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  • American Institute of Physics  (14,793)
  • American Meteorological Society
  • Annual Reviews
  • Copernicus
  • 2005-2009  (19,128)
  • 2005  (19,128)
  • 101
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    Annual Review of Genetics 39 (2005), S. 409-429 
    ISSN: 0066-4197
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: The lysis-lysogeny decision of bacteriophage lambda (??) is a paradigm for developmental genetic networks. There are three key features, which characterize the network. First, after infection of the host bacterium, a decision between lytic or lysogenic development is made that is dependent upon environmental signals and the number of infecting phages per cell. Second, the lysogenic prophage state is very stable. Third, the prophage enters lytic development in response to DNA-damaging agents. The CI and Cro regulators define the lysogenic and lytic states, respectively, as a bistable genetic switch. Whereas CI maintains a stable lysogenic state, recent studies indicate that Cro sets the lytic course not by directly blocking CI expression but indirectly by lowering levels of CII which activates cI transcription. We discuss how a relatively simple phage like ?? employs a complex genetic network in decision-making processes, providing a challenge for theoretical modeling.
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  • 102
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    Annual Review of Genetics 39 (2005), S. 309-338 
    ISSN: 0066-4197
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Orthologs and paralogs are two fundamentally different types of homologous genes that evolved, respectively, by vertical descent from a single ancestral gene and by duplication. Orthology and paralogy are key concepts of evolutionary genomics. A clear distinction between orthologs and paralogs is critical for the construction of a robust evolutionary classification of genes and reliable functional annotation of newly sequenced genomes. Genome comparisons show that orthologous relationships with genes from taxonomically distant species can be established for the majority of the genes from each sequenced genome. This review examines in depth the definitions and subtypes of orthologs and paralogs, outlines the principal methodological approaches employed for identification of orthology and paralogy, and considers evolutionary and functional implications of these concepts.
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  • 103
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    Annual Review of Genetics 39 (2005), S. 1-8 
    ISSN: 0066-4197
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: John Maynard Smith was one of the most original thinkers in evolutionary biology of the post neo-Darwinian synthesis age. He was able to define new problems with clarity and by doing so open up new research directions. He did this in a number of areas including game theory and evolution, the evolution of sex, animal behavior, evolutionary transitions and molecular evolution. Although he is best known for his research and his ideas, he was a great expositor and wrote many books, including introductory texts in the areas of evolution and genetics, ecology and mathematical modeling, as well as advanced expositions of research problems.
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  • 104
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    Annual Review of Genetics 39 (2005), S. 453-479 
    ISSN: 0066-4197
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Bacterial plasmids encode partitioning (par) loci that ensure ordered plasmid segregation prior to cell division. par loci come in two types: those that encode actin-like ATPases and those that encode deviant Walker-type ATPases. ParM, the actin-like ATPase of plasmid R1, forms dynamic filaments that segregate plasmids paired at mid-cell to daughter cells. Like microtubules, ParM filaments exhibit dynamic instability (i.e., catastrophic decay) whose regulation is an important component of the DNA segregation process. The Walker box ParA ATPases are related to MinD and form highly dynamic, oscillating filaments that are required for the subcellular movement and positioning of plasmids. The role of the observed ATPase oscillation is not yet understood. However, we propose a simple model that couples plasmid segregation to ParA oscillation. The model is consistent with the observed movement and localization patterns of plasmid foci and does not require the involvement of plasmid-specific host-encoded factors.
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  • 105
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    Annual Review of Genetics 39 (2005), S. 153-171 
    ISSN: 0066-4197
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Among many achievements in the neurodegeneration field in the past decade, two require special attention due to the huge impact on our understanding of molecular and cellular pathogenesis of human neurodegenerative diseases. First is defining specific mutations in familial neurodegenerative diseases and second is modeling these diseases in easily manipulable model organisms including the fruit fly, nematode, and yeast. The power of these genetic systems has revealed many genetic factors involved in the various pathways affected, as well as provided potential drug targets for therapeutics. This review focuses on fruit fly models of human neurodegenerative diseases, with emphasis on how fly models have provided new insights into various aspects of human diseases.
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  • 106
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    Annual Review of Genetics 39 (2005), S. 9-22 
    ISSN: 0066-4197
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: The zebrafish is an excellent model system for studying the molecular basis of inner ear development and function. The eggs develop ex utero and the ear is transparent for the first few weeks of life. Forward genetic screens and antisense technology have helped to elucidate the signaling pathways and molecules required for inner ear development and function. This review addresses the most recent advances in our understanding of how the ear forms and discusses the molecules in hair cells that are essential for sensing sound and movement in the zebrafish.
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  • 107
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    Annual Review of Genetics 39 (2005), S. 219-239 
    ISSN: 0066-4197
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: The myriad developmental roles served by the T-box family of transcription factor genes defy easy categorization. Present in all metazoans, the T-box genes are involved in early embryonic cell fate decisions, regulation of the development of extraembryonic structures, embryonic patterning, and many aspects of organogenesis. They are unusual in displaying dosage sensitivity in most instances. In humans, mutations in T-box genes are responsible for developmental dysmorphic syndromes, and several T-box genes have been implicated in neoplastic processes. T-box transcription factors function in many different signaling pathways, notably bone morphogenetic protein and fibroblast growth factor pathways. The few downstream target genes that have been identified indicate a wide range of downstream effectors.
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  • 108
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    Annual Review of Biophysics and Biomolecular Structure 34 (2005), S. 245-266 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: The conformation of the ligand in complex with a macromolecular target can be studied by nuclear magnetic resonance (NMR) in solution for both tightly and weakly forming complexes. In the weak binding regime (koff 〉 104 Hz), the structure of the bound ligand is accessible also for very large complexes (〉100 kDa), which are not amenable to NMR studies in the tight binding regime. Here I review the state-of-the-art NMR methodology used for screening ligands and for the structural investigation of bound ligand conformations, in both tight and weak binding regimes. The advantages and disadvantages of each approach are critically described. The NMR methodology used to investigate transiently forming complexes has expanded considerably in the past few years, opening new possibilities for a detailed description of ligand-target interactions. Novel methods for the determination of the bound ligand conformation, in particular transferred cross-correlated relaxation, are thoroughly reviewed, and their advantages with respect to established methodology are discussed, using the epothilone-tubulin complex as a primary example.
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    Annual Review of Biophysics and Biomolecular Structure 34 (2005), S. 221-243 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: The problem of how ions influence the folding of RNA into specific tertiary structures is being addressed from both thermodynamic (by how much do different salts affect the free energy change of folding) and structural (how are ions arranged on or near an RNA and what kinds of environments do they occupy) points of view. The challenge is to link these different approaches in a theoretical framework that relates the energetics of ion-RNA interactions to the spatial distribution of ions. This review distinguishes three different kinds of ion environments that differ in the extent of direct ion-RNA contacts and the degree to which the ion hydration is perturbed, and summarizes the current understanding of the way each environment relates to the overall energetics of RNA folding.
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    Annual Review of Biophysics and Biomolecular Structure 34 (2005), S. 21-42 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Molecular interactions are the language that molecules use to communicate recognition, binding, and regulation, events central to biological control mechanisms. Traditionally, such interactions involve direct, atom-to-atom, noncovalent contacts, or indirect contacts bridged by relatively fixed solvent molecules. Here we discuss a third class of molecular communication that, to date, has received less experimental attention, namely solvent-mediated communication between noncontacting macromolecules. This form of communication can be understood in terms of fundamental, well-established principles (coupled equilibria and linkage thermodynamics) that govern interactions between individual polymers and their solutions. In contrast to simple solutions used in laboratory studies, biological systems contain a multitude of nominally noninteracting biopolymers within the same solution environment. The exquisite control of biological function requires some form of communication between many of these solution components, even in the absence of direct and/or indirect contacts. Such communication must be considered when describing potential mechanisms of biological regulation.
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    Annual Review of Biophysics and Biomolecular Structure 34 (2005), S. 71-90 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Despite the central importance of peripheral membrane proteins to cellular signaling and metabolic pathways, the structures of protein-membrane interfaces remain largely inaccessible to high-resolution structural methods. In recent years a number of laboratories have contributed to the development of an electron paramagnetic resonance (EPR) power saturation approach that utilizes site-directed spin labeling to determine the key geometric parameters of membrane-docked proteins, including their penetration depths and angular orientations relative to the membrane surface. Representative applications to Ca2+-activated, membrane-docking C2 domains are described.
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  • 112
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    Annual Review of Cell and Developmental Biology 21 (2005), S. 247-269 
    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Approximately one percent of the human genome encodes proteins that either regulate or are regulated by direct interaction with members of the Rho family of small GTPases. Through a series of complex biochemical networks, these highly conserved molecular switches control some of the most fundamental processes of cell biology common to all eukaryotes, including morphogenesis, polarity, movement, and cell division. In the first part of this review, we present the best characterized of these biochemical pathways; in the second part, we attempt to integrate these molecular details into a biological context.
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    Annual Review of Cell and Developmental Biology 21 (2005), S. 529-550 
    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: The conserved protein-conducting channel, referred to as the Sec61 channel in eukaryotes or the SecY channel in eubacteria and archaea, translocates proteins across cellular membranes and integrates proteins containing hydrophobic transmembrane segments into lipid bilayers. Structural studies illustrate how the protein-conducting channel accomplishes these tasks. Three different mechanisms, each requiring a different set of channel binding partners, are employed to move polypeptide substrates: The ribosome feeds the polypeptide chain directly into the channel, a ratcheting mechanism is used by the eukaryotic endoplasmic reticulum chaperone BiP, and a pushing mechanism is utilized by the bacterial ATPase SecA. We review these translocation mechanisms, relating biochemical and genetic observations to the structures of the protein-conducting channel and its binding partners.
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  • 114
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    Annual Review of Cell and Developmental Biology 21 (2005), S. 35-56 
    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Apoptosis plays a central role in the development and homeostasis of metazoans. Research in the past two decades has led to the identification of hundreds of genes that govern the initiation, execution, and regulation of apoptosis. An earlier focus on the genetic and cell biological characterization has now been complemented by systematic biochemical and structural investigation, giving rise to an unprecedented level of clarity in many aspects of apoptosis. In this review, we focus on the molecular mechanisms of apoptosis by synthesizing available biochemical and structural information. We discuss the mechanisms of ligand binding to death receptors, actions of the Bcl-2 family of proteins, and caspase activation, inhibition, and removal of inhibition. Although an emphasis is given to the mammalian pathways, a comparative analysis is applied to related mechanistic information in Drosophila and Caenorhabditis elegans.
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  • 115
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    Annual Review of Cell and Developmental Biology 21 (2005), S. 347-380 
    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: The nuclear envelope (NE) is a highly specialized membrane that delineates the eukaryotic cell nucleus. It is composed of the inner and outer nuclear membranes, nuclear pore complexes (NPCs) and, in metazoa, the lamina. The NE not only regulates the trafficking of macromolecules between nucleoplasm and cytosol but also provides anchoring sites for chromatin and the cytoskeleton. Through these interactions, the NE helps position the nucleus within the cell and chromosomes within the nucleus, thereby regulating the expression of certain genes. The NE is not static, rather it is continuously remodeled during cell division. The most dramatic example of NE reorganization occurs during mitosis in metazoa when the NE undergoes a complete cycle of disassembly and reformation. Despite the importance of the NE for eukaryotic cell life, relatively little is known about its biogenesis or many of its functions. We thus are far from understanding the molecular etiology of a diverse group of NE-associated diseases.
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    Annual Review of Cell and Developmental Biology 21 (2005), S. 605-631 
    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Adult tissue-specific stem cells have the capacity to self-renew and generate functional differentiated cells that replenish lost cells throughout an organism's lifetime. Studies on stem cells from diverse systems have shown that stem cell function is controlled by extracellular cues from the niche and by intrinsic genetic programs within the stem cell. Here, we review the remarkable progress recently made in research regarding the stem cell niche. We compare the differences and commonalities of different stem cell niches in Drosophila ovary/testis and Caenorhabditis elegans distal tip, as well as in mammalian bone marrow, skin/hair follicle, intestine, brain, and testis. On the basis of this comparison, we summarize the common features, structure, and functions of the stem cell niche and highlight important niche signals that are conserved from Drosophila to mammals. We hope this comparative summary defines the basic elements of the stem cell niche, providing guiding principles for identification of the niche in other systems and pointing to areas for future studies.
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    Annual Review of Cell and Developmental Biology 21 (2005), S. 659-693 
    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: The TGF-?‚ family comprises many structurally related differentiation factors that act through a heteromeric receptor complex at the cell surface and an intracellular signal transducing Smad complex. The receptor complex consists of two type II and two type I transmembrane serine/threonine kinases. Upon phosphorylation by the receptors, Smad complexes translocate into the nucleus, where they cooperate with sequence-specific transcription factors to regulate gene expression. The vertebrate genome encodes many ligands, fewer type II and type I receptors, and only a few Smads. In contrast to the perceived simplicity of the signal transduction mechanism with few Smads, the cellular responses to TGF-?‚ ligands are complex and context dependent. This raises the question of how the specificity of the ligand-induced signaling is achieved. We review the molecular basis for the specificity and versatility of signaling by the many ligands through this conceptually simple signal transduction mechanism.
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    Annual Review of Cell and Developmental Biology 21 (2005), S. 81-103 
    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Sphingolipids and glycosphingolipids are membrane components of eukaryotic cell surfaces. Their constitutive degradation takes place on the surface of intra-endosomal and intra-lysosomal membrane structures. During endocytosis, these intra-lysosomal membranes are formed and prepared for digestion by a lipid-sorting process during which their cholesterol content decreases and the concentration of the negatively charged bis(monoacylglycero)phosphate (BMP)Đ??erroneously also called lysobisphosphatidic acid (LBPA)Đ??increases. Glycosphingolipid degradation requires the presence of water-soluble acid exohydrolases, sphingolipid activator proteins, and anionic phospholipids like BMP. The lysosomal degradation of sphingolipids with short hydrophilic head groups requires the presence of sphingolipid activator proteins (SAPs). These are the saposins (Saps) and the GM2 activator protein. Sphingolipid activator proteins are membrane-perturbing and lipid-binding proteins with different specificities for the bound lipid and the activated enzyme-catalyzed reaction. Their inherited deficiency leads to sphingolipid- and membrane-storage diseases. Sphingolipid activator proteins not only facilitate glycolipid digestion but also act as glycolipid transfer proteins facilitating the association of lipid antigens with immunoreceptors of the CD1 family.
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    Annual Review of Cell and Developmental Biology 21 (2005), S. 297-318 
    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: RNA silencing refers to a broad range of phenomena sharing the common feature that large, double-stranded RNAs or stem-loop precursors are processed to ca. 21Đ??26 nucleotide small RNAs, which then guide the cleavage of cognate RNAs, block productive translation of these RNAs, or induce methylation of specific target DNAs. Although the core mechanisms are evolutionarily conserved, epigenetic maintenance of silencing by amplification of small RNAs and the elaboration of mobile, RNA-based silencing signals occur predominantly in plants. Plant RNA silencing systems are organized into a network with shared components and overlapping functions. MicroRNAs, and probably trans-acting small RNAs, help regulate development at the posttranscriptional level. Small interfering RNAs associated with transgene- and virus-induced silencing function primarily in defending against foreign nucleic acids. Another system, which is concerned with RNA-directed methylation of DNA repeats, seems to have roles in epigenetic silencing of certain transposable elements and genes under their control.
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    Annual Review of Materials Research 35 (2005), S. 209-238 
    ISSN: 1531-7331
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: In recent years substantial progress has been made in the control of the properties of porous materials on the nano-, meso-, and macroscale. The feature of solids can, in favorable cases, be tailored to such an extent that one is justified in using the term engineering of porous catalytic materials. This review highlights recent developments concerning (a) the control of the pore structure of zeolites, (b) the creation of single site type catalysts based on ordered mesoporous oxides, (c) the catalytic potential of porous coordination compounds, and (d) the advances with respect to direct production of desired shapes of porous catalytic materials.
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    Annual Review of Materials Research 35 (2005), S. 427-464 
    ISSN: 1531-7331
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Catalyst life (with activity and selectivity) is one of the three essential properties of a practical catalyst, both in laboratory and industrial usage. For most catalysts in which the active phase is a metal, high activity requires a high metal surface area. In all cases, for long life, the metal surface area has to be maintained. The various modes of catalyst deactivation leading to loss of metal surface area are described (sintering, poisoning, coking, etc.). The choice of catalyst components for both active metal phases and for support phases is shown to be subject to thermodynamic and kinetic limits. Routes for the preparation of catalysts need to be and can be designed to give not only active, but also stable catalysts. Examples described include copper/zinc catalysts for hydrogenation/dehydrogenation reactions, iron catalysts for ammonia synthesis, nickel catalysts for hydrogenation reactions, automobile exhaust catalysts, and Raney catalysts.
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    Annual Review of Materials Research 35 (2005), S. 465-504 
    ISSN: 1531-7331
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: The key role of electron microscopy in understanding and creating advanced catalyst materials and processes in selective alkane oxidation, environmental control, and alternative energy sources is reviewed. In many technological processes, catalysts are increasingly nanoscale heterogeneous materials. With growing regulatory guidelines requiring efficient and environmentally compatible catalytic processes, it is crucial to have a fundamental understanding of the catalyst nanostructure and modes of operation under reaction conditions to design novel catalysts and processes. The review highlights the pioneering development and applications of atomic resolution in situ-environmental transmission electron microscopy (ETEM) for probing dynamic catalysis directly at the atomic level, high-resolution electron microscopy, and analytical spectroscopic methods in the development of alkane catalyzation, environmental protection, and new energy sources.
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    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 169-189 
    ISSN: 1543-592X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Plant secondary metabolites (PSMs) significantly impact the nutritional ecology of terrestrial vertebrate herbivores. Herbivores have a wide range of mechanisms (herbivore offenses) to mitigate the negative effects of PSMs. We discuss several behavioral and physiological offenses used by terrestrial vertebrates. Several newly recognized herbivore offenses such as regulated absorption and regulation of toxin intake are presented. We give a detailed description of the biotransformation system with respect to PSMs. We also summarize recent findings of plantĐ??animal interactions for lizards, birds, and mammals. Finally, we discuss some new tools that can be applied to long-standing questions of plantĐ??vertebrate interactions.
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    Annual Review of Fluid Mechanics 37 (2005), S. 99-128 
    ISSN: 0066-4189
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: This article reviews our current understanding of the physical mechanisms governing the movement of a tropical cyclone. In a barotropic framework, a tropical cyclone is basically "steered" by the surrounding flow but its movement is modified by the Coriolis force (referred to as the beta effect) and the horizontal vorticity gradient of the surrounding flow. In the presence of vertical wind shear and latent heat release, a tropical cyclone tends to move toward an area with a maximum in the time tendency of potential vorticity, which is mainly contributed by two processes: (a) advection that depends on the structures of the vortex and the environment surrounding the vortex in terms of their flow speed and vorticity gradient (including the beta effect), and (b) heating that results from a coupling between the latent heat released in the clouds and the vertical wind shear.
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    Annual Review of Fluid Mechanics 37 (2005), S. 263-293 
    ISSN: 0066-4189
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: The large-scale dynamics of the extratropical stratosphere are reviewed. The role of Rossby waves and vortex dynamics in shaping the winter stratospheric circulation and the dynamics of the longitudinal mean flow are first discussed separately. The important effects of two-way interaction between waves and mean flow are then described, with emphasis on how mechanisms discovered in simple models can be followed through to models that are closer to the real stratosphere. A final topic is the possible effect of the stratosphere on the troposphere, with emphasis on dynamical mechanisms for such an effect.
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    Annual Review of Fluid Mechanics 37 (2005), S. 71-98 
    ISSN: 0066-4189
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: The flow in turbomachines is unsteady due to the relative motion of the rows of blades. In the low-pressure turbine, the wakes from the upstream bladerows provide the dominant source of unsteadiness. Because much of the blade-surface boundary-layer flow is laminar, one of the most important consequences of this unsteadiness is the interaction of the wakes with the suction-side boundary layer of a downstream blade. This is important because the blade suctionĐ??side boundary layers are responsible for most of the loss of efficiency and because the combined effects of random (wake turbulence) and periodic disturbances (wake velocity defect and pressure fields) cause the otherwise laminar boundary layer to undergo transition and eventually become turbulent. This article summarizes the process of wake-induced boundary-layer transition in low-pressure turbines and the loss generation processes that result. Particular emphasis is placed on how the effects of wakes may be exploited to control loss generation and how this has enabled successful development of ultra-high-lift low-pressure turbines.
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    Annual Review of Fluid Mechanics 37 (2005), S. 43-69 
    ISSN: 0066-4189
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: We review major experimental and theoretical studies on microcirculation and hemorheology, focusing on mechanics of blood flow and the vascular wall. We discuss flow of the blood formed elements [red blood cells (RBCs), white blood cells or leukocytes (WBCs) and platelets] in individual arterioles, capillaries, and venules, and in microvascular networks. We also review mechanical and rheological properties of the formed elements and their interactions with the vascular wall. We discuss short-term and long-term regulation of the microvasculature; the modes of regulation include metabolic, myogenic, and shear-stress-dependent mechanisms as well as vascular adaptation such as angiogenesis and vascular remodeling.
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    Annual Review of Fluid Mechanics 37 (2005), S. 1-21 
    ISSN: 0066-4189
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: His contemporaries saw R.T. Jones as one of the notably creative aerodynamicists of the twentieth century. This essay reviews his remarkable life and career, including his years as a farm-country boy, college dropout, and fledgling airplane designer in Missouri, his time as an elevator operator and self-directed student in Washington, D.C., and his long professional career as an aerodynamicist at the Langley and Ames Aeronautical Laboratories and Stanford University. The focus in his career is on his fundamental discovery of the benefits of sweepback for the wings of high-speed airplanes. This includes speculation about his highly intuitive thought processes in arriving at his creative ideas. I also give an account of his work on blood flow and the mechanical heart, his avocational accomplishments as a maker of telescopes and violins, and his philosophical interest in human affairs.
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    Annual Review of Fluid Mechanics 37 (2005), S. 329-356 
    ISSN: 0066-4189
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
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    Annual Review of Genetics 39 (2005), S. 121-152 
    ISSN: 0066-4197
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Until around 1990, most multigene families were thought to be subject to concerted evolution, in which all member genes of a family evolve as a unit in concert. However, phylogenetic analysis of MHC and other immune system genes showed a quite different evolutionary pattern, and a new model called birth-and-death evolution was proposed. In this model, new genes are created by gene duplication and some duplicate genes stay in the genome for a long time, whereas others are inactivated or deleted from the genome. Later investigations have shown that most non-rRNA genes including highly conserved histone or ubiquitin genes are subject to this type of evolution. However, the controversy over the two models is still continuing because the distinction between the two models becomes difficult when sequence differences are small. Unlike concerted evolution, the model of birth-and-death evolution can give some insights into the origins of new genetic systems or new phenotypic characters.
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    Annual Review of Genetics 39 (2005), S. 615-651 
    ISSN: 0066-4197
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: In many multicellular organisms, males have one X chromosome and females have two. Dosage compensation refers to a regulatory mechanism that insures the equalization of X-linked gene products in males and females. The mechanism has been studied at the molecular level in model organisms belonging to three distantly related taxa; in these organisms, equalization is achieved by shutting down one of the two X chromosomes in the somatic cells of females, by decreasing the level of transcription of the two doses of X-linked genes in females relative to males, or by increasing the level of transcription of the single dose of X-linked genes in males. The study of dosage compensation in these different forms has revealed the existence of an amazing number of interacting chromatin remodeling mechanisms that affect the function of entire chromosomes.
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    Annual Review of Genetics 39 (2005), S. 293-307 
    ISSN: 0066-4197
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Although the sex of most animals is determined by genetic information, sex-determining genes had been identified only in mammals, several flies, and the worm Caenorhabditis elegans until the recent discovery of DMY (DM-domain gene on the Y chromosome) in the sex-determining region on the Y chromosome of the teleost fish medaka, Oryzias latipes. Functional and expression analyses of DMY have shown it to be the master gene for male sex determination in the medaka. The only sex-determining genes found so far in vertebrates are Sry and DMY. Therefore, the medaka is expected to become a good experimental animal for investigating the precise mechanisms involved in primary sex determination in nonmammalian vertebrates. This article reviews the origin of DMY and the sexual development of gonads in the medaka. The putative functions of DMY are also discussed.
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    Annual Review of Genetics 39 (2005), S. 241-262 
    ISSN: 0066-4197
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: The human and mouse genome sequences bring closer the goal of understanding how characteristics of adult mammalian physiology and pathology are encoded by DNA. Here we review the challenge of understanding how genes specify mammalian traits, with particular focus on the cells and behavior of the immune system. Summarized is the emerging experience, advantages, and limitations of using ethylnitrosourea (ENU) to modify the mouse genome and select informative variants by phenotypic screens, yielding two main conclusions. First, ENU-induced variation provides an eminently feasible route to understanding how the genome encodes important mammalian processes without any prior assumptions about genes, their chromosomal locations, or expression patterns. Second, ENU alleles match those arising by natural variation. By changing individual protein domains or splice products, these alleles reveal separate gene functions specified through protein combinations.
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    Annual Review of Entomology 50 (2005), S. 201-222 
    ISSN: 0066-4170
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Đ?“ Abstract?? Folsomia candida Willem 1902, a member of the order Collembola (colloquially called springtails), is a common and widespread arthropod that occurs in soils throughout the world. The species is parthenogenetic and is easy to maintain in the laboratory on a diet of granulated dry yeast. F. candida has been used as a "standard" test organism for more than 40 years for estimating the effects of pesticides and environmental pollutants on nontarget soil arthropods. However, it has also been employed as a model for the investigation of numerous other phenomena such as cold tolerance, quality as a prey item, and effects of microarthropod grazing on pathogenic fungi and mycorrhizae of plant roots. In this comprehensive review, aspects of the life history, ecology, and ecotoxicology of F. candida are covered. We focus on the recent literature, especially studies that have examined the effects of soil pollutants on reproduction in F. candida using the protocol published by the International Standards Organization in 1999.
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    Annual Review of Entomology 50 (2005), S. 247-269 
    ISSN: 0066-4170
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Đ?“ Abstract?? Published literature on thrips has been dominated by descriptive taxonomy, pest control work, and generalized synecology. The lack of studies examining the detailed biology or autecology of any species limits our understanding of how thrips live and the processes underlying their diversification. Similarly, the phylogenetic inadequacy of thrips classification limits our ability to examine the evolution of biological traits. The extent to which our knowledge of the biology of thrips has increased in recent years is reviewed, such as the behavior of particular species and their interactions with other organisms, including host plant associations, pollination, predation, and natural enemiesĐ??factors involved in driving diversification within this order of opportunistic insects.
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    Annual Review of Entomology 50 (2005), S. 347-370 
    ISSN: 0066-4170
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Đ?“ Abstract?? Females that place eggs under the care of conspecifics have been labeled egg dumpers. Egg dumping is an effective reproductive alternative that lowers risks for, and has the potential to increase fecundity in, its practitioners. Although insect egg dumpers can be social parasites of the maternal behavior of egg recipients, dumping is more likely to be a viable reproductive alternative when the costs to egg recipients are low and thus the defense by potential hosts against egg dumping intrusions is minimal. These conditions are met in insects that guard only eggs or in insects whose eggs hatch into self-supporting precocial young that need little beyond defense from parents. When this is the case, egg dumping is favored by natural and/or kin selection as a mechanism by which dumpers can avoid parental risks and increase fecundity, and egg recipients can enhance offspring survival by diluting predation.
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    Notes: Đ?“ Abstract?? The Bactrocera dorsalis complex of tropical fruit flies (Diptera: Tephritidae: Dacinae) contains 75 described species, largely endemic to Southeast Asia. Within the complex are a small number of polyphagous pests of international significance, including B. dorsalis sensu stricto, B. papayae, B. carambolae, and B. philippinensis. Most species within the complex were described in 1994 and since then substantial research has been undertaken in developing morphological and molecular diagnostic techniques for their recognition. Such techniques can now resolve most taxa adequately. Genetic evidence suggests that the complex has evolved in only the last few million years, and development of a phylogeny of the group is considered a high priority to provide a framework for future evolutionary and ecological studies. As model systems, mating studies on B. dorsalis s.s. and B. cacuminata have substantially advanced our understanding of insect use of plant-derived chemicals for mating, but such studies have not been applied to help resolve the limits of biological species within the complex. Although they are commonly regarded as major pests, there is little published evidence documenting economic losses caused by flies of the B. dorsalis complex. Quantification of economic losses caused by B. dorsalis complex species is urgently needed to prioritize research for quarantine and management. Although they have been documented as invaders, relatively little work has been done on the invasion biology of the complex and this is an area warranting further work.
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    Annual Review of Entomology 50 (2005), S. 53-70 
    ISSN: 0066-4170
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Đ?“ Abstract?? Effective indoor residual spraying against malaria vectors depends on whether mosquitoes rest indoors (i.e., endophilic behavior). This varies among species and is affected by insecticidal irritancy. Exophilic behavior has evolved in certain populations exposed to prolonged spraying programs. Optimum effectiveness of insecticide-treated nets presumably depends on vectors biting at hours when most people are in bed. Time of biting varies among different malaria vector species, but so far there is inconclusive evidence for these evolving so as to avoid bednets. Use of an untreated net diverts extra biting to someone in the same room who is without a net. Understanding choice of oviposition sites and dispersal behavior is important for the design of successful larval control programs including those using predatory mosquito larvae. Prospects for genetic control by sterile males or genes rendering mosquitoes harmless to humans will depend on competitive mating behavior. These methods are hampered by the immigration of monogamous, already-mated females.
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    Annual Review of Entomology 50 (2005), S. 153-179 
    ISSN: 0066-4170
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Đ?“ Abstract?? Residues of veterinary parasiticides in dung of treated livestock have nontarget effects on dung-breeding insects and dung degradation. Here, we review the nature and extent of these effects, examine the potential risks associated with different classes of chemicals, and describe how greater awareness of these nontarget effects has resulted in regulatory changes in the registration of veterinary products.
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    Annual Review of Entomology 50 (2005), S. 101-123 
    ISSN: 0066-4170
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Tsetse flies (Diptera: Glossinidae) constitute a small, ancient taxon of exclusively hematophagous insects that reproduce slowly and viviparously. Because tsetse flies are the only vectors of pathogenic African trypanosomes, they are a potent and constant threat to humans and livestock over much of sub-Saharan Africa. Despite their low fecundity, tsetse flies demonstrate great resilience, which makes population suppression expensive, transient, and beyond the capacities of private and public sectors to accomplish, except over small areas. Nevertheless, control measures that include genetic methods are under consideration at national and supranational levels. There is a pressing need for sufficient laboratory cultures of tsetse flies and financial support to carry out genetic research. Here we review tsetse genetics from organismal and population points of view and identify some research needs.
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    Annual Review of Entomology 50 (2005), S. 321-346 
    ISSN: 0066-4170
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Đ?“ Abstract?? Although the use of aggregation pheromones has been reported for hundreds of nonsocial arthropod species, the evolutionary ecological aspects of this behavior have received little attention. Despite the elaborate literature on mechanisms, robust data on costs and benefits of aggregation pheromones are scant. Existing literature indicates that, in contrast to the diversity of mechanisms, the ecological conditions in which aggregation pheromones are used are more alike. This points to a few general categories for costs and benefits of aggregation pheromones, and these are discussed. We subsequently review interspecific interactions that may be affected by the use of aggregation pheromones. We encounter a strikingly frequent association of aggregation pheromones with fungi and microorganisms and address cross-attraction by competitor species and exploitation by natural enemies. We show that aggregative behavior by individuals through the use of pheromones can profoundly affect ecological interactions and advocate further evolutionary and ecological investigations of pheromone-mediated aggregation.
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    Annual Review of Entomology 50 (2005), S. 371-393 
    ISSN: 0066-4170
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Đ?“ Abstract?? This review covers selected literature from 1982 to the present on some of the ecological, behavioral, and biochemical aspects of hydrocarbon use by insects and other arthropods. Major ecological and behavioral topics are species- and gender-recognition, nestmate recognition, task-specific cues, dominance and fertility cues, chemical mimicry, and primer pheromones. Major biochemical topics include chain length regulation, mechanism of hydrocarbon formation, timing of hydrocarbon synthesis and transport, and biosynthesis of volatile hydrocarbon pheromones of Lepidoptera and Coleoptera. In addition, a section is devoted to future research needs in this rapidly growing area of science.
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    Annual Review of Entomology 50 (2005), S. 395-420 
    ISSN: 0066-4170
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Đ?“ Abstract?? Pair formation in social insects mostly happens early in adult life and away from the social colony context, which precludes promiscuity in the usual sense. Termite males have continuous sperm production, but males of social Hymenoptera have fixed complements of sperm, except for a few species that mate before female dispersal and show male-fighting and lifelong sperm production. We develop an evolutionary framework for testing sexual selection and sperm competition theory across the advanced eusocial insects (ants, wasps, bees, termites) and highlight two areas related to premating sexual selection (sexual dimorphism and male mate number) that have remained understudied and in which considerable progress can be achieved with relatively simple approaches. We also infer that mating plugs may be relatively common, and we review further possibilities for postmating sexual selection, which gradually become less likely in termite evolution, but for which eusocial Hymenoptera provide unusual opportunities because they have clonal ejaculates and store viable sperm for up to several decades.
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    Annual Review of Entomology 50 (2005), S. 421-445 
    ISSN: 0066-4170
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Đ?“ Abstract?? Senescence (aging) is defined as a decline in performance and fitness with advancing age. Senescence is a nearly universal feature of multicellular organisms, and understanding why it occurs is a long-standing problem in biology. Here we present a concise review of both evolutionary and mechanistic theories of aging. We describe the development of the general evolutionary theory, along with the mutation accumulation, antagonistic pleiotropy, and disposable soma versions of the evolutionary model. The review of the mechanistic theories focuses on the oxidative stress resistance, cellular signaling, and dietary control mechanisms of life span extension. We close with a discussion of how an approach that makes use of both evolutionary and molecular analyses can address a critical question: Which of the mechanisms that can cause variation in aging actually do cause variation in natural populations?
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    Annual Review of Entomology 50 (2005), S. 479-503 
    ISSN: 0066-4170
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Đ?“ Abstract?? Weeds and arthropods interact in agricultural systems. Weeds can directly serve as food sources or provide other ecosystem resources for herbivorous arthropods, and indirectly serve carnivorous (beneficial) arthropods by providing food and shelter to their prey. Weeds can serve as alternative hosts for pest and beneficial arthropods when their preferred crop host is absent. Herbivory on crops by pest arthropods reduces the competitive ability of crop plants, leading to increased weed growth. Interactions between weeds and arthropods have several implications to integrated pest management (IPM). Pest and beneficial arthropod populations can be maintained in the absence of crop hosts. This statement also applies to all other pests that use weeds as a food source, including pathogens, nematodes, mollusks, and vertebrates. Weeds outside crop fields that maintain overwintering populations of arthropod pests are the major reason for the development of area-wide IPM programs for certain mobile arthropod pests. Weeds can serve as a source of increased diversity in agroecosystems. Increased diversity has been the rationale for enhancing biological control of arthropod pests through habitat management. The consequences of such approaches are difficult to predict on a multispecies IPM basis.
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    Annual Review of Entomology 50 (2005), S. 529-551 
    ISSN: 0066-4170
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Đ?“ Abstract?? Evolutionary ecology seeks to understand the selective reasons for the design features of the immune defense, especially with respect to parasitism. The molecular processes thereby set limitations, such as the failure to recognize an antigen, response specificity, the cost of defense, and the risk of autoimmunity. Sex, resource availability, and interference by parasites also affect a response. In turn, the defense repertoire consists of different kinds of immune responsesĐ??constitutive or induced, general or specificĐ??and involves memory and lasting protection. Because the situation often defies intuition, mathematical analysis is typically required to identify the costs and benefits of variation in design, but such studies are few. In all, insect immune defense is much more similar to that of vertebrates than previously thought. In addition, the field is now rapidly becoming revolutionized by molecular data and methods that allow unprecedented access to study evolution in action.
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    Annual Review of Immunology 23 (2005), S. 161-196 
    ISSN: 0732-0582
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Our views regarding the origins and functions of splenic marginal zone B cells have changed considerably over the past few years. Perspectives regarding the development and function of these cells vary considerably between investigators studying human and rodent immunology. Marginal zone B cells are now recognized to constitute a distinct naive B lymphoid lineage. Considerable progress has been made regarding the mechanisms involved in marginal zone B cell development in the mouse. Many of the molecular events that participate in the retention of this lineage of B cells in the marginal zone have been identified. Here, we discuss the functions of these cells in both innate and adaptive immunity. We also attempt to reconcile differing viewpoints regarding the generation and function of marginal zone B cells in rodents and primates.
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    Annual Review of Immunology 23 (2005), S. 487-513 
    ISSN: 0732-0582
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Helper T (Th) cellĐ??regulated B cell immunity progresses in an ordered cascade of cellular development that culminates in the production of antigen-specific memory B cells. The recognition of peptide MHC class II complexes on activated antigen-presenting cells is critical for effective Th cell selection, clonal expansion, and effector Th cell function development (Phase I). Cognate effector Th cellĐ??B cell interactions then promote the development of either short-lived plasma cells (PCs) or germinal centers (GCs) (Phase II). These GCs expand, diversify, and select high-affinity variants of antigen-specific B cells for entry into the long-lived memory B cell compartment (Phase III). Upon antigen rechallenge, memory B cells rapidly expand and differentiate into PCs under the cognate control of memory Th cells (Phase IV). We review the cellular and molecular regulators of this dynamic process with emphasis on the multiple memory B cell fates that develop in vivo.
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    Annual Review of Immunology 23 (2005), S. 415-445 
    ISSN: 0732-0582
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: The proliferation and differentiation of lymphocytes are regulated by receptors localized on the cell surface. Engagement of these receptors induces the activation of intracellular signaling proteins that transmit the receptor signals to distinct targets and control the cellular responses. The first signaling proteins to be discovered in higher organisms were the products of oncogenes. For example, the kinases Src and Abelson (Abl) were originally identified as oncogenes and were later characterized as important proteins for signal transduction in various cell types, including lymphocytes. Now, as many cellular signaling molecules have been discovered and ordered into certain pathways, we can better understand why particular signaling proteins are associated with tumorigenesis. In this review, we discuss recent progress in unraveling the molecular mechanisms of signaling pathways that control the proliferation and differentiation of early B cells. We point out the concepts of auto-inhibition and subcellular localization as crucial aspects in the regulation of B cell signaling.
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    Annual Review of Immunology 23 (2005), S. 683-747 
    ISSN: 0732-0582
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Multiple sclerosis (MS) develops in young adults with a complex predisposing genetic trait and probably requires an inciting environmental insult such as a viral infection to trigger the disease. The activation of CD4+ autoreactive T cells and their differentiation into a Th1 phenotype are a crucial events in the initial steps, and these cells are probably also important players in the long-term evolution of the disease. Damage of the target tissue, the central nervous system, is, however, most likely mediated by other components of the immune system, such as antibodies, complement, CD8+ T cells, and factors produced by innate immune cells. Perturbations in immunomodulatory networks that include Th2 cells, regulatory CD4+ T cells, NK cells, and others may in part be responsible for the relapsing-remitting or chronic progressive nature of the disease. However, an important paradigmatic shift in the study of MS has occurred in the past decade. It is now clear that MS is not just a disease of the immune system, but that factors contributed by the central nervous system are equally important and must be considered in the future.
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    Annual Review of Immunology 23 (2005), S. 651-682 
    ISSN: 0732-0582
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: CD8+ T cells play a critical role in antiviral immunity by exerting direct antiviral activity against infected cells. Because of their ability to recognize all types of viral proteins, they offer the promise of providing broad immunity to viruses that evade humoral immunity by varying their surface proteins. Consequently, there is considerable interest in developing vaccines that elicit effective antiviral TCD8+ responses. Generating optimal vaccines ultimately requires rational design based on detailed knowledge of how TCD8+ are activated in vivo under natural circumstances. Here we review recent progress obtained largely by in vivo studies in mice to understand the mechanistic basis for activation of naive TCD8+ in virus infections. These studies point the way to detailed understanding and provide some key information for vaccine development, although much remains to be learned to enable truly rational vaccine design.
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    Annual Review of Immunology 23 (2005), S. 945-974 
    ISSN: 0732-0582
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: The Notch pathway is gaining increasing recognition as a key regulator of developmental choices, differentiation, and function throughout the hematolymphoid system. Notch controls the generation of hematopoietic stem cells during embryonic development and may affect their subsequent homeostasis. Commitment to the T??cell lineage and subsequent stages of early thymopoiesis is critically regulated by Notch. Recent data indicate that Notch can also direct the differentiation and activity of peripheral T and B cells. Thus, the full spectrum of Notch effects is just beginning to be understood. In this review, we discuss this explosion of knowledge as well as current controversies and challenges in the field.
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    Annual Review of Physiology 67 (2005), S. 25-37 
    ISSN: 0066-4278
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Medicine , Biology
    Notes: Peter Hochachka was one of the most creative forces in the field of comparative physiology during the past half-century. His career was truly an exploratory adventure, in both intellectual and geographic senses. His broad comparative studies of metabolism in organisms as diverse as trout, tunas, oysters, squid, turtles, locusts, hummingbirds, seals, and humans revealed the adaptable features of enzymes and metabolic pathways that provide the biochemical bases for diverse lifestyles and environments. In its combined breadth and depth, no other corpus of work better illustrates the principle of "unity in diversity" that marks comparative physiology. Through his publications, his stimulating mentorship, his broad editorial services, and his continuousĐ??and highly infectiousĐ??enthusiasm for his field, Peter Hochachka served as one of the most influential leaders in the transformation of comparative physiology.
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    Annual Review of Physiology 67 (2005), S. 1-21 
    ISSN: 0066-4278
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Medicine , Biology
    Notes: My scientific life has been spent trying to understand how cells communicate with each other. This interest in cell signaling began with studies on the control of fluid secretion by an insect salivary gland, and the subsequent quest led to the discovery of inositol trisphosphate (IP3) and its role in calcium signaling, which effectively divided my scientific career into two distinct parts. The first part was primarily experimental and culminated in the discovery of IP3, which set the agenda for the second half during which I have enjoyed exploring the many functions of this remarkably versatile signaling system. It has been particularly exciting to find out how this IP3/Ca2+ signaling pathway has been adapted to control processes as diverse as fertilization, proliferation, cell contraction, secretion, and information processing in neuronal cells.
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    Notes: Over the past four years RNA interference (RNAi) has exploded onto the research scene as a new approach to manipulate gene expression in mammalian systems. More recently, RNAi has garnered much interest as a potential therapeutic strategy. In this review, we briefly summarize the current understanding of RNAi biology and examine how RNAi has been used to study the genetic basis of physiological and disease processes in mammalian systems. We also explore some of the new developments in the use of RNAi for disease therapy and highlight the key challenges that currently limit its application in the laboratory, as well as in the clinical setting.
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    Annual Review of Physiology 67 (2005), S. 259-284 
    ISSN: 0066-4278
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Medicine , Biology
    Notes: The stress response is subserved by the stress system, which is located both in the central nervous system and the periphery. The principal effectors of the stress system include corticotropin-releasing hormone (CRH); arginine vasopressin; the proopiomelanocortin-derived peptides ʼ̛-melanocyte-stimulating hormone and ?‚-endorphin, the glucocorticoids; and the catecholamines norepinephrine and epinephrine. Appropriate responsiveness of the stress system to stressors is a crucial prerequisite for a sense of well-being, adequate performance of tasks, and positive social interactions. By contrast, inappropriate responsiveness of the stress system may impair growth and development and may account for a number of endocrine, metabolic, autoimmune, and psychiatric disorders. The development and severity of these conditions primarily depend on the genetic vulnerability of the individual, the exposure to adverse environmental factors, and the timing of the stressful events, given that prenatal life, infancy, childhood, and adolescence are critical periods characterized by increased vulnerability to stressors.
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    Annual Review of Physiology 67 (2005), S. 285-308 
    ISSN: 0066-4278
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Medicine , Biology
    Notes: Tremendous progress has been made in elucidating numerous critical aspects of estrogen signaling. New tools and techniques have enabled detailed molecular analysis of components that direct estrogen responses. At the other end of the spectrum, generation of a multiplicity of transgenic animals has allowed analysis of the physiological roles of the estrogen-signaling components in biologically relevant models. Here, we review the ever-increasing body of knowledge in the field of estrogen biology, especially as applied to the female reproductive processes.
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    Annual Review of Physiology 67 (2005), S. 377-409 
    ISSN: 0066-4278
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Medicine , Biology
    Notes: In many species the pancreatic duct epithelium secretes HCO3 ions at a concentration of around 140 mM by a mechanism that is only partially understood. We know that HCO3 uptake at the basolateral membrane is achieved by Na+-HCO3 cotransport and also by a H+-ATPase and Na+/H+ exchanger operating together with carbonic anhydrase. At the apical membrane, the secretion of moderate concentrations of HCO3 can be explained by the parallel activity of a Cl/HCO3 exchanger and a Cl conductance, either the cystic fibrosis transmembrane conductance regulator (CFTR) or a Ca2+-activated Cl channel (CaCC). However, the sustained secretion of HCO3 into a HCO3 -rich luminal fluid cannot be explained by conventional Cl/HCO3 exchange. HCO3 efflux across the apical membrane is an electrogenic process that is facilitated by the depletion of intracellular Cl, but it remains to be seen whether it is mediated predominantly by CFTR or by an electrogenic SLC26 anion exchanger.
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    Annual Review of Physiology 67 (2005), S. 471-490 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Medicine , Biology
    Notes: The intestines play an important role in the absorption and secretion of nutrients. The colon is the final area for recapturing electrolytes and water prior to excretion, and in order to maintain this electrolyte homeostasis, a complex interaction between secretory and absorptive processes is necessary. Until recently it was thought that secretion and absorption were two distinct processes associated with either crypts or surface cells, respectively. Recently it was demonstrated that both the surface and crypt cells can perform secretory and absorptive functions and that, in fact, these functions can be going on simultaneously. This issue is important in the complexities associated with secretory diarrhea and also in attempting to develop treatment strategies for intestinal disorders. Here, we update the model of colonic secretion and absorption, discuss new issues of transporter activation, and identify some important new receptor pathways that are important modulators of the secretory and absorptive functions of the colon.
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    Annual Review of Physiology 67 (2005), S. 557-572 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Medicine , Biology
    Notes: Reabsorption of amino acids, similar to that of glucose, is a major task of the proximal kidney tubule. Various amino acids are actively transported across the luminal brush border membrane into proximal tubule epithelial cells, most of which by cotransport. An important player is the newly identified cotransporter (symporter) B0AT1 (SLC6A19), which imports a broad range of neutral amino acids together with Na+ across the luminal membrane and which is defective in Hartnup disorder. In contrast, cationic amino acids and cystine are taken up in exchange for recycled neutral amino acids by the heterodimeric cystinuria transporter. The basolateral release of some neutral amino acids into the extracellular space is mediated by unidirectional efflux transporters, analogous to GLUT2, that have not yet been definitively identified. Additionally, cationic amino acids and some other neutral amino acids leave the cell basolaterally via heterodimeric obligatory exchangers.
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    Annual Review of Physiology 67 (2005), S. 663-696 
    ISSN: 0066-4278
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Medicine , Biology
    Notes: Surfactant protein C (SP-C) is a hydrophobic 35-amino acid peptide that co-isolates with the phospholipid fraction of lung surfactant. SP-C represents a structurally and functionally challenging protein for the alveolar type 2 cell, which must synthesize, traffic, and process a 191Đ??197-amino acid precursor protein through the regulated secretory pathway. The current understanding of SP-C biosynthesis considers the SP-C proprotein (proSP-C) as a hybrid molecule that incorporates structural and functional features of both bitopic integral membrane proteins and more classically recognized luminal propeptide hormones, which are subject to post-translational processing and regulated exocytosis. Adding to the importance of a detailed understanding of SP-C biosynthesis has been the recent association of mutations in the proSP-C sequence with chronic interstitial pneumonias in children and adults. Many of these mutations involve either missense or deletion mutations located in a region of the proSP-C molecule that has structural homology to the BRI family of proteins linked to inherited degenerative dementias. This review examines the current state of SP-C biosynthesis with a focus on recent developments related to molecular and cellular mechanisms implicated in the emerging role of SP-C mutations in the pathophysiology of diffuse parenchymal lung disease.
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    Annual Review of Physiology 67 (2005), S. 595-621 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Medicine , Biology
    Notes: Exocytosis is fundamental in biology and requires an orchestra of proteins and other constituents to fuse a vesicle with the plasma membrane. Although the molecular fusion machinery appears to be well conserved in evolution, the process itself varies considerably with regard to the diversity of physico-chemical and structural factors that govern the delay between stimulus and fusion, the expansion of the fusion pore, the release of vesicle content, and, finally, its extracellular dispersion. Exocytosis of surfactant is unique in many of these aspects. This review deals with the secretory pathway of pulmonary surfactant from the type II cell to the air-liquid interface, with focus on the distinct mechanisms and regulation of lamellar body (LB) fusion and release. We also discuss the fate of secreted material until it is rearranged into units that finally function to reduce the surface tension in the lung.
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    Annual Review of Physiology 67 (2005), S. 759-778 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Medicine , Biology
    Notes: Numerous Cl channels have been identified in the kidney using physiological approaches and thus are thought to be involved in a range of physiological processes, including vectorial transepithelial Cl transport, cell volume regulation, and vesicular acidification. In addition, expression of genes from several Cl channel gene families has also been observed. However, the molecular characteristics of a number of Cl channels within the kidney are still unknown, and the physiological roles of Cl channels identified by molecular means remain to be determined. A gene knockout approach using mice might shed further light on the characteristics of these various Cl channels. In addition, study of diseases involving Cl channels (channelopathies) might clarify the physiological role of specific Cl channels. To date, more is known about CLC Cl channels than any other Cl channels within the kidney. This review focuses on the physiological roles of CLC Cl channels within the kidney, particularly kidney-specific ClC-K Cl channels, as well as the recently identified maxi anion channel in macula densa, which is involved in tubulo-glomerular feedback.
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    Annual Review of Physiology 67 (2005), S. 39-67 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Medicine , Biology
    Notes: Although well known as the location of the mechanism by which the cardiac sarcomere is activated by Ca2+ to generate force and shortening, the thin filament is now also recognized as a vital component determining the dynamics of contraction and relaxation. Molecular signaling in the thin filament involves steric, allosteric, and cooperative mechanisms that are modified by protein phosphorylation, sarcomere length and load, the chemical environment, and isoform composition. Approaches employing transgenesis and mutagenesis now permit investigation of these processes at the level of the systems biology of the heart. These studies reveal that the thin filaments are not merely slaves to the levels of Ca2+ determined by membrane channels, transporters and exchangers, but are actively involved in beat to beat control of cardiac function by neural and hormonal factors and by the Frank-Starling mechanism.
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    Annual Review of Physiology 67 (2005), S. 177-201 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Medicine , Biology
    Notes: Recent meta-analyses have shown that the effects of climate change are detectable and significant in their magnitude, but these studies have emphasized the utility of looking for large-scale patterns without necessarily understanding the mechanisms underlying these changes. Using a series of case studies, we explore the potential pitfalls when one fails to incorporate aspects of physiological performance when predicting the consequences of climate change on biotic communities. We argue that by considering the mechanistic details of physiological performance within the context of biophysical ecology (engineering methods of heat, mass and momentum exchange applied to biological systems), such approaches will be better poised to predict where and when the impacts of climate change will most likely occur.
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    Annual Review of Physiology 67 (2005), S. 491-514 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Medicine , Biology
    Notes: Vision at absolute threshold is based on signals produced in a tiny fraction of the rod photoreceptors. This requires that the rods signal the absorption of single photons, and that the resulting signals are transmitted across the retina and encoded in the activity sent from the retina to the brain. Behavioral and ganglion cell sensitivity has often been interpreted to indicate that these biophysical events occur noiselessly, i.e., that vision reaches limits to sensitivity imposed by the division of light into discrete photons and occasional photon-like noise events generated in the rod photoreceptors. We argue that this interpretation is not unique and provide a more conservative view of the constraints behavior and ganglion cell experiments impose on phototransduction and retinal processing. We summarize what is known about how these constraints are met and identify some of the outstanding open issues.
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    Annual Review of Physiology 67 (2005), S. 623-661 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Medicine , Biology
    Notes: Past studies have primarily focused on how altered lung vascular growth and development contribute to pulmonary hypertension. Recently, basic studies of vascular growth have led to novel insights into mechanisms underlying development of the normal pulmonary circulation and the essential relationship of vascular growth to lung alveolar development. These observations have led to new concepts underlying the pathobiology of developmental lung disease, especially the inhibition of lung growth that characterizes bronchopulmonary dysplasia (BPD). We speculate that understanding basic mechanisms that regulate and determine vascular growth will lead to new clinical strategies to improve the long-term outcome of premature babies with BPD.
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    Annual Review of Physiology 67 (2005), S. 719-758 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Medicine , Biology
    Notes: Calcium-activated chloride channels (CaCCs) play important roles in cellular physiology, including epithelial secretion of electrolytes and water, sensory transduction, regulation of neuronal and cardiac excitability, and regulation of vascular tone. This review discusses the physiological roles of these channels, their mechanisms of regulation and activation, and the mechanisms of anion selectivity and conduction. Despite the fact that CaCCs are so broadly expressed in cells and play such important functions, understanding these channels has been limited by the absence of specific blockers and the fact that the molecular identities of CaCCs remains in question. Recent status of the pharmacology and molecular identification of CaCCs is evaluated.
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    Annual Review of Physiology 67 (2005), S. 701-718 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Medicine , Biology
    Notes: The assembly of the cystic fibrosis transmembrane regulator (CFTR) chloride channel is of interest from the broad perspective of understanding how ion channels and ABC transporters are formed as well as dealing with the mis-assembly of CFTR in cystic fibrosis. CFTR is functionally distinct from other ABC transporters because it permits bidirectional permeation of anions rather than vectorial transport of solutes. This adaptation of the ABC transporter structure can be rationalized by considering CFTR as a hydrolyzable-ligand-gated channel with cytoplasmic ATP as ligand. Channel gating is initiated by ligand binding when the protein is also phosphorylated by protein kinase A and made reversible by ligand hydrolysis. The two nucleotide-binding sites play different roles in channel activation. CFTR self-associates, possibly as a function of its activation, but most evidence, including the low-resolution three-dimensional structure, indicates that the channel is monomeric. Domain assembly and interaction within the monomer is critical in maturation, stability, and function of the protein. Disease-associated mutations, including the most common, ??F508, interfere with domain folding and association, which occur both co- and post-translationally. Intermolecular interactions of mature CFTR have been detected primarily with the N- and C-terminal tails, and these interactions have some impact not only on channel function but also on localization and processing within the cell. The biosynthetic processing of the nascent polypeptide leading to channel assembly involves transient interactions with numerous chaperones and enzymes on both sides of the endoplasmic reticulum membrane.
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    Annual Review of Physiology 67 (2005), S. 809-839 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Medicine , Biology
    Notes: The CLC family comprises a group of integral membrane proteins whose major action is to translocate chloride (Cl) ions across the cell membranes. Recently, the structures of CLC orthologues from two bacterial species, Salmonella typhimurium and Escherichia coli, were solved, providing the first framework for understanding the operating mechanisms of these molecules. However, most of the previous mechanistic understanding of CLC channels came from electrophysiological studies of a branch of the channel family, the muscle-type CLC channels in vertebrate species. These vertebrate CLC channels were predicted to contain two identical but independent pores, and this hypothesis was confirmed by the solved bacterial CLC structures. The opening and closing of the vertebrate CLC channels are also known to couple to the permeant ions via their binding sites in the ion-permeation pathway. The bacterial CLC structures can probably serve as a structural model to explain the gating-permeation coupling mechanism. However, the CLC-ec1 protein in E. coli was most recently shown to be a Cl-H+ antiporter, but not an ion channel. The molecular basis to explain the difference between vertebrate and bacterial CLCs, especially the distinction between an ion channel and a transporter, remains a challenge in the structure/function studies for the CLC family.
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    Annual Review of Anthropology 34 (2005), S. 639-665 
    ISSN: 0084-6570
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Ethnic Sciences , Biology
    Notes: Despite the efforts of international health agencies to reduce global health inequalities, indigenous populations around the world remain largely unaffected by such initiatives. This chapter reviews the biomedical literature indexed by the PubMed database published between 1963 and 2003 on South American indigenous populations, a total of 1864 studies that include 63,563 study participants. Some language family groupings are better represented than are others, and lowland groups are better represented than are highland groups. Very few studies focus on major health threats (e.g., tuberculosis, influenza), public health interventions, or mestizo-indigenous epidemiological comparisons. The prevalence rates of three frequently studied infectionsĐ??parasitism, human T-cell lymphotropic viral infection (HTLV), and hepatitisĐ??are extraordinarily high, but these facts have been overlooked by national and international health agencies. This review underscores the urgent need for interventions based on known disease prevalence rates to reduce the burden of infectious diseases in indigenous communities.
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    Annual Review of Anthropology 34 (2005), S. 741-756 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Ethnic Sciences , Biology
    Notes: In the wake of critiques that have rendered problematic such familiar objects of study as culture and social structure, anthropologists seeking ways to engage ethnographically with the complexities of the contemporary world have fashioned new kinds of objects of study. These generally continue, however, to be framed as just thatĐ??as objects. Rather than pursue the "anthropology of" any particular object that preexists ethnography, anthropologists should find ways of bringing the openness and creativity of ethnographic work more boldly into the theoretical framing of what it is that they study. I propose here the notion of surfacing the body interior as one framing device that may help facilitate such ethnographic explorations into bodies, their interiors, and their surfaces as contingent configurations made and unmade through practices that are at once social, material, and representational.
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    Annual Review of Anthropology 34 (2005), S. 317-341 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Ethnic Sciences , Biology
    Notes: This essay reviews recent anthropological attention to the "beginnings" and "endings" of life. A large literature since the 1990s highlights the analytic trends and innovations that characterize anthropological attention to the cultural production of persons, the naturalization of life, and the emergence of new life forms. Part I of this essay outlines the coming-into-being, completion and attenuation of personhood and how life and death are attributed, contested, and enacted. Dominant themes include how connections are forged or severed between the living and the dead and the socio-politics of dead, dying, and decaying bodies. The culture of medicine is examined for its role in organizing and naming life and death. Part II is organized by the turn to biopolitical analyses stimulated by the work of Foucault. It encompasses the ways in which the biosciences and biotechnologies, along with state practices, govern forms of living and dying and new forms of life such as the stem cell, embryo, comatose, and brain dead, and it emphasizes the production of value. Much of this scholarship is informed by concepts of liminality (a period and state of being between social statuses) and subjectification (in which notions of self, citizenship, life and its management are linked to the production of knowledge and political forms of regulation).
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    Annual Review of Anthropology 34 (2005), S. 13 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Ethnic Sciences , Biology
    Notes: Scholarly interest in body size has increased in concert with recent efforts to shape and assess bodies in particular ways within industrialized social contexts. Attending to both overt and covert references to Eurocentric body projects, this chapter reviews literature in anthropology, sociology, and cultural studies that addresses the cultural politics of body size in various parts of the world. It begins with a discussion of biocultural paradigms, which accept certain biomedical categories even when challenging or reconfiguring their hegemonic power. Next is a survey of works analyzing body size within "non-Western" groups as well as European and North American subgroups. These studies often employ culturally powerful "Western" constructs as foils, an approach that risks cultural othering. The analysis then turns to the extensive literature that unpacks dominant Euro-American body practices and discourses. Here, diverse perspectives on several key concerns in sociocultural anthropology are considered; concepts of culture and power, theories of the body and embodiment, and understandings of human agency vary in instructive ways. The chapter concludes with a review of scholarship on postcolonial processes and representations that incorporates a critical perspective on Eurocentric preoccupations with body size.
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    Annual Review of Anthropology 34 (2005), S. 495-521 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Ethnic Sciences , Biology
    Notes: Immune function is notoriously complex, and current biomedical research elaborates this complexity by focusing on the cellular and molecular mechanisms that characterize immune defenses. However, the human immune system is a product of natural selection that develops and functions in whole organisms that are integral parts of their surrounding environments. A population-level, cross-cultural, adaptationist perspective is therefore a necessary complement to the micro levels of analysis currently favored by biomedical immunology. Prior field-based research on human immunity is reviewed to demonstrate the relevance of cultural ecological factors, with an emphasis on the ecologies of nutrition, infectious disease, reproduction, and psychosocial stress. Common themes and anthropological contributions are identified in an attempt to promote future research in human ecological immunology that integrates theory and method for a more contextualized understanding of this important physiological system.
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    Annual Review of Anthropology 34 (2005), S. 207 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Ethnic Sciences , Biology
    Notes: Perceptions of the emergence and spread of modern humans have changed recently through the reanalysis of fossils, an improved geochronological framework, and the discovery of a few specimens. Early modern humans in various portions of the Old World exhibit complex and varying mosaics of archaic, modern, and regional morphological characteristics. On the basis of this pattern, in conjunction with the emerging chronology of the earliest modern humans, the paleontological data indicate an assimilation model for modern human origins, in which the earliest modern humans emerged in eastern Africa, dispersed briefly into southwestern Asia, and then subsequently spread into the remainder of Africa and southern Asia, eventually into higher latitude Eurasia. The earliest modern humans outside of the core area of eastern Africa can be understood only if a variable degree of admixture with regional groups of late archaic humans occurred. Current and expected fossil and molecular data are unlikely to illuminate the degree of assimilation that took place in most regions of the Old World. However, the current chronological and phylogenetic framework provides the basis for ongoing investigation of the nature of this Late Pleistocene transitional period.
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    Annual Review of Anthropology 34 (2005), S. 549-573 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Ethnic Sciences , Biology
    Notes: This review examines literature on indigenous movements in Latin America from 1992 to 2004. It addresses ethnic identity and ethnic activism, in particular the reindianization processes occurring in indigenous communities throughout the region. We explore the impact that states and indigenous mobilizing efforts have had on each other, as well as the role of transnational nongovernmental organizations and para-statal organizations, neoliberalism more broadly, and armed conflict. Shifts in ethnoracial, political, and cultural indigenous discourses are examined, special attention being paid to new deployments of rhetorics concerned with political imaginaries, customary law, culture, and identity. Self-representational strategies will be numerous and dynamic, identities themselves multiple, fluid, and abundantly positional. The challenges these dynamics present for anthropological field research and ethnographic writing are discussed, as is the dialogue between scholars, indigenous and not, and activists, indigenous and not. Conclusions suggest potentially fruitful research directions for the future.
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    Annual Review of Earth and Planetary Sciences 33 (2005), S. 605-643 
    ISSN: 0084-6597
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Geosciences , Physics
    Notes: Various forms of atmospheric moist convection are reviewed through a consideration of three prevalent regimes: stratocumulus; trade-wind; and deep, precipitating, maritime convection. These regimes are chosen because they are structural components of the general circulation of the atmosphere and because they highlight distinguishing features of this polymorphous phenomenon. In particular, the ways in which varied forms of moist convection communicate with remote parts of the flow through mechanisms other than the rearrangement of fluid parcels are emphasized. These include radiative, gravity wave, and/or microphysical (precipitation) processes. For each regime, basic aspects of its phenomenology are presented along with theoretical frameworks that have arisen to help rationalize the phenomenology. Recent developments suggest that the increased capacity for numerical simulation and increasingly refined remote sensing capabilities bodes well for major advances in the coming years.
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    Annual Review of Earth and Planetary Sciences 33 (2005), S. 461-491 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Geosciences , Physics
    Notes: Recent developments in volcanic seismology include new techniques to improve earthquake locations that have changed clouds of earthquakes to lines (faults) for high-frequency events and small volumes for low-frequency (LF) events. Spatial mapping of the b-value shows regions of normal b and high b anomalies at depths of 3-4 and 7-10 km. Increases in b precede some eruptions. LF events and very-long-period (VLP) events have been recorded at many volcanoes, and models are becoming increasingly sophisticated. Deep long-period (LP) events are fairly common, but may represent several processes. Acoustic sensors have greatly improved the study of volcanic explosions. Volcanic tremor is stronger for fissure eruptions, phreatic eruptions, and higher gas contents. Path and site effects can be extreme at volcanoes. Seismicity at volcanoes is triggered by large earthquakes, although mechanisms are still uncertain. A number of volcanoes have significant deformation with very little seismicity. Tomography has benefited from improved techniques and better instrumental arrays.
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    Annual Review of Earth and Planetary Sciences 33 (2005), S. 571-604 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Geosciences , Physics
    Notes: Contrary to Earth, the interior of terrestrial planets is poorly known. This is mainly related to the lack of seismic data and of planetary seismic networks on these planets. So far, despite several attempts, only the Apollo Seismic Network has returned seismic information from the Moon. But even in this case, very few seismic signals were recorded after a propagation path through the deep interior and core owing to a hemispheric distribution of the stations on the near side and to a probably strongly attenuating lower mantle. This review presents the main results achieved by the analysis of the Apollo seismic data and the associated constraints on the internal structure of the Moon. It then presents the current knowledge on the Martian interior, the seismic activity of the planet, and possible source of seismic noise. This information can be used for preparing future Martian seismic network missions. A short review on existing space-qualified instruments and on possible seismic missions toward other telluric bodies, such as Venus, the giant planets' satellites, or small bodies, is then given.
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    Annual Review of Earth and Planetary Sciences 33 (2005), S. 493-530 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Geosciences , Physics
    Notes: We know that giant planets played a crucial role in the making of our Solar System. The discovery of giant planets orbiting other stars is a formidable opportunity to learn more about these objects, what their composition is, how various processes influence their structure and evolution, and most importantly how they form. Jupiter, Saturn, Uranus, and Neptune can be studied in detail, mostly from close spacecraft flybys. We can infer that they are all enriched in heavy elements compared to the Sun, with the relative global enrichments increasing with distance to the Sun. We can also infer that they possess dense cores of varied masses. The intercomparison of presently characterized extrasolar giant planets shows that they are also mainly made of hydrogen and helium, but that they either have significantly different amounts of heavy elements, have had different orbital evolutions, or both. Hence, many questions remain and need to be answered to make significant progress on the origins of planets.
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    Annual Review of Earth and Planetary Sciences 33 (2005), S. 645-671 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Geosciences , Physics
    Notes: The influence of surface orography on patterns of precipitation gives rise to some of the most pronounced climate gradients on Earth, and plays a fundamental role in the interaction between the atmosphere and the rest of the Earth System on a wide variety of time scales. The physical mechanisms involved comprise a rich set of interactions encompassing fluid dynamics, thermodynamics, and micron-scale cloud processes, as well as being dependent on the larger-scale patterns of the atmospheric general circulation. Investigations into orographic precipitation have pursued three parallel tracks of inquiry: observations, theory, and modeling. Significant advances have been made in each over the last few decades, and these are summarized and synthesized here. While many aspects of the basic mechanisms responsible for orographic precipitation have been understood, important issues remain unresolved. The sheer number of contributing processes, together with their convoluted interactions, make the quantitative prediction of precipitation in complex terrain a very hard task. However, while prediction of precipitation amounts for any given event may be difficult, various lines of evidence suggest that the patterns of orgraphic precipitation, even on scales of a few kilometers, are much more robust.
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    Annual Review of Earth and Planetary Sciences 33 (2005), S. 133-161 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Geosciences , Physics
    Notes: The bulk of the Đ♯50-km-thick Martian crust formed at Đ♯4.5 Gyr B.P., perhaps from a magma ocean. This crust is probably a basaltic andesite or andesite and is enriched in incompatible and heat-producing elements. Later additions of denser basalt to the crust were volumetrically minor, but resurfaced significant portions of the Northern hemisphere. A significant fraction of the total thickness of the crust was magnetized prior to 4 Gyr B.P., with the magnetization later selectively removed by large impacts. Early large impacts also modified the hemispheric contrast in crustal thickness (the dichotomy), which was possibly caused by long-wavelength mantle convection. Subsequent Noachian modification of the crust included further impacts, significant fluvial erosion, and volcanism associated with the formation of the Tharsis rise. Remaining outstanding questions include the origin of the dichotomy and the nature of the magnetic anomalies.
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    Annual Review of Earth and Planetary Sciences 33 (2005), S. 247-276 
    ISSN: 0084-6597
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Geosciences , Physics
    Notes: Processes operating beneath glaciers can have a greater influence on flow dynamics than those operating within them. The variety and complexity of these processes, which involve interactions among ice, water, and geological solids, resist efforts to establish simple truths and can lead to surprising outcomes. Thermal conditions at the ice-bed interface (melting or nonmelting) and the mechanical properties of the glacier substrate (soft or hard) determine which processes can be activated. The warm-soft case supports the greatest variety of processes and is the most important for fast-flow dynamics and for the mobilization of subglacial sediment. Process interactions can lead to oscillations and spatio-temporal switching behavior in glaciers and ice sheets as well as to the generation of subglacial landforms.
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    Annual Review of Earth and Planetary Sciences 33 (2005), S. 421-442 
    ISSN: 0084-6597
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Geosciences , Physics
    Notes: The Ediacara biota (575Đ??542 Ma) marks the first appearance of large, architecturally complex organisms in Earth history. Present evidence suggests that the Ediacara biota included a mixture of stem- and crown-group radial animals, stem-group bilaterian animals, "failed experiments" in animal evolution, and perhaps representatives of other eukaryotic kingdoms. These soft-bodied organisms were preserved under (or rarely within) event beds of sand or volcanic ash, and four distinct preservational styles (Flinders-, Fermeuse-, Conception-, and Nama-style) profoundly affected the types of organisms and features that could be preserved. Even the earliest Ediacaran communities (575Đ??565 Ma) show vertical and lateral niche subdivision of the sessile, benthic, filter-feeding organisms, which is strikingly like that of Phanerozoic and modern communities. Later biological and ecological innovations include mobility (〉555 Ma), calcification (550 Ma), and predation (〈549 Ma). The Ediacara biota abruptly disappeared 542 million years ago, probably as a consequence of mass extinction andor biological interactions with the rapidly evolving animals of the Cambrian explosion.
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    Annual Review of Earth and Planetary Sciences 33 (2005), S. 571-604 
    ISSN: 0084-6597
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Geosciences , Physics
    Notes: Contrary to Earth, the interior of terrestrial planets is poorly known. This is mainly related to the lack of seismic data and of planetary seismic networks on these planets. So far, despite several attempts, only the Apollo Seismic Network has returned seismic information from the Moon. But even in this case, very few seismic signals were recorded after a propagation path through the deep interior and core owing to a hemispheric distribution of the stations on the near side and to a probably strongly attenuating lower mantle. This review presents the main results achieved by the analysis of the Apollo seismic data and the associated constraints on the internal structure of the Moon. It then presents the current knowledge on the Martian interior, the seismic activity of the planet, and possible source of seismic noise. This information can be used for preparing future Martian seismic network missions. A short review on existing space-qualified instruments and on possible seismic missions toward other telluric bodies, such as Venus, the giant planets' satellites, or small bodies, is then given.
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    Annual Review of Neuroscience 28 (2005), S. 377-401 
    ISSN: 0147-006X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Plasticity is an intrinsic property of the human brain and represents evolution's invention to enable the nervous system to escape the restrictions of its own genome and thus adapt to environmental pressures, physiologic changes, and experiences. Dynamic shifts in the strength of preexisting connections across distributed neural networks, changes in task-related cortico-cortical and cortico-subcortical coherence and modifications of the mapping between behavior and neural activity take place in response to changes in afferent input or efferent demand. Such rapid, ongoing changes may be followed by the establishment of new connections through dendritic growth and arborization. However, they harbor the danger that the evolving pattern of neural activation may in itself lead to abnormal behavior. Plasticity is the mechanism for development and learning, as much as a cause of pathology. The challenge we face is to learn enough about the mechanisms of plasticity to modulate them to achieve the best behavioral outcome for a given subject.
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    Annual Review of Genomics and Human Genetics 6 (2005), S. 331-354 
    ISSN: 1527-8204
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Altering DNA copy number is one of the many ways that gene expression and function may be modified. Some variations are found among normal individuals (14, 35, 103), others occur in the course of normal processes in some species (33), and still others participate in causing various disease states. For example, many defects in human development are due to gains and losses of chromosomes and chromosomal segments that occur prior to or shortly after fertilization, whereas DNA dosage alterations that occur in somatic cells are frequent contributors to cancer. Detecting these aberrations, and interpreting them within the context of broader knowledge, facilitates identification of critical genes and pathways involved in biological processes and diseases, and provides clinically relevant information. Over the past several years array comparative genomic hybridization (array CGH) has demonstrated its value for analyzing DNA copy number variations. In this review we discuss the state of the art of array CGH and its applications in medical genetics and cancer, emphasizing general concepts rather than specific results.
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    Annual Review of Genomics and Human Genetics 6 (2005), S. 123-142 
    ISSN: 1527-8204
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: The ATP-binding cassette (ABC) superfamily of genes encode membrane proteins that transport a diverse set of substrates across membranes. Mutations in ABC transporters cause or contribute to many different Mendelian and complex disorders including adrenoleukodystrophy, cystic fibrosis, retinal degeneration, hypercholesterolemia, and cholestasis. The genes play important roles in protecting organisms from xenobiotics and transport compounds across the intestine, blood-brain barrier, and the placenta. There are 48 ABC genes in the human genome divided into seven subfamilies based on amino acid sequence similarities and phylogeny. These seven subfamilies are represented in all eukaryotic genomes and are therefore of ancient origin. Sequencing the genomes of numerous vertebrate organisms has allowed the complement of ABC transporters to be characterized and the evolution of the genes to be assessed. Most ABC transporters are conserved in all vertebrates, but there are also several examples of recent duplication and gene loss. For genes with a conserved ortholog, animal models have been identified or developed that can be used to probe the function and regulation of selected genes. Genes that are restricted to a specific group of animals may represent specialized functions that could provide insight into unique biological properties of that organism. Further characterization of all ABC transporters from the human genome and from model organisms will lead to additional insights into normal physiology and human disease.
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    Annual Review of Genomics and Human Genetics 6 (2005), S. 261-286 
    ISSN: 1527-8204
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Chemical genetics is an emerging approach for studying biological systems using chemical tools. This strategy aims to reveal the macromolecules responsible for regulating biological systems; thus, the approach shares much in common with genetics. In both strategies, one must (a) develop an assay that reports on a biological process of interest, (b) perturb this process systematically (with mutations or small molecules), and (c) determine the target of each perturbation to reveal macromolecules (i.e., proteins and genes) regulating the process of interest. In this review, we discuss advances and challenges in this field that have emerged over the past four years. Several technologies have converged, raising the hope that it may be possible to systematically apply chemical probes to biological processes.
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    Annual Review of Genomics and Human Genetics 6 (2005), S. 313-330 
    ISSN: 1527-8204
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
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    Annual Review of Genomics and Human Genetics 6 (2005), S. 93-122 
    ISSN: 1527-8204
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Psoriasis is an inflammatory/autoimmune disease and, as with many autoimmune diseases, is associated with alleles from the major histocompatibility complex (MHC). With psoriasis and autoimmune disease, the penetrance of the MHC-associated alleles is never 100%, even for monozygotic twins. This may be because development requires additional environmental and/or genetic modifiers or requires specific T-cell receptor arrangements. Families segregating single or multilocus susceptibility alleles other than the MHC have also been reported. Overlapping genetic locations of loci for different autoimmune diseases have been known for several years and are starting to reveal common genes or genetic variants. These include genes normally involved in preventing spontaneous T-cell activation or proliferation, immune synapse formation, or cytokine production via pathways such as those mediated by NF?”B and those involved in thymic selection. Autoimmunity may also involve dysregulation of genes or pathways regulated by the RUNX family of transcription factors. RUNX is involved in hematopoietic cell development, development of T cells in the thymus, chromatin remodeling, and gene silencing. Hence, its effect on cells of the immune system may be due to variable changes in gene expression and could account for variable body surface involvement and waxing and waning of disease.
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    Annual Review of Genomics and Human Genetics 6 (2005), S. 237-260 
    ISSN: 1527-8204
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Cystic fibrosis (CF) is the most common lethal autosomal recessive disorder in the Caucasian population, affecting about 30,000 individuals in the United States. The gene responsible for CF, the CF transmembrane conductance regulator (CFTR), was identified 15 years ago. Substantial variation in the many aspects of the CF phenotype among individuals with the same CFTR genotype demonstrates that factors independent of CFTR exert considerable influence on outcome in CF. To date, the majority of published studies investigating the cause of disease variability in CF report associations between candidate genes and some aspect of the CF phenotype. However, a definitive modifier gene for CF remains to be identified. Despite the challenges posed by searches for modifier effects, studies of affected twins and siblings indicate that genetic factors play a substantial role in intestinal manifestations. Identifying the factors contributing to variation in pulmonary disease, the primary cause of mortality, remains a challenge for CF research.
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    Annual Review of Genomics and Human Genetics 6 (2005), S. 69-92 
    ISSN: 1527-8204
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Mammalian X chromosome inactivation is one of the most striking examples of epigenetic gene regulation. Early in development one of the pair of Đ♯160-Mb X chromosomes is chosen to be silenced, and this silencing is then stably inherited through subsequent somatic cell divisions. Recent advances have revealed many of the chromatin changes that underlie this stable silencing of an entire chromosome. The key initiator of these changes is a functional RNA, XIST, which is transcribed from, and associates with, the inactive X chromosome, although the mechanism of association with the inactive X and recruitment of facultative heterochromatin remain to be elucidated. This review describes the unique evolutionary history and resulting genomic structure of the X chromosome as well as the current understanding of the factors and events involved in silencing an X chromosome in mammals.
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    Annual Review of Environment and Resources 30 (2005), S. 1-37 
    ISSN: 1543-5938
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Energy, Environment Protection, Nuclear Power Engineering
    Notes: The regional nature of several important air pollutants, which include acids, ozone, particulate matter, mercury, and persistent organics (POPs), is widely recognized by researchers and decision makers. Such pollutants are transported regionally over scales from about 100 to a few 1000s of kilometers, large enough to cross state, provincial, national, and even continental boundaries. Managing these regional pollutants requires overcoming political, economic, and cultural differences to establish cooperation between multiple jurisdictions, and it requires recognition of the linkages between pollutants and of impacts at different geographic scales. Here, regional dynamics of the pollutants are discussed, addressing them individually and as a tightly linked physical and chemical system. Collaborative efforts to characterize and manage regional pollution are presented, along with potential directions for future efforts.
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    Annual Review of Environment and Resources 30 (2005), S. 219-252 
    ISSN: 1543-5938
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Energy, Environment Protection, Nuclear Power Engineering
    Notes: The world's system of protected areas has grown exponentially over the past 25 years, particularly in developing countries where biodiversity is greatest. Concurrently, the mission of protected areas has expanded from biodiversity conservation to improving human welfare. The result is a shift in favor of protected areas allowing local resource use. Given the multiple purposes of many protected areas, measuring effectiveness is difficult. Our review of 49 tropical protected areas shows that parks are generally effective at curtailing deforestation within their boundaries. But deforestation in surrounding areas is isolating protected areas. Many initiatives now aim to link protected areas to local socioeconomic development. Some of these initiatives have been successful, but in general expectations need to be tempered regarding the capacity of protected areas to alleviate poverty. Greater attention must also be paid to the broader policy context of biodiversity loss, poverty, and unsustainable land use in developing countries.
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    Annual Review of Environment and Resources 30 (2005), S. 39-74 
    ISSN: 1543-5938
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Energy, Environment Protection, Nuclear Power Engineering
    Notes: Estimates of global wetland area range from 5.3 to 12.8 million km2. About half the global wetland area has been lost, but an international treaty (the 1971 Ramsar Convention) has helped 144 nations protect the most significant remaining wetlands. Because most nations lack wetland inventories, changes in the quantity and quality of the world's wetlands cannot be tracked adequately. Despite the likelihood that remaining wetlands occupy less than 9% of the earth's land area, they contribute more to annually renewable ecosystem services than their small area implies. Biodiversity support, water quality improvement, flood abatement, and carbon sequestration are key functions that are impaired when wetlands are lost or degraded. Restoration techniques are improving, although the recovery of lost biodiversity is challenged by invasive species, which thrive under disturbance and displace natives. Not all damages to wetlands are reversible, but it is not always clear how much can be retained through restoration. Hence, we recommend adaptive approaches in which alternative techniques are tested at large scales in actual restoration sites.
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    Annual Review of Environment and Resources 30 (2005), S. 253-289 
    ISSN: 1543-5938
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Energy, Environment Protection, Nuclear Power Engineering
    Notes: For years economists have urged policy makers to use market-based approaches such as cap-and-trade programs or emission taxes to control pollution. The sulfur dioxide (SO2) allowance market created by Title IV of the 1990 U.S. Clean Air Act Amendments represents the first real test of the wisdom of economists' advice. Subsequent urban and regional applications of nitrogen oxides (NOx) emission allowance trading took shape in the 1990s in the United States, culminating in a second large experiment in emissions trading in the eastern United States that began in 2003. This review provides an overview of the economic rationale for emissions trading and a description of the major U.S. programs to reduce SO2 and NOx pollution. We evaluate these programs along measures of performance, which include cost savings, environmental integrity, and incentives for technological innovation. We offer lessons for the design of future programs including, most importantly, those to reduce carbon dioxide.
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    Annual Review of Environment and Resources 30 (2005), S. 409-440 
    ISSN: 1543-5938
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Energy, Environment Protection, Nuclear Power Engineering
    Notes: Although human-induced changes to the global environment and natural biotic resources, collectively labeled "global change" and the "biodiversity crisis," have accelerated with industrialization over the past 300 years, such changes have a much longer history. Particularly since the rise of agriculturally based societies and associated population expansion during the early Holocene, humans have had cumulative and often irreversible impacts on natural landscapes and biotic resources worldwide. Archaeologists, often working closely with natural scientists in interdisciplinary projects, have accumulated a large body of empirical evidence documenting such changes as deforestation, spread of savannahs, increased rates of erosion, permanent rearrangements of landscapes for agriculture, resource depression and depletion (and in many cases, extinction) in prehistory. In some areas and time periods, environmental change led to long-term negative consequences for regional human populations, whereas in other cases, changes favored intensification of production and increased population sizes. Drawing upon case studies from North America, Mesoamerica, the Mediterranean, Near East, India, Australia, and the Pacific Islands, the diversity of types of prehistoric human-induced environmental change is assessed, along with the kinds of empirical evidence that support these interpretations. These findings have important implications both for the understanding of long-term human socioeconomic and political changes and for ecologists who need to assess current environmental dynamics in the context of longer-term environmental history.
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    Annual Review of Genomics and Human Genetics 6 (2005), S. 355-379 
    ISSN: 1527-8204
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Sulfatases are a highly conserved family of proteins that cleave sulfate esters from a wide range of substrates. The importance of sulfatases in human metabolism is underscored by the presence of at least eight human monogenic diseases caused by the deficiency of individual sulfatases. Sulfatase activity requires a unique posttranslational modification, which is impaired in patients with multiple sulfatase deficiency (MSD) due to a mutation of the sulfatase modifying factor 1 (SUMF1). Here we review current knowledge and future perspectives on the evolution of the sulfatase gene family, on the role of these enzymes in human metabolism, and on new developments in the therapy of sulfatase deficiencies.
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