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- Volume 50, 1996
Annual Review of Microbiology - Volume 50, 1996
Volume 50, 1996
- Preface
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- Review Articles
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MY ROLE IN THE DISCOVERY AND CLASSIFICATION OF THE ENTEROVIRUSES
Vol. 50 (1996), pp. 1–24More LessThe enteroviruses constitute one of the genera of the picornavirus family. The genus includes the polioviruses, the coxsackieviruses, and the echoviruses of humans, plus a number of enteroviruses of lower animals (e.g. monkeys, cattle, pigs, mice). Over 100 serotypes are recognized, of which the first to be discovered were the polioviruses. It was my good fortune to have been a scientist during the golden age of virology, when new techniques were being introduced into the field. These often led to the discovery of new viruses. This article details the isolation of the enteroviruses, their recognition as a separate genus of Picornaviridae, and my role in the process. Poliovirus, the most hazardous of the group, is almost gone from the world, but the other enteroviruses will be with us for some time. Several members of the Committee dealing with these agents—Enders, Sabin, Dalldorf, Syverton—have passed on, but the work of this Committee to which I was privileged to contribute will live long.
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MOLECULAR BIOLOGY OF MYCOPLASMAS
Vol. 50 (1996), pp. 25–57More LessAlthough mycoplasmas lack cell walls, they are in many respects similar to the gram-positive bacteria with which they share a common ancestor. The molecular biology of mycoplasmas is intriguing because the chromosome is uniquely small (<600 kb in some species) and extremely A-T rich (as high as 75 mol% in some species). Perhaps to accommodate DNA with a lower G + C content, most mycoplasmas do not have the “universal” genetic code. In these species, TGA is not a stop codon; instead it encodes tryptophan at a frequency 10 times greater than TGG, the usual codon for this amino acid. Because of the presence of TGA codons, the translation of mycoplasmal proteins terminates prematurely when cloned genes are expressed in other eubacteria, such as Escherichia coli. Many mycoplasmas possess strikingly dynamic chromosomes in which high-frequency changes result from errors in DNA repair or replication and from highly active recombination systems. Often, high-frequency changes in the mycoplasmal chromosome are associated with antigenic and phase variation, which regulate the production of factors critical to disease pathogenesis.
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LIVE ATTENUATED VARICELLA VACCINE
Vol. 50 (1996), pp. 59–100More LessVaricella-zoster virus (VZV) is a ubiquitous human pathogen that causes varicella, commonly called chicken pox; establishes latency; and reactivates as herpes zoster, referred to as shingles. A live attenuated varicella vaccine, derived from the Oka strain of VZV has clinical efficacy for the prevention of varicella. The vaccine induces persistent immunity to VZV in healthy children and adults. Immunization against VZV also has the potential to lower the risk of reactivation of latent virus. The varicella vaccine may eventually reduce or eliminate herpes zoster, which is a serious problem for elderly and immunocompromised individuals.
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OSMOADAPTATION BY RHIZOSPHERE BACTERIA
Vol. 50 (1996), pp. 101–136More LessThe osmolality of rhizosphere soil water is expected to be elevated in relation to bulk-soil water osmolality as a result of the exclusion of solutes by plant roots during water uptake, the release of plant root exudates, and the production of exopolymers by plant roots and rhizobacteria. In contrast, the osmolality of water within highly hydrated bulk soil is low (less than 50 Osm/kg); thus the ability to adapt to elevated osmolality is likely to be important for successful rhizosphere colonization by rhizobacteria. The present review focuses on the osmoadaptive responses of three gram-negative rhizobacterial genera: Rhizobium, Azospirillum, and Pseudomonas. Specifically, we examine the compatible solutes and osmoprotectants utilized by various species within these genera. The adaptation of rhizobacteria to hypoosmotic environments is also examined in the present review. In particular, we focus on the biosynthesis and accumulation of periplasmic glucans by rhizobacteria. Finally, the relationship between rhizobacterial osmoadaptation and selected plant-microbe interactions is considered.
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COBALAMIN (COENZYME B12): Synthesis and Biological Significance
JR Roth, JG Lawrence, and TA BobikVol. 50 (1996), pp. 137–181More LessThis review examines deoxyadenosylcobalamin (Ado-B12) biosynthesis, transport, use, and uneven distribution among living forms. We describe how genetic analysis of enteric bacteria has contributed to these issues. Two pathways for corrin ring formation have been found–an aerobic pathway (in P. denitrificans) and an anaerobic pathway (in P. shermanii and S. typhimurium)–that differ in the point of cobalt insertion. Analysis of B12 transport in E. coli reveals two systems: one (with two proteins) for the outer membrane, and one (with three proteins) for the inner membrane. To account for the uneven distribution of B12 in living forms, we suggest that the B12 synthetic pathway may have evolved to allow anaerobic fermentation of small molecules in the absence of an external electron acceptor. Later, evolution of the pathway produced siroheme, (allowing use of inorganic electron acceptors), chlorophyll (O2 production), and heme (aerobic respiration). As oxygen became a larger part of the atmosphere, many organisms lost fermentative functions and retained dependence on newer, B12 functions that did not involve fermentation. Paradoxically, Salmonella spp. synthesize B12 only anaerobically but can use B12 (for degradation of ethanolamine and propanediol) only with oxygen. Genetic analysis of the operons for these degradative functions indicate that anaerobic degradation is important. Recent results suggest that B12 can be synthesized and used during anaerobic respiration using tetrathionate (but not nitrate or fumarate) as an electron acceptor. The branch of enteric taxa from which Salmonella spp. and E. coli evolved appears to have lost the ability to synthesize B12 and the ability to use it in propanediol and glycerol degradation. Salmonella spp., but not E. coli, have acquired by horizontal transfer the ability to synthesize B12 and degrade propanediol. The acquired ability to degrade propanediol provides the selective force that maintains B12 synthesis in this group.
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MICROBIAL HYDROLYSIS OF POLYSACCHARIDES
Vol. 50 (1996), pp. 183–212More LessMicroorganisms are efficient degraders of starch, chitin, and the polysaccharides in plant cell walls. Attempts to purify hydrolases led to the realization that a microorganism may produce a multiplicity of enzymes, referred to as a system, for the efficient utilization of a polysaccharide. In order to fully characterize a particular enzyme, it must be obtained free of the other components of a system. Quite often, this proves to be very difficult because of the complexity of a system. This realization led to the cloning of the genes encoding them as an approach to eliminating other components. More than 400 such genes have been cloned and sequenced, and the enzymes they encode have been grouped into more than 50 families of related amino acid sequences. The enzyme systems revealed in this manner are complex on two quite different levels. First, many of the individual enzymes are complex, as they are modular proteins comprising one or more catalytic domains linked to ancillary domains that often include one or more substrate-binding domains. Second, the systems are complex, comprising from a few to 20 or more enzymes, all of which hydrolyze a particular substrate. Systems for the hydrolysis of plant cell walls usually contain more components than systems for the hydrolysis of starch and chitin because the cell walls contain several polysaccharides. In general, the systems produced by different microorganisms for the hydrolysis of a particular polysaccharide comprise similar enzymes from the same families.
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REGULATION OF PECTINOLYSIS IN ERWINIA CHRYSANTHEMI
Vol. 50 (1996), pp. 213–257More LessErwinia chrysanthemi is an enterobacterium that causes various plant diseases. Its pathogenicity results from the secretion of pectinolytic enzymes responsible for the disorganization of the plant cell wall. The E. chrysanthemi strain 3937 produces two pectin methylesterases, at least seven pectate lyases, a polygalacturonase, and a pectin lyase. The extracellular degradation of the pectin leads to the formation of oligogalacturonides that are catabolized through an intracellular pathway. The pectinase genes are expressed from independent cistrons, and their transcription is favored by environmental conditions such as presence of pectin and plant extracts, stationary growth phase, low temperature, oxygen or iron limitation, and so on. Moreover, transcription of the pectin lyase gene responds to DNA-damaging agents. The differential expressions of individual pectinase genes presumably reflect their role during plant infection. The regulation of pel genes requires several regulatory systems, including the KdgR repressor, which mediates the induction of all the pectinolysis genes in the presence of pectin catabolites. KdgR also controls the genes necessary for pectinase secretion and other pectin-inducible genes not yet characterized. PecS, a cytoplasmic protein homologous to other transcriptional regulators, can bind in vitro to the regulatory regions of pectinase and cellulase genes. The PecT protein, a member of the LysR family of transcriptional regulators, represses the expression of some pectinase genes and also affects other metabolic pathways of the bacteria. Other proteins involved in global regulations, such as CRP or HNS, can bind to the regulatory regions of the pectinase genes and affect their transcription.
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THE PATHOGENESIS OF TUBERCULOSIS
Vol. 50 (1996), pp. 259–284More LessTuberculosis patients relapse if treatment is not continued for 6 months, because chemotherapy fails to convert the patients' response from the necrotizing pattern characteristic of disease (Koch phenomenon) to the nonnecrotizing bactericidal function required for optimal immunity. We need to understand the nature of these two immunological states and how to convert one to the other. Studies in mice and humans implicate differences in cytokine profiles and in metabolism of adrenal steroids. Either enhanced susceptibility or protection can be evoked in mice with appropriate doses of a killed environmental saprophyte. This emphasizes the importance of shared epitopes and may explain the geographically variable efficacy of Mycobacterium bovis Bacillus Calmette Guérin vaccination. Unlike soluble antigens of M. tuberculosis itself, which tend to evoke necrosis, the shared mycobacterial epitopes evoke little skin-test reactivity in patients. Preparations of these epitopes show potential as immunotherapeutic agents to convert the response from necrotic to bactericidal mode.
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THE BIOCHEMISTRY AND GENETICS OF CAPSULAR POLYSACCHARIDE PRODUCTION IN BACTERIA
Vol. 50 (1996), pp. 285–315More LessBacterial polysaccharides are usually associated with the outer surface of the bacterium. They can form an amorphous layer of extracellular polysaccharide (EPS) surrounding the cell that may be further organized into a distinct structure termed a capsule. Additional polysaccharide molecules such as lipopolysaccharide (LPS) or lipooligosaccharide (LOS) may also decorate the cell surface. Polysaccharide capsules may mediate a number of biological processes, including invasive infections of human beings. Discussed here are the genetics and biochemistry of selected bacterial capsular polysaccharides and the basis of capsule diversity but not the genetics and biochemistry of LPS biosynthesis (for reviews see 100, 140).
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WHAT SIZE SHOULD A BACTERIUM BE? A Question of Scale
Vol. 50 (1996), pp. 317–348More LessThere are living prokaryotes (Bacteria and Archaea) that have cell sizes that range from 0.02–400 μm3. Over this tremendous range, various abilities to cope with the environment are needed. This review attempts to formulate some of the problems and some of the solutions. The smallest size for a free-living organism is suggested to be largely set by the catalytic efficiency of enzymes and protein synthetic machinery. Because of fluctuations in the environment, cells must maintain machinery to cope with various catastrophes; these mechanisms increase the minimum size of the cell. On the other hand, the largest cell is reasonably assumed to be limited by the ability of diffusion to bring nutrients to the appropriate part of the cell and to dispose of waste products. To explore the limitation imposed by diffusion, analysis is developed of diffusion processes through stirred and unstirred media, diffusion through media that contains obstacles, and the effect of size and shape.
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THE ROLE OF NUCLEIC ACID AMPLIFICATION AND DETECTION IN THE CLINICAL MICROBIOLOGY LABORATORY1
Vol. 50 (1996), pp. 349–373More LessClinical microbiology is in the midst of a new era. Methodology that is based on nucleic acid detection has slowly appeared in the diagnostic laboratory, and is revolutionizing our ability to assist physicians in the diagnosis and management of patients suffering from infectious diseases. Much like the introduction of immunoassays built around hybridoma technology in the 1980s, considerable doubt and promise exist hand in hand in the 1990s. Conventional testing that is technically straight forward, informative, and timely will always be a part of clinical microbiology; however, considerable room for improvement exists with organisms/diseases for which laboratory methods are limited. Nucleic acid methodology will have its greatest and long-awaited impact in this arena.
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BIOSYNTHESIS OF HALOGENATED METABOLITES BY BACTERIA
Vol. 50 (1996), pp. 375–399More LessHalogenated metabolites, originally thought to be infrequent in nature, are actually nothing unusual at all, and are produced by many different organisms, including bacteria. Whereas marine bacteria usually produce brominated compounds, terrestrial bacteria preferentially synthesize chlorometabolites, but fluoro- and iodometabolites can also be found. Haloperoxidases, enzymes capable of catalyzing the formation of carbon halogen bonds in the presence of hydrogen peroxide and halide ions (Cl−, Br− and I−) have been isolated and characterized from different bacteria. These enzymes turned out to be very unspecific and are obviously not the type of halogenating enzymes responsible for the formation of halometabolites in bacteria. A yet-unknown type of halogenating enzyme having both substrate and regio-specificity must be involved in the biosynthesis of halogenated compounds.
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TOWARDS A UNIFIED EVOLUTIONARY GENETICS OF MICROORGANISMS
Vol. 50 (1996), pp. 401–429More LessI propose here that evolutionary genetics, apart from improving our basic knowledge of the taxonomy and evolution of microbes (either eukaryotes or prokaryotes), can also greatly contribute to applied research in microbiology. Evolutionary genetics provides convenient guidelines for better interpreting genetic and molecular data dealing with microorganisms. The three main potential applications of evolutionary genetics in microbiology are (a) epidemiological follow-up (with the necessity of evaluating the stability off microbial genotypes over space and time); (b) taxonomy in the broad sense (better definition and sharper delimitation of preesently described taxa, research of hidden genetic subdivisions); and ( c) evaluation of the impact of the genetic diversity of microbes on their relevant properties (pathogenicity, resistance to drugs, etc). At present, two main kinds of population structure can be distinguished in natural microbial populations: (a) species that are not subdivided into discrete phylogenetic lineages (panmictic species or basically sexual species witth occasional bouts of short-term clonality fall into this category); (b) species that are strongly subdivided by either cryptic speciation or clonal evolution.
Improvements in available statistical methods are required to refine these distinctions and to better quantify the actual impact of gene exchange in natural microbial populations. Moreover, a codified selection of markers with appropriate molecular clocks (in other words: adapted levels of resolution) is sorely needed to answer distinct questions that address different scales of time and space: experimental, epidemic, and evolutionary. The problems raised by natural genetic diversity are very similar for all microbial species, in terms of both basic and applied science. Despite this fact, a regrettable compartmentalization among specialists has hampered progress in this field. I propose a synthetic approach, relying on the statistical improvements and technical standardizations called for above, to settle a unified evolutionary genetics of microorganisms, valid whatever the species studied, whether eukaryotic (parasitic protozoa and fungi) or prokaryotic (bacteria). Apart from benefits for basic evolutionary research, the anticipated payoff from this synthetic approach is to render routine and commonplace the use of microbial evolutionary genetics in the fields of epidemiology, medicine, and agronomy.
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MICROALGAL METABOLITES: A New Perspective
Vol. 50 (1996), pp. 431–465More LessOccurrence of secondary metabolites in microalgae (protoctista) is discussed with respect to the phylogenic or taxonomic relationships of organisms. Biosynthetic mechanisms of certain metabolites such as paralytic shellfish poisoning toxins and polyether toxins are also discussed, and genetic aspects of the secondary metabolite production as well.
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GENETICALLY ENGINEERED SYNTHESIS OF NATURAL PRODUCTS: From Alkaloids to Corrins
Vol. 50 (1996), pp. 467–490More LessBecause many natural products are of biological and medicinal importance, methods are continually being sought for studying their biosynthetic pathways, which may eventually result in increased production and the generation of novel compounds. Advances in genetic engineering have enabled the homologous or heterologous expression of many natural product biosynthetic genes from divergent sources, resulting in a supply of enzymes not readily available by isolation from the producing organism. Mixing and matching of these enzymes in cell-free reactions can provide information, not available by any other means, about enzyme mechanisms, pathway intermediates, and possible variations in the structure of the final product.
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BREAKING AND ENTERING: Host Penetration by the Fungal Rice Blast Pathogen Magnaporthe grisea
Vol. 50 (1996), pp. 491–512More Less▪ AbstractFungal plant pathogens have evolved diverse mechanisms for penetrating into host plant tissue, ranging from entry through natural plant openings to various mechanisms of direct penetration through the outer surface. The filamentous fungus Magnaporthe grisea can cause disease on many species of the grass (Poaceae) family. The disease on rice, Rice Blast, is of enormous economic importance and biological interest. The mechanism used by this pathogen for breaching the formidable host surface barriers has been studied cytologically and genetically as a model for plant pathology, and represents a remarkably sophisticated achievment of nature. The single-celled appressorium of M. grisea acts as a vessel for the generation and application of perhaps the highest turgor pressures known. The fungus requires and utilizes melanin-derived, osmotically generated pressures estimated at 80 bars to drive an actin-rich cellular protuberance through the surface of a rice leaf or plastic coverslip.
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MECHANISMS OF ADHESION BY ORAL BACTERIA
Vol. 50 (1996), pp. 513–552More LessAdherence to a surface is a key element for colonization of the human oral cavity by the more than 500 bacterial taxa recorded from oral samples. Three surfaces are available: teeth, epithelial mucosa, and the nascent surface created as each new bacterial cell binds to existing dental plaque. Oral bacteria exhibit specificity for their respective colonization sites. Such specificity is directed by adhesin-receptor cognate pairs on genetically distinct cells. Colonization is successful when adherent cells grow and metabolically participate in the oral bacterial community. The potential roles of adherence-relevant molecules are discussed in the context of the dynamic nature of the oral econiche.
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THE β-KETOADIPATE PATHWAY AND THE BIOLOGY OF SELF-IDENTITY
Vol. 50 (1996), pp. 553–590More LessThe β-ketoadipate pathway is a chromosomally encoded convergent pathway for aromatic compound degradation that is widely distributed in soil bacteria and fungi. One branch converts protocatechuate, derived from phenolic compounds including p-cresol, 4-hydroxybenzoate and numerous lignin monomers, to β-ketoadipate. The other branch converts catechol, generated from various aromatic hydrocarbons, amino aromatics, and lignin monomers, also to β-ketoadipate. Two additional steps accomplish the conversion of β-ketoadipate to tricarboxylic acid cycle intermediates. Enzyme studies and amino acid sequence data indicate that the pathway is highly conserved in diverse bacteria, including Pseudomonas putida, Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Rhodococcus erythropolis, and many others. The catechol branch of the β-ketoadipate pathway appears to be the evolutionary precursor for portions of the plasmid-borne ortho-pathways for chlorocatechol degradation. However, accumulating evidence points to an independent and convergent evolutionary origin for the eukaryotic β-ketoadipate pathway. In the face of enzyme conservation, the β-ketoadipate pathway exhibits many permutations in different bacterial groups with respect to enzyme distribution (isozymes, points of branch convergence), regulation (inducing metabolites, regulatory proteins), and gene organization. Diversity is also evident in the behavioral responses of different bacteria to β-ketoadipate pathway-associated aromatic compounds. The presence and versatility of transport systems encoded by β-ketoadipate pathway regulons is just beginning to be explored in various microbial groups. It appears that in the course of evolution, natural selection has caused the β-ketoadipate pathway to assume a characteristic set of features or identity in different bacteria. Presumably such identities have been shaped to optimally serve the diverse lifestyles of bacteria.
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LESSONS FROM A COOPERATIVE, BACTERIAL-ANIMAL ASSOCIATION: The Vibrio fischeri–Euprymna scolopes Light Organ Symbiosis
Vol. 50 (1996), pp. 591–624More LessAlthough the study of microbe-host interactions has been traditionally dominated by an interest in pathogenic associations, there is an increasing awareness of the importance of cooperative symbiotic interactions in the biology of many bacteria and their animal and plant hosts. This review examines a model system for the study of such symbioses, the light organ association between the bobtail squid Euprymna scolopes and the marine luminous bacterium Vibrio fischeri. Specifically, the initiation, establishment, and persistence of the benign bacterial infection of the juvenile host light organ are described, as are efforts to understand the mechanisms underlying this specific colonization program. Using molecular genetic techniques, mutant strains of V. fischeri have been constructed that are defective at specific stages of the development of the association. Some of the lessons that these mutants have begun to teach us about the complex and long-term nature of this cooperative venture are summarized.
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Previous Volumes
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Volume 78 (2024)
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Volume 77 (2023)
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Volume 76 (2022)
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Volume 75 (2021)
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Volume 74 (2020)
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Volume 73 (2019)
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Volume 72 (2018)
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Volume 71 (2017)
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Volume 70 (2016)
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Volume 69 (2015)
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Volume 68 (2014)
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Volume 67 (2013)
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Volume 66 (2012)
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Volume 65 (2011)
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Volume 64 (2010)
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Volume 63 (2009)
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Volume 62 (2008)
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Volume 61 (2007)
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Volume 60 (2006)
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Volume 59 (2005)
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Volume 58 (2004)
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Volume 57 (2003)
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Volume 56 (2002)
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Volume 55 (2001)
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Volume 54 (2000)
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Volume 53 (1999)
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Volume 52 (1998)
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Volume 51 (1997)
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Volume 50 (1996)
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Volume 49 (1995)
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Volume 48 (1994)
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Volume 47 (1993)
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Volume 46 (1992)
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Volume 45 (1991)
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Volume 44 (1990)
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Volume 43 (1989)
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Volume 42 (1988)
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Volume 41 (1987)
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Volume 40 (1986)
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Volume 39 (1985)
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Volume 38 (1984)
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Volume 37 (1983)
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Volume 36 (1982)
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Volume 35 (1981)
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Volume 34 (1980)
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Volume 33 (1979)
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Volume 32 (1978)
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Volume 31 (1977)
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Volume 30 (1976)
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Volume 29 (1975)
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Volume 28 (1974)
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Volume 27 (1973)
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Volume 26 (1972)
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Volume 25 (1971)
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Volume 24 (1970)
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Volume 23 (1969)
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Volume 22 (1968)
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Volume 21 (1967)
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Volume 20 (1966)
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Volume 19 (1965)
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Volume 18 (1964)
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Volume 17 (1963)
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Volume 16 (1962)
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Volume 15 (1961)
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Volume 14 (1960)
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Volume 13 (1959)
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Volume 12 (1958)
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Volume 11 (1957)
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Volume 10 (1956)
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Volume 9 (1955)
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Volume 8 (1954)
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Volume 7 (1953)
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Volume 6 (1952)
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Volume 5 (1951)
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Volume 4 (1950)
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Volume 3 (1949)
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Volume 2 (1948)
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Volume 1 (1947)
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Volume 0 (1932)