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1 Laboratory of Sericulture and Entomoresources, Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Japan
2 Shimadzu Corporation, Nakagyou, Kyoto 604-8511, Japan
3 Laboratory of Biodynamics, Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Japan
4 Central Laboratory and Greenhouse Complex, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand
Correspondence
Motoko Ikeda
mochiko{at}agr.nagoya-u.ac.jp
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ABSTRACT |
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 TOP ABSTRACT INTRODUCTIONMETHODSRESULTS AND DISCUSSIONREFERENCES |
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The GenBank/EMBL/DDBJ accession number for the HycuNPV N9 genome sequence is AP009046.
Supplementary material is available in JGV Online.
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INTRODUCTION |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTS AND DISCUSSIONREFERENCES |
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). Baculoviruses are subdivided into two genera, Nucleopolyhedrovirus (NPV) and Granulovirus (GV), based on the shape of occlusion bodies (OBs). The complete genomic sequences of 22 NPVs and seven GVs are currently listed in GenBank. Phylogenetic analysis based on the 29 core conserved baculovirus genes enables the classification of baculoviruses into five groups: group I and group II lepidopteran NPVs, hymenopteran NPVs, dipteran NPVs and GVs (de Jong et al., 2005; Herniou et al., 2004; Lauzon et al., 2005).
Hyphantria cunea NPV (HycuNPV) has been isolated from larvae of the fall webworm, H. cunea, in Japan (Aruga et al., 1960; Hukuhara & Hashimoto, 1966). H. cunea larvae are a serious pest for a variety of trees, including cherry, plane, mulberry and persimmon (Kunimi, 1998). Electron microscopic studies of HycuNPV OBs showed that virions contain multiple nucleocapsids, indicating that HycuNPV is a multicapsid (M) NPV. To develop HycuNPV as an effective biopesticide, we have characterized a number of HycuNPV clones isolated from H. cunea larvae in a mulberry field in Japan (Kamiya et al., 2003). The field isolates of HycuNPV showed a very high degree of genotypic variation, with 29 out of 30 clones exhibiting distinct restriction-endonuclease patterns. These variants were also different in the productivity of BVs and polyhedrin in cell culture and the virulence against H. cunea larvae (Kamiya et al., 2003). Among the 10 clones characterized biologically, clone N9 was the most virulent against H. cunea larvae and yielded the highest BV titre and a moderate amount of polyhedrin.
HycuNPV clone N9 was further characterized by sequencing several genes, including gp64, pcna, ep32, ie-1, iap-1, iap-2 and iap-3, and six homologous regions (hrs) (Felipe Alves et al., 2002a, b; Ikeda et al., 2004; Iwahori et al., 2002; GenBank accession no. AB175497
[GenBank]
). Based on the amino acid sequence identities of these genes, HycuNPV was found to be related closely to group I lepidopteran NPVs (group I NPVs), particularly to Orgyia pseudotsugata MNPV (OpMNPV). In addition, the structural organization of HycuNPV hrs (hycu-hrs), which were composed of 65–69 bp direct repeats, within which a 29–31 bp imperfect palindrome was embedded, is similar to those of group I NPVs, including Autographa californica MNPV (AcMNPV), Bombyx mori NPV (BmNPV) and OpMNPV (Felipe Alves et al., 2002a).
In previous studies, we have also shown that HycuNPV exhibits several distinct types of interactions with insect cells, which provides an excellent opportunity to analyse the mechanisms underlying host-specificity determination of baculoviruses at the molecular level. HycuNPV replicates to a high titre in Spilosoma imparilis SpIm cells (Kamiya et al., 2003), whereas Lymantria dispar Ld652Y cells infected with HycuNPV undergo apoptosis and yield few progeny virions (Ishikawa et al., 2003). In addition, HycuNPV infection triggers global protein-synthesis shutdown of B. mori BmN-4 cells and restricts replication of co-infected BmNPV that is productive in BmN-4 cells upon single infection (Shirata et al., 2004). HycuNPV infection of Ld652Y cells also results in a global protein-synthesis shutdown, which is rescued by hrf-1 (host-range factor 1) encoded by LdMNPV (Ishikawa et al., 2004).
A detailed genetic comparison of HycuNPV with other baculoviruses will be helpful in understanding the molecular mechanisms for host-specificity determination of HycuNPV. Such analysis will also provide valuable insights into baculovirus genomic alterations due to gene acquisitions and losses, which are involved in the improvement of adaptation of respective baculoviruses to their insect hosts. In this study, we analyse the complete nucleotide sequence and gene organization of the HycuNPV N9 genome and compare them with those of other baculovirus genomes sequenced so far.
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METHODS |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTS AND DISCUSSIONREFERENCES |
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), were grown in monolayer culture in MM medium (Mitsuhashi & Maramorosch, 1964) supplemented with 3 % fetal bovine serum. SpIm cells were infected with HycuNPV clone N9 (HycuNPV; Kamiya et al., 2003) at an m.o.i. of 5 and, at 72 h post-infection, the culture media containing budded viruses (BVs) were collected. BVs were precipitated by centrifugation at 106 300 g in an RPS27 rotor (Hitachi Koki) for 75 min through a 25 % (w/w) sucrose cushion and DNA was isolated from the BVs as described by O'Reilly et al. (1992).
Sequencing analysis.
A cosmid library of the HycuNPV genome was constructed (Felipe Alves et al., 2002a) and inserts of four clones, hc-2, hc-4, hc-5 and hc-7, were sequenced completely. These inserts covered the whole genome sequence of HycuNPV, with only one non-overlapping region between hc-2 and hc-4. Sequence of the non-overlapping region was determined by primer walking to fill in the non-overlapping region.
Sequences of hc-4 and hc-5 were determined by shotgun cloning at a redundancy of eight to ten, using a DYEnamic ET Terminator cycle sequencing kit (Amersham Biosciences) and a capillary sequencer (RISA-384; Shimadzu Corporation). Inserts of hc-2 and hc-7 were digested with restriction endonucleases and resultant DNA fragments were subcloned into pBluescript KS(+) (pBS; Stratagene). Sequencing of the insert DNA was performed by using a BigDye Terminator cycle sequencing ready reaction kit and an automated ABI Prism 310 genetic analyser (PE Applied Biosystems). Each DNA strand was sequenced more than three times. Sequences of restriction-endonuclease sites and the non-overlapping region between hc-2 and hc-4 were obtained by using sequence-specific primer sets. The contigs were assembled by DNASIS (Hitachi Software Engineering).
Similarity searches were performed by using the NCBI BLAST searches (version 2.2.12; Altschul et al., 1990). Open reading frames (ORFs) encoding more than 50 aa with minimum overlap were defined as putative genes. Multiple sequence alignments were performed by using CLUSTAL_X (Thompson et al., 1997).
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RESULTS AND DISCUSSION |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTS AND DISCUSSIONREFERENCES |
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. The first nucleotide of the sequence was designated by the first adenine of the translation-initiation codon of polh (polyhedrin). The ORFs are distributed on both strands of the DNA throughout the genome, i.e. 69 ORFs face in the clockwise direction and 79 ORFs face in the anticlockwise direction.
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. HycuNPV shares 130, 134, 131, 125, 125 and 122 ORFs with Choristoneura fumiferana MNPV (CfMNPV), OpMNPV, CfDEFNPV, Epiphyas postvittana MNPV (EppoMNPV), AcMNPV and BmNPV, respectively (Table 1). In total, 116 ORFs are conserved in HycuNPV and all other group I NPVs, including 29 ORFs that are conserved in all baculoviruses, 33 ORFs conserved in all lepidopteran baculoviruses only and 12 ORFs exclusive to the group I NPVs (see Supplementary Table S2 in JGV Online; de Jong et al., 2005; Herniou et al., 2003; Hyink et al., 2002). In addition, 26 ORFs are encoded by HycuNPV and one or more of the other group I NPVs (see Supplementary Table S3, available in JGV Online). Six ORFs are identified as being unique to HycuNPV (Tables 1 and 2). The six unique ORFs did not have any recognizable homologues in nucleotide sequence databases (GenBank/DDBJ/EMBL). HycuNPV ORF7 (Hycu7) and Hycu148 had early promoter motifs located upstream of the putative ATG initiation codon and Hycu121 had both early and late promoter motifs. No promoter motif was found for Hycu41, Hycu99 or Hycu100. HycuNPV did not encode a homologue of Ac44, which is conserved in all other completely sequenced group I NPVs (Bm35, Cf44, Cfdef44, Eppo41 and Op49), but with unknown function.
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). In general, hycu-hrs account for a total of 76 complete and 19 partial repeats, which represent a total of 5668 bp (4.3 % of the entire HycuNPV genome). ORFs account for 118 208 bp (88.9 %) and the remaining 9083 bp represents intergenic sequence (6.8 %).
Phylogenetic characterization of HycuNPV
A phylogenetic tree of 29 completely sequenced baculoviruses was constructed based on the amino acid sequences of 29 common ORFs (Fig. 2). Five groups described previously (de Jong et al., 2005; Herniou et al., 2004; Lauzon et al., 2005) were identified clearly in the tree. HycuNPV was included in group I NPVs, showing a close relationship with CfMNPV and OpMNPV. Based on the close phylogenetic relationships and conservation of several genes specific for group I NPVs, such as gp64, ie-2 and ptp-1 (Herniou et al., 2003), it is concluded that HycuNPV belongs to the group I NPVs.
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). H. cunea also attacks many kind of deciduous trees in North America and was introduced into Japan in the late 1940s (Kunimi, 1998).
Gene-parity plot analysis
The gene orders of HycuNPV and group I NPVs were compared by gene-parity plot analysis (Fig. 3). The result showed that the gene order of HycuNPV was inverted in most regions compared with those of other group I NPVs. In the case of AcMNPV and BmNPV, inversions around the polhs (Ac1-10 and Bm138-3) resulted in reverse ordering of most genes compared with those of HycuNPV. In the case of CfMNPV, CfDEFNPV, EppoMNPV and OpMNPV, the orientation of the first gene, polh, was set in the reverse direction in order to adjust most gene orders to match those of AcMNPV and BmNPV. In spite of the inverse orientation, linearity was observed in many parts of HycuNPV genome compared with those of other group I NPVs.
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) and OpMNPV (Ahrens et al., 1997).
Translocation of ctl-1 (conotoxin-like homologue 1) is observed when compared with CfMNPV (Cf131; Fig. 3a
) and with OpMNPV (Op136; Fig. 3b). In contrast, the location of ctl-1 of HycuNPV (Hycu143) is similar to that of AcMNPV, although a small inversion is observed between ctl-1 (Ac2) and bro (Ac3) (Table 1). Other group I NPVs, including CfDEFNPV, EppoMNPV and BmNPV, did not encode ctl-1 (see Supplementary Table S3, available in JGV Online).
ctl-2, the homologue of ctl-1, is found only in HycuNPV (Hycu123) and OpMNPV (Op30) among the group I NPVs and in the same context in both genomes (Supplementary Table S3). So far, two ctls, ctl-1 and ctl-2, are found only in the genomes of HycuNPV, OpMNPV and LdMNPV. Besides two ctls, hrf-1 (host-range factor 1) is present in the genomes of OpMNPV and LdMNPV. hrf-1 is a host-range gene that rescues AcMNPV replication in non-permissive Ld652Y cells derived from L. dispar. Herniou et al. (2003) suggested that there is a phylogenetic link between the presence of two ctls and hrf-1, because only OpMNPV and LdMNPV, which replicate successfully in larvae of the family Lymantriidae, L. dispar and O. pseudotsugata, encode these three genes. On the contrary, the present result shows that HycuNPV has two ctls, but hrf-1 is absent. This result suggests that hrf-1 may be lost in the HycuNPV lineage or may be acquired in the OpMNPV lineage apart from two ctls. The functions of the ctls are not known.
hrs
Consensus palindrome sequences (hrcons) present in hrs were compared among group I NPVs (Fig. 4). Each side of the hrcons, 1-GxTTTxC-7 and 22-TxGxAAAxC-30, was completely conserved, whereas the internal sequences diverged (Fig. 4a). HycuNPV hrcon (Hycuhrcon) showed high similarity to hrcons of AcMNPV (76.7 %), CfDEFNPV (76.7 %) and CfMNPV (76.7 %). The phylogenetic relationship of hrcons showed similar divergence to that of 29 conserved genes in group I NPVs (Fig. 2), suggesting that the hr sequence co-evolved with the virus genome.
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) and are not completely conserved in the palindrome sequences of group I NPVs (Fig. 4a). The homologous sequences of IBM in HycuNPV are 5'-ACTTGAAA-3' and 5'-TCTGGTAA-3' (underlined nucleotides indicate mismatch with AcMNPV IBM). Previous studies showed that expression of AcMNPV ie-0, ie-2 and pe-38, which contained the AcMNPV IBM sequence upstream of the CAGT transcription-initiation motif, was downregulated by AcMNPV IE-1 (Leisy et al., 1997). Sequences similar to those of HycuNPV IBM are present three to four bases upstream of the CAGT motif of hycu-ie-1, hycu-ie-2, hycu-pe38 and hycu-gp64. Whether or not HycuNPV IE-1 binds preferentially to the HycuNPV IBM and downregulates the expression of these genes remains to be elucidated.
The genomic contexts of HycuNPV hrs (hycu-hrs) were compared with those of other group I NPVs hrs (Fig. 5). The locations of hycu-hrs were more conserved in CfDEFNPV, EppoMNPV and OpMNPV than in AcMNPV, BmNPV and CfMNPV. In particular, both the number and the location of hycu-hrs showed high similarity to OpMNPV hrs (op-hrs) and the G-T repeated sequence. Among the six hycu-hrs, hycu-hr1, hycu-hr5 and hycu-hr6 were present at the same relative gene locations as op-hr1, op-hr5 and the G-T repeat, respectively. In addition, hycu-hr2 and hycu-hr3 were present at the same sites as op-hr2 and op-hr3, respectively, whilst an inversion (Op29–Op34) and certain insertions (Op28–31 and Op87) were observed in the vicinity of op-hr2 and op-hr3. The locations of five of six hycu-hrs were inconsistent with CfMNPV hrs (cf-hrs); however, the locations of both hycu-hrs and cf-hrs were well conserved in CfDEFNPV hrs (cfdef-hrs). This finding suggests that the locations of hrs are well conserved in a subgroup of group I NPVs that includes HycuNPV, CfMNPV, CfDEFNPV, EppoMNPV and OpMNPV, and that certain hrs are acquired and/or lost through evolution.
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). According to this hypothesis, it is possible that hycu-hr6 or cfdef-hr11 is acquired through recombination at the repeated sequence with a common or a specific ancestral NPV. Previous studies have demonstrated that hycu-hr6 enhances the hycu-gp64 early promoter and expression of Hycu-GP64, the envelope fusion protein of BVs, both in vivo and in vitro (Felipe Alves et al., 2002a, b; Nagai et al., 2006). Together, these results suggest that hycu-hr6 was acquired by HycuNPV and brought about enhancement of the expression of hycu-gp64 at the early phase of infection. Enhanced Hycu-GP64 production at the early phase of HycuNPV infection may increase virulence, as in AcMNPV-infected Heliothis virescens larvae (Washburn et al., 2003).
Baculovirus-repeated ORFs (BROs)
Baculovirus-repeated ORF genes (bros) were first identified in baculovirus genomes as a repetitive gene and constitute a gene family. Most BROs contain a 41 aa core sequence at the N-terminal half and several different domains throughout the sequence. Based on the similarity of those different domains, BROs were separated into four groups, I–IV, and the 41 aa core sequences were highly conserved among BROs in each group (Kuzio et al., 1999). HycuNPV encodes five BROs, named Hycu-BRO-a to Hycu-BRO-e according to the gene order. Hycu-BRO-b, -c, -d and -e showed the highest amino acid identities to Bm-BRO-a (74 % amino acid identity), Bm-BRO-e (85 %), Bm-BRO-a (67 %) and Ld-BRO-n (83 %), respectively, all of which was included in the group I BROs (Fig. 6a). Hycu-BRO-a showed similarity to the C-terminal sequences of Bm-BRO-d (29 % amino acid identity) and Ld-BRO-n (33 %), although the BRO-specific N-terminal sequence was truncated (Fig. 6b). Homologues of Hycu-BRO-a (Hycu38) that have the truncated N terminus were found in CfMNPV (Cf108), OpMNPV (Op116), CfDEFNPV (Cfdef112) and EppoMNPV (Eppo103). These Hycu-BRO-a homologues are located in the same genomic context (Table 1).
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). Functional analyses have revealed that Hycu-IAP-3 is able to block apoptosis induced by actinomycin D and rescues replication of p35-deficient mutant AcMNPV, whereas Hycu-IAP-1 and Hycu-IAP-2 cannot play such an essential role (Ikeda et al., 2004). The genomic contexts of these three iaps were well conserved in group I NPVs, except for iap-3, which was missing in both AcMNPV and BmNPV. Apart from iap-3, a cluster of other genes within the vicinity of iap-3 was missing in both AcMNPV and BmNPV (Table 1), suggesting that iap-3 was lost along with other genes in the cluster from the subgroup of group I NPVs including AcMNPV and BmNPV, or that the cluster was acquired by another subgroup of group I NPVs that includes HycuNPV, CfMNPV, CfDEFNPV, EppoMNPV and OpMNPV. iap-3 may not be required for both AcMNPV and BmNPV, because these viruses encode p35 as a functional anti-apoptotic gene. In contrast, p35 is not present in HycuNPV or other group I NPVs that encode iap-3. In addition, iap-4 is missing in HycuNPV, AcMNPV, BmNPV and CfMNPV. Taking into account the fact that iap-4 is present not only in OpMNPV, CfDEFNPV and EppoNPV genomes, but also in certain group II NPVs, iap-4s may have been lost from the genomes of HycuNPV, AcMNPV, BmNPV and CfMNPV.
Host-range genes
To date, five genes, p35, iap, helicase, hcf-1 (host cell-specific factor 1) and hrf-1, have been shown to be involved in host-range determination of AcMNPV (Miller & Lu, 1997). By carrying these host-range genes, AcMNPV is able to replicate in insects and their cell lines that are otherwise semi- or non-permissive for AcMNPV. p35, helicase and hcf-1 are encoded by the AcMNPV genome, and AcMNPV with a deletion and/or a mutation in these genes results in non-productive infection of normally permissive cells and insects. On the other hand, iap and hrf-1 are the host-range genes of OpMNPV and LdMNPV, respectively, and recombinant AcMNPVs expressing these genes replicate in non-permissive cells and insects. Previous results have shown that hycu-iap-3 in the HycuNPV genome is an essential gene for HycuNPV replication in SpIm cells, which are the conventional host cells of HycuNPV (Ikeda et al., 2004), indicating that hycu-iap-3 contributes to the host range of HycuNPV. HycuNPV does not encode homologues of other host-range genes, p35, hcf-1 and hrf-1.
Evolution of HycuNPV genome content
Based on the evolution of the genome content of group I NPVs suggested previously (de Jong et al., 2005; Herniou et al., 2003), HycuNPV genes that may have been acquired and lost through HycuNPV evolution and adaptation to the insect host are summarized. HycuNPV contains 15 genes (hycu-ie2, hycu24, hycu-gp64, hycu32, hycu40, hycu78, hycu79, hycu-gta, hycu117, hycu-odv-e26, hycu-ptp-1, hycu146, hycu-etm, hycu-ets and hycu-p15) acquired by the entire group I NPVs (Herniou et al., 2003) and three genes (hycu42, hycu118 and hycu119) acquired by the phylogenetic subgroup of group I NPVs that includes HycuNPV, CfMNPV, CfDEFNPV, EppoMNPV and OpMNPV (see Supplementary Table S3, available in JGV Online; Herniou et al., 2003). In contrast, seven genes (ac45, ac116, ac121, ac149, ac154, p43 and pk-2) acquired by another phylogenetic subgroup of group I NPVs, including AcMNPV and BmNPV (Herniou et al., 2003), are not found in HycuNPV. Three genes (op-iap-4, op4 and op5) acquired by the OpMNPV/EppoMNPV lineage (Herniou et al., 2003) are not found in HycuNPV, suggesting that these genes either were not acquired or have been lost by HycuNPV. HycuNPV does not contain homologues of 11 AcMNPV genes (ac7, ac58, ac84, ac97, ac107, ac112, ac118, ac140, ac152, hcf-1 and pnk), one BmNPV gene (bm111), seven CfMNPV genes (cf89, cf90, cf116, cf120, cf121, cf133 and cf143), two CfDEFNPV genes (cfdef19 and cfdef142) or six EppoMNPV genes (eppo9, eppo28, eppo43, eppo105, eppo113 and eppo132), which were acquired exclusively by the respective NPVs (de Jong et al., 2005; Herniou et al., 2003; Lauzon et al., 2005), but possesses the homologues of two OpMNPV genes, op68 and op-ep32, among seven genes (op28, op33, op66, op68, op-ep25, op-ep32 and p8.9) that were acquired by OpMNPV (Herniou et al., 2003; Lauzon et al., 2005). These two genes may be acquired by a common ancestor of HycuNPV and OpMNPV. Moreover, HycuNPV acquired six unique genes (Table 2).
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ACKNOWLEDGEMENTS |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTS AND DISCUSSIONREFERENCES |
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Received 9 February 2006;
accepted 25 April 2006.
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  S. Katsuma, T. Fujii, S. Kawaoka, and T. Shimada Bombyx mori nucleopolyhedrovirus SNF2 global transactivator homologue (Bm33) enhances viral pathogenicity in B. mori larvae J. Gen. Virol., December 1, 2008; 89(12): 3039 - 3046. [Abstract] [Full Text] [PDF]
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J. Huang, B. Hao, F. Deng, X. Sun, H. Wang, and Z. Hu Open reading frame Bm21 of Bombyx mori nucleopolyhedrovirus is not essential for virus replication in vitro, but its deletion extends the median survival time of infected larvae J. Gen. Virol., April 1, 2008; 89(4): 922 - 930. [Abstract] [Full Text] [PDF]
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