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Sun P, Kraus CN, Zhao W, Xu J, Suh S, Nguyen Q, Jia Y, Nair A, Oakes M, Tinoco R, Shiu J, Sun B, Elsensohn A, Atwood SX, Nie Q, Dai X. Single-cell and spatial transcriptomics of vulvar lichen sclerosus reveal multi-compartmental alterations in gene expression and signaling cross-talk. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.14.607986. [PMID: 39211101 PMCID: PMC11361165 DOI: 10.1101/2024.08.14.607986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Vulvar diseases are a critical yet often neglected area of women's health, profoundly affecting patients' quality of life and frequently resulting in long-term physical and psychological challenges. Lichen sclerosus (LS) is a chronic inflammatory skin disorder that predominantly affects the vulva, leading to severe itching, pain, scarring, and an increased risk of malignancy. Despite its profound impact on affected individuals, the molecular pathogenesis of vulvar LS (VLS) is not well understood, hindering the development of FDA-approved therapies. Here, we utilize single-cell and spatial transcriptomics to analyze lesional and non-lesional skin from VLS patients, as well as healthy control vulvar skin. Our findings demonstrate histologic, cellular, and molecular heterogeneities within VLS, yet highlight unifying molecular changes across keratinocytes, fibroblasts, immune cells, and melanocytes in lesional skin. They reveal cellular stress and damage in fibroblasts and keratinocytes, enhanced T cell activation and cytotoxicity, aberrant cell-cell signaling, and increased activation of the IFN, JAK/STAT, and p53 pathways in specific cell types. Using both monolayer and organotypic culture models, we also demonstrate that knockdown of select genes, which are downregulated in VLS lesional keratinocytes, partially recapitulates VLS-like stress-associated changes. Collectively, these data provide novel insights into the pathogenesis of VLS, identifying potential biomarkers and therapeutic targets for future research.
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2
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Wang J, Liu D, Tian E, Zhang Y, Guo Z, Chen J, Guo J, Zhou Z, Shi S, Lu Y, Zhang S. Molecular profile of vestibular compensation in the medial vestibular nucleus after unilateral labyrinthectomy. J Cell Mol Med 2024; 28:e18532. [PMID: 39039705 PMCID: PMC11263133 DOI: 10.1111/jcmm.18532] [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: 03/20/2024] [Revised: 05/30/2024] [Accepted: 06/04/2024] [Indexed: 07/24/2024] Open
Abstract
Long non-coding RNAs (lncRNAs) have emerged as crucial regulators in the central nervous system, yet their role in vestibular compensation remains elusive. To address this knowledge gap, we employed unilateral labyrinthectomy (UL) in rats to establish animal models of peripheral vestibular dysfunction. Utilizing ribonucleic acid sequencing (RNA-seq), we comprehensively analysed the expression profiles of genes dysregulated in the medial vestibular nucleus (MVN) of these rats at distinct time points: 4 h, 4 days, and 14 days post-UL. Through trans-target prediction analysis integrating differentially co-expressed messenger RNAs (mRNAs) and lncRNAs, we constructed lncRNA-mRNA regulatory networks. Validation of selected mRNAs and lncRNAs was performed using RT-qPCR. Our RNA-seq analysis revealed significant aberrant expression of 3054 lncRNAs and 1135 mRNAs compared to control samples. By applying weighted gene co-expression network analysis (WGCNA), we identified 11 co-expressed modules encompassing all genes. Notably, within the MEmagenta module, we observed an initial upregulation of differentially expressed genes (DEGs) at 4 h, followed by downregulation at 4- and 14-days post-UL. Our findings indicated that 3068 lncRNAs positively regulated 1259 DEGs, while 1482 lncRNAs negatively regulated 433 DEGs in the MVN. The RT-qPCR results corroborated the RNA-seq data, validating our findings. This study offers novel insights into the lncRNA-mRNA expression landscape during vestibular compensation, paving the way for further exploration of lncRNA functions in this context.
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Affiliation(s)
- Jun Wang
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Institute of Otorhinolaryngology, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubeiChina
| | - Dan Liu
- Department of OtorhinolaryngologyThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - E. Tian
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Institute of Otorhinolaryngology, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubeiChina
| | - Yuejin Zhang
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Department of Physiology, School of Basic MedicineHuazhong University of Science and TechnologyWuhanChina
| | - Zhaoqi Guo
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Institute of Otorhinolaryngology, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubeiChina
| | - Jingyu Chen
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Institute of Otorhinolaryngology, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubeiChina
| | - Jiaqi Guo
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Institute of Otorhinolaryngology, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubeiChina
| | - Zhanghong Zhou
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Institute of Otorhinolaryngology, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubeiChina
| | - Shiyu Shi
- Department of Rehabilitation, Liyuan Hospital of Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Yisheng Lu
- Department of Physiology, School of Basic MedicineHuazhong University of Science and TechnologyWuhanChina
| | - Sulin Zhang
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Institute of Otorhinolaryngology, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubeiChina
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3
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Xuan C, Cui H, Jin Z, Yue Y, Cao S, Cui S, Xu D. Glutamine ameliorates hyperoxia-induced hippocampal damage by attenuating inflammation and apoptosis via the MKP-1/MAPK signaling pathway in neonatal rats. Front Pharmacol 2023; 14:1096309. [PMID: 36817145 PMCID: PMC9932780 DOI: 10.3389/fphar.2023.1096309] [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: 11/12/2022] [Accepted: 01/20/2023] [Indexed: 02/05/2023] Open
Abstract
Glutamine (Gln) is an immunomodulatory protein that mediates oxidative stress, inflammation, and apoptosis, but has not been reported in the treatment of hyperoxia (Hyp)-induced brain injury. The aim of this study was to determine whether Gln could improve hyp-induced brain injury in neonatal rats to and later learning and memory dysfunction, and to explore its possible mechanisms. We prepared a model of neonatal rat brain injury caused by normobaric hyperoxia while administered with Gln for 7 days for evaluation. Learning memory function was assessed with the Morris water maze test. Histological analysis, protein expression analysis, oxidative stress and inflammation level analysis were performed using hippocampal tissue. Gln treatment significantly reduced brain tissue water content, oxidative stress levels, microglia activation and inflammatory factor expression, and attenuated tissue damage and apoptosis in the hippocampal region. Gln ameliorates hyp-induced learning, memory impairment in neonatal rats in water maze test. It also increased MKP-1 protein expression and decreased p-p38, p-ERK and p-JNK. Therefore, it is hypothesized that Gln may exert neuroprotective effects by increasing MKP-1 expression to negatively regulate MAPK signaling, with potential cognitive improvement in hyp-induced brain injury.
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Affiliation(s)
- Chouhui Xuan
- Department of Pediatrics, Yanbian University Hospital, Yanji, Jilin, China
| | - Haixia Cui
- Department of Clinical Laboratory, Yanbian University Hospital, Yanji, Jilin, China
| | - Zhengyong Jin
- Department of Pediatrics, Yanbian University Hospital, Yanji, Jilin, China
| | - Yuyang Yue
- Department of Dermatology, Yanbian University Hospital, Yanji, Jilin, China
| | - Shuxia Cao
- Department of Center of Morphological Experiment, Yanbian University, Yanji, Jilin, China
| | - Songbiao Cui
- Department of Neurology, Yanbian University Hospital, Yanji, Jilin, China,*Correspondence: Songbiao Cui, ; Dongyuan Xu,
| | - Dongyuan Xu
- Key Laboratory of Cellular Function and Pharmacology of Jilin Province, Yanbian University, Yanji, China,*Correspondence: Songbiao Cui, ; Dongyuan Xu,
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Biegler MT, Fedrigo O, Collier P, Mountcastle J, Haase B, Tilgner HU, Jarvis ED. Induction of an immortalized songbird cell line allows for gene characterization and knockout by CRISPR-Cas9. Sci Rep 2022; 12:4369. [PMID: 35288582 PMCID: PMC8921232 DOI: 10.1038/s41598-022-07434-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 02/14/2022] [Indexed: 12/20/2022] Open
Abstract
The zebra finch is one of the most commonly studied songbirds in biology, particularly in genomics, neuroscience and vocal communication. However, this species lacks a robust cell line for molecular biology research and reagent optimization. We generated a cell line, designated CFS414, from zebra finch embryonic fibroblasts using the SV40 large and small T antigens. This cell line demonstrates an improvement over previous songbird cell lines through continuous and density-independent growth, allowing for indefinite culture and monoclonal line derivation. Cytogenetic, genomic, and transcriptomic profiling established the provenance of this cell line and identified the expression of genes relevant to ongoing songbird research. Using this cell line, we disrupted endogenous gene sequences using S.aureus Cas9 and confirmed a stress-dependent localization response of a song system specialized gene, SAP30L. The utility of CFS414 cells enhances the comprehensive molecular potential of the zebra finch and validates cell immortalization strategies in a songbird species.
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Affiliation(s)
- Matthew T Biegler
- Laboratory of Neurogenetics of Language, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - Olivier Fedrigo
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, 10065, USA
| | - Paul Collier
- Center for Neurogenetics, Graduate School of Medical Sciences, Weil Cornell Medical Center, New York, NY, 10065, USA
| | | | - Bettina Haase
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, 10065, USA
| | - Hagen U Tilgner
- Center for Neurogenetics, Graduate School of Medical Sciences, Weil Cornell Medical Center, New York, NY, 10065, USA
| | - Erich D Jarvis
- Laboratory of Neurogenetics of Language, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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5
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Biegler MT, Cantin LJ, Scarano DL, Jarvis ED. Controlling for activity-dependent genes and behavioral states is critical for determining brain relationships within and across species. J Comp Neurol 2021; 529:3206-3221. [PMID: 33855704 PMCID: PMC8205984 DOI: 10.1002/cne.25157] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 03/16/2021] [Accepted: 03/19/2021] [Indexed: 12/16/2022]
Abstract
The genetic profile of vertebrate pallia has long driven debate on homology across distantly related clades. Based on an expression profile of the orphan nuclear receptor NR4A2 in mouse and chicken brains, Puelles et al. (The Journal of Comparative Neurology, 2016, 524, 665–703) concluded that the avian lateral mesopallium is homologous to the mammalian claustrum, and the medial mesopallium homologous to the insula cortex. They argued that their findings contradict conclusions by Jarvis et al. (The Journal of Comparative Neurology, 2013, 521, 3614–3665) and Chen et al. (The Journal of Comparative Neurology, 2013, 521, 3666–3701) that the hyperpallium densocellare is instead a mesopallium cell population, and by Suzuki and Hirata (Frontiers in Neuroanatomy, 2014, 8, 783) that the avian mesopallium is homologous to mammalian cortical layers 2/3. Here, we find that NR4A2 is an activity‐dependent gene and cannot be used to determine brain organization or species relationships without considering behavioral state. Activity‐dependent NR4A2 expression has been previously demonstrated in the rodent brain, with the highest induction occurring within the claustrum, amygdala, deep and superficial cortical layers, and hippocampus. In the zebra finch, we find that NR4A2 is constitutively expressed in the arcopallium, but induced in parts of the mesopallium, and in sparse cells within the hyperpallium, depending on animal stimulus or behavioral state. Basal and induced NR4A2 expression patterns do not discount the previously named avian hyperpallium densocellare as dorsal mesopallium and conflict with proposed homology between the avian mesopallium and mammalian claustrum/insula at the exclusion of other brain regions. Broadly, these findings highlight the importance of controlling for behavioral state and neural activity to genetically define brain cell population relationships within and across species.
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Affiliation(s)
- Matthew T Biegler
- Department of Neurobiology, Duke University Medical Center, Durham, North Carolina, USA.,Laboratory of Neurogenetics of Language, The Rockefeller University, New York, New York, USA
| | - Lindsey J Cantin
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, New York, USA
| | - Danielle L Scarano
- Department of Neurobiology, Duke University Medical Center, Durham, North Carolina, USA
| | - Erich D Jarvis
- Department of Neurobiology, Duke University Medical Center, Durham, North Carolina, USA.,Laboratory of Neurogenetics of Language, The Rockefeller University, New York, New York, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
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6
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Wang Y, Chung DH, Monteleone LR, Li J, Chiang Y, Toney MD, Beal PA. RNA binding candidates for human ADAR3 from substrates of a gain of function mutant expressed in neuronal cells. Nucleic Acids Res 2020; 47:10801-10814. [PMID: 31552420 PMCID: PMC6846710 DOI: 10.1093/nar/gkz815] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 08/26/2019] [Accepted: 09/16/2019] [Indexed: 12/18/2022] Open
Abstract
Human ADAR3 is a catalytically inactive member of the Adenosine Deaminase Acting on RNA (ADAR) protein family, whose active members catalyze A-to-I RNA editing in metazoans. Until now, the reasons for the catalytic incapability of ADAR3 has not been defined and its biological function rarely explored. Yet, its exclusive expression in the brain and involvement in learning and memory suggest a central role in the nervous system. Here we describe the engineering of a catalytically active ADAR3 enzyme using a combination of computational design and functional screening. Five mutations (A389V, V485I, E527Q, Q549R and Q733D) engender RNA deaminase in human ADAR3. By way of its catalytic activity, the ADAR3 pentamutant was used to identify potential binding targets for wild type ADAR3 in a human glioblastoma cell line. Novel ADAR3 binding sites discovered in this manner include the 3'-UTRs of the mRNAs encoding early growth response 1 (EGR1) and dual specificity phosphatase 1 (DUSP1); both known to be activity-dependent immediate early genes that respond to stimuli in the brain. Further studies reveal that the wild type ADAR3 protein can regulate transcript levels for DUSP1 and EGR1, suggesting a novel role ADAR3 may play in brain function.
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Affiliation(s)
- Yuru Wang
- Department of Chemistry, University of California, One Shields Ave, Davis, CA 95616, USA
| | - Dong Hee Chung
- Department of Chemistry, University of California, One Shields Ave, Davis, CA 95616, USA
| | - Leanna R Monteleone
- Department of Chemistry, University of California, One Shields Ave, Davis, CA 95616, USA
| | - Jie Li
- Department of Chemistry, University of California, One Shields Ave, Davis, CA 95616, USA
| | - Yao Chiang
- Department of Chemistry, University of California, One Shields Ave, Davis, CA 95616, USA
| | - Michael D Toney
- Department of Chemistry, University of California, One Shields Ave, Davis, CA 95616, USA
| | - Peter A Beal
- Department of Chemistry, University of California, One Shields Ave, Davis, CA 95616, USA
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Unno K, Pervin M, Taguchi K, Konishi T, Nakamura Y. Green Tea Catechins Trigger Immediate-Early Genes in the Hippocampus and Prevent Cognitive Decline and Lifespan Shortening. Molecules 2020; 25:molecules25071484. [PMID: 32218277 PMCID: PMC7181211 DOI: 10.3390/molecules25071484] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 03/21/2020] [Accepted: 03/23/2020] [Indexed: 12/14/2022] Open
Abstract
Senescence-accelerated mouse prone 10 (SAMP10) mice, after ingesting green tea catechins (GT-catechin, 60 mg/kg), were found to have suppressed aging-related decline in brain function. The dose dependence of brain function on GT-catechin indicated that intake of 1 mg/kg or more suppressed cognitive decline and a shortened lifespan. Mice that ingested 1 mg/kg GT-catechin had the longest median survival, but the dose was less effective at suppressing cognitive decline. The optimal dose for improving memory acquisition was 60 mg/kg, and memory retention was higher in mice that ingested 30 mg/kg or more. To elucidate the mechanism by which cognitive decline is suppressed by GT-catechin, changes in gene expression in the hippocampus of SAMP10 mice one month after ingesting GT-catechin were analyzed. The results show that the expression of immediate-early genes such as nuclear receptor subfamily 4 (Nr4a), FBJ osteosarcoma oncogene (Fos), early growth response 1 (Egr1), neuronal PAS domain protein 4 (Npas4), and cysteine-rich protein 61 (Cyr61) was significantly increased. These results suggest that GT-catechin suppresses age-related cognitive decline via increased expression of immediate-early genes that are involved in long-term changes in plasticity of synapses and neuronal circuits.
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Affiliation(s)
- Keiko Unno
- Tea Science Center, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan; (M.P.); (K.T.); (Y.N.)
- Correspondence: ; Tel.: +81-54-264-5822
| | - Monira Pervin
- Tea Science Center, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan; (M.P.); (K.T.); (Y.N.)
| | - Kyoko Taguchi
- Tea Science Center, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan; (M.P.); (K.T.); (Y.N.)
| | - Tomokazu Konishi
- Faculty of Bioresources Sciences, Akita Prefectural University, Shimoshinjo Nakano, Akita 010-0195, Japan;
| | - Yoriyuki Nakamura
- Tea Science Center, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan; (M.P.); (K.T.); (Y.N.)
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8
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Woolley SC, Woolley SMN. Integrating Form and Function in the Songbird Auditory Forebrain. THE NEUROETHOLOGY OF BIRDSONG 2020. [DOI: 10.1007/978-3-030-34683-6_5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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9
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Louder MIM, Lawson S, Lynch KS, Balakrishnan CN, Hauber ME. Neural mechanisms of auditory species recognition in birds. Biol Rev Camb Philos Soc 2019; 94:1619-1635. [PMID: 31066222 DOI: 10.1111/brv.12518] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 04/12/2019] [Accepted: 04/15/2019] [Indexed: 01/23/2023]
Abstract
Auditory communication in humans and other animals frequently takes place in noisy environments with many co-occurring signallers. Receivers are thus challenged to rapidly recognize salient auditory signals and filter out irrelevant sounds. Most bird species produce a variety of complex vocalizations that function to communicate with other members of their own species and behavioural evidence broadly supports preferences for conspecific over heterospecific sounds (auditory species recognition). However, it remains unclear whether such auditory signals are categorically recognized by the sensory and central nervous system. Here, we review 53 published studies that compare avian neural responses between conspecific versus heterospecific vocalizations. Irrespective of the techniques used to characterize neural activity, distinct nuclei of the auditory forebrain are consistently shown to be repeatedly conspecific selective across taxa, even in response to unfamiliar individuals with distinct acoustic properties. Yet, species-specific neural discrimination is not a stereotyped auditory response, but is modulated according to its salience depending, for example, on ontogenetic exposure to conspecific versus heterospecific stimuli. Neuromodulators, in particular norepinephrine, may mediate species recognition by regulating the accuracy of neuronal coding for salient conspecific stimuli. Our review lends strong support for neural structures that categorically recognize conspecific signals despite the highly variable physical properties of the stimulus. The available data are in support of a 'perceptual filter'-based mechanism to determine the saliency of the signal, in that species identity and social experience combine to influence the neural processing of species-specific auditory stimuli. Finally, we present hypotheses and their testable predictions, to propose next steps in species-recognition research into the emerging model of the neural conceptual construct in avian auditory recognition.
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Affiliation(s)
- Matthew I M Louder
- Department of Evolution, Ecology and Behavior, School of Integrative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, U.S.A
| | - Shelby Lawson
- Department of Evolution, Ecology and Behavior, School of Integrative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, U.S.A
| | - Kathleen S Lynch
- Department of Biology, Hofstra University, Hempstead, NY 11759, U.S.A
| | | | - Mark E Hauber
- Department of Evolution, Ecology and Behavior, School of Integrative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, U.S.A
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10
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Benítez-Burraco A, Kimura R. Robust Candidates for Language Development and Evolution Are Significantly Dysregulated in the Blood of People With Williams Syndrome. Front Neurosci 2019; 13:258. [PMID: 30971880 PMCID: PMC6444191 DOI: 10.3389/fnins.2019.00258] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 03/05/2019] [Indexed: 01/06/2023] Open
Abstract
Williams syndrome (WS) is a clinical condition, involving cognitive deficits and an uneven language profile, which has been the object of intense inquiry over the last decades. Although WS results from the hemideletion of around two dozen genes in chromosome 7, no gene has yet been probed to account for, or contribute significantly to, the language problems exhibited by the affected people. In this paper we have relied on gene expression profiles in the peripheral blood of WS patients obtained by microarray analysis and show that several robust candidates for language disorders and/or for language evolution in the species, all of them located outside the hemideleted region, are up- or downregulated in the blood of subjects with WS. Most of these genes play a role in the development and function of brain areas involved in language processing, which exhibit structural and functional anomalies in people with this condition. Overall, these genes emerge as robust candidates for language dysfunction in WS.
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Affiliation(s)
- Antonio Benítez-Burraco
- Department of Spanish, Linguistics, and Theory of Literature (Linguistics), Faculty of Philology, University of Seville, Seville, Spain
| | - Ryo Kimura
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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11
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Oshigiri T, Sasaki T, Sasaki M, Kataoka-Sasaki Y, Nakazaki M, Oka S, Morita T, Hirota R, Yoshimoto M, Yamashita T, Hashimoto-Torii K, Honmou O. Intravenous Infusion of Mesenchymal Stem Cells Alters Motor Cortex Gene Expression in a Rat Model of Acute Spinal Cord Injury. J Neurotrauma 2018; 36:411-420. [PMID: 29901416 DOI: 10.1089/neu.2018.5793] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Recent evidence has demonstrated that remote responses in the brain, as well as local responses in the injured spinal cord, can be induced after spinal cord injury (SCI). Intravenous infusion of mesenchymal stem cells (MSCs) has been shown to provide functional improvements in SCI through local therapeutic mechanisms that provide neuroprotection, stabilization of the blood-spinal cord barrier, remyelination, and axonal sprouting. In the present study, we examined the brain response that might be associated with the functional improvements induced by the infused MSCs after SCI. Genome-wide RNA profiling was performed in the motor cortex of SCI rats at 3 days post-MSC or vehicle infusion. Then, quantitative reverse transcription-polymerase chain reaction (qRT-PCR) data revealed that the "behaviorally-associated differentially expressed genes (DEGs)" were identified by the Pearson's correlation analysis with the behavioral function, suggesting that the "behaviorally-associated DEGs" may be related to the functional recovery after systemic infusion of MSCs in SCI. These results suggested that the infused MSCs alter the gene expression signature in the brain and that these expression changes may contribute to the improved function in SCI.
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Affiliation(s)
- Tsutomu Oshigiri
- 1 Department of Neural Regenerative Medicine, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, Sapporo, Japan.,2 Department of Orthopaedic Surgery, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Toru Sasaki
- 3 Center for Neuroscience Research, Children's Research Institute, Children's National Medical Center, Washington, DC
| | - Masanori Sasaki
- 1 Department of Neural Regenerative Medicine, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Yuko Kataoka-Sasaki
- 1 Department of Neural Regenerative Medicine, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Masahito Nakazaki
- 1 Department of Neural Regenerative Medicine, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Shinichi Oka
- 1 Department of Neural Regenerative Medicine, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Tomonori Morita
- 1 Department of Neural Regenerative Medicine, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, Sapporo, Japan.,2 Department of Orthopaedic Surgery, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Ryosuke Hirota
- 1 Department of Neural Regenerative Medicine, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, Sapporo, Japan.,2 Department of Orthopaedic Surgery, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Mitsunori Yoshimoto
- 2 Department of Orthopaedic Surgery, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Toshihiko Yamashita
- 2 Department of Orthopaedic Surgery, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Kazue Hashimoto-Torii
- 3 Center for Neuroscience Research, Children's Research Institute, Children's National Medical Center, Washington, DC.,4 Department of Pediatrics, Pharmacology, and Physiology, School of Medicine and Health Sciences, George Washington University, Washington, DC.,5 Department of Neurobiology, School of Medicine, Yale University, New Haven, Connecticut
| | - Osamu Honmou
- 1 Department of Neural Regenerative Medicine, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, Sapporo, Japan
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12
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Korlach J, Gedman G, Kingan SB, Chin CS, Howard JT, Audet JN, Cantin L, Jarvis ED. De novo PacBio long-read and phased avian genome assemblies correct and add to reference genes generated with intermediate and short reads. Gigascience 2018; 6:1-16. [PMID: 29020750 PMCID: PMC5632298 DOI: 10.1093/gigascience/gix085] [Citation(s) in RCA: 138] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 08/23/2017] [Indexed: 01/27/2023] Open
Abstract
Reference-quality genomes are expected to provide a resource for studying gene structure, function, and evolution. However, often genes of interest are not completely or accurately assembled, leading to unknown errors in analyses or additional cloning efforts for the correct sequences. A promising solution is long-read sequencing. Here we tested PacBio-based long-read sequencing and diploid assembly for potential improvements to the Sanger-based intermediate-read zebra finch reference and Illumina-based short-read Anna's hummingbird reference, 2 vocal learning avian species widely studied in neuroscience and genomics. With DNA of the same individuals used to generate the reference genomes, we generated diploid assemblies with the FALCON-Unzip assembler, resulting in contigs with no gaps in the megabase range, representing 150-fold and 200-fold improvements over the current zebra finch and hummingbird references, respectively. These long-read and phased assemblies corrected and resolved what we discovered to be numerous misassemblies in the references, including missing sequences in gaps, erroneous sequences flanking gaps, base call errors in difficult-to-sequence regions, complex repeat structure errors, and allelic differences between the 2 haplotypes. These improvements were validated by single long-genome and transcriptome reads and resulted for the first time in completely resolved protein-coding genes widely studied in neuroscience and specialized in vocal learning species. These findings demonstrate the impact of long reads, sequencing of previously difficult-to-sequence regions, and phasing of haplotypes on generating the high-quality assemblies necessary for understanding gene structure, function, and evolution.
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Affiliation(s)
| | - Gregory Gedman
- Laboratory of Neurogenetics of Language, Box 54, The Rockefeller University, New York, NY 10065, USA
| | | | | | - Jason T Howard
- Laboratory of Neurogenetics of Language, Box 54, The Rockefeller University, New York, NY 10065, USA
| | - Jean-Nicolas Audet
- Laboratory of Neurogenetics of Language, Box 54, The Rockefeller University, New York, NY 10065, USA.,Department of Biology, McGill University, Montreal, Quebec H3A 1B1, Canada
| | - Lindsey Cantin
- Laboratory of Neurogenetics of Language, Box 54, The Rockefeller University, New York, NY 10065, USA
| | - Erich D Jarvis
- Laboratory of Neurogenetics of Language, Box 54, The Rockefeller University, New York, NY 10065, USA.,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
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Ahmadiantehrani S, Gores EO, London SE. A complex mTOR response in habituation paradigms for a social signal in adult songbirds. ACTA ACUST UNITED AC 2018; 25:273-282. [PMID: 29764973 PMCID: PMC5959225 DOI: 10.1101/lm.046417.117] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 03/19/2018] [Indexed: 01/27/2023]
Abstract
Nonassociative learning is considered simple because it depends on presentation of a single stimulus, but it likely reflects complex molecular signaling. To advance understanding of the molecular mechanisms of one form of nonassociative learning, habituation, for ethologically relevant signals we examined song recognition learning in adult zebra finches. These colonial songbirds learn the unique song of individuals, which helps establish and maintain mate and other social bonds, and informs appropriate behavioral interactions with specific birds. We leveraged prior work demonstrating behavioral habituation for individual songs, and extended the molecular framework correlated with this behavior by investigating the mechanistic Target of Rapamycin (mTOR) signaling cascade. We hypothesized that mTOR may contribute to habituation because it integrates a variety of upstream signals and enhances associative learning, and it crosstalks with another cascade previously associated with habituation, ERK/ZENK. To begin probing for a possible role for mTOR in song recognition learning, we used a combination of song playback paradigms and bidirectional dysregulation of mTORC1 activation. We found that mTOR demonstrates the molecular signatures of a habituation mechanism, and that its manipulation reveals the complexity of processes that may be invoked during nonassociative learning. These results thus expand the molecular targets for habituation studies and raise new questions about neural processing of complex natural signals.
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Affiliation(s)
- Somayeh Ahmadiantehrani
- Department of Psychology, Institute for Mind and Biology, Grossman Institute for Neuroscience, Quantitative Biology and Human Behavior, University of Chicago, Chicago, Illinois 60637, USA
| | - Elisa O Gores
- Department of Psychology, Institute for Mind and Biology, Grossman Institute for Neuroscience, Quantitative Biology and Human Behavior, University of Chicago, Chicago, Illinois 60637, USA
| | - Sarah E London
- Department of Psychology, Institute for Mind and Biology, Grossman Institute for Neuroscience, Quantitative Biology and Human Behavior, University of Chicago, Chicago, Illinois 60637, USA
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14
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Pan WK, Zhang YF, Yu H, Gao Y, Zheng BJ, Li P, Xie C, Ge X. Identifying key genes associated with Hirschsprung's disease based on bioinformatics analysis of RNA-sequencing data. World J Pediatr 2017; 13:267-273. [PMID: 28120235 PMCID: PMC7091079 DOI: 10.1007/s12519-017-0002-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 08/25/2016] [Indexed: 01/17/2023]
Abstract
BACKGROUND Hirschsprung's disease (HSCR) is a type of megacolon induced by deficiency or dysfunction of ganglion cells in the distal intestine and is associated with developmental disorders of the enteric nervous system. To explore the mechanisms of HSCR, we analyzed the RNA-sequencing data of the expansion and the narrow segments of colon tissues separated from children with HSCR. METHODS RNA-sequencing of the expansion segments and the narrow segments of colon tissues isolated from children with HSCR was performed. After differentially expressed genes (DEGs) were identified using the edgeR package in R, functional and pathway enrichment analyses of DEGs were carried out using DAVID software. To further screen the key genes, protein-protein interaction (PPI) network and module analyses were conducted separately using Cytoscape software. RESULTS A total of 117 DEGs were identified in the expansion segment samples, including 47 up-regulated and 70 down-regulated genes. Functional enrichment analysis suggested that FOS and DUSP1 were implicated in response to endogenous stimulus. In the PPI network analysis, FOS (degree=20), EGR1 (degree=16), ATF3 (degree=9), NOS1 (degree=8), CCL5 (degree=8), DUSP1 (degree=7), CXCL3 (degree=6), VIP (degree=6), FOSB (degree=5), and NOS2 (degree=4) had higher degrees, which could interact with other genes. In addition, two significant modules (module 1 and module 2) were identified from the PPI network. CONCLUSIONS Several genes (including FOS, EGR1, ATF3, NOS1, CCL5, DUSP1, CXCL3, VIP, FOSB, and NOS2) might be involved in the development of HSCR through their effect on the nervous system.
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Affiliation(s)
- Wei-Kang Pan
- Department of Pediatric Surgery, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710004 China
| | - Ya-Fei Zhang
- Department of Endoscopy, Shaanxi Nuclear Industry 215 Hospital, Xianyang, 712000 China
| | - Hui Yu
- Department of Pediatric Surgery, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710004 China
| | - Ya Gao
- Department of Pediatric Surgery, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710004, China.
| | - Bai-Jun Zheng
- Department of Pediatric Surgery, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710004 China
| | - Peng Li
- Department of Pediatric Surgery, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710004 China
| | - Chong Xie
- Department of Pediatric Surgery, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710004 China
| | - Xin Ge
- Department of Pediatric Surgery, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710004 China
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15
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Wheatcroft D, Qvarnström A. A blueprint for vocal learning: auditory predispositions from brains to genomes. Biol Lett 2016; 11:rsbl.2015.0155. [PMID: 26246333 DOI: 10.1098/rsbl.2015.0155] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Memorizing and producing complex strings of sound are requirements for spoken human language. We share these behaviours with likely more than 4000 species of songbirds, making birds our primary model for studying the cognitive basis of vocal learning and, more generally, an important model for how memories are encoded in the brain. In songbirds, as in humans, the sounds that a juvenile learns later in life depend on auditory memories formed early in development. Experiments on a wide variety of songbird species suggest that the formation and lability of these auditory memories, in turn, depend on auditory predispositions that stimulate learning when a juvenile hears relevant, species-typical sounds. We review evidence that variation in key features of these auditory predispositions are determined by variation in genes underlying the development of the auditory system. We argue that increased investigation of the neuronal basis of auditory predispositions expressed early in life in combination with modern comparative genomic approaches may provide insights into the evolution of vocal learning.
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Affiliation(s)
- David Wheatcroft
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Anna Qvarnström
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
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16
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Chakraborty M, Walløe S, Nedergaard S, Fridel EE, Dabelsteen T, Pakkenberg B, Bertelsen MF, Dorrestein GM, Brauth SE, Durand SE, Jarvis ED. Core and Shell Song Systems Unique to the Parrot Brain. PLoS One 2015; 10:e0118496. [PMID: 26107173 PMCID: PMC4479475 DOI: 10.1371/journal.pone.0118496] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 01/19/2015] [Indexed: 11/19/2022] Open
Abstract
The ability to imitate complex sounds is rare, and among birds has been found only in parrots, songbirds, and hummingbirds. Parrots exhibit the most advanced vocal mimicry among non-human animals. A few studies have noted differences in connectivity, brain position and shape in the vocal learning systems of parrots relative to songbirds and hummingbirds. However, only one parrot species, the budgerigar, has been examined and no differences in the presence of song system structures were found with other avian vocal learners. Motivated by questions of whether there are important differences in the vocal systems of parrots relative to other vocal learners, we used specialized constitutive gene expression, singing-driven gene expression, and neural connectivity tracing experiments to further characterize the song system of budgerigars and/or other parrots. We found that the parrot brain uniquely contains a song system within a song system. The parrot "core" song system is similar to the song systems of songbirds and hummingbirds, whereas the "shell" song system is unique to parrots. The core with only rudimentary shell regions were found in the New Zealand kea, representing one of the only living species at a basal divergence with all other parrots, implying that parrots evolved vocal learning systems at least 29 million years ago. Relative size differences in the core and shell regions occur among species, which we suggest could be related to species differences in vocal and cognitive abilities.
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Affiliation(s)
- Mukta Chakraborty
- Department of Neurobiology, Duke University Medical Center, Durham, NC, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Solveig Walløe
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Research Laboratory for Stereology and Neuroscience, Bispebjerg University Hospital, Copenhagen, Denmark
| | - Signe Nedergaard
- Danish National Police, National Centre of Forensic Services, Vanloese, Denmark
| | - Emma E. Fridel
- Department of Neurobiology, Duke University Medical Center, Durham, NC, United States of America
| | - Torben Dabelsteen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Bente Pakkenberg
- Research Laboratory for Stereology and Neuroscience, Bispebjerg University Hospital, Copenhagen, Denmark
| | | | - Gerry M. Dorrestein
- Dutch Research Institute of Avian and Exotic Animals, Veldhoven, The Netherlands
| | - Steven E. Brauth
- University of Maryland, College Park, MA, United States of America
| | - Sarah E. Durand
- LaGuardia Community College, New York, NY, United States of America
| | - Erich D. Jarvis
- Department of Neurobiology, Duke University Medical Center, Durham, NC, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
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17
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Kanduri C, Kuusi T, Ahvenainen M, Philips AK, Lähdesmäki H, Järvelä I. The effect of music performance on the transcriptome of professional musicians. Sci Rep 2015; 5:9506. [PMID: 25806429 PMCID: PMC5380155 DOI: 10.1038/srep09506] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 02/27/2015] [Indexed: 12/31/2022] Open
Abstract
Music performance by professional musicians involves a wide-spectrum of cognitive and multi-sensory motor skills, whose biological basis is unknown. Several neuroscientific studies have demonstrated that the brains of professional musicians and non-musicians differ structurally and functionally and that musical training enhances cognition. However, the molecules and molecular mechanisms involved in music performance remain largely unexplored. Here, we investigated the effect of music performance on the genome-wide peripheral blood transcriptome of professional musicians by analyzing the transcriptional responses after a 2-hr concert performance and after a 'music-free' control session. The up-regulated genes were found to affect dopaminergic neurotransmission, motor behavior, neuronal plasticity, and neurocognitive functions including learning and memory. Particularly, candidate genes such as SNCA, FOS and DUSP1 that are involved in song perception and production in songbirds, were identified, suggesting an evolutionary conservation in biological processes related to sound perception/production. Additionally, modulation of genes related to calcium ion homeostasis, iron ion homeostasis, glutathione metabolism, and several neuropsychiatric and neurodegenerative diseases implied that music performance may affect the biological pathways that are otherwise essential for the proper maintenance of neuronal function and survival. For the first time, this study provides evidence for the candidate genes and molecular mechanisms underlying music performance.
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Affiliation(s)
- Chakravarthi Kanduri
- Department of Medical Genetics, Haartman Institute, University of Helsinki, P.O. Box 720, 00014 University of Helsinki, Finland
| | - Tuire Kuusi
- DocMus doctoral school, Sibelius Academy, University of the Arts, P.O. Box 30, FI 0097 Uniarts, Finland
| | - Minna Ahvenainen
- Department of Medical Genetics, Haartman Institute, University of Helsinki, P.O. Box 720, 00014 University of Helsinki, Finland
| | - Anju K. Philips
- Department of Medical Genetics, Haartman Institute, University of Helsinki, P.O. Box 720, 00014 University of Helsinki, Finland
| | - Harri Lähdesmäki
- Department of Information and Computer Science, Aalto University, FI-00076 AALTO, Finland
| | - Irma Järvelä
- Department of Medical Genetics, Haartman Institute, University of Helsinki, P.O. Box 720, 00014 University of Helsinki, Finland
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18
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Whitney O, Pfenning AR, Howard JT, Blatti CA, Liu F, Ward JM, Wang R, Audet JN, Kellis M, Mukherjee S, Sinha S, Hartemink AJ, West AE, Jarvis ED. Core and region-enriched networks of behaviorally regulated genes and the singing genome. Science 2014; 346:1256780. [PMID: 25504732 DOI: 10.1126/science.1256780] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Songbirds represent an important model organism for elucidating molecular mechanisms that link genes with complex behaviors, in part because they have discrete vocal learning circuits that have parallels with those that mediate human speech. We found that ~10% of the genes in the avian genome were regulated by singing, and we found a striking regional diversity of both basal and singing-induced programs in the four key song nuclei of the zebra finch, a vocal learning songbird. The region-enriched patterns were a result of distinct combinations of region-enriched transcription factors (TFs), their binding motifs, and presinging acetylation of histone 3 at lysine 27 (H3K27ac) enhancer activity in the regulatory regions of the associated genes. RNA interference manipulations validated the role of the calcium-response transcription factor (CaRF) in regulating genes preferentially expressed in specific song nuclei in response to singing. Thus, differential combinatorial binding of a small group of activity-regulated TFs and predefined epigenetic enhancer activity influences the anatomical diversity of behaviorally regulated gene networks.
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Affiliation(s)
- Osceola Whitney
- Department of Neurobiology, Howard Hughes Medical Institute, and Duke University Medical Center, Durham, NC 27710, USA.
| | - Andreas R Pfenning
- Department of Neurobiology, Howard Hughes Medical Institute, and Duke University Medical Center, Durham, NC 27710, USA. Computer Science and Artificial Intelligence Laboratory and the Broad Institute of MIT and Harvard, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Jason T Howard
- Department of Neurobiology, Howard Hughes Medical Institute, and Duke University Medical Center, Durham, NC 27710, USA
| | - Charles A Blatti
- Department of Computer Science, University of Illinois, Urbana-Champaign, IL, USA
| | - Fang Liu
- Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA
| | - James M Ward
- Department of Neurobiology, Howard Hughes Medical Institute, and Duke University Medical Center, Durham, NC 27710, USA
| | - Rui Wang
- Department of Neurobiology, Howard Hughes Medical Institute, and Duke University Medical Center, Durham, NC 27710, USA
| | - Jean-Nicoles Audet
- Department of Biology, McGill University, Montreal, Quebec H3A 1B1, Canada
| | - Manolis Kellis
- Computer Science and Artificial Intelligence Laboratory and the Broad Institute of MIT and Harvard, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Saurabh Sinha
- Department of Computer Science, University of Illinois, Urbana-Champaign, IL, USA
| | | | - Anne E West
- Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA.
| | - Erich D Jarvis
- Department of Neurobiology, Howard Hughes Medical Institute, and Duke University Medical Center, Durham, NC 27710, USA.
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19
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Boeckx C, Benítez-Burraco A. Globularity and language-readiness: generating new predictions by expanding the set of genes of interest. Front Psychol 2014; 5:1324. [PMID: 25505436 PMCID: PMC4243498 DOI: 10.3389/fpsyg.2014.01324] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 10/31/2014] [Indexed: 12/30/2022] Open
Abstract
This study builds on the hypothesis put forth in Boeckx and Benítez-Burraco (2014), according to which the developmental changes expressed at the levels of brain morphology and neural connectivity that resulted in a more globular braincase in our species were crucial to understand the origins of our language-ready brain. Specifically, this paper explores the links between two well-known 'language-related' genes like FOXP2 and ROBO1 implicated in vocal learning and the initial set of genes of interest put forth in Boeckx and Benítez-Burraco (2014), with RUNX2 as focal point. Relying on the existing literature, we uncover potential molecular links that could be of interest to future experimental inquiries into the biological foundations of language and the testing of our initial hypothesis. Our discussion could also be relevant for clinical linguistics and for the interpretation of results from paleogenomics.
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Affiliation(s)
- Cedric Boeckx
- Catalan Institute for Advanced Studies and Research (ICREA)Barcelona, Spain
- Department of Linguistics, Universitat de BarcelonaBarcelona, Spain
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20
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Wang CH, Zhang XL, Li Y, Wang GD, Wang XK, Dong J, Ning QF. Role of hippocampus mitogen-activated protein kinase phosphatase-1 mRNA expression and DNA methylation in the depression of the rats with chronic unpredicted stress. Cell Mol Neurobiol 2014; 35:473-82. [PMID: 25410305 DOI: 10.1007/s10571-014-0141-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 11/14/2014] [Indexed: 01/09/2023]
Abstract
Stressful life events especially the chronic unpredictable stress are the obvious precipitating factors of depression. The biological information transduction in cells plays an important role in the molecular biology mechanism of depression. Mitogen-activated protein kinase phosphatase-1 (MKP-1) regulates the cell physiological activity and involves in the adjustment of neural plasticity, function, and survival. This experiment tried to explore the possible effects of MKP-1 in hippocampus on depression of rats by determining the expression of MKP-1 mRNA and DNA methylation in MKP-1 gene promoter. The animal model was established by chronic unpredictable stress, and evaluated by open-field test and weight changes. All the rats were divided into the sham stimulation, the physiological saline, and the fluoxetine (1.25, 2.50, and 5.00 mg/kg) groups randomly. The expression of MKP-1 mRNA in the hippocampus was measured by RT-PCR and the methylation of MKP-1 promoter DNA was detected by COBRA. The chronic unpredicted stress (1) increased the animal movement scores in open-field test, and fluoxetine could prevent this increasement; (2) increased the body weight, and fluoxetine could not prevent this increasement; and (3) increased MKP-1 mRNA expression in the hippocampus, and fluoxetine could prevent it. However, fluoxetine did not influence the DNA methylation of MKP-1 gene promoter in the hippocampus during the chronic unpredicted stress. MKP-1 in the hippocampus might be involved in the etiology of depression, and DNA methylation of MKP-1 gene promoter in the hippocampus did not related with the depression.
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Affiliation(s)
- Chang-Hong Wang
- Department of Psychiatry, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, 453002, Henan, China
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21
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Chen CC, Winkler CM, Pfenning AR, Jarvis ED. Molecular profiling of the developing avian telencephalon: regional timing and brain subdivision continuities. J Comp Neurol 2014; 521:3666-701. [PMID: 23818174 PMCID: PMC3863995 DOI: 10.1002/cne.23406] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 06/19/2013] [Accepted: 06/21/2013] [Indexed: 12/30/2022]
Abstract
In our companion study (Jarvis et al. [2013] J Comp Neurol. doi: 10.1002/cne.23404) we used quantitative brain molecular profiling to discover that distinct subdivisions in the avian pallium above and below the ventricle and the associated mesopallium lamina have similar molecular profiles, leading to a hypothesis that they may form as continuous subdivisions around the lateral ventricle. To explore this hypothesis, here we profiled the expression of 16 genes at eight developmental stages. The genes included those that define brain subdivisions in the adult and some that are also involved in brain development. We found that phyletic hierarchical cluster and linear regression network analyses of gene expression profiles implicated single and mixed ancestry of these brain regions at early embryonic stages. Most gene expression-defined pallial subdivisions began as one ventral or dorsal domain that later formed specific folds around the lateral ventricle. Subsequently a clear ventricle boundary formed, partitioning them into dorsal and ventral pallial subdivisions surrounding the mesopallium lamina. These subdivisions each included two parts of the mesopallium, the nidopallium and hyperpallium, and the arcopallium and hippocampus, respectively. Each subdivision expression profile had a different temporal order of appearance, similar in timing to the order of analogous cell types of the mammalian cortex. Furthermore, like the mammalian pallium, expression in the ventral pallial subdivisions became distinct during prehatch development, whereas the dorsal portions did so during posthatch development. These findings support the continuum hypothesis of avian brain subdivision development around the ventricle and influence hypotheses on homologies of the avian pallium with other vertebrates.
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Affiliation(s)
- Chun-Chun Chen
- Department of Neurobiology, Howard Hughes Medical Institute, Duke University Medical Center, Durham, North Carolina, 27710
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22
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Jarvis ED, Yu J, Rivas MV, Horita H, Feenders G, Whitney O, Jarvis SC, Jarvis ER, Kubikova L, Puck AEP, Siang-Bakshi C, Martin S, McElroy M, Hara E, Howard J, Pfenning A, Mouritsen H, Chen CC, Wada K. Global view of the functional molecular organization of the avian cerebrum: mirror images and functional columns. J Comp Neurol 2014; 521:3614-65. [PMID: 23818122 DOI: 10.1002/cne.23404] [Citation(s) in RCA: 159] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 06/19/2013] [Accepted: 06/21/2013] [Indexed: 11/06/2022]
Abstract
Based on quantitative cluster analyses of 52 constitutively expressed or behaviorally regulated genes in 23 brain regions, we present a global view of telencephalic organization of birds. The patterns of constitutively expressed genes revealed a partial mirror image organization of three major cell populations that wrap above, around, and below the ventricle and adjacent lamina through the mesopallium. The patterns of behaviorally regulated genes revealed functional columns of activation across boundaries of these cell populations, reminiscent of columns through layers of the mammalian cortex. The avian functionally regulated columns were of two types: those above the ventricle and associated mesopallial lamina, formed by our revised dorsal mesopallium, hyperpallium, and intercalated hyperpallium; and those below the ventricle, formed by our revised ventral mesopallium, nidopallium, and intercalated nidopallium. Based on these findings and known connectivity, we propose that the avian pallium has four major cell populations similar to those in mammalian cortex and some parts of the amygdala: 1) a primary sensory input population (intercalated pallium); 2) a secondary intrapallial population (nidopallium/hyperpallium); 3) a tertiary intrapallial population (mesopallium); and 4) a quaternary output population (the arcopallium). Each population contributes portions to columns that control different sensory or motor systems. We suggest that this organization of cell groups forms by expansion of contiguous developmental cell domains that wrap around the lateral ventricle and its extension through the middle of the mesopallium. We believe that the position of the lateral ventricle and its associated mesopallium lamina has resulted in a conceptual barrier to recognizing related cell groups across its border, thereby confounding our understanding of homologies with mammals.
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Affiliation(s)
- Erich D Jarvis
- Department of Neurobiology, Howard Hughes Medical Institute, Duke University Medical Center, Durham, North Carolina, 27710
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23
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Smulders TV, Jarvis ED. Different mechanisms are responsible for dishabituation of electrophysiological auditory responses to a change in acoustic identity than to a change in stimulus location. Neurobiol Learn Mem 2013; 106:163-76. [PMID: 23999220 PMCID: PMC3986339 DOI: 10.1016/j.nlm.2013.08.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Revised: 07/09/2013] [Accepted: 08/22/2013] [Indexed: 01/03/2023]
Abstract
Repeated exposure to an auditory stimulus leads to habituation of the electrophysiological and immediate-early-gene (IEG) expression response in the auditory system. A novel auditory stimulus reinstates this response in a form of dishabituation. This has been interpreted as the start of new memory formation for this novel stimulus. Changes in the location of an otherwise identical auditory stimulus can also dishabituate the IEG expression response. This has been interpreted as an integration of stimulus identity and stimulus location into a single auditory object, encoded in the firing patterns of the auditory system. In this study, we further tested this hypothesis. Using chronic multi-electrode arrays to record multi-unit activity from the auditory system of awake and behaving zebra finches, we found that habituation occurs to repeated exposure to the same song and dishabituation with a novel song, similar to that described in head-fixed, restrained animals. A large proportion of recording sites also showed dishabituation when the same auditory stimulus was moved to a novel location. However, when the song was randomly moved among 8 interleaved locations, habituation occurred independently of the continuous changes in location. In contrast, when 8 different auditory stimuli were interleaved all from the same location, a separate habituation occurred to each stimulus. This result suggests that neuronal memories of the acoustic identity and spatial location are different, and that allocentric location of a stimulus is not encoded as part of the memory for an auditory object, while its acoustic properties are. We speculate that, instead, the dishabituation that occurs with a change from a stable location of a sound is due to the unexpectedness of the location change, and might be due to different underlying mechanisms than the dishabituation and separate habituations to different acoustic stimuli.
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Affiliation(s)
- Tom V Smulders
- Department of Neurobiology, Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC, USA; Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK.
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MAP kinase phosphatase 1 (MKP-1/DUSP1) is neuroprotective in Huntington's disease via additive effects of JNK and p38 inhibition. J Neurosci 2013; 33:2313-25. [PMID: 23392662 DOI: 10.1523/jneurosci.4965-11.2013] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
We previously demonstrated that sodium butyrate is neuroprotective in Huntington's disease (HD) mice and that this therapeutic effect is associated with increased expression of mitogen-activated protein kinase/dual-specificity phosphatase 1 (MKP-1/DUSP1). Here we show that enhancing MKP-1 expression is sufficient to achieve neuroprotection in lentiviral models of HD. Wild-type MKP-1 overexpression inhibited apoptosis in primary striatal neurons exposed to an N-terminal fragment of polyglutamine-expanded huntingtin (Htt171-82Q), blocking caspase-3 activation and significantly reducing neuronal cell death. This neuroprotective effect of MKP-1 was demonstrated to be dependent on its enzymatic activity, being ablated by mutation of its phosphatase domain and being attributed to inhibition of specific MAP kinases (MAPKs). Overexpression of MKP-1 prevented the polyglutamine-expanded huntingtin-induced activation of c-Jun N-terminal kinases (JNKs) and p38 MAPKs, whereas extracellular signal-regulated kinase (ERK) 1/2 activation was not altered by either polyglutamine-expanded Htt or MKP-1. Moreover, mutants of MKP-1 that selectively prevented p38 or JNK binding confirmed the important dual contributions of p38 and JNK regulation to MKP-1-mediated neuroprotection. These results demonstrate additive effects of p38 and JNK MAPK inhibition by MKP-1 without consequence to ERK activation in this striatal neuron-based paradigm. MKP-1 also provided neuroprotection in vivo in a lentiviral model of HD neuropathology in rat striatum. Together, these data extend previous evidence that JNK- and p38-mediated pathways contribute to HD pathogenesis and, importantly, show that therapies simultaneously inhibiting both JNK and p38 signaling pathways may lead to improved neuroprotective outcomes.
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Experience dependence of neural responses to different classes of male songs in the primary auditory forebrain of female songbirds. Behav Brain Res 2013; 243:184-90. [PMID: 23333401 DOI: 10.1016/j.bbr.2013.01.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Revised: 12/28/2012] [Accepted: 01/08/2013] [Indexed: 12/26/2022]
Abstract
There is both extensive species-specificity and critical experience-dependence in the recognition of own species songs in many songbird species. For example, female zebra finches Taeniopygia guttata raised by their parents show behavioral preferences for the songs of the father over unfamiliar conspecific males and for unfamiliar songs of conspecifics over heterospecifics. Behavioral discrimination between different species' songs is also displayed by females raised without exposure to any male songs but it is diminished in females raised by heterospecific foster parents. We tested whether neural responses in the female auditory forebrain paralleled each of these known behavioral patterns in song-class discrimination. We analyzed spike rates, above background levels, recorded from single units in the L2a subregion of the field L complex of female zebra finches. In subjects raised by genetic parents, spike rates were similar to songs of fathers and unfamiliar male zebra finches, and higher to unfamiliar conspecific over unfamiliar heterospecific songs. In females raised in isolation from male songs, we also found higher spike rates to unfamiliar conspecific over heterospecific songs. In females raised by heterospecific foster parents, spike rates were similar in response to songs of the foster father and unfamiliar males of the foster species, similar between unfamiliar songs of conspecifics and the heterospecific foster species, and higher to unfamiliar songs of the foster species over a third finch species. Thus, in parallel to the experience-dependence of females' behaviors in response to different male song classes, differences in social experiences can also alter neural response patterns to male song classes in the auditory forebrain of female zebra finches.
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26
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Aronov D, Fee MS. Natural changes in brain temperature underlie variations in song tempo during a mating behavior. PLoS One 2012; 7:e47856. [PMID: 23112858 PMCID: PMC3480430 DOI: 10.1371/journal.pone.0047856] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Accepted: 09/19/2012] [Indexed: 11/24/2022] Open
Abstract
The song of a male zebra finch is a stereotyped motor sequence whose tempo varies with social context--whether or not the song is directed at a female bird--as well as with the time of day. The neural mechanisms underlying these changes in tempo are unknown. Here we show that brain temperature recorded in freely behaving male finches exhibits a global increase in response to the presentation of a female bird. This increase strongly correlates with, and largely explains, the faster tempo of songs directed at a female compared to songs produced in social isolation. Furthermore, we find that the observed diurnal variations in song tempo are also explained by natural variations in brain temperature. Our findings suggest that brain temperature is an important variable that can influence the dynamics of activity in neural circuits, as well as the temporal features of behaviors that some of these circuits generate.
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Affiliation(s)
- Dmitriy Aronov
- Department of Brain and Cognitive Sciences, McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America.
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27
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Specialized motor-driven dusp1 expression in the song systems of multiple lineages of vocal learning birds. PLoS One 2012; 7:e42173. [PMID: 22876306 PMCID: PMC3410896 DOI: 10.1371/journal.pone.0042173] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Accepted: 07/04/2012] [Indexed: 11/19/2022] Open
Abstract
Mechanisms for the evolution of convergent behavioral traits are largely unknown. Vocal learning is one such trait that evolved multiple times and is necessary in humans for the acquisition of spoken language. Among birds, vocal learning is evolved in songbirds, parrots, and hummingbirds. Each time similar forebrain song nuclei specialized for vocal learning and production have evolved. This finding led to the hypothesis that the behavioral and neuroanatomical convergences for vocal learning could be associated with molecular convergence. We previously found that the neural activity-induced gene dual specificity phosphatase 1 (dusp1) was up-regulated in non-vocal circuits, specifically in sensory-input neurons of the thalamus and telencephalon; however, dusp1 was not up-regulated in higher order sensory neurons or motor circuits. Here we show that song motor nuclei are an exception to this pattern. The song nuclei of species from all known vocal learning avian lineages showed motor-driven up-regulation of dusp1 expression induced by singing. There was no detectable motor-driven dusp1 expression throughout the rest of the forebrain after non-vocal motor performance. This pattern contrasts with expression of the commonly studied activity-induced gene egr1, which shows motor-driven expression in song nuclei induced by singing, but also motor-driven expression in adjacent brain regions after non-vocal motor behaviors. In the vocal non-learning avian species, we found no detectable vocalizing-driven dusp1 expression in the forebrain. These findings suggest that independent evolutions of neural systems for vocal learning were accompanied by selection for specialized motor-driven expression of the dusp1 gene in those circuits. This specialized expression of dusp1 could potentially lead to differential regulation of dusp1-modulated molecular cascades in vocal learning circuits.
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28
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Chen CC, Wada K, Jarvis ED. Radioactive in situ hybridization for detecting diverse gene expression patterns in tissue. J Vis Exp 2012:3764. [PMID: 22566072 PMCID: PMC3466668 DOI: 10.3791/3764] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Knowing the timing, level, cellular localization, and cell type that a gene is expressed in contributes to our understanding of the function of the gene. Each of these features can be accomplished with in situ hybridization to mRNAs within cells. Here we present a radioactive in situ hybridization method modified from Clayton et al. (1988)1 that has been working successfully in our lab for many years, especially for adult vertebrate brains2-5. The long complementary RNA (cRNA) probes to the target sequence allows for detection of low abundance transcripts6,7. Incorporation of radioactive nucleotides into the cRNA probes allows for further detection sensitivity of low abundance transcripts and quantitative analyses, either by light sensitive x-ray film or emulsion coated over the tissue. These detection methods provide a long-term record of target gene expression. Compared with non-radioactive probe methods, such as DIG-labeling, the radioactive probe hybridization method does not require multiple amplification steps using HRP-antibodies and/or TSA kit to detect low abundance transcripts. Therefore, this method provides a linear relation between signal intensity and targeted mRNA amounts for quantitative analysis. It allows processing 100-200 slides simultaneously. It works well for different developmental stages of embryos. Most developmental studies of gene expression use whole embryos and non-radioactive approaches8,9, in part because embryonic tissue is more fragile than adult tissue, with less cohesion between cells, making it difficult to see boundaries between cell populations with tissue sections. In contrast, our radioactive approach, due to the larger range of sensitivity, is able to obtain higher contrast in resolution of gene expression between tissue regions, making it easier to see boundaries between populations. Using this method, researchers could reveal the possible significance of a newly identified gene, and further predict the function of the gene of interest.
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Affiliation(s)
- Chun-Chun Chen
- Department of Neurobiology, Howard Hughes Medical Institute, Duke University, USA
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29
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Detection of neural activity in the brains of Japanese honeybee workers during the formation of a "hot defensive bee ball". PLoS One 2012; 7:e32902. [PMID: 22431987 PMCID: PMC3303784 DOI: 10.1371/journal.pone.0032902] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2011] [Accepted: 02/06/2012] [Indexed: 11/22/2022] Open
Abstract
Anti-predator behaviors are essential to survival for most animals. The neural bases of such behaviors, however, remain largely unknown. Although honeybees commonly use their stingers to counterattack predators, the Japanese honeybee (Apis cerana japonica) uses a different strategy to fight against the giant hornet (Vespa mandarinia japonica). Instead of stinging the hornet, Japanese honeybees form a “hot defensive bee ball” by surrounding the hornet en masse, killing it with heat. The European honeybee (A. mellifera ligustica), on the other hand, does not exhibit this behavior, and their colonies are often destroyed by a hornet attack. In the present study, we attempted to analyze the neural basis of this behavior by mapping the active brain regions of Japanese honeybee workers during the formation of a hot defensive bee ball. First, we identified an A. cerana homolog (Acks = Apis cerana kakusei) of kakusei, an immediate early gene that we previously identified from A. mellifera, and showed that Acks has characteristics similar to kakusei and can be used to visualize active brain regions in A. cerana. Using Acks as a neural activity marker, we demonstrated that neural activity in the mushroom bodies, especially in Class II Kenyon cells, one subtype of mushroom body intrinsic neurons, and a restricted area between the dorsal lobes and the optic lobes was increased in the brains of Japanese honeybee workers involved in the formation of a hot defensive bee ball. In addition, workers exposed to 46°C heat also exhibited Acks expression patterns similar to those observed in the brains of workers involved in the formation of a hot defensive bee ball, suggesting that the neural activity observed in the brains of workers involved in the hot defensive bee ball mainly reflects thermal stimuli processing.
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Jeanneteau F, Deinhardt K. Fine-tuning MAPK signaling in the brain: The role of MKP-1. Commun Integr Biol 2011; 4:281-3. [PMID: 21980558 DOI: 10.4161/cib.4.3.14766] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Accepted: 01/07/2011] [Indexed: 12/30/2022] Open
Abstract
Mitogen-activated protein kinase (MAPK) signaling influences a variety of neuronal properties, including structural characteristics such as spine density, and physiological features like long-term potentiation. Spatiotemporal control of MAPK signaling is crucial to generate specific changes in neuronal physiology. However, while many studies have concentrated on the activation of MAPK signaling by trophic factors such as BDNF and neuronal activity, the mechanisms that lead to its termination have not been well described. Two recent reports begin to address this question by focusing on the role of the MAPK phosphatase, MKP-1, in neuronal function. The first study provides a cellular mechanism underlying MKP-1 action in the brain.1 The second study describes potential roles of MKP-1 during stress and major depression.2.
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Affiliation(s)
- Freddy Jeanneteau
- Molecular Neurobiology Program; Skirball Institute of Biomolecular Medicine; New York University Langone School of Medicine; New York, NY USA
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31
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Quantification of developmental birdsong learning from the subsyllabic scale to cultural evolution. Proc Natl Acad Sci U S A 2011; 108 Suppl 3:15572-9. [PMID: 21436035 DOI: 10.1073/pnas.1012941108] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Quantitative analysis of behavior plays an important role in birdsong neuroethology, serving as a common denominator in studies spanning molecular to system-level investigation of sensory-motor conversion, developmental learning, and pattern generation in the brain. In this review, we describe the role of behavioral analysis in facilitating cross-level integration. Modern sound analysis approaches allow investigation of developmental song learning across multiple time scales. Combined with novel methods that allow experimental control of vocal changes, it is now possible to test hypotheses about mechanisms of vocal learning. Further, song analysis can be done at the population level across generations to track cultural evolution and multigenerational behavioral processes. Complementing the investigation of song development with noninvasive brain imaging technology makes it now possible to study behavioral dynamics at multiple levels side by side with developmental changes in brain connectivity and in auditory responses.
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32
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Kopec CD, Bowers AC, Pai S, Brody CD. Semi-automated atlas-based analysis of brain histological sections. J Neurosci Methods 2011; 196:12-9. [PMID: 21194546 PMCID: PMC3075115 DOI: 10.1016/j.jneumeth.2010.12.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2010] [Revised: 11/26/2010] [Accepted: 12/01/2010] [Indexed: 10/18/2022]
Abstract
Quantifying the location and/or number of features in a histological section of the brain currently requires one to first, manually register a corresponding section from a tissue atlas onto the experimental section and second, count the features. No automated method exists for the first process (registering), and most automated methods for the second process (feature counting) operate reliably only in a high signal-to-noise regime. To reduce experimenter bias and inconsistencies and increase the speed of these analyses, we developed Atlas Fitter, a semi-automated, open-source MatLab-based software package that assists in rapidly registering atlas panels onto histological sections. We also developed CellCounter, a novel fully automated cell counting algorithm that is designed to operate on images with non-uniform background intensities and low signal-to-noise ratios.
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Affiliation(s)
- Charles D. Kopec
- HHMI/Princeton University, Lewis Thomas Lab, Department of Molecular Biology, Princeton University, Princeton, NJ 08544
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ 08544
| | - Amanda C. Bowers
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ 08544
| | - Shraddha Pai
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - Carlos D. Brody
- HHMI/Princeton University, Lewis Thomas Lab, Department of Molecular Biology, Princeton University, Princeton, NJ 08544
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ 08544
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Zapka M, Heyers D, Liedvogel M, Jarvis ED, Mouritsen H. Night-time neuronal activation of Cluster N in a day- and night-migrating songbird. Eur J Neurosci 2010; 32:619-24. [PMID: 20618826 PMCID: PMC2924469 DOI: 10.1111/j.1460-9568.2010.07311.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Magnetic compass orientation in a night-migratory songbird requires that Cluster N, a cluster of forebrain regions, is functional. Cluster N, which receives input from the eyes via the thalamofugal pathway, shows high neuronal activity in night-migrants performing magnetic compass-guided behaviour at night, whereas no activation is observed during the day, and covering up the birds’ eyes strongly reduces neuronal activation. These findings suggest that Cluster N processes light-dependent magnetic compass information in night-migrating songbirds. The aim of this study was to test if Cluster N is active during daytime migration. We used behavioural molecular mapping based on ZENK activation to investigate if Cluster N is active in the meadow pipit (Anthus pratensis), a day- and night-migratory species. We found that Cluster N of meadow pipits shows high neuronal activity under dim-light at night, but not under full room-light conditions during the day. These data suggest that, in day- and night-migratory meadow pipits, the light-dependent magnetic compass, which requires an active Cluster N, may only be used during night-time, whereas another magnetosensory mechanism and/or other reference system(s), like the sun or polarized light, may be used as primary orientation cues during the day.
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Affiliation(s)
- Manuela Zapka
- AG Neurosensorik, Institut für Biologie und Umweltwissenschaften, University of Oldenburg, D-26111 Oldenburg, Germany
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