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  • American Society for Microbiology  (15)
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  • 1
    Online Resource
    Online Resource
    Structural Variation in the Bacterial Community Associated with Airborne Particulate Matter in Beijing, China, during Hazy and Nonhazy Days
    American Society for Microbiology ; 2018
    In:  Applied and Environmental Microbiology Vol. 84, No. 9 ( 2018-05)
    Details
    In: Applied and Environmental Microbiology, American Society for Microbiology, Vol. 84, No. 9 ( 2018-05)
    Abstract: The structural variation of the bacterial community associated with particulate matter (PM) was assessed in an urban area of Beijing during hazy and nonhazy days. Sampling for different PM fractions (PM 2.5 [ 〈 2.5 μm], PM 10 [ 〈 10 μm], and total suspended particulate) was conducted using three portable air samplers from September 2014 to February 2015. The airborne bacterial community in these samples was analyzed using the Illumina MiSeq platform with bacterium-specific primers targeting the 16S rRNA gene. A total of 1,707,072 reads belonging to 6,009 operational taxonomic units were observed. The airborne bacterial community composition was significantly affected by PM fractions ( R = 0.157, P 〈 0.01). In addition, the relative abundances of several genera significantly differed between samples with various haze levels; for example, Methylobacillus , Tumebacillus , and Desulfurispora spp. increased in heavy-haze days. Canonical correspondence analysis and permutation tests showed that temperature, SO 2 concentration, relative humidity, PM 10 concentration, and CO concentration were significant factors that associated with airborne bacterial community composition. Only six genera increased across PM 10 samples ( Dokdonella , Caenimonas , Geminicoccus , and Sphingopyxis ) and PM 2.5 samples ( Cellulomonas and Rhizobacter ), while a large number of taxa significantly increased in total suspended particulate samples, such as Paracoccus , Kocuria , and Sphingomonas . Network analysis indicated that Paracoccus , Rubellimicrobium , Kocuria , and Arthrobacter were the key genera in the airborne PM samples. Overall, the findings presented here suggest that diverse airborne bacterial communities are associated with PM and provide further understanding of bacterial community structure in the atmosphere during hazy and nonhazy days. IMPORTANCE The results presented here represent an analysis of the airborne bacterial community associated with particulate matter (PM) and advance our understanding of the structural variation of these communities. We observed a shift in bacterial community composition with PM fractions but no significant difference with haze levels. This may be because the bacterial differences are obscured by high bacterial diversity in the atmosphere. However, we also observed that a few genera (such as Methylobacillus , Tumebacillus , and Desulfurispora ) increased significantly on heavy-haze days. In addition, Paracoccus , Rubellimicrobium , Kocuria , and Arthrobacter were the key genera in the airborne PM samples. Accurate and real-time techniques, such as metagenomics and metatranscriptomics, should be developed for a future survey of the relationship of airborne bacteria and haze.
    Type of Medium: Online Resource
    ISSN: 0099-2240 , 1098-5336
    URL: Article
    DOI: 10.1128/AEM.00004-18
    RVK:
    WA 15000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2018
    detail.hit.zdb_id: 223011-2
    detail.hit.zdb_id: 1478346-0
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  • 2
    Online Resource
    Online Resource
    Occurrence and Transmission of bla NDM -Carrying Enterobacteriaceae from Geese and the Surrounding Environment on a Commercial Goose Farm
    American Society for Microbiology ; 2021
    In:  Applied and Environmental Microbiology Vol. 87, No. 10 ( 2021-04-27)
    Details
    In: Applied and Environmental Microbiology, American Society for Microbiology, Vol. 87, No. 10 ( 2021-04-27)
    Abstract: We investigated the prevalence and transmission of NDM-producing Enterobacteriaceae in fecal samples of geese and environmental samples from a goose farm in southern China. The samples were cultivated on MacConkey agar plates supplemented with meropenem. Individual colonies were examined for bla NDM , and bla NDM -positive bacteria were characterized based on whole-genome sequencing (WGS) data from the Illumina and Oxford Nanopore Technologies (ONT) platforms. Of 117 samples analyzed, the carriage rates for New Delhi metallo-β-lactamase (NDM)-positive Enterobacteriaceae were 47.1, 18, and 50% in geese, inanimate environments (sewage, soil, fodder, and dust), and mouse samples, respectively. Two variants ( bla NDM-1 and bla NDM-5 , in 4 and 40 isolates, respectively) were found among 44 bla NDM -positive Enterobacteriaceae ; these variants belonged to eight species, and Escherichia coli was the most prevalent (50%). WGS analysis revealed that bla NDM coexisted with diverse antibiotic resistance genes (ARGs). Population structure analysis showed that most E. coli and Enterobacter sp. isolates were highly heterogeneous, while most Citrobacter sp. and P. stuartii isolates possessed extremely high genetic similarities. In addition, bla NDM-5 -positive ST4358/ST48 E. coli isolates were found to be clonally spread between geese and the environment and were highly genetically similar to those reported from ducks, farm environments, and humans in China. Plasmid analysis indicated that IncX3 pHNYX644-1-like ( n  = 40) and untypeable pM2-1-like plasmids ( n  = 4) mediated bla NDM spread. pM2-1-like plasmids possessed diverse ARGs, including bla NDM-1 , the arsenical and mercury resistance operons, and the maltose operon. Our findings revealed that the goose farm is a reservoir for NDM-positive Enterobacteriaceae . The bla NDM contamination of wild mice and the novel pM2-1-like plasmid described here likely adds to the risk for dissemination of bla NDM and associated resistance genes. IMPORTANCE Carbapenem-resistant bacteria, in particular NDM-producing Enterobacteriaceae , have become a great threat to global public. These bacteria have been found not only in hospital and community environments but also among food animal production chains, which are recognized as reservoirs for NDM-producing Enterobacteriaceae . However, the dissemination of NDM-producing bacteria in waterfowl farms has been less well explored. Our study demonstrates that the horizontal spread of bla NDM -carrying plasmids and the partial clonal spread of bla NDM -positive Enterobacteriaceae contribute to the widespread contamination of bla NDM in the goose farm ecosystem, including mice. Furthermore, we found a novel and transferable bla NDM-1 -carrying multidrug resistance (MDR) plasmid that possessed multiple environmental adaptation-related genes. The outcomes of this study contribute to a better understanding of the prevalence and transmission of bla NDM -carrying Enterobacteriaceae among diverse niches in the farm ecosystem.
    Type of Medium: Online Resource
    ISSN: 0099-2240 , 1098-5336
    URL: Article
    DOI: 10.1128/AEM.00087-21
    RVK:
    WA 15000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2021
    detail.hit.zdb_id: 223011-2
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  • 3
    Online Resource
    Online Resource
    Domains III and I-2α, at the Entrance of the Binding Cleft, Play an Important Role in Cold Adaptation of the Periplasmic Dipeptide-Binding Protein (DppA) from the Deep-Sea Psychrophilic Bacterium Pseudoalteromonas sp. Strain SM9913
    American Society for Microbiology ; 2010
    In:  Applied and Environmental Microbiology Vol. 76, No. 13 ( 2010-07), p. 4354-4361
    Details
    In: Applied and Environmental Microbiology, American Society for Microbiology, Vol. 76, No. 13 ( 2010-07), p. 4354-4361
    Abstract: The peptide transporter from a cold-adapted bacterium has never been reported. In the present study, the dpp operon from the psychrophilic bacterium Pseudoalteromonas sp. strain SM9913 was cloned and analyzed. The dipeptide binding protein DppA of SM9913 was overexpressed in Escherichia coli , and its cold adaptation characteristics were studied. The recombinant DppA of SM9913 ( Ps DppA) displayed the highest ligand-binding affinity at 15°C, whereas the recombinant DppA of E. coli ( Ec DppA) displayed the highest ligand-binding affinity at 35°C. Thermal and guanidium hydrochloride unfolding analyses indicated that Ps DppA has more structural instability than Ec DppA. Six domain-exchanged mutants of Ps DppA were expressed and purified. Analyses of these mutants indicated that domains III, I-2, and I-3 of Ps DppA were less stable than those from Ec DppA and that domains III and I-2 made a significant contribution to the high binding affinity of Ps DppA at low temperatures. Structural and sequence analyses suggested that the state transition-involved regions in domain III and the α part of domain I-2 are the hot spots of optimization during cold adaptation and that decreasing the side-chain size in these regions is an important strategy for the cold adaptation of Ps DppA.
    Type of Medium: Online Resource
    ISSN: 0099-2240 , 1098-5336
    URL: Article
    DOI: 10.1128/AEM.02884-09
    RVK:
    WA 15000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2010
    detail.hit.zdb_id: 223011-2
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  • 4
    Online Resource
    Online Resource
    Antibiotic Resistance Characteristics of Environmental Bacteria from an Oxytetracycline Production Wastewater Treatment Plant and the Receiving River
    American Society for Microbiology ; 2010
    In:  Applied and Environmental Microbiology Vol. 76, No. 11 ( 2010-06), p. 3444-3451
    Details
    In: Applied and Environmental Microbiology, American Society for Microbiology, Vol. 76, No. 11 ( 2010-06), p. 3444-3451
    Abstract: We characterized the bacterial populations in surface water receiving effluent from an oxytetracycline (OTC) production plant. Additional sampling sites included the receiving river water 5 km upstream and 20 km downstream from the discharge point. High levels of OTC were found in the wastewater (WW), and the antibiotic was still detectable in river water downstream (RWD), with undetectable levels in river water upstream (RWU). A total of 341 bacterial strains were isolated using nonselective media, with the majority being identified as Gammaproteobacteria . The MICs were determined for 10 antibiotics representing seven different classes of antibiotics, and the corresponding values were significantly higher for the WW and RWD isolates than for the RWU isolates. Almost all bacteria (97%) from the WW and RWD samples demonstrated multidrug-resistant (MDR) phenotypes, while in RWU samples, these were less frequent (28%). The WW and RWD isolates were analyzed for the presence of 23 tetracycline ( tet ) resistance genes. The majority of isolates (94.2% and 95.4% in WW and RWD, respectively) harbored the corresponding genes, with tet (A) being the most common (67.0%), followed by tet (W), tet (C), tet (J), tet (L), tet (D), tet (Y), and tet (K) (in the range between 21.0% and 40.6%). Class I integrons were detected in the majority of WW and RWD isolates (97.4% and 86.2%, respectively) but were not associated with the tet genes. We hypothesize that the strong selective pressure imposed by a high concentration of OTC contributes to the wide dissemination of tetracycline resistance genes and other antibiotic resistance genes, possibly through mobile genetic elements.
    Type of Medium: Online Resource
    ISSN: 0099-2240 , 1098-5336
    URL: Article
    DOI: 10.1128/AEM.02964-09
    RVK:
    WA 15000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2010
    detail.hit.zdb_id: 223011-2
    detail.hit.zdb_id: 1478346-0
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  • 5
    Online Resource
    Online Resource
    Gene Replacement for the Generation of Designed Novel Avermectin Derivatives with Enhanced Acaricidal and Nematicidal Activities
    American Society for Microbiology ; 2015
    In:  Applied and Environmental Microbiology Vol. 81, No. 16 ( 2015-08-15), p. 5326-5334
    Details
    In: Applied and Environmental Microbiology, American Society for Microbiology, Vol. 81, No. 16 ( 2015-08-15), p. 5326-5334
    Abstract: Avermectin (AVM) and ivermectin (IVM) are potent pesticides and acaricides which have been widely used during the past 30 years. As insect resistance to AVM and IVM is greatly increasing, alternatives are urgently needed. Here, we report two novel AVM derivatives, tenvermectin A (TVM A) and TVM B, which are considered a potential new generation of agricultural and veterinary drugs. The molecules of the TVMs were designed based on structure and pharmacological property comparisons among AVM, IVM, and milbemycin (MBM). To produce TVMs, a genetically engineered strain, MHJ1011, was constructed from Streptomyces avermitilis G8-17, an AVM industrial strain. In MHJ1011, the native aveA1 gene was seamlessly replaced with milA1 from Streptomyces hygroscopicus . The total titer of the two TVMs produced by MHJ1011 reached 3,400 mg/liter. Insecticidal tests proved that TVM had enhanced activities against Tetranychus cinnabarinus and Bursaphelenchus xylophilus , as desired. This study provides a typical example of exploration for novel active compounds through a new method of polyketide synthase (PKS) reassembly for gene replacement. The results of the insecticidal tests may be of use in elucidating the structure-activity relationship of AVMs and MBMs.
    Type of Medium: Online Resource
    ISSN: 0099-2240 , 1098-5336
    URL: Article
    DOI: 10.1128/AEM.01025-15
    RVK:
    WA 15000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2015
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  • 6
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    Glycine Betaine Monooxygenase, an Unusual Rieske-Type Oxygenase System, Catalyzes the Oxidative N -Demethylation of Glycine Betaine in Chromohalobacter salexigens DSM 3043
    American Society for Microbiology ; 2018
    In:  Applied and Environmental Microbiology Vol. 84, No. 13 ( 2018-07)
    Details
    In: Applied and Environmental Microbiology, American Society for Microbiology, Vol. 84, No. 13 ( 2018-07)
    Abstract: Although some bacteria, including Chromohalobacter salexigens DSM 3043, can use glycine betaine (GB) as a sole source of carbon and energy, little information is available about the genes and their encoded proteins involved in the initial step of the GB degradation pathway. In the present study, the results of conserved domain analysis, construction of in-frame deletion mutants, and an in vivo functional complementation assay suggested that the open reading frames Csal_1004 and Csal_1005, designated bmoA and bmoB , respectively, may act as the terminal oxygenase and the ferredoxin reductase genes in a novel Rieske-type oxygenase system to convert GB to dimethylglycine in C. salexigens DSM 3043. To further verify their function, BmoA and BmoB were heterologously overexpressed in Escherichia coli , and 13 C nuclear magnetic resonance analysis revealed that dimethylglycine was accumulated in E. coli BL21(DE3) expressing BmoAB or BmoA. In addition, His-tagged BmoA and BmoB were individually purified to electrophoretic homogeneity and estimated to be a homotrimer and a monomer, respectively. In vitro biochemical analysis indicated that BmoB is an NADH-dependent flavin reductase with one noncovalently bound flavin adenine dinucleotide (FAD) as its prosthetic group. In the presence of BmoB, NADH, and flavin, BmoA could aerobically degrade GB to dimethylglycine with the concomitant production of formaldehyde. BmoA exhibited strict substrate specificity for GB, and its demethylation activity was stimulated by Fe 2+ . Phylogenetic analysis showed that BmoA belongs to group V of the Rieske nonheme iron oxygenase (RO) family, and all the members in this group were able to use quaternary ammonium compounds as substrates. IMPORTANCE GB is widely distributed in nature. In addition to being accumulated intracellularly as a compatible solute to deal with osmotic stress, it can be utilized by many bacteria as a source of carbon and energy. However, very limited knowledge is presently available about the molecular and biochemical mechanisms for the initial step of the aerobic GB degradation pathway in bacteria. Here, we report the molecular and biochemical characterization of a novel two-component Rieske-type monooxygenase system, GB monooxygenase (BMO), which is responsible for oxidative demethylation of GB to dimethylglycine in C. salexigens DSM 3043. The results gained in this study extend our knowledge on the catalytic reaction of microbial GB degradation to dimethylglycine.
    Type of Medium: Online Resource
    ISSN: 0099-2240 , 1098-5336
    URL: Article
    DOI: 10.1128/AEM.00377-18
    RVK:
    WA 15000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2018
    detail.hit.zdb_id: 223011-2
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  • 7
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    Mechanistic Insights into Substrate Recognition and Catalysis of a New Ulvan Lyase of Polysaccharide Lyase Family 24
    American Society for Microbiology ; 2021
    In:  Applied and Environmental Microbiology Vol. 87, No. 12 ( 2021-05-26)
    Details
    In: Applied and Environmental Microbiology, American Society for Microbiology, Vol. 87, No. 12 ( 2021-05-26)
    Abstract: Ulvan is an important marine polysaccharide. Bacterial ulvan lyases play important roles in ulvan degradation and marine carbon cycling. Until now, only a small number of ulvan lyases have been characterized. Here, a new ulvan lyase, Uly1, belonging to polysaccharide lyase family 24 (PL24) from the marine bacterium Catenovulum maritimum , is characterized. The optimal temperature and pH for Uly1 to degrade ulvan are 40°C and pH 9.0, respectively. Uly1 degrades ulvan polysaccharides in the endolytic manner, mainly producing ΔRha3S, consisting of an unsaturated 4-deoxy- l - threo -hex-4-enopyranosiduronic acid and a 3-O-sulfated α- l -rhamnose. The structure of Uly1 was resolved at a 2.10-Å resolution. Uly1 adopts a seven-bladed β-propeller architecture. Structural and site-directed mutagenesis analyses indicate that four highly conserved residues, H128, H149, Y223, and R239, are essential for catalysis. H128 functions as both the catalytic acid and base, H149 and R239 function as the neutralizers, and Y223 plays a supporting role in catalysis. Structural comparison and sequence alignment suggest that Uly1 and many other PL24 enzymes may directly bind the substrate near the catalytic residues for catalysis, different from the PL24 ulvan lyase LOR_107, which adopts a two-stage substrate binding process. This study provides new insights into ulvan lyases and ulvan degradation. IMPORTANCE Ulvan is a major cell wall component of green algae of the genus Ulva. Many marine heterotrophic bacteria can produce extracellular ulvan lyases to degrade ulvan for a carbon nutrient. In addition, ulvan has a range of physiological bioactivities based on its specific chemical structure. Ulvan lyase thus plays an important role in marine carbon cycling and has great potential in biotechnological applications. However, only a small number of ulvan lyases have been characterized over the past 10 years. Here, based on biochemical and structural analyses, a new ulvan lyase of polysaccharide lyase family 24 is characterized, and its substrate recognition and catalytic mechanisms are revealed. Moreover, a new substrate binding process adopted by PL24 ulvan lyases is proposed. This study offers a better understanding of bacterial ulvan lyases and is helpful for studying the application potentials of ulvan lyases.
    Type of Medium: Online Resource
    ISSN: 0099-2240 , 1098-5336
    URL: Article
    DOI: 10.1128/AEM.00412-21
    RVK:
    WA 15000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2021
    detail.hit.zdb_id: 223011-2
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  • 8
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    High Diversity of Extended-Spectrum Beta-Lactamase-Producing Bacteria in an Urban River Sediment Habitat
    American Society for Microbiology ; 2010
    In:  Applied and Environmental Microbiology Vol. 76, No. 17 ( 2010-09), p. 5972-5976
    Details
    In: Applied and Environmental Microbiology, American Society for Microbiology, Vol. 76, No. 17 ( 2010-09), p. 5972-5976
    Abstract: Antibiotic-resistant bacteria (ARB) have been surveyed widely in water bodies, but few studies have determined the diversity of ARB in sediment, which is the most taxon-abundant habitat in aquatic environments. We isolated 56 extended-spectrum β-lactamase (ESBL)-producing bacteria from a single sediment sample taken from an urban river in China. All strains were confirmed for ESBL-producing capability by both the clavulanic acid combination disc method and MIC determination. Of the isolated strains, 39 were classified as Enterobacteriaceae (consisting of the genera Escherichia , Klebsiella , Serratia , and Aeromonas ) by 16S rRNA gene sequencing and biochemical analysis. The present study identifies, for the first time, ESBL-producing strains from the families Brucellaceae and Moraxellaceae . The bla CTX-M gene was the most dominant of the ESBL genes (45 strains), while the bla TEM gene was the second-most dominant (22 strains). A total of five types of bla CTX-M fragments were identified, with both known and novel sequences. A library of bla CTX-M cloned from the sediment DNA showed an even higher diversity of bla CTX-M sequences. The discovery of highly diverse ESBL-producing bacteria and ESBL genes, particularly bla CTX , in urban river sediment raises alarms for potential dissemination of ARB in communities through river environments.
    Type of Medium: Online Resource
    ISSN: 0099-2240 , 1098-5336
    URL: Article
    DOI: 10.1128/AEM.00711-10
    RVK:
    WA 15000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2010
    detail.hit.zdb_id: 223011-2
    detail.hit.zdb_id: 1478346-0
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  • 9
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    Microbial Diversity in Water and Sediment of Lake Chaka, an Athalassohaline Lake in Northwestern China
    American Society for Microbiology ; 2006
    In:  Applied and Environmental Microbiology Vol. 72, No. 11 ( 2006-11), p. 7430-7430
    Details
    In: Applied and Environmental Microbiology, American Society for Microbiology, Vol. 72, No. 11 ( 2006-11), p. 7430-7430
    Type of Medium: Online Resource
    ISSN: 0099-2240 , 1098-5336
    URL: Article
    DOI: 10.1128/AEM.02230-06
    RVK:
    WA 15000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2006
    detail.hit.zdb_id: 223011-2
    detail.hit.zdb_id: 1478346-0
    SSG: 12
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  • 10
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    Microbial Diversity in Water and Sediment of Lake Chaka, an Athalassohaline Lake in Northwestern China
    American Society for Microbiology ; 2006
    In:  Applied and Environmental Microbiology Vol. 72, No. 6 ( 2006-06), p. 3832-3845
    Details
    In: Applied and Environmental Microbiology, American Society for Microbiology, Vol. 72, No. 6 ( 2006-06), p. 3832-3845
    Abstract: We employed culture-dependent and -independent techniques to study microbial diversity in Lake Chaka, a unique hypersaline lake (32.5% salinity) in northwest China. It is situated at 3,214 m above sea level in a dry climate. The average water depth is 2 to 3 cm. Halophilic isolates were obtained from the lake water, and halotolerant isolates were obtained from the shallow sediment. The isolates exhibited resistance to UV and gamma radiation. Microbial abundance in the sediments ranged from 10 8 cells/g at the water-sediment interface to 10 7 cells/g at a sediment depth of 42 cm. A major change in the bacterial community composition was observed across the interface. In the lake water, clone sequences affiliated with the Bacteroidetes were the most abundant, whereas in the sediments, sequences related to low G+C gram-positive bacteria were predominant. A similar change was also present in the archaeal community. While all archaeal clone sequences in the lake water belonged to the Halobacteriales , the majority of the sequences in the sediments were related to those previously obtained from methanogenic soils and sediments. The observed changes in the microbial community structure across the water-sediment interface were correlated with a decrease in salinity from the lake water (32.5%) to the sediments (approximately 4%). Across the interface, the redox state also changed from oxic to anoxic and may also have contributed to the observed shift in the microbial community.
    Type of Medium: Online Resource
    ISSN: 0099-2240 , 1098-5336
    URL: Article
    DOI: 10.1128/AEM.02869-05
    RVK:
    WA 15000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2006
    detail.hit.zdb_id: 223011-2
    detail.hit.zdb_id: 1478346-0
    SSG: 12
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