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Houldcroft CJ, Underdown S. Infectious disease in the Pleistocene: Old friends or old foes? AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023; 182:513-531. [PMID: 38006200 DOI: 10.1002/ajpa.24737] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 03/01/2023] [Accepted: 03/14/2023] [Indexed: 11/26/2023]
Abstract
The impact of endemic and epidemic disease on humans has traditionally been seen as a comparatively recent historical phenomenon associated with the Neolithisation of human groups, an increase in population size led by sedentarism, and increasing contact with domesticated animals as well as species occupying opportunistic symbiotic and ectosymbiotic relationships with humans. The orthodox approach is that Neolithisation created the conditions for increasing population size able to support a reservoir of infectious disease sufficient to act as selective pressure. This orthodoxy is the result of an overly simplistic reliance on skeletal data assuming that no skeletal lesions equated to a healthy individual, underpinned by the assumption that hunter-gatherer groups were inherently healthy while agricultural groups acted as infectious disease reservoirs. The work of van Blerkom, Am. J. Phys. Anthropol., vol. suppl 37 (2003), Wolfe et al., Nature, vol. 447 (2007) and Houldcroft and Underdown, Am. J. Phys. Anthropol., vol. 160, (2016) has changed this landscape by arguing that humans and pathogens have long been fellow travelers. The package of infectious diseases experienced by our ancient ancestors may not be as dissimilar to modern infectious diseases as was once believed. The importance of DNA, from ancient and modern sources, to the study of the antiquity of infectious disease, and its role as a selective pressure cannot be overstated. Here we consider evidence of ancient epidemic and endemic infectious diseases with inferences from modern and ancient human and hominin DNA, and from circulating and extinct pathogen genomes. We argue that the pandemics of the past are a vital tool to unlock the weapons needed to fight pandemics of the future.
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Affiliation(s)
| | - Simon Underdown
- Human Origins and Palaeoenvironmental Research Group, School of Social Sciences, Oxford Brookes University, Oxford, UK
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
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2
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Hagen EH, Blackwell AD, Lightner AD, Sullivan RJ. Homo medicus: The transition to meat eating increased pathogen pressure and the use of pharmacological plants in Homo. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023; 180:589-617. [PMID: 36815505 DOI: 10.1002/ajpa.24718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 01/31/2023] [Accepted: 02/08/2023] [Indexed: 02/24/2023]
Abstract
The human lineage transitioned to a more carnivorous niche 2.6 mya and evolved a large body size and slower life history, which likely increased zoonotic pathogen pressure. Evidence for this increase includes increased zoonotic infections in modern hunter-gatherers and bushmeat hunters, exceptionally low stomach pH compared to other primates, and divergence in immune-related genes. These all point to change, and probably intensification, in the infectious disease environment of Homo compared to earlier hominins and other apes. At the same time, the brain, an organ in which immune responses are constrained, began to triple in size. We propose that the combination of increased zoonotic pathogen pressure and the challenges of defending a large brain and body from pathogens in a long-lived mammal, selected for intensification of the plant-based self-medication strategies already in place in apes and other primates. In support, there is evidence of medicinal plant use by hominins in the middle Paleolithic, and all cultures today have sophisticated, plant-based medical systems, add spices to food, and regularly consume psychoactive plant substances that are harmful to helminths and other pathogens. We propose that the computational challenges of discovering effective plant-based treatments, the consequent ability to consume more energy-rich animal foods, and the reduced reliance on energetically-costly immune responses helped select for increased cognitive abilities and unique exchange relationships in Homo. In the story of human evolution, which has long emphasized hunting skills, medical skills had an equal role to play.
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Affiliation(s)
- Edward H Hagen
- Department of Anthropology, Washington State University, Pullman, Washington, USA
| | - Aaron D Blackwell
- Department of Anthropology, Washington State University, Pullman, Washington, USA
| | - Aaron D Lightner
- Department of Anthropology, Washington State University, Pullman, Washington, USA
- Department of the Study of Religion, Aarhus University, Aarhus, Denmark
| | - Roger J Sullivan
- Department of Anthropology, California State University, Sacramento, California, USA
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3
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Carvalho PPD, Alves NA. Featuring ACE2 binding SARS-CoV and SARS-CoV-2 through a conserved evolutionary pattern of amino acid residues. J Biomol Struct Dyn 2022; 40:11719-11728. [PMID: 34486937 PMCID: PMC8425439 DOI: 10.1080/07391102.2021.1965028] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Spike (S) glycoproteins mediate the coronavirus entry into the host cell. The S1 subunit of S-proteins contains the receptor-binding domain (RBD) that is able to recognize different host receptors, highlighting its remarkable capacity to adapt to their hosts along the viral evolution. While RBD in spike proteins is determinant for the virus-receptor interaction, the active residues lie at the receptor-binding motif (RBM), a region located in RBD that plays a fundamental role binding the outer surface of their receptors. Here, we address the hypothesis that SARS-CoV and SARS-CoV-2 strains able to use angiotensin-converting enzyme 2 (ACE2) proteins have adapted their RBM along the viral evolution to explore specific conformational topology driven by the residues YGF to infect host cells. We also speculate that this YGF-based mechanism can act as a protein signature located at the RBM to distinguish coronaviruses able to use ACE2 as a cell entry receptor.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Patrícia P. D. Carvalho
- Departamento de Física, FFCLRP, Universidade de São Paulo, Ribeirão Preto, SP, Brazil,CONTACT Patrícia P. D. Carvalho ;
| | - Nelson A. Alves
- Departamento de Física, FFCLRP, Universidade de São Paulo, Ribeirão Preto, SP, Brazil,Nelson Alves
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4
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Santiago-Rodriguez TM, Hollister EB. Unraveling the viral dark matter through viral metagenomics. Front Immunol 2022; 13:1005107. [PMID: 36189246 PMCID: PMC9523745 DOI: 10.3389/fimmu.2022.1005107] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 08/31/2022] [Indexed: 11/13/2022] Open
Abstract
Viruses are part of the microbiome and have essential roles in immunology, evolution, biogeochemical cycles, health, and disease progression. Viruses influence a wide variety of systems and processes, and the continued discovery of novel viruses is anticipated to reveal new mechanisms influencing the biology of diverse environments. While the identity and roles of viruses continue to be discovered and understood through viral metagenomics, most of the sequences in virome datasets cannot be attributed to known viruses or may be only distantly related to species already described in public sequence databases, at best. Such viruses are known as the viral dark matter. Ongoing discoveries from the viral dark matter have provided insights into novel viruses from a variety of environments, as well as their potential in immunological processes, virus evolution, health, disease, therapeutics, and surveillance. Increased understanding of the viral dark matter will continue with a combination of cultivation, microscopy, sequencing, and bioinformatic efforts, which are discussed in the present review.
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5
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Khan T, Rahman M, Ahmed I, Al Ali F, Jithesh PV, Marr N. Human leukocyte antigen class II gene diversity tunes antibody repertoires to common pathogens. Front Immunol 2022; 13:856497. [PMID: 36003377 PMCID: PMC9393332 DOI: 10.3389/fimmu.2022.856497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 07/14/2022] [Indexed: 11/13/2022] Open
Abstract
Allelic diversity of human leukocyte antigen (HLA) class II genes may help maintain humoral immunity against infectious diseases. In this study, we investigated germline genetic variation in classical HLA class II genes and employed a systematic, unbiased approach to explore the relative contribution of this genetic variation in the antibody repertoire to various common pathogens. We leveraged a well-defined cohort of 800 adults representing the general Arab population in which genetic material is shared because of the high frequency of consanguineous unions. By applying a high-throughput method for large-scale antibody profiling to this well-defined cohort, we were able to dissect the overall effect of zygosity for classical HLA class II genes, as well as the effects associated with specific HLA class II alleles, haplotypes and genotypes, on the antimicrobial antibody repertoire breadth and antibody specificity with unprecedented resolution. Our population genetic studies revealed that zygosity of the classical HLA class II genes is a strong predictor of antibody responses to common human pathogens, suggesting that classical HLA class II gene heterozygosity confers a selective advantage. Moreover, we demonstrated that multiple HLA class II alleles can have additive effects on the antibody repertoire to common pathogens. We also identified associations of HLA-DRB1 genotypes with specific antigens. Our findings suggest that HLA class II gene polymorphisms confer specific humoral immunity against common pathogens, which may have contributed to the genetic diversity of HLA class II loci during hominine evolution.
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Affiliation(s)
| | | | | | | | - Puthen Veettil Jithesh
- Research Branch, Sidra Medicine, Doha, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Nico Marr
- Research Branch, Sidra Medicine, Doha, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
- *Correspondence: Nico Marr,
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6
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Dimka J, van Doren TP, Battles HT. Pandemics, past and present: The role of biological anthropology in interdisciplinary pandemic studies. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2022. [PMCID: PMC9082061 DOI: 10.1002/ajpa.24517] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Biological anthropologists are ideally suited for the study of pandemics given their strengths in human biology, health, culture, and behavior, yet pandemics have historically not been a major focus of research. The COVID‐19 pandemic has reinforced the need to understand pandemic causes and unequal consequences at multiple levels. Insights from past pandemics can strengthen the knowledge base and inform the study of current and future pandemics through an anthropological lens. In this paper, we discuss the distinctive social and epidemiological features of pandemics, as well as the ways in which biological anthropologists have previously studied infectious diseases, epidemics, and pandemics. We then review interdisciplinary research on three pandemics–1918 influenza, 2009 influenza, and COVID‐19–focusing on persistent social inequalities in morbidity and mortality related to sex and gender; race, ethnicity, and Indigeneity; and pre‐existing health and disability. Following this review of the current state of pandemic research on these topics, we conclude with a discussion of ways biological anthropologists can contribute to this field moving forward. Biological anthropologists can add rich historical and cross‐cultural depth to the study of pandemics, provide insights into the biosocial complexities of pandemics using the theory of syndemics, investigate the social and health impacts of stress and stigma, and address important methodological and ethical issues. As COVID‐19 is unlikely to be the last global pandemic, stronger involvement of biological anthropology in pandemic studies and public health policy and research is vital.
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Affiliation(s)
- Jessica Dimka
- Centre for Research on Pandemics and Society Oslo Metropolitan University Oslo Norway
| | | | - Heather T. Battles
- Anthropology, School of Social Sciences The University of Auckland Auckland New Zealand
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7
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Sanyal D, Banerjee S, Bej A, Chowdhury VR, Uversky VN, Chowdhury S, Chattopadhyay K. An integrated understanding of the evolutionary and structural features of the SARS-CoV-2 spike receptor binding domain (RBD). Int J Biol Macromol 2022; 217:492-505. [PMID: 35841961 PMCID: PMC9278002 DOI: 10.1016/j.ijbiomac.2022.07.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/29/2022] [Accepted: 07/04/2022] [Indexed: 12/23/2022]
Abstract
Conventional drug development strategies typically use pocket in protein structures as drug-target sites. They overlook the plausible effects of protein evolvability and resistant mutations on protein structure which in turn may impair protein-drug interaction. In this study, we used an integrated evolution and structure guided strategy to develop potential evolutionary-escape resistant therapeutics using receptor binding domain (RBD) of SARS-CoV-2 spike-protein/S-protein as a model. Deploying an ensemble of sequence space exploratory tools including co-evolutionary analysis and deep mutational scans we provide a quantitative insight into the evolutionarily constrained subspace of the RBD sequence-space. Guided by molecular simulation and structure network analysis we highlight regions inside the RBD, which are critical for providing structural integrity and conformational flexibility. Using fuzzy C-means clustering we combined evolutionary and structural features of RBD and identified a critical region. Subsequently, we used computational drug screening using a library of 1615 small molecules and identified one lead molecule, which is expected to target the identified region, critical for evolvability and structural stability of RBD. This integrated evolution-structure guided strategy to develop evolutionary-escape resistant lead molecules have potential general applications beyond SARS-CoV-2.
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Affiliation(s)
- Dwipanjan Sanyal
- Protein Folding and Dynamics Group, Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India
| | - Suharto Banerjee
- Protein Folding and Dynamics Group, Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India
| | - Aritra Bej
- Protein Folding and Dynamics Group, Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India
| | - Vaidehi Roy Chowdhury
- Protein Folding and Dynamics Group, Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA; Laboratory of New Methods in Biology, Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Moscow region 142290, Russia
| | - Sourav Chowdhury
- Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Krishnananda Chattopadhyay
- Protein Folding and Dynamics Group, Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India.
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8
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Nehra M, Kumar V, Kumar R, Dilbaghi N, Kumar S. Current Scenario of Pathogen Detection Techniques in Agro-Food Sector. BIOSENSORS 2022; 12:489. [PMID: 35884292 PMCID: PMC9313409 DOI: 10.3390/bios12070489] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/26/2022] [Accepted: 06/28/2022] [Indexed: 05/05/2023]
Abstract
Over the past-decade, agricultural products (such as vegetables and fruits) have been reported as the major vehicles for foodborne diseases, which are limiting food resources. The spread of infectious diseases due to foodborne pathogens poses a global threat to human health and the economy. The accurate and timely detection of infectious disease and of causative pathogens is crucial in the prevention and treatment of disease. Negligence in the detection of pathogenic substances can be catastrophic and lead to a pandemic. Despite the revolution in health diagnostics, much attention has been paid to the agro-food sector regarding the detection of food contaminants (such as pathogens). The conventional analytical techniques for pathogen detection are reliable and still in operation. However, laborious procedures and time-consuming detection via these approaches emphasize the need for simple, easy-to-use, and affordable detection techniques. The rapid detection of pathogens from food is essential to avoid the morbidity and mortality originating from the suboptimal nature of empiric pathogen treatment. This review critically discusses both the conventional and emerging bio-molecular approaches for pathogen detection in agro-food.
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Affiliation(s)
- Monika Nehra
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar 125001, Haryana, India; (M.N.); (V.K.); (N.D.)
- Department of Mechanical Engineering, University Institute of Engineering and Technology, Panjab University, Chandigarh 160014, India;
| | - Virendra Kumar
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar 125001, Haryana, India; (M.N.); (V.K.); (N.D.)
| | - Rajesh Kumar
- Department of Mechanical Engineering, University Institute of Engineering and Technology, Panjab University, Chandigarh 160014, India;
| | - Neeraj Dilbaghi
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar 125001, Haryana, India; (M.N.); (V.K.); (N.D.)
| | - Sandeep Kumar
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar 125001, Haryana, India; (M.N.); (V.K.); (N.D.)
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9
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La Marca AF, Lopes RDS, Lotufo ADP, Bartholomeu DC, Minussi CR. BepFAMN: A Method for Linear B-Cell Epitope Predictions Based on Fuzzy-ARTMAP Artificial Neural Network. SENSORS (BASEL, SWITZERLAND) 2022; 22:4027. [PMID: 35684648 PMCID: PMC9185646 DOI: 10.3390/s22114027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 05/22/2022] [Accepted: 05/24/2022] [Indexed: 12/02/2022]
Abstract
The public health system is extremely dependent on the use of vaccines to immunize the population from a series of infectious and dangerous diseases, preventing the system from collapsing and millions of people dying every year. However, to develop these vaccines and effectively monitor these diseases, it is necessary to use accurate diagnostic methods capable of identifying highly immunogenic regions within a given pathogenic protein. Existing experimental methods are expensive, time-consuming, and require arduous laboratory work, as they require the screening of a large number of potential candidate epitopes, making the methods extremely laborious, especially for application to larger microorganisms. In the last decades, researchers have developed in silico prediction methods, based on machine learning, to identify these markers, to drastically reduce the list of potential candidate epitopes for experimental tests, and, consequently, to reduce the laborious task associated with their mapping. Despite these efforts, the tools and methods still have low accuracy, slow diagnosis, and offline training. Thus, we develop a method to predict B-cell linear epitopes which are based on a Fuzzy-ARTMAP neural network architecture, called BepFAMN (B Epitope Prediction Fuzzy ARTMAP Artificial Neural Network). This was trained using a linear averaging scheme on 15 properties that include an amino acid ratio scale and a set of 14 physicochemical scales. The database used was obtained from the IEDB website, from which the amino acid sequences with the annotations of their positive and negative epitopes were taken. To train and validate the knowledge models, five-fold cross-validation and competition techniques were used. The BepiPred-2.0 database, an independent database, was used for the tests. In our experiment, the validation dataset reached sensitivity = 91.50%, specificity = 91.49%, accuracy = 91.49%, MCC = 0.83, and an area under the curve (AUC) ROC of approximately 0.9289. The result in the testing dataset achieves a significant improvement, with sensitivity = 81.87%, specificity = 74.75%, accuracy = 78.27%, MCC = 0.56, and AOC = 0.7831. These achieved values demonstrate that BepFAMN outperforms all other linear B-cell epitope prediction tools currently used. In addition, the architecture provides mechanisms for online training, which allow the user to find a new B-cell linear epitope, and to improve the model without need to re-train itself with the whole dataset. This fact contributes to a considerable reduction in the number of potential linear epitopes to be experimentally validated, reducing laboratory time and accelerating the development of diagnostic tests, vaccines, and immunotherapeutic approaches.
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Affiliation(s)
- Anthony F. La Marca
- Electrical Engineering Department, UNESP—São Paulo State University, Av. Brasil 56, Ilha Solteira 15385-000, Brazil; (A.F.L.M.); (A.D.P.L.)
| | - Robson da S. Lopes
- Computer Science Course, UFMT—Mato Grosso Federal University, Av. Valdon Varjão, 6390 Setor Industrial, Barra do Garças 78605-091, Brazil;
| | - Anna Diva P. Lotufo
- Electrical Engineering Department, UNESP—São Paulo State University, Av. Brasil 56, Ilha Solteira 15385-000, Brazil; (A.F.L.M.); (A.D.P.L.)
| | - Daniella C. Bartholomeu
- Parasite Immunology and Genomics Laboratory, Institute of Biological Sciences, Minas Gerais Federal University, Belo Horizonte 31270-901, Brazil;
| | - Carlos R. Minussi
- Electrical Engineering Department, UNESP—São Paulo State University, Av. Brasil 56, Ilha Solteira 15385-000, Brazil; (A.F.L.M.); (A.D.P.L.)
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10
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Ketz AC, Robinson SJ, Johnson CJ, Samuel MD. Pathogen‐mediated selection and management implications for white‐tailed deer exposed to chronic wasting disease. J Appl Ecol 2022. [DOI: 10.1111/1365-2664.14109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Alison C. Ketz
- Wisconsin Cooperative Research Unit Department of Forest and Wildlife Ecology University of Wisconsin Madison WI USA
| | - Stacie J. Robinson
- NOAA Hawaiian Monk Seal Research Program Pacific Islands Fisheries Science Center Honolulu HI USA
| | - Chad J. Johnson
- Medical Microbiology and Immunology University of Wisconsin Madison WI USA
| | - Michael D. Samuel
- Department of Forest and Wildlife Ecology University of Wisconsin Madison WI USA
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11
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Abstract
Blood group systems were the first phenotypic markers used in anthropology to decipher the origin of populations, their migratory movements, and their admixture. The recent emergence of new technologies based on the decoding of nucleic acids from an individual’s entire genome has relegated them to their primary application, blood transfusion. Thus, despite the finer mapping of the modern human genome in relation to Neanderthal and Denisova populations, little is known about red cell blood groups in these archaic populations. Here we analyze the available high-quality sequences of three Neanderthals and one Denisovan individuals for 7 blood group systems that are used today in transfusion (ABO including H/Se, Rh (Rhesus), Kell, Duffy, Kidd, MNS, Diego). We show that Neanderthal and Denisova were polymorphic for ABO and shared blood group alleles recurrent in modern Sub-Saharan populations. Furthermore, we found ABO-related alleles currently preventing from viral gut infection and Neanderthal RHD and RHCE alleles nowadays associated with a high risk of hemolytic disease of the fetus and newborn. Such a common blood group pattern across time and space is coherent with a Neanderthal population of low genetic diversity exposed to low reproductive success and with their inevitable demise. Lastly, we connect a Neanderthal RHD allele to two present-day Aboriginal Australian and Papuan, suggesting that a segment of archaic genome was introgressed in this gene in non-Eurasian populations. While contributing to both the origin and late evolutionary history of Neanderthal and Denisova, our results further illustrate that blood group systems are a relevant piece of the puzzle helping to decipher it.
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12
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Machado MR, Pantano S. Fighting viruses with computers, right now. Curr Opin Virol 2021; 48:91-99. [PMID: 33975154 DOI: 10.1016/j.coviro.2021.04.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/20/2021] [Accepted: 04/06/2021] [Indexed: 10/21/2022]
Abstract
The synergistic conjunction of various technological revolutions with the accumulated knowledge and workflows is rapidly transforming several scientific fields. Particularly, Virology can now feed from accurate physical models, polished computational tools, and massive computational power to readily integrate high-resolution structures into biological representations of unprecedented detail. That preparedness allows for the first time to get crucial information for vaccine and drug design from in-silico experiments against emerging pathogens of worldwide concern at relevant action windows. The present work reviews some of the main milestones leading to these breakthroughs in Computational Virology, providing an outlook for future developments in capacity building and accessibility to computational resources.
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Affiliation(s)
- Matías R Machado
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo, 11400, Uruguay.
| | - Sergio Pantano
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo, 11400, Uruguay.
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13
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Abstract
The medical, public health, and scientific communities are grappling with monumental imperatives to contain COVID-19, develop effective vaccines, identify efficacious treatments for the infection and its complications, and find biomarkers that detect patients at risk of severe disease. The focus of this communication is on a potential biomarker, short telomere length (TL), that might serve to identify patients more likely to die from the SARS-CoV-2 infection, regardless of age. The common thread linking these patients is lymphopenia, which largely reflects a decline in the numbers of CD4/CD8 T cells but not B cells. These findings are consistent with data that lymphocyte TL dynamics impose a limit on T-cell proliferation. They suggest that T-cell lymphopoiesis might stall in individuals with short TL who are infected with SARS-CoV-2.
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Affiliation(s)
- Abraham Aviv
- Center of Human Development and AgingRutgers, The State University of New JerseyNew Jersey Medical SchoolNewarkNJUSA
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14
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Harrison GF, Sanz J, Boulais J, Mina MJ, Grenier JC, Leng Y, Dumaine A, Yotova V, Bergey CM, Nsobya SL, Elledge SJ, Schurr E, Quintana-Murci L, Perry GH, Barreiro LB. Natural selection contributed to immunological differences between hunter-gatherers and agriculturalists. Nat Ecol Evol 2019; 3:1253-1264. [PMID: 31358949 PMCID: PMC6684323 DOI: 10.1038/s41559-019-0947-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 06/17/2019] [Indexed: 11/30/2022]
Abstract
The shift from a hunter-gatherer to an agricultural mode of subsistence is believed to have been associated with profound changes in the burden and diversity of pathogens across human populations. Yet, the extent to which the advent of agriculture affected the evolution of the human immune system remains unknown. Here we present a comparative study of variation in the transcriptional responses of peripheral blood mononuclear cells to bacterial and viral stimuli between Batwa rainforest hunter-gatherers and Bakiga agriculturalists from Uganda. We observed increased divergence between hunter-gatherers and agriculturalists in the early transcriptional response to viruses compared with that for bacterial stimuli. We demonstrate that a significant fraction of these transcriptional differences are under genetic control and we show that positive natural selection has helped to shape population differences in immune regulation. Across the set of genetic variants underlying inter-population immune-response differences, however, the signatures of positive selection were disproportionately observed in the rainforest hunter-gatherers. This result is counter to expectations on the basis of the popularized notion that shifts in pathogen exposure due to the advent of agriculture imposed radically heightened selective pressures in agriculturalist populations.
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Affiliation(s)
- Genelle F Harrison
- Department of Human Genetics, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
- Department of Genetics, CHU Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - Joaquin Sanz
- Department of Genetics, CHU Sainte-Justine Research Center, Montreal, Quebec, Canada
- Department of Biochemistry, Faculty of Medicine, Université de Montréal, Montréal, Quebec, Canada
| | - Jonathan Boulais
- Department of Genetics, CHU Sainte-Justine Research Center, Montreal, Quebec, Canada
- Department of Biochemistry, Faculty of Medicine, Université de Montréal, Montréal, Quebec, Canada
| | - Michael J Mina
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Genetics, Harvard Medical School and Division of Genetics, Brigham and Women's Hospital, Howard Hughes Medical Institute, Boston, MA, USA
| | | | - Yumei Leng
- Department of Genetics, Harvard Medical School and Division of Genetics, Brigham and Women's Hospital, Howard Hughes Medical Institute, Boston, MA, USA
| | - Anne Dumaine
- Department of Genetics, CHU Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - Vania Yotova
- Department of Genetics, CHU Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - Christina M Bergey
- Departments of Anthropology and Biology, Pennsylvania State University, University Park, PA, USA
| | - Samuel L Nsobya
- Department of Pathology, School Biomedical, Makerere University, Kampala, Uganda
| | - Stephen J Elledge
- Department of Genetics, Harvard Medical School and Division of Genetics, Brigham and Women's Hospital, Howard Hughes Medical Institute, Boston, MA, USA
| | - Erwin Schurr
- Department of Human Genetics, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - Lluis Quintana-Murci
- Unit of Human Evolutionary Genetics, Institut Pasteur, Paris, France
- Centre National de la Recherche Scientifique, UMR2000, Paris, France
- Center of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, Paris, France
| | - George H Perry
- Departments of Anthropology and Biology, Pennsylvania State University, University Park, PA, USA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Luis B Barreiro
- Department of Genetics, CHU Sainte-Justine Research Center, Montreal, Quebec, Canada.
- Department of Pediatrics, University of Montreal, Montreal, Quebec, Canada.
- Department of Medicine, Section of Genetic Medicine, University of Chicago, Chicago, IL, USA.
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15
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Emotional expressions of the sick face. Brain Behav Immun 2019; 80:286-291. [PMID: 30953768 DOI: 10.1016/j.bbi.2019.04.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 03/11/2019] [Accepted: 04/02/2019] [Indexed: 11/23/2022] Open
Abstract
To handle the substantial threat posed by infectious diseases, behaviors that promote avoidance of contagion are crucial. Based on the fact that sickness depresses mood and that emotional expressions reveal inner states of individuals to others, which in turn affect approach/avoidance behaviors, we hypothesized that facial expressions of emotion may play a role in sickness detection. Using an experimental model of sickness, 22 volunteers were intravenously injected with either endotoxin (lipopolysaccharide; 2 ng/kg body weight) and placebo using a randomized cross-over design. The volunteers were two hours later asked to keep a relaxed expression on their face while their facial photograph was taken. To assess the emotional expression of the sick face, 49 participants were recruited and were asked to rate the emotional expression of the facial photographs of the volunteers when sick and when healthy. Our results indicate that the emotional expression of faces changed two hours after being made temporarily sick by an endotoxin injection. Sick faces were perceived as more sick/less healthy, but also as expressing more negative emotions, such as sadness and disgust, and less happiness and surprise. The emotional expressions mediated 59.1% of the treatment-dependent change in rated health. The inclusion of physical features associated with emotional expressions to the mediation analysis supported these results. We conclude that emotional expressions may contribute to detection and avoidance of infectious individuals and thereby be part of a behavioral defense against disease.
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16
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Caballero A, Tabernero D, Buti M, Rodriguez-Frias F. Hepatitis B virus: The challenge of an ancient virus with multiple faces and a remarkable replication strategy. Antiviral Res 2018; 158:34-44. [PMID: 30059722 DOI: 10.1016/j.antiviral.2018.07.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 07/24/2018] [Accepted: 07/26/2018] [Indexed: 02/07/2023]
Abstract
The hepatitis B virus (HBV) is the prototype member of the Hepadnaviridae, an ancient family of hepatotropic DNA viruses, which may have originated from 360 to 430 million years ago and with evidence of endogenization in reptilian genomes >200 million years ago. The virus is currently estimated to infect more than 250 million humans. The extremely successful spread of this pathogen among the human population is explained by its multiple particulate forms, effective transmission strategies (particularly perinatal transmission), long induction period and low associated mortality. These characteristics confer selective advantages, enabling the virus to persist in small, disperse populations and spread worldwide, with high prevalence rates in many countries. The HBV replication strategy is remarkably complex and includes a multiplicity of particulate structures. In addition to the common virions containing DNA in a relaxed circular (rcDNA) or double-stranded linear (dslDNA) forms, the viral population includes virion-like particles containing RNA or "empty" (viral envelopes and capsids without genomes), subviral particles (only an envelope) and even naked capsids. Consequently, several forms of the genome coexist in a single infection: (i) the "traveler" forms found in serum, including rcDNA and dslDNA, which originate from retrotranscription of a messenger RNA (the pregenomic RNA, another form of the viral genome itself) and (ii) forms confined to the host cell nucleus, including covalently closed circular DNA (cccDNA), which leads to a minichromosome form associated with histones and viral proteins, and double-stranded DNA integrated into the host genome. This complex composition lends HBV a kind of "multiple personality". Are these additional particles and genomic forms simple intermediaries/artifacts or do they play a role in the viral life cycle?
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Affiliation(s)
- Andrea Caballero
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron and Universitat Autònoma de Barcelona (UAB), 119-129 Passeig Vall d'Hebron, Clinical Laboratories, 08035 Barcelona, Spain.
| | - David Tabernero
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron and Universitat Autònoma de Barcelona (UAB), 119-129 Passeig Vall d'Hebron, Clinical Laboratories, 08035 Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 3-5 Avenida Monforte de Lemos, pavilion 11, 28029 Madrid, Spain.
| | - Maria Buti
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 3-5 Avenida Monforte de Lemos, pavilion 11, 28029 Madrid, Spain; Liver Unit, Department of Internal Medicine, Hospital Universitari Vall d'Hebron and Universitat Autònoma de Barcelona (UAB), 119-129 Passeig Vall d'Hebron, General Hospital, Internal Medicine 2, 08035 Barcelona, Spain.
| | - Francisco Rodriguez-Frias
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron and Universitat Autònoma de Barcelona (UAB), 119-129 Passeig Vall d'Hebron, Clinical Laboratories, 08035 Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 3-5 Avenida Monforte de Lemos, pavilion 11, 28029 Madrid, Spain.
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17
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Mourant JR, Fenimore PW, Manore CA, McMahon BH. Decision Support for Mitigation of Livestock Disease: Rinderpest as a Case Study. Front Vet Sci 2018; 5:182. [PMID: 30234131 PMCID: PMC6129599 DOI: 10.3389/fvets.2018.00182] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 07/17/2018] [Indexed: 12/25/2022] Open
Abstract
A versatile, interactive model to predict geographically resolved epidemic progression after pathogen introduction into a population is presented. Deterministic simulations incorporating a compartmental disease model run rapidly, facilitating the analysis of mitigations such as vaccination and transmission reduction on epidemic spread and progression. We demonstrate the simulation model using rinderpest infection of cattle, a devastating livestock disease. Rinderpest has been extinguished in the wild, but it is still a threat due to stored virus in some laboratories. Comparison of simulations to historical outbreaks provides some validation of the model. Simulations of potential outbreaks demonstrate potential consequences of rinderpest virus release for a variety of possible disease parameters and mitigations. Our results indicate that a rinderpest outbreak could result in severe social and economic consequences.
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Affiliation(s)
- Judith R. Mourant
- Bioscience Division, Los Alamos National Laboratory (DOE), Los Alamos, NM, United States
| | - Paul W. Fenimore
- Theoretical Division, Los Alamos National Laboratory (DOE), Los Alamos, NM, United States
| | - Carrie A. Manore
- Theoretical Division, Los Alamos National Laboratory (DOE), Los Alamos, NM, United States
| | - Benjamin H. McMahon
- Theoretical Division, Los Alamos National Laboratory (DOE), Los Alamos, NM, United States
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18
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Brown MC, Holl EK, Boczkowski D, Dobrikova E, Mosaheb M, Chandramohan V, Bigner DD, Gromeier M, Nair SK. Cancer immunotherapy with recombinant poliovirus induces IFN-dominant activation of dendritic cells and tumor antigen-specific CTLs. Sci Transl Med 2017; 9:eaan4220. [PMID: 28931654 PMCID: PMC6034685 DOI: 10.1126/scitranslmed.aan4220] [Citation(s) in RCA: 169] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 04/10/2017] [Accepted: 08/07/2017] [Indexed: 12/11/2022]
Abstract
Tumors thrive in an immunosuppressive microenvironment that impedes antitumor innate and adaptive immune responses. Thus, approaches that can overcome immunosuppression and engage antitumor immunity are needed. This study defines the adjuvant and cancer immunotherapy potential of the recombinant poliovirus/rhinovirus chimera PVSRIPO. PVSRIPO is currently in clinical trials against recurrent World Health Organization grade IV malignant glioma, a notoriously treatment-refractory cancer. Cytopathogenic infection of neoplastic cells releases the proteome and exposes pathogen- and damage-associated molecular patterns. At the same time, sublethal infection of antigen-presenting cells, such as dendritic cells and macrophages, yields potent, sustained type I interferon-dominant activation in an immunosuppressed microenvironment and promotes the development of tumor antigen-specific T cell responses in vitro and antitumor immunity in vivo. PVSRIPO's immune adjuvancy stimulates canonical innate anti-pathogen inflammatory responses within the tumor microenvironment that culminate in dendritic cell and T cell infiltration. Our findings provide mechanistic evidence that PVSRIPO functions as a potent intratumor immune adjuvant that generates tumor antigen-specific cytotoxic T lymphocyte responses.
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Affiliation(s)
- Michael C Brown
- Department of Neurosurgery, Duke University School of Medicine, Durham, NC 27710, USA
| | - Eda K Holl
- Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
| | - David Boczkowski
- Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
| | - Elena Dobrikova
- Department of Neurosurgery, Duke University School of Medicine, Durham, NC 27710, USA
| | - Mubeen Mosaheb
- Department of Neurosurgery, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Vidya Chandramohan
- Department of Pathology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Darell D Bigner
- Department of Pathology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Matthias Gromeier
- Department of Neurosurgery, Duke University School of Medicine, Durham, NC 27710, USA.
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Smita K Nair
- Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA.
- Department of Pathology, Duke University School of Medicine, Durham, NC 27710, USA
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19
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Taylor JP. Reasoning Improves in Response to Threats of Contagion and Food Contamination. EVOLUTIONARY PSYCHOLOGICAL SCIENCE 2017. [DOI: 10.1007/s40806-017-0088-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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20
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Evolutionary Foundations of Psychiatric Compared to Nonpsychiatric Disorders. EVOLUTIONARY PSYCHOLOGY 2017. [DOI: 10.1007/978-3-319-60576-0_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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21
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Abstract
Human genetic variation is a determinant of nutrient efficacy and of tolerances and intolerances and has the potential to influence nutrient intake values (NIVs). Knowledge derived from the comprehensive identification of human genetic variation offers the potential to predict the physiological and pathological consequences of individual genetic differences and prevent and/or manage adverse outcomes through diet. Nutrients and genomes interact reciprocally; genomes confer differences in nutrient utilization, whereas nutrients effectively modify genome expression, stability, and viability. Understanding the interactions that occur among human genes, including all genetic variants thereof, and environmental exposures is enabling the development of genotype-specific nutritional regimens that prevent disease and promote wellness for individuals and populations throughout the life cycle. Genomic technologies may provide new criteria for establishing NIVs. The impact of a gene variant on NIVs will be dependent on its penetrance and prevalence within a population. Recent experiences indicate that few gene variants are anticipated to be sufficiently penetrant to affect average requirement (AR) values to a greater degree than environmental factors. If highly penetrant gene variants are identified that affect nutrient requirements, the prevalence of the variant in that country or region will determine the feasibility and necessity of deriving more than one AR or upper limit (UL) for affected genetic subgroups.
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Affiliation(s)
- Patrick J Stover
- Division of Nutritional Sciences, Cornell Uniersity, 315 Savage Hall, Ithaca, NY 14853, USA.
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22
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Parker MT. An Ecological Framework of the Human Virome Provides Classification of Current Knowledge and Identifies Areas of Forthcoming Discovery. THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2016; 89:339-351. [PMID: 27698618 PMCID: PMC5045143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Recent advances in sequencing technologies have opened the door for the classification of the human virome. While taxonomic classification can be applied to the viruses identified in such studies, this gives no information as to the type of interaction the virus has with the host. As follow-up studies are performed to address these questions, the description of these virus-host interactions would be greatly enriched by applying a standard set of definitions that typify them. This paper describes a framework with which all members of the human virome can be classified based on principles of ecology. The scaffold not only enables categorization of the human virome, but can also inform research aimed at identifying novel virus-host interactions.
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Affiliation(s)
- Michael T Parker
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
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23
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Rodriguez-Calvo T, Sabouri S, Anquetil F, von Herrath MG. The viral paradigm in type 1 diabetes: Who are the main suspects? Autoimmun Rev 2016; 15:964-9. [PMID: 27491567 DOI: 10.1016/j.autrev.2016.07.019] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 07/08/2016] [Indexed: 12/23/2022]
Abstract
Type 1 diabetes (T1D) is an autoimmune disease characterized by the loss of pancreatic beta cells in the islets of Langerhans. Although genetic predisposition plays an important role in T1D development, studies of identical twins suggest that environmental factors such as viruses and other pathogens may be critical triggers either through direct cytolytic effect and gradual beta cell destruction, or by bystander activation of the immune system. In addition, viruses may circumvent the host immune response and have the capacity to establish chronic lifelong infections. The association of various viral infections with the induction of T1D has been extensively studied at the serological and epidemiological level. However, there is still little evidence from studies of human pancreas to confirm their presence or a causal role in disease pathogenesis. In this review, we identify possible suspects for viral triggers of disease and explain their potential roles in the "viral paradigm" of T1D.
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Affiliation(s)
- Teresa Rodriguez-Calvo
- Type 1 Diabetes Center, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Somayeh Sabouri
- Type 1 Diabetes Center, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Florence Anquetil
- Type 1 Diabetes Center, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Matthias G von Herrath
- Type 1 Diabetes Center, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA; Novo Nordisk Diabetes Research & Development Center, Seattle, WA, USA.
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24
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Velazquez-Salinas L, Zarate S, Eschbaumer M, Pereira Lobo F, Gladue DP, Arzt J, Novella IS, Rodriguez LL. Selective Factors Associated with the Evolution of Codon Usage in Natural Populations of Arboviruses. PLoS One 2016; 11:e0159943. [PMID: 27455096 PMCID: PMC4959722 DOI: 10.1371/journal.pone.0159943] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 07/11/2016] [Indexed: 11/18/2022] Open
Abstract
Arboviruses (arthropod borne viruses) have life cycles that include both vertebrate and invertebrate hosts with substantial differences in vector and host specificity between different viruses. Most arboviruses utilize RNA for their genetic material and are completely dependent on host tRNAs for their translation, suggesting that virus codon usage could be a target for selection. In the current study we analyzed the relative synonymous codon usage (RSCU) patterns of 26 arboviruses together with 25 vectors and hosts, including 8 vertebrates and 17 invertebrates. We used hierarchical cluster analysis (HCA) and principal component analysis (PCA) to identify trends in codon usage. HCA demonstrated that the RSCU of arboviruses reflects that of their natural hosts, but not that of dead-end hosts. Of the two major components identified by PCA, the first accounted for 62.1% of the total variance, and among the 59 codons analyzed in this study, the leucine codon CTG had the highest correlation with the first principal component, however isoleucine had the highest correlation during amino acid analysis. Nucleotide and dinucleotide composition were the variables that explained most of the total codon usage variance. The results suggest that the main factors driving the evolution of codon usage in arboviruses is based on the nucleotide and dinucleotide composition present in the host. Comparing codon usage of arboviruses and potential vector hosts can help identifying potential vectors for emerging arboviruses.
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Affiliation(s)
- Lauro Velazquez-Salinas
- Foreign Animal Disease Research Unit, USDA/ARS Plum Island Animal Disease Center, Orient Point, New York, United States of America.,Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, Tennessee, United States of America
| | - Selene Zarate
- Autonomous University of Mexico City, Genomics Sciences Program, Mexico City, Mexico
| | - Michael Eschbaumer
- Foreign Animal Disease Research Unit, USDA/ARS Plum Island Animal Disease Center, Orient Point, New York, United States of America.,Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, Tennessee, United States of America
| | - Francisco Pereira Lobo
- Laboratório Multiusuário de Bioinformática, Embrapa Informática Agropecuária, Empresa Brasileira de Pesquisa Agropecuária (Embrapa) Campinas, Brazil
| | - Douglas P Gladue
- Foreign Animal Disease Research Unit, USDA/ARS Plum Island Animal Disease Center, Orient Point, New York, United States of America
| | - Jonathan Arzt
- Foreign Animal Disease Research Unit, USDA/ARS Plum Island Animal Disease Center, Orient Point, New York, United States of America
| | - Isabel S Novella
- Department of Medical Microbiology and Immunology, College of Medicine and Life Sciences, The University of Toledo, Toledo, Ohio, United States of America
| | - Luis L Rodriguez
- Foreign Animal Disease Research Unit, USDA/ARS Plum Island Animal Disease Center, Orient Point, New York, United States of America
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25
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Page AE, Viguier S, Dyble M, Smith D, Chaudhary N, Salali GD, Thompson J, Vinicius L, Mace R, Migliano AB. Reproductive trade-offs in extant hunter-gatherers suggest adaptive mechanism for the Neolithic expansion. Proc Natl Acad Sci U S A 2016; 113:4694-9. [PMID: 27071109 PMCID: PMC4855554 DOI: 10.1073/pnas.1524031113] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The Neolithic demographic transition remains a paradox, because it is associated with both higher rates of population growth and increased morbidity and mortality rates. Here we reconcile the conflicting evidence by proposing that the spread of agriculture involved a life history quality-quantity trade-off whereby mothers traded offspring survival for increased fertility, achieving greater reproductive success despite deteriorating health. We test this hypothesis by investigating fertility, mortality, health, and overall reproductive success in Agta hunter-gatherers whose camps exhibit variable levels of sedentarization, mobility, and involvement in agricultural activities. We conducted blood composition tests in 345 Agta and found that viral and helminthic infections as well as child mortality rates were significantly increased with sedentarization. Nonetheless, both age-controlled fertility and overall reproductive success were positively affected by sedentarization and participation in cultivation. Thus, we provide the first empirical evidence, to our knowledge, of an adaptive mechanism in foragers that reconciles the decline in health and child survival with the observed demographic expansion during the Neolithic.
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Affiliation(s)
- Abigail E Page
- Department of Anthropology, University College London, London WC1H 0BW, United Kingdom
| | - Sylvain Viguier
- Department of Anthropology, University College London, London WC1H 0BW, United Kingdom
| | - Mark Dyble
- Department of Anthropology, University College London, London WC1H 0BW, United Kingdom
| | - Daniel Smith
- Department of Anthropology, University College London, London WC1H 0BW, United Kingdom
| | - Nikhil Chaudhary
- Department of Anthropology, University College London, London WC1H 0BW, United Kingdom
| | - Gul Deniz Salali
- Department of Anthropology, University College London, London WC1H 0BW, United Kingdom
| | - James Thompson
- Department of Anthropology, University College London, London WC1H 0BW, United Kingdom
| | - Lucio Vinicius
- Department of Anthropology, University College London, London WC1H 0BW, United Kingdom
| | - Ruth Mace
- Department of Anthropology, University College London, London WC1H 0BW, United Kingdom
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26
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Houldcroft CJ, Underdown SJ. Neanderthal genomics suggests a pleistocene time frame for the first epidemiologic transition. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2016; 160:379-88. [PMID: 27063929 DOI: 10.1002/ajpa.22985] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 02/10/2016] [Accepted: 03/03/2016] [Indexed: 12/13/2022]
Abstract
High quality Altai Neanderthal and Denisovan genomes are revealing which regions of archaic hominin DNA have persisted in the modern human genome. A number of these regions are associated with response to infection and immunity, with a suggestion that derived Neanderthal alleles found in modern Europeans and East Asians may be associated with autoimmunity. As such Neanderthal genomes are an independent line of evidence of which infectious diseases Neanderthals were genetically adapted to. Sympathetically, human genome adaptive introgression is an independent line of evidence of which infectious diseases were important for AMH coming in to Eurasia and interacting with Neanderthals. The Neanderthals and Denisovans present interesting cases of hominin hunter-gatherers adapted to a Eurasian rather than African infectious disease package. Independent sources of DNA-based evidence allow a re-evaluation of the first epidemiologic transition and how infectious disease affected Pleistocene hominins. By combining skeletal, archaeological and genetic evidence from modern humans and extinct Eurasian hominins, we question whether the first epidemiologic transition in Eurasia featured a new package of infectious diseases or a change in the impact of existing pathogens. Coupled with pathogen genomics, this approach supports the view that many infectious diseases are pre-Neolithic, and the list continues to expand. The transfer of pathogens between hominin populations, including the expansion of pathogens from Africa, may also have played a role in the extinction of the Neanderthals and offers an important mechanism to understand hominin-hominin interactions well back beyond the current limits for aDNA extraction from fossils alone. Am J Phys Anthropol 160:379-388, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Charlotte J Houldcroft
- Division of Biological Anthropology, Department of Archaeology & Anthropology, University of Cambridge, Cambridge, CB2 3QG, UK.,Infection, Inflammation and Rheumatology Section, UCL Institute of Child Health, London, WC1N 1EH, UK
| | - Simon J Underdown
- Human Origins and Palaeoenvironmental Research Group (HOPE), Department of Anthropology & Geography, Oxford Brookes University, Oxford, OX3 0BP, UK
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27
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Froeschl G, Ntinginya NE, Sangare A, Lawala P, Mangu C, Dobler G, Heinrich N, Flach B, Nsojo A, Lennemann T. Integrating Local, National, and International Stakeholders in Outbreak Preparedness in Developing Countries: Conclusions from a Conference in Mbeya, Tanzania. Health Secur 2016; 14:29-34. [PMID: 26836445 DOI: 10.1089/hs.2015.0049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A conference called "Outbreaks in Tanzania-Are We Prepared?" was held in Mbeya, Tanzania, on September 14 and 15, 2015, accompanied by a training workshop on infection prevention and control for local stakeholders from September 16 to 18, 2015. The objective of the conference was to revisit past disease epidemics and to reflect on the current status of surveillance and outbreak preparedness in Tanzania, including an overview of agents relevant to biosecurity. The conference brought together national authorities of Tanzania, regional public health representatives, people from research and academic institutions, and international stakeholders. Key findings of the event were: (1) although national frameworks for surveillance and preparedness exist, their implementation presents challenges, and local health structures need support in implementation; (2) the ability to identify and properly manage infectious diseases of public health concern is crucial in empowering the local health workforce to contribute to surveillance measures, which in turn allows for realistic risk assessments and management algorithms; and (3) in settings of limited resources, research activities acquire an additional responsibility toward national surveillance and capacity building and should be integrated into national epidemic preparedness plans. This event was the first of its kind in Tanzania, facilitating direct discussion among regional, zonal, national, and international stakeholders on surveillance and outbreak preparedness. The conference's conclusions are relevant to strengthening health systems in other low- and middle-income countries.
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Abstract
The human-animal interface is as ancient as the first bipedal steps taken by humans. Born with the human species, it has grown and expanded with the human species' prehistoric and historical development to reach the unprecedented scope of current times. Several facets define the human-animal interface, guiding the scope and range of human interactions with animal species. These facets have not ceased to evolve and expand since their emergence, all the more favoring disease emergence. Placing the human-animal interface in its historical perspective allows us to realize its versatile and dynamic nature. Changes in the scope and range of domestication, agriculture, urbanization, colonization, trade, and industrialization have been accompanied by evolving risks for cross-species transmission of pathogens. Because these risks are unlikely to decrease, improving our technologies to identify and monitor pathogenic threats lurking at the human-animal interface should be a priority.
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29
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Cianciulli A, Calvello R, Panaro MA. Determinism and randomness in the evolution of introns and sine inserts in mouse and human mitochondrial solute carrier and cytokine receptor genes. Comput Biol Chem 2015; 55:49-59. [PMID: 25707022 DOI: 10.1016/j.compbiolchem.2015.02.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 02/02/2015] [Accepted: 02/13/2015] [Indexed: 12/16/2022]
Abstract
In the homologous genes studied, the exons and introns alternated in the same order in mouse and human. We studied, in both species: corresponding short segments of introns, whole corresponding introns and complete homologous genes. We considered the total number of nucleotides and the number and orientation of the SINE inserts. Comparisons of mouse and human data series showed that at the level of individual relatively short segments of intronic sequences the stochastic variability prevails in the local structuring, but at higher levels of organization a deterministic component emerges, conserved in mouse and human during the divergent evolution, despite the ample re-editing of the intronic sequences and the fact that processes such as SINE spread had taken place in an independent way in the two species. Intron conservation is negatively correlated with the SINE occupancy, suggesting that virus inserts interfere with the conservation of the sequences inherited from the common ancestor.
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Affiliation(s)
- Antonia Cianciulli
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari,via Orabona, 4, I-70126 Bari, Italy
| | - Rosa Calvello
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari,via Orabona, 4, I-70126 Bari, Italy
| | - Maria A Panaro
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari,via Orabona, 4, I-70126 Bari, Italy.
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30
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Abstract
The common cold is the most frequent, although generally mild, human disease. Human Rhinoviruses are the prevalent causative agents, but other viruses are also implicated. Being so common, viral colds, have significant implications on public health and quality of life, but may also be life-threatening for vulnerable groups of patients. Specific diagnosis and treatment of the common cold still remain unmet needs. Molecular diagnostic techniques allow specific detection of known pathogens as well as the identification of newly emerging viruses. Although a number of medications or natural treatments have been shown to have some effect, either on the number or on the severity of common colds, no single agent is considerably effective. Virus-specific management remains in most cases a challenging potential as many factors have to be taken into account, including the diversity of the viral genomes, the heterogeneity of affected individuals, as well as the complexity of this long standing host-virus relationship.
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Carter CJ. Susceptibility genes are enriched in those of the herpes simplex virus 1/host interactome in psychiatric and neurological disorders. Pathog Dis 2013; 69:240-61. [PMID: 23913659 DOI: 10.1111/2049-632x.12077] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2013] [Revised: 07/11/2013] [Accepted: 07/24/2013] [Indexed: 12/22/2022] Open
Abstract
Herpes simplex virus 1 (HSV-1) can promote beta-amyloid deposition and tau phosphorylation, demyelination or cognitive deficits relevant to Alzheimer's disease or multiple sclerosis and to many neuropsychiatric disorders with which it has been implicated. A seroprevalence much higher than disease incidence has called into question any primary causal role. However, as also the case with risk-promoting polymorphisms (also present in control populations), any causal effects are likely to be conditional. During its life cycle, the virus binds to many proteins and modifies the expression of multiple genes creating a host/pathogen interactome involving 1347 host genes. This data set is heavily enriched in the susceptibility genes for multiple sclerosis (P = 1.3E-99) > Alzheimer's disease > schizophrenia > Parkinsonism > depression > bipolar disorder > childhood obesity > chronic fatigue > autism > and anorexia (P = 0.047) but not attention deficit hyperactivity disorder, a relationship maintained for genome-wide association study data sets in multiple sclerosis and Alzheimer's disease. Overlapping susceptibility gene/interactome data sets disrupt signalling networks relevant to each disease, suggesting that disease susceptibility genes may filter the attentions of the pathogen towards particular pathways and pathologies. In this way, the same pathogen could contribute to multiple diseases in a gene-dependent manner and condition the risk-promoting effects of the genes whose function it disrupts.
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Reperant LA, Cornaglia G, Osterhaus ADME. The importance of understanding the human-animal interface : from early hominins to global citizens. Curr Top Microbiol Immunol 2013. [PMID: 23042568 DOI: 10.1007/82-2012-269] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2023]
Abstract
The complex relationships between the human and animal species have never ceased to evolve since the emergence of the human species and have resulted in a human-animal interface that has promoted the cross-species transmission, emergence and eventual evolution of a plethora of infectious pathogens. Remarkably, most of the characteristics of the human-animal interface-as we know it today-have been established long before the end of our species pre-historical development took place, to be relentlessly shaped throughout the history of our species. More recently, changes affecting the modern human population worldwide as well as their dramatic impact on the global environment have taken domestication, agriculture, urbanization, industrialization, and colonization to unprecedented levels. This has created a unique global multi-faceted human-animal interface, associated with a major epidemiological transition that is accompanied by an unexpected rise of new and emerging infectious diseases. Importantly, these developments are largely paralleled by medical, technological, and scientific progress, continuously spurred by our never-ending combat against pathogens. The human-animal interface has most likely contributed significantly to the evolutionary shaping and historical development of our species. Investment in a better understanding of this human-animal interface will offer humankind a future head-start in the never-ending battle against infectious diseases.
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Affiliation(s)
- Leslie A Reperant
- Department of Virology, Erasmus Medical Centre, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
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The importance of understanding the human-animal interface : from early hominins to global citizens. Curr Top Microbiol Immunol 2012; 365:49-81. [PMID: 23042568 PMCID: PMC7120531 DOI: 10.1007/82_2012_269] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The complex relationships between the human and animal species have never ceased to evolve since the emergence of the human species and have resulted in a human-animal interface that has promoted the cross-species transmission, emergence and eventual evolution of a plethora of infectious pathogens. Remarkably, most of the characteristics of the human-animal interface-as we know it today-have been established long before the end of our species pre-historical development took place, to be relentlessly shaped throughout the history of our species. More recently, changes affecting the modern human population worldwide as well as their dramatic impact on the global environment have taken domestication, agriculture, urbanization, industrialization, and colonization to unprecedented levels. This has created a unique global multi-faceted human-animal interface, associated with a major epidemiological transition that is accompanied by an unexpected rise of new and emerging infectious diseases. Importantly, these developments are largely paralleled by medical, technological, and scientific progress, continuously spurred by our never-ending combat against pathogens. The human-animal interface has most likely contributed significantly to the evolutionary shaping and historical development of our species. Investment in a better understanding of this human-animal interface will offer humankind a future head-start in the never-ending battle against infectious diseases.
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Abstract
Throughout the twentieth century, there were striking increases in the incidences of many chronic inflammatory disorders in the rich developed countries. These included autoimmune disorders such as Type 1 diabetes and multiple sclerosis. Although genetics and specific triggering mechanisms such as molecular mimicry and viruses are likely to be involved, the increases have been so rapid that any explanation that omits environmental change is incomplete. This chapter suggests that a series of environmental factors, most of them microbial, have led to a decrease in the efficiency of our immunoregulatory mechanisms because we are in a state of evolved dependence on organisms with which we co-evolved (and that had to be tolerated) as inducers of immunoregulatory circuits. These organisms ("Old Friends") are depleted from the modern urban environment. Rather than considering fetal programming by maternal microbial exposures, neonatal programming, the hygiene hypothesis, gut microbiota, and diet as separate and competing hypotheses, I attempt here to integrate these ideas under a single umbrella concept that can provide the missing immunoregulatory environmental factor that is needed to explain the recent increases in autoimmune disease.
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Affiliation(s)
- Graham A W Rook
- Department of Infection, Centre for Clinical Microbiology, University College London (UCL), London, UK.
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Costa L, Faustino MAF, Neves MGPMS, Cunha Â, Almeida A. Photodynamic inactivation of mammalian viruses and bacteriophages. Viruses 2012; 4:1034-74. [PMID: 22852040 PMCID: PMC3407894 DOI: 10.3390/v4071034] [Citation(s) in RCA: 141] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Revised: 06/12/2012] [Accepted: 06/13/2012] [Indexed: 11/16/2022] Open
Abstract
Photodynamic inactivation (PDI) has been used to inactivate microorganisms through the use of photosensitizers. The inactivation of mammalian viruses and bacteriophages by photosensitization has been applied with success since the first decades of the last century. Due to the fact that mammalian viruses are known to pose a threat to public health and that bacteriophages are frequently used as models of mammalian viruses, it is important to know and understand the mechanisms and photodynamic procedures involved in their photoinactivation. The aim of this review is to (i) summarize the main approaches developed until now for the photodynamic inactivation of bacteriophages and mammalian viruses and, (ii) discuss and compare the present state of the art of mammalian viruses PDI with phage photoinactivation, with special focus on the most relevant mechanisms, molecular targets and factors affecting the viral inactivation process.
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Affiliation(s)
- Liliana Costa
- Department of Biology and CESAM, University of Aveiro, 3810-193 Aveiro, Portugal; (L.C.); (A.C.)
| | - Maria Amparo F. Faustino
- Department of Chemistry and QOPNA, University of Aveiro, 3810-193 Aveiro, Portugal; (M.A.F.F.); (M.G.P.M.S.N.)
| | - Maria Graça P. M. S. Neves
- Department of Chemistry and QOPNA, University of Aveiro, 3810-193 Aveiro, Portugal; (M.A.F.F.); (M.G.P.M.S.N.)
| | - Ângela Cunha
- Department of Biology and CESAM, University of Aveiro, 3810-193 Aveiro, Portugal; (L.C.); (A.C.)
| | - Adelaide Almeida
- Department of Biology and CESAM, University of Aveiro, 3810-193 Aveiro, Portugal; (L.C.); (A.C.)
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Knapp LA, Innocent SHS. Molecules and mating: positive selection and reproductive behaviour in primates. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 739:218-36. [PMID: 22399405 DOI: 10.1007/978-1-4614-1704-0_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Sexual reproduction is generally thought to be more costly than asexual reproduction. However, it does have the advantage of accelerating rates of adaptation through processes such as recombination and positive selection. Comparative studies of the human and nonhuman primate genomes have demonstrated that positive selection has played an important role in the evolutionary history of humans and other primates. To date, many dozens of genes, thought to be affected by positive selection, have been identified. In this chapter, we will focus on genes that are associated with mating behaviours and reproductive processes, concentrating on genes that are most likely to enhance reproductive success and that also show evidence of positive selection. The genes encode phenotypic features that potentially influence mate choice decisions or impact the evolution and function of genes involved in the perception and regulation of, and the response to, phenotypic signals. We will also consider genes that influence precopulatory behavioural traits in humans and nonhuman primates, such as social bonding and aggression. The evolution of post-copulatory strategies such as sperm competition and selective abortion may also evolve in the presence of intense competition and these adaptations will also be considered. Although behaviour may not be solely determined by genes, the evidence suggests that the genes discussed in this chapter have some influence on human and nonhuman primate behaviour and that positive selection on these genes results in some degree of population differentiation and diversity.
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Affiliation(s)
- Leslie A Knapp
- Primate Immunogenetics and Molecular Ecology Research Group, Department of Biological Anthropology, University of Cambridge, Cambridge, UK.
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Robinson SJ, Samuel MD, Johnson CJ, Adams M, McKenzie DI. Emerging prion disease drives host selection in a wildlife population. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2012; 22:1050-9. [PMID: 22645831 DOI: 10.1890/11-0907.1] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Infectious diseases are increasingly recognized as an important force driving population dynamics, conservation biology, and natural selection in wildlife populations. Infectious agents have been implicated in the decline of small or endangered populations and may act to constrain population size, distribution, growth rates, or migration patterns. Further, diseases may provide selective pressures that shape the genetic diversity of populations or species. Thus, understanding disease dynamics and selective pressures from pathogens is crucial to understanding population processes, managing wildlife diseases, and conserving biological diversity. There is ample evidence that variation in the prion protein gene (PRNP) impacts host susceptibility to prion diseases. Still, little is known about how genetic differences might influence natural selection within wildlife populations. Here we link genetic variation with differential susceptibility of white-tailed deer to chronic wasting disease (CWD), with implications for fitness and disease-driven genetic selection. We developed a single nucleotide polymorphism (SNP) assay to efficiently genotype deer at the locus of interest (in the 96th codon of the PRNP gene). Then, using a Bayesian modeling approach, we found that the more susceptible genotype had over four times greater risk of CWD infection; and, once infected, deer with the resistant genotype survived 49% longer (8.25 more months). We used these epidemiological parameters in a multi-stage population matrix model to evaluate relative fitness based on genotype-specific population growth rates. The differences in disease infection and mortality rates allowed genetically resistant deer to achieve higher population growth and obtain a long-term fitness advantage, which translated into a selection coefficient of over 1% favoring the CWD-resistant genotype. This selective pressure suggests that the resistant allele could become dominant in the population within an evolutionarily short time frame. Our work provides a rare example of a quantifiable disease-driven selection process in a wildlife population, demonstrating the potential for infectious diseases to alter host populations. This will have direct bearing on the epidemiology, dynamics, and future trends in CWD transmission and spread. Understanding genotype-specific epidemiology will improve predictive models and inform management strategies for CWD-affected cervid populations.
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Affiliation(s)
- Stacie J Robinson
- Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Room 208 Russell Labs, 1630 Linden Drive, Madison, Wisconsin 53706, USA.
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Frías-Lasserre D. Non coding RNAs and viruses in the framework of the phylogeny of the genes, epigenesis and heredity. Int J Mol Sci 2012; 13:477-490. [PMID: 22312265 PMCID: PMC3269699 DOI: 10.3390/ijms13010477] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Revised: 12/22/2011] [Accepted: 12/23/2011] [Indexed: 01/21/2023] Open
Abstract
The origin of genes is one of the most enigmatic events in the origin of life. It has been suggested that noncoding (nc) RNA was probably a precursor in the formation of the first polypeptide, and also at the origin of the first manifestation of life and genes. ncRNAs are also becoming central for understanding gene expression and silencing. Indeed, before the discovery of ncRNAs, proteins were viewed as the major molecules in the regulation of gene expression and gene silencing; however, recent findings suggest that ncRNA also plays an important role in gene expression. Reverse transcription of RNA viruses and their integration into the genome of eukaryotes and also their relationship with the ncRNA suggest that their origin is basal in genome evolution, and also probably constitute the first mechanism of gene regulation. I am to review the different roles of ncRNAs in the framework of gene evolution, as well as the importance of ncRNAs and viruses in the epigenesis and in the non-Mendelian model of heredity and evolution.
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Affiliation(s)
- Daniel Frías-Lasserre
- Institute of Entomology, Metropolitan University of Educational Sciences, Avenue J.P. Alessandri 774 Ñuñoa, Código Postal 7760197, Santiago, Chile; E-Mail: ; Tel.: +56-2-2412457; Fax: +56-2-2412699
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Reperant LA, Cornaglia G, Osterhaus ADME. The Importance of Understanding the Human–Animal Interface. Curr Top Microbiol Immunol 2012. [DOI: 10.1007/978-3-662-45792-4_269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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40
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Yezli S, Otter JA. Minimum Infective Dose of the Major Human Respiratory and Enteric Viruses Transmitted Through Food and the Environment. FOOD AND ENVIRONMENTAL VIROLOGY 2011; 3:1-30. [PMID: 35255645 PMCID: PMC7090536 DOI: 10.1007/s12560-011-9056-7] [Citation(s) in RCA: 111] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2011] [Accepted: 02/26/2011] [Indexed: 05/18/2023]
Abstract
Viruses are a significant cause of morbidity and mortality around the world. Determining the minimum dose of virus particles that can initiate infection, termed the minimum infective dose (MID), is important for the development of risk assessment models in the fields of food and water treatment and the implementation of appropriate infection control strategies in healthcare settings. Both respiratory and enteric viruses can be shed at high titers from infected individuals even when the infection is asymptomatic. Presence of pre-existing antibodies has been shown to affect the infectious dose and to be protective against reinfection for many, but not all viruses. Most respiratory viruses appear to be as infective in humans as in tissue culture. Doses of <1 TCID50 of influenza virus, rhinovirus, and adenovirus were reported to infect 50% of the tested population. Similarly, low doses of the enteric viruses, norovirus, rotavirus, echovirus, poliovirus, and hepatitis A virus, caused infection in at least some of the volunteers tested. A number of factors may influence viruses' infectivity in experimentally infected human volunteers. These include host and pathogen factors as well as the experimental methodology. As a result, the reported infective doses of human viruses have to be interpreted with caution.
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Affiliation(s)
- Saber Yezli
- Bioquell UK Ltd, 52 Royce Close, West Portway, Andover, Hampshire, SP10 3TS, UK.
| | - Jonathan A Otter
- Bioquell UK Ltd, 52 Royce Close, West Portway, Andover, Hampshire, SP10 3TS, UK
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Liu Y, Li J. Short regions of sequence identity between the genomes of bacteria and human. Curr Microbiol 2010; 62:770-6. [PMID: 20972791 DOI: 10.1007/s00284-010-9783-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2010] [Accepted: 09/16/2010] [Indexed: 11/26/2022]
Abstract
The interaction between bacteria and human is still incomplete. With the recent availability of many microbial genomes and human genome, as well as the series of basic local alignment search tool (BLAST) programs, a new perspective to gain insight into the interaction between the bacteria and human is possible. This study is to determine the possibility of existence of sequence identity between the genomes of bacteria and human, and try to explain this phenomenon in term of bacteriophages and other genetic mobile elements. BLAST searches of the genomes of bacteria, bacteriophages, and plasmids against human genome were performed using the resources of the National Center for Biotechnology Information (NCBI). All studied bacteria contain variable numbers of short regions of sequence identity to the genome of human, which ranged from 27 to 84 nt. They were found at multiple sites within the human genome. The short regions of sequence identity existed between the genomes of bacteria and human, and a hypothesis that viruses, especially bacteriophages, might play a significant role in shaping the genomes of bacterial and human, and contribute to the short regions of sequence identity is developed.
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Affiliation(s)
- Yudong Liu
- Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100730, People's Republic of China
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42
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Rook GAW. The gut, immunoregulation and micro-organisms from man's evolutionary past. NUTR BULL 2010. [DOI: 10.1111/j.1467-3010.2010.01823.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Rook GAW. 99th Dahlem conference on infection, inflammation and chronic inflammatory disorders: darwinian medicine and the 'hygiene' or 'old friends' hypothesis. Clin Exp Immunol 2010; 160:70-9. [PMID: 20415854 PMCID: PMC2841838 DOI: 10.1111/j.1365-2249.2010.04133.x] [Citation(s) in RCA: 185] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2010] [Indexed: 12/18/2022] Open
Abstract
The current synthesis of the 'hygiene hypothesis' suggests that the recent increase in chronic inflammatory disorders is at least partly attributable to immunodysregulation resulting from lack of exposure to microorganisms that have evolved an essential role in the establishment of the immune system. This document provides a background for discussion of the following propositions. 1. The essential role of these organisms is an example of 'evolved dependence'. 2. The most relevant organisms are those that co-evolved with mammals, and already accompanied early hominids in the Paleolithic. 3. More recently evolved 'childhood infections' are not likely to have evolved this role, and recent epidemiology supports this contention. 4. This mechanism is interacting with other modern environmental changes that also lead to enhanced inflammatory responses [inappropriate diet, obesity, psychological stress, vitamin D deficiency, pollution (dioxins), etc.]. 5. The range of chronic inflammatory disorders that is affected is potentially larger than usually assumed [allergies, autoimmunity, inflammatory bowel disease, but also vascular disease, some cancers, depression/anxiety (when accompanied by raised inflammatory cytokines), and perhaps neurodegenerative disorders and type 2 diabetes].
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Affiliation(s)
- G A W Rook
- Department Infection, University College London (UCL), London, UK.
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44
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Mallet LV, Becq J, Deschavanne P. Whole genome evaluation of horizontal transfers in the pathogenic fungus Aspergillus fumigatus. BMC Genomics 2010; 11:171. [PMID: 20226043 PMCID: PMC2848249 DOI: 10.1186/1471-2164-11-171] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2010] [Accepted: 03/12/2010] [Indexed: 12/14/2022] Open
Abstract
Background Numerous cases of horizontal transfers (HTs) have been described for eukaryote genomes, but in contrast to prokaryote genomes, no whole genome evaluation of HTs has been carried out. This is mainly due to a lack of parametric methods specially designed to take the intrinsic heterogeneity of eukaryote genomes into account. We applied a simple and tested method based on local variations of genomic signatures to analyze the genome of the pathogenic fungus Aspergillus fumigatus. Results We detected 189 atypical regions containing 214 genes, accounting for about 1 Mb of DNA sequences. However, the fraction of atypical DNA detected was smaller than the average amount detected in the same conditions in prokaryote genomes (3.1% vs 5.6%). It appeared that about one third of these regions contained no annotated genes, a proportion far greater than in prokaryote genomes. When analyzing the origin of these HTs by comparing their signatures to a home made database of species signatures, 3 groups of donor species emerged: bacteria (40%), fungi (25%), and viruses (22%). It is to be noticed that though inter-domain exchanges are confirmed, we only put in evidence very few exchanges between eukaryotic kingdoms. Conclusions In conclusion, we demonstrated that HTs are not negligible in eukaryote genomes, bearing in mind that in our stringent conditions this amount is a floor value, though of a lesser extent than in prokaryote genomes. The biological mechanisms underlying those transfers remain to be elucidated as well as the biological functions of the transferred genes.
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Affiliation(s)
- Ludovic V Mallet
- Molécules thérapeutiques in silico (MTI), INSERM UMR-M 973, Université Paris Diderot-Paris 7, Bât Lamarck, 35 rue Hélène Brion, 75205 Paris Cedex 13, France
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Lewis-Rogers N, Crandall KA. Evolution of Picornaviridae: an examination of phylogenetic relationships and cophylogeny. Mol Phylogenet Evol 2009; 54:995-1005. [PMID: 19835964 DOI: 10.1016/j.ympev.2009.10.015] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2009] [Revised: 10/01/2009] [Accepted: 10/08/2009] [Indexed: 10/20/2022]
Abstract
Picornaviruses are responsible for some of the most common and debilitating illnesses affecting humans and animals worldwide. To extend our knowledge of the evolution of picornaviruses and their molecular epidemiology, phylogenetic relationships among 11 genera and the unassigned seal picornavirus type 1 were estimated from the conserved proteins 2C, 3C(pro), and 3D(pol). Each gene was analyzed separately and as a combined dataset. Different tree topologies were recovered from each gene. However, their sequences were determined to be combinable based on our finding of no recombination among genera and failing to reject the hypothesis of homogeneity among datasets using ILD tests. The combined data tree topology was identical to the 3D(pol) gene tree; a topology largely consistent with previous phylogenetic hypotheses based on 3D(pol) and the coding genome. Phylogenetic trees estimated from six phenotypic characters were not congruent with those recovered from molecular datasets; further supporting the hypothesis that viral phenotypes are highly plastic. Finally, we tested the hypothesis of host-virus cophylogeny. Both global and individual tests of the relationships between host and virus trees failed to detect a significant association. These results emphasize the importance of horizontal transmission among host species for picornavirus diversification rather than vertical transmission accompanying speciation.
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Affiliation(s)
- Nicole Lewis-Rogers
- Department of Biology, Brigham Young University, 401 WIDB, Provo, UT 84602, USA.
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46
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Kumlin U, Olofsson S, Dimock K, Arnberg N. Sialic acid tissue distribution and influenza virus tropism. Influenza Other Respir Viruses 2009; 2:147-54. [PMID: 19453419 PMCID: PMC4941897 DOI: 10.1111/j.1750-2659.2008.00051.x] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Abstract Avian influenza A viruses exhibit a strong preference for using α2,3‐linked sialic acid as a receptor. Until recently, the presumed lack of this receptor in human airways was believed to constitute an efficient barrier to avian influenza A virus infection of humans. Recent zoonotic outbreaks of avian influenza A virus have triggered researchers to analyse tissue distribution of sialic acid in further detail. Here, we review and extend the current knowledge about sialic acid distribution in human tissues, and discuss viruses with ocular tropism and their preference for α2,3‐linked sialic acid.
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Affiliation(s)
- Urban Kumlin
- Department of Clinical Microbiology, Division of Virology, Umeå University, Umeå, Sweden
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47
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Greger M. The Human/Animal Interface: Emergence and Resurgence of Zoonotic Infectious Diseases. Crit Rev Microbiol 2008; 33:243-99. [DOI: 10.1080/10408410701647594] [Citation(s) in RCA: 122] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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48
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Gage TB. Are modern environments really bad for us?: revisiting the demographic and epidemiologic transitions. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2006; Suppl 41:96-117. [PMID: 16369962 DOI: 10.1002/ajpa.20353] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
It is a common assumption that agriculture and modernization have been detrimental for human health. The theoretical argument is that humans are adapted to hunter-gatherer lifestyles, and that the agricultural and "modern" environments are novel and hence likely to be detrimental. In particular, changes in nutrition, and population size and distribution with the adoption of agriculture, are considered to increase the risk of infectious disease mortality. Similarly, changes due to modern lifestyles, notably changes in nutrition, smoking, exercise, and stress, are thought to be associated with an increased risk of degenerative disease mortality in the industrial environment. This paper reviews the available literature on the history and prehistory of total mortality (the demographic transition) and cause of death (the epidemiologic transition), and finds that neither agriculture nor modernization is associated with increases in mortality, i.e., declines in health. First, mortality does not appear to have increased during the transition to agriculture, or during the early phases of the industrial revolution. Clearly, infectious diseases have declined with modernization. Second, the empirical data, when uncorrected for misclassification of cause of death, do suggest an increase in degenerative disease mortality, at least until the mid 20th century, when these causes of death clearly began to decline. All studies that correct for misclassification of cause of death, however, find that the general decline in degenerative disease mortality began much earlier, perhaps as early as the 1850s in the developed countries. This is about the same time that infectious disease mortality began to decline in these countries. The exception is neoplasms, which increased with modernization until quite recently. Part of the increase in neoplasms may be attributable to increases in smoking during the course of modernization. Nevertheless, the overall risk of degenerative disease mortality appears to have declined with modernization. The fact that the decline in the risk of infectious disease mortality, and the decline in risk of degenerative disease mortality, are largely coordinated suggests that the causes of both declines may be related. Historical trends in morbidity, and potential causes of the decline in infectious and degenerative disease mortality, are briefly considered.
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Affiliation(s)
- Timothy B Gage
- Department of Anthropology and Department of Epidemiology, University at Albany-SUNY, Albany, New York 12222, USA.
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49
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COMMENTARIES ON Evolutionary Foundations of Cultural Variation: Evoked Culture and Mate Preferences. PSYCHOLOGICAL INQUIRY 2006. [DOI: 10.1207/s15327965pli1702_2] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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