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Xu S, Wang G, Feng Y, Zheng J, Huang L, Wang Y, Liu N. Silica Nanowires-Filled Glass Microporous Sensor for the Ultrasensitive Detection of Deoxyribonucleic Acid. ACS Sens 2024; 9:2050-2056. [PMID: 38632929 DOI: 10.1021/acssensors.4c00072] [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] [Indexed: 04/19/2024]
Abstract
DNA carries genetic information and can serve as an important biomarker for the early diagnosis and assessment of the disease prognosis. Here, we propose a bottom-up assembly method for a silica nanowire-filled glass microporous (SiNWs@GMP) sensor and develop a universal sensing platform for the ultrasensitive and specific detection of DNA. The three-dimensional network structure formed by SiNWs provides them with highly abundant and accessible binding sites, allowing for the immobilization of a large amount of capture probe DNA, thereby enabling more target DNA to hybridize with the capture probe DNA to improve detection performance. Therefore, the SiNWs@GMP sensor achieves ultrasensitive detection of target DNA. In the detection range of 1 aM to 100 fM, there is a good linear relationship between the decrease rate of current signal and the concentration of target DNA, and the detection limit is as low as 1 aM. The developed SiNWs@GMP sensor can distinguish target DNA sequences that are 1-, 3-, and 5-mismatched, and specifically recognize target DNA from complex mixed solution. Furthermore, based on this excellent selectivity and specificity, we validate the universality of this sensing strategy by detecting DNA (H1N1 and H5N1) sequences associated with the avian influenza virus. By replacing the types of nucleic acid aptamers, it is expected to achieve a wide range and low detection limit sensitive detection of various biological molecules. The results indicate that the developed universal sensing platform has ultrahigh sensitivity, excellent selectivity, stability, and acceptable reproducibility, demonstrating its potential application in DNA bioanalysis.
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Affiliation(s)
- Shiwei Xu
- Key Lab of Biohealth Materials and Chemistry of Wenzhou, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou, Zhejiang 325027, P. R. China
| | - Guofeng Wang
- Key Lab of Biohealth Materials and Chemistry of Wenzhou, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou, Zhejiang 325027, P. R. China
| | - Yueyue Feng
- Key Lab of Biohealth Materials and Chemistry of Wenzhou, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou, Zhejiang 325027, P. R. China
| | - Juanjuan Zheng
- Key Lab of Biohealth Materials and Chemistry of Wenzhou, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou, Zhejiang 325027, P. R. China
| | - Liying Huang
- Key Lab of Biohealth Materials and Chemistry of Wenzhou, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou, Zhejiang 325027, P. R. China
| | - Yajun Wang
- Key Lab of Biohealth Materials and Chemistry of Wenzhou, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou, Zhejiang 325027, P. R. China
| | - Nannan Liu
- Key Lab of Biohealth Materials and Chemistry of Wenzhou, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou, Zhejiang 325027, P. R. China
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Lv J, Wu X, Wu M, Wang X, Gong L, Li D, Qian R. Nanoconfined Electrokinetic Chromatography (NEC): Gradient Separation and Sensing of Short DNA Fragments at the Single-Molecule Level. Anal Chem 2024; 96:5702-5710. [PMID: 38538555 DOI: 10.1021/acs.analchem.4c00841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]
Abstract
Glass nanopipets have been demonstrated to be a powerful tool for the sensing and discrimination of biomolecules, such as DNA strands with different lengths or configurations. Despite progress made in nanopipet-based sensors, it remains challenging to develop effective strategies that separate and sense in one operation. In this study, we demonstrate an agarose gel-filled nanopipet that enables hyphenated length-dependent separation and electrochemical sensing of short DNA fragments based on the electrokinetic flow of DNA molecules in the nanoconfined channel at the tip of the nanopipet. This nanoconfined electrokinetic chromatography (NEC) method is used to distinguish the mixture of DNA strands without labels, and the ionic current signals measured in real time show that the mixed DNA strands pass through the tip hole in order according to the molecular weight. With NEC, gradient separation and electrochemical measurement of biomolecules can be achieved simultaneously at the single-molecule level, which is further applied for programmable gene delivery into single living cells. Overall, NEC provides a multipurpose platform integrating separation, sensing, single-cell delivery, and manipulation, which may bring new insights into advanced bioapplication.
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Affiliation(s)
- Jian Lv
- Key Laboratory for Advanced Materials, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Xue Wu
- Key Laboratory for Advanced Materials, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Mansha Wu
- Key Laboratory for Advanced Materials, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Xiaoyuan Wang
- Key Laboratory for Advanced Materials, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Lijuan Gong
- Key Laboratory for Advanced Materials, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Dawei Li
- Key Laboratory for Advanced Materials, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Ruocan Qian
- Key Laboratory for Advanced Materials, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
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Johnson CI, Hyde LE, Cornwall T, Spear M. Of mice (dogs, horses, sheep) and men: A novel comparative anatomy dissection course in a United Kingdom university. ANATOMICAL SCIENCES EDUCATION 2024; 17:506-513. [PMID: 38317576 DOI: 10.1002/ase.2392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 01/22/2024] [Accepted: 01/24/2024] [Indexed: 02/07/2024]
Abstract
At the University of Bristol, we established a novel dissection course to complement our anatomy degree. Students enrolled in this undergraduate course are trained as comparative anatomists, with equal time given to both human and veterinary anatomy. Historically, students opted to dissect either human or veterinary donors as part of the course. To fully reflect the comparative nature of the degree, the dissection course was redesigned so students could dissect both human and veterinary specimens as part of the same course. This facilitated a wide-ranging experience of anatomy, encouraging detailed knowledge of a multitude of species and allowing for multifaceted anatomy graduates to be ready for employment in a wide and competitive job market. Across three iterations of the amended version of the course, median marks ranged from 58.7% to 62.0%, with between 22 and 39 students enrolled. In comparison to the course prior to the introduction of the change, median marks ranged from 59.8% to 62.8%, with between 16 and 24 students enrolled. There was no significant difference between marks before or after the introduction of the concurrently comparative aspect. This paper describes the course, with learning materials and assessments considered, along with some reflection on its value. The course offers benefits to students by widening their perspective on anatomical knowledge and making them more equipped for the job market. It also broadens their understanding of form-function relationships. However, student feedback implied that having the choice between human or veterinary dissection was preferable, and this may outweigh the perceived benefits of the course.
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Affiliation(s)
| | - Lucy E Hyde
- School of Anatomy, University of Bristol, Bristol, UK
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Toda T, Bedrosian TA, Schafer ST, Cuoco MS, Linker SB, Ghassemzadeh S, Mitchell L, Whiteley JT, Novaresi N, McDonald AH, Gallina IS, Yoon H, Hester ME, Pena M, Lim C, Suljic E, AlFatah Mansour A, Boulard M, Parylak SL, Gage FH. Long interspersed nuclear elements safeguard neural progenitors from precocious differentiation. Cell Rep 2024; 43:113774. [PMID: 38349791 PMCID: PMC10948021 DOI: 10.1016/j.celrep.2024.113774] [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: 11/12/2022] [Revised: 11/30/2023] [Accepted: 01/24/2024] [Indexed: 02/15/2024] Open
Abstract
Long interspersed nuclear element-1 (L1 or LINE-1) is a highly abundant mobile genetic element in both humans and mice, comprising almost 20% of each genome. L1s are silenced by several mechanisms, as their uncontrolled expression has the potential to induce genomic instability. However, L1s are paradoxically expressed at high levels in differentiating neural progenitor cells. Using in vitro and in vivo techniques to modulate L1 expression, we report that L1s play a critical role in both human and mouse brain development by regulating the rate of neural differentiation in a reverse-transcription-independent manner.
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Affiliation(s)
- Tomohisa Toda
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA; Laboratory of Neural Epigenomics, Institute of Medical Physics and Micro-tissue Engineering, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany; Nuclear Architecture in Neural Plasticity and Aging Laboratory, German Center for Neurodegenerative Diseases, 01307 Dresden, Germany.
| | - Tracy A Bedrosian
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA; Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Simon T Schafer
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA; Department of Psychiatry and Psychotherapy, School of Medicine and Health, Technical University of Munich, Munich, Germany; TUM Center for Organoid Systems (COS), Munich Institute of Biomedical Engineering, Garching, Germany
| | - Michael S Cuoco
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA; Computational Neural DNA Dynamics Lab, Department of Cognitive Science, University of California, San Diego, San Diego, CA, USA; Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, San Diego, CA, USA
| | - Sara B Linker
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Saeed Ghassemzadeh
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Lisa Mitchell
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Jack T Whiteley
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Nicole Novaresi
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Aidan H McDonald
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Iryna S Gallina
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Hyojung Yoon
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Mark E Hester
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Monique Pena
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA; Department of Psychiatry and Psychotherapy, School of Medicine and Health, Technical University of Munich, Munich, Germany; TUM Center for Organoid Systems (COS), Munich Institute of Biomedical Engineering, Garching, Germany
| | - Christina Lim
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Emelia Suljic
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Abed AlFatah Mansour
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Matthieu Boulard
- Epigenetics & Neurobiology Unit, EMBL Rome, European Molecular Biology Laboratory, Via Ramarini 32, 00015 Monterotondo, Italy
| | - Sarah L Parylak
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Fred H Gage
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.
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Peyrégne S, Slon V, Kelso J. More than a decade of genetic research on the Denisovans. Nat Rev Genet 2024; 25:83-103. [PMID: 37723347 DOI: 10.1038/s41576-023-00643-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/19/2023] [Indexed: 09/20/2023]
Abstract
Denisovans, a group of now extinct humans who lived in Eastern Eurasia in the Middle and Late Pleistocene, were first identified from DNA sequences just over a decade ago. Only ten fragmentary remains from two sites have been attributed to Denisovans based entirely on molecular information. Nevertheless, there has been great interest in using genetic data to understand Denisovans and their place in human history. From the reconstruction of a single high-quality genome, it has been possible to infer their population history, including events of admixture with other human groups. Additionally, the identification of Denisovan DNA in the genomes of present-day individuals has provided insights into the timing and routes of dispersal of ancient modern humans into Asia and Oceania, as well as the contributions of archaic DNA to the physiology of present-day people. In this Review, we synthesize more than a decade of research on Denisovans, reconcile controversies and summarize insights into their population history and phenotype. We also highlight how our growing knowledge about Denisovans has provided insights into our own evolutionary history.
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Affiliation(s)
- Stéphane Peyrégne
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Viviane Slon
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Anatomy and Anthropology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- The Dan David Center for Human Evolution and Biohistory Research, Tel Aviv University, Tel Aviv, Israel
| | - Janet Kelso
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany.
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Wang K, Zhang H, Du Y. MEX3C induces cognitive impairment in mice through autophagy inhibition. Brain Behav 2023; 13:e3245. [PMID: 37652868 PMCID: PMC10636389 DOI: 10.1002/brb3.3245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 07/18/2023] [Accepted: 07/22/2023] [Indexed: 09/02/2023] Open
Abstract
BACKGROUND The muscle excess 3 (MEX3C) protein comprises one of two conserved KH hnRNP K homology domains of the Caenorhabditis elegans protein family, a gene involved in the metabolism of key RNAs at posttranscriptional levels during the development of C. elegans, but its function in mammals is unclear. METHODS AND RESULTS In this study, we found that MEX3C plays a key role in learning and cognitive function. The learning and cognitive abilities of MEX3C-knockout (KO) mice were significantly decreased relative to those of wild-type (WT) mice in behavioral experiments, including the shuttle box, Morris water maze, and new object recognition. Nissl staining showed a decrease in the number of Nissl bodies and in the maturation of hippocampal and cortical neurons. A Western blot analysis of the neuron-specific nuclear (NeuN) protein NEUN protein showed that the expression of that protein was decreased, which was consistent with the results of Nissl staining. Of note, the expression of sequestosome I p62 and Parkin BCL-2-associated X (Bax) Bax and B-cell lymphoma-2 (Bcl-2) Bcl-2 proteins also showed a downward trend, suggesting that the MEX3C gene may cause a decrease in the number and maturity of neuronal cells by increasing apoptosis through the inhibition of autophagy. In addition, Golgi staining showed that the complexity of neurons in the hippocampus and cerebral cortex was reduced, and the postsynaptic density protein 95 and growth-associated protein (GAP-43) also showed different degrees of reduction. CONCLUSION The KO of the MEX3C gene reduces the plasticity of synapses in various regions of the hippocampus, thereby affecting the function of the hippocampus and eventually causing the decline of cognitive function. On the other hand, compared with WT mice, MEX3C-KO mice showed increased anxiety-like behaviors in minefield and elevated plus maze tests.
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Affiliation(s)
- Kai Wang
- School of Clinical MedicineNingxia Medical UniversityNingxia YinchuanChina
| | - Hao‐Nan Zhang
- School of Clinical MedicineNingxia Medical UniversityNingxia YinchuanChina
| | - Yong Du
- Department of Pediatric SurgeryGeneral Hospital of Ningxia Medical UniversityNingxia YinchuanChina
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Soto DC, Uribe-Salazar JM, Shew CJ, Sekar A, McGinty S, Dennis MY. Genomic structural variation: A complex but important driver of human evolution. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023; 181 Suppl 76:118-144. [PMID: 36794631 PMCID: PMC10329998 DOI: 10.1002/ajpa.24713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 01/21/2023] [Accepted: 02/05/2023] [Indexed: 02/17/2023]
Abstract
Structural variants (SVs)-including duplications, deletions, and inversions of DNA-can have significant genomic and functional impacts but are technically difficult to identify and assay compared with single-nucleotide variants. With the aid of new genomic technologies, it has become clear that SVs account for significant differences across and within species. This phenomenon is particularly well-documented for humans and other primates due to the wealth of sequence data available. In great apes, SVs affect a larger number of nucleotides than single-nucleotide variants, with many identified SVs exhibiting population and species specificity. In this review, we highlight the importance of SVs in human evolution by (1) how they have shaped great ape genomes resulting in sensitized regions associated with traits and diseases, (2) their impact on gene functions and regulation, which subsequently has played a role in natural selection, and (3) the role of gene duplications in human brain evolution. We further discuss how to incorporate SVs in research, including the strengths and limitations of various genomic approaches. Finally, we propose future considerations in integrating existing data and biospecimens with the ever-expanding SV compendium propelled by biotechnology advancements.
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Affiliation(s)
- Daniela C. Soto
- Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, CA, USA
- Integrative Genetics and Genomics Graduate Group, University of California, Davis, CA, USA
| | - José M. Uribe-Salazar
- Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, CA, USA
- Integrative Genetics and Genomics Graduate Group, University of California, Davis, CA, USA
| | - Colin J. Shew
- Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, CA, USA
- Integrative Genetics and Genomics Graduate Group, University of California, Davis, CA, USA
| | - Aarthi Sekar
- Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, CA, USA
- Integrative Genetics and Genomics Graduate Group, University of California, Davis, CA, USA
| | - Sean McGinty
- Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, CA, USA
- Integrative Genetics and Genomics Graduate Group, University of California, Davis, CA, USA
| | - Megan Y. Dennis
- Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, CA, USA
- Integrative Genetics and Genomics Graduate Group, University of California, Davis, CA, USA
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Vanderhaeghen P, Polleux F. Developmental mechanisms underlying the evolution of human cortical circuits. Nat Rev Neurosci 2023; 24:213-232. [PMID: 36792753 PMCID: PMC10064077 DOI: 10.1038/s41583-023-00675-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/10/2023] [Indexed: 02/17/2023]
Abstract
The brain of modern humans has evolved remarkable computational abilities that enable higher cognitive functions. These capacities are tightly linked to an increase in the size and connectivity of the cerebral cortex, which is thought to have resulted from evolutionary changes in the mechanisms of cortical development. Convergent progress in evolutionary genomics, developmental biology and neuroscience has recently enabled the identification of genomic changes that act as human-specific modifiers of cortical development. These modifiers influence most aspects of corticogenesis, from the timing and complexity of cortical neurogenesis to synaptogenesis and the assembly of cortical circuits. Mutations of human-specific genetic modifiers of corticogenesis have started to be linked to neurodevelopmental disorders, providing evidence for their physiological relevance and suggesting potential relationships between the evolution of the human brain and its sensitivity to specific diseases.
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Affiliation(s)
- Pierre Vanderhaeghen
- VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.
- Department of Neurosciences, Leuven Brain Institute, KU Leuven, Leuven, Belgium.
| | - Franck Polleux
- Department of Neuroscience, Columbia University Medical Center, New York, NY, USA.
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA.
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Cobo-Simón M, Hart R, Ochman H. Escherichia Coli: What Is and Which Are? Mol Biol Evol 2023; 40:msac273. [PMID: 36585846 PMCID: PMC9830988 DOI: 10.1093/molbev/msac273] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 12/11/2022] [Accepted: 12/15/2022] [Indexed: 01/01/2023] Open
Abstract
Escherichia coli have served as important model organisms for over a century-used to elucidate key aspects of genetics, evolution, molecular biology, and pathogenesis. However, defining which strains actually belong to this species is erratic and unstable due to shifts in the characters and criteria used to distinguish bacterial species. Additionally, many isolates designated as E. coli are genetically more closely related to strains of Shigella than to other E. coli, creating a situation in which the entire genus of Shigella and its four species are encompassed within the single species E. coli. We evaluated all complete genomes assigned to E. coli and its closest relatives according to the biological species concept (BSC), using evidence of reproductive isolation and gene flow (i.e., homologous recombination in the case of asexual bacteria) to ascertain species boundaries. The BSC establishes a uniform, consistent, and objective principle that allows species-level classification across all domains of life and does not rely on either phenotypic or genotypic similarity to a defined type-specimen for species membership. Analyzing a total of 1,887 sequenced genomes and comparing our results to other genome-based classification methods, we found few barriers to gene flow among the strains, clades, phylogroups, or species within E. coli and Shigella. Due to the utility in recognizing which strains constitute a true biological species, we designate genomes that form a genetic cohesive group as members of E. coliBIO.
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Affiliation(s)
- Marta Cobo-Simón
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX
| | - Rowan Hart
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX
| | - Howard Ochman
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX
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Alternative telomere maintenance mechanism in Alligator sinensis provides insights into aging evolution. iScience 2022; 26:105850. [PMID: 36636341 PMCID: PMC9829719 DOI: 10.1016/j.isci.2022.105850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 11/27/2022] [Accepted: 12/16/2022] [Indexed: 12/25/2022] Open
Abstract
Lifespan is a life-history trait that undergoes natural selection. Telomeres are hallmarks of aging, and shortening rate predicts species lifespan, making telomere maintenance mechanisms throughout different lifespans a worthy topic for study. Alligators are suitable for the exploration of anti-aging molecular mechanisms, because they exhibit low or even negligible mortality in adults and no significant telomere shortening. Telomerase reverse transcriptase (TERT) expression is absent in the adult Alligator sinensis, as in humans. Selection analyses on telomere maintenance genes indicated that ATM, FANCE, SAMHD1, HMBOX1, NAT10, and MAP3K4 experienced positive selection on A. sinensis. Repressed pleiotropic ATM kinase in A. sinensis suggests their fitness optimum shift. In ATM downstream, Alternative Lengthening of Telomeres (ALT)-related genes were clustered in a higher expression pattern in A. sinensis, which covers 10-15% of human cancers showing no telomerase activities. In summary, we demonstrated how telomere shortening, telomerase activities, and ALT contributed to anti-aging strategies.
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Romero VI, Arias-Almeida B, Aguiar SA. NSD1 gene evolves under episodic selection within primates and mutations of specific exons in humans cause Sotos syndrome. BMC Genomics 2022; 23:849. [PMID: 36550402 PMCID: PMC9783842 DOI: 10.1186/s12864-022-09071-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Modern human brains and skull shapes differ from other hominids. Brain growth disorders as micro- (ASPM, MCPH1) and macrocephaly (NFIX, GLI3) have been highlighted as relevant for the evolution in humans due to the impact in early brain development. Genes associated with macrocephaly have been reported to cause this change, for example NSD1 which causes Sotos syndrome. RESULTS In this study we performed a systematic literature review, located the reported variants associated to Sotos syndrome along the gene domains, compared the sequences with close primates, calculated their similarity, Ka/Ks ratios, nucleotide diversity and selection, and analyzed the sequence and structural conservation with distant primates. We aimed to understand if NSD1 in humans differs from other primates since the evolution of NSD1 has not been analyzed in primates, nor if the localization of the mutations is limited to humans. Our study found that most variations causing Sotos syndrome are in exon 19, 22 and 10. In the primate comparison we did not detect Ka/Ks ratios > 1, but a high nucleotide diversity with non-synonymous variations in exons 10, 5, 9, 11 and 23, and sites under episodic selection in exon 5 and 23, and human, macaque/colobus/tarsier/galago and tarsier/lemur/colobus. Most of the domains are conserved in distant primates with a particular progressive development from a simple PWWP1 in O. garnetti to a complex structure in Human. CONCLUSION NSD1 is a chromatin modifier that suggests that the selection could influence brain development during modern human evolution and is not present in other primates; however, nowadays the nucleotide diversity is associated with Sotos syndrome.
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Affiliation(s)
- Vanessa I. Romero
- School of Medicine, Universidad San Francisco de Quito, Quito, Ecuador
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Dutrow EV, Emera D, Yim K, Uebbing S, Kocher AA, Krenzer M, Nottoli T, Burkhardt DB, Krishnaswamy S, Louvi A, Noonan JP. Modeling uniquely human gene regulatory function via targeted humanization of the mouse genome. Nat Commun 2022; 13:304. [PMID: 35027568 PMCID: PMC8758698 DOI: 10.1038/s41467-021-27899-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 12/16/2021] [Indexed: 01/22/2023] Open
Abstract
The evolution of uniquely human traits likely entailed changes in developmental gene regulation. Human Accelerated Regions (HARs), which include transcriptional enhancers harboring a significant excess of human-specific sequence changes, are leading candidates for driving gene regulatory modifications in human development. However, insight into whether HARs alter the level, distribution, and timing of endogenous gene expression remains limited. We examined the role of the HAR HACNS1 (HAR2) in human evolution by interrogating its molecular functions in a genetically humanized mouse model. We find that HACNS1 maintains its human-specific enhancer activity in the mouse embryo and modifies expression of Gbx2, which encodes a transcription factor, during limb development. Using single-cell RNA-sequencing, we demonstrate that Gbx2 is upregulated in the limb chondrogenic mesenchyme of HACNS1 homozygous embryos, supporting that HACNS1 alters gene expression in cell types involved in skeletal patterning. Our findings illustrate that humanized mouse models provide mechanistic insight into how HARs modified gene expression in human evolution.
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Affiliation(s)
- Emily V Dutrow
- Department of Genetics, Yale School of Medicine, New Haven, CT, 06510, USA
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Deena Emera
- Department of Genetics, Yale School of Medicine, New Haven, CT, 06510, USA
- Center for Reproductive Longevity and Equality, Buck Institute for Research on Aging, Novato, CA, 94945, USA
| | - Kristina Yim
- Department of Genetics, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Severin Uebbing
- Department of Genetics, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Acadia A Kocher
- Department of Genetics, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Martina Krenzer
- Department of Genetics, Yale School of Medicine, New Haven, CT, 06510, USA
- Neuroscience Research Training Program, Department of Psychiatry, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Timothy Nottoli
- Department of Comparative Medicine, Yale School of Medicine, New Haven, CT, 06510, USA
- Yale Genome Editing Center, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Daniel B Burkhardt
- Department of Genetics, Yale School of Medicine, New Haven, CT, 06510, USA
- Cellarity, Cambridge, MA, 02139, USA
| | - Smita Krishnaswamy
- Department of Genetics, Yale School of Medicine, New Haven, CT, 06510, USA
- Department of Computer Science, Yale University, New Haven, CT, 06520, USA
| | - Angeliki Louvi
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, 06510, USA
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, 06510, USA
| | - James P Noonan
- Department of Genetics, Yale School of Medicine, New Haven, CT, 06510, USA.
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, 06510, USA.
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA.
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13
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Yousaf A, Liu J, Ye S, Chen H. Current Progress in Evolutionary Comparative Genomics of Great Apes. Front Genet 2021; 12:657468. [PMID: 34456962 PMCID: PMC8385753 DOI: 10.3389/fgene.2021.657468] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 07/15/2021] [Indexed: 12/04/2022] Open
Abstract
The availability of high-quality genome sequences of great ape species provides unprecedented opportunities for genomic analyses. Herein, we reviewed the recent progress in evolutionary comparative genomic studies of the existing great ape species, including human, chimpanzee, bonobo, gorilla, and orangutan. We elaborate discovery on evolutionary history, natural selection, structural variations, and new genes of these species, which is informative for understanding the origin of human-specific phenotypes.
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Affiliation(s)
- Aisha Yousaf
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,China National Center for Bioinformation, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Junfeng Liu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,China National Center for Bioinformation, Beijing, China
| | - Sicheng Ye
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,China National Center for Bioinformation, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Hua Chen
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,China National Center for Bioinformation, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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14
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Raza RZ, Ma L, Zhang Z, Bao Y, Abbasi AA. Selection trends on nasal-associated SNP variants across human populations. Meta Gene 2021. [DOI: 10.1016/j.mgene.2021.100872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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15
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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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16
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Dannemann M, Gallego Romero I. Harnessing pluripotent stem cells as models to decipher human evolution. FEBS J 2021; 289:2992-3010. [PMID: 33876573 DOI: 10.1111/febs.15885] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/18/2021] [Accepted: 04/16/2021] [Indexed: 12/13/2022]
Abstract
The study of human evolution, long constrained by a lack of experimental model systems, has been transformed by the emergence of the induced pluripotent stem cell (iPSC) field. iPSCs can be readily established from noninvasive tissue sources, from both humans and other primates; they can be maintained in the laboratory indefinitely, and they can be differentiated into other tissue types. These qualities mean that iPSCs are rapidly becoming established as viable and powerful model systems with which it is possible to address questions in human evolution that were until now logistically and ethically intractable, especially in the quest to understand humans' place among the great apes, and the genetic basis of human uniqueness. In this review, we discuss the key lessons and takeaways of this nascent field; from the types of research, iPSCs make possible to lingering challenges and likely future directions. We provide a comprehensive overview of how the seemingly unlikely combination of iPSCs and explicit evolutionary frameworks is transforming what is possible in our understanding of humanity's past and present.
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Affiliation(s)
| | - Irene Gallego Romero
- Institute of Genomics, University of Tartu, Estonia.,Melbourne Integrative Genomics, The University of Melbourne, Parkville, Australia.,School of BioSciences, The University of Melbourne, Parkville, Australia.,The Centre for Stem Cell Systems, The University of Melbourne, Parkville, Australia
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17
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Repeated mutation of a developmental enhancer contributed to human thermoregulatory evolution. Proc Natl Acad Sci U S A 2021; 118:2021722118. [PMID: 33850016 PMCID: PMC8072367 DOI: 10.1073/pnas.2021722118] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Humans sweat to cool their bodies and have by far the highest eccrine sweat gland density among primates. Humans' high eccrine gland density has long been recognized as a hallmark human evolutionary adaptation, but its genetic basis has been unknown. In humans, expression of the Engrailed 1 (EN1) transcription factor correlates with the onset of eccrine gland formation. In mice, regulation of ectodermal En1 expression is a major determinant of natural variation in eccrine gland density between strains, and increased En1 expression promotes the specification of more eccrine glands. Here, we show that regulation of EN1 has evolved specifically on the human lineage to promote eccrine gland formation. Using comparative genomics and validation of ectodermal enhancer activity in mice, we identified a human EN1 skin enhancer, hECE18. We showed that multiple epistatically interacting derived substitutions in the human ECE18 enhancer increased its activity compared with nonhuman ape orthologs in cultured keratinocytes. Repression of hECE18 in human cultured keratinocytes specifically attenuated EN1 expression, indicating this element positively regulates EN1 in this context. In a humanized enhancer knock-in mouse, hECE18 increased developmental En1 expression in the skin to induce the formation of more eccrine glands. Our study uncovers a genetic basis contributing to the evolution of one of the most singular human adaptations and implicates multiple interacting mutations in a single enhancer as a mechanism for human evolutionary change.
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18
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Shi Y, Wu Q, Wang X. Modeling brain development and diseases with human cerebral organoids. Curr Opin Neurobiol 2020; 66:103-115. [PMID: 33130409 DOI: 10.1016/j.conb.2020.09.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 09/03/2020] [Accepted: 09/13/2020] [Indexed: 12/12/2022]
Abstract
Understanding the mechanisms that underlie human brain development and neurological and neuropsychiatric disorders is one of the key topics of neurobiology. Because of the poor accessibility of human and non-human primate brain tissues, the current perception and understanding of human brain development have been mainly derived from studies of rodents. However, some human-specific features of neural development cannot be well characterized by these animal models. Thanks to the advances in stem cell technologies, brain organoids are being under rapid development, showing the promising applications in decoding the human brain development and uncovering the pathology of brain diseases. In this review, we mainly summarized the recent advances in the development of brain organoid technology and discussed the limitations, applications and future prospects of this promising field.
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Affiliation(s)
- Yingchao Shi
- State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Brain-Intelligence Technology (Shanghai), Bioland Laboratory (Guangzhou), Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qian Wu
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, 100875, China; IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, 100875, China
| | - Xiaoqun Wang
- State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Brain-Intelligence Technology (Shanghai), Bioland Laboratory (Guangzhou), Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Advanced Innovation Center for Human Brain Protection, Beijing Institute for Brain Disorders, Capital Medical University, Beijing, 100069, China.
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19
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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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20
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Bastos RTDRM, Neto JV, Normando D. Dentofacial biometry as a discriminant factor in the identification of remote Amazon indigenous populations. Am J Orthod Dentofacial Orthop 2020; 157:619-630. [DOI: 10.1016/j.ajodo.2019.05.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 02/01/2019] [Accepted: 05/01/2019] [Indexed: 11/29/2022]
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21
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Tang H, Tang Y, Zeng T, Chen L. Gene expression analysis reveals the tipping points during infant brain development for human and chimpanzee. BMC Genomics 2020; 21:74. [PMID: 32138647 PMCID: PMC7057467 DOI: 10.1186/s12864-020-6465-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Accepted: 01/08/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Postpartum developmental delay has been proposed as an important phenotype of human evolution which contributes to many human-specific features including the increase in brain size and the advanced human-specific cognitive traits. However, the biological processes and molecular functions underlying early brain development still remain poorly understood, especially in human and primates. RESULTS In this paper, we comparatively and extensively studied dorsolarteral prefrontal cortex expression data in human and chimpanzee to investigate the critical processes or biological events during early brain development at a molecular level. By using the dynamic network biomarker (DNB) model, we found that there are tipping points around 3 months and 1 month, which are crucial periods in infant human and chimpanzee brain development, respectively. In particular, we shown that the human postnatal development and the corresponding expression changes are delayed 3 times relative to chimpanzee, and we also revealed that many common biological processes are highly involved in those critical periods for both human and chimpanzee, e.g., physiological system development functions, nervous system development, organismal development and tissue morphology. These findings support that the maximal rates of brain growth will be in those two critical periods for respective human and primates. In addition, different from chimpanzee, our analytic results also showed that human can further develop a number of advanced behavior functions around this tipping point (around 3 months), such as the ability of learning and memory. CONCLUSION This work not only provides biological insights into primate brain development at a molecular level but also opens a new way to study the criticality of nonlinear biological processes based on the observed omics data.
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Affiliation(s)
- Hui Tang
- Key Laboratory of Systems Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031 China
| | - Ying Tang
- Key Laboratory of Systems Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031 China
| | - Tao Zeng
- Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Shanghai, 201210 China
| | - Luonan Chen
- Key Laboratory of Systems Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031 China
- CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223 China
- Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Shanghai, 201210 China
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22
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Chai H. Determining primates bite force from histological tooth sections. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2020; 171:683-703. [PMID: 31912901 DOI: 10.1002/ajpa.24003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 10/06/2019] [Accepted: 12/16/2019] [Indexed: 11/09/2022]
Abstract
OBJECTIVES The ability to accurately estimate bite force (BF) in extant and fossil primates is valuable to biological anthropologists. BF is generally evaluated using complex jaw musculature and lever arm analyses employing numerous assumptions and requiring complete cranial morphology. Here, a simple method to determine BF from data measured on histological sections of fossil teeth is proposed. METHODS Published sections of molar teeth encompassing 27 different extinct and extant primates dating back to as early as 17 million years ago were examined. Focusing on the cusp region, the extracted data include characteristic enamel thickness dc and dentin horn angle φ. The occlusal force needed to fracture a cusp, PF , was determined from these variables with the aid of a finite element stress analysis similarly to a previous study on postcanine human teeth. The bite force was obtained by linking BF to PF using a universal constant. RESULTS The measured variables dc and φ are conclusively linked. This link produces a virtually constant fracture force PF and in turn bite force BF for all cusps in the molar row. An explicit formula tying BF to dc and φ was derived. For nonhominin taxa the bite force, molar crown area, and body mass are found to be intimately related. The case of hominins is more involved. The so determined BF is gender-averaged, with the bite force of males estimated to be ≈12% greater than that of females. CONCLUSIONS The use of "fracture mechanics" concepts from mechanics of materials facilitates determination of critical bite force in primates based on characteristic enamel thickness dc and dentin horn angle φ as extracted from histological sections of molar teeth. This novel approach enables quantitative insight into the role played by crown area, body mass and bite force on evolutionary trends. The conclusive link between cuspal enamel thickness and dentin horn angle facilitates optimal food processing without hindering cusp resilience. The proposed approach may be extended to mammals having asymmetric cusp structures.
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Affiliation(s)
- Herzl Chai
- School of Mechanical Engineering, Tel-Aviv University, Tel-Aviv, Israel
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23
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Wang Z, Liu Y, Yu L, Li Y, Qian G, Chang S. Nanopipettes: a potential tool for DNA detection. Analyst 2019; 144:5037-5047. [PMID: 31290857 DOI: 10.1039/c9an00633h] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
As the information in DNA is of practical value for clinical diagnosis, it is important to develop efficient and rapid methods for DNA detection. In the past decades, nanopores have been extensively explored for DNA detection due to their low cost and high efficiency. As a sub-group of the solid-state nanopore, nanopipettes exhibit great potential for DNA detection which is ascribed to their stability, ease of fabrication and good compatibility with other technologies, compared with biological and traditional solid-state nanopores. Herein, the review systematically summarizes the recent progress in DNA detection with nanopipettes and highlights those studies dedicated to improve the performance of DNA detection using nanopipettes through different approaches, including reducing the rate of DNA translocation, improving the spatial resolution of sensing nanopipettes, and controlling DNA molecules through novel techniques. Besides, some new perspectives of the integration of nanopipettes with other technologies are reviewed.
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Affiliation(s)
- Zhe Wang
- The State Key Laboratory of Refractories and Metallurgy, and Institute of Advanced Materials and Nanotechnology, Wuhan University of Science and Technology, Wuhan 430081, China.
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Merrick C, Filingeri D. The evolution of wetness perception: A comparison of arachnid, insect and human models. J Therm Biol 2019; 85:102412. [PMID: 31657753 DOI: 10.1016/j.jtherbio.2019.102412] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 09/03/2019] [Accepted: 09/06/2019] [Indexed: 12/22/2022]
Abstract
Hygroreceptors are a type of humidity sensor that have been identified in several invertebrate classes including Insecta and Arachnida. While their structure has been well researched, the nature of the mechanisms behind their function is debated as being either mechanical, evaporative, or psychrometric in insects and potentially also olfactory in arachnids. There is evidence that can be used to support or oppose each of these concepts, which also invites the possibility of multiple unified mechanisms occurring together. The integration of multiple sensory modalities has also formed the foundation of wetness perception in humans, led by thermal and tactile cues with supplementary information from vision and sound. These inputs are integrated by a vast neural network in the brain, which also occurs on a smaller scale in insects and arachnids. It is possible that as cerebral capacity increased throughout human evolution, this facilitated a preferable system of wetness perception via multisensory integration and rendered hygroreceptors obsolete. While this cerebral development hypothesis is only speculative, it gives a framework for further investigation. Additional research needs to be conducted to correctly classify hygroreceptor types in invertebrates and their relative prevalence before evolutionary associations can be made with vertebrate species. This integratory premise also applies to the human system, as knowing the relative contribution and compounding effects of each sensory modality on wetness perception will aid the overall understanding of the system and help to uncover the evolutionary development pathways underpinning each sense.
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Affiliation(s)
- Charlotte Merrick
- THERMOSENSELAB, Environmental Ergonomics Research Centre, Loughborough Design School, Loughborough University, Loughborough, United Kingdom.
| | - Davide Filingeri
- THERMOSENSELAB, Environmental Ergonomics Research Centre, Loughborough Design School, Loughborough University, Loughborough, United Kingdom.
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25
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Suzuki IK. Molecular drivers of human cerebral cortical evolution. Neurosci Res 2019; 151:1-14. [PMID: 31175883 DOI: 10.1016/j.neures.2019.05.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 05/30/2019] [Accepted: 05/31/2019] [Indexed: 01/10/2023]
Abstract
One of the most important questions in human evolutionary biology is how our ancestor has acquired an expanded volume of the cerebral cortex, which may have significantly impacted on improving our cognitive abilities. Recent comparative approaches have identified developmental features unique to the human or hominid cerebral cortex, not shared with other animals including conventional experimental models. In addition, genomic, transcriptomic, and epigenomic signatures associated with human- or hominid-specific processes of the cortical development are becoming identified by virtue of technical progress in the deep nucleotide sequencing. This review discusses ontogenic and phylogenetic processes of the human cerebral cortex, followed by the introduction of recent comprehensive approaches identifying molecular mechanisms potentially driving the evolutionary changes in the cortical development.
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Affiliation(s)
- Ikuo K Suzuki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 Japan; VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; Department of Neurosciences, Leuven Brain Institute, KULeuven, 3000 Leuven, Belgium; Université Libre de Bruxelles (U.L.B.), Institut de Recherches en Biologie Humaine et Moléculaire (IRIBHM), ULB Neuroscience Institute (UNI), 1070 Brussels, Belgium.
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26
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James WPT, Johnson RJ, Speakman JR, Wallace DC, Frühbeck G, Iversen PO, Stover PJ. Nutrition and its role in human evolution. J Intern Med 2019; 285:533-549. [PMID: 30772945 DOI: 10.1111/joim.12878] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Our understanding of human evolution has improved rapidly over recent decades, facilitated by large-scale cataloguing of genomic variability amongst both modern and archaic humans. It seems clear that the evolution of the ancestors of chimpanzees and hominins separated 7-9 million years ago with some migration out of Africa by the earlier hominins; Homo sapiens slowly emerged as climate change resulted in drier, less forested African conditions. The African populations expanded and evolved in many different conditions with slow mutation and selection rates in the human genome, but with much more rapid mutation occurring in mitochondrial DNA. We now have evidence stretching back 300 000 years of humans in their current form, but there are clearly four very different large African language groups that correlate with population DNA differences. Then, about 50 000-100 000 years ago a small subset of modern humans also migrated out of Africa resulting in a persistent signature of more limited genetic diversity amongst non-African populations. Hybridization with archaic hominins occurred around this time such that all non-African modern humans possess some Neanderthal ancestry and Melanesian populations additionally possess some Denisovan ancestry. Human populations both within and outside Africa also adapted to diverse aspects of their local environment including altitude, climate, UV exposure, diet and pathogens, in some cases leaving clear signatures of patterns of genetic variation. Notable examples include haemoglobin changes conferring resistance to malaria, other immune changes and the skin adaptations favouring the synthesis of vitamin D. As humans migrated across Eurasia, further major mitochondrial changes occurred with some interbreeding with ancient hominins and the development of alcohol intolerance. More recently, an ability to retain lactase persistence into adulthood has evolved rapidly under the environmental stimulus of pastoralism with the ability to husband lactating ruminants. Increased amylase copy numbers seem to relate to the availability of starchy foods, whereas the capacity to desaturase and elongate monounsaturated fatty acids in different societies seems to be influenced by whether there is a lack of supply of readily available dietary sources of long-chain polyunsaturated fatty acids. The process of human evolution includes genetic drift and adaptation to local environments, in part through changes in mitochondrial and nuclear DNA. These genetic changes may underlie susceptibilities to some modern human pathologies including folate-responsive neural tube defects, diabetes, other age-related pathologies and mental health disorders.
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Affiliation(s)
- W P T James
- London School of Hygiene and Tropical Medicine, London, UK
| | - R J Johnson
- Division of Renal Diseases and Hypertension, University of Colorado, Denver, CO, USA
| | - J R Speakman
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - D C Wallace
- Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA, USA
| | - G Frühbeck
- Endocrinology and Nutrition, Clinica Universidad de Navarra, Pamplona, Spain
| | - P O Iversen
- Department of Nutrition, University of Oslo, Oslo, Norway
| | - P J Stover
- Vice Chancellor and Dean for Agriculture and Life Sciences, Texas A&M AgriLife, College Station, TX, USA
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Schmitt JE, Neale MC, Clasen LS, Liu S, Seidlitz J, Pritikin JN, Chu A, Wallace GL, Lee NR, Giedd JN, Raznahan A. A Comprehensive Quantitative Genetic Analysis of Cerebral Surface Area in Youth. J Neurosci 2019; 39:3028-3040. [PMID: 30833512 PMCID: PMC6468099 DOI: 10.1523/jneurosci.2248-18.2019] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 01/21/2019] [Accepted: 01/29/2019] [Indexed: 11/21/2022] Open
Abstract
The genetics of cortical arealization in youth is not well understood. In this study, we use a genetically informative sample of 677 typically developing children and adolescents (mean age 12.72 years), high-resolution MRI, and quantitative genetic methodology to address several fundamental questions on the genetics of cerebral surface area. We estimate that >85% of the phenotypic variance in total brain surface area in youth is attributable to additive genetic factors. We also observed pronounced regional variability in the genetic influences on surface area, with the most heritable areas seen in primary visual and visual association cortex. A shared global genetic factor strongly influenced large areas of the frontal and temporal cortex, mirroring regions that are the most evolutionarily novel in humans relative to other primates. In contrast to studies on older populations, we observed statistically significant genetic correlations between measures of surface area and cortical thickness (rG = 0.63), suggestive of overlapping genetic influences between these endophenotypes early in life. Finally, we identified strong and highly asymmetric genetically mediated associations between Full-Scale Intelligence Quotient and left perisylvian surface area, particularly receptive language centers. Our findings suggest that spatially complex and temporally dynamic genetic factors are influencing cerebral surface area in our species.SIGNIFICANCE STATEMENT Over evolution, the human cortex has undergone massive expansion. In humans, patterns of neurodevelopmental expansion mirror evolutionary changes. However, there is a sparsity of information on how genetics impacts surface area maturation. Here, we present a systematic analysis of the genetics of cerebral surface area in youth. We confirm prior research that implicates genetics as the dominant force influencing individual differences in global surface area. We also find evidence that evolutionarily novel brain regions share common genetics, that overlapping genetic factors influence both area and thickness in youth, and the presence of strong genetically mediated associations between intelligence and surface area in language centers. These findings further elucidate the complex role that genetics plays in brain development and function.
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Affiliation(s)
- J Eric Schmitt
- Departments of Radiology and Psychiatry, Division of Neuroradiology, Brain Behavior Laboratory, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania 19104,
| | - Michael C Neale
- Departments of Psychiatry and Genetics, Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, Virginia 23298
| | - Liv S Clasen
- Developmental Neurogenomics Unit, Human Genetics Branch, National Institute of Mental Health, Bethesda, Maryland 20892
| | - Siyuan Liu
- Developmental Neurogenomics Unit, Human Genetics Branch, National Institute of Mental Health, Bethesda, Maryland 20892
| | - Jakob Seidlitz
- Developmental Neurogenomics Unit, Human Genetics Branch, National Institute of Mental Health, Bethesda, Maryland 20892
| | - Joshua N Pritikin
- Departments of Psychiatry and Genetics, Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, Virginia 23298
| | - Alan Chu
- Department of Radiology, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Gregory L Wallace
- Department of Speech, Language, and Hearing Sciences, George Washington University, Washington, DC 20052
| | - Nancy Raitano Lee
- Department of Psychology, Drexel University, Philadelphia, Pennsylvania 19104, and
| | - Jay N Giedd
- Department of Psychiatry, University of California at San Diego, La Jolla, California 92093
| | - Armin Raznahan
- Developmental Neurogenomics Unit, Human Genetics Branch, National Institute of Mental Health, Bethesda, Maryland 20892
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Lesciotto KM, Richtsmeier JT. Craniofacial skeletal response to encephalization: How do we know what we think we know? AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2019; 168 Suppl 67:27-46. [PMID: 30680710 PMCID: PMC6424107 DOI: 10.1002/ajpa.23766] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 11/16/2018] [Accepted: 11/21/2018] [Indexed: 12/17/2022]
Abstract
Dramatic changes in cranial capacity have characterized human evolution. Important evolutionary hypotheses, such as the spatial packing hypothesis, assert that increases in relative brain size (encephalization) have caused alterations to the modern human skull, resulting in a suite of traits unique among extant primates, including a domed cranial vault, highly flexed cranial base, and retracted facial skeleton. Most prior studies have used fossil or comparative primate data to establish correlations between brain size and cranial form, but the mechanistic basis for how changes in brain size impact the overall shape of the skull resulting in these cranial traits remains obscure and has only rarely been investigated critically. We argue that understanding how changes in human skull morphology could have resulted from increased encephalization requires the direct testing of hypotheses relating to interaction of embryonic development of the bones of the skull and the brain. Fossil and comparative primate data have thoroughly described the patterns of association between brain size and skull morphology. Here we suggest complementing such existing datasets with experiments focused on mechanisms responsible for producing the observed patterns to more thoroughly understand the role of encephalization in shaping the modern human skull.
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Affiliation(s)
- Kate M Lesciotto
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania
| | - Joan T Richtsmeier
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania
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29
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Human-Specific NOTCH2NL Genes Expand Cortical Neurogenesis through Delta/Notch Regulation. Cell 2018; 173:1370-1384.e16. [PMID: 29856955 PMCID: PMC6092419 DOI: 10.1016/j.cell.2018.03.067] [Citation(s) in RCA: 243] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 02/16/2018] [Accepted: 03/26/2018] [Indexed: 12/03/2022]
Abstract
The cerebral cortex underwent rapid expansion and increased complexity during recent hominid evolution. Gene duplications constitute a major evolutionary force, but their impact on human brain development remains unclear. Using tailored RNA sequencing (RNA-seq), we profiled the spatial and temporal expression of hominid-specific duplicated (HS) genes in the human fetal cortex and identified a repertoire of 35 HS genes displaying robust and dynamic patterns during cortical neurogenesis. Among them NOTCH2NL, human-specific paralogs of the NOTCH2 receptor, stood out for their ability to promote cortical progenitor maintenance. NOTCH2NL promote the clonal expansion of human cortical progenitors, ultimately leading to higher neuronal output. At the molecular level, NOTCH2NL function by activating the Notch pathway through inhibition of cis Delta/Notch interactions. Our study uncovers a large repertoire of recently evolved genes active during human corticogenesis and reveals how human-specific NOTCH paralogs may have contributed to the expansion of the human cortex. Identification of >35 HS protein-coding genes expressed during human corticogenesis NOTCH2NL human-specific paralogs of NOTCH2 expressed in human cortical progenitors NOTCH2NL genes expand human cortical progenitors and their neuronal output NOTCH2NL promotes Notch signaling through cis-inhibition of Delta/Notch interactions
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30
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Richtsmeier JT. A century of development. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2018; 165:726-740. [PMID: 29574839 PMCID: PMC6007869 DOI: 10.1002/ajpa.23379] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 12/02/2017] [Accepted: 12/09/2017] [Indexed: 12/13/2022]
Affiliation(s)
- Joan T Richtsmeier
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania 16802
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31
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Singh AN, Bhat V. Spectral peak enhancement of biological fluids by magnetron-sputtered silver nanoparticles. BIOINSPIRED BIOMIMETIC AND NANOBIOMATERIALS 2018. [DOI: 10.1680/jbibn.16.00023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Body fluids recovered from crime scenes are one of the most indispensable forms of evidence for forensic investigators. Such evidence, although obtained in minute quantities, is priceless in assisting the identification of a suspect and exonerating an innocent individual. This work delineates spectral enhancement of trace elements obtained from the crime scene by using spectroscopic techniques. Sputtering silver nanoparticles on the samples resulted in spectral peak enhancement, which is attributed to quantum confinement and a localized surface plasmon resonance effect. The specimen was characterized using UV/visible spectroscopy; for morphological studies, scanning electron microscopy was used, and chemical surface analysis of the sample was carried out using Fourier transform infrared–attenuated total reflection spectroscopy and surface-enhanced infrared absorption spectrographic analysis. Additional enhancement in the peaks was observed in samples obtained from diseased blood. The augmented spectral peak pattern ascertained in the diseased blood can be a tool for narrowing down the investigation to smaller radii. The findings of this analysis will certainly help forensic investigators in confronting the tough challenges concerning crime scene management of body fluids in the long run.
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Affiliation(s)
- Aditya Narayan Singh
- Institute of Research and Development, Gujarat Forensic Sciences University, Gandhinagar, India
| | - Vineet Bhat
- Institute of Forensic Science, Gujarat Forensic Sciences University, Gandhinagar, India
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32
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Abstract
Although most of wealth and innovation have been the result of human interaction and cooperation, we are not yet able to quantitatively predict the spatial distributions of three main elements of cities: population, roads, and socioeconomic interactions. By a simple model mainly based on spatial attraction and matching growth mechanisms, we reveal that the spatial scaling rules of these three elements are in a consistent framework, which allows us to use any single observation to infer the others. All numerical and theoretical results are consistent with empirical data from ten representative cities. In addition, our model can also provide a general explanation of the origins of the universal super- and sub-linear aggregate scaling laws and accurately predict kilometre-level socioeconomic activity. Our work opens a new avenue for uncovering the evolution of cities in terms of the interplay among urban elements, and it has a broad range of applications. Cities can be treated as dynamic complex systems being controlled by the interactions among people, whilst the detail remains largely unknown. Li et al. use spatial attraction together with matching growth to unify population, roads, and socioeconomic interactions crossing ten representative cities.
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33
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Peyrégne S, Boyle MJ, Dannemann M, Prüfer K. Detecting ancient positive selection in humans using extended lineage sorting. Genome Res 2017; 27:1563-1572. [PMID: 28720580 PMCID: PMC5580715 DOI: 10.1101/gr.219493.116] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 07/05/2017] [Indexed: 01/20/2023]
Abstract
Natural selection that affected modern humans early in their evolution has likely shaped some of the traits that set present-day humans apart from their closest extinct and living relatives. The ability to detect ancient natural selection in the human genome could provide insights into the molecular basis for these human-specific traits. Here, we introduce a method for detecting ancient selective sweeps by scanning for extended genomic regions where our closest extinct relatives, Neandertals and Denisovans, fall outside of the present-day human variation. Regions that are unusually long indicate the presence of lineages that reached fixation in the human population faster than expected under neutral evolution. Using simulations, we show that the method is able to detect ancient events of positive selection and that it can differentiate those from background selection. Applying our method to the 1000 Genomes data set, we find evidence for ancient selective sweeps favoring regulatory changes and present a list of genomic regions that are predicted to underlie positively selected human specific traits.
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Affiliation(s)
- Stéphane Peyrégne
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Michael James Boyle
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Michael Dannemann
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Kay Prüfer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
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34
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Hage SR, Gavrilov N, Nieder A. Developmental changes of cognitive vocal control in monkeys. ACTA ACUST UNITED AC 2017; 219:1744-9. [PMID: 27252457 DOI: 10.1242/jeb.137653] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 03/15/2016] [Indexed: 02/02/2023]
Abstract
The evolutionary origins of human language are obscured by the scarcity of essential linguistic characteristics in non-human primate communication systems. Volitional control of vocal utterances is one such indispensable feature of language. We investigated the ability of two monkeys to volitionally utter species-specific calls over many years. Both monkeys reliably vocalized on command during juvenile periods, but discontinued this controlled vocal behavior in adulthood. This emerging disability was confined to volitional vocal production, as the monkeys continued to vocalize spontaneously. In addition, they continued to use hand movements as instructed responses during adulthood. This greater vocal flexibility of monkeys early in ontogeny supports the neoteny hypothesis in human evolution. This suggests that linguistic capabilities were enabled via an expansion of the juvenile period during the development of humans.
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Affiliation(s)
- Steffen R Hage
- Animal Physiology, Institute of Neurobiology, University of Tübingen, Tübingen 72076, Germany
| | - Natalja Gavrilov
- Animal Physiology, Institute of Neurobiology, University of Tübingen, Tübingen 72076, Germany
| | - Andreas Nieder
- Animal Physiology, Institute of Neurobiology, University of Tübingen, Tübingen 72076, Germany
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35
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Pramanik S, Kutzner A, Heese K. Livebearing or egg-laying mammals: 27 decisive nucleotides of FAM168. Biosci Trends 2017; 11:169-178. [PMID: 28381702 DOI: 10.5582/bst.2016.01252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
In the present study, we determine comprehensive molecular phylogenetic relationships of the novel myelin-associated neurite-outgrowth inhibitor (MANI) gene across the entire eukaryotic lineage. Combined computational genomic and proteomic sequence analyses revealed MANI as one of the two members of the novel family with sequence similarity 168 member (FAM168) genes, consisting of FAM168A and FAM168B, having distinct genetic differences that illustrate diversification in its biological function and genetic taxonomy across the phylogenetic tree. Phylogenetic analyses based on coding sequences of these FAM168 genes revealed that they are paralogs and that the earliest emergence of these genes occurred in jawed vertebrates such as Callorhinchus milii. Surprisingly, these two genes are absent in other chordates that have a notochord at some stage in their lives, such as branchiostoma and tunicates. In the context of phylogenetic relationships among eukaryotic species, our results demonstrate the presence of FAM168 orthologs in vertebrates ranging from Callorhinchus milii to Homo sapiens, displaying distinct taxonomic clusters, comprised of fish, amphibians, reptiles, birds, and mammals. Analyses of individual FAM168 exons in our sample provide new insights into the molecular relationships between FAM168A and FAM168B (MANI) on the one hand and livebearing and egg-laying mammals on the other hand, demonstrating that a distinctive intermediate exon 4, comprised of 27 nucleotides, appears suddenly only in FAM168A and there in the livebearing mammals only but is absent from all other species including the egg-laying mammals.
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Affiliation(s)
- Subrata Pramanik
- Graduate School of Biomedical Science and Engineering, Hanyang University
| | - Arne Kutzner
- Department of Information Systems, College of Engineering, Hanyang University
| | - Klaus Heese
- Graduate School of Biomedical Science and Engineering, Hanyang University
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36
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Hage SR, Nieder A. Dual Neural Network Model for the Evolution of Speech and Language. Trends Neurosci 2016; 39:813-829. [DOI: 10.1016/j.tins.2016.10.006] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 10/14/2016] [Accepted: 10/20/2016] [Indexed: 12/31/2022]
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37
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Kupferman J, Polleux F. Genomic remodelling in the primate brain. Nature 2016; 539:171-172. [DOI: 10.1038/539171a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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38
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Barbosa M, Vieira EP, Quintão CCA, Normando D. Facial biometry of Amazon indigenous people of the Xingu River - Perspectives on genetic and environmental contributions to variation in human facial morphology. Orthod Craniofac Res 2016; 19:169-79. [PMID: 27132798 DOI: 10.1111/ocr.12125] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/03/2016] [Indexed: 11/28/2022]
Abstract
OBJECTIVE To evaluate facial morphology of non-mixed indigenous people living in the Xingu region. Studies on these populations report that the total genetic diversity is as high as that observed for other continental populations. On the other hand, eating habits are different between indigenous and urban population, as indigenous people still have traditional habits. SETTING AND SAMPLE POPULATION The sample consisted of 106 indigenous subjects, in permanent dentition stage, belonging to four groups: Arara-Laranjal (n = 35), Arara-Iriri (n = 20), Xikrin-Kaiapó (n = 24), and Assurini (n = 27). MATERIAL AND METHODS Standardized facial photographs were obtained, and fourteen measurements were analyzed. Intra- and intergroup homogeneities were examined by discriminant analysis, followed by anova and Kruskal-Wallis tests. Sexual dimorphism to each village was analyzed by Student's t-test or Mann-Whitney test, at p < 0.05. RESULTS Significant facial differences were found between male and female, indicating that sex data should not be grouped for intergroup comparison. Discriminant analysis showed a large intergroup heterogeneity, while an intragroup homogeneity was found, especially for females. It was also observed that some morphological features of the face are specific to some villages, regardless of ethnicity. CONCLUSIONS Facial morphological characteristics were strongly different among groups, even comparing villages from the same ethnicity. Furthermore, a low diversity within groups was observed. Our findings, supported by previous reports on genetics and eating habits in these populations, reinforce the role of the genetic determination on craniofacial morphology.
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Affiliation(s)
- M Barbosa
- Federal University of Pará, Belém, PA, Brazil
| | - E P Vieira
- Federal University of Pará, Belém, PA, Brazil
| | | | - D Normando
- Federal University of Pará, Belém, PA, Brazil
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39
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Ardila A. The Evolutionary Concept of "Preadaptation" Applied to Cognitive Neurosciences. Front Neurosci 2016; 10:103. [PMID: 27013963 PMCID: PMC4794492 DOI: 10.3389/fnins.2016.00103] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 02/29/2016] [Indexed: 11/17/2022] Open
Affiliation(s)
- Alfredo Ardila
- Communication Sciences and Disorders, Florida International University Miami, FL, USA
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40
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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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41
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Mechanisms of Long Non-coding RNAs in Mammalian Nervous System Development, Plasticity, Disease, and Evolution. Neuron 2015; 88:861-877. [DOI: 10.1016/j.neuron.2015.09.045] [Citation(s) in RCA: 303] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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42
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Gea J, Pascual S, Casadevall C, Orozco-Levi M, Barreiro E. Muscle dysfunction in chronic obstructive pulmonary disease: update on causes and biological findings. J Thorac Dis 2015; 7:E418-38. [PMID: 26623119 DOI: 10.3978/j.issn.2072-1439.2015.08.04] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Respiratory and/or limb muscle dysfunction, which are frequently observed in chronic obstructive pulmonary disease (COPD) patients, contribute to their disease prognosis irrespective of the lung function. Muscle dysfunction is caused by the interaction of local and systemic factors. The key deleterious etiologic factors are pulmonary hyperinflation for the respiratory muscles and deconditioning secondary to reduced physical activity for limb muscles. Nonetheless, cigarette smoke, systemic inflammation, nutritional abnormalities, exercise, exacerbations, anabolic insufficiency, drugs and comorbidities also seem to play a relevant role. All these factors modify the phenotype of the muscles, through the induction of several biological phenomena in patients with COPD. While respiratory muscles improve their aerobic phenotype (percentage of oxidative fibers, capillarization, mitochondrial density, enzyme activity in the aerobic pathways, etc.), limb muscles exhibit the opposite phenotype. In addition, both muscle groups show oxidative stress, signs of damage and epigenetic changes. However, fiber atrophy, increased number of inflammatory cells, altered regenerative capacity; signs of apoptosis and autophagy, and an imbalance between protein synthesis and breakdown are rather characteristic features of the limb muscles, mostly in patients with reduced body weight. Despite that significant progress has been achieved in the last decades, full elucidation of the specific roles of the target biological mechanisms involved in COPD muscle dysfunction is still required. Such an achievement will be crucial to adequately tackle with this relevant clinical problem of COPD patients in the near-future.
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Affiliation(s)
- Joaquim Gea
- Servei de Pneumologia, Muscle & Respiratory System Research Unit (URMAR), Hospital del Mar-I.M.I.M., Experimental Sciences and Health Department (CEXS), Universitat Pompeu Fabra, CIBERES, ISCIII, Barcelona, Catalonia, Spain
| | - Sergi Pascual
- Servei de Pneumologia, Muscle & Respiratory System Research Unit (URMAR), Hospital del Mar-I.M.I.M., Experimental Sciences and Health Department (CEXS), Universitat Pompeu Fabra, CIBERES, ISCIII, Barcelona, Catalonia, Spain
| | - Carme Casadevall
- Servei de Pneumologia, Muscle & Respiratory System Research Unit (URMAR), Hospital del Mar-I.M.I.M., Experimental Sciences and Health Department (CEXS), Universitat Pompeu Fabra, CIBERES, ISCIII, Barcelona, Catalonia, Spain
| | - Mauricio Orozco-Levi
- Servei de Pneumologia, Muscle & Respiratory System Research Unit (URMAR), Hospital del Mar-I.M.I.M., Experimental Sciences and Health Department (CEXS), Universitat Pompeu Fabra, CIBERES, ISCIII, Barcelona, Catalonia, Spain
| | - Esther Barreiro
- Servei de Pneumologia, Muscle & Respiratory System Research Unit (URMAR), Hospital del Mar-I.M.I.M., Experimental Sciences and Health Department (CEXS), Universitat Pompeu Fabra, CIBERES, ISCIII, Barcelona, Catalonia, Spain
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43
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Nakagome S, Alkorta-Aranburu G, Amato R, Howie B, Peter BM, Hudson RR, Di Rienzo A. Estimating the Ages of Selection Signals from Different Epochs in Human History. Mol Biol Evol 2015; 33:657-69. [PMID: 26545921 DOI: 10.1093/molbev/msv256] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Genetic variation harbors signatures of natural selection driven by selective pressures that are often unknown. Estimating the ages of selection signals may allow reconstructing the history of environmental changes that shaped human phenotypes and diseases. We have developed an approximate Bayesian computation (ABC) approach to estimate allele ages under a model of selection on new mutations and under demographic models appropriate for human populations. We have applied it to two resequencing data sets: An ultra-high depth data set from a relatively small sample of unrelated individuals and a lower depth data set in a larger sample with transmission information. In addition to evaluating the accuracy of our method based on simulations, for each SNP, we assessed the consistency between the posterior probabilities estimated by the ABC approach and the ancient DNA record, finding good agreement between the two types of data and methods. Applying this ABC approach to data for eight single nucleotide polymorphisms (SNPs), we were able to rule out an onset of selection prior to the dispersal out-of-Africa for three of them and more recent than the spread of agriculture for an additional three SNPs.
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Affiliation(s)
| | | | - Roberto Amato
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, United Kingdom
| | - Bryan Howie
- Department of Human Genetics, University of Chicago
| | | | - Richard R Hudson
- Department of Human Genetics, University of Chicago Department of Ecology and Evolution, University of Chicago
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44
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Ashfaq M, Prosser S, Nasir S, Masood M, Ratnasingham S, Hebert PDN. High diversity and rapid diversification in the head louse, Pediculus humanus (Pediculidae: Phthiraptera). Sci Rep 2015; 5:14188. [PMID: 26373806 PMCID: PMC4570997 DOI: 10.1038/srep14188] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 08/18/2015] [Indexed: 12/15/2022] Open
Abstract
The study analyzes sequence variation of two mitochondrial genes (COI, cytb) in Pediculus humanus from three countries (Egypt, Pakistan, South Africa) that have received little prior attention, and integrates these results with prior data. Analysis indicates a maximum K2P distance of 10.3% among 960 COI sequences and 13.8% among 479 cytb sequences. Three analytical methods (BIN, PTP, ABGD) reveal five concordant OTUs for COI and cytb. Neighbor-Joining analysis of the COI sequences confirm five clusters; three corresponding to previously recognized mitochondrial clades A, B, C and two new clades, "D" and "E", showing 2.3% and 2.8% divergence from their nearest neighbors (NN). Cytb data corroborate five clusters showing that clades "D" and "E" are both 4.6% divergent from their respective NN clades. Phylogenetic analysis supports the monophyly of all clusters recovered by NJ analysis. Divergence time estimates suggest that the earliest split of P. humanus clades occurred slightly more than one million years ago (MYa) and the latest about 0.3 MYa. Sequence divergences in COI and cytb among the five clades of P. humanus are 10X those in their human host, a difference that likely reflects both rate acceleration and the acquisition of lice clades from several archaic hominid lineages.
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Affiliation(s)
- Muhammad Ashfaq
- Biodiversity Institute of Ontario, University of Guelph, Guelph, ON, Canada
| | - Sean Prosser
- Biodiversity Institute of Ontario, University of Guelph, Guelph, ON, Canada
| | - Saima Nasir
- Pakistan Council for Science and Technology, Islamabad, Pakistan
| | - Mariyam Masood
- National Institute for Biotechnology and Genetic Engineering, Jhang Road, Faisalabad, Pakistan
| | | | - Paul D N Hebert
- Biodiversity Institute of Ontario, University of Guelph, Guelph, ON, Canada
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de Souza BS, Bichara LM, Guerreiro JF, Quintão CCA, Normando D. Occlusal and facial features in Amazon indigenous: An insight into the role of genetics and environment in the etiology dental malocclusion. Arch Oral Biol 2015; 60:1177-86. [DOI: 10.1016/j.archoralbio.2015.04.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 03/31/2015] [Accepted: 04/15/2015] [Indexed: 10/23/2022]
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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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47
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Wu DD, Ye LQ, Li Y, Sun YB, Shao Y, Chen C, Zhu Z, Zhong L, Wang L, Irwin DM, Zhang YE, Zhang YP. Integrative analyses of RNA editing, alternative splicing, and expression of young genes in human brain transcriptome by deep RNA sequencing. J Mol Cell Biol 2015; 7:314-25. [DOI: 10.1093/jmcb/mjv043] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 04/16/2015] [Indexed: 12/31/2022] Open
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Rieux A, Eriksson A, Li M, Sobkowiak B, Weinert LA, Warmuth V, Ruiz-Linares A, Manica A, Balloux F. Improved calibration of the human mitochondrial clock using ancient genomes. Mol Biol Evol 2014; 31:2780-92. [PMID: 25100861 PMCID: PMC4166928 DOI: 10.1093/molbev/msu222] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Reliable estimates of the rate at which DNA accumulates mutations (the substitution rate) are crucial for our understanding of the evolution and past demography of virtually any species. In humans, there are considerable uncertainties around these rates, with substantial variation among recent published estimates. Substitution rates have traditionally been estimated by associating dated events to the root (e.g., the divergence between humans and chimpanzees) or to internal nodes in a phylogenetic tree (e.g., first entry into the Americas). The recent availability of ancient mitochondrial DNA sequences allows for a more direct calibration by assigning the age of the sequenced samples to the tips within the human phylogenetic tree. But studies also vary greatly in the methodology employed and in the sequence panels analyzed, making it difficult to tease apart the causes for the differences between previous estimates. To clarify this issue, we compiled a comprehensive data set of 350 ancient and modern human complete mitochondrial DNA genomes, among which 146 were generated for the purpose of this study and estimated substitution rates using calibrations based both on dated nodes and tips. Our results demonstrate that, for the same data set, estimates based on individual dated tips are far more consistent with each other than those based on nodes and should thus be considered as more reliable.
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Affiliation(s)
- Adrien Rieux
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Anders Eriksson
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Mingkun Li
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Benjamin Sobkowiak
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Lucy A Weinert
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Vera Warmuth
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Andres Ruiz-Linares
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Andrea Manica
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - François Balloux
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
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49
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del Rosario RCH, Rayan NA, Prabhakar S. Noncoding origins of anthropoid traits and a new null model of transposon functionalization. Genome Res 2014; 24:1469-84. [PMID: 25043600 PMCID: PMC4158753 DOI: 10.1101/gr.168963.113] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Little is known about novel genetic elements that drove the emergence of anthropoid primates. We exploited the sequencing of the marmoset genome to identify 23,849 anthropoid-specific constrained (ASC) regions and confirmed their robust functional signatures. Of the ASC base pairs, 99.7% were noncoding, suggesting that novel anthropoid functional elements were overwhelmingly cis-regulatory. ASCs were highly enriched in loci associated with fetal brain development, motor coordination, neurotransmission, and vision, thus providing a large set of candidate elements for exploring the molecular basis of hallmark primate traits. We validated ASC192 as a primate-specific enhancer in proliferative zones of the developing brain. Unexpectedly, transposable elements (TEs) contributed to >56% of ASCs, and almost all TE families showed functional potential similar to that of nonrepetitive DNA. Three L1PA repeat-derived ASCs displayed coherent eye-enhancer function, thus demonstrating that the "gene-battery" model of TE functionalization applies to enhancers in vivo. Our study provides fundamental insights into genome evolution and the origins of anthropoid phenotypes and supports an elegantly simple new null model of TE exaptation.
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Affiliation(s)
- Ricardo C H del Rosario
- Computational and Systems Biology, Genome Institute of Singapore, #02-01 Genome, Singapore 138672
| | - Nirmala Arul Rayan
- Computational and Systems Biology, Genome Institute of Singapore, #02-01 Genome, Singapore 138672
| | - Shyam Prabhakar
- Computational and Systems Biology, Genome Institute of Singapore, #02-01 Genome, Singapore 138672
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50
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Chouinard-Decorte F, McKay DR, Reid A, Khundrakpam B, Zhao L, Karama S, Rioux P, Sprooten E, Knowles E, Kent JW, Curran JE, Göring HHH, Dyer TD, Olvera RL, Kochunov P, Duggirala R, Fox PT, Almasy L, Blangero J, Bellec P, Evans AC, Glahn DC. Heritable changes in regional cortical thickness with age. Brain Imaging Behav 2014; 8:208-16. [PMID: 24752552 PMCID: PMC4205107 DOI: 10.1007/s11682-014-9296-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 02/05/2014] [Indexed: 01/15/2023]
Abstract
It is now well established that regional indices of brain structure such as cortical thickness, surface area or grey matter volume exhibit spatially variable patterns of heritability. However, a recent study found these patterns to change with age during development, a result supported by gene expression studies. Changes in heritability have not been investigated in adulthood so far and could have important implications in the study of heritability and genetic correlations in the brain as well as in the discovery of specific genes explaining them. Herein, we tested for genotype by age (G ×A) interactions, an extension of genotype by environment interactions, through adulthood and healthy aging in 902 subjects from the Genetics of Brain Structure (GOBS) study. A "jackknife" based method for the analysis of stable cortical thickness clusters (JASC) and scale selection is also introduced. Although additive genetic variance remained constant throughout adulthood, we found evidence for incomplete pleiotropy across age in the cortical thickness of paralimbic and parieto-temporal areas. This suggests that different genetic factors account for cortical thickness heritability at different ages in these regions.
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Affiliation(s)
- Francois Chouinard-Decorte
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada
| | - D. Reese McKay
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT 06571, USA
- Olin Neuropsychiatry Research Center, Institute of Living, Hartford, CT 06106, USA
| | - Andrew Reid
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada
| | - Budhachandra Khundrakpam
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada
| | - Lu Zhao
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada
| | - Sherif Karama
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada
- Department of Psychiatry, Douglas Mental Health University Institute, McGill University, Montreal, QC H4H 1R2, Canada
| | - Pierre Rioux
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada
| | - Emma Sprooten
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT 06571, USA
- Olin Neuropsychiatry Research Center, Institute of Living, Hartford, CT 06106, USA
| | - Emma Knowles
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT 06571, USA
- Olin Neuropsychiatry Research Center, Institute of Living, Hartford, CT 06106, USA
| | - Jack W. Kent
- Department of Genetics, Texas Biomedical Research Institute, PO Box 760549, San Antonio, TX 78245, USA
| | - Joanne E. Curran
- Department of Genetics, Texas Biomedical Research Institute, PO Box 760549, San Antonio, TX 78245, USA
| | - Harald H. H. Göring
- Department of Genetics, Texas Biomedical Research Institute, PO Box 760549, San Antonio, TX 78245, USA
| | - Thomas D. Dyer
- Department of Genetics, Texas Biomedical Research Institute, PO Box 760549, San Antonio, TX 78245, USA
| | - Rene L. Olvera
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT 06571, USA
- Olin Neuropsychiatry Research Center, Institute of Living, Hartford, CT 06106, USA
- Department of Psychiatry, Douglas Mental Health University Institute, McGill University, Montreal, QC H4H 1R2, Canada
- Department of Genetics, Texas Biomedical Research Institute, PO Box 760549, San Antonio, TX 78245, USA
- Maryland Psychiatric Research Center, Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD 2120, USA
- Research Imaging Institute, University of Texas Health Science Center San Antonio, 8403 Floyd Curl Dr, San Antonio, TX 78229, USA
- Geriatric Institute Research Center, Université de Montréal, Montréal, QC H3W 1W5, Canada
- Department of Psychiatry, University of Texas Health Science Center San Antonio, 7703 Floyd Curl Drive, San Antonio, TX H3W 1W5, USA
| | - Peter Kochunov
- Maryland Psychiatric Research Center, Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD 2120, USA
| | - Ravi Duggirala
- Department of Genetics, Texas Biomedical Research Institute, PO Box 760549, San Antonio, TX 78245, USA
| | - Peter T. Fox
- Research Imaging Institute, University of Texas Health Science Center San Antonio, 8403 Floyd Curl Dr, San Antonio, TX 78229, USA
| | - Laura Almasy
- Department of Genetics, Texas Biomedical Research Institute, PO Box 760549, San Antonio, TX 78245, USA
| | - John Blangero
- Department of Genetics, Texas Biomedical Research Institute, PO Box 760549, San Antonio, TX 78245, USA
| | - Pierre Bellec
- Geriatric Institute Research Center, Université de Montréal, Montréal, QC H3W 1W5, Canada
| | - Alan C. Evans
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada
| | - David C. Glahn
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT 06571, USA
- Olin Neuropsychiatry Research Center, Institute of Living, Hartford, CT 06106, USA
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