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Doubovikov ED, Serdyukova NA, Greenberg SB, Gascoigne DA, Minhaj MM, Aksenov DP. Electric Field Effects on Brain Activity: Implications for Epilepsy and Burst Suppression. Cells 2023; 12:2229. [PMID: 37759452 PMCID: PMC10527339 DOI: 10.3390/cells12182229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/07/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023] Open
Abstract
Electric fields are now considered a major mechanism of epileptiform activity. However, it is not clear if another electrophysiological phenomenon, burst suppression, utilizes the same mechanism for its bursting phase. Thus, the purpose of this study was to compare the role of ephaptic coupling-the recruitment of neighboring cells via electric fields-in generating bursts in epilepsy and burst suppression. We used local injections of the GABA-antagonist picrotoxin to elicit epileptic activity and a general anesthetic, sevoflurane, to elicit burst suppression in rabbits. Then, we applied an established computational model of pyramidal cells to simulate neuronal activity in a 3-dimensional grid, with an additional parameter to trigger a suppression phase based on extra-cellular calcium dynamics. We discovered that coupling via electric fields was sufficient to produce bursting in scenarios where inhibitory control of excitatory neurons was sufficiently low. Under anesthesia conditions, bursting occurs with lower neuronal recruitment in comparison to seizures. Our model predicts that due to the effect of electric fields, the magnitude of bursts during seizures should be roughly 2-3 times the magnitude of bursts that occur during burst suppression, which is consistent with our in vivo experimental results. The resulting difference in magnitude between bursts during anesthesia and epileptiform bursts reflects the strength of the electric field effect, which suggests that burst suppression and epilepsy share the same ephaptic coupling mechanism.
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Affiliation(s)
- Evan D. Doubovikov
- Department of Radiology, NorthShore University HealthSystem, Evanston, IL 60201, USA
| | - Natalya A. Serdyukova
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
- Department of Pediatrics, NorthShore University HealthSystem, Evanston, IL 60201, USA
| | - Steven B. Greenberg
- Department of Anesthesiology, NorthShore University HealthSystem, Evanston, IL 60201, USA
| | - David A. Gascoigne
- Department of Radiology, NorthShore University HealthSystem, Evanston, IL 60201, USA
| | - Mohammed M. Minhaj
- Department of Anesthesiology, NorthShore University HealthSystem, Evanston, IL 60201, USA
| | - Daniil P. Aksenov
- Department of Radiology, NorthShore University HealthSystem, Evanston, IL 60201, USA
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
- Department of Anesthesiology, NorthShore University HealthSystem, Evanston, IL 60201, USA
- Pritzker School of Medicine, University of Chicago, Chicago, IL 60637, USA
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2
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Aksenov DP, Li L, Serdyukova NA, Gascoigne DA, Doubovikov ED, Drobyshevsky A. Functional Deficiency of Interneurons and Negative BOLD fMRI Response. Cells 2023; 12:cells12050811. [PMID: 36899947 PMCID: PMC10000915 DOI: 10.3390/cells12050811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 02/20/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
The functional deficiency of the inhibitory system typically appears during development and can progress to psychiatric disorders or epilepsy, depending on its severity, in later years. It is known that interneurons, the major source of GABAergic inhibition in the cerebral cortex, can make direct connections with arterioles and participate in the regulation of vasomotion. The goal of this study was to mimic the functional deficiency of interneurons through the use of localized microinjections of the GABA antagonist, picrotoxin, in such a concentration that it did not elicit epileptiform neuronal activity. First, we recorded the dynamics of resting-state neuronal activity in response to picrotoxin injections in the somatosensory cortex of an awake rabbit; second, we assessed the altered neuronal and hemodynamic responses to whisker stimulation using BOLD fMRI and electrophysiology recordings; third, we evaluated brain tissue oxygen levels before and after picrotoxin injection. Our results showed that neuronal activity typically increased after picrotoxin administration, the BOLD responses to stimulation became negative, and the oxygen response was nearly abolished. Vasoconstriction during the resting baseline was not observed. These results indicate that picrotoxin provoked imbalanced hemodynamics either due to increased neuronal activity, decreased vascular response, or a combination of both.
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Affiliation(s)
- Daniil P. Aksenov
- Department of Radiology, NorthShore University HealthSystem, Evanston, IL 60201, USA
- Department of Anesthesiology, NorthShore University HealthSystem, Evanston, IL 60201, USA
- Pritzker School of Medicine, University of Chicago, Chicago, IL 60637, USA
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
- Correspondence:
| | - Limin Li
- Department of Radiology, NorthShore University HealthSystem, Evanston, IL 60201, USA
| | - Natalya A. Serdyukova
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
- Department of Pediatrics, NorthShore University HealthSystem, Evanston, IL 60201, USA
| | - David A. Gascoigne
- Department of Radiology, NorthShore University HealthSystem, Evanston, IL 60201, USA
| | - Evan D. Doubovikov
- Department of Radiology, NorthShore University HealthSystem, Evanston, IL 60201, USA
| | - Alexander Drobyshevsky
- Pritzker School of Medicine, University of Chicago, Chicago, IL 60637, USA
- Department of Pediatrics, NorthShore University HealthSystem, Evanston, IL 60201, USA
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3
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Beklemisheva VR, Lemskaya NA, Prokopov DY, Perelman PL, Romanenko SA, Proskuryakova AA, Serdyukova NA, Utkin YA, Nie W, Ferguson-Smith MA, Yang F, Graphodatsky AS. Maps of Constitutive-Heterochromatin Distribution for Four Martes Species (Mustelidae, Carnivora, Mammalia) Show the Formative Role of Macrosatellite Repeats in Interspecific Variation of Chromosome Structure. Genes (Basel) 2023; 14:489. [PMID: 36833416 PMCID: PMC9957230 DOI: 10.3390/genes14020489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/08/2023] [Accepted: 02/09/2023] [Indexed: 02/17/2023] Open
Abstract
Constitutive-heterochromatin placement in the genome affects chromosome structure by occupying centromeric areas and forming large blocks. To investigate the basis for heterochromatin variation in the genome, we chose a group of species with a conserved euchromatin part: the genus Martes [stone marten (M. foina, 2n = 38), sable (M. zibellina, 2n = 38), pine marten (M. martes, 2n = 38), and yellow-throated marten (M. flavigula, 2n = 40)]. We mined the stone marten genome for the most abundant tandem repeats and selected the top 11 macrosatellite repetitive sequences. Fluorescent in situ hybridization revealed distributions of the tandemly repeated sequences (macrosatellites, telomeric repeats, and ribosomal DNA). We next characterized the AT/GC content of constitutive heterochromatin by CDAG (Chromomycin A3-DAPI-after G-banding). The euchromatin conservatism was shown by comparative chromosome painting with stone marten probes in newly built maps of the sable and pine marten. Thus, for the four Martes species, we mapped three different types of tandemly repeated sequences critical for chromosome structure. Most macrosatellites are shared by the four species with individual patterns of amplification. Some macrosatellites are specific to a species, autosomes, or the X chromosome. The variation of core macrosatellites and their prevalence in a genome are responsible for the species-specific variation of the heterochromatic blocks.
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Affiliation(s)
- Violetta R. Beklemisheva
- Department of Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Natalya A. Lemskaya
- Department of Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Dmitry Yu. Prokopov
- Department of Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Polina L. Perelman
- Department of Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Svetlana A. Romanenko
- Department of Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Anastasia A. Proskuryakova
- Department of Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Natalya A. Serdyukova
- Department of Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Yaroslav A. Utkin
- Department of Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Wenhui Nie
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Malcolm A. Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Fentang Yang
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo 255049, China
| | - Alexander S. Graphodatsky
- Department of Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
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4
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Aksenov DP, Rutila K, Li L, Miller MJ, Gascoigne DA, Serdyukova NA, Doubovikov ED, Linsenmeier RA, Drobyshevsky A. Brain Tissue Oxygen and BOLD fMRI Under Different Levels of Neuronal Activity. Adv Exp Med Biol 2023; 1438:3-8. [PMID: 37845431 DOI: 10.1007/978-3-031-42003-0_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
Localized increases in neuronal activity are supported by the hemodynamic response, which delivers oxygen to the brain tissue to support synaptic functions, action potentials and other neuronal processes. However, it remains unknown if changes in baseline neuronal activity, which are expected to reflect neuronal metabolic demand, alter the relationship between the local hemodynamic and oxygen behaviour. In order to better characterize this system, we examine here the relationship between brain tissue oxygen (PO2) and hemodynamic responses (BOLD functional MRI) under different levels of neuronal activity. By comparing the stimulus-evoked responses during different levels of baseline neuronal activity, the awake state vs isoflurane anesthesia, we were able to measure how a known change in neuronal demand affected tissue PO2 as well as the hemodynamic response to stimulation. We observed a high correlation between stimulus-evoked PO2 and BOLD responses in the awake state. Moreover, we found that the evoked PO2 and BOLD responses were still present despite the elevated tissue oxygen baseline and decreased baseline of neuronal activity under low concentration isoflurane, and that the magnitudes of these responses decreased by similar proportions but the relationship between these signals was distorted. Our findings point to distortion of the BOLD-PO2 relationship due to anesthesia. The feedback mechanism to adjust the level of brain tissue oxygen, as well as the correlation between BOLD and PO2 responses, are impaired even by a small dose of anesthetics.
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Affiliation(s)
- D P Aksenov
- Department of Radiology, NorthShore University HealthSystem, Evanston, IL, USA.
- Department of Anesthesiology, NorthShore University HealthSystem, Evanston, IL, USA.
- University of Chicago, Pritzker School of Medicine, Chicago, IL, USA.
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA.
| | - K Rutila
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - L Li
- Department of Radiology, NorthShore University HealthSystem, Evanston, IL, USA
| | - M J Miller
- Department of Radiology, NorthShore University HealthSystem, Evanston, IL, USA
| | - D A Gascoigne
- Department of Radiology, NorthShore University HealthSystem, Evanston, IL, USA
| | - N A Serdyukova
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
- Department of Neurobiology, Northwestern University, Evanston, IL, USA
| | - E D Doubovikov
- Department of Radiology, NorthShore University HealthSystem, Evanston, IL, USA
| | - R A Linsenmeier
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
- Department of Neurobiology, Northwestern University, Evanston, IL, USA
| | - A Drobyshevsky
- University of Chicago, Pritzker School of Medicine, Chicago, IL, USA
- Department of Pediatrics, NorthShore University HealthSystem, Evanston, IL, USA
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5
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Aksenov DP, Doubovikov ED, Serdyukova NA, Gascoigne DA, Linsenmeier RA, Drobyshevsky A. Brain tissue oxygen dynamics while mimicking the functional deficiency of interneurons. Front Cell Neurosci 2022; 16:983298. [PMID: 36339824 PMCID: PMC9630360 DOI: 10.3389/fncel.2022.983298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 10/06/2022] [Indexed: 11/13/2022] Open
Abstract
The dynamic interaction between excitatory and inhibitory activity in the brain is known as excitatory-inhibitory balance (EIB). A significant shift in EIB toward excitation has been observed in numerous pathological states and diseases, such as autism or epilepsy, where interneurons may be dysfunctional. The consequences of this on neurovascular interactions remains to be elucidated. Specifically, it is not known if there is an elevated metabolic consumption of oxygen due to increased excitatory activity. To investigate this, we administered microinjections of picrotoxin, a gamma aminobutyric acid (GABA) antagonist, to the rabbit cortex in the awake state to mimic the functional deficiency of GABAergic interneurons. This caused an observable shift in EIB toward excitation without the induction of seizures. We used chronically implanted electrodes to measure both neuronal activity and brain tissue oxygen concentrations (PO2) simultaneously and in the same location. Using a high-frequency recording rate for PO2, we were able to detect two important phenomena, (1) the shift in EIB led to a change in the power spectra of PO2 fluctuations, such that higher frequencies (8-15 cycles per minute) were suppressed and (2) there were brief periods (dips with a duration of less than 100 ms associated with neuronal bursts) when PO2 dropped below 10 mmHg, which we defined as the threshold for hypoxia. The dips were followed by an overshoot, which indicates either a rapid vascular response or decrease in oxygen consumption. Our results point to the essential role of interneurons in brain tissue oxygen regulation in the resting state.
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Affiliation(s)
- Daniil P. Aksenov
- Department of Radiology, NorthShore University HealthSystem, Evanston, IL, United States,Department of Anesthesiology, NorthShore University HealthSystem, Evanston, IL, United States,Pritzker School of Medicine, University of Chicago, Chicago, IL, United States,*Correspondence: Daniil P. Aksenov,
| | - Evan D. Doubovikov
- Department of Radiology, NorthShore University HealthSystem, Evanston, IL, United States
| | - Natalya A. Serdyukova
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, United States,Department of Pediatrics, NorthShore University HealthSystem, Evanston, IL, United States
| | - David A. Gascoigne
- Department of Radiology, NorthShore University HealthSystem, Evanston, IL, United States
| | - Robert A. Linsenmeier
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, United States
| | - Alexander Drobyshevsky
- Pritzker School of Medicine, University of Chicago, Chicago, IL, United States,Department of Pediatrics, NorthShore University HealthSystem, Evanston, IL, United States
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6
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Romanenko SA, Fedorova YE, Serdyukova NA, Zaccaroni M, Stanyon R, Graphodatsky AS. Evolutionary rearrangements of X chromosomes in voles (Arvicolinae, Rodentia). Sci Rep 2020; 10:13235. [PMID: 32764633 PMCID: PMC7413345 DOI: 10.1038/s41598-020-70226-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Accepted: 07/20/2020] [Indexed: 11/09/2022] Open
Abstract
Euchromatic segments of the X chromosomes of placental mammals are the most conservative elements of the karyotype, only rarely subjected to either inter- or intrachromosomal rearrangements. Here, using microdissection-derived set of region-specific probes of Terricola savii we detailed the evolutionary rearrangements found in X chromosomes in 20 vole species (Arvicolinae, Rodentia). We show that the evolution of X chromosomes in this taxon was accompanied by multiple para- and pericentric inversions and centromere shifts. The contribution of intrachromosomal rearrangements to the karyotype evolution of Arvicolinae species was approximately equivalent in both the separate autosomal conserved segments and the X chromosomes. Intrachromosmal rearrangements and structural reorganization of the X chromosomes was likely accompanied by an accumulation, distribution, and evolution of repeated sequences.
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Affiliation(s)
| | - Yulia E Fedorova
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | | | - Marco Zaccaroni
- Department of Biology, University of Florence, Florence, Italy
| | - Roscoe Stanyon
- Department of Biology, University of Florence, Florence, Italy
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7
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Romanenko SA, Serdyukova NA, Perelman PL, Trifonov VA, Golenishchev FN, Bulatova NS, Stanyon R, Graphodatsky AS. Multiple intrasyntenic rearrangements and rapid speciation in voles. Sci Rep 2018; 8:14980. [PMID: 30297915 PMCID: PMC6175948 DOI: 10.1038/s41598-018-33300-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 09/26/2018] [Indexed: 11/09/2022] Open
Abstract
Remarkably stable genomic chromosome elements (evolutionary conserved segments or syntenies) are the basis of large-scale chromosome architecture in vertebrate species. However, these syntenic elements harbour evolutionary important changes through intrachromosomal rearrangements such as inversions and centromere repositioning. Here, using FISH with a set of 20 region-specific probes on a wide array of 28 species, we analyzed evolution of three conserved syntenic regions of the Arvicolinae ancestral karyotype. Inside these syntenies we uncovered multiple, previously cryptic intrachromosomal rearrangements. Although in each of the three conserved blocks we found inversions and centromere repositions, the blocks experienced different types of rearrangements. In two syntenies centromere repositioning predominated, while in the third region, paracentric inversions were more frequent, whereas pericentric inversions were not detected. We found that some of the intrachromosomal rearrangements, mainly paracentric inversions, were synapomorphic for whole arvicoline genera or tribes: genera Alexandromys and Microtus, tribes Ellobini and Myodini. We hypothesize that intrachromosomal rearrangements within conserved syntenic blocks are a major evolutionary force modulating genome architecture in species-rich and rapidly-evolving rodent taxa. Inversions and centromere repositioning may impact speciation and provide a potential link between genome evolution, speciation, and biogeography.
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Affiliation(s)
- Svetlana A Romanenko
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, Russia.
- Novosibirsk State University, Novosibirsk, Russia.
| | | | - Polina L Perelman
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Vladimir A Trifonov
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | | | - Nina Sh Bulatova
- A.N. Severtsov Institute of Ecology and Evolution, RAS, Moscow, Russia
| | - Roscoe Stanyon
- Department of Biology, Anthropology Laboratories, University of Florence, Florence, Italy
| | - Alexander S Graphodatsky
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
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8
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Kukekova AV, Johnson JL, Xiang X, Feng S, Liu S, Rando HM, Kharlamova AV, Herbeck Y, Serdyukova NA, Xiong Z, Beklemischeva V, Koepfli KP, Gulevich RG, Vladimirova AV, Hekman JP, Perelman PL, Graphodatsky AS, O'Brien SJ, Wang X, Clark AG, Acland GM, Trut LN, Zhang G. Red fox genome assembly identifies genomic regions associated with tame and aggressive behaviours. Nat Ecol Evol 2018; 2:1479-1491. [PMID: 30082739 DOI: 10.1038/s41559-018-0611-6] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 06/18/2018] [Indexed: 12/30/2022]
Abstract
Strains of red fox (Vulpes vulpes) with markedly different behavioural phenotypes have been developed in the famous long-term selective breeding programme known as the Russian farm-fox experiment. Here we sequenced and assembled the red fox genome and re-sequenced a subset of foxes from the tame, aggressive and conventional farm-bred populations to identify genomic regions associated with the response to selection for behaviour. Analysis of the re-sequenced genomes identified 103 regions with either significantly decreased heterozygosity in one of the three populations or increased divergence between the populations. A strong positional candidate gene for tame behaviour was highlighted: SorCS1, which encodes the main trafficking protein for AMPA glutamate receptors and neurexins and suggests a role for synaptic plasticity in fox domestication. Other regions identified as likely to have been under selection in foxes include genes implicated in human neurological disorders, mouse behaviour and dog domestication. The fox represents a powerful model for the genetic analysis of affiliative and aggressive behaviours that can benefit genetic studies of behaviour in dogs and other mammals, including humans.
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Affiliation(s)
- Anna V Kukekova
- Animal Sciences Department, College of ACES, University of Illinois at Urbana, Champaign, IL, USA.
| | - Jennifer L Johnson
- Animal Sciences Department, College of ACES, University of Illinois at Urbana, Champaign, IL, USA
| | - Xueyan Xiang
- China National Genebank, BGI -Shenzhen, Shenzhen, China
| | - Shaohong Feng
- China National Genebank, BGI -Shenzhen, Shenzhen, China
| | - Shiping Liu
- China National Genebank, BGI -Shenzhen, Shenzhen, China
| | - Halie M Rando
- Animal Sciences Department, College of ACES, University of Illinois at Urbana, Champaign, IL, USA
| | - Anastasiya V Kharlamova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Yury Herbeck
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Natalya A Serdyukova
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Zijun Xiong
- China National Genebank, BGI -Shenzhen, Shenzhen, China.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Violetta Beklemischeva
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Klaus-Peter Koepfli
- Smithsonian Conservation Biology Institute, National Zoological Park, Washington DC, USA.,Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, Saint Petersburg, Russia
| | - Rimma G Gulevich
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Anastasiya V Vladimirova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Jessica P Hekman
- Animal Sciences Department, College of ACES, University of Illinois at Urbana, Champaign, IL, USA.,The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Polina L Perelman
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Aleksander S Graphodatsky
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Stephen J O'Brien
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, Saint Petersburg, Russia.,Guy Harvey Oceanographic Center, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale, FL, USA
| | - Xu Wang
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.,Department of Pathobiology, Auburn University, Auburn, AL, USA
| | - Andrew G Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Gregory M Acland
- Baker Institute for Animal Health, Cornell University, College of Veterinary Medicine, Ithaca, NY, USA
| | - Lyudmila N Trut
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Guojie Zhang
- China National Genebank, BGI -Shenzhen, Shenzhen, China. .,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China. .,Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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9
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Bikchurina TI, Tishakova KV, Kizilova EA, Romanenko SA, Serdyukova NA, Torgasheva AA, Borodin PM. Chromosome Synapsis and Recombination in Male-Sterile and Female-Fertile Interspecies Hybrids of the Dwarf Hamsters ( Phodopus, Cricetidae). Genes (Basel) 2018; 9:genes9050227. [PMID: 29693587 PMCID: PMC5977167 DOI: 10.3390/genes9050227] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 04/09/2018] [Accepted: 04/18/2018] [Indexed: 02/06/2023] Open
Abstract
Hybrid sterility is an important step in the speciation process. Hybrids between dwarf hamsters Phodopus sungorus and P.campbelli provide a good model for studies in cytological and genetic mechanisms of hybrid sterility. Previous studies in hybrids detected multiple abnormalities of spermatogenesis and a high frequency of dissociation between the X and Y chromosomes at the meiotic prophase. In this study, we found that the autosomes of the hybrid males and females underwent paring and recombination as normally as their parental forms did. The male hybrids showed a significantly higher frequency of asynapsis and recombination failure between the heterochromatic arms of the X and Y chromosomes than the males of the parental species. Female hybrids as well as the females of the parental species demonstrated a high incidence of centromere misalignment at the XX bivalent and partial asynapsis of the ends of its heterochromatic arms. In all three karyotypes, recombination was completely suppressed in the heterochromatic arm of the X chromosome, where the pseudoautosomal region is located. We propose that this recombination pattern speeds up divergence of the X- and Y-linked pseudoautosomal regions between the parental species and results in their incompatibility in the male hybrids.
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Affiliation(s)
- Tatiana I Bikchurina
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Department, Novosibirsk 630090, Russia.
- Novosibirsk State University, Novosibirsk 630090, Russia.
| | - Katerina V Tishakova
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Department, Novosibirsk 630090, Russia.
- Novosibirsk State University, Novosibirsk 630090, Russia.
| | - Elena A Kizilova
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Department, Novosibirsk 630090, Russia.
- Novosibirsk State University, Novosibirsk 630090, Russia.
| | - Svetlana A Romanenko
- Novosibirsk State University, Novosibirsk 630090, Russia.
- Institute of Cell and Molecular Biology, Russian Academy of Sciences, Siberian Department, Novosibirsk 630090, Russia.
| | - Natalya A Serdyukova
- Institute of Cell and Molecular Biology, Russian Academy of Sciences, Siberian Department, Novosibirsk 630090, Russia.
| | - Anna A Torgasheva
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Department, Novosibirsk 630090, Russia.
- Novosibirsk State University, Novosibirsk 630090, Russia.
| | - Pavel M Borodin
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Department, Novosibirsk 630090, Russia.
- Novosibirsk State University, Novosibirsk 630090, Russia.
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10
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Moskalev AА, Kudryavtseva AV, Graphodatsky AS, Beklemisheva VR, Serdyukova NA, Krutovsky KV, Sharov VV, Kulakovskiy IV, Lando AS, Kasianov AS, Kuzmin DA, Putintseva YA, Feranchuk SI, Shaposhnikov MV, Fraifeld VE, Toren D, Snezhkina AV, Sitnik VV. De novo assembling and primary analysis of genome and transcriptome of gray whale Eschrichtius robustus. BMC Evol Biol 2017; 17:258. [PMID: 29297306 PMCID: PMC5751776 DOI: 10.1186/s12862-017-1103-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Background Gray whale, Eschrichtius robustus (E. robustus), is a single member of the family Eschrichtiidae, which is considered to be the most primitive in the class Cetacea. Gray whale is often described as a “living fossil”. It is adapted to extreme marine conditions and has a high life expectancy (77 years). The assembly of a gray whale genome and transcriptome will allow to carry out further studies of whale evolution, longevity, and resistance to extreme environment. Results In this work, we report the first de novo assembly and primary analysis of the E. robustus genome and transcriptome based on kidney and liver samples. The presented draft genome assembly is complete by 55% in terms of a total genome length, but only by 24% in terms of the BUSCO complete gene groups, although 10,895 genes were identified. Transcriptome annotation and comparison with other whale species revealed robust expression of DNA repair and hypoxia-response genes, which is expected for whales. Conclusions This preliminary study of the gray whale genome and transcriptome provides new data to better understand the whale evolution and the mechanisms of their adaptation to the hypoxic conditions. Electronic supplementary material The online version of this article (doi: 10.1186/s12862-017-1103-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alexey А Moskalev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russian Federation. .,Institute of Biology of Komi Science Center of Ural Branch of RAS, Syktyvkar, 167982, Russian Federation.
| | - Anna V Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russian Federation
| | - Alexander S Graphodatsky
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, 630090, Russian Federation.,Novosibirsk State University, Novosibirsk, 630090, Russian Federation
| | | | - Natalya A Serdyukova
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, 630090, Russian Federation
| | - Konstantin V Krutovsky
- Department of Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, Göttingen, 37077, Germany.,Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russian Federation.,Genome Research and Education Center, Siberian Federal University, Krasnoyarsk, 660036, Russian Federation.,Department of Ecosystem Science and Management, Texas A&M University, College Station, 77843-2138, TX, USA
| | - Vadim V Sharov
- Genome Research and Education Center, Siberian Federal University, Krasnoyarsk, 660036, Russian Federation.,Department of High Performance Computing, Institute of Space and Information Technologies, Siberian Federal University, Krasnoyarsk, 660074, Russian Federation
| | - Ivan V Kulakovskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russian Federation.,Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russian Federation.,Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, 143026, Russia
| | - Andrey S Lando
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russian Federation
| | - Artem S Kasianov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russian Federation.,Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, 143026, Russia
| | - Dmitry A Kuzmin
- Genome Research and Education Center, Siberian Federal University, Krasnoyarsk, 660036, Russian Federation.,Department of High Performance Computing, Institute of Space and Information Technologies, Siberian Federal University, Krasnoyarsk, 660074, Russian Federation
| | - Yuliya A Putintseva
- Genome Research and Education Center, Siberian Federal University, Krasnoyarsk, 660036, Russian Federation
| | - Sergey I Feranchuk
- Genome Research and Education Center, Siberian Federal University, Krasnoyarsk, 660036, Russian Federation.,Irkutsk National Research Technical University, Irkutsk, 664074, Russian Federation.,Limnological Institute, Siberian Branch of Russian Academy of Sciences, Irkutsk, 664033, Russian Federation
| | - Mikhail V Shaposhnikov
- Institute of Biology of Komi Science Center of Ural Branch of RAS, Syktyvkar, 167982, Russian Federation
| | - Vadim E Fraifeld
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Center for Multidisciplinary Research on Aging, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel
| | - Dmitri Toren
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Center for Multidisciplinary Research on Aging, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel
| | - Anastasia V Snezhkina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russian Federation
| | - Vasily V Sitnik
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, 143026, Russia
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11
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Romanenko SA, Serdyukova NA, Perelman PL, Pavlova SV, Bulatova NS, Golenishchev FN, Stanyon R, Graphodatsky AS. Intrachromosomal Rearrangements in Rodents from the Perspective of Comparative Region-Specific Painting. Genes (Basel) 2017; 8:E215. [PMID: 28867774 PMCID: PMC5615349 DOI: 10.3390/genes8090215] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 08/22/2017] [Accepted: 08/23/2017] [Indexed: 01/31/2023] Open
Abstract
It has long been hypothesized that chromosomal rearrangements play a central role in different evolutionary processes, particularly in speciation and adaptation. Interchromosomal rearrangements have been extensively mapped using chromosome painting. However, intrachromosomal rearrangements have only been described using molecular cytogenetics in a limited number of mammals, including a few rodent species. This situation is unfortunate because intrachromosomal rearrangements are more abundant than interchromosomal rearrangements and probably contain essential phylogenomic information. Significant progress in the detection of intrachromosomal rearrangement is now possible, due to recent advances in molecular biology and bioinformatics. We investigated the level of intrachromosomal rearrangement in the Arvicolinae subfamily, a species-rich taxon characterized by very high rate of karyotype evolution. We made a set of region specific probes by microdissection for a single syntenic region represented by the p-arm of chromosome 1 of Alexandromys oeconomus, and hybridized the probes onto the chromosomes of four arvicolines (Microtus agrestis, Microtus arvalis, Myodes rutilus, and Dicrostonyx torquatus). These experiments allowed us to show the intrachromosomal rearrangements in the subfamily at a significantly higher level of resolution than previously described. We found a number of paracentric inversions in the karyotypes of M. agrestis and M. rutilus, as well as multiple inversions and a centromere shift in the karyotype of M. arvalis. We propose that during karyotype evolution, arvicolines underwent a significant number of complex intrachromosomal rearrangements that were not previously detected.
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Affiliation(s)
- Svetlana A Romanenko
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia.
- Synthetic Biological Unit, Novosibirsk State University, 630090 Novosibirsk, Russia.
| | - Natalya A Serdyukova
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia.
| | - Polina L Perelman
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia.
- Synthetic Biological Unit, Novosibirsk State University, 630090 Novosibirsk, Russia.
| | - Svetlana V Pavlova
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, 119071 Moscow, Russia.
| | - Nina S Bulatova
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, 119071 Moscow, Russia.
| | | | - Roscoe Stanyon
- Department of Biology, Anthropology Laboratories, University of Florence, 50122 Florence, Italy.
| | - Alexander S Graphodatsky
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia.
- Synthetic Biological Unit, Novosibirsk State University, 630090 Novosibirsk, Russia.
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12
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Gladkikh OL, Romanenko SA, Lemskaya NA, Serdyukova NA, O’Brien PCM, Kovalskaya JM, Smorkatcheva AV, Golenishchev FN, Perelman PL, Trifonov VA, Ferguson-Smith MA, Yang F, Graphodatsky AS. Rapid Karyotype Evolution in Lasiopodomys Involved at Least Two Autosome - Sex Chromosome Translocations. PLoS One 2016; 11:e0167653. [PMID: 27936177 PMCID: PMC5147937 DOI: 10.1371/journal.pone.0167653] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 11/17/2016] [Indexed: 11/21/2022] Open
Abstract
The generic status of Lasiopodomys and its division into subgenera Lasiopodomys (L. mandarinus, L. brandtii) and Stenocranius (L. gregalis, L. raddei) are not generally accepted because of contradictions between the morphological and molecular data. To obtain cytogenetic evidence for the Lasiopodomys genus and its subgenera and to test the autosome to sex chromosome translocation hypothesis of sex chromosome complex origin in L. mandarinus proposed previously, we hybridized chromosome painting probes from the field vole (Microtus agrestis, MAG) and the Arctic lemming (Dicrostonyx torquatus, DTO) onto the metaphases of a female Mandarin vole (L. mandarinus, 2n = 47) and a male Brandt's vole (L. brandtii, 2n = 34). In addition, we hybridized Arctic lemming painting probes onto chromosomes of a female narrow-headed vole (L. gregalis, 2n = 36). Cross-species painting revealed three cytogenetic signatures (MAG12/18, 17a/19, and 22/24) that could validate the genus Lasiopodomys and indicate the evolutionary affinity of L. gregalis to the genus. Moreover, all three species retained the associations MAG1bc/17b and 2/8a detected previously in karyotypes of all arvicolins studied. The associations MAG2a/8a/19b, 8b/21, 9b/23, 11/13b, 12b/18, 17a/19a, and 5 fissions of ancestral segments appear to be characteristic for the subgenus Lasiopodomys. We also validated the autosome to sex chromosome translocation hypothesis on the origin of complex sex chromosomes in L. mandarinus. Two translocations of autosomes onto the ancestral X chromosome in L. mandarinus led to a complex of neo-X1, neo-X2, and neo-X3 elements. Our results demonstrate that genus Lasiopodomys represents a striking example of rapid chromosome evolution involving both autosomes and sex chromosomes. Multiple reshuffling events including Robertsonian fusions, chromosomal fissions, inversions and heterochromatin expansion have led to the formation of modern species karyotypes in a very short time, about 2.4 MY.
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Affiliation(s)
- Olga L. Gladkikh
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Svetlana A. Romanenko
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
- * E-mail:
| | - Natalya A. Lemskaya
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Natalya A. Serdyukova
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Patricia C. M. O’Brien
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Julia M. Kovalskaya
- Severtzov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | | | | | - Polina L. Perelman
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Vladimir A. Trifonov
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Malcolm A. Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Fengtang Yang
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Alexander S. Graphodatsky
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
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13
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Romanenko SA, Lemskaya NA, Trifonov VA, Serdyukova NA, O'Brien PCM, Bulatova NS, Golenishchev FN, Ferguson-Smith MA, Yang F, Graphodatsky AS. Genome-wide comparative chromosome maps of Arvicola amphibius, Dicrostonyx torquatus, and Myodes rutilus. Chromosome Res 2015; 24:145-59. [PMID: 26611440 DOI: 10.1007/s10577-015-9504-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 11/05/2015] [Accepted: 11/09/2015] [Indexed: 11/25/2022]
Abstract
The subfamily Arvicolinae consists of a great number of species with highly diversified karyotypes. In spite of the wide use of arvicolines in biological and medicine studies, the data on their karyotype structures are limited. Here, we made a set of painting probes from flow-sorted chromosomes of a male Palearctic collared lemming (Dicrostonyx torquatus, DTO). Together with the sets of painting probes made previously from the field vole (Microtus agrestis, MAG) and golden hamster (Mesocricetus auratus, MAU), we carried out a reciprocal chromosome painting between these three species. The three sets of probes were further hybridized onto the chromosomes of the Eurasian water vole (Arvicola amphibius) and northern red-backed vole (Myodes rutilus). We defined the diploid chromosome number in D. torquatus karyotype as 2n = 45 + Bs and showed that the system of sex chromosomes is X1X2Y1. The probes developed here provide a genomic tool-kit, which will help to investigate the evolutionary biology of the Arvicolinae rodents. Our results show that the syntenic association MAG1/17 is present not only in Arvicolinae but also in some species of Cricetinae; and thus, should not be considered as a cytogenetic signature for Arvicolinae. Although cytogenetic signature markers for the genera have not yet been found, our data provides insight into the likely ancestral karyotype of Arvicolinae. We conclude that the karyotypes of modern voles could have evolved from a common ancestral arvicoline karyotype (AAK) with 2n = 56 mainly by centric fusions and fissions.
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Affiliation(s)
- Svetlana A Romanenko
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, 630090, Russia. .,Novosibirsk State University, Novosibirsk, 630090, Russia.
| | - Natalya A Lemskaya
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, 630090, Russia
| | - Vladimir A Trifonov
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, 630090, Russia.,Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Natalya A Serdyukova
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, 630090, Russia
| | - Patricia C M O'Brien
- Department of Veterinary Medicine, Cambridge Resource Centre for Comparative Genomics, University of Cambridge, Madingley Road, Cambridge, CB3 OES, UK
| | - Nina Sh Bulatova
- A. N. Severtsov Institute of Ecology and Evolution, Moscow, 119071, Russia
| | | | - Malcolm A Ferguson-Smith
- Department of Veterinary Medicine, Cambridge Resource Centre for Comparative Genomics, University of Cambridge, Madingley Road, Cambridge, CB3 OES, UK
| | - Fengtang Yang
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
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14
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Romanenko SA, Biltueva LS, Serdyukova NA, Kulemzina AI, Beklemisheva VR, Gladkikh OL, Lemskaya NA, Interesova EA, Korentovich MA, Vorobieva NV, Graphodatsky AS, Trifonov VA. Segmental paleotetraploidy revealed in sterlet (Acipenser ruthenus) genome by chromosome painting. Mol Cytogenet 2015; 8:90. [PMID: 26587056 PMCID: PMC4652396 DOI: 10.1186/s13039-015-0194-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 11/07/2015] [Indexed: 11/21/2022] Open
Abstract
Background Acipenseriformes take a basal position among Actinopteri and demonstrate a striking ploidy variation among species. The sterlet (Acipenser ruthenus, Linnaeus, 1758; ARUT) is a diploid 120-chromosomal sturgeon distributed in Eurasian rivers from Danube to Enisey. Despite a high commercial value and a rapid population decline in the wild, many genomic characteristics of sterlet (as well as many other sturgeon species) have not been studied. Results Cell lines from different tissues of 12 sterlet specimens from Siberian populations were established following an optimized protocol. Conventional cytogenetic studies supplemented with molecular cytogenetic investigations on obtained fibroblast cell lines allowed a detailed description of sterlet karyotype and a precise localization of 18S/28S and 5S ribosomal clusters. Localization of sturgeon specific HindIII repetitive elements revealed an increased concentration in the pericentromeric region of the acrocentric ARUT14, while the total sterlet repetitive DNA fraction (C0t30) produced bright signals on subtelomeric segments of small chromosomal elements. Chromosome and region specific probes ARUT1p, 5, 6, 7, 8 as well as 14 anonymous small sized chromosomes (probes A-N) generated by microdissection were applied in chromosome painting experiments. According to hybridization patterns all painting probes were classified into two major groups: the first group (ARUT5, 6, 8 as well as microchromosome specific probes C, E, F, G, H, and I) painted only a single region each on sterlet metaphases, while probes of the second group (ARUT1p, 7 as well as microchromosome derived probes A, B, D, J, K, M, and N) marked two genomic segments each on different chromosomes. Similar results were obtained on male and female metaphases. Conclusions The sterlet genome represents a complex mosaic structure and consists of diploid and tetraploid chromosome segments. This may be regarded as a transition stage from paleotetraploid (functional diploid) to diploid genome condition. Molecular cytogenetic and genomic studies of other 120- and 240-chromosomal sturgeons are needed to reconstruct genome evolution of this vertebrate group.
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Affiliation(s)
- Svetlana A Romanenko
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia ; Novosibirsk State University, Novosibirsk, Russia
| | - Larisa S Biltueva
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | | | | | | | - Olga L Gladkikh
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | | | - Elena A Interesova
- Novosibirsk Branch of the Federal State Budgetary Scientific Institution "State Scientific-and-Production Centre for Fisheries (Gosrybcenter)", Novosibirsk, Russia ; Tomsk State University, Tomsk, Russia
| | - Marina A Korentovich
- Federal State Budgetary Scientific Institution "State Scientific-and-Production Centre for Fisheries (Gosrybcenter)", Tyumen, Russia
| | - Nadezhda V Vorobieva
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia ; Novosibirsk State University, Novosibirsk, Russia
| | - Alexander S Graphodatsky
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia ; Novosibirsk State University, Novosibirsk, Russia
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15
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Aksenov DP, Serdyukova NA, Bloedel JR, Bracha V. Glutamate neurotransmission in the cerebellar interposed nuclei: involvement in classically conditioned eyeblinks and neuronal activity. J Neurophysiol 2004; 93:44-52. [PMID: 15331619 DOI: 10.1152/jn.00586.2004] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The cerebellar interposed nuclei (IN) are critical components of a neural network that controls the expression of classically conditioned eyeblinks. The IN receive 2 major inputs: the massive, gamma-aminobutyric acid (GABA)-mediated input from the Purkinje cells of the cerebellar cortex and the relatively weaker, glutamate-mediated input from collaterals of mossy and climbing fiber cerebellar afferent systems. To elucidate the role of IN glutamate neurotransmission in conditioned response (CR) expression, effects of blocking fast glutamatergic neurotransmission in the IN with gamma-d-glutamylglycine (DGG) on the expression of conditioned eyeblinks and on cerebellar nuclear neuronal activity were examined. Surprisingly, blocking fast glutamate receptors in the IN did not abolish CRs. DGG decreased CR incidence and slightly increased CR latency. In contrast, identical amounts of DGG applied to the cerebellar cortex abolished CRs. Similar to the behavioral effects, DGG had unexpectedly mild effects on IN neurons. At the population level, the baseline firing frequency of IN cells was not affected. After DGG injections, the incidence of excitatory modulation of cell activity in the interstimulus interval decreased but was not abolished. A combined block of fast glutamate and GABA(A) neurotransmission using a mixture of DGG and picrotoxin dramatically reduced CR incidence, increased the firing frequency of all cell types, and virtually abolished all modulation of neuronal activity. These results indicate that fast glutamate neurotransmission in the IN plays only an accessory role both in the expression of behavioral CRs and in the generation of associated neuronal activity in the IN.
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Affiliation(s)
- D P Aksenov
- Department of Biomedical Sciences, 2032 Vet Med, Iowa State University, Ames, IA 50011, USA
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16
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Abstract
C-banding and fluorescence in situ hybridization (FISH) document the distribution of constitutive heterochromatin and six highly repeated DNA families (MSAT2570, MSAT21, MSAT160, MS2, MS4 and STR47) in the chromosomes of nine species of Microtus (M. chrotorrhinus, M. rossiaemeridionalis, M. arvalis, M. ilaeus, M. transcaspicus, M. cabrerae, M. pennsylvanicus, M. miurus and M. ochrogaster). Autosomal heterochromatin is largely centromeric and contains different repeated families in different species. Similarly, large C-band positive blocks on the sex chromosomes of four species contain different repeated DNAs. This interspecific variation in the chromosomal distribution and copy number of the repeats suggests that a common ancestor to modern species contained most of the repetitive families, and that descendant species selectively amplified or deleted different repeats on different chromosomes.
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Affiliation(s)
- William S Modi
- Basic Research Program, SAIC Frederick, National Cancer Institute at Frederick, Frederick, MD 21702, USA.
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17
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Graphodatsky AS, Sablina OV, Meyer MN, Malikov VG, Isakova EA, Trifonov VA, Polyakov AV, Lushnikova TP, Vorobieva NV, Serdyukova NA, Perelman PL, Borodin PM, Benda P, Frynta D, Leikepová L, Munclinger P, Piálek J, Sádlová J, Zima J. Comparative cytogenetics of hamsters of the genus Calomyscus. Cytogenet Cell Genet 2000; 88:296-304. [PMID: 10828614 DOI: 10.1159/000015513] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Karyotypes of Calomyscus from different regions of Turkmenistan, Iran, and Azerbaijan were studied using chromosome banding (G- and C-banding) and analyses of meiosis in laboratory hybrids. Extensive variation in the diploid number and the number of autosomal arms (FNa) was revealed (2n = 30, FNa = 44; 2n = 32, FNa = 42; 2n = 44, FNa = 46; 2n = 44, FNa = 58; 2n = 37, FNa = 44; 2n = 50, FNa = 50; 2n = 52, FNa = 56). Centric and tandem fusions and heterochromatin changes were identified as the major modes of karyotype evolution in this group. Natural hybrids between individuals with different karyotypes were recorded, and regular chromosome pairing in meiosis was observed in laboratory hybrids. Fluorescence in situ hybridization with a 353-bp BspRI complex tandem repeat indicated that chromosomal repatterning occurred recently within the genus. There is no unequivocal evidence suggesting the role of chromosomal change in the speciation of the populations of Calomyscus examined.
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Affiliation(s)
- A S Graphodatsky
- Institute of Cytology and Genetics, Russian Academy of Sciences, Novosibirsk, Russia
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18
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Rogatcheva MB, Serdyukova NA, Biltueva LS, Perelman PL, Borodin PM, Oda S, Graphodatsky AS. Localization of the genes for major ribosomal RNA on chromosomes of the house musk shrew, Suncus murinus, at meiotic and mitotic cells by fluorescence in situ hybridization and silver staining. Genes Genet Syst 1997; 72:215-8. [PMID: 9418261 DOI: 10.1266/ggs.72.215] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The genes for major ribosomal RNA were localized on chromosomes 5pter-p15, 9q64-qter, and 13q38-qter of the house musk shrew, Suncus murinus (Insectivora, Soricidae) by silver staining of mitotic metaphase and meiotic pachytene spreads and fluorescence in situ hybridization using the human 28S-RNA genes as a probe to mitotic metaphase spreads. The data presented indicate a correlation between sites of in situ hybridization and silver staining. The finding of nuclear materials in mitosis was in a good agreement with observation in meiosis: same chromosomes carried active NORs in both meiotic and mitotic cells.
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Affiliation(s)
- M B Rogatcheva
- School of Agricultural Sciences, Nagoya University, Japan
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