* Department of Microbiology and Parasitology, and Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia; and Faculty of Pharmacy and Pharmaceutical Sciences, Fukuyama University, Fukuyama, Hiroshima, Japan
Correspondence: E-mail: r.shao{at}uq.edu.au.
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Abstract |
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Key Words: concerted evolution duplicate control regions gene rearrangement Ixodes ticks
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Introduction |
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CRs may contain the initiation sites of mt gene transcription. Two of the three transcription-initiation sites in the mt genome of Homo sapiens are in the CR (Taanman 1999). All of the transcription-initiation sites identified so far in other vertebrates are in the CR (Tracy and Stern 1995). Two of the five initiation sites in the mt genome of Drosophila melanogaster are in the CR (Berthier et al. 1986). The sea urchin, Paracentrotus lividus, is the only exception known so far: neither of its two known transcription-initiation sites is in the CR (Cantatore et al. 1990).
CRs may also contain the initiation sites for the replication of mt genomes. Two models have been proposed for the replication of mt genomes in mammals: the strand-displacement model (Clayton 1982) and the strand-coupled model (Holt, Lorimer, and Jacobs 2000). According to the strand-displacement model, replication of one strand (the leading strand) initiates at the CR, whereas replication of the other strand (the lagging strand) initiates at a site distant from the CR. According to the strand-coupled model, replications of both strands initiate at the CR. These two models agree that the replication of the leading strand initiates at the CR, although they disagree on the initiation sites of the replication of the lagging strand, and there is also debate over which model predominates in mammalian cells (Bogenhagen and Clayton 2003; Holt and Jacobs 2003). The replication mechanism of mammalian mt genomes is thought to be conserved in vertebrates (Shadel and Clayton 1997) but not conserved in invertebrates (Rubenstein, Brutlag, and Clayton 1977). However, it is known that replications of leading strands in the mt genomes of fruitflies also initiate at the CR (Goddard and Wolstenholme 1980).
The mt genomes of most metazoa studied to date have only one CR. However, the mt genomes of some snakes (Kumazawa et al. 1996), sea cucumbers (Arndt and Smith 1998), metastriate ticks (Black and Roehrdanz 1998; Campbell and Barker 1999), Amazona parrots (Eberhard, Wright, and Bermingham 2001), a fish (Lee et al. 2001), a thrips (Shao and Barker 2003), and a sea firefly (Ogoh and Ohmiya 2004) have duplicate CRs; that is, two separate CRs with identical or highly similar nucleotide (nt) sequences. The lineage of snakes has had duplicate CRs for over 70 Myr, whereas the lineage of metastriate ticks has had duplicate CRs for over 210 Myr (Kumazawa et al. 1996; Campbell and Barker 1999). Some humans with mt disorders also have mt genomes with duplicate CRs; these patients usually have a mixture of wild-type mt genomes (one CR), partially deleted mt genomes (one CR), and partially duplicated mt genomes (two CRs) in their clinically affected tissues (Schon, Bonilla, and DiMauro 1997).
The presence of duplicate CRs in the mt genomes of metazoa is an intriguing mutational phenomenon in light of the otherwise extreme economy of these genomes. This phenomenon raises at least four functional and evolutionary questions (Kumazawa et al. 1996, 1998; Tang et al. 2000; Umeda et al. 2001). Why do some mt genomes, but not others, have duplicate CRs? How did mt genomes with duplicate CRs evolve? How could the nt sequences of duplicate CRs remain identical or highly similar over evolutionary time? Are duplicate CRs phylogenetic markers? Here, we present analyses of the entire and/or partial mtDNA sequences of 14 species of Ixodes ticks. We show that the Australasian Ixodes have duplicate CRs that evolved in concert in each species. Further, we address the four questions above with accumulated mtDNA sequences of metazoa with duplicate CRs and two recently published experiments on the replication of mt genomes in human cell lines with duplicate CRs.
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Materials and Methods |
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Results |
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Duplicate CRs of Australasian Ixodes Ticks
The two CRs of the seven Australasian Ixodes species sequenced in this study were 349 to 476 bp long (table 2). The nt sequences of CR#1 and CR#2 of a species were 87% to 95% similar. The nt sequences of CR#1 and CR#2 of a species were more similar to each other than were the CR#1 sequences or the CR#2 sequences of different species. Consider I. cornuatus and I. myrmecobii, which are apparently sister species (fig. 2). CR#1 and CR#2 of I. cornuatus were 95% similar, and CR#1 and CR#2 of I. myrmecobii were 90% similar. However, CR#1 of I. cornuatus and CR#1 of I. myrmecobii were only 81% similar, and CR#2 of I. cornuatus and CR#2 of I. myrmecobii were only 78% similar. Seven motifs, 5 to 18 nts long, respectively, were conserved among CR#1 and CR#2 of the seven Australasian Ixodes species we sequenced (fig. 3); these motifs were also partially conserved in the other Ixodes species, which have one CR (data not shown). The conservation of these motifs indicates that they may have roles in the control of replication and/or transcription of the mt genome of these ticks.
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Species of the four major lineages of ticks in our CR-sequence tree differ in the copy number of CR and the arrangement of genes in mt genomes (figs. 1 and 2). The most parsimonious explanation for the evolution of the copy number of CR and the arrangement of mt genes in ticks is that (1) the most recent common ancestor of ticks had one CR and the arrangement of mt genes of the hypothetical ancestor of the arthropods, which has persisted in the horseshoe crab, Limulus polyphemus (Lavrov, Boore, and Brown 2000 [fig. 2]); (2) the CR duplicated in the lineage of the Australasian Ixodes ticks but no genes rearranged; (3) the CR duplicated and several genes rearranged in the lineage of the metastriate ticks; and (4) a single CR and the ancestral arrangement of genes of ticks persisted unchanged in the other Ixodes species and the soft ticks.
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Discussion |
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In addition to the Australasian Ixodes ticks and the metastriate ticks, duplicate CRs have also been found in the mt genomes of some snakes (Kumazawa et al. 1996), sea cucumbers (Arndt and Smith 1998), Amazona parrots (Eberhard, Wright, and Bermingham 2001), a fish (Lee et al. 2001), a plague thrips (Shao and Barker 2003), and a sea firefly (Ogoh and Ohmiya 2004 [table 2]). Once duplicate CRs occur in an mt genome, they may evolve either in concert or independently. Independent evolution leads to the divergence of the nt sequences of the two CRs and, eventually, degeneration or deletion of one of the CRs (Bensch and Harlid 2000). Concerted evolution, however, keeps the nt sequences of the two CRs highly similar. Kumazawa et al. (1996) and Arndt and Smith (1998) proposed concerted evolution as an explanation for the high similarity of the nt sequences of the two CRs in the snakes and the sea cucumbers they studied. Black and Roehrdanz (1998) and Eberhard, Wright, and Bermingham (2001) showed that the two CRs evolved in concert in each species of the metastriate ticks and the Amazona parrots. Black and Roehrdanz (1998) and Eberhard, Wright, and Bermingham (2001) studied two and four species, respectively. In the present study, we studied 26 species of ticks: 15 had duplicate CRs, and 11 had one CR. Our study, together with previous studies, shows conclusively that duplicate CRs in the mt genomes of metazoa tend to evolve in concert in each species rather than independently.
The presence of duplicate CRs in the mt genome of metazoa is an intriguing mutational phenomenon in light of the otherwise extreme economy of these genomes. This phenomenon raises several functional and evolutionary questions.
Why Do Some mt Genomes, but Not Others, Have Duplicate CRs?
Replication of the mt genomes of the mammals and fruitflies studied initiates at the CR (Goddard and Wolstenholme 1980; Clayton 1982; Holt, Lorimer, and Jacobs 2000). So, it is probably reasonable to speculate that mt genomes with duplicate CRs may have a selective advantage over mt genomes with one CR. For example, an mt genome with two CRs may replicate more efficiently than an mt genome with one CR (Kumazawa et al. 1996; Arndt and Smith 1998; Umeda et al. 2001). Initiation of replication is apparently a rate-limiting step in the replication of the mt genome of D. melanogastor (Rubenstein, Brutlag, and Clayton 1977). If replication can initiate at both CRs, then mt genomes with two CRs could start more replication per unit time than could mt genomes with one CR. Thus, mt genomes with two CRs may "out compete" mt genomes with one CR.
Our knowledge of the replication of metazoan mt genomes is almost entirely from studies of mammals and fruitflies that have one CR. It is not clear yet how mt genomes with two CRs replicate. Nevertheless, two recent experimental studies indicate that an mt genome with two CRs may replicate more efficiently than an mt genome with one CR. Tang et al. (2000) found that the population of mt genomes in human cell lines, which was originally a mixture of genomes with one CR and genomes with two CRs, shifted over time, towards mt genomes with two CRs. This finding suggests that cells may favor mt genomes with two CRs. Tang et al. (2000) proposed that mt genomes with duplicate CRs would have a selective advantage over those with one CR if the two types of genomes were competing for a finite amount of replication factor(s). Further, Umeda et al. (2001) showed that in human cell lines that had partially duplicated mt genomes, the two CRs were equally efficient at starting replication. It is not known, however, whether the two CRs in an mt genome can be active simultaneously, and if so, whether the two CRs start replication simultaneously or sequentially.
How Did mt Genomes with Duplicate CRs Evolve?
Three mechanisms may account for mt genomes with duplicate CRs: tandem duplication, dimerization, and illegitimate recombination (reviewed in Boore [2000]). The tandem duplication mechanism starts with replication errors, such as imprecise termination and/or slipped-strand mispairing. If these errors occur in the section that has the CR, then the replication will generate an mt genome with two tandem-repeated sections, and each section contains a CR. Dimerization occurs when two linearized monomeric mt genomes join "head-to-tail" to form a large circular mt genome. A dimeric mt genome would have two CRs and two copies of each gene. Illegitimate recombination occurs when a section of one mt genome is cleaved out and then introduced into another mt genome. If this section contains the CR, then the mt genome that receives the cleaved section of genome will have two CRs. Obviously, illegitimate recombination may also cause tandem duplications if the introduced section is next to its counterpart in the receipt mt genome.
A single event of tandem duplication followed by deletions of redundant copies of genes can account for the duplicate CRs and/or gene rearrangements in the mt genomes of all of the metazoa known that have duplicate CRs, except the plague thrips and the sea firefly (see Supplementary Material online). However, different genes would have been duplicated and deleted in each of these metazoan lineages. Moreover, the two CRs are in different positions in each lineage. The mt genomes of the plague thrips and the sea firefly are highly rearranged, and, therefore, multiple events of tandem duplication and deletions, and/or illegitimate recombination, may have occurred in the evolution of these genomes (Shao and Barker 2003; Ogoh and Ohmiya 2004).
How Do Duplicate CRs Evolve in Concert?
Kumazawa et al. (1998) proposed two mechanisms for the concerted evolution of duplicate CRs: tandem duplication and gene conversion. The tandem duplication mechanism starts with a replication error. Replication of a strand that starts in one CR, say CR#1, pauses at the other CR, CR#2. Then the newly synthesized fragment is unwound from the template strand. The two ends of this fragment reanneal to CR#1, and the rest of the fragment forms a loop. Replication of this strand then restarts, and a new strand with three CRs (CR#1, CR#2, and CR#1 with CR#2 in the loop) is synthesized. If the loop is deleted, then replication of the next strand will generate an mt genome with two identical or nearly identical CRs. The gene conversion mechanism involves homologous recombination. The crossing over of nicked strands between the two CRs of an mt genome forms a Holliday structure, which leads to two heteroduplex intermediate CRs. Subsequent DNA repairs replace the nt sequence of one CR with that of the other and lead to two identical CRs in an mt genome.
The tandem duplication mechanism is a less plausible explanation, in our view, for the concerted evolution of duplicate CRs than is the gene conversion mechanism. For the tandem duplication mechanism to account for the concerted evolution of duplicate CRs in each species, the same replication errors must occur over and over again, and independently in each species. This circumstance is less likely. Further, as discussed above, each tandem duplication event could potentially lead to rearrangement of mt genes in a species. However, we did not find differences in mt gene arrangement among the seven species of the Australasian Ixodes ticks (two species sequenced entirely; five species sequenced partially), among the eight species of the metastriate ticks (four species sequenced entirely and others sequenced partially), or among three species of the Amazona parrots (all sequenced partially [table 2]). Rather, gene conversion is a more plausible mechanism for the concerted evolution of duplicate CRs. Indeed, recombination (homologous and/or nonhomologous) may be an indispensable part of the mtDNA replication and repair machinery of metazoa (Rokas, Ladoukakis, and Zouros 2003). Further, gene conversion can account for the high similarity of the nt sequences of the CRs in each species and the conservation of the gene arrangement among species of the Australasian Ixodes ticks, the metastriate ticks, and the Amazona parrots, respectively.
Are Duplicate CRs Phylogenetic Markers?
Mitochondrial genomes with duplicate CRs may be a synapomorphy for the Australasian Ixodes ticks (fig. 2). Further, duplicate CRs, together with gene rearrangements, is probably a synapomorphy for the metastriate ticks. Kumazawa et al. (1996) suggested that duplicate CRs might be a synapomorphy for the snakes they studied from three genera of two families. Taken together, these studies indicate that duplicate CRs are informative phylogenetic markers at low taxonomic levels such as within a genus, within a family, or among families.
Intriguingly, Mindell, Sorenson, and Dimcheff (1998) and Bensch and Harlid (2000) found that birds from four orders had a novel mt gene arrangement. This novel gene arrangement had a control region (CR) plus a degenerate control region (NC), whereas the typical mt genome of birds has only one CR at the position of NC. These authors showed that the novel gene arrangement evolved by convergence in these lineages of birds and, therefore, was not a synapomorphy. The Amazona parrots also had a novel gene arrangement (Eberhard, Wright, and Bermingham 2001). However, instead of a CR and an NC, the Amazona parrots had two CRs, CR#1 and CR#2, in the positions of CR and NC in the mt genomes of the four orders of birds studied by Mindell, Sorenson, and Dimcheff (1998) and Bensch and Harlid (2000). The two CRs share high similarity of nt sequences and have evolved in concert (Eberhard, Wright, and Bermingham 2001).
The novel gene arrangement of birds with a CR and an NC was thought to have evolved independently at least five times in the four orders of birds by tandem duplications followed by deletions of genes (Mindell, Sorenson, and Dimcheff 1998; Bensch and Harlid 2000). As discussed above, tandem duplication is a mechanism that involves replication errors. If the novel gene arrangement in birds evolved five times independently, then the same replication errors, same tandem duplications and, subsequently, deletions of the same genes, would have to occur five times independently in the four orders of birds. This circumstance is unlikely, in our view.
Boore (2000) proposed a much more parsimonious explanation for the evolution of the novel mt gene arrangement in the four orders of birds. A gene arrangement with duplicate CRs, CR#1 and CR#2, such as that of the Amazona parrots, may be ancestral for all birds. The two CRs may have evolved in concert in some lineages of birds, whereas in other lineages, they may have evolved independently. In the lineages of birds that have two CRs that have evolved independently, one of the two CRs would eventually be deleted or would degenerate; this would lead to either the typical or the novel gene arrangement of birds observed by Mindell, Sorenson, and Dimcheff (1998) and Bensch and Harlid (2000). The apparent convergent evolution in birds of genomes with a CR and an NC suggests that duplicate CRs may not be a reliable phylogenetic marker at high taxonomic levels, such as among orders.
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Conclusion |
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Acknowledgements |
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Footnotes |
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Diethard Tautz, Associate Editor
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References |
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Arndt, A., and M. J. Smith. 1998. Mitochondrial gene rearrangement in the sea cucumber genus Cucumaria. Mol. Biol. Evol. 15:10091016.[Abstract]
Attardi, G. 1985. Animal mitochondrial DNA: an extreme example of genetic economy. Int. Rev. Cytol. 93:93145.[ISI][Medline]
Barker, S. C., and A. Murrell. 2004. Systematics and evolution of ticks with a list of valid genus and species names. Parasitology 129(Suppl.).
Bensch, S., and A. Harlid. 2000. Mitochondrial genomic rearrangements in songbirds. Mol. Biol. Evol. 17:107113.
Berthier, F., M. Renaud, S. Alziari, and R. Durand. 1986. RNA mapping on Drosophila mitochondrial DNA: precursors and template strands. Nucleic Acids Res. 14:45194533.[Abstract]
Black, W. C., and R. L. Roehrdanz. 1998. Mitochondrial gene order is not conserved in arthropods: prostriate and metastriate tick mitochondrial genomes. Mol. Biol. Evol. 15:17721785.
Bogenhagen, D. F., and D. A. Clayton. 2003. The mitochondrial DNA replication bubble has not burst. Trends Biochem. Sci. 28:357360.[CrossRef][ISI][Medline]
Boore, J. L. 1999. Animal mitochondrial genomes. Nucleic Acids Res. 27:17671780.
. 2000. The duplication/random loss model for gene rearrangement exemplified by mitochondrial genomes of deuterostome animals. Pp. 133147 in D. Sankoff and J. H. Nadeau, eds. Comparative genomics. Kluwer Academic Publishers, Dordrecht, The Netherlands.
Campbell, N. J. H., and S. C. Barker. 1999. The novel mitochondrial gene arrangement of the cattle tick, Boophilus microplus: Fivefold tandem repetition of a coding region. Mol. Biol. Evol. 16:732740.[Abstract]
Cantatore, P., M. Roberti, P. Loguercio Polosa, A. Mustich, and M. N. Gadaleta. 1990. Mapping and characterization of Paracentrotus lividus mitochondrial transcripts: multiple and overlapping transcription units. Curr. Genet. 17:235245.[ISI][Medline]
Clayton, D. A. 1982. Replication of animal mitochondrial DNA. Cell 28:693705.[ISI][Medline]
Eberhard, J. R., T. F. Wright, and E. Bermingham. 2001. Duplication and concerted evolution of the mitochondrial control region in the parrot genus Amazona. Mol. Biol. Evol. 18:13301342.
Goddard, J. M., and D. R. Wolstenholme. 1980. Origin and direction of replication in the mitochondrial DNA molecules from the genus Drosophila. Nucleic Acids Res. 8:741757.[Abstract]
Holt, I. J., and H. T. Jacobs. 2003. Response: the mitochondrial DNA replication bubble has not burst. Trends Biochem. Sci. 28:355356.[CrossRef][ISI][Medline]
Holt, I. J., H. E. Lorimer, and H. T. Jacobs. 2000. Coupled leading- and lagging-strand synthesis of mammalian mitochondrial DNA. Cell 100:515524.[ISI][Medline]
Kumazawa, Y., H. Ota, M. Nishida, and T. Ozawa. 1996. Gene rearrangements in snake mitochondrial genomes: highly concerted evolution of control-region-like sequences duplicated and inserted into a tRNA gene cluster. Mol. Biol. Evol. 13:12421254.[Abstract]
. 1998. The complete nucleotide sequence of a snake (Dinodon semicarinatus) mitochondrial genome with two identical control regions. Genetics 150:313329.
Lanave, C., G. Preparata, C. Saccone, and G. Serio. 1984. A new method for calculating evolutionary substitution rates. J. Mol. Evol. 20:8693.[ISI][Medline]
Lavrov, D. V., J. L. Boore, and W. M. Brown. 2000. The complete mitochondrial DNA sequence of the horseshoe crab Limulus polyphemus. Mol. Biol. Evol. 5:813824.
Lee, J. S., M. Miya, Y. S. Lee, C. G. Kim, E. H. Park, Y. Aoki, and M. Nishida. 2001. The complete DNA sequence of the mitochondrial genome of the self-fertilizing fish Rivulus marmoratus (Cyprinodontiformes, Rivulidae) and the first description of duplication of a control region in fish. Gene 280:17.[CrossRef][ISI][Medline]
Lopez, J. V., N. Yuhki, R. Masuda, W. Modi, and S. J. Obrien. 1994. Numt, a recent transfer and tandem amplification of mitochondrial-DNA to the nuclear genome of the domestic cat. J. Mol. Evol. 39:174190.[ISI][Medline]
Mindell, D. P., M. D. Sorenson, and D. E. Dimcheff. 1998. Multiple independent origins of mitochondrial gene order in birds. Proc. Natl. Acad. Sci. USA 95:1069310697.
Ogoh, K., and Y. Ohmiya. 2004. Complete mitochondrial DNA sequence of the sea-firefly, Vargula hilgendorfii (Crustacea, Ostracoda) with duplicate control regions. Gene 327:131139.[CrossRef][ISI][Medline]
Rokas, A., E. Ladoukakis, and E. Zouros. 2003. Animal mitochondrial DNA recombination revisited. Trends Ecol. Evol. 18:411417.[CrossRef][ISI]
Rubenstein, J. L., D. Brutlag, and D. A. Clayton. 1977. The mitochondrial DNA of Drosophila melanogaster exists in two distinct and stable superhelical forms. Cell 12:471482.[CrossRef][ISI][Medline]
Schon, E. A., E. Bonilla, and S. DiMauro. 1997. Mitochondrial DNA mutations and pathogenesis. J. Bioenerg. Biomembr. 29:131149.[CrossRef][ISI][Medline]
Shadel, G. S., and D. A. Clayton. 1997. Mitochondrial DNA maintenance in vertebrates. Annu. Rev. Biochem. 66:409435.[CrossRef][ISI][Medline]
Shao, R., Y. Aoki, H. Mitani, N. Tabuchi, S. C. Barker, and M. Fukunaga. 2004. The mitochondrial genomes of soft ticks have an arrangement of genes that has remained unchanged for over 400 million years. Insect Mol. Biol. 13:219224.[CrossRef][ISI][Medline]
Shao, R., and S. C. Barker. 2003. The highly rearranged mitochondrial genome of the plague thrips, Thrips imaginis (Insecta: Thysanoptera): convergence of two novel gene boundaries and an extraordinary arrangement of rRNA genes. Mol. Biol. Evol. 20:362370.
Shao, R., N. J. H. Campbell, E. R. Schmidt, and S. C. Barker. 2001. Increased rate of gene rearrangement in the mitochondrial genomes of three orders of hemipteroid insects. Mol. Biol. Evol. 18:18281832.
Swofford, D. L. 2000. PAUP*: phylogenetic analysis using parsimony (*and other methods). Sinauer Associates, Sunderland, Mass.
Taanman, J. W. 1999. The mitochondrial genome: structure, transcription, translation and replication. Biochim. Biophys. Acta 1410:103123.[ISI][Medline]
Tang, Y. Y., G. Manfredi, M. Hirano, and E. A. Schon. 2000. Maintenance of human rearranged mitochondrial DNAs in long-term cultured transmitochondrial cell lines. Mol. Biol. Cell 11:23492358.
Thompson, J. D., T. J. Gibson, F. Plewniak, F. Jeanmougin, and D. G. Higgins. 1997. The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25:48764882.
Tracy, R. L., and D. B. Stern. 1995. Mitochondrial transcription initiation: promoter structures and RNA polymerases. Curr. Genet. 28:205216.[ISI][Medline]
Umeda, S., Y. Tang, M. Okamoto, N. Hamasaki, E. A. Schon, and D. Kang. 2001. Both heavy strand replication origins are active in partially duplicated human mitochondrial DNAs. Biochem. Biophys. Res. Commun. 286:681687.[CrossRef][ISI][Medline]
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