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Alicea B, Bastani S, Gordon NK, Crawford-Young S, Gordon R. The Molecular Basis of Differentiation Wave Activity in Embryogenesis. Biosystems 2024; 243:105272. [PMID: 39033973 DOI: 10.1016/j.biosystems.2024.105272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 07/10/2024] [Accepted: 07/11/2024] [Indexed: 07/23/2024]
Abstract
As development varies greatly across the tree of life, it may seem difficult to suggest a model that proposes a single mechanism for understanding collective cell behaviors and the coordination of tissue formation. Here we propose a mechanism called differentiation waves, which unify many disparate results involving developmental systems from across the tree of life. We demonstrate how a relatively simple model of differentiation proceeds not from function-related molecular mechanisms, but from so-called differentiation waves. A phenotypic model of differentiation waves is introduced, and its relation to molecular mechanisms is proposed. These waves contribute to a differentiation tree, which is an alternate way of viewing cell lineage and local action of the molecular factors. We construct a model of differentiation wave-related molecular mechanisms (genome, epigenome, and proteome) based on bioinformatic data from the nematode Caenorhabditis elegans. To validate this approach across different modes of development, we evaluate protein expression across different types of development by comparing Caenorhabditis elegans with several model organisms: fruit flies (Drosophila melanogaster), yeast (Saccharomyces cerevisiae), and mouse (Mus musculus). Inspired by gene regulatory networks, two Models of Interactive Contributions (fully-connected MICs and ordered MICs) are used to suggest potential genomic contributions to differentiation wave-related proteins. This, in turn, provides a framework for understanding differentiation and development.
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Affiliation(s)
- Bradly Alicea
- Orthogonal Research and Education Lab, Champaign-Urbana, IL, USA; OpenWorm Foundation, Boston, MA, USA; University of Illinois Urbana-Champaign, USA.
| | - Suroush Bastani
- Orthogonal Research and Education Lab, Champaign-Urbana, IL, USA.
| | | | | | - Richard Gordon
- Gulf Specimen Marine Laboratory & Aquarium, Panacea, FL, USA.
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2
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Boggi B, Sharpen JDA, Taylor G, Drosou K. A novel integrated extraction protocol for multi-omic studies in heavily degraded samples. Sci Rep 2024; 14:17477. [PMID: 39080329 PMCID: PMC11289452 DOI: 10.1038/s41598-024-67104-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 07/08/2024] [Indexed: 08/02/2024] Open
Abstract
The combination of multi-omic techniques, such as genomics, transcriptomics, proteomics, metabolomics and epigenomics, has revolutionised studies in medical research. These techniques are employed to support biomarker discovery, better understand molecular pathways and identify novel drug targets. Despite concerted efforts in integrating omic datasets, there is an absence of protocols that integrate all four biomolecules in a single extraction process. Here, we demonstrate for the first time a minimally destructive integrated protocol for the simultaneous extraction of artificially degraded DNA, proteins, lipids and metabolites from pig brain samples. We used an MTBE-based approach to separate lipids and metabolites, followed by subsequent isolation of DNA and proteins. We have validated this protocol against standalone extraction protocols and show comparable or higher yields of all four biomolecules. This integrated protocol is key to facilitating the preservation of irreplaceable samples while promoting downstream analyses and successful data integration by removing bias from univariate dataset noise and varied distribution characteristics.
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Affiliation(s)
- Byron Boggi
- Faculty of Biology, Medicine and Health, Division of Cell Matrix Biology and Regenerative Medicine, University of Manchester, Manchester, M13 9PL, UK
| | - Jack D A Sharpen
- Faculty of Biology, Medicine and Health, Division of Cell Matrix Biology and Regenerative Medicine, University of Manchester, Manchester, M13 9PL, UK
| | - George Taylor
- Faculty of Biology, Medicine and Health, Research and Innovation, University of Manchester, Manchester, M13 9PG, UK
| | - Konstantina Drosou
- Faculty of Biology, Medicine and Health, Division of Cell Matrix Biology and Regenerative Medicine, University of Manchester, Manchester, M13 9PL, UK.
- Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, UK.
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3
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Stabile AM, Pistilli A, Mariangela R, Rende M, Bartolini D, Di Sante G. New Challenges for Anatomists in the Era of Omics. Diagnostics (Basel) 2023; 13:2963. [PMID: 37761332 PMCID: PMC10529314 DOI: 10.3390/diagnostics13182963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/08/2023] [Accepted: 09/10/2023] [Indexed: 09/29/2023] Open
Abstract
Anatomic studies have traditionally relied on macroscopic, microscopic, and histological techniques to investigate the structure of tissues and organs. Anatomic studies are essential in many fields, including medicine, biology, and veterinary science. Advances in technology, such as imaging techniques and molecular biology, continue to provide new insights into the anatomy of living organisms. Therefore, anatomy remains an active and important area in the scientific field. The consolidation in recent years of some omics technologies such as genomics, transcriptomics, proteomics, and metabolomics allows for a more complete and detailed understanding of the structure and function of cells, tissues, and organs. These have been joined more recently by "omics" such as radiomics, pathomics, and connectomics, supported by computer-assisted technologies such as neural networks, 3D bioprinting, and artificial intelligence. All these new tools, although some are still in the early stages of development, have the potential to strongly contribute to the macroscopic and microscopic characterization in medicine. For anatomists, it is time to hitch a ride and get on board omics technologies to sail to new frontiers and to explore novel scenarios in anatomy.
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Affiliation(s)
- Anna Maria Stabile
- Department of Medicine and Surgery, Section of Human, Clinical and Forensic Anatomy, University of Perugia, 60132 Perugia, Italy; (A.M.S.); (A.P.); (R.M.); (M.R.)
| | - Alessandra Pistilli
- Department of Medicine and Surgery, Section of Human, Clinical and Forensic Anatomy, University of Perugia, 60132 Perugia, Italy; (A.M.S.); (A.P.); (R.M.); (M.R.)
| | - Ruggirello Mariangela
- Department of Medicine and Surgery, Section of Human, Clinical and Forensic Anatomy, University of Perugia, 60132 Perugia, Italy; (A.M.S.); (A.P.); (R.M.); (M.R.)
| | - Mario Rende
- Department of Medicine and Surgery, Section of Human, Clinical and Forensic Anatomy, University of Perugia, 60132 Perugia, Italy; (A.M.S.); (A.P.); (R.M.); (M.R.)
| | - Desirée Bartolini
- Department of Medicine and Surgery, Section of Human, Clinical and Forensic Anatomy, University of Perugia, 60132 Perugia, Italy; (A.M.S.); (A.P.); (R.M.); (M.R.)
- Department of Pharmaceutical Sciences, University of Perugia, 06126 Perugia, Italy
| | - Gabriele Di Sante
- Department of Medicine and Surgery, Section of Human, Clinical and Forensic Anatomy, University of Perugia, 60132 Perugia, Italy; (A.M.S.); (A.P.); (R.M.); (M.R.)
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4
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Adedara IA, Mohammed KA, Canzian J, Rosemberg DB, Aschner M, Farombi EO, Rocha JB. Nauphoeta cinerea as an emerging model in neurotoxicology. ADVANCES IN NEUROTOXICOLOGY 2023; 9:181-196. [PMID: 37389201 PMCID: PMC10310038 DOI: 10.1016/bs.ant.2023.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/01/2023]
Affiliation(s)
- Isaac A. Adedara
- Drug Metabolism and Toxicology Research Laboratories, Department of Biochemistry, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Laboratory of Experimental Neuropsychobiology, Department of Biochemistry and Molecular Biology, Federal University of Santa Maria, Santa Maria, Brazil
| | - Khadija A. Mohammed
- Drug Metabolism and Toxicology Research Laboratories, Department of Biochemistry, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Julia Canzian
- Laboratory of Experimental Neuropsychobiology, Department of Biochemistry and Molecular Biology, Federal University of Santa Maria, Santa Maria, Brazil
| | - Denis B. Rosemberg
- Laboratory of Experimental Neuropsychobiology, Department of Biochemistry and Molecular Biology, Federal University of Santa Maria, Santa Maria, Brazil
| | - Michael Aschner
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Ebenezer O. Farombi
- Drug Metabolism and Toxicology Research Laboratories, Department of Biochemistry, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Joao Batista Rocha
- Department of Biochemical and Molecular Biology, Federal University of Santa Maria, Santa Maria, Brazil
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5
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Serrano C, Lopes-Marques M, Amorim A, João Prata M, Azevedo L. A partial duplication of an X-linked gene exclusive of a primate lineage (Macaca). Gene 2023; 851:146997. [DOI: 10.1016/j.gene.2022.146997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/12/2022] [Accepted: 10/18/2022] [Indexed: 11/04/2022]
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6
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DeCasien AR, Trujillo AE, Janiak MC, Harshaw EP, Caes ZN, Galindo GA, Petersen RM, Higham JP. Equivocal evidence for a link between megalencephaly-related genes and primate brain size evolution. Sci Rep 2022; 12:10902. [PMID: 35764790 PMCID: PMC9239989 DOI: 10.1038/s41598-022-12953-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 05/19/2022] [Indexed: 11/08/2022] Open
Abstract
A large brain is a defining feature of modern humans, and much work has been dedicated to exploring the molecular underpinnings of this trait. Although numerous studies have focused on genes associated with human microcephaly, no studies have explicitly focused on genes associated with megalencephaly. Here, we investigate 16 candidate genes that have been linked to megalencephaly to determine if: (1) megalencephaly-associated genes evolved under positive selection across primates; and (2) selection pressure on megalencephaly-associated genes is linked to primate brain size. We found evidence for positive selection for only one gene, OFD1, with 1.8% of the sites estimated to have dN/dS values greater than 1; however, we did not detect a relationship between selection pressure on this gene and brain size across species, suggesting that selection for changes to non-brain size traits drove evolutionary changes to this gene. In fact, our primary analyses did not identify significant associations between selection pressure and brain size for any candidate genes. While we did detect positive associations for two genes (GPC3 and TBC1D7) when two phyletic dwarfs (i.e., species that underwent recent evolutionary decreases in brain size) were excluded, these associations did not withstand FDR correction. Overall, these results suggest that sequence alterations to megalencephaly-associated genes may have played little to no role in primate brain size evolution, possibly due to the highly pleiotropic effects of these genes. Future comparative studies of gene expression levels may provide further insights. This study enhances our understanding of the genetic underpinnings of brain size evolution in primates and identifies candidate genes that merit further exploration.
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Affiliation(s)
- Alex R DeCasien
- Department of Anthropology, New York University, New York, USA.
- New York Consortium in Evolutionary Primatology (NYCEP), New York, USA.
- Section on Developmental Neurogenomics, National Institute of Mental Health (NIMH), Bethesda, USA.
| | - Amber E Trujillo
- Department of Anthropology, New York University, New York, USA
- New York Consortium in Evolutionary Primatology (NYCEP), New York, USA
| | - Mareike C Janiak
- School of Science, Engineering and Environment, University of Salford, Salford, UK
- Department of Anthropology, Rutgers University, New Brunswick, USA
| | - Etta P Harshaw
- Department of Art History, University of Southern California, Los Angeles, USA
- Eleanor Roosevelt High School, New York, USA
| | - Zosia N Caes
- Department of Chemistry, Yale University, New Haven, USA
- Columbia Secondary School for Math, Science, and Engineering, New York, USA
| | | | - Rachel M Petersen
- Department of Anthropology, New York University, New York, USA
- New York Consortium in Evolutionary Primatology (NYCEP), New York, USA
- Department of Biological Sciences, Vanderbilt University, Nashville, USA
| | - James P Higham
- Department of Anthropology, New York University, New York, USA
- New York Consortium in Evolutionary Primatology (NYCEP), New York, USA
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7
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Xiao X, Zhang CY, Zhang Z, Hu Z, Li M, Li T. Revisiting tandem repeats in psychiatric disorders from perspectives of genetics, physiology, and brain evolution. Mol Psychiatry 2022; 27:466-475. [PMID: 34650204 DOI: 10.1038/s41380-021-01329-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 09/16/2021] [Accepted: 09/28/2021] [Indexed: 01/28/2023]
Abstract
Genome-wide association studies (GWASs) have revealed substantial genetic components comprised of single nucleotide polymorphisms (SNPs) in the heritable risk of psychiatric disorders. However, genetic risk factors not covered by GWAS also play pivotal roles in these illnesses. Tandem repeats, which are likely functional but frequently overlooked by GWAS, may account for an important proportion in the "missing heritability" of psychiatric disorders. Despite difficulties in characterizing and quantifying tandem repeats in the genome, studies have been carried out in an attempt to describe impact of tandem repeats on gene regulation and human phenotypes. In this review, we have introduced recent research progress regarding the genomic distribution and regulatory mechanisms of tandem repeats. We have also summarized the current knowledge of the genetic architecture and biological underpinnings of psychiatric disorders brought by studies of tandem repeats. These findings suggest that tandem repeats, in candidate psychiatric risk genes or in different levels of linkage disequilibrium (LD) with psychiatric GWAS SNPs and haplotypes, may modulate biological phenotypes related to psychiatric disorders (e.g., cognitive function and brain physiology) through regulating alternative splicing, promoter activity, enhancer activity and so on. In addition, many tandem repeats undergo tight natural selection in the human lineage, and likely exert crucial roles in human brain evolution. Taken together, the putative roles of tandem repeats in the pathogenesis of psychiatric disorders is strongly implicated, and using examples from previous literatures, we wish to call for further attention to tandem repeats in the post-GWAS era of psychiatric disorders.
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Affiliation(s)
- Xiao Xiao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Chu-Yi Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Zhuohua Zhang
- Institute of Molecular Precision Medicine and Hunan Key Laboratory of Molecular Precision Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Zhonghua Hu
- Institute of Molecular Precision Medicine and Hunan Key Laboratory of Molecular Precision Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China. .,Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China. .,Department of Critical Care Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China. .,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China. .,Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, Hunan, China. .,Eye Center of Xiangya Hospital and Hunan Key Laboratory of Ophthalmology, Central South University, Changsha, Hunan, China. .,National Clinical Research Center on Mental Disorders, Changsha, Hunan, China.
| | - Ming Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China. .,CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China. .,KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.
| | - Tao Li
- Affiliated Mental Health Center & Hangzhou Seventh People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China. .,Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Guangzhou, China.
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8
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Wang Y, Zhao B, Choi J, Lee EA. Genomic approaches to trace the history of human brain evolution with an emerging opportunity for transposon profiling of ancient humans. Mob DNA 2021; 12:22. [PMID: 34663455 PMCID: PMC8525043 DOI: 10.1186/s13100-021-00250-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 09/27/2021] [Indexed: 12/17/2022] Open
Abstract
Transposable elements (TEs) significantly contribute to shaping the diversity of the human genome, and lines of evidence suggest TEs as one of driving forces of human brain evolution. Existing computational approaches, including cross-species comparative genomics and population genetic modeling, can be adapted for the study of the role of TEs in evolution. In particular, diverse ancient and archaic human genome sequences are increasingly available, allowing reconstruction of past human migration events and holding the promise of identifying and tracking TEs among other evolutionarily important genetic variants at an unprecedented spatiotemporal resolution. However, highly degraded short DNA templates and other unique challenges presented by ancient human DNA call for major changes in current experimental and computational procedures to enable the identification of evolutionarily important TEs. Ancient human genomes are valuable resources for investigating TEs in the evolutionary context, and efforts to explore ancient human genomes will potentially provide a novel perspective on the genetic mechanism of human brain evolution and inspire a variety of technological and methodological advances. In this review, we summarize computational and experimental approaches that can be adapted to identify and validate evolutionarily important TEs, especially for human brain evolution. We also highlight strategies that leverage ancient genomic data and discuss unique challenges in ancient transposon genomics.
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Affiliation(s)
- Yilan Wang
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA
| | - Boxun Zhao
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA
| | - Jaejoon Choi
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Eunjung Alice Lee
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA.
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA.
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9
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Abstract
The human brain is characterized by the large size and intricate folding of its cerebral cortex, which are fundamental for our higher cognitive function and frequently altered in pathological dysfunction. Cortex folding is not unique to humans, nor even to primates, but is common across mammals. Cortical growth and folding are the result of complex developmental processes that involve neural stem and progenitor cells and their cellular lineages, the migration and differentiation of neurons, and the genetic programs that regulate and fine-tune these processes. All these factors combined generate mechanical stress and strain on the developing neural tissue, which ultimately drives orderly cortical deformation and folding. In this review we examine and summarize the current knowledge on the molecular, cellular, histogenic and mechanical mechanisms that are involved in and influence folding of the cerebral cortex, and how they emerged and changed during mammalian evolution. We discuss the main types of pathological malformations of human cortex folding, their specific developmental origin, and how investigating their genetic causes has illuminated our understanding of key events involved. We close our review by presenting the state-of-the-art animal and in vitro models of cortex folding that are currently used to study these devastating developmental brain disorders in children, and what are the main challenges that remain ahead of us to fully understand brain folding.
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Affiliation(s)
- Lucia Del Valle Anton
- Instituto de Neurociencias, Agencia Estatal Consejo Superior de Investigaciones Científicas, San Juan de Alicante, Alicante, Spain
| | - Victor Borrell
- Instituto de Neurociencias, Agencia Estatal Consejo Superior de Investigaciones Científicas, San Juan de Alicante, Alicante, Spain
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10
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Bueichekú E, Gonzalez-de-Echavarri JM, Ortiz-Teran L, Montal V, d'Oleire Uquillas F, De Marcos L, Orwig W, Kim CM, Ortiz-Teran E, Basaia S, Diez I, Sepulcre J. Divergent connectomic organization delineates genetic evolutionary traits in the human brain. Sci Rep 2021; 11:19692. [PMID: 34608211 PMCID: PMC8490416 DOI: 10.1038/s41598-021-99082-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 09/07/2021] [Indexed: 02/08/2023] Open
Abstract
The relationship between human brain connectomics and genetic evolutionary traits remains elusive due to the inherent challenges in combining complex associations within cerebral tissue. In this study, insights are provided about the relationship between connectomics, gene expression and divergent evolutionary pathways from non-human primates to humans. Using in vivo human brain resting-state data, we detected two co-existing idiosyncratic functional systems: the segregation network, in charge of module specialization, and the integration network, responsible for information flow. Their topology was approximated to whole-brain genetic expression (Allen Human Brain Atlas) and the co-localization patterns yielded that neuron communication functionalities-linked to Neuron Projection-were overrepresented cell traits. Homologue-orthologue comparisons using dN/dS-ratios bridged the gap between neurogenetic outcomes and biological data, summarizing the known evolutionary divergent pathways within the Homo Sapiens lineage. Evidence suggests that a crosstalk between functional specialization and information flow reflects putative biological qualities of brain architecture, such as neurite cellular functions like axonal or dendrite processes, hypothesized to have been selectively conserved in the species through positive selection. These findings expand our understanding of human brain function and unveil aspects of our cognitive trajectory in relation to our simian ancestors previously left unexplored.
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Affiliation(s)
- Elisenda Bueichekú
- Gordon Center for Medical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, USA
| | - Jose M Gonzalez-de-Echavarri
- Gordon Center for Medical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, USA
- Barcelona βeta Brain Research Center, Barcelona, Spain
| | - Laura Ortiz-Teran
- Gordon Center for Medical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, USA
- Department of Radiology, Division of Nuclear Medicine and Molecular Imaging, Brigham and Women's Hospital, Harvard Medical School, Boston, USA
| | - Victor Montal
- Gordon Center for Medical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, USA
- Memory Unit, Department of Neurology, Hospital de la Santa Creu i Sant Pau, Biomedical Research Institute Sant Pau, Universitat Autonoma de Barcelona, Barcelona, Spain
- Centro de Investigacón Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Federico d'Oleire Uquillas
- Gordon Center for Medical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, USA
- Princeton Neuroscience Institute, Princeton University, Princeton, USA
| | - Lola De Marcos
- Gordon Center for Medical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, USA
- University of Navarra School of Medicine, University of Navarra, Pamplona, Navarra, Spain
| | - William Orwig
- Gordon Center for Medical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, USA
| | - Chan-Mi Kim
- Gordon Center for Medical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, USA
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, USA
| | - Elena Ortiz-Teran
- Gordon Center for Medical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, USA
- Facultad de Ciencias Jurídicas y Sociales, Universidad Rey Juan Carlos, Madrid, Spain
| | - Silvia Basaia
- Gordon Center for Medical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, USA
- Neuroimaging Research Unit, San Raffaele Scientific Institute, Vita-Salute San Raffaele University, Milan, Italy
| | - Ibai Diez
- Gordon Center for Medical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, USA
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, USA
| | - Jorge Sepulcre
- Gordon Center for Medical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, USA.
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, USA.
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11
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Vancamp P, Spirhanzlova P, Sébillot A, Butruille L, Gothié JD, Le Mével S, Leemans M, Wejaphikul K, Meima M, Mughal BB, Roques P, Remaud S, Fini JB, Demeneix BA. The pyriproxyfen metabolite, 4'-OH-PPF, disrupts thyroid hormone signaling in neural stem cells, modifying neurodevelopmental genes affected by ZIKA virus infection. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 285:117654. [PMID: 34289950 DOI: 10.1016/j.envpol.2021.117654] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/25/2021] [Accepted: 06/11/2021] [Indexed: 06/13/2023]
Abstract
North-Eastern Brazil saw intensive application of the insecticide pyriproxyfen (PPF) during the microcephaly outbreak caused by the Zika virus (ZIKV). ZIKV requires the neural RNA-binding protein Musashi-1 to replicate. Thyroid hormone (TH) represses MSI1. PPF is a suspected TH disruptor. We hypothesized that co-exposure to the main metabolite of PPF, 4'-OH-PPF, could exacerbate ZIKV effects through increased MSI1 expression. Exposing an in vivo reporter model, Xenopus laevis, to 4'-OH-PPF decreased TH signaling and increased msi1 mRNA and protein, confirming TH-antagonistic properties. Next, we investigated the metabolite's effects on mouse subventricular zone-derived neural stem cells (NSCs). Exposure to 4'-OH-PPF dose-dependently reduced neuroprogenitor proliferation and dysregulated genes implicated in neurogliogenesis. The highest dose induced Msi1 mRNA and protein, increasing cell apoptosis and the ratio of neurons to glial cells. Given these effects of the metabolite alone, we considered if combined infection with ZIKV worsened neurogenic events. Only at the fourth and last day of incubation did co-exposure of 4'-OH-PPF and ZIKV decrease viral replication, but viral RNA copies stayed within the same order of magnitude. Intracellular RNA content of NSCs was decreased in the combined presence of 4'-OH-PPF and ZIKV, suggesting a synergistic block of transcriptional machinery. Seven out of 12 tested key genes in TH signaling and neuroglial commitment were dysregulated by co-exposure, of which four were unaltered when exposed to 4'-OH-PPF alone. We conclude that 4'-OH-PPF is an active TH-antagonist, altering NSC processes known to underlie correct cortical development. A combination of the TH-disrupting metabolite and ZIKV could aggravate the microcephaly phenotype.
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Affiliation(s)
- Pieter Vancamp
- Laboratory Molecular Physiology and Adaptation, CNRS UMR 7221, Muséum National d'Histoire Naturelle, Department Adaptations of Life, F-75005, Paris, France
| | - Petra Spirhanzlova
- Laboratory Molecular Physiology and Adaptation, CNRS UMR 7221, Muséum National d'Histoire Naturelle, Department Adaptations of Life, F-75005, Paris, France
| | - Anthony Sébillot
- Laboratory Molecular Physiology and Adaptation, CNRS UMR 7221, Muséum National d'Histoire Naturelle, Department Adaptations of Life, F-75005, Paris, France
| | - Lucile Butruille
- Laboratory Molecular Physiology and Adaptation, CNRS UMR 7221, Muséum National d'Histoire Naturelle, Department Adaptations of Life, F-75005, Paris, France
| | - Jean-David Gothié
- Laboratory Molecular Physiology and Adaptation, CNRS UMR 7221, Muséum National d'Histoire Naturelle, Department Adaptations of Life, F-75005, Paris, France
| | - Sébastien Le Mével
- Laboratory Molecular Physiology and Adaptation, CNRS UMR 7221, Muséum National d'Histoire Naturelle, Department Adaptations of Life, F-75005, Paris, France
| | - Michelle Leemans
- Laboratory Molecular Physiology and Adaptation, CNRS UMR 7221, Muséum National d'Histoire Naturelle, Department Adaptations of Life, F-75005, Paris, France
| | - Karn Wejaphikul
- Department of Internal Medicine, Academic Center for Thyroid Diseases, Erasmus Medical Center, Rotterdam, the Netherlands; Department of Pediatrics, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Marcel Meima
- Department of Internal Medicine, Academic Center for Thyroid Diseases, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Bilal B Mughal
- Laboratory Molecular Physiology and Adaptation, CNRS UMR 7221, Muséum National d'Histoire Naturelle, Department Adaptations of Life, F-75005, Paris, France
| | - Pierre Roques
- Immunology of Viral Infections and Autoimmune Diseases, IDMIT Department, IBFJ, CEA, Université Paris Sud, INSERM U1184, 92265, Fontenay-aux-Roses, France
| | - Sylvie Remaud
- Laboratory Molecular Physiology and Adaptation, CNRS UMR 7221, Muséum National d'Histoire Naturelle, Department Adaptations of Life, F-75005, Paris, France
| | - Jean-Baptiste Fini
- Laboratory Molecular Physiology and Adaptation, CNRS UMR 7221, Muséum National d'Histoire Naturelle, Department Adaptations of Life, F-75005, Paris, France
| | - Barbara A Demeneix
- Laboratory Molecular Physiology and Adaptation, CNRS UMR 7221, Muséum National d'Histoire Naturelle, Department Adaptations of Life, F-75005, Paris, France.
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12
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Pervaiz N, Kang H, Bao Y, Abbasi AA. Molecular evolutionary analysis of human primary microcephaly genes. BMC Ecol Evol 2021; 21:76. [PMID: 33941077 PMCID: PMC8091745 DOI: 10.1186/s12862-021-01801-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 04/22/2021] [Indexed: 12/05/2022] Open
Abstract
Background There has been a rapid increase in the brain size relative to body size during mammalian evolutionary history. In particular, the enlarged and globular brain is the most distinctive anatomical feature of modern humans that set us apart from other extinct and extant primate species. Genetic basis of large brain size in modern humans has largely remained enigmatic. Genes associated with the pathological reduction of brain size (primary microcephaly-MCPH) have the characteristics and functions to be considered ideal candidates to unravel the genetic basis of evolutionary enlargement of human brain size. For instance, the brain size of microcephaly patients is similar to the brain size of Pan troglodyte and the very early hominids like the Sahelanthropus tchadensis and Australopithecus afarensis. Results The present study investigates the molecular evolutionary history of subset of autosomal recessive primary microcephaly (MCPH) genes; CEP135, ZNF335, PHC1, SASS6, CDK6, MFSD2A, CIT, and KIF14 across 48 mammalian species. Codon based substitutions site analysis indicated that ZNF335, SASS6, CIT, and KIF14 have experienced positive selection in eutherian evolutionary history. Estimation of divergent selection pressure revealed that almost all of the MCPH genes analyzed in the present study have maintained their functions throughout the history of placental mammals. Contrary to our expectations, human-specific adoptive evolution was not detected for any of the MCPH genes analyzed in the present study. Conclusion Based on these data it can be inferred that protein-coding sequence of MCPH genes might not be the sole determinant of increase in relative brain size during primate evolutionary history. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01801-0.
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Affiliation(s)
- Nashaiman Pervaiz
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Hongen Kang
- China National Center for Bioinformation and National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yiming Bao
- China National Center for Bioinformation and National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Amir Ali Abbasi
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan.
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13
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Franchini LF. Genetic Mechanisms Underlying Cortical Evolution in Mammals. Front Cell Dev Biol 2021; 9:591017. [PMID: 33659245 PMCID: PMC7917222 DOI: 10.3389/fcell.2021.591017] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 01/08/2021] [Indexed: 12/13/2022] Open
Abstract
The remarkable sensory, motor, and cognitive abilities of mammals mainly depend on the neocortex. Thus, the emergence of the six-layered neocortex in reptilian ancestors of mammals constitutes a fundamental evolutionary landmark. The mammalian cortex is a columnar epithelium of densely packed cells organized in layers where neurons are generated mainly in the subventricular zone in successive waves throughout development. Newborn cells move away from their site of neurogenesis through radial or tangential migration to reach their specific destination closer to the pial surface of the same or different cortical area. Interestingly, the genetic programs underlying neocortical development diversified in different mammalian lineages. In this work, I will review several recent studies that characterized how distinct transcriptional programs relate to the development and functional organization of the neocortex across diverse mammalian lineages. In some primates such as the anthropoids, the neocortex became extremely large, especially in humans where it comprises around 80% of the brain. It has been hypothesized that the massive expansion of the cortical surface and elaboration of its connections in the human lineage, has enabled our unique cognitive capacities including abstract thinking, long-term planning, verbal language and elaborated tool making capabilities. I will also analyze the lineage-specific genetic changes that could have led to the modification of key neurodevelopmental events, including regulation of cell number, neuronal migration, and differentiation into specific phenotypes, in order to shed light on the evolutionary mechanisms underlying the diversity of mammalian brains including the human brain.
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Affiliation(s)
- Lucía Florencia Franchini
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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14
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Dimovasili C, Fadouloglou VE, Kefala A, Providaki M, Kotsifaki D, Kanavouras K, Sarrou I, Plaitakis A, Zaganas I, Kokkinidis M. Crystal structure of glutamate dehydrogenase 2, a positively selected novel human enzyme involved in brain biology and cancer pathophysiology. J Neurochem 2021; 157:802-815. [PMID: 33421122 DOI: 10.1111/jnc.15296] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 12/04/2020] [Accepted: 01/06/2021] [Indexed: 01/01/2023]
Abstract
INTRODUCTION Mammalian glutamate dehydrogenase (hGDH1 in human cells) interconverts glutamate to α-ketoglutarate and ammonia while reducing NAD(P) to NAD(P)H. During primate evolution, humans and great apes have acquired hGDH2, an isoenzyme that underwent rapid evolutionary adaptation concomitantly with brain expansion, thereby acquiring unique catalytic and regulatory properties that permitted its function under conditions inhibitory to its ancestor hGDH1. Although the 3D-structures of GDHs, including hGDH1, have been determined, attempts to determine the hGDH2 structure were until recently unsuccessful. Comparison of the hGDH1/hGDH2 structures would enable a detailed understanding of their evolutionary differences. This work aimed at the determination of the hGDH2 crystal structure and the analysis of its functional implications. Recombinant hGDH2 was produced in the Spodoptera frugiperda ovarian cell line Sf21, using the Baculovirus expression system. Purification was achieved via a two-step chromatography procedure. hGDH2 was crystallized, X-ray diffraction data were collected using synchrotron radiation and the structure was determined by molecular replacement. The hGDH2 structure is reported at a resolution of 2.9 Å. The enzyme adopts a novel semi-closed conformation, which is an intermediate between known open and closed GDH1 conformations, differing from both. The structure enabled us to dissect previously reported biochemical findings and to structurally interpret the effects of evolutionary amino acid substitutions, including Arg470His, on ADP affinity. In conclusion, our data provide insights into the structural basis of hGDH2 properties, the functional evolution of hGDH isoenzymes, and open new prospects for drug design, especially for cancer therapeutics.
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Affiliation(s)
- Christina Dimovasili
- Neurology Laboratory, Medical School, University of Crete, Heraklion, Crete, Greece.,Departments of Psychiatry and Neuroscience, Center for Molecular Biology and Genetics of Neurodegeneration, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Vasiliki E Fadouloglou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece.,Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | - Aikaterini Kefala
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece.,Department of Biology, University of Crete, Heraklion, Crete, Greece
| | - Mary Providaki
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece
| | - Dina Kotsifaki
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece
| | - Konstantinos Kanavouras
- Neurology Laboratory, Medical School, University of Crete, Heraklion, Crete, Greece.,Department of Neurology, "G. Gennimatas" General Hospital, Athens, Greece
| | - Iosifina Sarrou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece.,Center for Free-Electron Laser Science/DESY, Hamburg, Germany
| | - Andreas Plaitakis
- Neurology Laboratory, Medical School, University of Crete, Heraklion, Crete, Greece
| | - Ioannis Zaganas
- Neurology Laboratory, Medical School, University of Crete, Heraklion, Crete, Greece
| | - Michael Kokkinidis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece.,Department of Biology, University of Crete, Heraklion, Crete, Greece
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15
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Liu Y, Konopka G. An integrative understanding of comparative cognition: lessons from human brain evolution. Integr Comp Biol 2020; 60:991-1006. [PMID: 32681799 PMCID: PMC7608741 DOI: 10.1093/icb/icaa109] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
A comprehensive understanding of animal cognition requires the integration of studies on behavior, electrophysiology, neuroanatomy, development, and genomics. Although studies of comparative cognition are receiving increasing attention from organismal biologists, most current studies focus on the comparison of behaviors and anatomical structures to understand their adaptative values. However, to understand the most potentially complex cognitive program of the human brain a greater synthesis of a multitude of disciplines is needed. In this review, we start with extensive neuroanatomic comparisons between humans and other primates. One likely specialization of the human brain is the expansion of neocortex, especially in regions for high-order cognition (e.g., prefrontal cortex). We then discuss how such an expansion can be linked to heterochrony of the brain developmental program, resulting in a greater number of neurons and enhanced computational capacity. Furthermore, alteration of gene expression in the human brain has been associated with positive selection in DNA sequences of gene regulatory regions. These results not only imply that genes associated with brain development are a major factor in the evolution of cognition, but also that high-quality whole-genome sequencing and gene manipulation techniques are needed for an integrative and functional understanding of comparative cognition in non-model organisms.
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Affiliation(s)
- Yuxiang Liu
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Genevieve Konopka
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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16
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Wang W, Wang GZ. Twin-peak temporal regulation during human neocortical development. Cell Discov 2019; 5:61. [PMID: 31871735 PMCID: PMC6915741 DOI: 10.1038/s41421-019-0129-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 09/11/2019] [Indexed: 01/05/2023] Open
Abstract
Understanding the temporal and spatial expression patterns of the human cerebral cortex is essential for expanding knowledge of its functionality. Previous analysis focused on the differentially expressed genes (DEGs) among cortical subregions revealed an hourglass model for interareal differences. However, the overall pattern of transcriptional differences during the development of every region remains to be fully explored. Here, analysing more than 800 neocortex samples from lifespan transcriptional profiles revealed that excitatory neurons are more regulated than inhibitory neurons in the foetal brain. Developmental DEGs tend to be resting state or memory encoding-related and are also involved in autism and Alzheimer’s disease. In addition, twin peaks of DEGs occur during the development of each neocortex region, with a first peak appearing in the perinatal period and an unexpected second peak appearing around childhood. Genes in these peaks have similar functions, but the second peak is more inhibitory neuron related. All these results emphasize the significance of this unique temporal regulatory pattern for human neocortical development.
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Affiliation(s)
- Wei Wang
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031 China
| | - Guang-Zhong Wang
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031 China
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17
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Dos Santos M, West SA. The coevolution of cooperation and cognition in humans. Proc Biol Sci 2019; 285:rspb.2018.0723. [PMID: 29848655 DOI: 10.1098/rspb.2018.0723] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 05/03/2018] [Indexed: 11/12/2022] Open
Abstract
Cooperative behaviours in archaic hunter-gatherers could have been maintained partly due to the gains from cooperation being shared with kin. However, the question arises as to how cooperation was maintained after early humans transitioned to larger groups of unrelated individuals. We hypothesize that after cooperation had evolved via benefits to kin, the consecutive evolution of cognition increased the returns from cooperating, to the point where benefits to self were sufficient for cooperation to remain stable when group size increased and relatedness decreased. We investigate the theoretical plausibility of this hypothesis, with both analytical modelling and simulations. We examine situations where cognition either (i) increases the benefits of cooperation, (ii) leads to synergistic benefits between cognitively enhanced cooperators, (iii) allows the exploitation of less intelligent partners, and (iv) the combination of these effects. We find that cooperation and cognition can coevolve-cooperation initially evolves, favouring enhanced cognition, which favours enhanced cooperation, and stabilizes cooperation against a drop in relatedness. These results suggest that enhanced cognition could have transformed the nature of cooperative dilemmas faced by early humans, thereby explaining the maintenance of cooperation between unrelated partners.
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Affiliation(s)
- Miguel Dos Santos
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
| | - Stuart A West
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
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18
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Evolution and genomics of the human brain. NEUROLOGÍA (ENGLISH EDITION) 2018. [DOI: 10.1016/j.nrleng.2015.06.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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19
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Levchenko A, Kanapin A, Samsonova A, Gainetdinov RR. Human Accelerated Regions and Other Human-Specific Sequence Variations in the Context of Evolution and Their Relevance for Brain Development. Genome Biol Evol 2018; 10:166-188. [PMID: 29149249 PMCID: PMC5767953 DOI: 10.1093/gbe/evx240] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/14/2017] [Indexed: 12/24/2022] Open
Abstract
The review discusses, in a format of a timeline, the studies of different types of genetic variants, present in Homo sapiens, but absent in all other primate, mammalian, or vertebrate species, tested so far. The main characteristic of these variants is that they are found in regions of high evolutionary conservation. These sequence variations include single nucleotide substitutions (called human accelerated regions), deletions, and segmental duplications. The rationale for finding such variations in the human genome is that they could be responsible for traits, specific to our species, of which the human brain is the most remarkable. As became obvious, the vast majority of human-specific single nucleotide substitutions are found in noncoding, likely regulatory regions. A number of genes, associated with these human-specific alleles, often through novel enhancer activity, were in fact shown to be implicated in human-specific development of certain brain areas, including the prefrontal cortex. Human-specific deletions may remove regulatory sequences, such as enhancers. Segmental duplications, because of their large size, create new coding sequences, like new functional paralogs. Further functional study of these variants will shed light on evolution of our species, as well as on the etiology of neurodevelopmental disorders.
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Affiliation(s)
- Anastasia Levchenko
- Institute of Translational Biomedicine, Saint Petersburg State University, Russia
| | - Alexander Kanapin
- Institute of Translational Biomedicine, Saint Petersburg State University, Russia
- Department of Oncology, University of Oxford, United Kingdom
| | - Anastasia Samsonova
- Institute of Translational Biomedicine, Saint Petersburg State University, Russia
- Department of Oncology, University of Oxford, United Kingdom
| | - Raul R Gainetdinov
- Institute of Translational Biomedicine, Saint Petersburg State University, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow, Russia
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20
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Brattås PL, Jönsson ME, Fasching L, Nelander Wahlestedt J, Shahsavani M, Falk R, Falk A, Jern P, Parmar M, Jakobsson J. TRIM28 Controls a Gene Regulatory Network Based on Endogenous Retroviruses in Human Neural Progenitor Cells. Cell Rep 2017; 18:1-11. [PMID: 28052240 DOI: 10.1016/j.celrep.2016.12.010] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 10/26/2016] [Accepted: 12/02/2016] [Indexed: 11/30/2022] Open
Abstract
Endogenous retroviruses (ERVs), which make up 8% of the human genome, have been proposed to participate in the control of gene regulatory networks. In this study, we find a region- and developmental stage-specific expression pattern of ERVs in the developing human brain, which is linked to a transcriptional network based on ERVs. We demonstrate that almost 10,000, primarily primate-specific, ERVs act as docking platforms for the co-repressor protein TRIM28 in human neural progenitor cells, which results in the establishment of local heterochromatin. Thereby, TRIM28 represses ERVs and consequently regulates the expression of neighboring genes. These results uncover a gene regulatory network based on ERVs that participates in control of gene expression of protein-coding transcripts important for brain development.
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Affiliation(s)
- Per Ludvik Brattås
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, BMC A11, Lund University, 221 84 Lund, Sweden
| | - Marie E Jönsson
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, BMC A11, Lund University, 221 84 Lund, Sweden
| | - Liana Fasching
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, BMC A11, Lund University, 221 84 Lund, Sweden
| | - Jenny Nelander Wahlestedt
- Developmental and Regenerative Neurobiology, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, BMC A11, Lund University, 221 84 Lund, Sweden
| | - Mansoureh Shahsavani
- Department of Neuroscience, Karolinska Institute, Retziusväg 8, 171 77 Stockholm, Sweden
| | - Ronny Falk
- Department of Neuroscience, Karolinska Institute, Retziusväg 8, 171 77 Stockholm, Sweden
| | - Anna Falk
- Department of Neuroscience, Karolinska Institute, Retziusväg 8, 171 77 Stockholm, Sweden
| | - Patric Jern
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden
| | - Malin Parmar
- Developmental and Regenerative Neurobiology, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, BMC A11, Lund University, 221 84 Lund, Sweden
| | - Johan Jakobsson
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, BMC A11, Lund University, 221 84 Lund, Sweden.
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21
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Affiliation(s)
- Chet C. Sherwood
- Department of Anthropology and Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, DC 20052
| | - Aida Gómez-Robles
- Department of Anthropology and Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, DC 20052
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, United Kingdom
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22
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Abstract
What made us human? Gene expression changes clearly played a significant part in human evolution, but pinpointing the causal regulatory mutations is hard. Comparative genomics enabled the identification of human accelerated regions (HARs) and other human-specific genome sequences. The major challenge in the past decade has been to link diverged sequences to uniquely human biology. This review discusses approaches to this problem, progress made at the molecular level, and prospects for moving towards genetic causes for uniquely human biology.
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Affiliation(s)
- Lucía F Franchini
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Katherine S Pollard
- Gladstone Institutes, San Francisco, CA, 94158, USA. .,Department of Epidemiology & Biostatistics, Institute for Human Genetics, Institute for Computational Health Sciences, University of California, San Francisco, CA, 94158, USA.
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23
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Correlates and catalysts of hominin evolution in Africa. Theory Biosci 2017; 136:123-140. [PMID: 28597395 DOI: 10.1007/s12064-017-0250-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 05/28/2017] [Indexed: 10/19/2022]
Abstract
Hominin evolution in the African Pliocene and Pleistocene was accompanied and mediated by changes in the abiotic and biotic spheres. It has been hypothesized that such environmental changes were catalysts of hominin morphological evolution and speciations. Whereas there is little doubt that ecological changes were relevant to shaping the trajectories of mammalian evolution, testing specific hypotheses with data from the fossil record has yielded ambiguous results regarding environmental disruption as a primary catalyst. Proposed mechanisms for abiotic and biotic causes of evolution are not always consistent with the timing and trends exhibited by the African fossil record of hominins and other mammals. Analyses of fossil and genetic data suggest that much of hominin evolution, and by extension mammalian evolution, was autocatalytic, driven by feedback loops within a species or lineage, irrespective of changes in the external environment.
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24
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Sato M. Early Origin and Evolution of the Angelman Syndrome Ubiquitin Ligase Gene Ube3a. Front Cell Neurosci 2017; 11:62. [PMID: 28326016 PMCID: PMC5339648 DOI: 10.3389/fncel.2017.00062] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 02/22/2017] [Indexed: 12/20/2022] Open
Abstract
The human Ube3a gene encodes an E3 ubiquitin ligase and exhibits brain-specific genomic imprinting. Genetic abnormalities that affect the maternal copy of this gene cause the neurodevelopmental disorder Angelman syndrome (AS), which is characterized by severe mental retardation, speech impairment, seizure, ataxia and some unique behavioral phenotypes. In this review article, I highlight the evolution of the Ube3a gene and its imprinting to provide evolutionary insights into AS. Recent comparative genomic studies have revealed that Ube3a is most phylogenetically similar to HECTD2 among the human HECT (homologous to the E6AP carboxyl terminus) family of E3 ubiquitin ligases, and its distant evolutionary origin can be traced to common ancestors of fungi and animals. Moreover, a gene more similar to Ube3a than HECTD2 is found in a range of eukaryotes from amoebozoans to basal metazoans, but is lost in later lineages. Unlike in mice and humans, Ube3a expression is biallelic in birds, monotremes, marsupials and insects. The imprinting domain that governs maternal expression of Ube3a was formed from non-imprinted elements following multiple chromosomal rearrangements after diversification of marsupials and placental mammals. Hence, the evolutionary origins of Ube3a date from long before the emergence of the nervous system, although its imprinted expression was acquired relatively recently. These observations suggest that exogenous expression and functional analyses of ancient Ube3a orthologs in mammalian neurons will facilitate the evolutionary understanding of AS.
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Affiliation(s)
- Masaaki Sato
- Graduate School of Science and Engineering and Brain and Body System Science Institute, Saitama UniversitySaitama, Japan
- RIKEN Brain Science InstituteWako, Japan
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25
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Climbing Brain Levels of Organisation from Genes to Consciousness. Trends Cogn Sci 2017; 21:168-181. [PMID: 28161289 DOI: 10.1016/j.tics.2017.01.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 12/24/2016] [Accepted: 01/04/2017] [Indexed: 12/24/2022]
Abstract
Given the tremendous complexity of brain organisation, here I propose a strategy that dynamically links stages of brain organisation from genes to consciousness, at four privileged structural levels: genes; transcription factors (TFs)-gene networks; synaptic epigenesis; and long-range connectivity. These structures are viewed as nested and reciprocally inter-regulated, with a hierarchical organisation that proceeds on different timescales during the course of evolution and development. Interlevel bridging mechanisms include intrinsic variation-selection mechanisms, which offer a community of bottom-up and top-down models linking genes to consciousness in a stepwise manner.
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26
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Creanza N, Feldman MW. Worldwide genetic and cultural change in human evolution. Curr Opin Genet Dev 2016; 41:85-92. [PMID: 27644074 DOI: 10.1016/j.gde.2016.08.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Revised: 08/04/2016] [Accepted: 08/19/2016] [Indexed: 01/04/2023]
Abstract
Both genetic variation and certain culturally transmitted phenotypes show geographic signatures of human demographic history. As a result of the human cultural predisposition to migrate to new areas, humans have adapted to a large number of different environments. Migration to new environments alters genetic selection pressures, and comparative genetic studies have pinpointed numerous likely targets of this selection. However, humans also exhibit many cultural adaptations to new environments, such as practices related to clothing, shelter, and food. Human culture interacts with genes and the environment in complex ways, and studying genes and culture together can deepen our understanding of human evolution.
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Affiliation(s)
- Nicole Creanza
- Department of Biology Stanford University, Gilbert Hall, 371 Serra Mall, Stanford, CA 94305, United States; Department of Biological Sciences, Vanderbilt University, 465 21st Ave. South, Nashville, TN 37212, United States.
| | - Marcus W Feldman
- Department of Biology Stanford University, Gilbert Hall, 371 Serra Mall, Stanford, CA 94305, United States
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27
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Pervaiz N, Abbasi AA. Molecular evolution of WDR62, a gene that regulates neocorticogenesis. Meta Gene 2016; 9:1-9. [PMID: 27114917 PMCID: PMC4833054 DOI: 10.1016/j.mgene.2016.02.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 02/23/2016] [Indexed: 02/02/2023] Open
Abstract
Human brain evolution is characterized by dramatic expansion in cerebral cortex size. WDR62 (WD repeat domain 62) is one of the important gene in controlling human cortical development. Mutations in WDR62 lead to primary microcephaly, a neurodevelopmental disease characterized by three to four fold reduction in cerebral cortex size of affected individuals. This study analyzes comparative protein evolutionary rate to provide a useful insight into the molecular evolution of WDR62 and hence pinpointed human specific amino acid replacements. Comparative analysis of human WDR62 with two archaic humans (Neanderthals and Denisovans) and modern human populations revealed that five hominin specific amino acid residues (human specific amino acids shared with two archaic humans) might have been accumulated in the common ancestor of extinct archaic humans and modern humans about 550,000–765,000 years ago. Collectively, the data demonstrates an acceleration of WDR62 sequence evolution in hominin lineage and suggests that the ability of WDR62 protein to mediate the neurogenesis has been altered in the course of hominin evolution. We trace the evolutionary history of WDR62 and its putative paralogs. We identify accelerated sequence evolution in human WDR62. We pinpoint eight human specific amino acid sites that reside on the C-terminal. Out of eight, six sites are shared with archaic humans.
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Affiliation(s)
- Nashaiman Pervaiz
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Amir Ali Abbasi
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
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Benítez-Burraco A, Uriagereka J. The Immune Syntax Revisited: Opening New Windows on Language Evolution. Front Mol Neurosci 2016; 8:84. [PMID: 26793054 PMCID: PMC4707268 DOI: 10.3389/fnmol.2015.00084] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 12/14/2015] [Indexed: 01/29/2023] Open
Abstract
Recent research has added new dimensions to our understanding of classical evolution, according to which evolutionary novelties result from gene mutations inherited from parents to offspring. Language is surely one such novelty. Together with specific changes in our genome and epigenome, we suggest that two other (related) mechanisms may have contributed to the brain rewiring underlying human cognitive evolution and, specifically, the changes in brain connectivity that prompted the emergence of our species-specific linguistic abilities: the horizontal transfer of genetic material by viral and non-viral vectors and the brain/immune system crosstalk (more generally, the dialogue between the microbiota, the immune system, and the brain).
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Affiliation(s)
| | - Juan Uriagereka
- Department of Linguistics, University of Maryland College Park, MD, USA
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Abstract
The recent finding that the human version of a neurodevelopmental enhancer of the Wnt receptor Frizzled 8 (FZD8) gene alters neural progenitor cell cycle timing and brain size is a step forward to understanding human brain evolution. The human brain is distinctive in terms of its cognitive abilities as well as its susceptibility to neurological disease. Identifying which of the millions of genomic changes that occurred during human evolution led to these and other uniquely human traits is extremely challenging. Recent studies have demonstrated that many of the fastest evolving regions of the human genome function as gene regulatory enhancers during embryonic development and that the human‐specific mutations in them might alter expression patterns. However, elucidating molecular and cellular effects of sequence or expression pattern changes is a major obstacle to discovering the genetic bases of the evolution of our species. There is much work to do before human‐specific genetic and genomic changes are linked to complex human traits. Also watch the Video Abstract.
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Affiliation(s)
- Lucía F Franchini
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Katherine S Pollard
- Gladstone Institutes, San Francisco, CA, USA.,Institute for Human Genetics, Department of Epidemiology & Biostatistics, University of California, San Francisco, CA, USA
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30
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Rosales-Reynoso MA, Juárez-Vázquez CI, Barros-Núñez P. Evolution and genomics of the human brain. Neurologia 2015; 33:254-265. [PMID: 26304653 DOI: 10.1016/j.nrl.2015.06.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 06/01/2015] [Indexed: 01/20/2023] Open
Abstract
Most living beings are able to perform actions that can be considered intelligent or, at the very least, the result of an appropriate reaction to changing circumstances in their environment. However, the intelligence or intellectual processes of humans are vastly superior to those achieved by all other species. The adult human brain is a highly complex organ weighing approximately 1500g, which accounts for only 2% of the total body weight but consumes an amount of energy equal to that required by all skeletal muscle at rest. Although the human brain displays a typical primate structure, it can be identified by its specific distinguishing features. The process of evolution and humanisation of the Homo sapiens brain resulted in a unique and distinct organ with the largest relative volume of any animal species. It also permitted structural reorganization of tissues and circuits in specific segments and regions. These steps explain the remarkable cognitive abilities of modern humans compared not only with other species in our genus, but also with older members of our own species. Brain evolution required the coexistence of two adaptation mechanisms. The first involves genetic changes that occur at the species level, and the second occurs at the individual level and involves changes in chromatin organisation or epigenetic changes. The genetic mechanisms include: a) genetic changes in coding regions that lead to changes in the sequence and activity of existing proteins; b) duplication and deletion of previously existing genes; c) changes in gene expression through changes in the regulatory sequences of different genes; and d) synthesis of non-coding RNAs. Lastly, this review describes some of the main documented chromosomal differences between humans and great apes. These differences have also contributed to the evolution and humanisation process of the H. sapiens brain.
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Affiliation(s)
- M A Rosales-Reynoso
- División de Medicina Molecular, Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social, Guadalajara, Jalisco, México
| | - C I Juárez-Vázquez
- División de Medicina Molecular, Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social, Guadalajara, Jalisco, México
| | - P Barros-Núñez
- División de Genética, Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social, Guadalajara, Jalisco, México.
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31
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Shi L, Lin Q, Su B. Estrogen regulation of microcephaly genes and evolution of brain sexual dimorphism in primates. BMC Evol Biol 2015; 15:127. [PMID: 26123139 PMCID: PMC4487212 DOI: 10.1186/s12862-015-0398-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 05/29/2015] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Sexual dimorphism in brain size is common among primates, including humans, apes and some Old World monkeys. In these species, the brain size of males is generally larger than that of females. Curiously, this dimorphism has persisted over the course of primate evolution and human origin, but there is no explanation for the underlying genetic controls that have maintained this disparity in brain size. RESULTS In the present study, we tested the effect of the female hormone (estradiol) on seven genes known to be related to brain size in both humans and nonhuman primates, and we identified half estrogen responsive elements (half EREs) in the promoter regions of four genes (MCPH1, ASPM, CDK5RAP2 and WDR62). Likewise, at sequence level, it appears that these half EREs are generally conserved across primates. Later testing via a reporter gene assay and cell-based endogenous expression measurement revealed that estradiol could significantly suppress the expression of the four affected genes involved in brain size. More intriguingly, when the half EREs were deleted from the promoters, the suppression effect disappeared, suggesting that the half EREs mediate the regulation of estradiol on the brain size genes. We next replicated these experiments using promoter sequences from chimpanzees and rhesus macaques, and observed a similar suppressive effect of estradiol on gene expression, suggesting that this mechanism is conserved among primate species that exhibit brain size dimorphism. CONCLUSIONS Brain size dimorphism among certain primates, including humans, is likely regulated by estrogen through its sex-dependent suppression of brain size genes during development.
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Affiliation(s)
- Lei Shi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 East Jiao-Chang Road, Kunming, 650223, Yunnan, PR China. .,Yunnan Key Laboratory of Primate Biomedical Research, Kunming, 650000, China.
| | - Qiang Lin
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 East Jiao-Chang Road, Kunming, 650223, Yunnan, PR China. .,Yunnan Key Laboratory of Primate Biomedical Research, Kunming, 650000, China. .,Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, 100101, China.
| | - Bing Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 East Jiao-Chang Road, Kunming, 650223, Yunnan, PR China. .,Yunnan Key Laboratory of Primate Biomedical Research, Kunming, 650000, China.
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32
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Pulvers JN, Journiac N, Arai Y, Nardelli J. MCPH1: a window into brain development and evolution. Front Cell Neurosci 2015; 9:92. [PMID: 25870538 PMCID: PMC4376118 DOI: 10.3389/fncel.2015.00092] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 02/28/2015] [Indexed: 12/21/2022] Open
Abstract
The development of the mammalian cerebral cortex involves a series of mechanisms: from patterning, progenitor cell proliferation and differentiation, to neuronal migration. Many factors influence the development of the cerebral cortex to its normal size and neuronal composition. Of these, the mechanisms that influence the proliferation and differentiation of neural progenitor cells are of particular interest, as they may have the greatest consequence on brain size, not only during development but also in evolution. In this context, causative genes of human autosomal recessive primary microcephaly, such as ASPM and MCPH1, are attractive candidates, as many of them show positive selection during primate evolution. MCPH1 causes microcephaly in mice and humans and is involved in a diverse array of molecular functions beyond brain development, including DNA repair and chromosome condensation. Positive selection of MCPH1 in the primate lineage has led to much insight and discussion of its role in brain size evolution. In this review, we will present an overview of MCPH1 from these multiple angles, and whilst its specific role in brain size regulation during development and evolution remain elusive, the pieces of the puzzle will be discussed with the aim of putting together the full picture of this fascinating gene.
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Affiliation(s)
| | - Nathalie Journiac
- U1141 Inserm Paris, France ; Université Paris Diderot, Sorbonne Paris Cité, UMRS 1141 Paris, France
| | - Yoko Arai
- Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot, Sorbonne Paris Cité Paris, France
| | - Jeannette Nardelli
- U1141 Inserm Paris, France ; Université Paris Diderot, Sorbonne Paris Cité, UMRS 1141 Paris, France
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Amlien IK, Fjell AM, Tamnes CK, Grydeland H, Krogsrud SK, Chaplin TA, Rosa MGP, Walhovd KB. Organizing Principles of Human Cortical Development--Thickness and Area from 4 to 30 Years: Insights from Comparative Primate Neuroanatomy. Cereb Cortex 2014; 26:257-267. [PMID: 25246511 DOI: 10.1093/cercor/bhu214] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The human cerebral cortex undergoes a protracted, regionally heterogeneous development well into young adulthood. Cortical areas that expand the most during human development correspond to those that differ most markedly when the brains of macaque monkeys and humans are compared. However, it remains unclear to what extent this relationship derives from allometric scaling laws that apply to primate brains in general, or represents unique evolutionary adaptations. Furthermore, it is unknown whether the relationship only applies to surface area (SA), or also holds for cortical thickness (CT). In 331 participants aged 4 to 30, we calculated age functions of SA and CT, and examined the correspondence of human cortical development with macaque to human expansion, and with expansion across nonhuman primates. CT followed a linear negative age function from 4 to 30 years, while SA showed positive age functions until 12 years with little further development. Differential cortical expansion across primates was related to regional maturation of SA and CT, with age trajectories differing between high- and low-expanding cortical regions. This relationship adhered to allometric scaling laws rather than representing uniquely macaque-human differences: regional correspondence with human development was as large for expansion across nonhuman primates as between humans and macaque.
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Affiliation(s)
- Inge K Amlien
- Research Group for Lifespan Changes in Brain and Cognition, Department of Psychology, University of Oslo, Oslo, Norway
| | - Anders M Fjell
- Research Group for Lifespan Changes in Brain and Cognition, Department of Psychology, University of Oslo, Oslo, Norway.,Department of Physical Medicine and Rehabilitation, Unit of Neuropsychology, Oslo University Hospital, Oslo, Norway
| | - Christian K Tamnes
- Research Group for Lifespan Changes in Brain and Cognition, Department of Psychology, University of Oslo, Oslo, Norway
| | - Håkon Grydeland
- Research Group for Lifespan Changes in Brain and Cognition, Department of Psychology, University of Oslo, Oslo, Norway
| | - Stine K Krogsrud
- Research Group for Lifespan Changes in Brain and Cognition, Department of Psychology, University of Oslo, Oslo, Norway
| | - Tristan A Chaplin
- Department of Physiology.,Monash Vision Group, Monash University, Clayton, VIC, Australia.,ARC Centre of Excellence for Integrative Brain Function, Clayton, VIC, Australia
| | - Marcello G P Rosa
- Department of Physiology.,Monash Vision Group, Monash University, Clayton, VIC, Australia.,ARC Centre of Excellence for Integrative Brain Function, Clayton, VIC, Australia
| | - Kristine B Walhovd
- Research Group for Lifespan Changes in Brain and Cognition, Department of Psychology, University of Oslo, Oslo, Norway.,Department of Physical Medicine and Rehabilitation, Unit of Neuropsychology, Oslo University Hospital, Oslo, Norway
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34
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Dwivedi SK, Jalan S. Emergence of clustering: role of inhibition. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 90:032803. [PMID: 25314478 DOI: 10.1103/physreve.90.032803] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Indexed: 05/11/2023]
Abstract
Though biological and artificial complex systems having inhibitory connections exhibit a high degree of clustering in their interaction pattern, the evolutionary origin of clustering in such systems remains a challenging problem. Using genetic algorithm we demonstrate that inhibition is required in the evolution of clique structure from primary random architecture, in which the fitness function is assigned based on the largest eigenvalue. Further, the distribution of triads over nodes of the network evolved from mixed connections reveals a negative correlation with its degree providing insight into origin of this trend observed in real networks.
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Affiliation(s)
- Sanjiv K Dwivedi
- Complex Systems Lab, School of Basic Sciences, Indian Institute of Technology Indore, M-Block, IET-DAVV Campus Khandwa Road, Indore-452017, India
| | - Sarika Jalan
- Complex Systems Lab, School of Basic Sciences, Indian Institute of Technology Indore, M-Block, IET-DAVV Campus Khandwa Road, Indore-452017, India
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35
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Buckner RL, Krienen FM. The evolution of distributed association networks in the human brain. Trends Cogn Sci 2013; 17:648-65. [DOI: 10.1016/j.tics.2013.09.017] [Citation(s) in RCA: 475] [Impact Index Per Article: 43.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 09/28/2013] [Accepted: 09/30/2013] [Indexed: 01/25/2023]
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36
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Barry G. Lamarckian evolution explains human brain evolution and psychiatric disorders. Front Neurosci 2013; 7:224. [PMID: 24324395 PMCID: PMC3840504 DOI: 10.3389/fnins.2013.00224] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 11/05/2013] [Indexed: 01/05/2023] Open
Affiliation(s)
- Guy Barry
- Neuroscience Division, Garvan Institute of Medical Research Darlinghurst, NSW, Australia
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37
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Gilmore EC, Walsh CA. Genetic causes of microcephaly and lessons for neuronal development. WILEY INTERDISCIPLINARY REVIEWS. DEVELOPMENTAL BIOLOGY 2013; 2:461-78. [PMID: 24014418 PMCID: PMC3767923 DOI: 10.1002/wdev.89] [Citation(s) in RCA: 165] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The study of human developmental microcephaly is providing important insights into brain development. It has become clear that developmental microcephalies are associated with abnormalities in cellular production, and that the pathophysiology of microcephaly provides remarkable insights into how the brain generates the proper number of neurons that determine brain size. Most of the genetic causes of 'primary' developmental microcephaly (i.e., not associated with other syndromic features) are associated with centrosomal abnormalities. In addition to other functions, centrosomal proteins control the mitotic spindle, which is essential for normal cell proliferation during mitosis. However, the brain is often uniquely affected when microcephaly genes are mutated implying special centrosomal-related functions in neuronal production. Although models explaining how this could occur have some compelling data, they are not without controversy. Interestingly, some of the microcephaly genes show evidence that they were targets of evolutionary selection in primates and human ancestors, suggesting potential evolutionary roles in controlling neuronal number and brain volume across species. Mutations in DNA repair pathway genes also lead to microcephaly. Double-stranded DNA breaks appear to be a prominent type of damage that needs to be repaired during brain development, yet why defects in DNA repair affect the brain preferentially and if DNA repair relates to centrosome function, are not clearly understood.
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Affiliation(s)
- Edward C Gilmore
- Division of Pediatric Neurology, Department of Pediatrics, Case Western Reserve University, Cleveland, OH, USA
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38
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Affiliation(s)
- Simon E Fisher
- Department of Language and Genetics, Max Planck Institute for Psycholinguistics, Nijmegen, Netherlands. imon.fi
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39
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Shi L, Li M, Lin Q, Qi X, Su B. Functional divergence of the brain-size regulating gene MCPH1 during primate evolution and the origin of humans. BMC Biol 2013; 11:62. [PMID: 23697381 PMCID: PMC3674976 DOI: 10.1186/1741-7007-11-62] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 05/09/2013] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND One of the key genes that regulate human brain size, MCPH1 has evolved under strong Darwinian positive selection during the evolution of primates. During this evolution, the divergence of MCPH1 protein sequences among primates may have caused functional changes that contribute to brain enlargement. RESULTS To test this hypothesis, we used co-immunoprecipitation and reporter gene assays to examine the activating and repressing effects of MCPH1 on a set of its down-stream genes and then compared the functional outcomes of a series of mutant MCPH1 proteins that carry mutations at the human- and great-ape-specific sites. The results demonstrate that the regulatory effects of human MCPH1 and rhesus macaque MCPH1 are different in three of eight down-stream genes tested (p73, cyclinE1 and p14ARF), suggesting a functional divergence of MCPH1 between human and non-human primates. Further analyses of the mutant MCPH1 proteins indicated that most of the human-specific mutations could change the regulatory effects on the down-stream genes. A similar result was also observed for one of the four great-ape-specific mutations. CONCLUSIONS Collectively, we propose that during primate evolution in general and human evolution in particular, the divergence of MCPH1 protein sequences under Darwinian positive selection led to functional modifications, providing a possible molecular mechanism of how MCPH1 contributed to brain enlargement during primate evolution and human origin.
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Affiliation(s)
- Lei Shi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 East Jiao-Chang Road, Kunming, Yunnan 650223, PR China
| | - Ming Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 East Jiao-Chang Road, Kunming, Yunnan 650223, PR China
- University of the Chinese Academy of Sciences, No.19A Yuquan Road, Shijingshan District, Beijing, 100049, China
| | - Qiang Lin
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 East Jiao-Chang Road, Kunming, Yunnan 650223, PR China
- University of the Chinese Academy of Sciences, No.19A Yuquan Road, Shijingshan District, Beijing, 100049, China
| | - Xuebin Qi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 East Jiao-Chang Road, Kunming, Yunnan 650223, PR China
| | - Bing Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 East Jiao-Chang Road, Kunming, Yunnan 650223, PR China
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40
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Wu DD, Zhang YP. Evolution and function of de novo originated genes. Mol Phylogenet Evol 2013; 67:541-5. [DOI: 10.1016/j.ympev.2013.02.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Revised: 02/10/2013] [Accepted: 02/13/2013] [Indexed: 01/08/2023]
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41
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Parham P, Moffett A. Variable NK cell receptors and their MHC class I ligands in immunity, reproduction and human evolution. Nat Rev Immunol 2013; 13:133-44. [PMID: 23334245 DOI: 10.1038/nri3370] [Citation(s) in RCA: 354] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Natural killer (NK) cells have roles in immunity and reproduction that are controlled by variable receptors that recognize MHC class I molecules. The variable NK cell receptors found in humans are specific to simian primates, in which they have progressively co-evolved with MHC class I molecules. The emergence of the MHC-C gene in hominids drove the evolution of a system of NK cell receptors for MHC-C molecules that is most elaborate in chimpanzees. By contrast, the human system of MHC-C receptors seems to have been subject to different selection pressures that have acted in competition on the immunological and reproductive functions of MHC class I molecules. We suggest that this compromise facilitated the development of the bigger brains that enabled archaic and modern humans to migrate out of Africa and populate other continents.
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Affiliation(s)
- Peter Parham
- Department of Structural Biology, Stanford University, Stanford, California 94305, USA.
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42
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Abstract
What evolutionary events led to the emergence of human cognition? Although the genetic differences separating modern humans from both non-human primates (for example, chimpanzees) and archaic hominins (Neanderthals and Denisovans) are known, linking human-specific mutations to the cognitive phenotype remains a challenge. One strategy is to focus on human-specific changes at the level of intermediate phenotypes, such as gene expression and metabolism, in conjunction with evolutionary changes in gene regulation involving transcription factors, microRNA and proximal regulatory elements. In this Review we show how this strategy has yielded some of the first hints about the mechanisms of human cognition.
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43
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Montgomery SH, Mundy NI. Microcephaly genes and the evolution of sexual dimorphism in primate brain size. J Evol Biol 2013; 26:906-11. [PMID: 23305468 DOI: 10.1111/jeb.12091] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Accepted: 11/24/2012] [Indexed: 12/29/2022]
Abstract
Microcephaly genes are amongst the most intensively studied genes with candidate roles in brain evolution. Early controversies surrounded the suggestion that they experienced differential selection pressures in different human populations, but several association studies failed to find any link between variation in microcephaly genes and brain size in humans. Recently, however, sex-dependent associations were found between variation in three microcephaly genes and human brain size, suggesting that these genes could contribute to the evolution of sexually dimorphic traits in the brain. Here, we test the hypothesis that microcephaly genes contribute to the evolution of sexual dimorphism in brain mass across anthropoid primates using a comparative approach. The results suggest a link between selection pressures acting on MCPH1 and CENPJ and different scores of sexual dimorphism.
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Affiliation(s)
- S H Montgomery
- Department of Zoology, University of Cambridge, Cambridge, UK.
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44
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Borrell V, Reillo I. Emerging roles of neural stem cells in cerebral cortex development and evolution. Dev Neurobiol 2012; 72:955-71. [PMID: 22684946 DOI: 10.1002/dneu.22013] [Citation(s) in RCA: 133] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Expansion and folding of the cerebral cortex are landmark features of mammalian brain evolution, which are recapitulated during embryonic development. Neural stem cells and their derived germinal cells are coordinated during cerebral cortex development to produce the appropriate amounts and types of neurons. This process is further complicated in gyrencephalic species, where newborn neurons must disperse in the tangential axis to expand the cerebral cortex in surface area. Here, we review advances that have been made over the last decade in understanding the nature and diversity of telencephalic neural stem cells and their roles in cortical development, and we discuss recent progress on how newly identified types of cortical progenitor cell populations may have evolved to drive the expansion and folding of the mammalian cerebral cortex.
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Affiliation(s)
- Víctor Borrell
- Developmental Neurobiology Unit, Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas-Universidad Miguel Hernández, 03550 Sant Joan d'Alacant, Spain.
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45
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Barry G, Mattick JS. The role of regulatory RNA in cognitive evolution. Trends Cogn Sci 2012; 16:497-503. [PMID: 22940578 DOI: 10.1016/j.tics.2012.08.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Revised: 08/12/2012] [Accepted: 08/13/2012] [Indexed: 12/18/2022]
Abstract
The evolution of the human brain has resulted in the emergence of higher-order cognitive abilities, such as reasoning, planning and social awareness. Although there has been a concomitant increase in brain size and complexity, and component diversification, we argue that RNA regulation of epigenetic processes, RNA editing, and the controlled mobilization of transposable elements have provided the major substrates for cognitive advance. We also suggest that these expanded capacities and flexibilities have led to the collateral emergence of psychiatric fragilities and conditions.
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Affiliation(s)
- Guy Barry
- Institute for Molecular Bioscience, The University of Queensland, Brisbane Queensland, 4072, Australia.
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46
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Morales Roselló J, Hervás Marín D, Fillol Crespo M, Perales Marín A. Doppler changes in the vertebral, middle cerebral, and umbilical arteries in fetuses delivered after 34 weeks: relationship to severity of growth restriction. Prenat Diagn 2012; 32:960-7. [DOI: 10.1002/pd.3941] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Revised: 06/21/2012] [Accepted: 06/21/2012] [Indexed: 01/07/2023]
Affiliation(s)
- José Morales Roselló
- Servicio de Obstetricia y Ginecología; Hospital Universitario y Politécnico La Fe; Valencia Spain
- Servicio de Obstetricia y Ginecología; Hospital de La Plana; Villarreal Spain
| | - David Hervás Marín
- Unidad de Bioestadística; Instituto de Investigación Sanitaria La Fe; Valencia Spain
| | | | - Alfredo Perales Marín
- Servicio de Obstetricia y Ginecología; Hospital Universitario y Politécnico La Fe; Valencia Spain
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Zeng H, Shen EH, Hohmann JG, Oh SW, Bernard A, Royall JJ, Glattfelder KJ, Sunkin SM, Morris JA, Guillozet-Bongaarts AL, Smith KA, Ebbert AJ, Swanson B, Kuan L, Page DT, Overly CC, Lein ES, Hawrylycz MJ, Hof PR, Hyde TM, Kleinman JE, Jones AR. Large-scale cellular-resolution gene profiling in human neocortex reveals species-specific molecular signatures. Cell 2012; 149:483-96. [PMID: 22500809 DOI: 10.1016/j.cell.2012.02.052] [Citation(s) in RCA: 264] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2011] [Revised: 11/02/2011] [Accepted: 02/01/2012] [Indexed: 12/30/2022]
Abstract
Although there have been major advances in elucidating the functional biology of the human brain, relatively little is known of its cellular and molecular organization. Here we report a large-scale characterization of the expression of ∼1,000 genes important for neural functions by in situ hybridization at a cellular resolution in visual and temporal cortices of adult human brains. These data reveal diverse gene expression patterns and remarkable conservation of each individual gene's expression among individuals (95%), cortical areas (84%), and between human and mouse (79%). A small but substantial number of genes (21%) exhibited species-differential expression. Distinct molecular signatures, comprised of genes both common between species and unique to each, were identified for each major cortical cell type. The data suggest that gene expression profile changes may contribute to differential cortical function across species, and in particular, a shift from corticosubcortical to more predominant corticocortical communications in the human brain.
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Affiliation(s)
- Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA 98103, USA.
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Noack RA. Solving the "human problem": the frontal feedback model. Conscious Cogn 2012; 21:1043-67. [PMID: 22330981 DOI: 10.1016/j.concog.2012.01.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Revised: 01/16/2012] [Accepted: 01/16/2012] [Indexed: 12/14/2022]
Abstract
This paper argues that humans possess unique cognitive abilities due to the presence of a functional system that exists in the human brain that is absent in the non-human brain. This system, the frontal feedback system, was born in the hominin brain when the great phylogenetic expansion of the prefrontal cortex relative to posterior sensory regions surpassed a critical threshold. Surpassing that threshold effectively reversed the preferred direction of information flow in the highest association regions of the neocortex, producing the frontal feedback system. This reversal was from the caudo-rostral bias characteristic of non-human, or pre-human, brain dynamics to a rostro-caudal bias characteristic of modern human brain dynamics. The frontal feedback system works through frontal motor routines, or action schemes, manipulating the release and reconstruction of stored sensory memories in posterior sensory areas. As an obligatory feature of frontal feedback, a central character, or self, emerges within this cortical network that manifests itself as agent in these reconstructions as well as in the experience of sensory perceptions. Dynamical-systems modeling of cortical interactions is combined in the paper with recent neuroimaging studies of "resting-state" brain activity to bridge the gap between microscopic and macroscopic levels of cortical behavior. This synthesis is used to support the proposal of an information flow reversal occurring in the hominin brain and also to explain how such a reversal generates the wide variety of cognitive and experiential phenomena that many consider to be uniquely human.
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Database independent proteomics analysis of the ostrich and human proteome. Proc Natl Acad Sci U S A 2011; 109:407-12. [PMID: 22198768 DOI: 10.1073/pnas.1108399108] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Mass spectrometry (MS)-based proteome analysis relies heavily on the presence of complete protein databases. Such a strategy is extremely powerful, albeit not adequate in the analysis of unpredicted postgenome events, such as posttranslational modifications, which exponentially increase the search space. Therefore, it is of interest to explore "database-free" approaches. Here, we sampled the ostrich and human proteomes with a method facilitating de novo sequencing, utilizing the protease Lys-N in combination with electron transfer dissociation. By implementing several validation steps, including the combined use of collision-induced dissociation/electron transfer dissociation data and a cross-validation with conventional database search strategies, we identified approximately 2,500 unique de novo peptide sequences from the ostrich sample with over 900 peptides generating full backbone sequence coverage. This dataset allowed the appropriate positioning of ostrich in the evolutionary tree. The described database-free sequencing approach is generically applicable and has great potential in important proteomics applications such as in the analysis of variable parts of endogenous antibodies or proteins modified by a plethora of complex posttranslational modifications.
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