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Qu Y, Chen C, Xiong Y, She H, Zhang YE, Cheng Y, DuBay S, Li D, Ericson PGP, Hao Y, Wang H, Zhao H, Song G, Zhang H, Yang T, Zhang C, Liang L, Wu T, Zhao J, Gao Q, Zhai W, Lei F. Rapid phenotypic evolution with shallow genomic differentiation during early stages of high elevation adaptation in Eurasian Tree Sparrows. Natl Sci Rev 2019; 7:113-127. [PMID: 34692022 PMCID: PMC8289047 DOI: 10.1093/nsr/nwz138] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 08/31/2019] [Accepted: 09/01/2019] [Indexed: 02/06/2023] Open
Abstract
Abstract
Known as the ‘third polar region’, the Qinghai-Tibet Plateau represents one of the harshest highland environments in the world and yet a number of organisms thrive there. Previous studies of birds, animals and humans have focused on well-differentiated populations in later stages of phenotypic divergence. The adaptive processes during the initial phase of highland adaptation remain poorly understood. We studied a human commensal, the Eurasian Tree Sparrow, which has followed human agriculture to the Qinghai-Tibet Plateau. Despite strong phenotypic differentiation at multiple levels, in particular in muscle-related phenotypes, highland and lowland populations show shallow genomic divergence and the colonization event occurred within the past few thousand years. In a one-month acclimation experiment investigating phenotypic plasticity, we exposed adult lowland tree sparrows to a hypoxic environment and did not observe muscle changes. Through population genetic analyses, we identified a signature of polygenic adaptation, whereby shifts in allele frequencies are spread across multiple loci, many of which are associated with muscle-related processes. Our results reveal a case of positive selection in which polygenic adaptation appears to drive rapid phenotypic evolution, shedding light on early stages of adaptive evolution to a novel environment.
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Affiliation(s)
- Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chunhai Chen
- BGI Genomics, BGI-Shenzhen, Shenzhen 518084, China
| | - Ying Xiong
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huishang She
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yong E Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Yalin Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shane DuBay
- Committee on Evolutionary Biology, University of Chicago, Chicago, IL 60637, USA
- Life Sciences Section, Integrative Research Center, Field Museum of Natural History, Chicago, IL 60605, USA
| | - Dongming Li
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Per G P Ericson
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-104 05 Stockholm, Sweden
| | - Yan Hao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongyuan Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Hongfeng Zhao
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hailin Zhang
- BGI Genomics, BGI-Shenzhen, Shenzhen 518084, China
| | - Ting Yang
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Chi Zhang
- BGI Genomics, BGI-Shenzhen, Shenzhen 518084, China
| | - Liping Liang
- BGI Genomics, BGI-Shenzhen, Shenzhen 518084, China
| | - Tianyu Wu
- BGI Genomics, BGI-Shenzhen, Shenzhen 518084, China
| | - Jinyang Zhao
- BGI Genomics, BGI-Shenzhen, Shenzhen 518084, China
| | - Qiang Gao
- BGI Genomics, BGI-Shenzhen, Shenzhen 518084, China
| | - Weiwei Zhai
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
- Human Genetics, Genome Institute of Singapore, Agency for Science, Technology, and Research, Singapore 138672, Singapore
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
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2
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Gazal S, Espinoza JR, Austerlitz F, Marchant D, Macarlupu JL, Rodriguez J, Ju-Preciado H, Rivera-Chira M, Hermine O, Leon-Velarde F, Villafuerte FC, Richalet JP, Gouya L. The Genetic Architecture of Chronic Mountain Sickness in Peru. Front Genet 2019; 10:690. [PMID: 31417607 PMCID: PMC6682665 DOI: 10.3389/fgene.2019.00690] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 07/02/2019] [Indexed: 12/23/2022] Open
Abstract
Chronic mountain sickness (CMS) is a pathological condition resulting from chronic exposure to high-altitude hypoxia. While its prevalence is high in native Andeans (>10%), little is known about the genetic architecture of this disease. Here, we performed the largest genome-wide association study (GWAS) of CMS (166 CMS patients and 146 controls living at 4,380 m in Peru) to detect genetic variants associated with CMS. We highlighted four new candidate loci, including the first CMS-associated variant reaching GWAS statistical significance (rs7304081; P = 4.58 × 10−9). By looking at differentially expressed genes between CMS patients and controls around these four loci, we suggested AEBP2, CAST, and MCTP2 as candidate CMS causal genes. None of the candidate loci were under strong natural selection, consistent with the observation that CMS affects fitness mainly after the reproductive years. Overall, our results reveal new insights on the genetic architecture of CMS and do not provide evidence that CMS-associated variants are linked to a strong ongoing adaptation to high altitude.
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Affiliation(s)
- Steven Gazal
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, United States.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, United States.,INSERM, Infection, Antimicrobials, Modelling, Evolution (IAME), UMR 1137, Paris, France.,Plateforme de génomique constitutionnelle du GHU Nord, Assistance Publique des Hôpitaux de Paris (APHP), Hôpital Bichat, Paris, France
| | - Jose R Espinoza
- Laboratorio de Biotecnología Molecular-LID, Departamento de Ciencias Celulares y Moleculares, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Frédéric Austerlitz
- UMR CNRS 7206 Eco-Anthropologie et Ethnobiologie, Musée de l'Homme, Paris, France
| | - Dominique Marchant
- Université Paris 13, Sorbonne Paris Cité, INSERM UMR 1272 Hypoxie et Poumon, Bobigny, France
| | - Jose Luis Macarlupu
- Laboratorio de Fisiología Comparada/Fisiología de Adaptación a la Altura-LID, Departamento de Ciencias Biológicas y Fisiológicas, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Jorge Rodriguez
- Laboratorio de Biotecnología Molecular-LID, Departamento de Ciencias Celulares y Moleculares, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Hugo Ju-Preciado
- Laboratorio de Fisiología Comparada/Fisiología de Adaptación a la Altura-LID, Departamento de Ciencias Biológicas y Fisiológicas, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Maria Rivera-Chira
- Laboratorio de Fisiología Comparada/Fisiología de Adaptación a la Altura-LID, Departamento de Ciencias Biológicas y Fisiológicas, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Olivier Hermine
- Université Paris Descartes, Institut National de la Santé et de la Recherche Médicale Unité 1163, Centre National de la Recherche Scientifique, Equipes de Recherche Labellisées 8254, Institut Imagine, Paris, France.,Laboratoire d'Excellence, Globule Rouge-Excellence, Paris, France
| | - Fabiola Leon-Velarde
- Laboratorio de Fisiología Comparada/Fisiología de Adaptación a la Altura-LID, Departamento de Ciencias Biológicas y Fisiológicas, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Francisco C Villafuerte
- Laboratorio de Fisiología Comparada/Fisiología de Adaptación a la Altura-LID, Departamento de Ciencias Biológicas y Fisiológicas, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Jean-Paul Richalet
- Université Paris 13, Sorbonne Paris Cité, INSERM UMR 1272 Hypoxie et Poumon, Bobigny, France.,Laboratoire d'Excellence, Globule Rouge-Excellence, Paris, France
| | - Laurent Gouya
- Laboratoire d'Excellence, Globule Rouge-Excellence, Paris, France.,Université Paris Diderot, INSERM U1149, Hème, fer et pathologies inflammatoires, Assistance Publique des Hôpitaux de Paris (APHP), Hôpital Louis Mourier, Paris, France
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3
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Ivy CM, Scott GR. Ventilatory acclimatization to hypoxia in mice: Methodological considerations. Respir Physiol Neurobiol 2016; 235:95-103. [PMID: 27989891 DOI: 10.1016/j.resp.2016.10.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 09/30/2016] [Accepted: 10/27/2016] [Indexed: 01/15/2023]
Abstract
We examined ventilatory acclimatization to hypoxia (VAH) in CD1 mice, and contrasted results obtained using the barometric method on unrestrained mice with pneumotachography and pulse oximetry on restrained mice. Responses to progressive step reductions in O2 fraction (21%-8%) were assessed in mice acclimated to normoxia and hypobaric hypoxia (barometric pressure of 60kPa for 6-8 weeks). Hypoxia acclimation increased the hypoxic ventilatory response (primarily by increasing breathing frequency rather than tidal volume), arterial O2 saturation (SaO2) and heart rate in deep hypoxia, hypoxic chemosensitivity (ventilatory O2/CO2 equivalents versus SaO2), and respiratory water loss, and it blunted the hypoxic depression of metabolism and body temperature. Although some effects of hypoxia acclimation were qualitatively similar between methods, the effects were often greater in magnitude when assessed using pneumotachography. Furthermore, whereas hypoxia acclimation reduced ventilatory O2 equivalent and increased pulmonary O2 extraction in barometric experiments, it had the opposite effects in pneumotachography experiments. Our findings highlight the importance of considering the impact of how breathing is measured on the apparent responses to hypoxia.
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Affiliation(s)
- Catherine M Ivy
- Department of Biology, McMaster University, Hamilton, ON, Canada.
| | - Graham R Scott
- Department of Biology, McMaster University, Hamilton, ON, Canada
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4
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Samillan V, Haider T, Vogel J, Leuenberger C, Brock M, Schwarzwald C, Gassmann M, Ostergaard L. Combination of erythropoietin and sildenafil can effectively attenuate hypoxia-induced pulmonary hypertension in mice. Pulm Circ 2014; 3:898-907. [PMID: 25006406 DOI: 10.1086/674758] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Accepted: 08/22/2013] [Indexed: 12/12/2022] Open
Abstract
Pulmonary hypertension (PH) is an incurable disease that often leads to right ventricular hypertrophy and right heart failure. This study investigated single versus combined therapy with sildenafil and erythropoietin on hypoxia-induced pulmonary hypertension in mice. Mice were randomized into 5 groups and exposed to either hypoxia (10% oxygen) or normoxia for a total of 5 weeks. Hypoxic mice were treated with saline solution, erythropoietin (500 IU/kg 3 times weekly), sildenafil (10 mg/kg daily), or a combination of the two drugs for the last 2 weeks of hypoxic exposure. We measured right ventricular pressures using right heart catheterization, and the ventilatory response to hypoxia was recorded via whole-body plethysmography. Histological analyses were performed to elucidate changes in pulmonary morphology and appearance of right heart hypertrophy. Plasma levels of cardiotrophin-1 and atrial natriuretic peptide were quantified. Treatment with either erythropoietin or sildenafil alone lowered the hypoxia-induced increase of pulmonary pressure and reduced pulmonary edema formation, pulmonary vascular remodeling, and right ventricular hypertrophy. Notably, the combination of the two drugs had the most prominent effect. Changes in cardiotrophin-1 and atrial natriuretic protein levels confirmed these observations. The combination treatment with erythropoietin and sildenafil demonstrated an attenuation of the development of hypoxia-induced PH in mice that was superior to that observed for either drug when given alone.
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Affiliation(s)
- Victor Samillan
- Institute for Veterinary Physiology, Vetsuisse Faculty, Zurich, Switzerland ; Zurich Center for Integrative Human Physiology, Zurich, Switzerland ; Human Physiology Department, Medical School, Universidad Alas Peruanas, Lima, Peru
| | - Thomas Haider
- Institute for Veterinary Physiology, Vetsuisse Faculty, Zurich, Switzerland ; Zurich Center for Integrative Human Physiology, Zurich, Switzerland
| | - Johannes Vogel
- Institute for Veterinary Physiology, Vetsuisse Faculty, Zurich, Switzerland ; Zurich Center for Integrative Human Physiology, Zurich, Switzerland
| | - Caroline Leuenberger
- Institute for Veterinary Physiology, Vetsuisse Faculty, Zurich, Switzerland ; Institute of Human Movement Sciences and Sport, ETH Zurich, Zurich, Switzerland
| | - Matthias Brock
- Institute for Veterinary Physiology, Vetsuisse Faculty, Zurich, Switzerland ; Division of Pulmonology, University Hospital Zurich, Zurich, Switzerland
| | - Colin Schwarzwald
- Equine Department, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Max Gassmann
- Institute for Veterinary Physiology, Vetsuisse Faculty, Zurich, Switzerland ; Zurich Center for Integrative Human Physiology, Zurich, Switzerland ; Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Louise Ostergaard
- Institute for Veterinary Physiology, Vetsuisse Faculty, Zurich, Switzerland ; Zurich Center for Integrative Human Physiology, Zurich, Switzerland
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5
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Substance P differentially modulates firing rate of solitary complex (SC) neurons from control and chronic hypoxia-adapted adult rats. PLoS One 2014; 9:e88161. [PMID: 24516602 PMCID: PMC3917864 DOI: 10.1371/journal.pone.0088161] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 01/03/2014] [Indexed: 11/19/2022] Open
Abstract
NK1 receptors, which bind substance P, are present in the majority of brainstem regions that contain CO2/H(+)-sensitive neurons that play a role in central chemosensitivity. However, the effect of substance P on the chemosensitive response of neurons from these regions has not been studied. Hypoxia increases substance P release from peripheral afferents that terminate in the caudal nucleus tractus solitarius (NTS). Here we studied the effect of substance P on the chemosensitive responses of solitary complex (SC: NTS and dorsal motor nucleus) neurons from control and chronic hypoxia-adapted (CHx) adult rats. We simultaneously measured intracellular pH and electrical responses to hypercapnic acidosis in SC neurons from control and CHx adult rats using the blind whole cell patch clamp technique and fluorescence imaging microscopy. Substance P significantly increased the basal firing rate in SC neurons from control and CHx rats, although the increase was smaller in CHx rats. However, substance P did not affect the chemosensitive response of SC neurons from either group of rats. In conclusion, we found that substance P plays a role in modulating the basal firing rate of SC neurons but the magnitude of the effect is smaller for SC neurons from CHx adult rats, implying that NK1 receptors may be down regulated in CHx adult rats. Substance P does not appear to play a role in modulating the firing rate response to hypercapnic acidosis of SC neurons from either control or CHx adult rats.
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6
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Naeije R, Vanderpool R. Pulmonary Hypertension and Chronic Mountain Sickness. High Alt Med Biol 2013; 14:117-25. [DOI: 10.1089/ham.2012.1124] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Affiliation(s)
- Robert Naeije
- Department of Pathophysiology, Faculty of Medicine, Free University of Brussels, Brussels, Belgium
| | - Rebecca Vanderpool
- Department of Pathophysiology, Faculty of Medicine, Free University of Brussels, Brussels, Belgium
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7
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Teppema LJ, Dahan A. The Ventilatory Response to Hypoxia in Mammals: Mechanisms, Measurement, and Analysis. Physiol Rev 2010; 90:675-754. [DOI: 10.1152/physrev.00012.2009] [Citation(s) in RCA: 257] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The respiratory response to hypoxia in mammals develops from an inhibition of breathing movements in utero into a sustained increase in ventilation in the adult. This ventilatory response to hypoxia (HVR) in mammals is the subject of this review. The period immediately after birth contains a critical time window in which environmental factors can cause long-term changes in the structural and functional properties of the respiratory system, resulting in an altered HVR phenotype. Both neonatal chronic and chronic intermittent hypoxia, but also chronic hyperoxia, can induce such plastic changes, the nature of which depends on the time pattern and duration of the exposure (acute or chronic, episodic or not, etc.). At adult age, exposure to chronic hypoxic paradigms induces adjustments in the HVR that seem reversible when the respiratory system is fully matured. These changes are orchestrated by transcription factors of which hypoxia-inducible factor 1 has been identified as the master regulator. We discuss the mechanisms underlying the HVR and its adaptations to chronic changes in ambient oxygen concentration, with emphasis on the carotid bodies that contain oxygen sensors and initiate the response, and on the contribution of central neurotransmitters and brain stem regions. We also briefly summarize the techniques used in small animals and in humans to measure the HVR and discuss the specific difficulties encountered in its measurement and analysis.
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Affiliation(s)
- Luc J. Teppema
- Department of Anesthesiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Albert Dahan
- Department of Anesthesiology, Leiden University Medical Center, Leiden, The Netherlands
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8
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Nichols NL, Wilkinson KA, Powell FL, Dean JB, Putnam RW. Chronic hypoxia suppresses the CO2 response of solitary complex (SC) neurons from rats. Respir Physiol Neurobiol 2009; 168:272-80. [PMID: 19619674 DOI: 10.1016/j.resp.2009.07.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2008] [Revised: 07/12/2009] [Accepted: 07/13/2009] [Indexed: 11/17/2022]
Abstract
We studied the effect of chronic hypobaric hypoxia (CHx; 10-11% O(2)) on the response to hypercapnia (15% CO(2)) of individual solitary complex (SC) neurons from adult rats. We simultaneously measured the intracellular pH and firing rate responses to hypercapnia of SC neurons in superfused medullary slices from control and CHx-adapted adult rats using the blind whole cell patch clamp technique and fluorescence imaging microscopy. We found that CHx caused the percentage of SC neurons inhibited by hypercapnia to significantly increase from about 10% up to about 30%, but did not significantly alter the percentage of SC neurons activated by hypercapnia (50% in control vs. 35% in CHx). Further, the magnitudes of the responses of SC neurons from control rats (chemosensitivity index for activated neurons of 166+/-11% and for inhibited neurons of 45+/-15%) were the same in SC neurons from CHx-adapted rats. This plasticity induced in chemosensitive SC neurons by CHx appears to involve intrinsic changes in neuronal properties since they were the same in synaptic blockade medium.
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Affiliation(s)
- Nicole L Nichols
- Department of Neuroscience, Cell Biology & Physiology, Wright State University Boonshoft School of Medicine, 3640 Colonel Glenn Highway, Dayton, OH 45435, USA
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9
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Frappell PB, León-Velarde F, Rivera-Ch M. Oxygen transport at high altitude--an integrated perspective. Introduction. Respir Physiol Neurobiol 2007; 158:115-20. [PMID: 17889816 DOI: 10.1016/j.resp.2007.08.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2007] [Accepted: 08/13/2007] [Indexed: 10/22/2022]
Affiliation(s)
- Peter B Frappell
- Adaptational and Evolutionary Respiratory Physiology Laboratory, Department of Zoology, La Trobe University, Melbourne, Victoria, Australia.
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