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Zakharenko LP, Petrovskii DV, Bykov RA. The P-Element Has Not Significant Effect on the Drosophila simulans Viability. Mol Biol 2023. [DOI: 10.1134/s0026893323020231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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Bertocchi NÁ, Oliveira TDD, Deprá M, Goñi B, Valente VLS. Interpopulation variation of transposable elements of the hAT superfamily in Drosophila willistoni (Diptera: Drosophilidae): in-situ approach. Genet Mol Biol 2022; 45:e20210287. [PMID: 35297941 PMCID: PMC8961557 DOI: 10.1590/1678-4685-gmb-2021-0287] [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: 09/10/2021] [Accepted: 01/31/2022] [Indexed: 11/22/2022] Open
Abstract
Transposable elements are abundant and dynamic part of the genome, influencing
organisms in different ways through their presence or mobilization, or by acting
directly on pre- and post-transcriptional regulatory regions. We compared and
evaluated the presence, structure, and copy number of three hAT
superfamily transposons (hobo, BuT2, and mar)
in five strains of Drosophila willistoni
species. These D. willistoni strains are
of different geographical origins, sampled across the north-south occurrence of
this species. We used sequenced clones of the hAT elements in
fluorescence in-situ hybridizations in the polytene chromosomes
of three strains of D. willistoni. We also analyzed the
structural characteristics and number of copies of these hAT
elements in the 10 currently available sequenced genomes of the
willistoni group. We found that hobo,
BuT2, and mar were widely distributed in
D. willistoni polytene chromosomes and sequenced genomes of
the willistoni group, except for mar, which is
restricted to the subgroup willistoni. Furthermore, the
elements hobo, BuT2, and mar have different
evolutionary histories. The transposon differences among D.
willistoni strains, such as variation in the number, structure, and
chromosomal distribution of hAT transposons, could reflect the
genomic and chromosomal plasticity of D. willistoni species in
adapting to highly variable environments.
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Affiliation(s)
- Natasha Ávila Bertocchi
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
| | - Thays Duarte de Oliveira
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Biologia Animal, Porto Alegre, RS, Brazil
| | - Maríndia Deprá
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil.,Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Biologia Animal, Porto Alegre, RS, Brazil
| | - Beatriz Goñi
- Universidad de la República, Facultad de Ciencias, Montevideo, Uruguay
| | - Vera Lúcia S Valente
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil.,Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Biologia Animal, Porto Alegre, RS, Brazil
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Bernardo LP, Mombach DM, Loreto ELS. Characterization of Herves-like transposable elements (hATs) in Drosophila species and their evolutionary scenario. INSECT MOLECULAR BIOLOGY 2019; 28:616-627. [PMID: 30793407 DOI: 10.1111/imb.12577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A monophyletic group of Drosophila hAT transposable elements, referred to as Herves-like, was characterized and found to be present in 46% of 57 screened Drosophila species. A remarkable characteristic of these elements is the presence of a long array of minisatellite repeats (MnRs) in both subterminal extremities of the elements. The copy number of these minisatellites was highly variable between and within populations. Twenty-three strains of Drosophila willistoni, covering its geographic distribution, were screened for polymorphism in the copy number of 5' MnRs, showing a variation from 7 to 20 repeat copies. These MnRs are well conserved among Drosophila species and probably function as transposase binding sequences, as provided by short subterminal repeats in other hAT elements. Miniature inverted repeat transposable elements were found in 27% of species carrying Herves-like elements. Phylogenetic analysis showed incongruences between transposable elements and species phylogenies, suggesting that at least four horizontal transfer events have occurred.
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Affiliation(s)
- L P Bernardo
- PPG Biodiverdade Animal, Universidade Federal de Santa Maria (UFSM), Santa Maria, Brazil
| | - D M Mombach
- Department of Biochemistry and Molecular Biology, CCNE, Univeridade Federal de Santa Maria, Santa Maria, Brazil
| | - E L S Loreto
- Department of Biochemistry and Molecular Biology, CCNE, Univeridade Federal de Santa Maria, Santa Maria, Brazil
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Simão MC, Haudry A, Granzotto A, de Setta N, Carareto CMA. Helena and BS: Two Travellers between the Genera Drosophila and Zaprionus. Genome Biol Evol 2018; 10:2671-2685. [PMID: 30165545 PMCID: PMC6179348 DOI: 10.1093/gbe/evy184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2018] [Indexed: 12/20/2022] Open
Abstract
The frequency of horizontal transfers of transposable elements (HTTs) varies among the types of elements according to the transposition mode and the geographical and temporal overlap of the species involved in the transfer. The drosophilid species of the genus Zaprionus and those of the melanogaster, obscura, repleta, and virilis groups of the genus Drosophila investigated in this study shared space and time at some point in their evolutionary history. This is particularly true of the subgenus Zaprionus and the melanogaster subgroup, which overlapped both geographically and temporally in Tropical Africa during their period of origin and diversification. Here, we tested the hypothesis that this overlap may have facilitated the transfer of retrotransposons without long terminal repeats (non-LTRs) between these species. We estimated the HTT frequency of the non-LTRs BS and Helena at the genome-wide scale by using a phylogenetic framework and a vertical and horizontal inheritance consistence analysis (VHICA). An excessively low synonymous divergence among distantly related species and incongruities between the transposable element and species phylogenies allowed us to propose at least four relatively recent HTT events of Helena and BS involving ancestors of the subgroup melanogaster and ancestors of the subgenus Zaprionus during their concomitant diversification in Tropical Africa, along with older possible events between species of the subgenera Drosophila and Sophophora. This study provides the first evidence for HTT of non-LTRs retrotransposons between Drosophila and Zaprionus, including an in-depth reconstruction of the time frame and geography of these events.
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Affiliation(s)
- Maryanna C Simão
- Universidade Estadual Paulista (Unesp), Instituto de Biociências Letras e Ciências Exatas (Ibilce), Câmpus São José do Rio Preto, SP, Brazil
| | - Annabelle Haudry
- Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, France
| | - Adriana Granzotto
- Universidade Estadual Paulista (Unesp), Instituto de Biociências Letras e Ciências Exatas (Ibilce), Câmpus São José do Rio Preto, SP, Brazil
| | - Nathalia de Setta
- Universidade Federal do ABC (UFABC), Centro de Ciências Naturais e Humanas (CCNH), São Bernardo do Campo, SP, Brazil
| | - Claudia M A Carareto
- Universidade Estadual Paulista (Unesp), Instituto de Biociências Letras e Ciências Exatas (Ibilce), Câmpus São José do Rio Preto, SP, Brazil
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Sun T, Renner SS, Xu Y, Qin Y, Wu J, Sun G. Two hAT transposon genes were transferred from Brassicaceae to broomrapes and are actively expressed in some recipients. Sci Rep 2016; 6:30192. [PMID: 27452947 PMCID: PMC4958966 DOI: 10.1038/srep30192] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 06/30/2016] [Indexed: 11/23/2022] Open
Abstract
A growing body of evidence is pointing to an important role of horizontal gene transfer (HGT) in the evolution of higher plants. However, reports of HGTs of transposable elements (TEs) in plants are still scarce, and only one case is known of a class II transposon horizontally transferred between grasses. To investigate possible TE transfers in dicots, we performed transcriptome screening in the obligate root parasite Phelipanche aegyptiaca (Orobanchaceae), data-mining in the draft genome assemblies of four other Orobanchaceae, gene cloning, gene annotation in species with genomic information, and a molecular phylogenetic analysis. We discovered that the broomrape genera Phelipanche and Orobanche acquired two related nuclear genes (christened BO transposase genes), a new group of the hAT superfamily of class II transposons, from Asian Sisymbrieae or a closely related tribe of Brassicaceae, by HGT. The collinearity of the flanking genes, lack of a classic border structure, and low expression levels suggest that BO transposase genes cannot transpose in Brassicaceae, whereas they are highly expressed in P. aegyptiaca.
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Affiliation(s)
- Ting Sun
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Kaifeng 475004, China
- University of the Chinese Academy of Sciences, Beijing 100039, China
| | - Susanne S. Renner
- Systematic Botany and Mycology, University of Munich (LMU), Munich 80638, Germany
| | - Yuxing Xu
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- University of the Chinese Academy of Sciences, Beijing 100039, China
| | - Yan Qin
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Jianqiang Wu
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Guiling Sun
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Kaifeng 475004, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
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Abstract
hAT transposons are ancient in their origin and they are widespread across eukaryote kingdoms. They can be present in large numbers in many genomes. However, only a few active forms of these elements have so far been discovered indicating that, like all transposable elements, there is selective pressure to inactivate them. Nonetheless, there have been sufficient numbers of active hAT elements and their transposases characterized that permit an analysis of their structure and function. This review analyzes these and provides a comparison with the several domesticated hAT genes discovered in eukaryote genomes. Active hAT transposons have also been developed as genetic tools and understanding how these may be optimally utilized in new hosts will depend, in part, on understanding the basis of their function in genomes.
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hobo-brothers elements and their time and place for horizontal transfer. Genetica 2013; 141:471-8. [PMID: 24158527 DOI: 10.1007/s10709-013-9746-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 10/18/2013] [Indexed: 01/02/2023]
Abstract
Transposable elements (TEs) are ubiquitous components of nearly all genomes studied. These elements are highly variable in copy number, molecular structure and transposition strategies. They can move within and between genomes, thus increasing their copy numbers and avoiding being eliminated by stochastic and deterministic processes. hobo is a class II element isolated from Drosophila melanogaster. Previous phylogenetic analyses have shown that the canonical hobo element from D. melanogaster has a sister group formed by sequences found in D. willistoni (called howilli2) and D. mojavensis (called homo1). In the present study, we investigated 36 Drosophilidae species for sequences similar to howilli2 and homo1 using degenerate primers. Additionally, in silico searches were performed in 21 available Drosophila genomes. The obtained sequences formed a monophyletic sister group with the canonical hobo element; we termed these sequences 'hobo-brothers' elements. These elements showed a patch distribution and incongruities with the TE and host species phylogenies, suggesting possible cases of horizontal transfer (HT). Species that possess hobo-brothers sequences are from the New World, mainly Neotropical areas. In addition, the estimated divergence of the sequences found showed that these elements are or were recently active; the large number of HT events observed suggests that these elements could be experiencing an expansion process in Neotropical genomes. A comparison of these results with the literature is discussed with regard to the importance of the time and location of horizontal transposon transfer events.
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Ladevèze V, Chaminade N, Lemeunier F, Periquet G, Aulard S. General survey of hAT transposon superfamily with highlight on hobo element in Drosophila. Genetica 2012; 140:375-92. [DOI: 10.1007/s10709-012-9687-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Accepted: 10/10/2012] [Indexed: 11/30/2022]
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Merlo MA, Cross I, Palazón JL, Ubeda-Manzanaro M, Sarasquete C, Rebordinos L. Evidence for 5S rDNA horizontal transfer in the toadfish Halobatrachus didactylus (Schneider, 1801) based on the analysis of three multigene families. BMC Evol Biol 2012; 12:201. [PMID: 23039906 PMCID: PMC3544641 DOI: 10.1186/1471-2148-12-201] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Accepted: 10/03/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Batrachoididae family is a group of marine teleosts that includes several species with more complicated physiological characteristics, such as their excretory, reproductive, cardiovascular and respiratory systems. Previous studies of the 5S rDNA gene family carried out in four species from the Western Atlantic showed two types of this gene in two species but only one in the other two, under processes of concerted evolution and birth-and-death evolution with purifying selection. Here we present results of the 5S rDNA and another two gene families in Halobatrachus didactylus, an Eastern Atlantic species, and draw evolutionary inferences regarding the gene families. In addition we have also mapped the genes on the chromosomes by two-colour fluorescence in situ hybridization (FISH). RESULTS Two types of 5S rDNA were observed, named type α and type β. Molecular analysis of the 5S rDNA indicates that H. didactylus does not share the non-transcribed spacer (NTS) sequences with four other species of the family; therefore, it must have evolved in isolation. Amplification with the type β specific primers amplified a specific band in 9 specimens of H. didactylus and two of Sparus aurata. Both types showed regulatory regions and a secondary structure which mark them as functional genes. However, the U2 snRNA gene and the ITS-1 sequence showed one electrophoretic band and with one type of sequence. The U2 snRNA sequence was the most variable of the three multigene families studied. Results from two-colour FISH showed no co-localization of the gene coding from three multigene families and provided the first map of the chromosomes of the species. CONCLUSIONS A highly significant finding was observed in the analysis of the 5S rDNA, since two such distant species as H. didactylus and Sparus aurata share a 5S rDNA type. This 5S rDNA type has been detected in other species belonging to the Batrachoidiformes and Perciformes orders, but not in the Pleuronectiformes and Clupeiformes orders. Two hypotheses have been outlined: one is the possible vertical permanence of the shared type in some fish lineages, and the other is the possibility of a horizontal transference event between ancient species of the Perciformes and Batrachoidiformes orders. This finding opens a new perspective in fish evolution and in the knowledge of the dynamism of the 5S rDNA. Cytogenetic analysis allowed some evolutionary trends to be roughed out, such as the progressive change in the U2 snDNA and the organization of (GATA)n repeats, from dispersed to localized in one locus. The accumulation of (GATA)n repeats in one chromosome pair could be implicated in the evolution of a pair of proto-sex chromosomes. This possibility could situate H. didactylus as the most highly evolved of the Batrachoididae family in terms of sex chromosome biology.
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Affiliation(s)
- Manuel A Merlo
- Laboratorio Genética, Facultad de Ciencias del Mar y Ambientales, CACYTMAR, Universidad de Cádiz, Puerto Real (Cádiz), 11510, Spain
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Commar LS, Galego LGDC, Ceron CR, Carareto CMA. Taxonomic and evolutionary analysis of Zaprionus indianus and its colonization of Palearctic and Neotropical regions. Genet Mol Biol 2012; 35:395-406. [PMID: 22888286 PMCID: PMC3389525 DOI: 10.1590/s1415-47572012000300003] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Accepted: 02/28/2012] [Indexed: 11/21/2022] Open
Abstract
Zaprionus indianus is a dipteran (Drosophilidae) with a wide distribution throughout the tropics and temperate Palearctic and Nearctic regions. There have been proposals to reclassify the genus Zaprionus as a subgenus or group of the genus Drosophila because various molecular markers have indicated a close relationship between Zaprionus species and the immigrans-Hirtodrosophila radiation within Drosophila. These markers, together with alloenzymes and quantitative traits, have been used to describe the probable scenario for the expansion of Zaprionus indianus from its center of dispersal (Africa) to regions of Asia (ancient dispersal) and the Americas (recent dispersal). The introduction of Z. indianus into Brazil was first reported in 1999 and the current consensus is that the introduced flies came from high-latitude African populations through the importation of fruit. Once in Brazil, Z. indianus spread rapidly throughout the Southeast and then to the rest of the country, in association with highway-based fruit commerce. These and other aspects of the evolutionary biology of Z. indianus are addressed in this review, including a description of a probable route for this species’ dispersal during its recent expansion.
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Affiliation(s)
- Leliane Silva Commar
- Departamento de Biologia, Universidade Estadual Paulista "Júlio de Mesquita Filho", São José do Rio Preto, SP, Brazil
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de Setta N, Van Sluys MA, Capy P, Carareto CMA. Copia retrotransposon in the Zaprionus genus: another case of transposable element sharing with the Drosophila melanogaster subgroup. J Mol Evol 2011; 72:326-38. [PMID: 21347850 DOI: 10.1007/s00239-011-9435-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2010] [Accepted: 02/07/2011] [Indexed: 11/24/2022]
Abstract
Copia is a retrotransposon that appears to be distributed widely among the Drosophilidae subfamily. Evolutionary analyses of regulatory regions have indicated that the Copia retrotransposon evolved through both positive and purifying selection, and that horizontal transfer (HT) could also explain its patchy distribution of the among the subfamilies of the melanogaster subgroup. Additionally, Copia elements could also have transferred between melanogaster subgroup and other species of Drosophilidae-D. willistoni and Z. tuberculatus. In this study, we surveyed seven species of the Zaprionus genus by sequencing the LTR-ULR and reverse transcriptase regions, and by using RT-PCR in order to understand the distribution and evolutionary history of Copia in the Zaprionus genus. The Copia element was detected, and was transcriptionally active, in all species investigated. Structural and selection analysis revealed Zaprionus elements to be closely related to the most ancient subfamily of the melanogaster subgroup, and they seem to be evolving mainly under relaxed purifying selection. Taken together, these results allowed us to classify the Zaprionus sequences as a new subfamily-ZapCopia, a member of the Copia retrotransposon family of the melanogaster subgroup. These findings indicate that the Copia retrotransposon is an ancient component of the genomes of the Zaprionus species and broaden our understanding of the diversity of retrotransposons in the Zaprionus genus.
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Affiliation(s)
- Nathalia de Setta
- Laboratory of Molecular Evolution, Department of Biology, UNESP, São Paulo State University, 15054-000 São José do Rio Preto, SP, Brazil
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Dittmar T, Zänker KS. Horizontal gene transfers with or without cell fusions in all categories of the living matter. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2011; 714:5-89. [PMID: 21506007 PMCID: PMC7120942 DOI: 10.1007/978-94-007-0782-5_2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
This article reviews the history of widespread exchanges of genetic segments initiated over 3 billion years ago, to be part of their life style, by sphero-protoplastic cells, the ancestors of archaea, prokaryota, and eukaryota. These primordial cells shared a hostile anaerobic and overheated environment and competed for survival. "Coexist with, or subdue and conquer, expropriate its most useful possessions, or symbiose with it, your competitor" remain cellular life's basic rules. This author emphasizes the role of viruses, both in mediating cell fusions, such as the formation of the first eukaryotic cell(s) from a united crenarchaeon and prokaryota, and the transfer of host cell genes integrated into viral (phages) genomes. After rising above the Darwinian threshold, rigid rules of speciation and vertical inheritance in the three domains of life were established, but horizontal gene transfers with or without cell fusions were never abolished. The author proves with extensive, yet highly selective documentation, that not only unicellular microorganisms, but the most complex multicellular entities of the highest ranks resort to, and practice, cell fusions, and donate and accept horizontally (laterally) transferred genes. Cell fusions and horizontally exchanged genetic materials remain the fundamental attributes and inherent characteristics of the living matter, whether occurring accidentally or sought after intentionally. These events occur to cells stagnating for some 3 milliard years at a lower yet amazingly sophisticated level of evolution, and to cells achieving the highest degree of differentiation, and thus functioning in dependence on the support of a most advanced multicellular host, like those of the human brain. No living cell is completely exempt from gene drains or gene insertions.
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Affiliation(s)
- Thomas Dittmar
- Inst. Immunologie, Universität Witten/Herdecke, Stockumer Str. 10, Witten, 58448 Germany
| | - Kurt S. Zänker
- Institute of Immunologie, University of Witten/Herdecke, Stockumer Str. 10, Witten, 58448 Germany
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Benedict M, Eckerstorfer M, Franz G, Gaugitsch H, Greiter A, Heissenberger A, Knols B, Kumschick S, Nentwig W, Rabitsch W. Defining Environment Risk Assessment Criteria for Genetically Modified Insects to be placed on the EU Market. ACTA ACUST UNITED AC 2010. [DOI: 10.2903/sp.efsa.2010.en-71] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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