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Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
Correspondence
Umesh Varshney
varshney{at}mcbl.iisc.ernet.in
or
uvarshney{at}gmail.com
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ABSTRACT |
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 TOP ABSTRACT INTRODUCTIONMETHODSRESULTSDISCUSSIONREFERENCES |
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INTRODUCTION |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTSDISCUSSIONREFERENCES |
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). Nitric oxide deaminates cytosine to uracil, adenine to hypoxanthine, and guanine to xanthine (Wink et al., 1991). Oxidative stress results in formation of abasic sites, single- and double-stranded breaks in DNA and damage to nitrogenous bases such as the conversion of guanine to 7,8-dihydro-8-oxoguanine (8-oxoG). In addition, reaction of nitric oxide with molecular oxygen or superoxide anion forming peroxynitrite may induce inter-strand G–G cross-links and also polyamine DNA cross-links (Hartman et al., 1986; Shapiro et al., 1977). Failure to repair DNA damage is both cytotoxic and mutagenic. Thus DNA lesions are often subject to overlapping repair processes (Cooke et al., 2003).
Mycobacterium tuberculosis, which resides in the host macrophages, is one of the most successful pathogens. It not only tolerates the hostile environment within macrophages but also survives environmental stresses like exposure to UV, dehydration and low temperature during host exchanges (Manganelli et al., 2004). Although the DNA damage response mechanisms in M. tuberculosis are not well understood, it is clear that for its persistence in the host, DNA repair strategies are vital for this pathogen (Mizrahi & Andersen, 1998).
The genome sequences of M. tuberculosis (Cole et al., 1998), Mycobacterium leprae (Cole et al., 2001; Smith et al., 1997) and Mycobacterium smegmatis (http://www.tigr.org) have suggested that mismatch repair enzymes are missing in these organisms (Mizrahi & Andersen, 1998), and the role of RecA has been found to be minimal in mutation prevention (Boshoff et al., 2003; Rand et al., 2003). Thus, among the major DNA repair pathways, the base excision repair (BER) and the nucleotide excision repair (NER) pathways presumably contribute significantly to the maintenance of the genomic integrity in these bacteria. The high G+C content (
65 mol%) of the genomes of mycobacteria puts them at a greater risk of cytosine deamination (to uracil), and oxidative damage of guanosine (to 8-oxoG). The pathways that repair uracil and 8-oxoG are initiated by uracil DNA glycosylase (Ung or UDG; Lindahl, 1979; Duncan, 1981; Krokan et al., 1997) and formamidopyrimidine DNA glycosylase (Fpg or MutM, Bailly et al., 1989; Tchou et al., 1991; Graves et al., 1992), respectively, which are also two important BER enzymes in mycobacteria (Venkatesh et al., 2003; Jain et al., 2007). On the other hand, UvrB is a central player in NER (Skorvaga et al., 2002).
Earlier studies have shown that a uvrB-deficient strain of M. tuberculosis (Darwin et al., 2003) is markedly attenuated for survival in mice (Darwin & Nathan, 2005). However, there appear to have been no studies in which the relative importance of the DNA repair pathways in survival of mycobacteria has been compared in an isogenic strain background. Mutants of M. tuberculosis defective in ung or fpg have not been explored. Similarly, mutants of M. smegmatis defective in NER have been hitherto unavailable.
In this study, we generated a uvrB-deficient strain of M. smegmatis, and compared the relative fitness of this strain with those deficient in Ung (ung–) or Fpg (fpg–), the two important BER pathway enzymes, under commonly encountered conditions that damage DNA.
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METHODS |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTSDISCUSSIONREFERENCES |
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, and the details of various strains generated from M. smegmatis mc2155 (Snapper et al., 1990) are listed in Table 2. M. smegmatis strains were grown in LB containing 0.2 % (v/v) Tween 80 (LBT) or Middlebrook 7H9 (Difco) containing 0.2 % (v/v) glycerol and 0.2 % Tween 80. For growth on solid surfaces, 1.5 % agar was included in the media. When specified, 7H10 medium (Difco) containing 0.5 % (v/v) glycerol and 0.05 % Tween 80 was used to obtain isolated colonies from glycerol stocks of various strains. Media were supplemented with hygromycin, gentamicin and kanamycin at 50, 5 and 50 µg ml–1, respectively, as needed.
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) by its homology to M. tuberculosis uvrB (Rv1633; Cole et al., 1998) and the relevant part of it was PCR amplified using primers UvrB-Fp1 (5'-AGCCTGCAGTGGTGTTGCTCGGCGC-3', which anneals 160 bp downstream of the start codon in the UvrB ORF) and UvrB-Rp1 (5'-GCCAGCTCGAACTGCAGGTCG-3', which anneals 70 bp upstream of the stop codon) and DyNAzyme EXT DNA polymerase (Finnzymes). PCR was carried out in a 50 µl reaction containing 1.5 U DyNAzyme EXT DNA polymerase (Finnzymes), 250 ng M. smegmatis SN2 genomic DNA, 20 pmol of each primer, 3.5 mM MgSO4, 5 % DMSO, DyNAzyme EXT reaction buffer and 200 µM dNTPs. After initial denaturation for 4 min at 94 °C, 30 cycles of incubations were carried out at 94 °C for 1 min, 64 °C for 30 s and 72 °C for 2 min, followed by a final extension step at 72 °C for 10 min. The amplicon (1.9 kb) was digested with PstI and cloned into similarly digested pUC4k (Vieira & Messing, 1982), resulting in pUC4k-MsmUvrB, which was then digested with SphI (internal to Msm-uvrB), blunt-ended with T4 DNA polymerase and ligated to a kanamycin cassette (1.3 kb HincII fragment from pUC4k) to generate pUC4k-Msm-uvrB : : kanR. A 3.2 kb BamHI fragment from this construct containing Msm-uvrB : : kanR was then mobilized into the BamHI site of pPR27 (Pelicic et al., 1997) to generate pPR-Msm-uvrB : : kanR, which was introduced into M. smegmatis mc2155 by electroporation (Hatfull & Jacobs, 2002) to generate the knockout strain using a protocol described before (Pelicic et al., 1997; Venkatesh et al., 2003).
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2.5 µg) were digested with an excess of restriction enzymes (20 U), separated on a 0.7 % agarose gel using TBE buffer, transferred (Reed & Mann, 1985) to nylon membrane (Biodyne B, Pall Gelman Laboratory) and subjected to hybridization (Vasanthakrishna et al., 1997) with radiolabelled probe prepared by PCR using [
-32P]dCTP and primers UvrB-Fp2 (5'-CGCACCGGCAAACCCTTCG-3') and UvrB-Rp2 (5'-CGCGAATTCAGTCACGACGAC-3') (Sambrook et al., 1989) using PCR product obtained by the same primers under standard conditions as template.
Generation of the uvrB-complemented strain.
DNA oligomers UvrB-Fp3 (5'-CTATAAGCTTCGGGATCGGTATTG-3', which anneals 244 bp upstream of the start codon in ORF) and UvrB-RP3 (5'-CGCTCGCTGTTTCGGTCACTTCAG-3', which anneals 15 bp downstream of the termination codon) were used to PCR amplify Mtu-uvrB (Rv1633) from M. tuberculosis H37Rv genomic DNA (250 ng) using 1 U DyNAzyme EXT (Finnzyme) in a 50 µl reaction. The PCR conditions included an initial step of heating at 94 °C for 4 min followed by 30 cycles of incubations at 94 °C for 1 min, 47 °C for 30 s and 72 °C for 2 min 45 s and a final extension at 72 °C for 10 min. The amplicon (2.2 kb) was digested with HindIII, ethanol precipitated, phosphorylated with polynucleotide kinase, gel purified and cloned between the AgeI (blunt-ended) and HindIII sites of pMV361 (hygR) (Stover et al., 1991) to generate pMV-Mtu-uvrB, which was then introduced into M. smegmatis (uvrB : : kan) by electroporation for its ectopic integration into the chromosome at the L5 att site to generate the uvrB–(L5att : : uvrB) strain. The vector alone (pMV361, hygR) was also electroporated into the uvrB : : kan strain to generate the uvrB : : kan L5att : : pMV361 (referred to as uvrB–) strain. The strain designations have been defined in Table 2
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Generation of the ung-complemented strain.
The M. smegmatis ung ORF along with 700 bp of upstream and 663 bp of downstream sequences was released as 2.1 kb fragment from pPRmsUng (Venkatesh et al., 2003) by digestion with NcoI and XbaI, blunt-ended using Klenow fragment of DNA polymerase I and subcloned into PvuII-digested pMV361 (Stover et al., 1991) to generate pMVMsm-ung (hygR), which was then introduced into M. smegmatis ung : : kan by electroporation to generate M. smegmatis ung : : kan (L5att : : ung), referred to as [ung–(L5att : : ung)], containing an ectopic copy of ung at the L5att site (Table 2).
Assay for UV sensitivity.
An early-exponential-phase culture (OD595 0.4) of M. smegmatis was serially diluted 1 : 5 in LBT in a 96-well plate. Samples from the third dilution onwards were spotted on LBT agar plates with a 48-pronged spotter (Sigma) and plates were exposed to UV C in a biosafety cabinet to UV intensities of 0, 30 or 60 J m–2 (as measured with a dosimeter), then incubated at 37 °C for 3 days.
Determination of mutation rates.
Mutation rates were determined according to David (1970). Briefly, isolated colonies of the various M. smegmatis strains were grown to saturation in 7H9 medium containing 0.2 % glycerol, 0.1 % Tween 80 and 10 % ADC (Difco) along with the appropriate antibiotics for 48 h. Subsequently, for each strain, 12 independent tubes containing 2 ml each of the same medium but without antibiotics were inoculated with 1500–2000 bacteria by diluting from the freshly prepared saturated cultures, and grown for 6 days at 37 °C with vigorous shaking. Absence of spontaneous mutants in the inoculum (used to develop the 6 day cultures) was confirmed by plating an equivalent aliquot of the culture on 7H10 containing 0.5 % glycerol, 10 % OADC (Difco) and 100 µg rifampicin ml–1. At the end of the 6 day growth, small aliquots from cultures were used to determine total viable counts by dilution plating on LBT agar, and the cells from the remainder of the cultures were harvested and plated on 7H10 containing 0.5 % glycerol, 10 % OADC and 100 µg rifampicin ml–1. The plates were incubated for 3–5 days and the colonies appearing on the plates were counted. The mutation rates for each replicate of the strain were determined and mean mutation rates were calculated (David, 1970).
Effect of acidified sodium nitrite.
Isolated colonies of M. smegmatis strains were grown in triplicate in 7H9 medium with appropriate antibiotics to saturation (55–60 h). The cultures were serially diluted 1 : 100 in LBT (pH 5.5) with 0.5 % (w/v) BSA, supplemented with 0, 0.5, 1.5 or 2.5 mM freshly prepared sodium nitrite (Merck, India), seeded in the microtitre wells of honeycomb plates and incubated in a Bioscreen C kinetic growth reader at 37 °C with constant shaking at maximum amplitude. Growth was monitored by the machine, which measured OD600 at 3 h intervals for 39 h.
Effect of hydrogen peroxide on bacterial growth.
The effect of H2O2 on growth was determined in a manner similar to that of acidified sodium nitrite except that the saturated cultures of M. smegmatis strains were diluted in LBT with 0.5 % BSA containing 0, 0.5, 1.0 or 1.5 mM H2O2 (Calbiochem).
Effect of hypoxic stress on bacterial survival.
M. smegmatis strains were grown to an OD600 of 0.5–0.6 (1.5-2.0x108 c.f.u. ml–1) in Dubos medium with 10 % ADC and diluted 1 : 100 in triplicate in screw-cap flat-bottom culture tubes containing 20 ml of the same medium and 10 ml of air space (headspace ratio 0.5; Dick et al., 1998). The tubes were sealed and the cultures were grown with slow stirring using a multipoint magnetic board at 37 °C for 10 days. Total viable counts of these cultures were determined by dilution plating on LBT agar. The cultures (from hypoxic conditions) were also diluted 1 : 100 in triplicate in fresh Dubos medium (with ADC) and recovered aerobically under vigorous shaking conditions at 37 °C. Total viable counts of the recovered cultures were determined at 3, 6, 12 and 24 h by dilution plating and plotted as log10 c.f.u. ml–1.
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RESULTS |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTSDISCUSSIONREFERENCES |
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95 % similarity and 92 % identity) and the nucleotide sequence level (85.3 %). The genomic contexts of uvrB in M. tuberculosis and M. smegmatis are shown in Fig. 1(a). The M. smegmatis uvrB knockout strain was generated by insertion of a kanamycin resistance (kanR) cassette (1.3 kb) within the ORF of uvrB (Fig. 1b). The disruption of chromosomal uvrB was confirmed by genomic blot analysis. As expected (Fig. 1b), a ScaI/BamHI double digest resulted in detection of a 2.5 kb fragment (Fig. 1c, lane 1) from the wild-type and a 3.8 kb fragment from the knockout strains (lanes 2 and 3). The NarI digests also showed the expected fragment sizes of 2.3 kb for the wild-type (lane 4) and 3.6 kb for the knockout strain (lanes 5 and 6). These results confirmed the authenticity of the uvrB gene knockout. Assays of Fpg and Ung activity (performed as previously described: Venkatesh et al., 2003; Jain et al., 2007) confirmed that neither of these activities was disrupted in the uvrB deletion mutant (data not shown).
Analysis of the mutation rates
To investigate the effect of the UvrB deficiency (deficiency of NER) on the mutation rates of the strain and to compare it with those of strains deficient in the BER pathways (ung– and fpg–) in M. smegmatis, we determined the mutation rates of the bacterial cultures by scoring for appearance of rifampicin-resistant colonies in the various strains. As shown in Table 3, the loss of Fpg or UvrB proteins resulted in a 2.5-fold increase in the mutation rates compared to the wild-type strain. On the other hand, under the same conditions, the deficiency of Ung resulted in a 9-fold increase in the mutation rate.
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). We compared the sensitivity to UV radiation of M. smegmatis strains deficient in DNA repair enzymes. All the strains showed similar growth when not exposed to UV (Fig. 2, 0 J m–2). However, the strain deficient in uvrB was highly sensitive to UV C radiation even at 30 J m–2. The other strains showed no visible growth defect even at the higher dose of 60 J m–2. Based on earlier studies in other organisms (Czeczot et al., 1991; Scott et al., 1999; Huang et al., 2006), it was not unexpected that the deficiency of Ung and Fpg did not result in any increased sensitivity of M. smegmatis to UV C radiation. However, these observations highlight that the NER pathway provides the major means to protect M. smegmatis against DNA damage caused by UV radiation. As a control, integration of a single copy of the uvrB gene (from M. tuberculosis) at the L5 att site in the knockout strain rescued the phenotype (bottom row in Fig. 2), suggesting that the UV sensitivity of the strain was due to UvrB deficiency and not an indirect consequence of chromosomal alteration at the uvrB locus.
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; O'Brien et al., 1994). RNI can cause deamination of various bases in DNA or could react with oxygen to form peroxynitrite, causing oxidative damage to cells. Earlier work (Venkatesh et al., 2003; Darwin & Nathan, 2005) has shown that mycobacterial strains deficient in Ung or UvrB (M. smegmatis and M. tuberculosis, respectively) are susceptible to nitric oxide stress. We compared the effect of nitric oxide on strains of M. smegmatis deficient in Fpg, Ung, and UvrB at initial culture pH of 5.5. Representative growth curves are presented in Fig. 3. As seen in Fig. 3(a), the medium pH of 5.5 itself had an effect on the growth profile of the strains, and the growth of the strain deficient in NER was the most compromised. While the supplementation of the medium with increasing amounts of sodium nitrite (Fig. 3b–d) resulted in additional compromise in the growth of the NER-deficient strain, the effect of the reagent on the ung– strain was more pronounced (e.g. compare its growth with that of the wild-type strain in panels a and c). The effect of the reagent on the fpg– strain was the least pronounced. Thus, the ung– and uvrB– but not the fpg– strains, under the conditions used, are sensitive to growth in acidified nitrite. As a control, at the highest concentration of the reagent used, the ung–, uvrB– and fpg– strains grew like the wild-type parent when complemented with, respectively, an ectopically inserted copy of ung or uvrB at the L5 att site in the chromosome, and fpg on a vector, pTK-Mtu-fpg (Fig. 3e). It may be noted that the pH of the medium changes to neutral during the mid-exponential phase of the culture.
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). Such analyses have not been carried out for the strains deficient in Ung and UvrB. As shown by the representative data in Fig. 4, all the strains showed similar growth kinetics in the absence of H2O2 (Fig. 4a). Addition of the increasing amounts of H2O2 (0.5, 1 and 1.5 mM) to the growth medium revealed that the NER-deficient strain was the most sensitive to the reagent, and at 1.5 mM H2O2 it failed to grow (Fig. 4b–d). At 1 mM H2O2, a small effect could also be detected for the fpg– strain but not the ung– strain (Fig. 4c). However, at 1.5 mM H2O2, growth of both the fpg– and the ung– strains was also severely impaired. As a control, growth of the complemented strains was similar to that of the wild-type strain even at the highest concentration of the reagent used (Fig. 4e). These observations show that among the strains tested, the uvrB– strain is highly susceptible to H2O2.
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; Wayne & Hayes, 1996). Earlier reports (Dick et al., 1998; Mayuri et al., 2002) have described adaptation of these growth conditions for M. smegmatis and shown that several physiological changes that the bacterium undergoes during such a growth are common to those encountered by M. tuberculosis under the same conditions. Considering that hypoxic conditions are known to induce DNA damage (Moller et al., 2001; Grishko et al., 2001) it was of interest to subject the various DNA-repair-deficient M. smegmatis strains to the hypoxic growth model of Wayne. As shown in Fig. 5(a), evaluation of the total viable counts of the various cultures at the end of the growth regimen revealed that in comparison with the WT strain the uvrB– strain was the least fit for survival under hypoxia. Although the ung– strain also showed impaired survival under these conditions, the fpg– strain was unaffected. Importantly, complementation of the uvrB– and the ung– strains with the uvrB and ung genes restored their survival level to the WT level. The complementation of the fpg– strain with a plasmid-borne copy of fpg resulted in a slight decrease in total viable counts (in comparison to the fpg– strain). The reasons for this are not clear. Notwithstanding this observation, it is clear that of all the strains, the uvrB– strain is most sensitive to hypoxia as well.
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). As expected, all the complemented strains recovered as well as the WT strain. |
DISCUSSION |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTSDISCUSSIONREFERENCES |
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As expected for the G+C-rich genomes of M. tuberculosis and M. smegmatis, the Ung- and Fpg-mediated repair pathways represent two of the crucial BER pathways in these bacteria (Venkatesh et al., 2003; Jain et al., 2007). Neither of these repair pathways has been investigated in M. tuberculosis. On the other hand, while the consequences of NER deficiency have been investigated previously (Darwin & Nathan, 2005) in a transposon insertion mutant of M. tuberculosis (Darwin et al., 2003), its significance had not been reported in M. smegmatis. In this study, we have generated an uvrB knockout strain of M. smegmatis to allow a direct comparison of the significance of different DNA repair pathways in mycobacteria.
We previously reported an increase in mutation frequencies of about 8- and 3.8-fold in Ung- and Fpg-deficient strains, respectively (Venkatesh et al., 2003; Jain et al., 2007). As mutation frequency analysis can be influenced by various factors, for a comparative analysis of the mutator phenotypes, in this study we carried out mutation rate analyses (David, 1970). This analysis revealed that Ung, Fpg and UvrB deficiencies resulted in a 9-, 2.6- and 2.5-fold increase, respectively, in the mutation rates above the WT reference (Table 3). However, compared with Ung- and Fpg-deficient strains, the UvrB-deficient strain was more sensitive to exposure to UV, low pH, H2O2 and hypoxia (Figs 2, 3, 4 and 5), emphasizing a vital role of NER in mycobacteria. It may be noted that the susceptibility of M. smegmatis to H2O2 is in contrast to the observations made with a uvrB-deficient strain of M. tuberculosis (Darwin & Nathan, 2005). The reasons for this observed difference are unclear, but it may well be that the culture age and the growth conditions play a role in susceptibility to H2O2 (e.g. the presence of catalase, a component of OADC supplement, in the culture medium of M. tuberculosis may neutralize H2O2). Also, while mutational analysis with the NER-deficient strain of M. tuberculosis has not been carried out, our observations on the remaining phenotypes of NER-deficient M. smegmatis reinforce the observations made with the uvrB transposon mutant of M. tuberculosis isolated by Darwin et al. (2003) and then extensively characterized by Darwin & Nathan (2005). Further, while a direct comparison of the effects of the BER and NER such as that carried out in this study is not available, studies in Escherichia coli have shown that NER deficiency resulted in only a marginal increase in mutation frequencies (Pienkowska et al., 1993). Interestingly, Hall (1995) showed that NER deficiency in a tryptophan auxotroph of E. coli resulted in a >100-fold increase in mutation rates of trpA46 to trpA+ under tryptophan starvation. However, under tryptophan-sufficiency conditions the mutation rates were not affected by NER deficiency.
It has also been shown that NER plays a major role in repair of 8-oxoG, cyclo-dA and cyclo-dG (Scott et al., 1999; Kuraoka et al., 2000). In fact, overlapping functions of Fpg and NER have also been suggested by other studies (Kow et al., 1990; Asad et al., 2000). Deamination of guanine to xanthine can also result in depurination to form abasic sites in DNA (Tamir et al., 1996), which could be substrates for NER (Lin & Sancar, 1989). These observations support our findings on the sensitivity of NER-deficient bacteria to H2O2.
It is significant that uvrA and uvrB are induced in mycobacteria upon treatment with DNA-damaging agents like mitomycin C as well as upon infecting human macrophages (Rand et al., 2003; Graham & Clark-Curtiss, 1999). Thus, NER seems to be central to DNA repair mechanisms in mycobacteria. Taken together, these and earlier observations (Darwin & Nathan, 2005) show that mycobacteria deficient in NER could be a good candidate for development of attenuated strains, and development of inhibitors against NER proteins may allow an efficient method of killing mycobacteria.
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ACKNOWLEDGEMENTS |
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Edited by: G. R. Stewart
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Received 15 April 2008;
revised 13 May 2008;
accepted 22 May 2008.
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