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Applied and Environmental Microbiology, March 2006, p. 1878-1885, Vol. 72, No. 3
0099-2240/06/$08.00+0 doi:10.1128/AEM.72.3.1878-1885.2006
Copyright © 2006, American Society for Microbiology. All Rights Reserved.
In Vivo Himar1-Based Transposon Mutagenesis of Francisella tularensis
Tamara M. Maier,
Roger Pechous,
Monika Casey,
Thomas C. Zahrt, and
D. W. Frank*
Department of Microbiology and Molecular Genetics, Medical College of Wisconsin, 8701 Watertown Plank Rd., Milwaukee, Wisconsin 53226
Received 4 October 2005/
Accepted 27 December 2005

ABSTRACT
Francisella tularensis is the intracellular pathogen that causes
human tularemia. It is recognized as a potential agent of bioterrorism
due to its low infectious dose and multiple routes of entry.
We report the development of a
Himar1-based random mutagenesis
system for
F. tularensis (
HimarFT). In vivo mutagenesis of
F. tularensis live vaccine strain (LVS) with
HimarFT occurs at
high efficiency. Approximately 12 to 15% of cells transformed
with the delivery plasmid result in transposon insertion into
the genome. Results from Southern blot analysis of 33 random
isolates suggest that single insertions occurred, accompanied
by the loss of the plasmid vehicle in most cases. Nucleotide
sequence analysis of rescued genomic DNA with
HimarFT indicates
that the orientation of integration was unbiased and that insertions
occurred in open reading frames and intergenic and repetitive
regions of the chromosome. To determine the utility of the system,
transposon mutagenesis was performed, followed by a screen for
growth on Chamberlain's chemically defined medium (CDM) to isolate
auxotrophic mutants. Several mutants were isolated that grew
on complex but not on the CDM. We genetically complemented two
of the mutants for growth on CDM with a newly constructed plasmid
containing a nourseothricin resistance marker. In addition,
uracil or aromatic amino acid supplementation of CDM supported
growth of isolates with insertions in
pyrD,
carA, or
aroE1 supporting
the functional assignment of genes within each biosynthetic
pathway. A mutant containing an insertion in
aroE1 demonstrated
delayed replication in macrophages and was restored to the parental
growth phenotype when provided with the appropriate plasmid
in
trans. Our results suggest that a comprehensive library of
mutants can be generated in
F. tularensis LVS, providing an
additional genetic tool to identify virulence determinants required
for survival within the host.

INTRODUCTION
Francisella tularensis is the etiologic agent of human tularemia.
Four subspecies of
F. tularensis have been recognized, including
(i) the virulent type A
F. tularensis subsp.
tularensis, (ii)
the less virulent type B
F. tularensis subsp.
holarctica, (iii)
F. tularensis subsp.
mediasiatica, and (iv)
F. tularensis subsp.
novicida. The
F. tularensis LVS (live vaccine strain) is derived
from
F. tularensis subsp.
holarctica. This strain demonstrates
an attenuated phenotype in humans but remains virulent for mice,
making it a potential model system to identify virulence factors
(
13,
23). Although
Francisella replicates in several cell types
including macrophages (
4,
22,
25), hepatocytes (
17), and amoebae
(
1), the virulence determinants that contribute to its intracellular
lifestyle remain an active area of investigation. Approaches
to identify and functionally characterize specific genes involved
in intracellular maintenance and replication will contribute
toward a general understanding of
Francisella and host biology.
There has been steady progress toward the development and use of genetic methods to manipulate Francisella. Chemically induced or spontaneous mutants have been reported for both Francisella novicida (40) and F. tularensis LVS (10, 50). Tn10- or Tn1721-based transposon shuttle mutagenesis has been performed in F. tularensis subsp. novicida (5, 7-9, 18, 27, 41), but the observed instability of the transposons is problematic (35). Recently, transposon-transposase complexes were used to construct stable Tn5-derived insertion mutants in F. tularensis LVS in vivo (31). The functional aspects of candidate virulence genes have been tested using allelic replacement strategies (26, 35), and genetic strategies to complement attenuated mutants to wild-type have been developed (7, 36, 37, 42). The recent availability of genomic sequence information and chip arrays provides additional opportunities to identify genomic and transcript expression differences between subspecies and strains. As the mechanisms of pathogenesis remain poorly understood, particularly for the highly virulent type A strains of F. tularensis, random mutagenesis strategies may facilitate the discovery of new genes involved in maintaining an intracellular lifestyle. The identification of virulence factors should, in turn, facilitate the rational design of therapeutics or vaccines.
In previous work we constructed shuttle plasmids with expanded capabilities for use in Francisella (37). In this study, we report the utilization of a conditionally replicating derivative for delivery of a modified Himar1 (HimarFT) into F. tularensis LVS in vivo. Our results demonstrate that HimarFT-based mutagenesis of F. tularensis LVS results in random, single, stable insertions at high efficiency, providing a new genetic tool for the potential identification of coding regions important for pathogenesis.

MATERIALS AND METHODS
Bacterial strains, plasmids, and growth conditions.
All bacterial strains and plasmids used in this study are listed
in Table
1.
F. tularensis LVS was routinely grown at 37°C
in modified Mueller-Hinton (MH) broth or on agar (Difco Laboratories)
as previously described (
37). In some experiments, cysteine
heart agar (Difco) with 5% defibrinated horse blood (Becton
Dickinson) was used. Screening for auxotrophic mutants was performed
with Chamberlain's chemically defined medium (CDM) (
15). Strains
containing temperature-sensitive plasmid derivatives were grown
at 30°C (permissive temperature) or 40°C (nonpermissive
temperature). When required, medium was supplemented with kanamycin
(10 µg ml
1) or nourseothricin (5 µg ml
1).
Selection for nourseothricin resistance was performed at 30°C.
Escherichia coli was grown aerobically in Luria-Bertani (LB)
medium (Difco) at 37°C, supplemented with kanamycin (50
µg ml
1), ampicillin (100 µg ml
1),
or nourseothricin (50 µg ml
1). Kanamycin and ampicillin
were purchased from Sigma-Aldrich (St. Louis, Mo.) or United
States Biochemical Corporation (Cleveland, Ohio). Nourseothricin
was purchased from WERNER BioAgents (Jena, Germany).
DNA manipulation and transformation.
Purification and manipulation of plasmid or genomic DNA, electroporation
of
F. tularensis LVS, and chemical transformation of
E. coli were performed as described previously (
37). Custom oligonucleotide
primers (Table
1) were synthesized by Operon (Huntsville, AL).
DNA maps were constructed using MacPlasmap Pro (CGC Scientific,
Inc., Ballwin, Mo.).
To determine insertion locations in Francisella, genomic DNA was isolated from each mutant strain, digested with SpeI, and treated with T4 DNA ligase. HimarFT-containing fragments were recovered as plasmid DNA in E. coli DH5
pir (14). Analysis of genomic DNA adjacent to insertions was performed as previously described (37). The HimarFT insertion site sequences were compared against the F. tularensis LVS genome at http://bbrp.llnl.gov/bbrp/bin/f.tularensis_blast and the F. tularensis Schu S4 genome available at http://artedi.ebc.uu.se/Projects/Francisella/blast/.
Southern blot analysis.
Genomic DNA (0.5 µg) was digested with SpeI overnight, resolved on a 0.7% agarose gel, and transferred to a positively charged nylon membrane (Roche Diagnostics Corporation, Indianapolis, IN) using an LKB 2016 VacuGene Vacuum Blotting System (Pharmacia). Blots were probed with DNA fragments randomly labeled using a DIG High Prime DNA Labeling and Detection Starter Kit II (Roche); probes detected either the HimarFT transposon with a 634-bp fragment recognizing the neomycin phosphotransferase (npt) gene responsible for kanamycin resistance or the pFNLTP16 vehicle with a 624-bp fragment recognizing the ß-lactamase (bla) gene responsible for ampicillin resistance. Gel processing, probe labeling, and detection were performed as recommended by the manufacturer.
Construction and transposition of Himar1 derivatives.
All Himar1 derivatives are listed in Table 1. The vehicle pFNLTP16 is a derivative of pFNLTP9 (37) in which npt was removed by inverse PCR and multiple cloning sites were added (Fig. 1). The pMiniHimar plasmid containing Himar1 was linearized and ligated to pFNLTP16 to generate pFNLTP16 H1 (Fig. 1). Derivatives of pFNLTP16 H1 were generated by cloning promoters for groEL (pgro) and/or acpA (pacp) (21, 48) upstream of npt and/or tnp, respectively (Fig. 1). A derivative of pFNLTP16 H3 containing a 1.3-kb fragment encoding nourseothricin resistance, including the translation elongation factor promoter and terminator (24), was amplified from pAG36 (Euroscarf) to construct pFNLTP25 H3.
Several transposition conditions were tested to determine the
optimal growth medium and length of time for outgrowth. For
optimal transposition, 100 ng of each transposon-containing
plasmid was electroporated into newly prepared electrocompetent
F. tularensis LVS. After outgrowth at 30°C on a shaker for
5 h, dilutions were plated on MH medium containing kanamycin
and incubated at 40°C to select for
Himar1 integration and
loss of plasmid (one-step protocol) or incubated at 30°C
to obtain replicating plasmid before secondary selection for
plasmid loss at 40°C (two-step protocol). In addition, dilutions
were plated onto MH medium with or without kanamycin to determine
total CFU transformed or total potential recipients, respectively.
Colonies grown for 3 or 4 days at 40°C were picked and struck
onto MH medium containing kanamycin and grown at 37°C to
recover individual clones containing
Himar1 insertions in the
genome.
Complementation of HimarFT auxotrophic mutants.
The transposon insertion was mapped in each auxotrophic mutant identified. Wild-type aroE1 or pyrDF and predicted promoter regions were amplified from F. tularensis LVS genomic DNA and cloned into pFNLTP23 (see Fig. 4), a derivative of pFNLTP8 (37) containing the gene encoding nourseothricin acetyltransferase. After electroporation into the respective F. tularensis LVS HimarFT mutant strains, the ability to restore growth on CDM was determined. To functionally complement carA, pyrD, or aroE1 mutant strains, uracil (50 µg ml1) or a mixture of phenylalanine and tryptophan (100 µg ml1 each) was added to CDM. The intracellular growth phenotype was determined by measuring bacterial replication over 3 days in the murine BALB/c macrophage cell line J774A.1 as described previously (37).
Nucleotide sequence accession numbers.
Sequence information for pFNLTP16 H3 and pFNLTP23 is available
from the GenBank database under accession numbers DQ236098 and
DQ266433, respectively.

RESULTS
Construction of a Himar1 transposon for use in Francisella.
Initial attempts to isolate
Himar1 insertions in
Francisella using pMiniHimar (Table
1), a plasmid unable to replicate in
Francisella, were unsuccessful. This result could be due to
failures in (i) transposon delivery, (ii) expression of the
transposase, (iii) expression of the selection marker, or (iv)
a combination of these factors. To address delivery of the transposon,
Himar1 derivatives were cloned into the temperature-sensitive
shuttle plasmid pFNLTP16 (Fig.
1), a derivative of pFNLTP9 in
which
npt had been removed. This plasmid can be efficiently
electroporated into
Francisella species and maintained at a
permissive (30°C) but not at a nonpermissive (40°C)
temperature (
37). To ensure transcriptional initiation of the
selectable marker and transposase, the
Francisella promoter
for
groEL (p
gro) (
21) was cloned upstream of
npt (pFNLTP16 H3
and H4), and/or the promoter for
acpA (p
acp) (
48) was cloned
upstream of
tnp (pFNLTP16 H2 and H4) (Fig.
1). Previous experiments
demonstrated that both p
gro and p
acp drive the expression of
gfp cloned into pFNLTP6 in
F. tularensis LVS (
37).
Optimization of Himar1 transposition in F. tularensis LVS.
One-step and two-step transposition protocols were tested using various pFNLTP16 Himar1 derivatives, including those that had been modified by the addition of one or both Francisella promoters. All derivatives were electroporated into F. tularensis LVS to determine if Kmr colonies could be recovered at 40°C in a one-step procedure. Transposition was not detected with pFNLTP16, pMiniHimar, pFNLTP16 H1, or pFNLTP16 H2. However, Kmr isolates were recovered at high efficiency using the pFNLTP16 H3 or H4 derivatives (Table 2). The efficiency of plating at the nonpermissive temperature was approximately 12 to 15% of that observed at the permissive temperature (Table 2). Loss of plasmid DNA was investigated using a derivative of pFNLTP16 H3 that contains the nourseothricin resistance cassette as a selectable marker (pFNLTP25 H3) (Table 1). After electroporation and growth at the nonpermissive temperature, 100 kanamycin-resistant isolates were picked onto MH medium containing either nourseothricin or kanamycin. All isolates retained kanamycin resistance, but none was able to grow on medium with nourseothricin, consistent with Himar1 transposition and loss of the plasmid vehicle. Isolates from an electroporation plated at permissive temperature grew on medium containing kanamycin or nourseothricin, a result consistent with plasmid maintenance (data not shown).
To determine if the frequency of transposition could be further
improved, the procedure was repeated for all transposon derivatives
using a two-step method. Strains were first selected for inheritance
and maintenance of plasmid DNA at 30°C. Cultures were then
shifted to the restrictive temperature (40°C) to inhibit
subsequent plasmid replication. As in the one-step protocol,
Km
r colonies were obtained only with the pFNLTP16 H3 and H4
derivatives after incubation at 40°C. Plasmid DNA, however,
remained detectable in these isolates. The presence of plasmid
DNA may be due to a residual plasmid-containing subpopulation
that should be lost by subsequent replication cycles at 40°C.
Since the retention of plasmid-encoded Km
r could be problematic
in subsequent screening steps, we concluded that a one-step
protocol using pFNLTP16 H3 was optimal for the delivery and
transposition of
HimarFT into
F. tularensis LVS.
Verification of HimarFT transposition in F. tularensis LVS.
Southern blot analysis was performed on genomic DNA from 33 random Kmr colonies recovered after a one-step transposition protocol with pFNLTP16 H3. Hybridization of SpeI-digested genomic DNA with a probe specific to npt present on HimarFT resulted in single bands of various sizes, as shown for 15 representative isolates (Fig. 2A). No signal was obtained with a probe specific to the ß-lactamase gene (bla) present on pFNLTP16 for 31 of these random isolates (data not shown). DNA from two isolates hybridized to the plasmid-specific probe, suggesting that plasmid DNA was incompletely resolved during subsequent replication.
Rescue of HimarFT and DNA sequence analysis of insertions.
HimarFT insertion sites were mapped by ligation of SpeI-digested
genomic fragments and recovery of plasmid DNA in
E. coli DH5

pir.
Nucleotide sequence analysis was performed with primers annealing
to
HimarFT and reading into flanking genomic DNA. When insertion
locations were mapped to the
F. tularensis LVS genome (Fig.
2B), a random distribution of
HimarFT insertion was observed
with no apparent regional bias. A variety of insertions occurred
with no observed preference for the open reading frame (ORF)
or transposon orientation (Fig.
2C). Of the 31 rescued genomic
insertions, 19 possessed
HimarFT insertions in a predicted ORF
(Table
3).
HimarFT inserted into genes involved in secretion,
transport, energy production, metabolism, cell division, and
protein turnover. Eight insertions mapped to intergenic regions,
and two were located in repetitive regions of the
F. tularensis LVS genome. The remaining two isolates likely represent aberrant
transposition events. We detected one deletion and one duplication
of flanking genomic sequence. The typical TA insertion site
for
Himar1 transposons was present in all but one isolate.
Stability of HimarFT insertions in F. tularensis LVS.
Five
HimarFT mutants were serially passaged in MH broth without
kanamycin for 5 days. After

40 generations, cultures passaged
in the absence of selective pressure maintained the kanamycin
marker. A Southern blot comparing the genomic DNA isolated from
cultures grown under kanamycin selection and those isolated
after 5 days without kanamycin confirmed that the insertion
site was identical (Fig.
3). These results indicate that once
transposition and plasmid loss has occurred, the kanamycin marker
remains stably integrated within the genome.
Phenotypic screen for auxotrophic mutants after HimarFT transposition.
To test the utility of
HimarFT, a one-step mutagenesis protocol
was performed, and Km
r colonies were screened for growth by
replica plating onto Chamberlain's CDM. From approximately 6,500
clones, three isolates were obtained that failed to grow on
CDM. Each strain possessed a single insertion of
HimarFT, as
shown by Southern blot analysis with the
npt probe (Fig.
2A,
lanes 13 to 15). A hybridization signal was undetectable with
the
bla probe (data not shown).
HimarFT insertions resulting
in auxotrophy mapped to
carA (required for carbamoyl phosphate
synthesis, an intermediate in arginine and pyrimidine synthesis),
pyrD (required for pyrimidine synthesis), and
aroE1 (required
for the shikimate pathway involved in aromatic amino acid, ubiquinone/menaquinone,
and folate synthesis, respectively) based on the annotated Schu
S4 genome (Table
3).
Complementation of the auxotrophic HimarFT mutants.
To genetically complement HimarFT insertion strains, we constructed a plasmid expressing nourseothricin resistance as the selective marker (pFNLTP23). Nourseothricin is an aminoglycoside that inhibits a broad spectrum of organisms, including bacteria, protozoa, yeasts, viruses, and plants. Treatment with nourseothricin is postulated to inhibit protein synthesis by inducing miscoding events. It is an attractive marker for research because it is not used in human or veterinary medicine and has not been shown to display cross-resistance (24). The MIC of nourseothricin for F. tularensis LVS is approximately 2 to 5 µg ml1 when it is incorporated in complex medium (data not shown). No cross-resistance to kanamycin was observed in strain LVS.
DNA fragments containing the coding sequences and putative promoter regions for the HimarFT-interrupted ORFs were amplified from the genome and cloned into pFNLTP23 for complementation (Fig. 4A). F. tularensis LVS containing pFNLTP23 grew on defined medium (Fig. 4B, sector 2), while the auxotrophic mutants containing pFNLTP23 were unable to grow (Fig. 4B, sectors 3 and 5). When pyrDF and aroE1 (including
300 bp upstream) were provided in trans, they restored the ability of pyrD::HimarFT and aroE1::HimarFT, respectively, to grow on CDM (Fig. 4B, sectors 4 and 6). We were unable to genetically test complementation of carAB::HimarFT as several attempts to clone this fragment in pFNLTP23 were unsuccessful. However, the addition of uracil to CDM functionally complemented both carAB and pyrD insertion strains (Fig. 4C), consistent with the predicted function of these genes in pyrimidine biosynthesis (12). Similarly, aroE1::HimarFT grew on CDM supplemented with phenylalanine and tryptophan (data not shown).
To determine if any of the auxotrophic mutants possessed intracellular replication defects, a growth analysis was performed in J774A.1 macrophages. Strains with insertions in pyrD or carA were indistinguishable from LVS when replication in macrophages was assessed (data not shown). In contrast, aroEI::HimarFT pFNLTP23 exhibited a distinct delay in replication compared to LVS pFNLTP23 (Fig. 4D). This delay is specific to intracellular growth since no growth difference was seen at 37°C in MH broth between LVS and aroEI::HimarFT with or without pFNLTP23 (data not shown). The replication defect of aroEI::HimarFT pFNLTP23 in J774A.1 macrophages was complemented with the cloned gene in trans (Fig. 4D).

DISCUSSION
Himar1 has been useful for in vitro (
2,
3,
45) and in vivo (
6,
49,
51,
54) transposon mutagenesis of a variety of bacteria.
Moreover, since
Himar1 does not require host-specific factors
for transposition and displays a lack of site specificity, it
seemed ideal for mutagenesis of the AT-rich
Francisella genome
(
32-
34). The modified
Himar1 transposon developed in this study
(
HimarFT) allows efficient in vivo random mutagenesis of
F. tularensis LVS. Analysis of 31 insertions from a single transposition
reaction suggested that
HimarFT could transpose randomly within
the
F. tularensis LVS genome with no known sequence specificity
apart from the TA dinucleotide previously reported to be required
for all
mariner transposition events (
19,
33). The frequency
of insertion for
HimarFT, either 15% of transformed cells or
2
x 10
5 of potential recipient organisms, is comparable
to other reported in vivo random mutagenesis systems in
Francisella (
31) or in other bacteria (
49,
51,
54). This frequency allows
saturation mutagenesis to be conducted in
Francisella from a
single electroporation, an advantage over transposon-transposase
complexes (
31).
Implementing a transposon mutagenesis strategy in diverse organisms may require optimization of several parameters, including expression of the transposase and antibiotic resistance marker for selection. Alteration or substitution of promoter sequences has been used in prior studies to eliminate host restriction (49, 51, 54). Recent studies indicate that this could also be a limitation encountered in Francisella. Interestingly, detection of EZ::TN insertions in the Francisella genome appears to be limited to transcriptionally active regions, perhaps due to poor expression of the resistance marker in single copy. In HimarFT, the orientation of the groEL promoter relative to npt and tnp may result in sufficient expression of both genes, as the addition of the acpA promoter upstream of tnp does not affect the frequency of transposition. This configuration may actually limit tnp expression to a single event per plasmid.
Although single, stable genomic insertions were identified in most cases, spurious events were also detected using HimarFT as constructed. Isolates were obtained that possessed rearrangements adjacent to the insertion or parts of the delivery vehicle. This is not specific to Francisella or HimarFT but is common for transposon mutagenesis (6, 11, 16, 20, 38, 53). Additionally, two isolates appeared to maintain plasmid sequences, due possibly to reversion of the temperature-sensitive mutation within RepA. We anticipate that spurious events represent only a minority of the HimarFT-containing clones in a genomic library, some of which may not generate a phenotype during subsequent screening steps.
Auxotrophy is one phenotype that has been considered for the development of a suitable attenuated vaccine candidate. Both the shikimate and the purine biosynthetic pathways have been proposed as targets to generate vaccine strains in Francisella (30, 47). The attenuation of growth in vivo while maintaining the expression of protective antigens is important in considering immunization strategies (28, 43). Mutants of the aro pathway in Listeria monocytogenes are attenuated in virulence in epithelial cell culture and in mice (52), while Mycobacterium tuberculosis requires this pathway for viability (44). Disruption of carA or pyrD did not result in any phenotypic change for entry or replication within macrophages in F. tularensis LVS. In contrast, disruption of aroE1 results in delayed or reduced replication in F. tularensis LVS, a characteristic fully reversible when aroE1 is provided in trans. Further analysis of LVS aroE::HimarFT in mice will be necessary to better delineate the in vivo phenotype and its potential as a live vaccine.
Isolation of auxotrophs in other bacteria often results in 1 to 2% recovery (6, 29). We had expected to obtain more auxotrophs in our screen, consistent with the F. tularensis Schu S4 genomic analysis that identified approximately 350 enzymes postulated to participate in metabolism (34). Although
6,500 clones were analyzed on CDM, replica plating resulted in crowding on the assay medium, reducing the ability to detect loss of growth. We arrayed the library in a 96-well format and repeated the screen for growth on CDM. From 5,467 clones, eight isolates grew on complex medium and reproducibly failed to grow on CDM (0.15%) (data not shown). All insertions mapped within genes annotated as components of biosynthetic pathways. Additionally, different insertions in carB and aroE1 were identified in the second screen. A similar frequency of auxotrophy (0.5%) was reported in a screen of Xenorhabdus nematophila transposon mutants on a defined medium supplemented with all 20 L-amino acids (39). The complexity of the CDM and the exclusion of essential genes from our screen may influence the total number of auxotrophs that could be isolated by insertional mutagenesis.
The in vivo HimarFT mutagenesis system utilized in this study for Francisella expands the array of newly developed tools to analyze gene function in this intracellular pathogen. Continued development of random mutagenesis strategies should accelerate the discovery of determinants required for virulence and replication and perhaps guide future work toward a defined vaccine strain.

ACKNOWLEDGMENTS
This work was supported by the Center for Biopreparedness and
Infectious Disease at the Medical College of Wisconsin and the
Great Lakes Regional Center of Excellence (GLRCE) for Biodefense
and Emerging Infectious Disease Research (DP5, to T.C.Z. and
D.W.F.). T.M.M. is supported by a GLRCE Career Development Fellowship
(CDP9).
We thank Rachel H. Becker and Renee Penoske for their technical assistance and Eric J. Rubin for the pMiniHimar used in this study.

FOOTNOTES
* Corresponding author. Mailing address: Department of Microbiology and Molecular Genetics, Medical College of Wisconsin, 8701 Watertown Plank Rd., Milwaukee, WI 53226. Phone: (414) 456-8766. Fax: (414) 456-6535. E-mail:
frankd{at}mcw.edu.


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Applied and Environmental Microbiology, March 2006, p. 1878-1885, Vol. 72, No. 3
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