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  • Articles  (14,929)
  • Wiley-Blackwell  (12,970)
  • Annual Reviews
  • 1995-1999  (14,929)
  • 1980-1984
  • 1935-1939
  • 1999  (2,543)
  • 1997  (12,386)
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  • 1995-1999  (14,929)
  • 1980-1984
  • 1935-1939
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Journal
  • 1
    Electronic Resource
    Electronic Resource
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 26 (1997), S. 1-25 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
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  • 2
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 26 (1997), S. 27-45 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract The scope and utility of phage display is reviewed with emphasis on medical applications and structure-based ligand and drug design, from literature mostly after 1994. General principles by which phage-displayed peptides achieve affinity and selectivity for targets are described, along with selected structural or mechanistic studies of the binding of peptides or proteins discovered or engineered by phage display. Such engineered proteins whose wild-type or mutant crystal or 2D-NMR structures yield insight about the basis for enhanced affinity or altered specificity include antibodies, zinc fingers, human growth hormone, protein A, and atrial natriuretic peptide. Structures of complexes of de novo phage-discovered peptide ligands with targets such as the Src SH3 domain, streptavidin, and erythropoietin receptor reveal the structural basis for receptor-peptide recognition in these systems.
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  • 3
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 26 (1997), S. 83-112 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Chromatin structure is now believed to be dynamic and intimately related with cellular processes such as transcription. Over the past few years, high-resolution structures for the histones have become available. These structures and their implications for nucleosome organization are reviewed here.
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  • 4
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    Annual Review of Biophysics and Biomolecular Structure 26 (1997), S. 113-137 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract The evidence showing that the self-assembly of complex RNAs occurs in discrete transitions, each relating to the folding of sub-systems of increasing size and complexity starting from a state with most of the secondary structure, is reviewed. The reciprocal influence of the concentration of magnesium ions and nucleotide mutations on tertiary structure is analyzed. Several observations demonstrate that detrimental mutations can be rescued by high magnesium concentrations, while stabilizing mutations lead to a lesser dependence on magnesium ion concentration. Recent data point to the central controlling and monitoring roles of RNA-binding proteins that can bind to the different folding stages, either before full establishment of the secondary structure or at the molten globule state before the cooperative transition to the final three-dimensional structure.
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  • 5
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    Annual Review of Biophysics and Biomolecular Structure 26 (1997), S. 139-156 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract One of the fundamental properties of the RNA helix is its intrinsic resistance to bend- or twist-deformations. Results of a variety of physical measurements point to a persistence length of 700-800 A for double-stranded RNA in the presence of magnesium cations, approximately 1.5-2.0-fold larger than the corresponding value for DNA. Although helix flexibility represents an important, quantifiable measure of the forces of interaction within the helix, it must also be considered in describing conformational variation of nonhelix elements (e.g. internal loops, branches), since the latter always reflect the properties of the flanking helices; that is, such elements are never completely rigid. For one important element of tertiary structure, namely, the core of yeast tRNAPhe, the above consideration has led to the conclusion that the core is not substantially more flexible than an equivalent length of pure helix.
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  • 6
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    Annual Review of Biophysics and Biomolecular Structure 26 (1997), S. 157-179 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Phospholamban is a 52-amino-acid protein that assembles into a pentamer in sarcoplasmic reticulum membranes. The protein has a role in the regulation of the resident calcium ATPase through an inhibitory association that can be reversed by phosphorylation. The phosphorylation of phospholamban is initiated by beta-adrenergic stimulation, identifying phospholamban as an important component in the stimulation of cardiac activity by beta-agonists. It is this role of phospholamban that has motivated studies in recent decades. There is evidence that phospholamban may also function as a Ca2+-selective ion channel. The structural properties of phospholamban have been studied by mutagenesis, modeling, and spectroscopy, resulting in a new view of the organization of this key molecule in membranes.
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  • 7
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 26 (1997), S. 181-222 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Innovative algorithms have been developed during the past decade for simulating Newtonian physics for macromolecules. A major goal is alleviation of the severe requirement that the integration timestep be small enough to resolve the fastest components of the motion and thus guarantee numerical stability. This timestep problem is challenging if strictly faster methods with the same all-atom resolution at small timesteps are sought. Mathematical techniques that have worked well in other multiple-timescale contexts-where the fast motions are rapidly decaying or largely decoupled from others-have not been as successful for biomolecules, where vibrational coupling is strong. This review examines general issues that limit the timestep and describes available methods (constrained, reduced-variable, implicit, symplecttic, multiple-timestep, and normal-mode-based schemes). A section compares results of selected integrators for a model dipeptide, assessing physical and numerical performance. Included is our dual timestep method LN, which relies on an approximate linearization of the equations of motion every Deltat interval (5 fs or less), the solution of which is obtained by explicit integration at the inner timestep Deltatau (e.g., 0.5 fs). LN is computationally competitive, providing 4-5 speedup factors, and results are in good agreement, in comparison to 0.5 fs trajectories. These collective algorithmic efforts help fill the gap between the time range that can be simulated and the timespans of major biological interest (milliseconds and longer). Still, only a hierarchy of models and methods, along with experimentational improvements, will ultimately give theoretical modeling the status of partner with experiment.
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  • 8
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    Annual Review of Biophysics and Biomolecular Structure 26 (1997), S. 223-258 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Two sensory rhodopsins (SRI and SRII) mediate color-sensitive phototaxis responses in halobacteria. These seven-helix receptor proteins, structurally and functionally similar to animal visual pigments, couple retinal photoisomerization to receptor activation and are complexed with membrane-embedded transducer proteins (HtrI and HtrII) that modulate a cytoplasmic phosphorylation cascade controlling the flagellar motor. The Htr proteins resemble the chemotaxis transducers from Escherichia coli. The SR-Htr signaling complexes allow studies of the biophysical chemistry of signal generation and relay, from the photobiophysics of initial excitation of the receptors to the final output at the level of the flagellar motor switch, revealing fundamental principles of sensory transduction and more broadly the nature of dynamic interactions between membrane proteins. We review here recent advances that have led to new insights into the molecular mechanism of signaling by these membrane complexes.
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  • 9
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    Annual Review of Biophysics and Biomolecular Structure 26 (1997), S. 259-288 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract A characteristic feature of cellular signal transduction pathways in eukaryotes is the separation of catalysis from target recognition. Several modular domains that recognize short peptide sequences and target signaling proteins to these sequences have been identified. The structural bases of the specificities of recognition by SH2, SH3, and PTB domains have been elucidated by X-ray crystallography and NMR, and these results are reviewed here. In addition, the mechanism of cooperative interactions between these domains is discussed.
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  • 10
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    Annual Review of Biophysics and Biomolecular Structure 26 (1997), S. 357-371 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Zinc-finger domains are small metal-binding modules that are found in a wide range of gene regulatory proteins. Peptides corresponding to these domains have provided valuable model systems for examining a number of biophysical parameters entirely unrelated to their nucleic acid binding properties. These include the chemical basis for metal-ion affinity and selectivity, thermodynamic properties related to hydrophobic packing and beta-sheet propensities, and constraints on the generation of ligand-binding and potential catalytic sites. These studies have laid the foundation for applications such as the generation of optically detected zinc probes and the design of metal-binding peptides and proteins with desired spectroscopic and chemical properties.
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  • 11
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    Annual Review of Biophysics and Biomolecular Structure 26 (1997), S. 327-355 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Over the past two decades, nanosecond absorption and vibrational spectroscopies have developed into powerful tools for monitoring the secondary, tertiary, and quaternary structural relaxations of biological macromolecules under near-physiological conditions of solvent and temperature. Observed through such methods, the dynamic response of a biomolecule to photoinitiated excursions from equilibrium can reveal valuable information about the structure-function relationship, information beyond that obtained from the static structures provided by X-ray crystallography, nuclear magnetic resonance spectroscopy, and other steady-state methods. Most recently, the development of ultra-sensitive polarization techniques for absorption spectroscopy has greatly enhanced the amount of time-resolved structural information that can be obtained from the broadened electronic spectra of biomolecules. This review examines nanosecond absorption, vibrational, and polarized absorption methods, and their applications to protein function and folding, emphasizing the complementary nature of information obtained from electronic and vibrational spectra measured on the nanosecond time scale.
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  • 12
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    Annual Review of Biophysics and Biomolecular Structure 26 (1997), S. 289-325 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Eukaryotes have three distinct RNA polymerases that catalyze transcription of nuclear genes. RNA polymerase II is responsible for transcribing nuclear genes encoding the messenger RNAs and several small nuclear RNAs. Like RNA polymerases I and III, polymerase II cannot recognize its target promoter directly and initiate transcription without accessory factors. Instead, this large multisubunit enzyme relies on general transcription factors and transcriptional activators and coactivators to regulate transcription from class II promoters. X-ray crystallography and nuclear magnetic resonance spectroscopy have been used to study complexes of general transcription factors and transcriptional activators with their specific DNA targets. This work has provided important structural insights into transcription initiation by polymerase II and the more general problem of DNA sequence recognition.
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  • 13
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    Annual Review of Biophysics and Biomolecular Structure 26 (1997), S. 47-82 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Researchers have made good progress in unraveling the molecular mechanisms of excitation-contraction (EC) coupling in striated muscle. Despite this progress, paradoxes abound. In skeletal muscle, the existence of a mechanical coupling between membrane charge movement and activation of sarcoplasmic reticulum (SR) release channels is essentially established, but the contribution of Ca2+-induced Ca2+ release (CICR) to the transient and steady-state components of Ca2+ release remains controversial. In cardiac muscle, the role of CICR as the primary mechanism of EC coupling is well established, but the stability and tight coupling between membrane Ca2+ current and release are paradoxical. Answers may lie in microdomain issues, and in the examination of discrete elementary release events, although quantitative treatments are needed. This review explores the theoretical and experimental methods used and the observations made in the study of microdomain Ca2+.
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  • 14
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    Annual Review of Biophysics and Biomolecular Structure 26 (1997), S. 373-399 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Measurements of trajectories of individual proteins or lipids in the plasma membrane of cells show a variety of types of motion. Brownian motion is observed, but many of the particles undergo non-Brownian motion, including directed motion, confined motion, and anomalous diffusion. The variety of motion leads to significant effects on the kinetics of reactions among membrane-bound species and requires a revision of existing views of membrane structure and dynamics.
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  • 15
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    Annual Review of Biophysics and Biomolecular Structure 26 (1997), S. 495-540 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract This review focuses on the recent advances in EPR spectroscopy as they are applied both to photoinduced electron transfer in the photosynthetic apparatus and to biomimetic systems. The review deals with time-resolved direct-detection cw and pulsed EPR and ENDOR methods, both at conventional bands [X-(9.5 GHz), K-(24 GHz), and Q-(35 GHz)] and at high frequency bands (W-band, 95 GHz, and even highter frequency bands). EPR studies on photosynthetic and model systems in their doublet, triplet and radical pair states are surveyed, including their static and dynamic properties. Applications of time-resolved EPR in studying photoinduced electron and energy transfer in isotropic and anisotropic environments, and the concepts of electron spin polarization and magnetic field effects in photochemical reactions are also reviewed.
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  • 16
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    Annual Review of Biophysics and Biomolecular Structure 26 (1997), S. 541-566 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Surface plasmon resonance biosensors have become increasingly popular for the qualitative and quantitative characterization of the specific binding of a mobile reactant to a binding partner immobilized on the sensor surface. This article reviews the use of this new technique to measure the binding affinities and the kinetic constants of reversible interactions between biological macromolecules. Immobilization techniques, the most commonly employed experimental strategies, and various analytical approaches are summarized. In recent years, several sources of potential artifacts have been identified: immobilization of the binding partner, steric hindrance of binding to adjacent binding sites at the sensor surface, and finite rate of mass transport of the mobile reactant to the sensor surface. Described here is the influence of these artifacts on the measured binding kinetics and equilibria, together with suggested control experiments.
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  • 17
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    Annual Review of Biophysics and Biomolecular Structure 26 (1997), S. 597-627 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Analysis of the structures in the Protein Databank, released in June 1996, shows that the number of different protein folds, i.e. the number of different arrangements of major secondary structures and/or chain topologies, is 327. Of these folds, approximately 25% belong to the all-alpha class, 20% belong to the all-beta class, 30% belong to the alpha/beta class, and 25% belong to the alpha + beta class. We describe the types of folds now known for the all-beta and all-alpha classes, emphasizing those that have been discovered recently. Detailed theories for the physical determinants of the structures of most of these folds now exist, and these are reviewed.
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  • 18
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    Annual Review of Biophysics and Biomolecular Structure 28 (1999), S. 1-27 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract The Raman spectrum of a protein or nucleic acid consists of numerous discrete bands representing molecular normal modes of vibration and serves as a sensitive and selective fingerprint of three-dimensional structure, intermolecular interactions, and dynamics. Recent improvements in instrumentation, coupled with innovative approaches in experimental design, dramatically increase the power and scope of the method, particularly for investigations of large supramolecular assemblies. Applications are considered that involve the use of (a) time-resolved Raman spectroscopy to elucidate assembly pathways in icosahedral viruses, (b) polarized Raman microspectroscopy to determine detailed structural parameters in filamentous viruses, (c) ultraviolet-resonance Raman spectroscopy to probe selective DNA and protein residues in nucleoprotein complexes, and (d) difference Raman methods to understand mechanisms of protein/DNA recognition in gene regulatory and chromosomal complexes.
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    Annual Review of Biophysics and Biomolecular Structure 28 (1999), S. 29-56 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Transcription in eukaryotes is frequently regulated by a mechanism termed combinatorial control, whereby several different proteins must bind DNA in concert to achieve appropriate regulation of the downstream gene. X-ray crystallographic studies of multiprotein complexes bound to DNA have been carried out to investigate the molecular determinants of complex assembly and DNA binding. This work has provided important insights into the specific protein-protein and protein-DNA interactions that govern the assembly of multiprotein regulatory complexes. The results of these studies are reviewed here, and the general insights into the mechanism of combinatorial gene regulation are discussed.
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    Annual Review of Biophysics and Biomolecular Structure 28 (1999), S. 75-100 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Analytical ultracentrifugation is a classical method of biochemistry and molecular biology. Because it is a primary technique, sedimentation can provide first-principle hydrodynamic and first-principle thermodynamic information for nearly any molecule, in a wide range of solvents and over a wide range of solute concentrations. For many questions, it is the technique of choice. This review stresses what information is available from analytical ultracentrifugation and how that information is being extracted and used in contemporary applications.
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    Annual Review of Biophysics and Biomolecular Structure 28 (1999), S. 129-153 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Measurement of the distance between two spin label probes in proteins permits the spatial orientation of elements of defined secondary structure. By using site-directed spin labeling, it is possible to determine multiple distance constraints and thereby build tertiary and quaternary structural models as well as measure the kinetics of structural changes. New analytical methods for determining interprobe distances and relative orientations for uniquely oriented spin labels have been developed using global analysis of multifrequency electron paramagnetic resonance data. New methods have also been developed for determining interprobe distances for randomly oriented spin labels. These methods are being applied to a wide range of structural problems, including peptides, soluble proteins, and membrane proteins, that are not readily characterized by other structural techniques.
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    Annual Review of Biophysics and Biomolecular Structure 28 (1999), S. 155-179 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Current computer simulations of biomolecules typically make use of classical molecular dynamics methods, as a very large number (tens to hundreds of thousands) of atoms are involved over timescales of many nanoseconds. The methodology for treating short-range bonded and van der Waals interactions has matured. However, long-range electrostatic interactions still represent a bottleneck in simulations. In this article, we introduce the basic issues for an accurate representation of the relevant electrostatic interactions. In spite of the huge computational time demanded by most biomolecular systems, it is no longer necessary to resort to uncontrolled approximations such as the use of cutoffs. In particular, we discuss the Ewald summation methods, the fast particle mesh methods, and the fast multipole methods. We also review recent efforts to understand the role of boundary conditions in systems with long-range interactions, and conclude with a short perspective on future trends.
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    Annual Review of Biophysics and Biomolecular Structure 28 (1999), S. 101-128 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Recent structural and biochemical studies have begun to illuminate how cells solve the problems of recognizing and removing damaged DNA bases. Bases damaged by environmental, chemical, or enzymatic mechanisms must be efficiently found within a large excess of undamaged DNA. Structural studies suggest that a rapid damage-scanning mechanism probes for both conformational deviations and local deformability of the DNA base stack. At susceptible lesions, enzyme-induced conformational changes lead to direct interactions with specific damaged bases. The diverse array of damaged DNA bases are processed through a two-stage pathway in which damage-specific enzymes recognize and remove the base lesion, creating a common abasic site intermediate that is processed by damage-general repair enzymes to restore the correct DNA sequence.
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    Annual Review of Biophysics and Biomolecular Structure 28 (1999), S. 181-204 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract A significant number of exciting papain-like cysteine protease structures have been determined by crystallographic methods over the last several years. This trove of data allows for an analysis of the structural features that empower these molecules as they efficiently carry out their specialized tasks. Although the structure of the paradigm for the family, papain, has been known for twenty years, recent efforts have reaped several structures of specialized mammalian enzymes. This review first covers the commonalities of architecture and purpose of the papain-like cysteine proteases. From that broad platform, each of the lysosomal enzymes for which there is an X-ray structure (or structures) is then examined to gain an understanding of what structural features are used to customize specificity and activity. Structure-based design of inhibitors to control pathological cysteine protease activity will also be addressed.
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    Annual Review of Biophysics and Biomolecular Structure 28 (1999), S. 269-293 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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    Notes: Abstract For nuclear magnetic resonance determinations of the conformation of oligosaccharides in solution, simple molecular mechanics calculations and nuclear Overhauser enhancement measurements are adequate for small oligosaccharides that adopt single, relatively rigid conformations. Polysaccharides and larger or more flexible oligosaccharides generally require additional types of data, such as scalar and dipolar coupling constants, which are most conveniently measured in 13C-enriched samples. Nuclear magnetic resonance relaxation data provide information on the dynamics of oligosaccharides, which involves several different types of internal motion. Oligosaccharides complexed with lectins and antibodies have been successfully studied both by X-ray crystallography and by nuclear magnetic resonance spectroscopy. The complexes have been shown to be stabilized by a combination of polar hydrogen bonding interactions and van der Waals attractions. Although theoretical calculations of the conformation and stability of free oligosaccharides and of complexes with proteins can be carried out by molecular mechanics methods, the role of solvent water for these highly polar molecules continues to present computational problems.
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    Annual Review of Biophysics and Biomolecular Structure 28 (1999), S. 295-317 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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    Notes: Abstract Proteasomes are large multisubunit proteases that are found in the cytosol, both free and attached to the endoplasmic reticulum, and in the nucleus of eukaryotic cells. Their ubiquitous presence and high abundance in these compartments reflects their central role in cellular protein turnover. Proteasomes recognize, unfold, and digest protein substrates that have been marked for degradation by the attachment of a ubiquitin moiety. Individual subcomplexes of the complete 26S proteasome are involved in these different tasks: The ATP-dependent 19S caps are believed to unfold substrates and feed them to the actual protease, the 20S proteasome. This core particle appears to be more ancient than the ubiquitin system. Both prokaryotic and archaebacterial ancestors have been identified. Crystal structures are now available for the E. coli proteasome homologue and the T. acidophilum and S. cerevisiae 20S proteasomes. All three enzymes are cylindrical particles that have their active sites on the inner walls of a large central cavity. They share the fold and a novel catalytic mechanism with an N-terminal nucleophilic threonine, which places them in the family of Ntn (N terminal nucleophile) hydrolases. Evolution has added complexity to the comparatively simple prokaryotic prototype. This minimal proteasome is a homododecamer made from two hexameric rings stacked head to head. Its heptameric version is the catalytic core of archaebacterial proteasomes, where it is sandwiched between two inactive antichambers that are made up from a different subunit. In eukaryotes, both subunits have diverged into seven different subunits each, which are present in the particle in unique locations such that a complex dimer is formed that has six active sites with three major specificities that can be attributed to individual subunits. Genetic, biochemical, and high-resolution electron microscopy data, but no crystal structures, are available for the 19S caps. A first step toward a mechanistic understanding of proteasome activation and regulation has been made with the elucidation of the X-ray structure of the alternative, mammalian proteasome activator PA28.
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    Annual Review of Cell and Developmental Biology 13 (1997), S. 1-23 
    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Abstract Transcriptional regulation is important in all eukaryotic organisms for cell growth, development, and responses to environmental change. Saccharomyces cerevisiae, or bakers' yeast, has provided a powerful system for genetic analysis of transcriptional regulation, and findings from the study of this model system have proven broadly applicable to higher organisms. Transcriptional regulation requires the interactions of regulatory proteins with various components of the transcription machinery. Recently, genetic analysis of a diverse set of transcriptional regulatory responses has converged with studies of the function of the RNA polymerase II carboxy-terminal domain (CTD) to reveal regulatory roles for proteins associated with the CTD. These proteins, designated Srb/mediator proteins, are broadly involved in both positive and negative regulatory responses in vivo. This review focuses on the connections between genetic analysis of transcriptional regulation and the functions of the Srb/mediator proteins associated with the RNA polymerase II CTD.
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    Annual Review of Cell and Developmental Biology 13 (1997), S. 53-82 
    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Abstract Most animal species exhibit left-right asymmetry in their body plans and show a strong bias for one handedness over the other. The mechanism of handedness choice, recognized as an intriguing problem over a century ago, is still a mystery. However, from recent advances in understanding when and how asymmetry arises in both invertebrates and vertebrates, developmental pathways for establishment and maintenance of left-right differences are beginning to take shape, and speculations can be made on the initial choice mechanism.
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    Annual Review of Cell and Developmental Biology 13 (1997), S. 83-117 
    ISSN: 1081-0706
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    Topics: Biology , Medicine
    Notes: Abstract The polymerization dynamics of microtubules are central to their biological functions. Polymerization dynamics allow microtubules to adopt spatial arrangements that can change rapidly in response to cellular needs and, in some cases, to perform mechanical work. Microtubules utilize the energy of GTP hydrolysis to fuel a unique polymerization mechanism termed dynamic instability. In this review, we first describe progress toward understanding the mechanism of dynamic instability of pure tubulin and then discuss the function and regulation of microtubule dynamic instability in living cells.
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    Annual Review of Cell and Developmental Biology 13 (1997), S. 25-51 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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    Notes: Abstract Mitochondria import most of their proteins from the cytosol. Dynamic protein complexes in the mitochondrial outer and inner membranes are responsible for the specific recognition and membrane translocation of preproteins. The preprotein translocase of the outer mitochondrial membrane contains several import receptors and a general import pore. The preprotein translocase of the inner membrane consists of a channel interacting with preproteins in transit and an import motor that includes the matrix heat shock protein Hsp70. Acidic patches of import components are thought to guide the import of positively charged signal sequences (acid chain hypothesis). Energy input is derived from the inner membrane potential and ATP. Proteins in the mitochondrial matrix are required for proteolytic processing and folding of imported proteins. The dynamic nature of the membrane translocase permits sorting of preproteins at distinct stages of the import pathway.
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    Annual Review of Cell and Developmental Biology 13 (1997), S. 119-146 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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    Notes: Abstract Adherens junctions are specialized forms of cadherin-based adhesive contacts important for tissue organization in developing and adult organisms. Cadherins form protein complexes with cytoplasmic proteins (catenins) that convert the specific, homophilic-binding capacity of the extracellular domain into stable cell adhesion. The extracellular domains of cadherins form parallel dimers that possess intrinsic homophilic-binding activity. Cytoplasmic interactions can influence the function of the ectodomain by a number of potential mechanisms, including redistribution of binding sites into clusters, providing cytoskeletal anchorage, and mediating physiological regulation of cadherin function. Adherens junctions are likely to serve specific, specialized functions beyond the basic adhesive process. These functions include coupling cytoskeletal force generation to strongly adherent sites on the cell surface and the regulation of intracellular signaling events.
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    Annual Review of Cell and Developmental Biology 13 (1997), S. 147-170 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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    Notes: Abstract The Drosophila ovary provides a favorable model system in which to study cellular morphogenesis. The development of a mature egg involves a syncytium of 16 germline cells and over 1000 somatically derived follicle cells. Intercellular transport, stable intercellular bridges, cell migrations, cell shape changes, and specific subcellular localization of many embryonic patterning determinants contribute to egg development and require a dynamic cytoskeleton. We discuss many of the recent genetic and cell biological studies that have led to insights into how the actin cytoskeleton is assembled and regulated during the morphogenesis of the Drosophila egg.
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    Annual Review of Cell and Developmental Biology 13 (1997), S. 333-361 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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    Notes: Abstract Notch, LIN-12, and GLP-1 are receptors that mediate a broad range of cell interactions during Drosophila and nematode development. Signaling by these receptors relies on a conserved pathway with three core components: DSL ligand, LNG receptor, and a CSL effector that links the receptor to its transcriptional response. Although key functional regions have been identified in each class of proteins, the mechanism for signal transduction is not yet understood. Diverse regulatory mechanisms influence signaling by the LIN-12/Notch pathway. Inductive signaling relies on the synthesis of ligand and receptor in distinct but neighboring cells. By contrast, lateral signaling leads to the transformation of equivalent cells that express both ligand and receptor into nonequivalent cells that express either ligand or receptor. This transformation appears to rely on regulatory feedback loops within the LIN-12/Notch pathway. In addition, the pathway can be regulated by intrinsic factors that are asymmetrically segregated during cell division or by extrinsic cues via other signaling pathways. Specificity in the pathway does not appear to reside in the particular ligand or receptor used for a given cell-cell interaction. The existence of multiple ligands and receptors may have evolved from the stringent demands placed upon the regulation of genes encoding them.
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    Annual Review of Cell and Developmental Biology 13 (1997), S. 363-393 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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    Notes: Abstract Molecules involved in cell adhesion processes are often both structurally and functionally modular, with subdomains that are members of large protein families. Recently, high-resolution structures have been determined for representative members of many of these families including fragments of integrins, cadherins, fibronectin-like domains, and immunoglobulin-like domains. These structures have enhanced our understanding of cell adhesion processes at several levels. In almost all cases, ligand-binding sites have been visualized and provide insight into how these molecules mediate biologically important interactions. Metal-binding sites have been identified and characterized, allowing assessment of the role of bound ions in cell adhesion processes. Many of these structures serve as templates for modeling homologous domains in other proteins or, when the structure of a fragment consisting of more than one domain is determined, the structure of multidomain arrays of homologous domains. Knowledge of atomic structure also allows rational design of drugs that either mimic or target specific binding sites. In many cases, high-resolution structures have revealed unexpected relationships that pose questions about the evolutionary origin of specific domains. This review briefly describes several recently determined structures of cell adhesion molecules, summarizes some of the main results of each structure, and highlights common features of different systems.
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    Annual Review of Cell and Developmental Biology 13 (1997), S. 395-424 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Abstract Bacteria usually divide by building a central septum across the middle of the cell. This review focuses on recent results indicating that the tubulin-like FtsZ protein plays a central role in cytokinesis as a major component of a contractile cytoskeleton. Assembly of this cytoskeletal element abutting the membrane is a key point for regulation. The characterization of FtsZ homologues in Mycoplasmas, Archaea, and chloroplasts implies that the constriction mechanism is conserved and that FtsZ can constrict in the absence of peptidoglycan synthesis. In most Eubacteria, the internal cytoskeleton must also regulate synthesis of septal peptidoglycan. The Escherichia coli septum-specific penicillin-binding protein 3 (PBP3) forms a complex with other enzymes involved in murein metabolism, suggesting a centrally located transmembrane complex capable of splicing multiple new strands of peptidoglycan into the cell wall. Important questions remain about the spatial and temporal control of bacterial division.
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    Annual Review of Cell and Developmental Biology 13 (1997), S. 425-456 
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    Notes: Abstract NCAM, L1, and DCC-immunoglobulin cell adhesion molecules (Ig CAMs)-are widely expressed during development. Many workers have dismissed a role for such molecules in the control of axonal growth and guidance because they do not show highly restricted expression patterns. Yet evidence from a number of model systems suggests all three CAMs play a role in the development of specific projections in the nervous system. For example, there is a reduction in mossy fiber tracts in the hippocampus of mice that lack NCAM, a requirement for DCC in the response of commissural neurons to a floor plate-derived chemoattractant, and a loss of corticospinal tracts in humans who carry mutations in the L1 gene. The above paradox might be explained by the observation that differential post-translational processing can modulate CAMs function and that alternative splicing can generate functionally distinct isoforms of a CAM. Activation of the FGF tyrosine kinase receptor is required for the responses stimulated by NCAM and L1, and the importance of regulated tyrosine phosphorylation for growth and guidance is underscored by the involvement of receptor tyrosine phosphatases in this process.
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    Annual Review of Cell and Developmental Biology 13 (1997), S. 513-609 
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    Notes: Abstract Src family protein tyrosine kinases are activated following engagement of many different classes of cellular receptors and participate in signaling pathways that control a diverse spectrum of receptor-induced biological activities. While several of these kinases have evolved to play distinct roles in specific receptor pathways, there is considerable redundancy in the functions of these kinases, both with respect to the receptor pathways that activate these kinases and the downstream effectors that mediate their biological activities. This chapter reviews the evidence implicating Src family kinases in specific receptor pathways and describes the mechanisms leading to their activation, the targets that interact with these kinases, and the biological events that they regulate.
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    Notes: Abstract The chemosensory pathway of bacterial chemotaxis has become a paradigm for the two-component superfamily of receptor-regulated phosphorylation pathways. This simple pathway illustrates many of the fundamental principles and unanswered questions in the field of signaling biology. A molecular description of pathway function has progressed rapidly because it is accessible to diverse structural, biochemical, and genetic approaches. As a result, structures are emerging for most of the pathway elements, biochemical studies are elucidating the mechanisms of key signaling events, and genetic methods are revealing the intermolecular interactions that transmit information between components. Recent advances include (a) the first molecular picture of a conformational transmembrane signal in a cell surface receptor, (b) four new structures of kinase domains and adaptation enzymes, and (c) significant new insights into the mechanisms of receptor-mediated kinase regulation, receptor adaptation, and the phospho-activation of signaling proteins. Overall, the chemosensory pathway and the propulsion system it regulates provide an ideal system in which to probe molecular principles underlying complex cellular signaling and behavior.
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    Annual Review of Cell and Developmental Biology 13 (1997), S. 611-667 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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    Notes: Abstract The organizer is formed in an equatorial sector of the blastula stage amphibian embryo by cells that have responded to two maternal agents: a general meso-endoderm inducer (involving the TFG-beta signaling pathway) and a dorsal modifier (probably involving the Wnt signaling pathway). The meso-endoderm inducer is secreted by most vegetal cells, those containing maternal materials that had been localized in the vegetal hemisphere of the oocyte during oogenesis. As a consequence of the inducer's distribution and action, the competence domains of prospective ectoderm, mesoderm, and endoderm are established in an animal-to-vegetal order in the blastula. The dorsal modifier signal is secreted by a sector of cells of the animal and vegetal hemispheres on one side of the blastula. These cells contain maternal materials transported there in the first cell cycle from the vegetal pole of the egg along microtubules aligned by cortical rotation. The Nieuwkoop center is the region of blastula cells secreting both maternal signals, and hence specifying the organizer in an equatorial sector. Final steps of organizer formation at the late blastula or early gastrula stage may involve locally secreted zygotic signals as well. At the gastrula stage, the organizer secretes a variety of zygotic proteins that act as antagonists to various members of the BMP and Wnt families of ligands, which are secreted by cells of the competence domains surrounding the organizer. BMPs and Wnts favor ventral development, and cells near the organizer are protected from these agents by the organizer's inducers. The nearby cells are derepressed in their inherent capacity for dorsal development, which is apparent in the neural induction of the ectoderm, dorsalization of the mesoderm, and anteriorization of the endoderm. The organizer also engages in extensive specialized morphogenesis, which brings it within range of responsive cell groups. It also self-differentiates to a variety of axial tissues of the body.
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    Annual Review of Cell and Developmental Biology 15 (1999), S. 185-230 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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    Notes: Abstract Ubiquitous among eukaryotes, the ADF/cofilins are essential proteins responsible for the high turnover rates of actin filaments in vivo. In vertebrates, ADF and cofilin are products of different genes. Both bind to F-actin cooperatively and induce a twist in the actin filament that results in the loss of the phalloidin-binding site. This conformational change may be responsible for the enhancement of the off rate of subunits at the minus end of ADF/cofilin-decorated filaments and for the weak filament-severing activity. Binding of ADF/cofilin is competitive with tropomyosin. Other regulatory mechanisms in animal cells include binding of phosphoinositides, phosphorylation by LIM kinases on a single serine, and changes in pH. Although vertebrate ADF/cofilins contain a nuclear localization sequence, they are usually concentrated in regions containing dynamic actin pools, such as the leading edge of migrating cells and neuronal growth cones. ADF/cofilins are essential for cytokinesis, phagocytosis, fluid phase endocytosis, and other cellular processes dependent upon actin dynamics.
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    Annual Review of Cell and Developmental Biology 15 (1999), S. 393-410 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Abstract Endoderm, one of the three principal germ layers, contributes to all organs of the alimentary tract. For simplicity, this review divides formation of endodermal organs into four fundamental steps: (a) formation of endoderm during gastrulation, (b) morphogenesis of a gut tube from a sheet of cells, (c) budding of organ domains from the tube, and (d) differentiation of organ-specific cell types within the growing buds. We discuss possible mechanisms that regulate how undifferentiated endoderm becomes specified into a myriad of cell types that populate the respiratory and gastrointestinal tracts.
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    Annual Review of Cell and Developmental Biology 15 (1999), S. 291-339 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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    Notes: Abstract Information can be transferred between the nucleus and the cytoplasm by translocating macromolecules across the nuclear envelope. Communication of extracellular or intracellular changes to the nucleus frequently leads to a transcriptional response that allows cells to survive in a continuously changing environment. Eukaryotic cells have evolved ways to regulate this movement of macromolecules between the cytoplasm and the nucleus such that the transfer of information occurs only under conditions in which a transcriptional response is required. This review focuses on the ways in which cells regulate movement of proteins across the nuclear envelope and the significance of this regulation for controlling diverse biological processes.
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    Annual Review of Cell and Developmental Biology 15 (1999), S. 469-517 
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    Notes: Abstract In Dictyostelium amoebae, cell-type differentiation, spatial patterning, and morphogenesis are controlled by a combination of cell-autonomous mechanisms and intercellular signaling. A chemotactic aggregation of ~105 cells leads to the formation of a multicellular organism. Cell-type differentiation and cell sorting result in a small number of defined cell types organized along an anteroposterior axis. Finally, a mature fruiting body is created by the terminal differentiation of stalk and spore cells. Analysis of the regulatory program demonstrates a role for several molecules, including GSK-3, signal transducers and activators of transcription (STAT) factors, and cAMP-dependent protein kinase (PKA), that control spatial patterning in metazoans. Unexpectedly, two component systems containing histidine kinases and response regulators also play essential roles in controlling Dictyostelium development. This review focuses on the role of cAMP, which functions intracellularly to mediate the activity of PKA, an essential component in aggregation, cell-type specification, and terminal differentiation. Cytoplasmic cAMP levels are controlled through both the regulated activation of adenylyl cyclases and the degradation by a phosphodiesterase containing a two-component system response regulator. Extracellular cAMP regulates G-protein-dependent and -independent pathways to control aggregation as well as the activity of GSK-3 and the transcription factors GBF and STATa during multicellular development. The integration of these pathways with others regulated by the morphogen DIF-1 to control cell fate decisions are discussed.
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    Annual Review of Cell and Developmental Biology 15 (1999), S. 799-842 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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    Notes: Abstract Cotranslational protein translocation across and integration into the membrane of the endoplasmic reticulum (ER) occur at sites termed translocons. Translocons are composed of several ER membrane proteins that associate to form an aqueous pore through which secretory proteins and lumenal domains of membrane proteins pass from the cytoplasm to the ER lumen. These sites are not passive holes in the bilayer, but instead are quite dynamic both structurally and functionally. Translocons cycle between ribosome-bound and ribosome-free states, and convert between translocation and integration modes of operation. These changes in functional state are accompanied by structural rearrangements that alter translocon conformation, composition, and interactions with ligands such as the ribosome and BiP. Recent studies have revealed that the translocon is a complex and sophisticated molecular machine that regulates the movement of polypeptides through the bilayer, apparently in both directions as well as laterally into the bilayer, all while maintaining the membrane permeability barrier.
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    Annual Review of Cell and Developmental Biology 15 (1999), S. 733-798 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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    Notes: Abstract Synaptic vesicles, which have been a paradigm for the fusion of a vesicle with its target membrane, also serve as a model for understanding the formation of a vesicle from its donor membrane. Synaptic vesicles, which are formed and recycled at the periphery of the neuron, contain a highly restricted set of neuronal proteins. Insight into the trafficking of synaptic vesicle proteins has come from studying not only neurons but also neuroendocrine cells, which form synaptic-like microvesicles (SLMVs). Formation and recycling of synaptic vesicles/SLMVs takes place from the early endosome and the plasma membrane. The cytoplasmic machinery of synaptic vesicle/SLMV formation and recycling has been studied by a variety of experimental approaches, in particular using cell-free systems. This has revealed distinct machineries for membrane budding and fission. Budding is mediated by clathrin and clathrin adaptors, whereas fission is mediated by dynamin and its interacting protein SH3p4, a lysophosphatidic acid acyl transferase.
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    Annual Review of Astronomy and Astrophysics 35 (1997), S. xiii 
    ISSN: 0066-4146
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    Topics: Physics
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    Annual Review of Astronomy and Astrophysics 35 (1997), S. 33-67 
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    Topics: Physics
    Notes: Abstract To what extent are changes in the Earth's global environment linked with fluctuations in its primary energy source, the radiation from a variable star, the Sun? A firm scientific basis for policy making with regard to anthropogenic greenhouse warming of climate and chlorofluorocarbon depletion of ozone requires a reliable answer to this question. Reduction of the vulnerability of spacecraft operations and communications to space weather necessitates knowledge of solar induced variability in Earth's upper atmosphere. Toward these goals, solar radiation monitoring and studies of solar variability mechanisms facilitate an understanding of the sources and amplitudes of the Sun's changing radiation. Interdisciplinary studies that link these changes with a wide array of terrestrial phenomena over the longer time scales of global change and the shorter time scales of space weather address the relevance of solar radiation variability for Earth. However, although numerous associations are apparent between solar and terrestrial fluctuations, full comprehension of the physical mechanisms responsible for the many facets of radiative Sun-Earth coupling remains to be accomplished.
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    Annual Review of Astronomy and Astrophysics 35 (1997), S. 267-307 
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    Topics: Physics
    Notes: Abstract The properties of galaxies that are lower in surface brightness than the dark night sky are reviewed. There are substantial selection effects against the discovery of galaxies that are unevolved or diffuse; these systems are missing from most wide field catalogs. Low surface brightness galaxies make up a significant amount of the luminosity density of the local universe. They contribute substantial but poorly determined amounts to the census of baryons and dark matter. Low surface brightness galaxies are also relevant to the interpretation of quasar absorption lines and to the understanding of rapidly evolving galaxy populations in the more distant universe. Theories of galaxy formation and evolution must accomodate the properties of these diffuse stellar systems.
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    Annual Review of Astronomy and Astrophysics 35 (1997), S. 357-388 
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    Topics: Physics
    Notes: Abstract Compact groups of galaxies have posed a number of challenging questions. Intensive observational and theoretical studies are now providing answers to many of these and, at the same time, are revealing unexpected new clues about the nature and role of these systems. Most compact groups contain a high fraction of galaxies having morphological or kinematical peculiarities, nuclear radio and infrared emission, and starburst or active galactic nuclei (AGN) activity. They contain large quantities of diffuse gas and are dynamically dominated by dark matter. They most likely form as subsystems within looser associations and evolve by gravitational processes. Strong galaxy interactions result and merging is expected to lead to the ultimate demise of the group. Compact groups are surprisingly numerous and may play a significant role in galaxy evolution.
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    Annual Review of Astronomy and Astrophysics 35 (1997), S. 557-605 
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    Notes: Abstract Three cases for mixing not present in standard stellar models are presented: Light element depletion in low mass main-sequence stars, deep mixing in massive stars, and deep mixing in low mass giants. The review begins with the mixing indicators and the predictions of standard models. The observational evidence for anomalous mixing is then presented, followed by the physics of mixing outside the standard model. The status of theoretical models that include extra mixing is then examined.
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    Annual Review of Astronomy and Astrophysics 37 (1999), S. 37-64 
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    Topics: Physics
    Notes: Abstract I present the general picture of how galactic magnetic fields grow in disks according to the alpha-Omega dynamo theory. Emphasis is placed on following the lines of force during the dynamo process. The dynamo equation is presented together with a simple growing solution for the galactic disk. Then I take up the various critical questions that have been raised concerning the galactic dynamo theory. These are (1) the importance of the escape of flux from the disk in order for the magnetic field to grow; (2) the physics of turbulent diffusion and its mixing of field lines together so that the rms field is possibly greater than the mean field; (3) whether magnetic reconnection plays a role in the galactic dynamo; (4) whether small-scale fields can grow large enough to swamp the dynamo. Then I discuss the possible seed fields from which the dynamo starts and their relation to the primordial hypothesis. Finally I take up the question of the final evolution of the galactic field after the alpha effect saturates. My conclusion is that all these problems warrant attention but none of them seem to be serious enough to cast any real doubt on the dynamo as the most likely generator of galactic fields.
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    Annual Review of Astronomy and Astrophysics 37 (1999), S. 97-125 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Physics
    Notes: Abstract Advances in wide-angle astrometric measurements of three to four orders of magnitude in the last thirty years have resulted in a redefinition of the fundamental astronomical reference frame. This new frame, the International Celestial Reference Frame (ICRF), is based on the radio positions of 212 compact extragalactic radio sources. The ICRF defines the direction of the axes of the International Celestial Reference System (ICRS) with a precision of approximately 20 muas. At optical wavelengths, the Hipparcos catalog is the realization of this frame. The precision with which the ICRF is now determined requires that the ICRS models for precession, nutation, and others, be revised. Increases in the precision of measurements from astrometric space missions will further improve the celestial reference frame and may require its redefinition within the next ten years. These improvements will again challenge the models for the celestial reference system.
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    Annual Review of Astronomy and Astrophysics 37 (1999), S. 409-443 
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    Topics: Physics
    Notes: Abstract Black holes of stellar mass and neutron stars in binary systems are first detected as hard X-ray sources using high-energy space telescopes. Relativistic jets in some of these compact sources are found by means of multiwavelength observations with ground-based telescopes. The X-ray emission probes the inner accretion disk and immediate surroundings of the compact object, whereas the synchrotron emission from the jets is observed in the radio and infrared bands, and in the future could be detected at even shorter wavelengths. Black-hole X-ray binaries with relativistic jets mimic, on a much smaller scale, many of the phenomena seen in quasars and are thus called microquasars. Because of their proximity, their study opens the way for a better understanding of the relativistic jets seen elsewhere in the Universe. From the observation of two-sided moving jets it is inferred that the ejecta in microquasars move with relativistic speeds similar to those believed to be present in quasars. The simultaneous multiwavelength approach to microquasars reveals in short timescales the close connection between instabilities in the accretion disk seen in the X-rays, and the ejection of relativistic clouds of plasma observed as synchrotron emission at longer wavelengths. Besides contributing to a deeper understanding of accretion disks and jets, microquasars may serve in the future to determine the distances of jet sources using constraints from special relativity, and the spin of black holes using general relativity.
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    Annual Review of Astronomy and Astrophysics 37 (1999), S. 603-648 
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    Topics: Physics
    Notes: Abstract Far-ultraviolet radiation is a ubiquitous, if unanticipated, phenomenon in elliptical galaxies and early-type spiral bulges. It is the most variable photometric feature associated with old stellar populations. Recent observational and theoretical evidence shows that it is produced mainly by low-mass, small-envelope, helium-burning stars in extreme horizontal branch and subsequent phases of evolution. These are probably descendants of the dominant, metal rich population of the galaxies. Their lifetime UV outputs are remarkably sensitive to their physical properties and hence to the age and the helium and metal abundances of their parents. UV spectra are therefore exceptionally promising diagnostics of old stellar populations, although their calibration requires a much improved understanding of giant branch mass loss, helium enrichment, and atmospheric diffusion.
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    Annual Review of Fluid Mechanics 29 (1997), S. 515-567 
    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: Abstract Modern helicopter aerodynamics is challenging because the flow field generated by a helicopter is extremely complicated and difficult to measure, model, and predict; moreover, experiments are expensive and difficult to conduct. In this article we discuss the basic principles of modern helicopter aerodynamics. Many sophisticated experimental and computational techniques have been employed in an effort to predict performance parameters. Of particular interest is the structure of the rotor wake, which is highly three-dimensional and unsteady, and the rotor-blade pressure distribution, which is significantly affected by the strength and position of the wake. We describe the various modern methods of computation and experiment which span the range from vortex techniques to full three-dimensional Navier-Stokes computations, and from classical probe methods to laser velocimetry techniques. Typical results for the structure of the wake and the blade pressure distribution in both hover and forward flight are presented Despite the complexity of the helicopter flow, significant progress has been made within the last ten years and the future will likely bring marked advances.
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    Annual Review of Fluid Mechanics 31 (1999), S. 95-123 
    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: Abstract Nuclear magnetic resonance (NMR) measurements of flowing materials are reviewed with emphasis on applications to multiphase flows. After a brief presentation of NMR physics, experimental considerations related to flow measurements are discussed. Both imaging and non-imaging NMR as well as topics such as Earth's field NMR and rapid imaging are covered. Specific topics that follow are tagging and time-of-flight, phase measurement of velocity, diffusion, turbulence, and calibration and validations. Finally, recent applications are reviewed in the areas of sedimentation, suspension flows in Couette and pipe geometries, rheometers and viscometers, liquid-liquid multiphase flows, porous media flow, granular flows, and turbulence.
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    Annual Review of Fluid Mechanics 31 (1999), S. 171-199 
    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: Abstract In this review, we describe the dynamics and thermodynamics of liquid and vapor flow through hot fractured rock. Such flows occur in geothermal reservoirs and have important implications for geothermal power generation; we describe both forced flows associated with liquid injection into such systems, and natural convective flows associated with the vertical heat transfer through such systems. First we focus on permeable media and describe the heat transfer of single-phase liquid or vapor flow through a medium of different temperature. Then we consider the dynamics and thermodynamics of a liquid front as it advances into a superheated region and boils. The morphological stability of such an interface is discussed, and we describe conditions under which the interface breaks down to form a two-phase zone between the liquid and vapor. We next examine the heat transfer and boiling in gravity-driven flows advancing through a superheated permeable rock, identifying that at large times such currents asymptote to a family of similarity solutions. In the second part of the review, we describe the analogous heat transfer and boiling processes associated with liquid flow along a fracture embedded in an impermeable rock. We describe some simple asymptotic solutions for the temperature distribution in the bounding rock, which reveal that in the fracture, a two-phase boiling region develops between the purely liquid and purely vapor zones. Model predictions are successfully tested with laboratory experiments. In the final section of the review, we briefly discuss natural convective flows, illustrating how single-phase and two-phase convective regions interact and in some cases produce instability.
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    Annual Review of Fluid Mechanics 31 (1999), S. 347-384 
    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: Abstract We discuss the thickness of the liquid layer entrained by a solid drawn out of a bath, focusing on the case where the solid is a fiber or a wire. Slow withdrawals out of a pure or a complex fluid are described as well as quick coatings. We specify the general laws of entrainment and stress the cases where the fiber curvature plays a role. We finally give an overview on the further evolution of the coated film.
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    Annual Review of Fluid Mechanics 31 (1999), S. 239-272 
    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: Abstract Noncircular jets have been the topic of extensive research in the last fifteen years. These jets were identified as an efficient technique of passive flow control that allows significant improvements of performance in various practical systems at a relatively low cost because noncircular jets rely solely on changes in the geometry of the nozzle. The applications of noncircular jets discussed in this review include improved large- and small-scale mixing in low- and high-speed flows, and enhanced combustor performance, by improving combustion efficiency, reducing combustion instabilities and undesired emissions. Additional applications include noise suppression, heat transfer, and thrust vector control (TVC). The flow patterns associated with noncircular jets involve mechanisms of vortex evolution and interaction, flow instabilities, and fine-scale turbulence augmentation. Stability theory identified the effects of initial momentum thickness distribution, aspect ratio, and radius of curvature on the initial flow evolution. Experiments revealed complex vortex evolution and interaction related to self-induction and interaction between azimuthal and axial vortices, which lead to axis switching in the mean flow field. Numerical simulations described the details and clarified mechanisms of vorticity dynamics and effects of heat release and reaction on noncircular jet behavior. The research on noncircular jets has also led to technology transfer. A topic that started as an academic curiosity-an interesting flow phenomenon-subsequently has had various industrial applications. The investigations reviewed include experimental, theoretical, numerical, and technological aspects of the subject.
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    Annual Review of Fluid Mechanics 31 (1999), S. 385-416 
    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: Abstract An overview of preconditioning for the steady-state compressible inviscid fluid dynamic equations is presented. Extensions to the Navier-Stokes equations are also considered. These preconditioners are necessary for many algorithms in order to have the correct behavior at low speeds and to converge to the solution of the incompressible equations as the Mach number goes to zero. In addition, the preconditioning accelerates the convergence to a steady state for problems in which a significant portion of the flow is low speed. This low speed preconditioner can be combined with Jacobi and line preconditioners to damp high frequencies at all speeds. This is necessary for use with multigrid methods. Such combined methods are also better at accelerating problems with high aspect ratios. Details of the implementation are presented including several different variants for the preconditioning matrix.
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    Annual Review of Fluid Mechanics 31 (1999), S. 537-566 
    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: Abstract The paper reviews striking features of swirling flows-collapse, swirl generation, vortex breakdown, hysteresis, and axisymmetry breaking-and the mechanisms involved with the help of conical similarity solutions of the Navier-Stokes equations. The strong accumulation of axial and angular momenta, observed in tornadoes and flows over delta wings, corresponds to collapse, i.e. the singularity development in these solutions. Bifurcation of swirl explains the threshold character of swirl development in capillary and electrovortex flows. Analytical solutions for fold catastrophes and hysteresis reveal why there are so few stable states and why the jump transitions between the states occur-features typical of tornadoes, of flows over delta wings, and in vortex devices. Finally, the divergent instability explains such effects as the splitting of a tornado and the development of spiral branches in tree and near-wall swirling flows.
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    Annual Review of Genetics 31 (1997), S. 527-546 
    ISSN: 0066-4197
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Abstract The general goal of genetic studies of learning and memory is to develop and test theories that explain the animal's behavior in neuroanatomical, neurophysiological, cellular, and molecular terms. In this review we describe the role that gene targeting and other transgenic techniques have had in the study of mammalian learning and memory. We focus especially on the hippocampus, a brain structure that is thought to be central to the processing and temporary storage of complex information. We also discuss the main issues that confront this young field, as well as our vision for its future.
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    Annual Review of Genetics 31 (1997), S. 33-60 
    ISSN: 0066-4197
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Abstract Production of red blood cells (erythropoiesis) in the vertebrate embryo is critical to its survival and subsequent development. As red cells are the first blood cells to appear in embryogenesis, their origin reflects commitment of mesoderm to an hematopoietic fate and provides an avenue by which to examine the development of the hematopoietic system, including the hematopoietic stem cell (HSC). We discuss the genetics of erythropoiesis as studied in two systems: the mouse and zebrafish (Danio rerio). In the mouse, targeted disruption has established several genes as essential at different stages of hematopoiesis or erythroid precursor cell maturation. In the zebrafish, numerous mutants displaying a wide range of phenotypes have been isolated, although the affected genes are unknown. In comparing mouse knockout and zebrafish mutant phenotypes, we propose a pathway for erythropoiesis that emphasizes the apparent similarity of the mutants and the complementary nature of investigation in the two species. We speculate that further genetic studies in mouse and zebrafish will identify the majority of essential genes and define a regulatory network for hematopoiesis in vertebrates.
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    Annual Review of Genetics 31 (1997), S. 61-89 
    ISSN: 0066-4197
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Abstract During this decade, there have been major advancements in the understanding of genetic loci involved in synthesis of the family of Mg-tetrapyrroles known as chlorophylls and bacteriochlorophylls. Molecular genetic analysis of Mg-tetrapyrrole biosynthesis was initiated by the performance of detailed sequence and mutational analysis of the photosynthesis gene cluster from Rhodobacter capsulatus. These studies provided the first detailed understanding of genes involved in bacteriochlorophyll a biosynthesis. In the short time since these studies were initiated, most of the chlorophyll biosynthesis genes have been identified by virtue of their ability to complement bacteriochlorophyll a biosynthesis mutants as well as by sequence homology comparisons. This review is centered on a discussion of our current understanding of bacterial, algal, and plant genes that code for enzymes in the Mg-branch of the tetrapyrrole biosynthetic pathway that are responsible for synthesis of chlorophylls and bacteriochlorophylls.
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    Annual Review of Genetics 31 (1997), S. 91-111 
    ISSN: 0066-4197
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Abstract Gene amplification is a common feature of the genome of prokaryotic organisms. In this review, we analyze different instances of gene amplification in a variety of prokaryotes, including their mechanisms of generation and biological role. Growing evidence supports the concept that gene amplification be considered not as a mutation but rather as a dynamic genomic state related to the adaptation of bacterial populations to changing environmental conditions or biological interactions. In this context, the potentially amplifiable DNA regions impose a defined dynamic structure on the genome. If such structure has indeed been selected during evolution, it is a particularly challenging hypothesis.
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    Annual Review of Genetics 33 (1999), S. 57-88 
    ISSN: 0066-4197
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Abstract A decade of research on adaptive mutation has revealed a plethora of mutagenic mechanisms that may be important in evolution. The DNA synthesis associated with recombination could be an important source of spontaneous mutation in cells that are not proliferating. The movement of insertion elements can be responsive to environmental conditions. Insertion elements not only activate and inactivate genes, they also provide sequence homology that allows large-scale genomic rearrangements. Some conjugative plasmids can recombine with their host's chromosome, and may acquire chromosomal genes that could then spread through the population and even to other species. Finally, a subpopulation of transient hypermutators could be a source of multiple variant alleles, providing a mechanism for rapid evolution under adverse conditions.
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    Annual Review of Genetics 33 (1999), S. 133-170 
    ISSN: 0066-4197
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Abstract Lentiviruses are associated with chronic diseases of the hematological and neurological systems in animals and man. In particular, human immunodeficiency virus type 1 (HIV-1) is the etiological agent of the global AIDS epidemic. The genomes of lentiviruses are complex, encoding a number of regulatory and accessory proteins not found in other retroviruses. This complexity is reflected in their replication cycle, which reveals intricate regulatory pathways and unique mechanisms for viral persistence. In this review, we highlight some of these unique features for HIV-1, with particular focus on the transcriptional and posttranscriptional control of gene expression. Although our understanding of the biology of HIV-1 is far from complete, the knowledge gained thus far has already led to novel strategies for both virus intervention and exploiting the lentiviruses for therapeutic applications.
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    Annual Review of Genetics 33 (1999), S. 193-227 
    ISSN: 0066-4197
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Abstract The stability of mRNA in prokaryotes depends on multiple factors and it has not yet been possible to describe the process of mRNA degradation in terms of a unique pathway. However, important advances have been made in the past 10 years with the characterization of the cis-acting RNA elements and the trans-acting cellular proteins that control mRNA decay. The trans-acting proteins are mainly four nucleases, two endo- (RNase E and RNase III) and two exonucleases (PNPase and RNase II), and poly(A) polymerase. RNase E and PNPase are found in a multienzyme complex called the degradosome. In addition to the host nucleases, phage T4 encodes a specific endonuclease called RegB. The cis-acting elements that protect mRNA from degradation are stable stem-loops at the 5' end of the transcript and terminators or REP sequences at their 3' end. The rate-limiting step in mRNA decay is usually an initial endonucleolytic cleavage that often occurs at the 5' extremity. This initial step is followed by directional 3' to 5' degradation by the two exonucleases. Several examples, reviewed here, indicate that mRNA degradation is an important step at which gene expression can be controlled. This regulation can be either global, as in the case of growth rate-dependent control, or specific, in response to changes in the environmental conditions.
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    Annual Review of Genetics 33 (1999), S. 449-477 
    ISSN: 0066-4197
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Abstract Due to the increase of human migrations, the appearance of emerging and reemerging endemies, growing antibiotic resistance, and climatic changes, infectious diseases most probably constitute the major challenge for medicine in the next century. The advent of molecular methods of pathogen characterization has considerably improved our knowledge of the epidemiology of these diseases. However, the use of concepts of evolutionary genetics for interpreting "molecular epidemiology" data remains limited, although the application of such methods would broaden considerably the scope of this field of research, and allow epidemiologic and taxonomic approaches to be ascertained on a much firmer basis. In turn, pathogens, hosts, and vectors provide fascinating models for basic research. The artificial character of the border between "basic" and "applied" research is especially apparent with regard to the "integrated genetic epidemiology of infectious diseases" concept. The goal of this chapter is to evaluate the respective impact, on the transmission and pathogenicity of infectious diseases, of the host's, the pathogen's, and the vector's (for vector-borne diseases) genetic diversity, and the interactions between these three parameters (coevolution phenomena).
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    Annual Review of Biophysics and Biomolecular Structure 26 (1997), S. 401-424 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Phage display makes large-peptide diversity libraries readily attainable for identifying novel peptide ligands for receptors and other protein or non-protein targets. This technology kindles enthusiasm for the idea that large and protein-protein interaction surfaces (epitopes) can be distilled down to small pharmacophores. These may be accessible to organic scaffolding, yielding new orally active drugs that might otherwise have taken greater time and effort to be discovered through chemical-library screening. This review, though not comprehensive with respect to the explosive volume of phage display work over the last few years, focuses on recent developments in phage-displayed peptide technology.
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    Annual Review of Biophysics and Biomolecular Structure 26 (1997), S. 425-459 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Oil-water partitioning, solubilities, and vapor pressure experiments on small-molecule compounds are often used as models to obtain energies for biomolecular modeling. For example, measured partition coefficients, K, are often inserted into the formula -RTlnK to obtain quantities thought to represent microscopic contact interaction free energies. We review evidence here that this procedure does not always give microscopically meaningful free energies. Some partitioning processes, particularly involving polymeric solvents such as octanol or hexadecane, are governed not only by translational entropies and contact interactions, but also by free energies resulting from changes in the conformations of the polymer chains upon solute insertion. The Flory-Huggins theory is more suitable for these situations than is the classical approach. We discuss the physical bases for both approaches.
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    Annual Review of Biophysics and Biomolecular Structure 26 (1997), S. 461-493 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Ten years have passed since the initial reports that antibodies could be programmed to have enzymatic activity by immunization with a transition-site analog. Much of the research over the last decade has focused on defining the scope and generality of antibody catalysis; however, during the past two years the first few crystal structures of catalytic antibody transition-state analogs have been reported. This review analyzes four such structures of catalytic antibodies that catalyze markedly different reactions, including ester hydrolysis, sulfide oxidation, and a pericyclic rearrangement. Structure-function relations for these catalysts are discussed and compared to the structure and function of natural enzymes, as well as the chemistry that occurs in solution.
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    Annual Review of Biophysics and Biomolecular Structure 26 (1997), S. 567-596 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Recent advances in ultrasensitive instrumentation have allowed for the detection, identification, and dynamic studies of single molecules in the condensed phase. This measurement capability provides a new set of tools for scientists to address important current problems and to explore new frontiers in many scientific disciplines, such as chemistry, molecular biology, molecular medicine, and nanostructured materials. This review focuses on the methodologies and biological applications of single-molecule detection based on laser-induced fluorescence.
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    Annual Review of Biophysics and Biomolecular Structure 26 (1997), S. 629-658 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract This chapter reviews the dynamics information obtained from experimental magnetic resonance studies of site-specifically labeled duplex DNA. A previous review (43) discusses the dynamics of duplex DNA; it develops a theory that shows how magnetic resonance experiments are used to detect those dynamics. The methods for obtaining information about dynamics as well as a summary of what is now known about the site-specific dynamics of DNA are presented. This review contains two methods sections which present results using electron paramagnetic resonance and nuclear magnetic resonance active probes.
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    Annual Review of Biophysics and Biomolecular Structure 28 (1999), S. 57-73 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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    Notes: Abstract An RNA fold is the result of packing together two or more coaxial helical stacks. To date, four RNA folds have been determined at near-atomic resolution by X-ray crystallography: transfer RNA, the hammerhead ribozyme, the P4-P6 domain of the Tetrahymena group I intron, and the hepatitis delta virus ribozyme. All four folds result in RNAs that are considerably more compact than isolated A-form duplexes. These structures illustrate, to varying degrees, three modes of fold stabilization: association of complementary molecular surfaces, stabilization of close RNA packing by binding of cations, and stabilization through pseudoknotting.
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    Annual Review of Biophysics and Biomolecular Structure 28 (1999), S. 205-234 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract The F0F1 ATP synthase is a large multisubunit complex that couples translocation of protons down an electrochemical gradient to the synthesis of ATP. Recent advances in structural analyses have led to the demonstration that the enzyme utilizes a rotational catalytic mechanism. Kinetic and biochemical evidence is consistent with the expected equal participation of the three catalytic sites in the alpha3beta3 hexamer, which operate in sequential, cooperative reaction pathways. The rotation of the core gamma subunit plays critical roles in establishing the conformation of the sites and the cooperative interactions. Mutational analyses have shown that the rotor subunits are responsible for coupling and in doing so transmit specific conformational information between transport and catalysis.
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    Annual Review of Biophysics and Biomolecular Structure 28 (1999), S. 235-268 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Solid-state nuclear magnetic resonance (NMR) is rapidly emerging as a successful and important technique for protein and peptide structural elucidation from samples in anisotropic environments. Because of the diversity of nuclei and nuclear spin interactions that can be observed, and because of the broad range of sample conditions that can be studied by solid-state NMR, the potential for gaining structural constraints is great. Structural constraints in the form of orientational, distance, and torsional constraints can be obtained on proteins in crystalline, liquid-crystalline, or amorphous preparations. Great progress in the past few years has been made in developing techniques for obtaining these constraints, and now it has also been clearly demonstrated that these constraints can be assembled into uniquely defined three-dimensional structures at high resolution. Although much progress toward the development of solid-state NMR as a routine structural tool has been documented, the future is even brighter with the continued development of the experiments, of NMR hardware, and of the molecular biological methods for the preparation of labeled samples.
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    Annual Review of Biophysics and Biomolecular Structure 28 (1999), S. 319-365 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Stably folded membrane proteins reside in a free energy minimum determined by the interactions of the peptide chains with each other, the lipid bilayer hydrocarbon core, the bilayer interface, and with water. The prediction of three-dimensional structure from sequence requires a detailed understanding of these interactions. Progress toward this objective is summarized in this review by means of a thermodynamic framework for describing membrane protein folding and stability. The framework includes a coherent thermodynamic formalism for determining and describing the energetics of peptide-bilayer interactions and a review of the properties of the environment of membrane proteins-the bilayer milieu. Using a four-step thermodynamic cycle as a guide, advances in three main aspects of membrane protein folding energetics are discussed: protein binding and folding in bilayer interfaces, transmembrane helix insertion, and helix-helix interactions. The concepts of membrane protein stability that emerge provide insights to fundamental issues of protein folding.
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    Annual Review of Biophysics and Biomolecular Structure 28 (1999), S. 367-399 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Bacteriorhodopsin is the best understood ion transport protein and has become a paradigm for membrane proteins in general and transporters in particular. Models up to 2.5 A resolution of bacteriorhodopsin's structure have been published during the last three years and are basic for understanding its function. Thus one focus of this review is to summarize and to compare these models in detail. Another focus is to follow the protein through its catalytic cycle in summarizing more recent developments. We focus on literature published since 1995; a comprehensive series of reviews was published in 1995 (112).
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    Annual Review of Cell and Developmental Biology 13 (1997), S. 203-229 
    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Abstract To grow and develop optimally, all organisms need to perceive and process information from both their biotic and abiotic surroundings. A particularly important environmental cue is light, to which organisms respond in many different ways. Because they are photosynthetic and non-motile, plants need to be especially plastic in response to their light environment. The diverse responses of plants to light require sophisticated sensing of its intensity, direction, duration, and wavelength. The action spectra of light responses provided assays to identify three photoreceptor systems absorbing in the red/far-red, blue/near-ultraviolet, and ultraviolet spectral ranges. Following absorption of light, photoreceptors interact with other signal transduction elements, which eventually leads to many molecular and morphological responses. While a complete signal transduction cascade is not known yet, molecular genetic studies using the model plant Arabidopsis have led to substantial progress in dissecting the signal transduction network. Important gains have been made in determining the function of the photoreceptors, the terminal response pathways, and the intervening signal transduction components.
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    Annual Review of Cell and Developmental Biology 13 (1997), S. 231-259 
    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Abstract Adipose tissue has long been known to house the largest energy reserves in the animal body. Recent research indicates that in addition to this role, the adipocyte functions as a global regulator of energy metabolism. Adipose tissue is exquisitely sensitive to a variety of endocrine and paracrine signals, e.g. insulin, glucagon, glucocorticoids, and tumor necrosis factor (TNF), that combine to control both the secretion of other regulatory factors and the recruitment and differentiation of new adipocytes. The process of adipocyte differentiation is controlled by a cascade of transcription factors, most notably those of the C/EBP and PPAR families, which combine to regulate each other and to control the expression of adipocyte-specific genes. One such gene, i.e. the obese gene, was recently identified and found to encode a hormone, referred to as leptin, that plays a major role in the regulation of energy intake and expenditure. The hormonal and transcriptional control of adipocyte differentiation is discussed, as is the role of leptin and other factors secreted by the adipocyte that participate in the regulation of adipose homeostasis.
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    Annual Review of Cell and Developmental Biology 15 (1999), S. 661-703 
    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Abstract The [PSI+] factor of the yeast Saccharomyces cerevisiae is an epigenetic regulator of translation termination. More than three decades ago, genetic analysis of the transmission of [PSI+] revealed a complex and often contradictory series of observations. However, many of these discrepancies may now be reconciled by a revolutionary hypothesis: protein conformation-based inheritance (the prion hypothesis). This model predicts that a single protein can stably exist in at least two distinct physical states, each associated with a different phenotype. Propagation of one of these traits is achieved by a self-perpetuating change in the protein from one form to the other. Mounting genetic and biochemical evidence suggests that the determinant of [PSI+] is the nuclear encoded Sup35p, a component of the translation termination complex. Here we review the series of experiments supporting the yeast prion hypothesis and provide another look at the 30 years of work preceding this theory in light of our current state of knowledge.
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    Annual Review of Astronomy and Astrophysics 35 (1997), S. 1-32 
    ISSN: 0066-4146
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Physics
    Notes: Abstract Eta Carinae (Eta) is one of the most remarkable of all well-studied stars and perhaps the most poorly understood. Observations with the Hubble Space Telescope and other modern instruments have solved a few of the mysteries concerning this object while opening a comparable number of new ones. In this review we first recount some essential background information concerning Eta, then we sketch most of the observational developments of the past few years, related to the star itself and to its ejecta. Throughout, we propose a series of specific unsolved observational and theoretical problems that seem especially interesting or important at this time.
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    Annual Review of Astronomy and Astrophysics 35 (1997), S. 137-177 
    ISSN: 0066-4146
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Physics
    Notes: Abstract As progressively cooler stellar and substellar objects are discovered, the presence first of molecules and then of condensed particulates greatly complicates the understanding of their physical properties. Accurate model atmospheres that include these processes are the key to establishing their atmospheric parameters. They play a crucial role in determining structural characteristics by setting the surface conditions of model interiors and providing transformations to the various observational planes. They can reveal the spectroscopic properties of brown dwarfs and help establish their detectability. In this paper, we review the current state-of-the-art theory and modeling of the atmospheres of very low mass stars, including the coolest known M dwarfs, M subdwarfs, and brown dwarfs, i.e. Teff〈= 4,000 K and -4.0 〈= [M/H] 〈= +0.0. We discuss ongoing efforts to incorporate molecular and grain opacities in cool stellar spectra, as well as the latest progress in (a) deriving the effective temperature scale of M dwarfs, (b) reproducing the lower main sequences of metal-poor subdwarfs in the halo and globular clusters, and (c) results of the models related to the search for brown dwarfs.
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    Annual Review of Astronomy and Astrophysics 35 (1997), S. 179-215 
    ISSN: 0066-4146
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Physics
    Notes: Abstract All neutral atomic hydrogen gas and a large fraction of the molecular gas in the Milky Way Galaxy and external galaxies lie in PDRs, and PDRs are the origin of most of the nonstellar infrared (IR) and the millimeter CO emission from a galaxy. On the surfaces (Av〈 1-3) of interstellar clouds, the absorption of far ultraviolet (FUV) photons (hnu〈 13.6 eV) by gas and dust grains leads to intense emission of [C II] 158 mum, [O I] 63, 146 mum, and H2 rovibrational transitions, as well as IR dust continuum and polycyclic aromatic hydrocarbon (PAH) emission features. Deeper in PDRs, CO rotational and [C I] 370, 609 mum lines originate. The transition of H to H2 and C+ to CO occurs within PDRs. Theoretical models compared with observations diagnose such physical parameters as the density and temperature structure, the elemental abundances, and the FUV radiation field in PDRs. Applications include clouds next to H II regions, reflection nebulae, planetary nebulae, red giant outflows, circumstellar gas around young stars, diffuse clouds, the warm neutral medium (WNM), and molecular clouds in the interstellar radiation field: in summary, much of the interstellar medium in galaxies. This review focuses on dense PDRs in the Milky Way Galaxy. Theoretical PDR models help explain the observed correlation of the CO J = 1-0 luminosity with the molecular mass and also suggest FUV-induced feedback mechanisms that may regulate star formation rates and the column density through giant molecular clouds.
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    Annual Review of Astronomy and Astrophysics 35 (1997), S. 389-443 
    ISSN: 0066-4146
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Physics
    Notes: Abstract The physical properties of the faint blue galaxy population are reviewed in the context of observational progress made via deep spectroscopic surveys and Hubble Space Telescope imaging of field galaxies at various limits and theoretical models for the integrated star formation history of the universe. Notwithstanding uncertainties in the properties of the local population of galaxies, convincing evidence has emerged from several independent studies for a rapid decline in the volume-averaged star-formation rate of field galaxies since a redshift z = 1. Together with the small angular sizes and modest mean redshift of the faintest detectable sources, these results can be understood in hierarchical models where the bulk of the star formation occurred at redshifts between z = 1-2. The physical processes responsible for the subsequent demise of the faint blue galaxy population remain unclear. Considerable progress will be possible when the evolutionary trends can be monitored in the context of independent physical parameters such as the underlying galactic mass.
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    Annual Review of Astronomy and Astrophysics 35 (1997), S. 503-556 
    ISSN: 0066-4146
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Physics
    Notes: Abstract The metallicity of stars in the Galaxy ranges from [Fe/H] = -4 to +0.5 dex, and the solar iron abundance is epsilon(Fe) = 7.51 +- 0.01 dex. The average values of [Fe/H] in the solar neighborhood, the halo, and Galactic bulge are -0.2, -1.6, and -0.2 dex respectively. Detailed abundance analysis reveals that the Galactic disk, halo, and bulge exhibit unique abundance patterns of O, Mg, Si, Ca, and Ti and neutron-capture elements. These signatures show that environment plays an important role in chemical evolution and that supernovae come in many flavors with a range of element yields. The 300-fold dispersion in heavy element abundances of the most metal-poor stars suggests incomplete mixing of ejecta from individual supernova, with vastly different yields, in clouds of ~106 M . The composition of Orion association stars indicates that star-forming regions are significantly self-enriched on time scales of 80 million years. The rapid self-enrichment and inhomogeneous chemical evolution models are required to match observed abundance trends and the dispersion in the age-metallicity relation.
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    Annual Review of Astronomy and Astrophysics 37 (1999), S. 127-189 
    ISSN: 0066-4146
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Physics
    Notes: Abstract Gravitational lenses can provide crucial information on the geometry of the Universe, on the cosmological scenario of formation of its structures as well as on the history of its components with look-back time. In this review, I focus on the most recent results obtained during the last five years from the analysis of the weak lensing regime. The potential of weak lensing as a probe of dark matter and the study of the coupling between light and mass on scales of clusters of galaxies, large-scale structures and galaxies is discussed first. Then I present the impact of weak lensing for the study of distant galaxies and of the population of lensed sources as a function of redshift. Finally, I discuss the potential of weak lensing to constrain the cosmological parameters, either from pure geometrical effects observed in peculiar lenses, or from the coupling of weak lensing with the CMB.
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    Annual Review of Astronomy and Astrophysics 37 (1999), S. 533-602 
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    Annual Review of Fluid Mechanics 31 (1999), S. 1-53 
    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: Abstract Because of mean distortion, most turbulent flows are anisotropic. Two-point descriptions, forming the heart of this review of anisotropic models, capture the continuum of anisotropically structured turbulent scales and, moreover, allow exact treatment of the linear terms representing mean distortion, only needing closure assumptions for the nonlinear part of the model. The rapid-distortion limit, in which nonlinear terms are neglected, is the main subject of Section 2, while Section 3 introduces nonlinearity. It is shown that, even with significant nonlinearity, many features of turbulence can, at least qualitatively, be understood using linear theory alone, e.g. the directionality of velocity fluctuations and correlation lengths induced by strong mean shear near a wall or straining by duct flow, whereas some, e.g. wave resonances in rotating turbulence, involve a subtle combination of linear and nonlinear terms. The importance of linear effects is reflected in the triadic models of Section 3, which contain no approximations of the linear terms and whose anisotropic nonlinear closures are heavily dependent on linear theory. Despite being fundamentally less satisfactory (because they involve additional ad hoc hypotheses to compensate for the lack of two-point information), one-point models dominate industrial calculations because they are robust, well-established, and computationally relatively cheap. Although there are too many spectral degrees of freedom for a one-point model to reproduce two-point results in all circumstances, two-point theories-in particular RDT-have been exploited to develop new one-point models, as discussed in Section 4. Given the significant limitation of classical two-point models to homogeneous turbulence, some inhomogeneous extensions are described in Section 5.
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    Annual Review of Fluid Mechanics 31 (1999), S. 201-238 
    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: Abstract Natural ventilation of buildings is the flow generated by temperature differences and by the wind. The governing feature of this flow is the exchange between an interior space and the external ambient. Although the wind may often appear to be the dominant driving mechanism, in many circumstances temperature variations play a controlling feature on the ventilation since the directional buoyancy force has a large influence on the flow patterns within the space and on the nature of the exchange with the outside. Two forms of ventilation are discussed: mixing ventilation, in which the interior is at an approximately uniform temperature, and displacement ventilation, where there is strong internal stratification. The dynamics of these buoyancy-driven flows are considered, and the effects of wind on them are examined. The aim behind this work is to give designers rules and intuition on how air moves within a building; the research reveals a fascinating branch of fluid mechanics.
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    Annual Review of Fluid Mechanics 31 (1999), S. 301-346 
    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: Abstract This review deals primarily with the bifurcation, stability, and evolution of gravity and capillary-gravity waves. Recent results on the bifurcation of various types of capillary-gravity waves, including two-dimensional solitary waves at the minimum of the dispersion curve, are reviewed. A survey of various mechanisms (including the most recent ones) to explain the frequency downshift phenomenon is provided. Recent significant results are given on "horseshoe" patterns, which are three-dimensional structures observable on the sea surface under the action of wind or in wave tank experiments. The so-called short-crested waves are then discussed. Finally, the importance of surface tension effects on steep waves is studied.
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    Annual Review of Fluid Mechanics 31 (1999), S. 459-494 
    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: Abstract A review of planetary-entry gas dynamics is presented. Evolution of a blunt-body flowfield from a free molecular flow environment to a continuum environment is described. Simulations of near-wake flow phenomena, important for defining aerobrake payload environments, are also discussed. Some topics to be highlighted include aerodynamic coefficient predictions with emphasis on high-temperature gas effects; surface heating and temperature predictions for thermal protection system (TPS) design in a high-temperature, thermochemical nonequilibrium environment; and thermochemical models required for numerical flow simulation. Recent applications involving atmospheric entry into Jupiter (Galileo), Mars (Pathfinder and Global Surveyor), and a planned mission in which dust from the tail of a comet will be returned to Earth (Stardust) will provide context for this discussion.
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    Annual Review of Genetics 31 (1997), S. 493-525 
    ISSN: 0066-4197
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Abstract A handful of autosomal genes in the mammalian genome are inherited in a silent state from one of the two parents, and in a fully active form from the other, thereby rendering the organism functionally hemizygous for imprinted genes. To date 19 imprinted genes have been identified; 5 are expressed from the maternal chromosome while the rest are expressed from the paternal chromosome. Allele-specific methylation of CpG residues, established in one of the germlines and maintained throughout embryogenesis, has been clearly implicated in the maintenance of imprinting in somatic cells. Although the function of imprinting remains a subject of some debate, the process is thought to have an important role in regulating the rate of fetal growth.
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    Annual Review of Genetics 31 (1997), S. 571-610 
    ISSN: 0066-4197
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Abstract The inactive X chromosome differs from the active X in a number of ways; some of these, such as allocyclic replication and altered histone acetylation, are associated with all types of epigenetic silencing, whereas others, such as DNA methylation, are of more restricted use. These features are acquired progressively by the inactive X after onset of initiation. Initiation of X-inactivation is controlled by the X-inactivation center (Xic) and influenced by the X chromosome controlling element (Xce), which causes primary nonrandom X-inactivation. Other examples of nonrandom X-inactivation are also presented in this review. The definition of a major role for Xist, a noncoding RNA, in X-inactivation has enabled investigation of the mechanism leading to establishment of the heterochromatinized X-chromosome and also of the interactions between X-inactivation and imprinting as well as between X-inactivation and developmental processes in the early embryo.
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    Annual Review of Genetics 31 (1997), S. 635-662 
    ISSN: 0066-4197
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Abstract Gene mutations provide valuable clues to cellular metabolism. In humans such insights come mainly from genetic disorders. Ataxia-telangiectasia (A-T) and Nijmegen breakage syndrome (NBS) are two distinct, but closely related, single gene disorders that highlight a complex junction of several signal transduction pathways. These pathways appear to control defense mechanisms against specific types of damage to cellular macromolecules, and probably regulate the processing of certain types of DNA damage or normal intermediates of DNA metabolism. A-T is characterized primarily by cerebellar degeneration, immunodeficiency, genome instability, clinical radiosensitivity, and cancer predisposition. NBS shares all these features except cerebellar deterioration. The cellular phenotypes of A-T and NBS are almost indistinguishable, however, and include chromosomal instability, radiosensitivity, and defects in cell cycle checkpoints normally induced by ionizing radiation. The recent identification of the gene responsible for A-T, ATM, has revealed its product to be a large, constitutively expressed phosphoprotein with a carboxy-terminal region similar to the catalytic domain of phosphatidylinositol 3-kinases (PI 3-kinases). ATM is a member of a family of proteins identified in various organisms, which share the PI 3-kinase domain and are involved in regulation of cell cycle progression and response to genotoxic agents. Some of these proteins, most notably the DNA-dependent protein kinase, have an associated protein kinase activity, and preliminary data indicate this activity in ATM as well. Mutations in A-T patients are null alleles that truncate or destabilize the ATM protein. Atm-deficient mice recapitulate the human phenotype with slower nervous-system degeneration. Two ATM interactors, c-Abl and p53, underscore its role in cellular responses to genotoxic stress. The complexity of ATM's structure and mode of action make it a paradigm of multifaceted signal transduction proteins involved in many physiological pathways via multiple protein-protein interactions. The as yet unknown NBS protein may be a component in an ATM-based complex, with a key role in sensing and processing specific DNA damage or intermediates and signaling their presence to the cell cycle machinery.
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    Annual Review of Genetics 31 (1997), S. 1-31 
    ISSN: 0066-4197
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Abstract Eubacterial plasmids and chromosomes encode multiple killer genes belonging to the hok gene family. The plasmid-encoded killer genes mediate plasmid stabilization by killing plasmid-free cells. This review describes the genetics, molecular biology, and evolution of the hok gene family. The complicated antisense RNA-regulated control-loop that regulates posttranscriptional and postsegregational activation of killer mRNA translation in plasmid-free cells is described in detail. Nucleotide covariations in the mRNAs reveal metastable stem-loop structures that are formed at the mRNA 5' ends in the nascent transcripts. The metastable structures prevent translation and antisense RNA binding during transcription. Coupled nucleotide covariations provide evidence for a phylogenetically conserved mRNA folding pathway that involves sequential dynamic RNA rearrangements. Our analyses have elucidated an intricate mechanism by which translation of an antisense RNA-regulated mRNA can be conditionally activated. The complex phylogenetic relationships of the plasmid- and chromosome-encoded systems are also presented and discussed.
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    Annual Review of Genetics 33 (1999), S. 1-27 
    ISSN: 0066-4197
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Abstract This review of plant population genetics focuses on the genetic foundations of the processes that have led to documentable improvements in cultivated plants since the earliest domestications took place perhaps 13,000 years ago. Nearly all human civilizations have depended heavily on inbreeding plants (particularly wheat, barley, soybeans and other inbreeding legumes), as well as outbreeding vegetatively propagated species (white potatoes, yams) as their dietary standbys. The principal exception is maize (corn), an annual seed-produced outbreeder in nature. It is noteworthy that maize joined wheat, rice, and barley as a truly major crop worldwide only after its conversion to self-pollination combined with hybridization between favorably interacting inbred lines increased yield of maize several-fold in the twentieth century.
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    Annual Review of Genetics 33 (1999), S. 29-55 
    ISSN: 0066-4197
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Abstract The immune response is regulated not only by cell proliferation and differentiation, but also by programmed cell death, or apoptosis. In response to various stimuli, death factors bind to their respective receptors and activate the apoptotic death program in target cells. A cascade of specific proteases termed caspases mediates the apoptotic process. The activated caspases cleave various cellular components, a process that leads to morphological changes of the cells and nuclei, as well as to degradation of the chromosomal DNA. Loss-of-function mutations in the signaling molecules involved in apoptosis cause hyper-proliferation of cells in mouse and human. In contrast, exaggeration of this death cascade causes the destruction of various tissues.
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    Annual Review of Genetics 33 (1999), S. 89-131 
    ISSN: 0066-4197
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Abstract The past decade has witnessed extraordinary progress in retinal disease gene identification, the analysis of animal and tissue culture models of disease processes, and the integration of this information with clinical observations and with retinal biochemistry and physiology. During this period over twenty retinal disease genes were identified and for many of these genes there are now significant insights into their role in disease. This review presents an overview of the basic and clinical biology of the retina, summarizes recent progress in understanding the molecular mechanisms of inherited retinal diseases, and offers an assessment of the role that genetics will play in the next phase of research in this area.
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