observed an almost equal number of de novo and constant CNVs (107 and 111, respectively, i.e. 49% and 51%). Twice as many de novo CNVs emerged during the second half of the sampling schedule as in the first part. It suggests a dynamic generation of de novo CNVs in the bovine genome that becomes more frequent as the age of the animal progresses. In a second experiment de novo CNVs were detected through in vitro ageing of bovine fibroblasts by sampling passage #5, #15 and #25. De novo CNVs also became more frequent, but the proportion of them was only ~25% of the total number of CNVs (21 out of 85). Temporal generation of de novo CNVs resulted in increasing genome coverage. Genes and quantitative trait loci overlapping de novo CNVs were further investigated for ageing related functions.
Collapse
|
222
|
Naslavsky MS, Yamamoto GL, Almeida TF, Ezquina SAM, Sunaga DY, Pho N, Bozoklian D, Sandberg TOM, Brito LA, Lazar M, Bernardo DV, Amaro E, Duarte YAO, Lebrão ML, Passos‐Bueno MR, Zatz M. Exomic variants of an elderly cohort of Brazilians in the ABraOM database. Hum Mutat 2017; 38:751-763. [DOI: 10.1002/humu.23220] [Citation(s) in RCA: 149] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 03/14/2017] [Accepted: 03/19/2017] [Indexed: 01/03/2023]
Affiliation(s)
- Michel Satya Naslavsky
- Human Genome and Stem Cell Research Center Biosciences Institute, University of São Paulo São Paulo Brazil
- Hospital Israelita Albert Einstein São Paulo Brazil
| | - Guilherme Lopes Yamamoto
- Human Genome and Stem Cell Research Center Biosciences Institute, University of São Paulo São Paulo Brazil
- Department of Clinical Genetics Children's Hospital Medical School University of São Paulo São Paulo Brazil
| | - Tatiana Ferreira Almeida
- Human Genome and Stem Cell Research Center Biosciences Institute, University of São Paulo São Paulo Brazil
| | - Suzana A. M. Ezquina
- Human Genome and Stem Cell Research Center Biosciences Institute, University of São Paulo São Paulo Brazil
| | - Daniele Yumi Sunaga
- Human Genome and Stem Cell Research Center Biosciences Institute, University of São Paulo São Paulo Brazil
| | - Nam Pho
- Department of Biomedical Informatics Harvard Medical School Boston Massachusetts
| | - Daniel Bozoklian
- Human Genome and Stem Cell Research Center Biosciences Institute, University of São Paulo São Paulo Brazil
| | | | - Luciano Abreu Brito
- Human Genome and Stem Cell Research Center Biosciences Institute, University of São Paulo São Paulo Brazil
| | - Monize Lazar
- Human Genome and Stem Cell Research Center Biosciences Institute, University of São Paulo São Paulo Brazil
| | - Danilo Vicensotto Bernardo
- Laboratório de Estudos em Antropologia Biológica Bioarqueologia e Evolução Humana, Instituto de Ciências Humanas e da Informação, Universidade Federal do Rio Grande Rio Grande Rio Grande de Sul Brazil
| | - Edson Amaro
- Hospital Israelita Albert Einstein São Paulo Brazil
- Radiology Institute Medical School, University of São Paulo São Paulo Brazil
| | - Yeda A. O. Duarte
- Department of Epidemiology Public Health School University of São Paulo São Paulo Brazil
- School of Nursing University of São Paulo São Paulo Brazil
| | - Maria Lúcia Lebrão
- Department of Epidemiology Public Health School University of São Paulo São Paulo Brazil
| | - Maria Rita Passos‐Bueno
- Human Genome and Stem Cell Research Center Biosciences Institute, University of São Paulo São Paulo Brazil
| | - Mayana Zatz
- Human Genome and Stem Cell Research Center Biosciences Institute, University of São Paulo São Paulo Brazil
| |
Collapse
|
223
|
Moskalev A, Chernyagina E, Kudryavtseva A, Shaposhnikov M. Geroprotectors: A Unified Concept and Screening Approaches. Aging Dis 2017; 8:354-363. [PMID: 28580190 PMCID: PMC5440114 DOI: 10.14336/ad.2016.1022] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 10/22/2016] [Indexed: 12/20/2022] Open
Abstract
Although the geroprotectors discovery is a new biomedicine trend and more than 200 compounds can slow aging and increase the lifespan of the model organism, there are still no geroprotectors on the market. The reasons may be partly related to the lack of a unified concept of geroprotector, accepted by the scientific community. Such concept as a system of criteria for geroprotector identification and classification can form a basis for an analytical model of anti-aging drugs, help to consolidate the efforts of various research initiatives in this area and compare their results. Here, we review the existing classification and characteristics of geroprotectors based on their effect on the survival of a group of individuals or pharmaceutics classes, according to the proposed mechanism of their geroprotective action or theories of aging. After discussing advantages and disadvantages of these approaches, we offer a new concept based on the maintenance of homeostatic capacity because aging can be considered as exponential shrinkage of homeostatic capacity leading to the onset of age-related diseases and death. Besides, we review the most promising current screening approaches to finding new geroprotectors. Establishing the classification of existing geroprotectors based on physiology and current understanding of the nature of aging is essential for putting the existing knowledge into a single system. This system could be useful to formulate standards for finding and creating new geroprotectors. Standardization, in turn, would allow easier comparison and combination of experimental data obtained by different research groups.
Collapse
Affiliation(s)
- Alexey Moskalev
- 1Laboratory of postgenomic studies, Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, Moscow, 119991, Russia.,2Laboratory of genetics of aging and longevity, Moscow Institute of Physics and Technology, Dolgoprudny, 141700, Russia.,3Laboratory of molecular radiobiology and gerontology, Institute of Biology of Komi Science Center of Ural Branch of Russian Academy of Sciences, Syktyvkar, 167982, Russia
| | - Elizaveta Chernyagina
- 2Laboratory of genetics of aging and longevity, Moscow Institute of Physics and Technology, Dolgoprudny, 141700, Russia
| | - Anna Kudryavtseva
- 1Laboratory of postgenomic studies, Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, Moscow, 119991, Russia
| | - Mikhail Shaposhnikov
- 3Laboratory of molecular radiobiology and gerontology, Institute of Biology of Komi Science Center of Ural Branch of Russian Academy of Sciences, Syktyvkar, 167982, Russia
| |
Collapse
|
224
|
Arnold P, Amson E, Fischer MS. Differential scaling patterns of vertebrae and the evolution of neck length in mammals. Evolution 2017; 71:1587-1599. [PMID: 28323340 DOI: 10.1111/evo.13232] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 03/06/2017] [Indexed: 12/13/2022]
Abstract
Almost all mammals have seven vertebrae in their cervical spines. This consistency represents one of the most prominent examples of morphological stasis in vertebrae evolution. Hence, the requirements associated with evolutionary modifications of neck length have to be met with a fixed number of vertebrae. It has not been clear whether body size influences the overall length of the cervical spine and its inner organization (i.e., if the mammalian neck is subject to allometry). Here, we provide the first large-scale analysis of the scaling patterns of the cervical spine and its constituting cervical vertebrae. Our findings reveal that the opposite allometric scaling of C1 and C2-C7 accommodate the increase of neck bending moment with body size. The internal organization of the neck skeleton exhibits surprisingly uniformity in the vast majority of mammals. Deviations from this general pattern only occur under extreme loading regimes associated with particular functional and allometric demands. Our results indicate that the main source of variation in the mammalian neck stems from the disparity of overall cervical spine length. The mammalian neck reveals how evolutionary disparity manifests itself in a structure that is otherwise highly restricted by meristic constraints.
Collapse
Affiliation(s)
- Patrick Arnold
- Institut für Spezielle Zoologie und Evolutionsbiologie mit Phyletischem Museum, Friedrich-Schiller-Universität Jena, Erbert-Straße 1, D-07743, Jena, Germany.,Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany
| | - Eli Amson
- AG Morphologie und Formengeschichte, Bild Wissen Gestaltung-ein interdisziplinäres Labor & Institut für Biologie, Humboldt-Universität zu Berlin, Philippstraße 12/13, D-10115, Berlin, Germany
| | - Martin S Fischer
- Institut für Spezielle Zoologie und Evolutionsbiologie mit Phyletischem Museum, Friedrich-Schiller-Universität Jena, Erbert-Straße 1, D-07743, Jena, Germany
| |
Collapse
|
225
|
Yapuncich GS, Seiffert ER, Boyer DM. Quantification of the position and depth of the flexor hallucis longus groove in euarchontans, with implications for the evolution of primate positional behavior. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2017; 163:367-406. [PMID: 28345775 DOI: 10.1002/ajpa.23213] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 02/28/2017] [Accepted: 03/10/2017] [Indexed: 12/12/2022]
Abstract
OBJECTIVE On the talus, the position and depth of the groove for the flexor hallucis longus tendon have been used to infer phylogenetic affinities and positional behaviors of fossil primates. This study quantifies aspects of the flexor hallucis longus groove (FHLG) to test if: (1) a lateral FHLG is a derived strepsirrhine feature, (2) a lateral FHLG reflects inverted and abducted foot postures, and (3) a deeper FHLG indicates a larger muscle. METHODS We used linear measurements of microCT-generated models from a sample of euarchontans (n = 378 specimens, 125 species) to quantify FHLG position and depth. Data are analyzed with ANOVA, Ordinary and Phylogenetic Generalized Least Squares, and Bayesian Ancestral State Reconstruction (ASR). RESULTS Extant strepsirrhines, adapiforms, plesiadapiforms, dermopterans, and Ptilocercus exhibit lateral FHLGs. Extant anthropoids, subfossil lemurs, and Tupaia have medial FHLGs. FHLGs of omomyiforms and basal fossil anthropoids are intermediate between those of strepsirrhines and extant anthropoids. FHLG position has few correlations with pedal inversion features. Relative FHLG depth is not significantly correlated with body mass. ASRs support a directional model for FHLG position and a random walk model for FHLG depth. CONCLUSIONS The prevalence of lateral FHLGs in many non-euprimates suggests a lateral FHLG is not a derived strepsirrhine feature. The lack of correlations with pedal inversion features suggests a lateral FHLG is not a sufficient indicator of strepsirrhine-like foot postures. Instead, a lateral FHLG may reduce the risk of tendon displacement in abducted foot postures on large diameter supports. A deep FHLG does not indicate a larger muscle, but likely reduces bowstringing during plantarflexion.
Collapse
Affiliation(s)
- Gabriel S Yapuncich
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina
| | - Erik R Seiffert
- Department of Cell and Neurobiology, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Doug M Boyer
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina
| |
Collapse
|
226
|
Primate brain size is predicted by diet but not sociality. Nat Ecol Evol 2017; 1:112. [DOI: 10.1038/s41559-017-0112] [Citation(s) in RCA: 236] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 02/07/2017] [Indexed: 01/24/2023]
|
227
|
Abstract
Rodents are the most commonly used model organisms in studies of aging in vertebrates. However, there are species that may suit this role much better. Most birds (Aves), having higher rate of metabolism, live two-to-three times longer than mammals of the same size. This mini-review briefly covers several evolutionary, ecological, and physiological aspects that may contribute to the phenomenon of birds' longevity. The role of different molecular mechanisms known to take part in the process of aging according to various existing theories, e.g. telomere shortening, protection against reactive oxygen species, and formation of advanced glycation end-products is discussed. We also address some features of birds' aging that make this group unique and perspective model organisms in longevity studies.
Collapse
Affiliation(s)
- D Y Travin
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, 119991, Russia
| | | |
Collapse
|
228
|
Fabris F, Magalhães JPD, Freitas AA. A review of supervised machine learning applied to ageing research. Biogerontology 2017; 18:171-188. [PMID: 28265788 PMCID: PMC5350215 DOI: 10.1007/s10522-017-9683-y] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 02/21/2017] [Indexed: 11/30/2022]
Abstract
Broadly speaking, supervised machine learning is the computational task of learning correlations between variables in annotated data (the training set), and using this information to create a predictive model capable of inferring annotations for new data, whose annotations are not known. Ageing is a complex process that affects nearly all animal species. This process can be studied at several levels of abstraction, in different organisms and with different objectives in mind. Not surprisingly, the diversity of the supervised machine learning algorithms applied to answer biological questions reflects the complexities of the underlying ageing processes being studied. Many works using supervised machine learning to study the ageing process have been recently published, so it is timely to review these works, to discuss their main findings and weaknesses. In summary, the main findings of the reviewed papers are: the link between specific types of DNA repair and ageing; ageing-related proteins tend to be highly connected and seem to play a central role in molecular pathways; ageing/longevity is linked with autophagy and apoptosis, nutrient receptor genes, and copper and iron ion transport. Additionally, several biomarkers of ageing were found by machine learning. Despite some interesting machine learning results, we also identified a weakness of current works on this topic: only one of the reviewed papers has corroborated the computational results of machine learning algorithms through wet-lab experiments. In conclusion, supervised machine learning has contributed to advance our knowledge and has provided novel insights on ageing, yet future work should have a greater emphasis in validating the predictions.
Collapse
Affiliation(s)
- Fabio Fabris
- School of Computing, University of Kent, Canterbury, Kent CT2 7NF UK
| | - João Pedro de Magalhães
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, L7 8TX UK
| | - Alex A. Freitas
- School of Computing, University of Kent, Canterbury, Kent CT2 7NF UK
| |
Collapse
|
229
|
Benton MC, Sutherland HG, Macartney-Coxson D, Haupt LM, Lea RA, Griffiths LR. Methylome-wide association study of whole blood DNA in the Norfolk Island isolate identifies robust loci associated with age. Aging (Albany NY) 2017; 9:753-768. [PMID: 28255110 PMCID: PMC5391229 DOI: 10.18632/aging.101187] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 02/28/2017] [Indexed: 01/07/2023]
Abstract
Epigenetic regulation of various genomic functions, including gene expression, provide mechanisms whereby an organism can dynamically respond to changes in its environment and modify gene expression accordingly. One epigenetic mechanism implicated in human aging and age-related disorders is DNA methylation. Isolated populations such as Norfolk Island (NI) should be advantageous for the identification of epigenetic factors related to aging due to reduced genetic and environmental variation. Here we conducted a methylome-wide association study of age using whole blood DNA in 24 healthy female individuals from the NI genetic isolate (aged 24-47 years). We analysed 450K methylation array data using a machine learning approach (GLMnet) to identify age-associated CpGs. We identified 497 CpG sites, mapping to 422 genes, associated with age, with 11 sites previously associated with age. The strongest associations identified were for a single CpG site in MYOF and an extended region within the promoter of DDO. These hits were validated in curated public data from 2316 blood samples (MARMAL-AID). This study is the first to report robust age associations for MYOF and DDO, both of which have plausible functional roles in aging. This study also illustrates the value of genetic isolates to reveal new associations with epigenome-level data.
Collapse
Affiliation(s)
- Miles C Benton
- Genomics Research Centre, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Kelvin Grove, Queensland, 4059, Australia
| | - Heidi G Sutherland
- Genomics Research Centre, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Kelvin Grove, Queensland, 4059, Australia
| | - Donia Macartney-Coxson
- Kenepuru Science Centre, Institute of Environmental Science and Research, Wellington 5240, New Zealand
| | - Larisa M Haupt
- Genomics Research Centre, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Kelvin Grove, Queensland, 4059, Australia
| | - Rodney A Lea
- Genomics Research Centre, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Kelvin Grove, Queensland, 4059, Australia
| | - Lyn R Griffiths
- Genomics Research Centre, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Kelvin Grove, Queensland, 4059, Australia
| |
Collapse
|
230
|
Kuehne A, Hildebrand J, Soehle J, Wenck H, Terstegen L, Gallinat S, Knott A, Winnefeld M, Zamboni N. An integrative metabolomics and transcriptomics study to identify metabolic alterations in aged skin of humans in vivo. BMC Genomics 2017; 18:169. [PMID: 28201987 PMCID: PMC5312537 DOI: 10.1186/s12864-017-3547-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 02/02/2017] [Indexed: 11/12/2022] Open
Abstract
Background Aging human skin undergoes significant morphological and functional changes such as wrinkle formation, reduced wound healing capacity, and altered epidermal barrier function. Besides known age-related alterations like DNA-methylation changes, metabolic adaptations have been recently linked to impaired skin function in elder humans. Understanding of these metabolic adaptations in aged skin is of special interest to devise topical treatments that potentially reverse or alleviate age-dependent skin deterioration and the occurrence of skin disorders. Results We investigated the global metabolic adaptions in human skin during aging with a combined transcriptomic and metabolomic approach applied to epidermal tissue samples of young and old human volunteers. Our analysis confirmed known age-dependent metabolic alterations, e.g. reduction of coenzyme Q10 levels, and also revealed novel age effects that are seemingly important for skin maintenance. Integration of donor-matched transcriptome and metabolome data highlighted transcriptionally-driven alterations of metabolism during aging such as altered activity in upper glycolysis and glycerolipid biosynthesis or decreased protein and polyamine biosynthesis. Together, we identified several age-dependent metabolic alterations that might affect cellular signaling, epidermal barrier function, and skin structure and morphology. Conclusions Our study provides a global resource on the metabolic adaptations and its transcriptional regulation during aging of human skin. Thus, it represents a first step towards an understanding of the impact of metabolism on impaired skin function in aged humans and therefore will potentially lead to improved treatments of age related skin disorders. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3547-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Andreas Kuehne
- Institute of Molecular Systems Biology, ETH Zurich, Auguste-Piccard-Hof 1, 8093, Zürich, Switzerland.,PhD Program Systems Biology, Life Science Zurich Graduate School, Zurich, Switzerland
| | - Janosch Hildebrand
- Coburg University of Applied Sciences and Arts, Friedrich-Streib-Straße 2, Coburg, 96450, Germany
| | - Joern Soehle
- Beiersdorf AG, R&D, Skin Research Center, Unnastrasse 48, Hamburg, 20253, Germany
| | - Horst Wenck
- Beiersdorf AG, R&D, Skin Research Center, Unnastrasse 48, Hamburg, 20253, Germany
| | - Lara Terstegen
- Beiersdorf AG, R&D, Skin Research Center, Unnastrasse 48, Hamburg, 20253, Germany
| | - Stefan Gallinat
- Beiersdorf AG, R&D, Skin Research Center, Unnastrasse 48, Hamburg, 20253, Germany
| | - Anja Knott
- Beiersdorf AG, R&D, Skin Research Center, Unnastrasse 48, Hamburg, 20253, Germany
| | - Marc Winnefeld
- Beiersdorf AG, R&D, Skin Research Center, Unnastrasse 48, Hamburg, 20253, Germany.
| | - Nicola Zamboni
- Institute of Molecular Systems Biology, ETH Zurich, Auguste-Piccard-Hof 1, 8093, Zürich, Switzerland.
| |
Collapse
|
231
|
Tollis M, Schiffman JD, Boddy AM. Evolution of cancer suppression as revealed by mammalian comparative genomics. Curr Opin Genet Dev 2017; 42:40-47. [DOI: 10.1016/j.gde.2016.12.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 12/19/2016] [Accepted: 12/21/2016] [Indexed: 02/05/2023]
|
232
|
Abstract
Maximal lifespan of mammalian species, even if closely related, may differ more than 10-fold, however the nature of the mechanisms that determine this variability is unresolved. Here, we assess the relationship between maximal lifespan duration and concentrations of more than 20,000 lipid compounds, measured in 669 tissue samples from 6 tissues of 35 species representing three mammalian clades: primates, rodents and bats. We identify lipids associated with species' longevity across the three clades, uncoupled from other parameters, such as basal metabolic rate, body size, or body temperature. These lipids clustered in specific lipid classes and pathways, and enzymes linked to them display signatures of greater stabilizing selection in long-living species, and cluster in functional groups related to signaling and protein-modification processes. These findings point towards the existence of defined molecular mechanisms underlying variation in maximal lifespan among mammals.
Collapse
|
233
|
Wan C, Freitas AA. An empirical evaluation of hierarchical feature selection methods for classification in bioinformatics datasets with gene ontology-based features. Artif Intell Rev 2017. [DOI: 10.1007/s10462-017-9541-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
234
|
Gervasi SS, Stephens PR, Hua J, Searle CL, Xie GY, Urbina J, Olson DH, Bancroft BA, Weis V, Hammond JI, Relyea RA, Blaustein AR. Linking Ecology and Epidemiology to Understand Predictors of Multi-Host Responses to an Emerging Pathogen, the Amphibian Chytrid Fungus. PLoS One 2017; 12:e0167882. [PMID: 28095428 PMCID: PMC5240985 DOI: 10.1371/journal.pone.0167882] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Accepted: 11/22/2016] [Indexed: 12/12/2022] Open
Abstract
Variation in host responses to pathogens can have cascading effects on populations and communities when some individuals or groups of individuals display disproportionate vulnerability to infection or differ in their competence to transmit infection. The fungal pathogen, Batrachochytrium dendrobatidis (Bd) has been detected in almost 700 different amphibian species and is implicated in numerous global amphibian population declines. Identifying key hosts in the amphibian-Bd system–those who are at greatest risk or who pose the greatest risk for others–is challenging due in part to many extrinsic environmental factors driving spatiotemporal Bd distribution and context-dependent host responses to Bd in the wild. One way to improve predictive risk models and generate testable mechanistic hypotheses about vulnerability is to complement what we know about the spatial epidemiology of Bd with data collected through comparative experimental studies. We used standardized pathogen challenges to quantify amphibian survival and infection trajectories across 20 post-metamorphic North American species raised from eggs. We then incorporated trait-based models to investigate the predictive power of phylogenetic history, habitat use, and ecological and life history traits in explaining responses to Bd. True frogs (Ranidae) displayed the lowest infection intensities, whereas toads (Bufonidae) generally displayed the greatest levels of mortality after Bd exposure. Affiliation with ephemeral aquatic habitat and breadth of habitat use were strong predictors of vulnerability to and intensity of infection and several other traits including body size, lifespan, age at sexual maturity, and geographic range also appeared in top models explaining host responses to Bd. Several of the species examined are highly understudied with respect to Bd such that this study represents the first experimental susceptibility data. Combining insights gained from experimental studies with observations of landscape-level disease prevalence may help explain current and predict future pathogen dynamics in the Bd system.
Collapse
Affiliation(s)
- Stephanie S. Gervasi
- Monell Chemical Senses Center, Philadelphia, Pennsylvania, United States of America
- * E-mail:
| | - Patrick R. Stephens
- Odum School of Ecology, University of Georgia, Athens, Georgia, United States of America
| | - Jessica Hua
- Biological Sciences Department, Binghamton University, Binghamton, New York, United States of America
| | - Catherine L. Searle
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America
| | - Gisselle Yang Xie
- Department of Integrative Biology, Oregon State University, Corvallis, Oregon, United States of America
| | - Jenny Urbina
- Environmental Sciences Graduate Program, Oregon State University, Corvallis, Oregon, United States of America
| | - Deanna H. Olson
- United States Forest Service, Pacific Northwest Research Station, Corvallis, Oregon, United States of America
| | - Betsy A. Bancroft
- Biology Department, Gonzaga University, Spokane, Washington, United States of America
| | - Virginia Weis
- Department of Integrative Biology, Oregon State University, Corvallis, Oregon, United States of America
| | - John I. Hammond
- Department of Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Rick A. Relyea
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York, United States of America
| | - Andrew R. Blaustein
- Department of Integrative Biology, Oregon State University, Corvallis, Oregon, United States of America
| |
Collapse
|
235
|
Early-life adversity accelerates cellular ageing and affects adult inflammation: Experimental evidence from the European starling. Sci Rep 2017; 7:40794. [PMID: 28094324 PMCID: PMC5240102 DOI: 10.1038/srep40794] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 12/09/2016] [Indexed: 12/31/2022] Open
Abstract
Early-life adversity is associated with accelerated cellular ageing during development and increased inflammation during adulthood. However, human studies can only establish correlation, not causation, and existing experimental animal approaches alter multiple components of early-life adversity simultaneously. We developed a novel hand-rearing paradigm in European starling nestlings (Sturnus vulgaris), in which we separately manipulated nutritional shortfall and begging effort for a period of 10 days. The experimental treatments accelerated erythrocyte telomere attrition and increased DNA damage measured in the juvenile period. For telomere attrition, amount of food and begging effort exerted additive effects. Only the combination of low food amount and high begging effort increased DNA damage. We then measured two markers of inflammation, high-sensitivity C-reactive protein and interleukin-6, when the birds were adults. The experimental treatments affected both inflammatory markers, though the patterns were complex and different for each marker. The effect of the experimental treatments on adult interleukin-6 was partially mediated by increased juvenile DNA damage. Our results show that both nutritional input and begging effort in the nestling period affect cellular ageing and adult inflammation in the starling. However, the pattern of effects is different for different biomarkers measured at different time points.
Collapse
|
236
|
Kural KC, Tandon N, Skoblov M, Kel-Margoulis OV, Baranova AV. Pathways of aging: comparative analysis of gene signatures in replicative senescence and stress induced premature senescence. BMC Genomics 2016; 17:1030. [PMID: 28105936 PMCID: PMC5249001 DOI: 10.1186/s12864-016-3352-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Background In culturing normal diploid cells, senescence may either happen naturally, in the form of replicative senescence, or it may be a consequence of external challenges such as oxidative stress. Here we present a comparative analysis aimed at reconstruction of molecular cascades specific for replicative (RS) and stressinduced senescence (SIPS) in human fibroblasts. Results An involvement of caspase-3/keratin-18 pathway and serine/threonine kinase Aurora A/ MDM2 pathway was shared between RS and SIPS. Moreover, stromelysin/MMP3 and N-acetylglucosaminyltransferase enzyme MGAT1, which initiates the synthesis of hybrid and complex Nglycans, were identified as key orchestrating components in RS and SIPS, respectively. In RS only, Aurora-B driven cell cycle signaling was deregulated in concert with the suppression of anabolic branches of the fatty acids and estrogen metabolism. In SIPS, Aurora-B signaling is deprioritized, and the synthetic branches of cholesterol metabolism are upregulated, rather than downregulated. Moreover, in SIPS, proteasome/ubiquitin ligase pathways of protein degradation dominate the regulatory landscape. This picture indicates that SIPS proceeds in cells that are actively fighting stress which facilitates premature senescence while failing to completely activate the orderly program of RS. The promoters of genes differentially expressed in either RS or SIPS are unusually enriched by the binding sites for homeobox family proteins, with particular emphasis on HMX1, IRX2, HDX and HOXC13. Additionally, we identified Iroquois Homeobox 2 (IRX2) as a master regulator for the secretion of SPP1-encoded osteopontin, a stromal driver for tumor growth that is overexpressed by both RS and SIPS fibroblasts. The latter supports the hypothesis that senescence-specific de-repression of SPP1 aids in SIPS-dependent stromal activation. Conclusions Reanalysis of previously published experimental data is cost-effective approach for extraction of additional insignts into the functioning of biological systems. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3352-4) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Kamil C Kural
- School of Systems Biology, George Mason University, Manassas, VA, 20110, USA
| | | | - Mikhail Skoblov
- Research Centre for Medical Genetics, Moscow, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny, 141700, Russia
| | | | - Ancha V Baranova
- School of Systems Biology, George Mason University, Manassas, VA, 20110, USA. .,Research Centre for Medical Genetics, Moscow, Russia. .,Moscow Institute of Physics and Technology, Dolgoprudny, 141700, Russia.
| |
Collapse
|
237
|
Liu H, Guo M, Xue T, Guan J, Luo L, Zhuang Z. Screening lifespan-extending drugs in Caenorhabditis elegans via label propagation on drug-protein networks. BMC SYSTEMS BIOLOGY 2016; 10:131. [PMID: 28155715 PMCID: PMC5260106 DOI: 10.1186/s12918-016-0362-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Background One of the most challenging tasks in the exploration of anti-aging is to discover drugs that can promote longevity and delay the incidence of age-associated diseases of human. Up to date, a number of drugs, including some antioxidants, metabolites and synthetic compounds, have been found to effectively delay the aging of nematodes and insects. Results We proposed a label propagation algorithm on drug-protein network to infer drugs that can extend the lifespan of C. elegans. We collected a set of drugs of which functions on lifespan extension of C. elegans have been reliably determined, and then built a large-scale drug-protein network by collecting a set of high-confidence drugprotein interactions. A label propagation algorithm was run on the drug-protein bipartite network to predict new drugs with lifespan-extending effect on C. elegans. We calibrated the performance of the proposed method by conducting performance comparison with two classical models, kNN and SVM. We also showed that the screened drugs significantly mediate in the aging-related pathways, and have higher chemical similarities to the effective drugs than ineffective drugs in promoting longevity of C. elegans. Moreover, we carried out wet-lab experiments to verify a screened drugs, 2- Bromo-4’-nitroacetophenone, and found that it can effectively extend the lifespan of C. elegans. These results showed that our method is effective in screening lifespanextending drugs in C. elegans. Conclusions In this paper, we proposed a semi-supervised algorithm to predict drugs with lifespan-extending effects on C. elegans. In silico empirical evaluations and in vivo experiments in C. elegans have demonstrated that our method can effectively narrow down the scope of candidate drugs needed to be verified by wet lab experiments. Electronic supplementary material The online version of this article (doi:10.1186/s12918-016-0362-4) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Hui Liu
- Changzhou University, Jiangsu, 213164, China.,Changzhou NO. 7 People's Hospital, Changzhou, Jiangsu, 213011, China
| | | | - Ting Xue
- Changzhou University, Jiangsu, 213164, China
| | - Jihong Guan
- Department of Computer Science and Technology, Tongji University, Shanghai, 201804, China
| | - Libo Luo
- Changzhou NO. 7 People's Hospital, Changzhou, Jiangsu, 213011, China. @fudan.edu.cn
| | - Ziheng Zhuang
- Changzhou University, Jiangsu, 213164, China. .,Changzhou NO. 7 People's Hospital, Changzhou, Jiangsu, 213011, China.
| |
Collapse
|
238
|
Malik A, Domankevich V, Lijuan H, Xiaodong F, Korol A, Avivi A, Shams I. Genome maintenance and bioenergetics of the long-lived hypoxia-tolerant and cancer-resistant blind mole rat, Spalax: a cross-species analysis of brain transcriptome. Sci Rep 2016; 6:38624. [PMID: 27934892 PMCID: PMC5146665 DOI: 10.1038/srep38624] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 11/08/2016] [Indexed: 01/09/2023] Open
Abstract
The subterranean blind mole rat, Spalax, experiences acute hypoxia-reoxygenation cycles in its natural subterranean habitat. At the cellular level, these conditions are known to promote genomic instability, which underlies both cancer and aging. However, Spalax is a long-lived animal and is resistant to both spontaneous and induced cancers. To study this apparent paradox we utilized a computational procedure that allows detecting differences in transcript abundance between Spalax and the closely related above-ground Rattus norvegicus in individuals of different ages. Functional enrichment analysis showed that Spalax whole brain tissues maintain significantly higher normoxic mRNA levels of genes associated with DNA damage repair and DNA metabolism, yet keep significantly lower mRNA levels of genes involved in bioenergetics. Many of the genes that showed higher transcript abundance in Spalax are involved in DNA repair and metabolic pathways that, in other species, were shown to be downregulated under hypoxia, yet are required for overcoming replication- and oxidative-stress during the subsequent reoxygenation. We suggest that these differentially expressed genes may prevent the accumulation of DNA damage in mitotic and post-mitotic cells and defective resumption of replication in mitotic cells, thus maintaining genome integrity as an adaptation to acute hypoxia-reoxygenation cycles.
Collapse
Affiliation(s)
- Assaf Malik
- Institue of Evolution, University of Haifa, Haifa 3498838, Israel.,Bioinformatics Core Unit, University of Haifa, Haifa 3498838, Israel
| | - Vered Domankevich
- Institue of Evolution, University of Haifa, Haifa 3498838, Israel.,Deparment of Evolutionary and Environmental Biology, University of Haifa, Haifa 3498838, Israel
| | - Han Lijuan
- BGI-Tech, BGI-Shenzhen, Shenzhen 518083, China
| | | | - Abraham Korol
- Institue of Evolution, University of Haifa, Haifa 3498838, Israel.,Deparment of Evolutionary and Environmental Biology, University of Haifa, Haifa 3498838, Israel
| | - Aaron Avivi
- Institue of Evolution, University of Haifa, Haifa 3498838, Israel
| | - Imad Shams
- Institue of Evolution, University of Haifa, Haifa 3498838, Israel.,Deparment of Evolutionary and Environmental Biology, University of Haifa, Haifa 3498838, Israel
| |
Collapse
|
239
|
Distinct epigenomes in CD4 + T cells of newborns, middle-ages and centenarians. Sci Rep 2016; 6:38411. [PMID: 27917918 PMCID: PMC5137168 DOI: 10.1038/srep38411] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 11/09/2016] [Indexed: 12/22/2022] Open
Abstract
Age-related variations in genes and microRNAs expression and DNA methylation have been reported respectively; however, their interactions during aging are unclear. We therefore investigated alterations in the transcriptomes, miRNAomes and DNA methylomes in the same CD4+T cells from newborn (NB), middle-aged (MA) and long-lived (LL) individuals to elucidate the molecular changes and their interactions. A total 659 genes showed significantly expression changes across NB, MA and LL individuals, in which we identified four age-related co-expression modules with three hub networks of co-expressed genes and non-coding RNAs. Moreover, we identified 9835 differentially methylated regions (DMRs) including 7015 hypermethylated and 2820 hypomethylated DMRs in the NB compared with the MA, and 12,362 DMRs including 4809 hypermethylated and 7553 hypomethylated DMRs in the MA compared with the LL. The integrated analysis revealed a potential relationship between genes transcription and DNA methylation for many age- or immune-related genes, suggesting that DNA methylation-dependent transcription regulation is involved in development and functions of T cells during aging. Our results reveals age-related transcription and methylation changes and their interactions in human T cells from the cradle to the grave. Longitudinal work is required to establish the relationship between identified age-associated genes/DNA methylation and T cells aging phenotypes.
Collapse
|
240
|
Delhaye J, Salamin N, Roulin A, Criscuolo F, Bize P, Christe P. Interspecific correlation between red blood cell mitochondrial ROS production, cardiolipin content and longevity in birds. AGE (DORDRECHT, NETHERLANDS) 2016; 38:433-443. [PMID: 27572896 PMCID: PMC5266217 DOI: 10.1007/s11357-016-9940-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 07/22/2016] [Indexed: 05/29/2023]
Abstract
Mitochondrial respiration releases reactive oxygen species (ROS) as by-products that can damage the soma and may in turn accelerate ageing. Hence, according to "the oxidative stress theory of ageing", longer-lived organisms may have evolved mechanisms that improve mitochondrial function, reduce ROS production and/or increase cell resistance to oxidative damage. Cardiolipin, an important mitochondrial inner-membrane phospholipid, has these properties by binding and stabilizing mitochondrial inner-membrane proteins. Here, we investigated whether ROS production, cardiolipin content and cell membrane resistance to oxidative attack in freshly collected red blood cells (RBCs) are associated with longevity (range 5-35 years) in 21 bird species belonging to seven Orders. After controlling for phylogeny, body size and oxygen consumption, variation in maximum longevity was significantly explained by mitochondrial ROS production and cardiolipin content, but not by membrane resistance to oxidative attack. RBCs of longer-lived species produced less ROS and contained more cardiolipin than RBCs of shorter-lived species did. These results support the oxidative stress theory of ageing and shed light on mitochondrial cardiolipin as an important factor linking ROS production to longevity.
Collapse
Affiliation(s)
- Jessica Delhaye
- Department of Ecology and Evolution, Quartier Sorge, bâtiment Biophore, University of Lausanne, 1015, Lausanne, Switzerland.
| | - Nicolas Salamin
- Department of Ecology and Evolution, Quartier Sorge, bâtiment Biophore, University of Lausanne, 1015, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge, 1015, Lausanne, Switzerland
| | - Alexandre Roulin
- Department of Ecology and Evolution, Quartier Sorge, bâtiment Biophore, University of Lausanne, 1015, Lausanne, Switzerland
| | | | - Pierre Bize
- Department of Ecology and Evolution, Quartier Sorge, bâtiment Biophore, University of Lausanne, 1015, Lausanne, Switzerland
- Institute of Biological and Environmental Sciences, University of Aberdeen, AB24 2TZ, Aberdeen, UK
| | - Philippe Christe
- Department of Ecology and Evolution, Quartier Sorge, bâtiment Biophore, University of Lausanne, 1015, Lausanne, Switzerland
| |
Collapse
|
241
|
|
242
|
Ma S, Upneja A, Galecki A, Tsai YM, Burant CF, Raskind S, Zhang Q, Zhang ZD, Seluanov A, Gorbunova V, Clish CB, Miller RA, Gladyshev VN. Cell culture-based profiling across mammals reveals DNA repair and metabolism as determinants of species longevity. eLife 2016; 5:e19130. [PMID: 27874830 PMCID: PMC5148604 DOI: 10.7554/elife.19130] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Accepted: 11/21/2016] [Indexed: 12/30/2022] Open
Abstract
Mammalian lifespan differs by >100 fold, but the mechanisms associated with such longevity differences are not understood. Here, we conducted a study on primary skin fibroblasts isolated from 16 species of mammals and maintained under identical cell culture conditions. We developed a pipeline for obtaining species-specific ortholog sequences, profiled gene expression by RNA-seq and small molecules by metabolite profiling, and identified genes and metabolites correlating with species longevity. Cells from longer lived species up-regulated genes involved in DNA repair and glucose metabolism, down-regulated proteolysis and protein transport, and showed high levels of amino acids but low levels of lysophosphatidylcholine and lysophosphatidylethanolamine. The amino acid patterns were recapitulated by further analyses of primate and bird fibroblasts. The study suggests that fibroblast profiling captures differences in longevity across mammals at the level of global gene expression and metabolite levels and reveals pathways that define these differences.
Collapse
Affiliation(s)
- Siming Ma
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, United States
| | - Akhil Upneja
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, United States
| | - Andrzej Galecki
- Department of Pathology, University of Michigan Medical School, Ann Arbor, United States
- Geriatrics Center, University of Michigan Medical School, Ann Arbor, United States
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, United States
| | - Yi-Miau Tsai
- Department of Pathology, University of Michigan Medical School, Ann Arbor, United States
- Geriatrics Center, University of Michigan Medical School, Ann Arbor, United States
| | - Charles F Burant
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, United States
| | - Sasha Raskind
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, United States
| | - Quanwei Zhang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, United States
| | - Zhengdong D Zhang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, United States
| | - Andrei Seluanov
- Department of Biology, University of Rochester, Rochester, United States
| | - Vera Gorbunova
- Department of Biology, University of Rochester, Rochester, United States
| | | | - Richard A Miller
- Department of Pathology, University of Michigan Medical School, Ann Arbor, United States
- Geriatrics Center, University of Michigan Medical School, Ann Arbor, United States
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, United States
| |
Collapse
|
243
|
Martinez PA, Jacobina UP, Fernandes RV, Brito C, Penone C, Amado TF, Fonseca CR, Bidau CJ. A comparative study on karyotypic diversification rate in mammals. Heredity (Edinb) 2016; 118:366-373. [PMID: 27804966 DOI: 10.1038/hdy.2016.110] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 09/19/2016] [Accepted: 09/27/2016] [Indexed: 01/23/2023] Open
Abstract
Chromosomal rearrangements have a relevant role in organismic evolution. However, little is known about the mechanisms that lead different phylogenetic clades to have different chromosomal rearrangement rates. Here, we investigate the causes behind the wide karyotypic diversity exhibited by mammals. In particular, we analyzed the role of metabolic, reproductive, biogeographic and genomic characteristics on the rates of macro- and microstructural karyotypic diversification (rKD) using comparative phylogenetic methods. We found evidence that reproductive characteristics such as larger litter size per year and longevity, by allowing a higher number of meioses in absolute time, favor a higher probability of chromosomal change. Furthermore, families with large geographic distributions but containing species with restricted geographic ranges showed a greater probability of fixation of macrostructural chromosomal changes in different geographic areas. Finally, rKD does not evolve by Brownian motion because the mutation rate depends on the concerted evolution of repetitive sequences. The decisive factors of rKD evolution will be natural selection, genetic drift and meiotic drive that will eventually allow or not the fixation of the rearrangements. Our results indicate that mammalian karyotypic diversity is influenced by historical and adaptive mechanisms where reproductive and genomic factors modulate the rate of chromosomal change.
Collapse
Affiliation(s)
- P A Martinez
- PIBi Lab-Laboratorio de Pesquisas Integrativas em Biodiversidade, Pós-Graduação em Ecologia e Conservação, Universidade Federal de Sergipe, São Cristovão, Brazil
| | | | - R V Fernandes
- Departamento de Ecologia, Universidade Federal do Rio Grande do Norte, Natal, Brazil
| | - C Brito
- Departamento de Ecologia, Universidade Federal do Rio Grande do Norte, Natal, Brazil
| | - C Penone
- Institute of Plant Science, University of Bern, Bern, Switzerland
| | - T F Amado
- BioMa-Biodiversity and Macroecology Lab, Department of Biology and Geology, Physics and Inorganic Chemistry, Rey Juan Carlos University, Mostoles, Spain
| | - C R Fonseca
- Departamento de Ecologia, Universidade Federal do Rio Grande do Norte, Natal, Brazil
| | - C J Bidau
- Paraná y Los Claveles, Garupá, Argentina
| |
Collapse
|
244
|
Fabris F, Freitas AA, Tullet JMA. An Extensive Empirical Comparison of Probabilistic Hierarchical Classifiers in Datasets of Ageing-Related Genes. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2016; 13:1045-1058. [PMID: 26661786 DOI: 10.1109/tcbb.2015.2505288] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
This study comprehensively evaluates the performance of five types of probabilistic hierarchical classification methods used for predicting Gene Ontology (GO) terms related to ageing. Of those tested, a new hybrid of a Local Hierarchical Classifier (LHC) and the Predictive Clustering Tree algorithm (LHC-PCT) had the best predictive accuracy results. We also tested the impact of two types of variations in most hierarchical classification algorithms, namely: (a) changing the base algorithm (we tested Naive Bayes and Support Vector Machines), and the impact of (b) using or not the Correlation based Feature Selection (CFS) algorithm in a pre-processing step. In total, we evaluated the predictive performance of 17 variations of hierarchical classifiers across 15 datasets of ageing and longevity-related genes. We conclude that the LHC-PCT algorithm ranks better across several tests (seven out of 12). In addition, we interpreted the models generated by the PCT algorithm to show how hierarchical classification algorithms can be used to extract biological insights out of the ageing-related datasets that we compiled.
Collapse
|
245
|
Kim Y, Nam HG, Valenzano DR. The short-lived African turquoise killifish: an emerging experimental model for ageing. Dis Model Mech 2016; 9:115-29. [PMID: 26839399 PMCID: PMC4770150 DOI: 10.1242/dmm.023226] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Human ageing is a fundamental biological process that leads to functional decay, increased risk for various diseases and, ultimately, death. Some of the basic biological mechanisms underlying human ageing are shared with other organisms; thus, animal models have been invaluable in providing key mechanistic and molecular insights into the common bases of biological ageing. In this Review, we briefly summarise the major applications of the most commonly used model organisms adopted in ageing research and highlight their relevance in understanding human ageing. We compare the strengths and limitations of different model organisms and discuss in detail an emerging ageing model, the short-lived African turquoise killifish. We review the recent progress made in using the turquoise killifish to study the biology of ageing and discuss potential future applications of this promising animal model.
Collapse
Affiliation(s)
- Yumi Kim
- Max Planck Institute for Biology of Ageing, D50931, Cologne, Germany Department of New Biology, DGIST, 711-873, Daegu, Republic of Korea
| | - Hong Gil Nam
- Department of New Biology, DGIST, 711-873, Daegu, Republic of Korea Center for Plant Aging Research, Institute for Basic Science, 711-873, Daegu, Republic of Korea
| | | |
Collapse
|
246
|
Mohlhenrich ER, Mueller RL. Genetic drift and mutational hazard in the evolution of salamander genomic gigantism. Evolution 2016; 70:2865-2878. [DOI: 10.1111/evo.13084] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Revised: 09/27/2016] [Accepted: 09/27/2016] [Indexed: 12/25/2022]
|
247
|
Karabekmez ME, Kirdar B. A novel topological centrality measure capturing biologically important proteins. MOLECULAR BIOSYSTEMS 2016; 12:666-73. [PMID: 26699451 DOI: 10.1039/c5mb00732a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Topological centrality in protein interaction networks and its biological implications have widely been investigated in the past. In the present study, a novel metric of centrality-weighted sum of loads eigenvector centrality (WSL-EC)-based on graph spectra is defined and its performance in identifying topologically and biologically important nodes is comparatively investigated with common metrics of centrality in a human protein-protein interaction network. The metric can capture nodes from peripherals of the network differently from conventional eigenvector centrality. Different metrics were found to selectively identify hub sets that are significantly associated with different biological processes. The widely accepted metrics degree centrality, betweenness centrality, subgraph centrality and eigenvector centrality are subject to a bias towards super-hubs, whereas WSL-EC is not affected by the presence of super-hubs. WSL-EC outperforms other metrics of centrality in detecting biologically central nodes such as pathogen-interacting, cancer, ageing, HIV-1 or disease-related proteins and proteins involved in immune system processes and autoimmune diseases in the human interactome.
Collapse
Affiliation(s)
| | - Betul Kirdar
- Bogazici University, Department of Chemical Engineering, Istanbul, Turkey.
| |
Collapse
|
248
|
Miller EM. The reproductive ecology of iron in women. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2016; 159:S172-95. [PMID: 26808104 DOI: 10.1002/ajpa.22907] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Reproductive ecology focuses on the sensitivity of human reproduction to environmental variation. While reproductive ecology has historically focused on the relationship between energy status and reproductive outcomes, iron status is equally critical to women's reproductive health, given the wide-ranging detrimental effects of iron-deficiency anemia on maternal and infant well-being. This review interprets the vast literature on iron status and women's reproduction through an evolutionary framework. First, it will critique the evidence for iron deficiency caused by blood loss during menstruation, reinterpreting the available data as ecological variation in menses within and between populations of women. Second, it will highlight the scant but growing evidence that iron status is implicated in fertility, a relationship that has deep evolutionary roots. Third, this review proposes a new hypothesis for the transfer of iron from mother to infant via pregnancy and breastfeeding: reproductive iron withholding. In this hypothesis, mothers transfer iron to infants in a manner that helps infants avoid iron-mediated infection and oxidative stress, but trades off with potential risk of maternal and infant iron deficiency. Finally, this review explores two main factors that can modify the relationship between iron status and the gestation-lactation cycle: (1) the relationship between long-term reproductive effort (parity) and iron status and (2) supplementation schemes before and during pregnancy. The review concludes by suggesting continued research into iron homeostasis in women using evolutionary, ecological, and biocultural frameworks.
Collapse
Affiliation(s)
- Elizabeth M Miller
- Department of Anthropology, University of South Florida, Tampa, FL, 33620
| |
Collapse
|
249
|
Castillo-Morales A, Monzón-Sandoval J, de Sousa AA, Urrutia AO, Gutierrez H. Neocortex expansion is linked to size variations in gene families with chemotaxis, cell-cell signalling and immune response functions in mammals. Open Biol 2016; 6:160132. [PMID: 27707894 PMCID: PMC5090057 DOI: 10.1098/rsob.160132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Accepted: 09/08/2016] [Indexed: 11/30/2022] Open
Abstract
Increased brain size is thought to have played an important role in the evolution of mammals and is a highly variable trait across lineages. Variations in brain size are closely linked to corresponding variations in the size of the neocortex, a distinct mammalian evolutionary innovation. The genomic features that explain and/or accompany variations in the relative size of the neocortex remain unknown. By comparing the genomes of 28 mammalian species, we show that neocortical expansion relative to the rest of the brain is associated with variations in gene family size (GFS) of gene families that are significantly enriched in biological functions associated with chemotaxis, cell-cell signalling and immune response. Importantly, we find that previously reported GFS variations associated with increased brain size are largely accounted for by the stronger link between neocortex expansion and variations in the size of gene families. Moreover, genes within these families are more prominently expressed in the human neocortex during early compared with adult development. These results suggest that changes in GFS underlie morphological adaptations during brain evolution in mammalian lineages.
Collapse
Affiliation(s)
- Atahualpa Castillo-Morales
- Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK School of Life Sciences, University of Lincoln, Lincoln LN6 7TS, UK Milner Centre for Evolution, University of Bath, Bath BA2 7YA, UK
| | - Jimena Monzón-Sandoval
- Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK School of Life Sciences, University of Lincoln, Lincoln LN6 7TS, UK Milner Centre for Evolution, University of Bath, Bath BA2 7YA, UK
| | | | - Araxi O Urrutia
- Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK Milner Centre for Evolution, University of Bath, Bath BA2 7YA, UK
| | | |
Collapse
|
250
|
Gao L, Duan DD, Zhang JQ, Zhou YZ, Qin XM, Du GH. A Bioinformatic Approach for the Discovery of Antiaging Effects of Baicalein from Scutellaria baicalensis Georgi. Rejuvenation Res 2016; 19:414-422. [DOI: 10.1089/rej.2015.1760] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Affiliation(s)
- Li Gao
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan, P.R. China
| | - Dan-dan Duan
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan, P.R. China
- College of Chemistry and Chemical Engineering, Shanxi University, Taiyuan, P.R. China
| | - Jian-qin Zhang
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan, P.R. China
| | - Yu-zhi Zhou
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan, P.R. China
| | - Xue-mei Qin
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan, P.R. China
| | - Guan-hua Du
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan, P.R. China
- Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, P.R. China
| |
Collapse
|