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Romanenko SA, Kliver SF, Serdyukova NA, Perelman PL, Trifonov VA, Seluanov A, Gorbunova V, Azpurua J, Pereira JC, Ferguson-Smith MA, Graphodatsky AS. Integration of fluorescence in situ hybridization and chromosome-length genome assemblies revealed synteny map for guinea pig, naked mole-rat, and human. Sci Rep 2023; 13:21055. [PMID: 38030702 PMCID: PMC10687270 DOI: 10.1038/s41598-023-46595-x] [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: 06/08/2023] [Accepted: 11/02/2023] [Indexed: 12/01/2023] Open
Abstract
Descriptions of karyotypes of many animal species are currently available. In addition, there has been a significant increase in the number of sequenced genomes and an ever-improving quality of genome assembly. To close the gap between genomic and cytogenetic data we applied fluorescent in situ hybridization (FISH) and Hi-C technology to make the first full chromosome-level genome comparison of the guinea pig (Cavia porcellus), naked mole-rat (Heterocephalus glaber), and human. Comparative chromosome maps obtained by FISH with chromosome-specific probes link genomic scaffolds to individual chromosomes and orient them relative to centromeres and heterochromatic blocks. Hi-C assembly made it possible to close all gaps on the comparative maps and to reveal additional rearrangements that distinguish the karyotypes of the three species. As a result, we integrated the bioinformatic and cytogenetic data and adjusted the previous comparative maps and genome assemblies of the guinea pig, naked mole-rat, and human. Syntenic associations in the two hystricomorphs indicate features of their putative ancestral karyotype. We postulate that the two approaches applied in this study complement one another and provide complete information about the organization of these genomes at the chromosome level.
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Affiliation(s)
- Svetlana A Romanenko
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia.
| | - Sergei F Kliver
- Center for Evolutionary Hologenomics, The Globe Institute, The University of Copenhagen, Copenhagen, Denmark
| | - Natalia A Serdyukova
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia
| | - Polina L Perelman
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia
| | - Vladimir A Trifonov
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Andrei Seluanov
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Vera Gorbunova
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Jorge Azpurua
- Department of Biochemistry and Molecular Medicine, The George Washington University, Washington, DC, USA
| | - Jorge C Pereira
- Animal and Veterinary Research Centre, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Malcolm A Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Alexander S Graphodatsky
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia
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Stokes JV, Levin ML, Cross CE, Ross AL, Snellgrove AN, Willeford BV, Alugubelly N, Varela‐Stokes AS. Evaluating the Clinical and Immune Responses to Spotted Fever Rickettsioses in the Guinea Pig-Tick-Rickettsia System. Curr Protoc 2022; 2:e584. [PMID: 36383032 PMCID: PMC9828190 DOI: 10.1002/cpz1.584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The guinea pig was the original animal model developed for investigating spotted fever rickettsiosis (SFR). This model system has persisted on account of the guinea pig's conduciveness to tick transmission of SFR agents and ability to recapitulate SFR in humans through clinical signs that include fever, unthriftiness, and in some cases the development of an eschar. The guinea pig is the smallest animal model for SFR that allows the collection of multiple blood and skin samples antemortem for longitudinal studies. This unit provides the basic protocols necessary to establish, maintain, and utilize a guinea pig-tick-Rickettsia model for monitoring the course of infection and immune response to an infection by spotted fever group Rickettsia (SFGR) that can be studied at biosafety level 2 (BSL-2) and arthropod containment level 2 (ACL-2); adaptations must be made for BSL-3 agents. The protocols cover methods for tick feeding and colony development, laboratory infection of ticks, tick transmission of Rickettsia to guinea pigs, and monitoring of the course of infection through clinical signs, rickettsial burden, and immune response. It should be feasible to adapt these methods to study other tick-borne pathogens. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Tick transmission of SFGR to guinea pigs Support Protocol 1: Laboratory infection of ticks by injection Alternate Protocol 1: Needle inoculation of SFGR to guinea pigs Basic Protocol 2: Monitoring the course of guinea pig rickettsial infection: clinical signs Basic Protocol 3: Monitoring the course of guinea pig rickettsial infection: collection of biological specimens Support Protocol 2: Guinea pig anesthesia Basic Protocol 4: Monitoring rickettsial burden in guinea pigs by multiplex qPCR Basic Protocol 5: Monitoring guinea pig immune response to infection: blood leukocytes by flow cytometry Basic Protocol 6: Monitoring immune response to guinea pig rickettsial infection: leukocyte infiltration of skin at the tick bite site by flow cytometry Basic Protocol 7: Monitoring the immune response to guinea pig rickettsial infection: antibody titer by ELISA Support Protocol 4: Coating ELISA Plates Alternate Protocol 2: Monitoring immune response to guinea pig rickettsial infection: antibody titer by immunofluorescence assay.
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Affiliation(s)
- John V. Stokes
- Department of Comparative Pathobiology, Cummings School of Veterinary MedicineTufts UniversityNorth GraftonMassachusettsUSA
| | - Michael L. Levin
- Division of Vector‐Borne DiseasesCenters for Disease Control and PreventionAtlantaGeorgiaUSA
| | - Claire E. Cross
- Department of Pathology, Microbiology, and ImmunologyVanderbilt UniversityNashvilleTennesseeUSA
| | - Anne‐Marie L. Ross
- Department of Comparative Biomedical SciencesMississippi State UniversityMississippi StateMississippiUSA
| | - Alyssa N. Snellgrove
- Division of Vector‐Borne DiseasesCenters for Disease Control and PreventionAtlantaGeorgiaUSA
| | - Bridget V. Willeford
- Laboratory Animal ResourcesMississippi State UniversityMississippi StateMississippiUSA
| | | | - Andrea S. Varela‐Stokes
- Department of Comparative Pathobiology, Cummings School of Veterinary MedicineTufts UniversityNorth GraftonMassachusettsUSA
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Wahl D, Moreno JA, Santangelo KS, Zhang Q, Afzali MF, Walsh MA, Musci RV, Cavalier AN, Hamilton KL, LaRocca TJ. Nontransgenic Guinea Pig Strains Exhibit Hallmarks of Human Brain Aging and Alzheimer's Disease. J Gerontol A Biol Sci Med Sci 2022; 77:1766-1774. [PMID: 35323931 PMCID: PMC9434446 DOI: 10.1093/gerona/glac073] [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: 12/29/2021] [Indexed: 11/14/2022] Open
Abstract
Older age is the primary risk factor for most chronic diseases, including Alzheimer's disease (AD). Current preclinical models to study brain aging and AD are mainly transgenic and harbor mutations intended to mirror brain pathologies associated with human brain aging/AD (eg, by increasing production of the amyloid precursor protein, amyloid beta [Aβ], and/or phosphorylated tau, all of which are key pathological mediators of AD). Although these models may provide insight on pathophysiological processes in AD, none completely recapitulate the disease and its strong age-dependence, and there has been limited success in translating preclinical results and treatments to humans. Here, we describe 2 nontransgenic guinea pig (GP) models, a standard PigmEnTed (PET) strain, and lesser-studied Dunkin-Hartley (DH) strain, that may naturally mimic key features of brain aging and AD in humans. We show that brain aging in PET GP is transcriptomically similar to human brain aging, whereas older DH brains are transcriptomically more similar to human AD. Both strains/models also exhibit increased neurofilament light chain (NFL, a marker of neuronal damage) with aging, and DH animals display greater S100 calcium-binding protein B (S100β), ionized calcium-binding adapter molecule 1 (Iba1), and Aβ and phosphorylated tau-which are all important markers of neuroinflammation-associated AD. Collectively, our results suggest that both the PET and DH GP may be useful, nontransgenic models to study brain aging and AD, respectively.
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Affiliation(s)
- Devin Wahl
- Department of Health and Exercise Science, Colorado State University, Fort Collins, Colorado, USA
- Center for Healthy Aging, Colorado State University, Fort Collins, Colorado, USA
| | - Julie A Moreno
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Kelly S Santangelo
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Qian Zhang
- Department of Health and Exercise Science, Colorado State University, Fort Collins, Colorado, USA
| | - Maryam F Afzali
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Maureen A Walsh
- Department of Health and Exercise Science, Colorado State University, Fort Collins, Colorado, USA
| | - Robert V Musci
- Department of Health and Exercise Science, Colorado State University, Fort Collins, Colorado, USA
| | - Alyssa N Cavalier
- Department of Health and Exercise Science, Colorado State University, Fort Collins, Colorado, USA
| | - Karyn L Hamilton
- Department of Health and Exercise Science, Colorado State University, Fort Collins, Colorado, USA
- Center for Healthy Aging, Colorado State University, Fort Collins, Colorado, USA
| | - Thomas J LaRocca
- Address correspondence to: Thomas J. LaRocca, PhD, Department of Health and Exercise Science, Center for Healthy Aging, Colorado State University, 1582 Campus Delivery, Fort Collins, CO 80523-1582, USA. E-mail:
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Convergent evolution of a genomic rearrangement may explain cancer resistance in hystrico- and sciuromorpha rodents. NPJ Aging Mech Dis 2021; 7:20. [PMID: 34471123 PMCID: PMC8410860 DOI: 10.1038/s41514-021-00072-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 06/21/2021] [Indexed: 11/09/2022] Open
Abstract
The rodents of hystricomorpha and sciuromorpha suborders exhibit remarkably lower incidence of cancer. The underlying genetic basis remains obscure. We report a convergent evolutionary split of human 3p21.31, a locus hosting a large number of tumour-suppressor genes (TSGs) and frequently deleted in several tumour types, in hystrico- and sciuromorphs. Analysis of 34 vertebrate genomes revealed that the synteny of 3p21.31 cluster is functionally and evolutionarily constrained in most placental mammals, but exhibit large genomic interruptions independently in hystricomorphs and sciuromorphs, owing to relaxation of underlying constraints. Hystrico- and sciuromorphs, therefore, escape from pro-tumorigenic co-deletion of several TSGs in cis. The split 3p21.31 sub-clusters gained proximity to proto-oncogene clusters from elsewhere, which might further nullify pro-tumorigenic impact of copy number variations due to co-deletion or co-amplification of genes with opposing effects. The split of 3p21.31 locus coincided with the accelerated rate of its gene expression and the body mass evolution of ancestral hystrico- and sciuromorphs. The genes near breakpoints were associated with the traits specific to hystrico- and sciuromorphs, implying adaptive significance. We conclude that the convergently evolved chromosomal interruptions of evolutionarily constrained 3p21.31 cluster might have impacted evolution of cancer resistance, body mass variation and ecological adaptations in hystrico- and sciuromorphs.
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Complex Structure of Lasiopodomys mandarinus vinogradovi Sex Chromosomes, Sex Determination, and Intraspecific Autosomal Polymorphism. Genes (Basel) 2020; 11:genes11040374. [PMID: 32235544 PMCID: PMC7230192 DOI: 10.3390/genes11040374] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 03/23/2020] [Accepted: 03/27/2020] [Indexed: 11/21/2022] Open
Abstract
The mandarin vole, Lasiopodomys mandarinus, is one of the most intriguing species among mammals with non-XX/XY sex chromosome system. It combines polymorphism in diploid chromosome numbers, variation in the morphology of autosomes, heteromorphism of X chromosomes, and several sex chromosome systems the origin of which remains unexplained. Here we elucidate the sex determination system in Lasiopodomys mandarinus vinogradovi using extensive karyotyping, crossbreeding experiments, molecular cytogenetic methods, and single chromosome DNA sequencing. Among 205 karyotyped voles, one male and three female combinations of sex chromosomes were revealed. The chromosome segregation pattern and karyomorph-related reproductive performances suggested an aberrant sex determination with almost half of the females carrying neo-X/neo-Y combination. The comparative chromosome painting strongly supported this proposition and revealed the mandarin vole sex chromosome systems originated due to at least two de novo autosomal translocations onto the ancestral X chromosome. The polymorphism in autosome 2 was not related to sex chromosome variability and was proved to result from pericentric inversions. Sequencing of microdissection derived of sex chromosomes allowed the determination of the coordinates for syntenic regions but did not reveal any Y-specific sequences. Several possible sex determination mechanisms as well as interpopulation karyological differences are discussed.
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Lindsay CD, Timperley CM. TRPA1 and issues relating to animal model selection for extrapolating toxicity data to humans. Hum Exp Toxicol 2019; 39:14-36. [PMID: 31578097 DOI: 10.1177/0960327119877460] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The transient receptor potential ankyrin 1 (TRPA1) ion channel is a sensor for irritant chemicals, has ancient lineage, and is distributed across animal species including humans, where it features in many organs. Its activation by a diverse panel of electrophilic molecules (TRPA1 agonists) through electrostatic binding and/or covalent attachment to the protein causes the sensation of pain. This article reviews the species differences between TRPA1 channels and their responses, to assess the suitability of different animals to model the effects of TRPA1-activating electrophiles in humans, referring to common TRPA1 activators (exogenous and endogenous) and possible mechanisms of action relating to their toxicology. It concludes that close matching of in vitro and in vivo models will help optimise the identification of relevant biochemical and physiological responses to benchmark the efficacy of potential therapeutic drugs, including TRPA1 antagonists, to counter the toxic effects of those electrophiles capable of harming humans. The analysis of the species issue provided should aid the development of medical treatments to counter poisoning by such chemicals.
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Affiliation(s)
- C D Lindsay
- Chemical, Biological and Radiological (CBR) Division, Defence Science and Technology Laboratory (Dstl), Salisbury, UK
| | - C M Timperley
- Chemical, Biological and Radiological (CBR) Division, Defence Science and Technology Laboratory (Dstl), Salisbury, UK
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Kresnoadi U, Raharjo T, Rostiny R. Effects of mangosteen peel extract combined with demineralized freeze-dried bovine bone xenograft on osteocalcin, collagen 1, and osteoblast as alveolar bone regeneration in socket preservation. J Indian Prosthodont Soc 2018; 18:117-121. [PMID: 29692564 PMCID: PMC5903174 DOI: 10.4103/jips.jips_326_17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 01/29/2018] [Indexed: 11/18/2022] Open
Abstract
Background: Tooth extraction will provoke changes in alveolar bone morphology and dimensions. Postextraction bone resorption can lead to significant problems for restorative dentistry. Therefore, the extracted tooth socket needs to be preserved to reduce alveolar ridge bone resorption. This research aimed to analyze the expression and levels of osteocalcin, collagen 1, and osteoblasts in extracted tooth sockets filled with a combination of mangosteen peel extract and demineralized freeze-dried bovine bone xenograft (DFDBBX). Material and Methods: Fifty-six Cavia cobaya, whose lower left incisors had been extracted, were divided into eight groups according to the substance used to fill their sockets on days 7 and 30, Poly ethylene glycol, DFDBBX, mangosteen peel extract, or a combination of mangosteen peel extract and DFDBBX. This research was conducted in several stages; the application of mangosteen peel extract combined with graft material was performed as the form of tooth extraction socket preservation. The C. cobaya rats were subsequently examined by immunohistochemical methods to measure osteocalcin and collagen 1 expressions, whereas histological examination was conducted to calculate the number of osteoblasts in accordance with the duration of the research. Results: On days 7 and 30, the group treated with a combination of DFDBBX and mangosteen peel extract which had the highest expression and levels of osteocalcin, collagen 1, and osteoblasts. Conclusion: The administration of mangosteen peel extract combined with DFDBBX as a means of tooth extraction socket preservation can increase osteocalcin and collagen 1 expression. Consequently, osteoblasts as a means of alveolar bone regeneration will increase in number.
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Affiliation(s)
- Utari Kresnoadi
- Department of Prosthodontic, Faculty of Dental Medicine, Universitas Airlangga, Surabaya 60132, Indonesia
| | - Tika Raharjo
- Department of Prosthodontic, Faculty of Dental Medicine, Universitas Airlangga, Surabaya 60132, Indonesia
| | - Rostiny Rostiny
- Department of Prosthodontic, Faculty of Dental Medicine, Universitas Airlangga, Surabaya 60132, Indonesia
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Karyotype diversity suggests that Laonastes aenigmamus (Laotian rock rat) (Rodentia, Diatomyidae) is a multi-specific genus. Chromosome Res 2016; 24:379-92. [PMID: 27193170 DOI: 10.1007/s10577-016-9527-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 04/21/2016] [Accepted: 04/25/2016] [Indexed: 12/18/2022]
Abstract
Laonastes aenigmamus (Khanyou) is a recently described rodent species living in geographically separated limestone formations of the Khammuan Province in Lao PDR. Chromosomes of 21 specimens of L. aenigmamus were studied using chromosome banding as well as fluorescent in situ hybridization (FISH) techniques using human painting, telomere repeats, and 28S rDNA probes. Four different karyotypes were established. Study with human chromosome paints and FISH revealed that four large chromosomes were formed by multiple common tandem fusions, with persistence of some interstitial telomeres. The rearrangements separating the different karyotypes (I to IV) were also reconstructed. Various combinations of Robertsonian translocations or tandem fusions involving the same chromosomes differentiate these karyotypes. These rearrangements create a strong gametic barrier, which isolates specimens with karyotype II from the others. C-banding and FISH with telomere repeats also exhibit large and systematized differences between karyotype II and others. These data indicate an ancient reproductive separation and suggest that Laonastes is not a mono-specific genus.
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