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Strekalova T, Moskvin O, Jain AY, Gorbunov N, Gorlova A, Sadovnik D, Umriukhin A, Cespuglio R, Yu WS, Tse ACK, Kalueff AV, Lesch KP, Lim LW. Molecular signature of excessive female aggression: study of stressed mice with genetic inactivation of neuronal serotonin synthesis. J Neural Transm (Vienna) 2023; 130:1113-1132. [PMID: 37542675 PMCID: PMC10460733 DOI: 10.1007/s00702-023-02677-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 07/21/2023] [Indexed: 08/07/2023]
Abstract
Aggression is a complex social behavior, critically involving brain serotonin (5-HT) function. The neurobiology of female aggression remains elusive, while the incidence of its manifestations has been increasing. Yet, animal models of female aggression are scarce. We previously proposed a paradigm of female aggression in the context of gene x environment interaction where mice with partial genetic inactivation of tryptophan hydroxylase-2 (Tph2+/- mice), a key enzyme of neuronal 5-HT synthesis, are subjected to predation stress resulting in pathological aggression. Using deep sequencing and the EBSeq method, we studied the transcriptomic signature of excessive aggression in the prefrontal cortex of female Tph2+/- mice subjected to rat exposure stress and food deprivation. Challenged mutants, but not other groups, displayed marked aggressive behaviors. We found 26 genes with altered expression in the opposite direction between stressed groups of both Tph2 genotypes. We identified several molecular markers, including Dgkh, Arfgef3, Kcnh7, Grin2a, Tenm1 and Epha6, implicated in neurodevelopmental deficits and psychiatric conditions featuring impaired cognition and emotional dysregulation. Moreover, while 17 regulons, including several relevant to neural plasticity and function, were significantly altered in stressed mutants, no alteration in regulons was detected in stressed wildtype mice. An interplay of the uncovered pathways likely mediates partial Tph2 inactivation in interaction with severe stress experience, thus resulting in excessive female aggression.
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Affiliation(s)
- Tatyana Strekalova
- Division of Molecular Psychiatry, Center of Mental Health, University Hospital of Würzburg, Würzburg, Germany
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University, Maastricht, The Netherlands
| | - Oleg Moskvin
- Primate Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Singapore Medical School, BluMaiden Biosciences, Singapore, Singapore
| | - Aayushi Y Jain
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Nikita Gorbunov
- Division of Molecular Psychiatry, Center of Mental Health, University Hospital of Würzburg, Würzburg, Germany
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University, Maastricht, The Netherlands
| | - Anna Gorlova
- Laboratory of Psychiatric Neurobiology, Institute of Molecular Medicine and Department of Normal Physiology, Sechenov Moscow State Medical University, Moscow, Russia
| | - Daria Sadovnik
- Laboratory of Psychiatric Neurobiology, Institute of Molecular Medicine and Department of Normal Physiology, Sechenov Moscow State Medical University, Moscow, Russia
| | - Aleksei Umriukhin
- Laboratory of Psychiatric Neurobiology, Institute of Molecular Medicine and Department of Normal Physiology, Sechenov Moscow State Medical University, Moscow, Russia
| | - Raymond Cespuglio
- Laboratory of Psychiatric Neurobiology, Institute of Molecular Medicine and Department of Normal Physiology, Sechenov Moscow State Medical University, Moscow, Russia
- Neuroscience Research Center of Lyon, Beliv Plateau, Claude-Bernard Lyon-1 University, Bron, France
| | - Wing Shan Yu
- Neuromodulation Laboratory, School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
| | - Anna Chung Kwan Tse
- Neuromodulation Laboratory, School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
| | - Allan V Kalueff
- Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - Klaus-Peter Lesch
- Division of Molecular Psychiatry, Center of Mental Health, University Hospital of Würzburg, Würzburg, Germany.
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University, Maastricht, The Netherlands.
| | - Lee Wei Lim
- Neuromodulation Laboratory, School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China.
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Dudek SM, Phoenix AN, Scappini E, Shepeleva DV, Herbeck YE, Trut LN, Farris S, Kukekova AV. Defining hippocampal area CA2 in the fox (Vulpes vulpes) brain. Hippocampus 2023; 33:700-711. [PMID: 37159095 PMCID: PMC10274530 DOI: 10.1002/hipo.23546] [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: 02/06/2023] [Revised: 04/05/2023] [Accepted: 04/21/2023] [Indexed: 05/10/2023]
Abstract
Since 1959, the Russian Farm-Fox study has bred foxes to be either tame or, more recently, aggressive, and scientists have used them to gain insight into the brain structures associated with these behavioral features. In mice, hippocampal area CA2 has emerged as one of the essential regulators of social aggression, and so to eventually determine whether we could identify differences in CA2 between tame and aggressive foxes, we first sought to identify CA2 in foxes (Vulpes vulpes). As no clearly defined area of CA2 has been described in species such as cats, dogs, or pigs, it was not at all clear whether CA2 could be identified in foxes. In this study, we cut sections of temporal lobes from male and female red foxes, perpendicular to the long axis of the hippocampus, and stained them with markers of CA2 pyramidal cells commonly used in tissue from rats and mice. We observed that antibodies against Purkinje cell protein 4 best stained the pyramidal cells in the area spanning the end of the mossy fibers and the beginning of the pyramidal cells lacking mossy fibers, resembling the pattern seen in rats and mice. Our findings indicate that foxes do have a "molecularly defined" CA2, and further, they suggest that other carnivores like dogs and cats might as well. With this being the case, these foxes could be useful in future studies looking at CA2 as it relates to aggression.
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Affiliation(s)
- Serena M Dudek
- National Institute of Environmental Health Sciences, NIH, Research Triangle Park, Durham, North Carolina, USA
| | - Ashley N Phoenix
- National Institute of Environmental Health Sciences, NIH, Research Triangle Park, Durham, North Carolina, USA
| | - Erica Scappini
- National Institute of Environmental Health Sciences, NIH, Research Triangle Park, Durham, North Carolina, USA
| | - Darya V Shepeleva
- Siberian Branch of the Russian Academy of Sciences, Institute of Cytology and Genetics, Novosibirsk, Russian Federation
| | - Yury E Herbeck
- Siberian Branch of the Russian Academy of Sciences, Institute of Cytology and Genetics, Novosibirsk, Russian Federation
- Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food & Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Lyudmila N Trut
- Siberian Branch of the Russian Academy of Sciences, Institute of Cytology and Genetics, Novosibirsk, Russian Federation
| | - Shannon Farris
- Fralin Biomedical Research Institute, Virginia Tech, Roanoke, Virginia, USA
| | - Anna V Kukekova
- Department of Animal Science, The University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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3
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Rogers Flattery CN, Abdulla M, Barton SA, Michlich JM, Trut LN, Kukekova AV, Hecht EE. The brain of the silver fox (Vulpes vulpes): a neuroanatomical reference of cell-stained histological and MRI images. Brain Struct Funct 2023; 228:1177-1189. [PMID: 37160458 PMCID: PMC11192273 DOI: 10.1007/s00429-023-02648-5] [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: 07/27/2022] [Accepted: 04/21/2023] [Indexed: 05/11/2023]
Abstract
Although the silver fox (Vulpes vulpes) has been largely overlooked by neuroscientists, it has the potential to serve as a powerful model for the investigation of brain-behavior relationships. The silver fox is a melanistic variant of the red fox. Within this species, the long-running Russian farm-fox experiment has resulted in different strains bred to show divergent behavior. Strains bred for tameness, aggression, or without selection on behavior present an excellent opportunity to investigate neuroanatomical changes underlying behavioral characteristics. Here, we present a histological and MRI neuroanatomical reference of a fox from the conventional strain, which is bred without behavioral selection. This can provide an anatomical basis for future studies of the brains of foxes from this particular experiment, as well as contribute to an understanding of fox brains in general. In addition, this can serve as a resource for comparative neuroscience and investigations into neuroanatomical variation among the family Canidae, the order Carnivora, and mammals more broadly.
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Affiliation(s)
| | - Munawwar Abdulla
- Department of Human Evolutionary Biology, Harvard University, 11 Divinity Ave, Cambridge, MA, 02138, USA
| | - Sophie A Barton
- Department of Human Evolutionary Biology, Harvard University, 11 Divinity Ave, Cambridge, MA, 02138, USA
| | - Jenny M Michlich
- Department of Human Evolutionary Biology, Harvard University, 11 Divinity Ave, Cambridge, MA, 02138, USA
| | - Lyudmila N Trut
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Anna V Kukekova
- Department of Animal Sciences, College of ACES, University of Illinois at Urbana-Champaign, Urbana, USA
| | - Erin E Hecht
- Department of Human Evolutionary Biology, Harvard University, 11 Divinity Ave, Cambridge, MA, 02138, USA.
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4
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Hecht EE, Barton SA, Rogers Flattery CN, Meza Meza A. The evolutionary neuroscience of domestication. Trends Cogn Sci 2023; 27:553-567. [PMID: 37087363 DOI: 10.1016/j.tics.2023.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/17/2023] [Accepted: 03/22/2023] [Indexed: 04/24/2023]
Abstract
How does domestication affect the brain? This question has broad relevance. Domesticated animals play important roles in human society, and substantial recent work has addressed the hypotheses that a domestication syndrome links phenotypes across species, including Homo sapiens. Surprisingly, however, neuroscience research on domestication remains largely disconnected from current knowledge about how and why brains change in evolution. This article aims to bridge that gap. Examination of recent research reveals some commonalities across species, but ultimately suggests that brain changes associated with domestication are complex and variable. We conclude that interactions between behavioral, metabolic, and life-history selection pressures, as well as the role the role of experience and environment, are currently largely overlooked and represent important directions for future research.
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Affiliation(s)
- Erin E Hecht
- Department of Human Evolutionary Biology, Harvard University, 11 Divinity Avenue, Cambridge, MA 02171, USA.
| | - Sophie A Barton
- Department of Human Evolutionary Biology, Harvard University, 11 Divinity Avenue, Cambridge, MA 02171, USA
| | | | - Araceli Meza Meza
- Department of Human Evolutionary Biology, Harvard University, 11 Divinity Avenue, Cambridge, MA 02171, USA
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Odintsova VV, Hagenbeek FA, van der Laan CM, van de Weijer S, Boomsma DI. Genetics and epigenetics of human aggression. HANDBOOK OF CLINICAL NEUROLOGY 2023; 197:13-44. [PMID: 37633706 DOI: 10.1016/b978-0-12-821375-9.00005-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/28/2023]
Abstract
There is substantial variation between humans in aggressive behavior, with its biological etiology and molecular genetic basis mostly unknown. This review chapter offers an overview of genomic and omics studies revealing the genetic contribution to aggression and first insights into associations with epigenetic and other omics (e.g., metabolomics) profiles. We allowed for a broad phenotype definition including studies on "aggression," "aggressive behavior," or "aggression-related traits," "antisocial behavior," "conduct disorder," and "oppositional defiant disorder." Heritability estimates based on family and twin studies in children and adults of this broadly defined phenotype of aggression are around 50%, with relatively small fluctuations around this estimate. Next, we review the genome-wide association studies (GWAS) which search for associations with alleles and also allow for gene-based tests and epigenome-wide association studies (EWAS) which seek to identify associations with differently methylated regions across the genome. Both GWAS and EWAS allow for construction of Polygenic and DNA methylation scores at an individual level. Currently, these predict a small percentage of variance in aggression. We expect that increases in sample size will lead to additional discoveries in GWAS and EWAS, and that multiomics approaches will lead to a more comprehensive understanding of the molecular underpinnings of aggression.
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Affiliation(s)
- Veronika V Odintsova
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands; Amsterdam Reproduction and Development (AR&D) Research Institute, Amsterdam, The Netherlands; Mental Health Division, Amsterdam Public Health (APH) Research Institute, Amsterdam, The Netherlands
| | - Fiona A Hagenbeek
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands; Mental Health Division, Amsterdam Public Health (APH) Research Institute, Amsterdam, The Netherlands
| | - Camiel M van der Laan
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands; Netherlands Institute for the Study of Crime and Law Enforcement (NSCR), Amsterdam, The Netherlands
| | - Steve van de Weijer
- Netherlands Institute for the Study of Crime and Law Enforcement (NSCR), Amsterdam, The Netherlands
| | - Dorret I Boomsma
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands; Amsterdam Reproduction and Development (AR&D) Research Institute, Amsterdam, The Netherlands.
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Lin S, Yi S, Qiu P. Comprehensive analysis of TCGA data reveals correlation between DNA methylation and alternative splicing. BMC Genomics 2022; 23:758. [PMID: 36401166 PMCID: PMC9675104 DOI: 10.1186/s12864-022-08992-w] [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: 04/11/2022] [Accepted: 11/05/2022] [Indexed: 11/21/2022] Open
Abstract
The effect of DNA methylation on the regulation of gene expression has been extensively discussed in the literature. However, the potential association between DNA methylation and alternative splicing is not understood well. In this study, we integrated multiple omics data types from The Cancer Genome Atlas (TCGA) and systematically examined the relationship between DNA methylation and alternative splicing. Using the methylation data and exon expression data, we identified many CpG sites significantly associated with exon expression in various types of cancers. We further observed that the direction and strength of significant CpG-exon correlation tended to be consistent across different cancer contexts, indicating that some CpG-exon correlation patterns reflect fundamental biological mechanisms that transcend tissue- and cancer- types. We also discovered that CpG sites correlated with exon expressions were more likely to be associated with patient survival outcomes compared to CpG sites that did not correlate with exon expressions. Furthermore, we found that CpG sites were more strongly correlated with exon expression than expression of isoforms harboring the corresponding exons. This observation suggests that a major effect of CpG methylation on alternative splicing may be related to the inclusion or exclusion of exons, which subsequently impacts the relative usage of various isoforms. Overall, our study revealed correlation patterns between DNA methylation and alternative splicing, which provides new insights into the role of methylation in the transcriptional process.
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Affiliation(s)
- Shuting Lin
- grid.213917.f0000 0001 2097 4943School of Biological Sciences, Georgia Institute of Technology, Atlanta, USA
| | - Soojin Yi
- grid.133342.40000 0004 1936 9676Ecology, Evolution, Marine Biology, University of California, Santa Barbara, Santa Barbara, USA
| | - Peng Qiu
- grid.213917.f0000 0001 2097 4943Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, USA
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Transcription Factors as Important Regulators of Changes in Behavior through Domestication of Gray Rats: Quantitative Data from RNA Sequencing. Int J Mol Sci 2022; 23:ijms232012269. [PMID: 36293128 PMCID: PMC9603081 DOI: 10.3390/ijms232012269] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/28/2022] [Accepted: 10/12/2022] [Indexed: 11/16/2022] Open
Abstract
Studies on hereditary fixation of the tame-behavior phenotype during animal domestication remain relevant and important because they are of both basic research and applied significance. In model animals, gray rats Rattus norvegicus bred for either an enhancement or reduction in defensive response to humans, for the first time, we used high-throughput RNA sequencing to investigate differential expression of genes in tissue samples from the tegmental region of the midbrain in 2-month-old rats showing either tame or aggressive behavior. A total of 42 differentially expressed genes (DEGs; adjusted p-value < 0.01 and fold-change > 2) were identified, with 20 upregulated and 22 downregulated genes in the tissue samples from tame rats compared with aggressive rats. Among them, three genes encoding transcription factors (TFs) were detected: Ascl3 was upregulated, whereas Fos and Fosb were downregulated in tissue samples from the brains of tame rats brain. Other DEGs were annotated as associated with extracellular matrix components, transporter proteins, the neurotransmitter system, signaling molecules, and immune system proteins. We believe that these DEGs encode proteins that constitute a multifactorial system determining the behavior for which the rats have been artificially selected. We demonstrated that several structural subtypes of E-box motifs—known as binding sites for many developmental TFs of the bHLH class, including the ASCL subfamily of TFs—are enriched in the set of promoters of the DEGs downregulated in the tissue samples of tame rats’. Because ASCL3 may act as a repressor on target genes of other developmental TFs of the bHLH class, we hypothesize that the expression of TF gene Ascl3 in tame rats indicates longer neurogenesis (as compared to aggressive rats), which is a sign of neoteny and domestication. Thus, our domestication model shows a new function of TF ASCL3: it may play the most important role in behavioral changes in animals.
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Trieu-Duc V, Oshima K, Matsumura K, Iwasaki Y, Chiu MT, Nikaido M, Okada N. Alternative splicing plays key roles in response to stress across different stages of fighting in the fish Betta splendens. BMC Genomics 2022; 22:920. [PMID: 35637454 PMCID: PMC9150285 DOI: 10.1186/s12864-022-08609-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 05/06/2022] [Indexed: 12/13/2022] Open
Abstract
Background Aggression is an evolutionarily conserved behavior critical for animal survival. In the fish Betta splendens, across different stages of fighting interactions, fighting opponents suffer from various stressors, especially from the great demand for oxygen. Using RNA sequencing, we profiled differential alternative splicing (DAS) events in the brains of fish collected before fighting, during fighting, and after fighting to study the involvement of alternative splicing (AS) in the response to stress during the fight. Results We found that fighting interactions induced the greatest increase in AS in the ‘during-fighting’ fish, followed by that of the ‘after-fighting’ fish. Intron retention (IR) was the most enriched type among all the basic AS events. DAS genes were mainly associated with synapse assembly, ion transport, and regulation of protein secretion. We further observed that IR events significantly differentiated between winners and losers for 19 genes, which were associated with messenger RNA biogenesis, DNA repair, and transcription machinery. These genes share many common features, including shorter intron length and higher GC content. Conclusions This study is the first comprehensive view of AS induced by fighting interactions in a fish species across different stages of those interactions, especially with respect to IR events in winners and losers. Together, these findings facilitate future investigations into transcriptome complexity and AS regulation in response to stress under the context of aggression in vertebrates. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08609-2.
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Affiliation(s)
- Vu Trieu-Duc
- School of Pharmacy, Kitasato University, Tokyo, Japan.,Life Sciences and Biotechnology Department, Tokyo Institute of Technology, Tokyo, Japan.,Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | | | | | - Yuri Iwasaki
- Nagahama Institute of Bio-Science and Technology, Nagahama, Japan
| | - Ming-Tzu Chiu
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Masato Nikaido
- Life Sciences and Biotechnology Department, Tokyo Institute of Technology, Tokyo, Japan
| | - Norihiro Okada
- School of Pharmacy, Kitasato University, Tokyo, Japan. .,Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan. .,Nagahama Institute of Bio-Science and Technology, Nagahama, Japan.
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Konner M. Is History the Same as Evolution? No. Is it Independent of Evolution? Certainly Not. EVOLUTIONARY PSYCHOLOGY 2022; 20:14747049211069137. [PMID: 35253457 PMCID: PMC10523472 DOI: 10.1177/14747049211069137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 12/08/2021] [Accepted: 12/08/2021] [Indexed: 11/15/2022] Open
Abstract
History is full of violence and oppression within and between groups, and although group conflicts enhance within-group cooperation (mediated by oxytocin, which promotes parochial altruism) the hierarchy within groups ensures that spoils accrue very unevenly. Darwin suggested, and we now know, that sexual selection is as powerful as selection by mortality, and the main purpose of survival is reproduction. Male reproductive skew is greater than that among females in all societies, but the difference became much greater after the hunting-gathering era, and the rise of so-called "civilization" was everywhere a process of predatory expansion, producing kingdoms and empires where top males achieved astounding heights of reproductive success. This was shown by historical and ethnographic data now strongly confirmed by genomic science. Psychological research confirms that group identity, out-group stigmatization, leadership characterized by charisma, the will to power, narcissism, sociopathy, and cruelty, and followership characterized by hypnotic obedience, loss of individuality, and cruelty are integral parts of human nature. We can thank at least ten or twelve millennia of microevolutionary processes such as those described above, all more prominent in males than females. Followers in wars have faced a difficult risk-benefit analysis, but if they survived and won they too could increase their reproductive success through the rape and other sexual exploitation that have accompanied almost all wars. For modern leaders, social monogamy and contraception have separated autocracy from reproductive success, but only partly, and current worldwide autocratic trends still depend on the evolved will to power, obedience, and cruelty.
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Affiliation(s)
- Melvin Konner
- Department of Anthropology, Program in Neuroscience & Behavioral Biology, Atlanta, Georgia, USA
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Fallahshahroudi A, Johnsson M, Sorato E, Ubhayasekera SJKA, Bergquist J, Altimiras J, Jensen P. Effects of the domestic thyroid stimulating hormone receptor (TSHR) variant on the hypothalamic-pituitary-thyroid axis and behavior in chicken. Genetics 2021; 217:1-9. [PMID: 33683367 DOI: 10.1093/genetics/iyaa050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 12/21/2020] [Indexed: 12/18/2022] Open
Abstract
Domestic chickens are less fearful, have a faster sexual development, grow bigger, and lay more eggs than their primary ancestor, the red junglefowl. Several candidate genetic variants selected during domestication have been identified, but only a few studies have directly linked them with distinct phenotypic traits. Notably, a variant of the thyroid stimulating hormone receptor (TSHR) gene has been under strong positive selection over the past millennium, but it's function and mechanisms of action are still largely unresolved. We therefore assessed the abundance of the domestic TSHR variant and possible genomic selection signatures in an extensive data set comprising multiple commercial and village chicken populations as well as wild-living extant members of the genus Gallus. Furthermore, by mean of extensive backcrossing we introgressed the wild-type TSHR variant from red junglefowl into domestic White Leghorn chickens and investigated gene expression, hormone levels, cold adaptation, and behavior in chickens possessing either the wild-type or domestic TSHR variant. While the domestic TSHR was the most common variant in all studied domestic populations and in one of two red junglefowl population, it was not detected in the other Gallus species. Functionally, the individuals with the domestic TSHR variant had a lower expression of the TSHR in the hypothalamus and marginally higher in the thyroid gland than wild-type TSHR individuals. Expression of TSHB and DIO2, two regulators of sexual maturity and reproduction in birds, was higher in the pituitary gland of the domestic-variant chickens. Furthermore, the domestic variant was associated with higher activity in the open field test. Our findings confirm that the spread of the domestic TSHR variant is limited to domesticated chickens, and to a lesser extent, their wild counterpart, the red junglefowl. Furthermore, we showed that effects of genetic variability in TSHR mirror key differences in gene expression and behavior previously described between the red junglefowl and domestic chicken.
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Affiliation(s)
- Amir Fallahshahroudi
- Department of Medical Biochemistry and Microbiology, Biomedical Center (BMC), Uppsala University, Uppsala 752 37, Sweden
| | - Martin Johnsson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala 750 07, Sweden
| | - Enrico Sorato
- Reneco International Wildlife Consultants, Abu Dhabi, UAE
| | | | - Jonas Bergquist
- Department of Chemistry, Biomedical Center (BMC), Uppsala University, Uppsala 75124, Sweden
| | - Jordi Altimiras
- AVIAN Behavioural Genomics and Physiology Group, Department of Physics, Chemistry and Biology (IFM), Linköping University, Linköping 58183, Sweden
| | - Per Jensen
- AVIAN Behavioural Genomics and Physiology Group, Department of Physics, Chemistry and Biology (IFM), Linköping University, Linköping 58183, Sweden
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11
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Huang M, Lai H, Yu Y, Chen X, Wang T, Feng Q. Deep-gated recurrent unit and diet network-based genome-wide association analysis for detecting the biomarkers of Alzheimer's disease. Med Image Anal 2021; 73:102189. [PMID: 34343841 DOI: 10.1016/j.media.2021.102189] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 05/30/2021] [Accepted: 07/16/2021] [Indexed: 01/01/2023]
Abstract
Genome-wide association analysis (GWAS) is a commonly used method to detect the potential biomarkers of Alzheimer's disease (AD). Most existing GWAS methods entail a high computational cost, disregard correlations among imaging data and correlations among genetic data, and ignore various associations between longitudinal imaging and genetic data. A novel GWAS method was proposed to identify potential AD biomarkers and address these problems. A network based on a gated recurrent unit was applied without imputing incomplete longitudinal imaging data to integrate the longitudinal data of variable lengths and extract an image representation. In this study, a modified diet network that can considerably reduce the number of parameters in the genetic network was proposed to perform GWAS between image representation and genetic data. Genetic representation can be extracted in this way. A link between genetic representation and AD was established to detect potential AD biomarkers. The proposed method was tested on a set of simulated data and a real AD dataset. Results of the simulated data showed that the proposed method can accurately detect relevant biomarkers. Moreover, the results of real AD dataset showed that the proposed method can detect some new risk-related genes of AD. Based on previous reports, no research has incorporated a deep-learning model into a GWAS framework to investigate the potential information on super-high-dimensional genetic data and longitudinal imaging data and create a link between imaging genetics and AD for detecting potential AD biomarkers. Therefore, the proposed method may provide new insights into the underlying pathological mechanism of AD.
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Affiliation(s)
- Meiyan Huang
- School of Biomedical Engineering, Southern Medical University, Guangzhou 510515, China; Guangdong Provincial Key Laboratory of Medical Image Processing, Southern Medical University, Guangzhou 510515, China; Guangdong Province Engineering Laboratory for Medical Imaging and Diagnostic Technology, Southern Medical University, Guangzhou 510515, China.
| | - Haoran Lai
- School of Biomedical Engineering, Southern Medical University, Guangzhou 510515, China.
| | - Yuwei Yu
- School of Biomedical Engineering, Southern Medical University, Guangzhou 510515, China.
| | - Xiumei Chen
- School of Biomedical Engineering, Southern Medical University, Guangzhou 510515, China.
| | - Tao Wang
- School of Biomedical Engineering, Southern Medical University, Guangzhou 510515, China.
| | - Qianjin Feng
- School of Biomedical Engineering, Southern Medical University, Guangzhou 510515, China; Guangdong Provincial Key Laboratory of Medical Image Processing, Southern Medical University, Guangzhou 510515, China; Guangdong Province Engineering Laboratory for Medical Imaging and Diagnostic Technology, Southern Medical University, Guangzhou 510515, China.
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12
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Hecht EE, Kukekova AV, Gutman DA, Acland GM, Preuss TM, Trut LN. Neuromorphological Changes following Selection for Tameness and Aggression in the Russian Farm-Fox experiment. J Neurosci 2021; 41:6144-6156. [PMID: 34127519 PMCID: PMC8276742 DOI: 10.1523/jneurosci.3114-20.2021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 05/11/2021] [Accepted: 05/17/2021] [Indexed: 01/13/2023] Open
Abstract
The Russian farm-fox experiment is an unusually long-running and well-controlled study designed to replicate wolf-to-dog domestication. As such, it offers an unprecedented window onto the neural mechanisms governing the evolution of behavior. Here we report evolved changes to gray matter morphology resulting from selection for tameness versus aggressive responses toward humans in a sample of 30 male fox brains. Contrasting with standing ideas on the effects of domestication on brain size, tame foxes did not show reduced brain volume. Rather, gray matter volume in both the tame and aggressive strains was increased relative to conventional farm foxes bred without deliberate selection on behavior. Furthermore, tame- and aggressive-enlarged regions overlapped substantially, including portions of motor, somatosensory, and prefrontal cortex, amygdala, hippocampus, and cerebellum. We also observed differential morphologic covariation across distributed gray matter networks. In one prefrontal-cerebellum network, this covariation differentiated the three populations along the tame-aggressive behavioral axis. Surprisingly, a prefrontal-hypothalamic network differentiated the tame and aggressive foxes together from the conventional strain. These findings indicate that selection for opposite behaviors can influence brain morphology in a similar way.SIGNIFICANCE STATEMENT Domestication represents one of the largest and most rapid evolutionary shifts of life on earth. However, its neural correlates are largely unknown. Here we report the neuroanatomical consequences of selective breeding for tameness or aggression in the seminal Russian farm-fox experiment. Compared with a population of conventional farm-bred control foxes, tame foxes show neuroanatomical changes in the PFC and hypothalamus, paralleling wolf-to-dog shifts. Surprisingly, though, aggressive foxes also show similar changes. Moreover, both strains show increased gray matter volume relative to controls. These results indicate that similar brain adaptations can result from selection for opposite behavior, that existing ideas of brain changes in domestication may need revision, and that significant neuroanatomical change can evolve very quickly, within the span of <100 generations.
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Affiliation(s)
- Erin E Hecht
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138
| | - Anna V Kukekova
- Department of Animal Sciences, College of Agriculture, Consumer, and Environmental Sciences, University of IL Urbana-Champaign, Urbana, IL 61801
| | | | - Gregory M Acland
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, 14853
| | - Todd M Preuss
- Yerkes National Primate Research Center, Emory University, Atlanta, GA 30322
| | - Lyudmila N Trut
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia, 630090
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13
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Romero-Diaz C, Xu C, Campos SM, Herrmann MA, Kusumi K, Hews DK, Martins EP. Brain transcriptomic responses of Yarrow's spiny lizard, Sceloporus jarrovii, to conspecific visual or chemical signals. GENES BRAIN AND BEHAVIOR 2021; 20:e12753. [PMID: 34036739 DOI: 10.1111/gbb.12753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 05/20/2021] [Accepted: 05/24/2021] [Indexed: 11/24/2022]
Abstract
Species with multimodal communication integrate information from social cues in different modalities into behavioral responses that are mediated by changes in gene expression in the brain. Differences in patterns of gene expression between signal modalities may shed light on the neuromolecular mechanisms underlying multisensory processing. Here, we use RNA-Seq to analyze brain transcriptome responses to either chemical or visual social signals in a territorial lizard with multimodal communication. Using an intruder challenge paradigm, we exposed 18 wild-caught, adult, male Sceloporus jarrovii to either male conspecific scents (femoral gland secretions placed on a small pebble), the species-specific push-up display (a programmed robotic model), or a control (an unscented pebble). We conducted differential expression analysis with both a de novo S. jarrovii transcriptome assembly and the reference genome of a closely related species, Sceloporus undulatus. Despite some inter-individual variation, we found significant differences in gene expression in the brain across signal modalities and the control in both analyses. The most notable differences occurred between chemical and visual stimulus treatments, closely followed by visual stimulus versus the control. Altered expression profiles could explain documented aggression differences in the immediate behavioral response to conspecific signals from different sensory modalities. Shared differentially expressed genes between visually- or chemically-stimulated males are involved in neural activity and neurodevelopment and several other differentially expressed genes in stimulus-challenged males are involved in conserved signal-transduction pathways associated with the social stress response, aggression and the response to territory intruders across vertebrates.
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Affiliation(s)
| | - Cindy Xu
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Stephanie M Campos
- Center for Behavioral Neuroscience, Neuroscience Institute, Georgia State University, Atlanta, Georgia, USA
| | - Morgan A Herrmann
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Kenro Kusumi
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Diana K Hews
- Department of Biology, Indiana State University, Terre Haute, Indiana, USA
| | - Emília P Martins
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
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14
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Šimić G, Vukić V, Kopić J, Krsnik Ž, Hof PR. Molecules, Mechanisms, and Disorders of Self-Domestication: Keys for Understanding Emotional and Social Communication from an Evolutionary Perspective. Biomolecules 2020; 11:E2. [PMID: 33375093 PMCID: PMC7822183 DOI: 10.3390/biom11010002] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/18/2020] [Accepted: 12/20/2020] [Indexed: 12/16/2022] Open
Abstract
The neural crest hypothesis states that the phenotypic features of the domestication syndrome are due to a reduced number or disruption of neural crest cells (NCCs) migration, as these cells differentiate at their final destinations and proliferate into different tissues whose activity is reduced by domestication. Comparing the phenotypic characteristics of modern and prehistoric man, it is clear that during their recent evolutionary past, humans also went through a process of self-domestication with a simultaneous prolongation of the period of socialization. This has led to the development of social abilities and skills, especially language, as well as neoteny. Disorders of neural crest cell development and migration lead to many different conditions such as Waardenburg syndrome, Hirschsprung disease, fetal alcohol syndrome, DiGeorge and Treacher-Collins syndrome, for which the mechanisms are already relatively well-known. However, for others, such as Williams-Beuren syndrome and schizophrenia that have the characteristics of hyperdomestication, and autism spectrum disorders, and 7dupASD syndrome that have the characteristics of hypodomestication, much less is known. Thus, deciphering the biological determinants of disordered self-domestication has great potential for elucidating the normal and disturbed ontogenesis of humans, as well as for the understanding of evolution of mammals in general.
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Affiliation(s)
- Goran Šimić
- Department of Neuroscience, Croatian Institute for Brain Research, University of Zagreb Medical School, 10000 Zagreb, Croatia; (V.V.); (J.K.); (Ž.K.)
| | - Vana Vukić
- Department of Neuroscience, Croatian Institute for Brain Research, University of Zagreb Medical School, 10000 Zagreb, Croatia; (V.V.); (J.K.); (Ž.K.)
| | - Janja Kopić
- Department of Neuroscience, Croatian Institute for Brain Research, University of Zagreb Medical School, 10000 Zagreb, Croatia; (V.V.); (J.K.); (Ž.K.)
| | - Željka Krsnik
- Department of Neuroscience, Croatian Institute for Brain Research, University of Zagreb Medical School, 10000 Zagreb, Croatia; (V.V.); (J.K.); (Ž.K.)
| | - Patrick R. Hof
- Nash Family Department of Neuroscience, Friedman Brain Institute, and Ronald M. Loeb Center for Alzheimer’s disease, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
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15
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Zhao Y, Chen H, Li C, Chen S, Xiao H. Comparative Transcriptomics Reveals the Molecular Genetic Basis of Cave Adaptability in Sinocyclocheilus Fish Species. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.589039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Cavefish evolved a series of distinct survival mechanisms for adaptation to cave habitat. Such mechanisms include loss of eyesight and pigmentation, sensitive sensory organs, unique dietary preferences, and predation behavior. Thus, it is of great interest to understand the mechanisms underlying these adaptability traits of troglobites. The teleost genus Sinocyclocheilus (Cypriniformes: Cyprinidae) is endemic to China and has more than 70 species reported (including over 30 cavefish species). High species diversity and diverse phenotypes make the Sinocyclocheilus as an outstanding model for studying speciation and adaptive evolution. In this study, we conducted a comparative transcriptomics study on the brain tissues of two Sinocyclocheilus species (surface-dwelling species – Sinocyclocheilus malacopterus and semi-cave-dwelling species – Sinocyclocheilus rhinocerous living in the same water body. A total of 425,188,768 clean reads were generated, which contributed to 102,839 Unigenes. Bioinformatic analysis revealed a total of 3,289 differentially expressed genes (DEGs) between two species Comparing to S. malacopterus, 2,598 and 691 DEGs were found to be respectively, down-regulated and up-regulated in S. rhinocerous. Furthermore, it is also found tens of DEGs related to cave adaptability such as insulin secretion regulation (MafA, MafB, MafK, BRSK, and CDK16) and troglomorphic traits formation (CEP290, nmnat1, coasy, and pqbp1) in the cave-dwelling S. rhinocerous. Interestingly, most of the DEGs were found to be down-regulated in cavefish species and this trend of DEGs expression was confirmed through qPCR experiments. This study would provide an appropriate genetic basis for future studies on the formation of troglomorphic traits and adaptability characters of troglobites, and improve our understanding of mechanisms of cave adaptation.
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Green MT, Martin RE, Kinkade JA, Schmidt RR, Bivens NJ, Tuteja G, Mao J, Rosenfeld CS. Maternal oxycodone treatment causes pathophysiological changes in the mouse placenta. Placenta 2020; 100:96-110. [PMID: 32891007 PMCID: PMC8112023 DOI: 10.1016/j.placenta.2020.08.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 08/03/2020] [Accepted: 08/05/2020] [Indexed: 12/17/2022]
Abstract
INTRODUCTION Pregnant women are increasingly being prescribed and abusing opioid drugs. As the primary communication organ between mother and conceptus, the placenta may be vulnerable to opioid effects but also holds the key to better understanding how these drugs affect long-term offspring health. We hypothesized that maternal treatment with oxycodone (OXY), the primary opioid at the center of the current crisis, deleteriously affects placental structure and gene expression patterns. METHODS Female mice were treated daily with 5 mg OXY/kg or saline solution (Control, CTL) for two weeks prior to breeding and until placenta were collected at embryonic age 12.5. A portion of the placenta was fixed for histology, and the remainder was frozen for RNA isolation followed by RNAseq. RESULTS Maternal OXY treatment reduced parietal trophoblast giant cell (pTGC) area and decreased the maternal blood vessel area within the labyrinth region. OXY exposure affected placental gene expression profiles in a sex dependent manner with female placenta showing up-regulation of many placental enriched genes, including Ceacam11, Ceacam14, Ceacam12, Ceacam13, Prl7b1, Prl2b1, Ctsq, and Tpbpa. In contrast, placenta of OXY exposed males had alteration of many ribosomal proteins. Weighted correlation network analysis revealed that in OXY female vs. CTL female comparison, select modules correlated with OXY-induced placental histological changes. Such associations were lacking in the male OXY vs. CTL male comparison. DISCUSSION Results suggest OXY exposure alters placental histology. In response to OXY exposure, female placenta responds by upregulating placental enriched transcripts that are either unchanged or downregulated in male placenta. Such changes may shield female offspring from developmental origins of health and disease-based diseases.
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Affiliation(s)
- Madison T Green
- Christopher S Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA; Biomedical Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Rachel E Martin
- Christopher S Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA; Biomedical Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Jessica A Kinkade
- Christopher S Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA; Biomedical Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Robert R Schmidt
- Christopher S Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA; Biomedical Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Nathan J Bivens
- DNA Core Facility, University of Missouri, Columbia, MO, 65211, USA
| | - Geetu Tuteja
- Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 50011, USA
| | - Jiude Mao
- Christopher S Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA; Biomedical Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Cheryl S Rosenfeld
- Christopher S Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA; Biomedical Sciences, University of Missouri, Columbia, MO, 65211, USA; Informatics Institute, University of Missouri, Columbia, MO, 65211, USA; Thompson Center for Autism and Neurobehavioral Disorders, University of Missouri, Columbia, MO, 65211, USA; Genetics Area Program, University of Missouri, Columbia, MO, 65211, USA.
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17
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Charvet CJ. Closing the gap from transcription to the structural connectome enhances the study of connections in the human brain. Dev Dyn 2020; 249:1047-1061. [PMID: 32562584 DOI: 10.1002/dvdy.218] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 06/02/2020] [Accepted: 06/09/2020] [Indexed: 12/11/2022] Open
Abstract
The brain is composed of a complex web of networks but we have yet to map the structural connections of the human brain in detail. Diffusion MR imaging is a high-throughput method that relies on the principle of diffusion to reconstruct tracts (ie, pathways) across the brain. Although diffusion MR tractography is an exciting method to explore the structural connectivity of the brain in development and across species, the tractography has at times led to questionable interpretations. There are at present few if any alternative methods to trace structural pathways in the human brain. Given these limitations and the potential of diffusion MR imaging to map the human connectome, it is imperative that we develop new approaches to validate neuroimaging techniques. I discuss our recent studies integrating neuroimaging with transcriptional and anatomical variation across humans and other species over the course of development and in adulthood. Developing a novel framework to harness the potential of diffusion MR tractography provides new and exciting opportunities to study the evolution of developmental mechanisms generating variation in connections and bridge the gap between model systems to humans.
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18
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Simpson JH. Fear and Foxes: An Educational Primer for Use with "Anterior Pituitary Transcriptome Suggests Differences in ACTH Release in Tame and Aggressive Foxes". Genetics 2020; 215:15-24. [PMID: 32371439 PMCID: PMC7198266 DOI: 10.1534/genetics.120.303046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 03/26/2020] [Indexed: 01/11/2023] Open
Abstract
The way genes contribute to behavior is complicated. Although there are some single genes with large contributions, most behavioral differences are due to small effects from many interacting genes. This makes it hard to identify the genes that cause behavioral differences. Mutagenesis screens in model organisms, selective breeding experiments in animals, comparisons between related populations with different behaviors, and genome-wide association studies in humans are promising and complementary approaches to understanding the heritable aspects of complex behaviors. To connect genes to behaviors requires measuring behavioral differences, locating correlated genetic changes, determining when, where, and how these candidate genes act, and designing causative confirmatory experiments. This area of research has implications from basic discovery science to human mental health.
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Affiliation(s)
- Julie H Simpson
- Department of Molecular, Cellular and Developmental Biology and Neuroscience Research Institute, University of California, Santa Barbara, California 93106-9625
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