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Annual Review of Plant Biology - Volume 56, 2005
Volume 56, 2005
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PHYTOREMEDIATION
Vol. 56 (2005), pp. 15–39More LessPhytoremediation
the use of plants and their associated microbes for environmental cleanup , the use of plants and their associated microbes for environmental cleanup, has gained acceptance in the past 10 years as a cost-effective, noninvasive alternative or complementary technology for engineering-based remediation methods. Plants can be used for pollutant stabilization, extraction, degradation, or volatilization. These different phytoremediation technologies are reviewed here, including their applicability for various organic and inorganic pollutants, and most suitable plant species. To further enhance the efficiency of phytoremediation, there is a need for better knowledge of the processes that affect pollutant availability, rhizosphere processes, pollutant uptake, translocation, chelation, degradation, and volatilization. For each of these processes I review what is known so far for inorganic and organic pollutants, the remaining gaps in our knowledge, and the practical implications for designing phytoremediation strategies. Transgenic approaches to enhance these processes are also reviewed and discussed.
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CALCIUM OXALATE IN PLANTS: Formation and Function
Vol. 56 (2005), pp. 41–71More LessCalcium oxalate
a highly insoluble crystalline salt of oxalic acid and calcium (CaOx) crystals are distributed among all taxonomic levels of photosynthetic organisms from small algae to angiosperms and giant gymnosperms. Accumulation of crystals by these organisms can be substantial. Major functions of CaOx crystal formation in plants include high-capacity calcium (Ca) regulation and protection against herbivory. Ultrastructural and developmental analyses have demonstrated that this biomineralization process is not a simple random physical-chemical precipitation of endogenously synthesized oxalic acida strong and the simplest dicarboxylic acid, often thought of as a toxin or end product of metabolism, but which is also synthesized when calcium oxalate crystals are induced to form in plants and environmentally derived Ca. Instead, crystals are formed in specific shapes and sizes. Genetic regulation of CaOx formation is indicated by constancy of crystal morphology within species, cell specialization, and the remarkable coordination of crystal growth and cell expansion. Using a variety of approaches, researchers have begun to unravel the exquisite control mechanisms exerted by cells specialized for CaOx formation that include the machinery for uptake and accumulation of Ca, oxalic acid biosynthetic pathways, and regulation of crystal growth.
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STARCH DEGRADATION
Vol. 56 (2005), pp. 73–98More LessRecent research reveals that starch degradation in Arabidopsis leaves at night is significantly different from the “textbook” version of this process. Although parts of the pathway are now understood, other parts remain to be discovered. Glucans derived from starch granules are hydrolyzed via β-amylase to maltose, which is exported from the chloroplast. In the cytosol maltose is the substrate for a transglucosylation reaction, producing glucose and a glucosylated acceptor molecule. The enzyme that attacks the starch granule to release glucans is not known, nor is the nature of the cytosolic acceptor molecule. An Arabidopsis-type pathway may operate in leaves of other species, and in nonphotosynthetic organs that accumulate starch transiently. However, in starch-storing organs such as cereal endosperms and legume seeds, the process differs from that in Arabidopsis and may more closely resemble the textbook pathway. We discuss the differences in relation to the biology of each system.
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CO2 CONCENTRATING MECHANISMS IN ALGAE: Mechanisms, Environmental Modulation, and Evolution
Vol. 56 (2005), pp. 99–131More LessThe evolution of organisms capable of oxygenic photosynthesis paralleled a long-term reduction in atmospheric CO2 and the increase in O2. Consequently, the competition between O2 and CO2 for the active sites of RUBISCO
ribulose bisphosphate carboxylase/oxygenase became more and more restrictive to the rate of photosynthesis. In coping with this situation, many algae and some higher plants acquired mechanisms that use energy to increase the CO2 concentrations (CO2 concentrating mechanisms, CCMsCO2 concentrating mechanism ) in the proximity of RUBISCO. A number of CCM variants are now found among the different groups of algae. Modulating the CCMs may be crucial in the energetic and nutritional budgets of a cell, and a multitude of environmental factors can exert regulatory effects on the expression of the CCM components. We discuss the diversity of CCMs, their evolutionary origins, and the role of the environment in CCM modulation.
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SOLUTE TRANSPORTERS OF THE PLASTID ENVELOPE MEMBRANE
Vol. 56 (2005), pp. 133–164More LessPlastids
semi-autonomous, membrane-bound organelles of plant cells that carry out a large number of biosynthetic and other functions such as photosynthesis (chloroplasts), ammonia and sulfur assimilation, and starch storage (amyloplasts) are metabolically extraordinarily active and versatile organelles that are found in all plant cells with the exception of angiosperm pollen grains. Many of the plastid-localized biochemical pathways depend on precursors from the cytosol and, in turn, many cytosolic pathways depend on the supply of precursor molecules from the plastid stroma. Hence, a massive traffic of metabolites occurs across the permeability barrier between plastids and cytosol that is called the plastid envelope membrane. Many of the known plastid envelope solute transportersintegral membrane proteins that catalyze the transport of solutes across biological lipid-bilayer membranes have been identified by biochemical purification and peptide sequencing. This approach is of limited use for less abundant proteins and for proteins of plastid subtypes that are difficult to isolate in preparative amounts. Hence, the majority of plastid envelope membrane transporters are not yet identified at the molecular level. The availability of fully sequenced plant genomes, the progress in bioinformaticsresearch, development, or application of computational tools and approaches to explore biological data such as genome sequences or proteomics data to predict membrane transporters localized in plastids, and the development of highly sensitive proteomicssystematic, comprehensive analysis of the full set of proteins (the proteome) in an organism, a specific cell or tissue, or a cellular fraction such as internal membrane systems techniques open new avenues toward identifying additional, to date unknown, plastid envelope membrane transporters.
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ABSCISIC ACID BIOSYNTHESIS AND CATABOLISM
Vol. 56 (2005), pp. 165–185More LessThe level of abscisic acid (ABA
abscisic acid ) in any particular tissue in a plant is determined by the rate of biosynthesis and catabolism of the hormone. Therefore, identifying all the genes involved in the metabolism is essential for a complete understanding of how this hormone directs plant growth and development. To date, almost all the biosynthetic genes have been identified through the isolation of auxotrophic mutants. On the other hand, among several ABA catabolic pathways, current genomic approaches revealed that Arabidopsis CYP707A genes encode ABA 8′-hydroxylases, which catalyze the first committed step in the predominant ABA catabolic pathway. Identification of ABA metabolic genes has revealed that multiple metabolic steps are differentially regulated to fine-tune the ABA level at both transcriptional and post-transcriptional levels. Furthermore, recent ongoing studies have given new insights into the regulation and site of ABA metabolism in relation to its physiological roles.
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REDOX REGULATION: A Broadening Horizon
Vol. 56 (2005), pp. 187–220More LessInitially discovered in the context of photosynthesis, regulation by change in the redox state of thiol groups (S−S ↔ 2SH) is now known to occur throughout biology. Several systems, each linking a hydrogen donor to an intermediary disulfide protein, act to effect changes that alter the activity of target proteins: the ferredoxin/thioredoxin
a small protein, reduced enzymatically by NADPH or ferredoxin, that is active in thiol/disulfide exchange and results in regulation or substrate conversion system, comprised of reduced ferredoxin, a thioredoxin, and the enzyme, ferredoxin-thioredoxin reductase; the NADP/thioredoxin system, including NADPH, a thioredoxin, and NADP-thioredoxin reductase; and the glutathione/glutaredoxina small protein, reduced by glutathione, that is active in thiol/disulfide exchange and results in regulation or substrate conversion system, composed of reduced glutathione and a glutaredoxin. A related disulfide protein, protein disulfide isomerase (PDI) acts in protein assembly. Regulation linked to plastoquinone and signaling induced by reactive oxygen species (ROSreactive oxygen species ) and other agents are also being actively investigated. Progress made on these systems has linked redox to the regulation of an increasing number of processes not only in plants, but in other types of organisms as well. Research in areas currently under exploration promises to provide a fuller understanding of the role redox plays in cellular processes, and to further the application of this knowledge to technology and medicine.
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ENDOCYTOTIC CYCLING OF PM PROTEINS
Vol. 56 (2005), pp. 221–251More LessPlasma membrane protein internalization and recycling mechanisms in plants share many features with other eukaryotic organisms. However, functional and structural differences at the cellular and organismal level mandate specialized mechanisms for uptake, sorting, trafficking, and recycling in plants. Recent evidence of plasma membrane cycling of members of the PIN auxin efflux facilitator family and the KAT1 inwardly rectifying potassium channel demonstrates that endocytotic cycling of some form occurs in plants. However, the mechanisms underlying protein internalization and the signals that stimulate endocytosis of proteins from the cell-environment interface are poorly understood. Here we summarize what is known of endocytotic cycling in animals and compare those mechanisms with what is known in plants. We discuss plant orthologs of mammalian-trafficking proteins involved in endocytotic cycling. The use of the styryl dye FM4-64 to define the course of endocytotic uptake and the fungal toxin brefeldin A to dissect the internalization pathways are particularly emphasized. Additionally, we discuss progress in identifying distinct endosomal populations marked by the small GTPases Ara6 and Ara7 as well as recently described examples of apparent cycling of plasma membrane proteins.
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MOLECULAR PHYSIOLOGY OF LEGUME SEED DEVELOPMENT
Vol. 56 (2005), pp. 253–279More LessLegume seed development is characterized by progressive differentiation of organs and tissues resulting in developmental gradients
A developmental gradient results from the gradual differentiation of different organs or within a single-seed organ and is reflected by heterogeneous populations of cells of different physiological age accumulating different amounts of substances, e.g., mRNAs, proteins, and starch. . The whole process is prone to metabolic control, and distinct metabolite profiles specify the differentiation state. Whereas early embryo growth is mainly maternally controlled, the transition into maturation implies a switch to filial control. A signaling network involving sugars, ABAabscisic acid , and SnRK1 kinases governs maturation. Processes of maturation are activated by changing oxygen/energy levels and/or a changing nutrient state, which trigger responses at the level of transcription and protein phosphorylation. This way seed metabolism becomes adapted to altering conditions. In maturing cotyledons photoheterotrophic metabolismPhotoheterotrophic metabolism occurs in green seeds in which specific photoheterotrophic plastids import sugars, are photosynthetically active, and produce oxygen, thereby supporting respiration and overall metabolic activity. improves internal oxygen supply and biosynthetic fluxes and influences assimilate partitioning. Transgenic legumes with changed metabolic pathways and seed composition provide suitable models to study pathway regulation and metabolic control. At the same time, desirable improvements of seed quality and yield may be achieved.
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CYTOKINESIS IN HIGHER PLANTS
Vol. 56 (2005), pp. 281–299More LessCytokinesis partitions the cytoplasm between two or more nuclei. In higher plants, cytokinesis is initiated by cytoskeleton-assisted targeted delivery of membrane vesicles to the plane of cell division, followed by local membrane fusion to generate tubulo-vesicular networks. This initial phase of cytokinesis is essentially the same in diverse modes of plant cytokinesis whereas the subsequent transformation of the tubulo-vesicular networks into the partitioning membrane may be different between systems. This review focuses on membrane and cytoskeleton dynamics in cell plate
a transient membrane compartment that is formed by the fusion of cytokinetic vesicles and eventually matures into the plasma membranes and cross-wall between daughter cells formation and expansion during somatic cytokinesis.
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EVOLUTION OF FLAVORS AND SCENTS
Vol. 56 (2005), pp. 301–325More LessThe world is filled with flavors and scents, which are the result of volatile compounds produced and emitted by plants. These specialized metabolites
A metabolite, usually a small molecule, which is not a building block of proteins, lipids, or sugars, but that plays another role in the organism. Usually, but not always, its occurrence is restricted. are the products of specific metabolic pathways. The terpenoid, fatty acid, and phenylpropanoid pathways contribute greatly to production of volatile compounds. Mechanisms that lead to evolution of volatile production in plants include gene duplication and divergence, convergent evolution, repeated evolutionThis occurs when a new and identical (or very similar) genetic function arises independently in the same gene family from two or more orthologous or paralogous genes that did not share the same function. , and alteration of gene expression, caused by a number of factors, followed by change in enzyme specificity. Many examples of these processes are now available for three important gene families involved in production of volatile metabolites: the small molecule O-methyltransferases, the acyltransferasesAn enzyme that catalyzes the formation of esters and amides via transfer from the co-enzyme A derivate of acid moieties to a receptive alcohol. , and the terpene synthasesA member of the large family of enzymes that catalyze the formation of terpenoid (isoprenoid) specialized metabolites from geranyl diphosphate, farnesyl diphosphate, or geranylgeranyl diphosphate via a carbocation intermediate. . Examples of these processes in these gene families are found in roses, Clarkia breweri, and sweet basil, among others. Finally, evolution of volatile emission will be an exciting field of study for the foreseeable future.
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BIOLOGY OF CHROMATIN DYNAMICS
Vol. 56 (2005), pp. 327–351More LessDuring the development of a multicellular organism, cell differentiation involves activation and repression of transcription programs that must be stably maintained during subsequent cell divisions. Chromatin remodeling plays a crucial role in regulating chromatin states that conserve transcription programs and provide a mechanism for chromatin states to be maintained as cells proliferate, a process referred to as epigenetic inheritance
inheritance of a gene activity state that is not specified by DNA sequence . A large number of factors and protein complexes are now known to be involved in regulating the dynamic states of chromatin structure. Their biological functions and molecular mechanisms are beginning to be revealed.
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SHOOT BRANCHING
Vol. 56 (2005), pp. 353–374More LessAll plant shoots can be described as a series of developmental modules termed phytomers, which are produced from shoot apical meristems. A phytomer generally consists of a leaf, a stem segment, and a secondary shoot meristem. The fate and activity adopted by these secondary, axillary shoot meristems is the major source of evolutionary and environmental diversity in shoot system architecture. Axillary meristem fate and activity are regulated by the interplay of genetic programs with the environment. Recent results show that these inputs are channeled through interacting hormonal and transcription factor regulatory networks. Comparison of the factors involved in regulating the function of diverse axillary meristem types both within and between species is gradually revealing a pattern in which a common basic program has been modified to produce a range of axillary meristem types.
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PROTEIN SPLICING ELEMENTS AND PLANTS: From Transgene Containment to Protein Purification
Vol. 56 (2005), pp. 375–392More LessProtein splicing
the process in which an intein excises itself from a precursor molecule with the concomitant ligation of the flanking protein sequences elements, termed inteinsa protein splicing element , have been discovered in all the domains of life. Basic research on inteins has led to a greater understanding of how they mediate the protein splicing process. Because inteins are natural protein engineering elements they have been harnessed for use in a number of applications, including protein purification, protein semisynthesis, and in vivo and in vitro protein modifications. This review focuses on the use of inteins in plants. A split-gene technique utilizes inteins to reconstitute the activity of a transgene product with the goal of limiting the spread of transgenes from a genetically modified plant to a weedy relative. Furthermore, merging the intein tag for protein purification with the large protein yields possible with plants has the potential to produce pharmaceutically important proteins. Finally, relevant techniques that may be used in plants in the future are discussed.
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MOLECULAR GENETIC ANALYSES OF MICROSPOROGENESIS AND MICROGAMETOGENESIS IN FLOWERING PLANTS
Vol. 56 (2005), pp. 393–434More LessIn flowering plants, male reproductive development requires the formation of the stamen, including the differentiation of anther tissues. Within the anther, male meiosis produces microspores, which further develop into pollen grains, relying on both sporophytic and gametophytic gene functions. The mature pollen is released when the anther dehisces, allowing pollination to occur. Molecular studies have identified a large number of genes that are expressed during stamen and pollen development. Genetic analyses have demonstrated the function of some of these genes in specifying stamen identity, regulating anther cell division and differentiation, controlling male meiosis, supporting pollen development, and promoting anther dehiscence. These genes encode a variety of proteins, including transcriptional regulators, signal transduction proteins, regulators of protein degradation, and enzymes for the biosynthesis of hormones. Although much has been learned in recent decades, much more awaits to be discovered and understood; the future of the study of plant male reproduction remains bright and exciting with the ever-growing tool kits and rapidly expanding information and resources for gene function studies.
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PLANT-SPECIFIC CALMODULIN-BINDING PROTEINS
Vol. 56 (2005), pp. 435–466More LessCalmodulin
CaM is a ubiquitous Ca2+ sensor protein (16 to 18 kD) with no catalytic activity that can, upon binding Ca2+, activate target proteins involved in various cellular processes. The CaM prototype is comprised of two globular domains connected with a long flexible helix. Each globular domain contains a pair of intimately linked EF hands. One EF hand motif is composed of a specialized helix-loop-helix structure that binds one molecule of Ca2+. (CaMcalmodulin ) is the most prominent Ca2+ transducer in eukaryotic cells, regulating the activity of numerous proteins with diverse cellular functions. Many features of CaM and its downstream targets are similar in plants and other eukaryotes. However, plants possess a unique set of CaM-related proteins, and several unique CaM target proteins. This review discusses recent progress in identifying plant-specific CaM-binding proteins and their roles in response to biotic and abiotic stresses and development. The review also addresses aspects emerging from recent structural studies of CaM interactions with target proteins relevant to plants.
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SELF-INCOMPATIBILITY IN PLANTS
Vol. 56 (2005), pp. 467–489More LessSexual reproduction in many flowering plants involves self-incompatibility (SI
self-incompatibility ), which is one of the most important systems to prevent inbreeding. In many species, the self-/nonself-recognition of SI is controlled by a single polymorphic locus, the S-locus. Molecular dissection of the S-locus revealed that SI represents not one system, but a collection of divergent mechanisms. Here, we discuss recent advances in the understanding of three distinct SI mechanisms, each controlled by two separate determinant genes at the S-locus. In the Brassicaceae, the determinant genes encode a pollen ligand and its stigmatic receptor kinase; their interaction induces incompatible signaling(s) within the stigma papilla cells. In the Solanaceae-type SI, the determinants are a ribonuclease and an F-box protein, suggesting the involvement of RNA and protein degradation in the system. In the Papaveraceae, the only identified female determinant induces a Ca2+-dependent signaling network that ultimately results in the death of incompatible pollen.
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REMEMBERING WINTER: Toward a Molecular Understanding of Vernalization
Vol. 56 (2005), pp. 491–508More LessExposure to the prolonged cold of winter is an important environmental cue that favors flowering in the spring in many types of plants. The process by which exposure to cold promotes flowering is known as vernalization. In Arabidopsis and certain cereals, the block to flowering in plants that have not been vernalized is due to the expression of flowering repressors. The promotion of flowering is due to the cold-mediated suppression of these repressors. Recent work has demonstrated that covalent modifications of histones in the chromatin of target loci are part of the molecular mechanism by which certain repressors are silenced during vernalization.
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NEW INSIGHTS TO THE FUNCTION OF PHYTOPATHOGENIC BACTERIAL TYPE III EFFECTORS IN PLANTS
Vol. 56 (2005), pp. 509–531More LessPhytopathogenic bacteria use the type III secretion system (TTSS
type III secretion system ) to inject effector proteins into plant cells. This system is essential for bacteria to multiply in plant tissue and to promote the development of disease symptoms. Until recently, little was known about the function of TTSS effectors in bacterial-plant interactions. New studies dissecting the molecular and biochemical action of TTSS effectors show that these proteins contribute to bacterial pathogenicity by interfering with plant defense signal transduction. These investigations provide us with a fresh view of how bacteria manipulate plant physiology to colonize their hosts.
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Previous Volumes
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Volume 75 (2024)
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Volume 74 (2023)
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Volume 73 (2022)
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Volume 72 (2021)
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Volume 71 (2020)
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Volume 70 (2019)
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Volume 69 (2018)
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Volume 68 (2017)
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Volume 67 (2016)
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Volume 66 (2015)
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Volume 65 (2014)
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Volume 64 (2013)
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Volume 63 (2012)
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Volume 62 (2011)
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Volume 61 (2010)
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Volume 60 (2009)
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Volume 59 (2008)
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Volume 58 (2007)
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Volume 57 (2006)
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Volume 56 (2005)
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Volume 55 (2004)
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Volume 54 (2003)
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Volume 53 (2002)
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Volume 52 (2001)
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Volume 51 (2000)
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Volume 50 (1999)
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Volume 49 (1998)
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Volume 48 (1997)
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Volume 47 (1996)
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Volume 46 (1995)
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Volume 45 (1994)
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Volume 44 (1993)
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Volume 43 (1992)
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Volume 42 (1991)
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Volume 41 (1990)
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Volume 40 (1989)
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Volume 39 (1988)
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Volume 38 (1987)
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Volume 37 (1986)
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Volume 36 (1985)
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Volume 35 (1984)
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Volume 34 (1983)
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Volume 33 (1982)
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Volume 32 (1981)
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Volume 31 (1980)
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Volume 30 (1979)
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Volume 29 (1978)
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Volume 28 (1977)
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Volume 27 (1976)
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Volume 26 (1975)
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Volume 25 (1974)
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Volume 24 (1973)
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Volume 23 (1972)
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Volume 22 (1971)
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Volume 21 (1970)
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Volume 20 (1969)
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Volume 19 (1968)
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Volume 18 (1967)
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Volume 17 (1966)
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Volume 16 (1965)
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Volume 15 (1964)
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Volume 14 (1963)
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Volume 13 (1962)
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Volume 12 (1961)
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Volume 11 (1960)
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Volume 10 (1959)
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Volume 9 (1958)
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Volume 8 (1957)
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Volume 7 (1956)
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Volume 6 (1955)
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Volume 5 (1954)
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Volume 4 (1953)
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Volume 3 (1952)
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Volume 2 (1951)
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Volume 1 (1950)
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Volume 0 (1932)