bluuebunny/crossref_metadata_2025 huggingface dataset:
LUMINOUS INFRARED GALAXIES
Authors: Sanders D. B. , Mirabel I. F.
Published: July 2002

▪ Abstract  At luminosities above 1011 [Formula: see text], infrared galaxies become the dominant population of extragalactic objects in the local Universe (z ≲ 0.3), being more numerous than optically selected starburst and Seyfert galaxies and quasi-stellar objects at comparable bolometric luminosity. The trigger for the intense infrared emission appears to be the strong interaction/merger of molecular gas-rich spirals, and the bulk of the infrared luminosity for all but the most luminous objects is due to dust heating from an intense starburst within giant molecular clouds. At the highest luminosities (Lir > 1012 [Formula: see text]), nearly all objects appear to be advanced mergers powered by a mixture of circumnuclear starburst and active galactic nucleus energy sources, both of which are fueled by an enormous concentration of molecular gas that has been funneled into the merger nucleus. These ultraluminous infrared galaxies may represent an important stage in the formation of quasi-stellar objects and powerful radio galaxies. They may also represent a primary stage in the formation of elliptical galaxy cores, the formation of globular clusters, and the metal enrichment of the intergalactic medium.
Elemental Abundances in Quasistellar Objects: Star Formation and Galactic Nuclear Evolution at High Redshifts
Authors: Hamann Fred , Ferland Gary
Published: July 2002

▪ Abstract  Quasar (QSO) elemental abundances provide unique probes of high-redshift star formation and galaxy evolution. There is growing evidence from both the emission and intrinsic absorption lines that QSO environments have roughly solar or higher metallicities out to redshifts >4. The range is not well known, but solar to a few times solar metallicity appears to be typical. There is also evidence for higher metallicities in more luminous objects and for generally enhanced N/C and Fe/α abundances compared with solar ratios.

These results identify QSOs with vigorous, high-redshift star formation—consistent with the early evolution of massive galactic nuclei or dense protogalactic clumps. However, the QSOs offer new constraints. For example, (a) most of the enrichment and star formation must occur before the QSOs “turn on” or become observable, on time scales of [Formula: see text] 1 Gyr at least at the highest redshifts. (b) The tentative result for enhanced Fe/α suggests that the first local star formation began at least ∼1 Gyr before the QSO epoch. (c) The star formation must ultimately be extensive to reach high metallicities; that is, a substantial fraction of the local gas must be converted into stars and stellar remnants. The exact fraction depends on the shape of the initial mass function (IMF). (d) The highest derived metallicities require IMFs that are weighted slightly more toward massive stars than in the solar neighborhood. (e) High metallicities also require deep gravitational potentials. By analogy with the well-known mass–metallicity relation among low-redshift galaxies, metal-rich QSOs should reside in galaxies (or protogalaxies) that are minimally as massive (or as tightly bound) as our own Milky Way.
THE AMP-ACTIVATED/SNF1 PROTEIN KINASE SUBFAMILY: Metabolic Sensors of the Eukaryotic Cell?
Authors: Hardie D. Grahame , Carling David , Carlson Marian
Published: July 2002

Mammalian AMP-activated protein kinase and yeast SNF1 protein kinase are the central components of kinase cascades that are highly conserved between animals, fungi, and plants. The AMP-activated protein kinase cascade acts as a metabolic sensor or “fuel gauge” that monitors cellular AMP and ATP levels because it is activated by increases in the AMP:ATP ratio. Once activated, the enzyme switches off ATP-consuming anabolic pathways and switches on ATP-producing catabolic pathways, such as fatty acid oxidation. The SNF1 complex in yeast is activated in response to the stress of glucose deprivation. In this case the intracellular signal or signals have not been identified; however, SNF1 activation is associated with depletion of ATP and elevation of AMP. The SNF1 complex acts primarily by inducing expression of genes required for catabolic pathways that generate glucose, probably by triggering phosphorylation of transcription factors. SNF1-related protein kinases in higher plants are likely to be involved in the response of plant cells to environmental and/or nutritional stress.
Nuclear-Receptor Ligands and Ligand-Binding Domains
Authors: Weatherman Ross V. , Fletterick Robert J. , Scanlan Thomas S.
Published: July 2002

▪ Abstract  The determination of several structures of nuclear receptor ligand binding domains (LBD) has led to new insights into the mechanism of action of this very important class of receptors. This review describes and compares the different LBD structures and their relationship to the function of the nuclear receptors. The role of the ligand in the LBD structures and the implications of ligand structure on receptor activity are also discussed. Structural information regarding interactions between the LBD and coactivator proteins and the potential role of these interactions in ligand agonism and antagonism is reviewed. Different pathways for nuclear receptor signaling and the use of new ligands to investigate these pathways are also described.
Mechanisms of Viral Membrane Fusion and Its Inhibition
Authors: Eckert Debra M. , Kim Peter S.
Published: July 2002

▪ Abstract  Viral envelope glycoproteins promote viral infection by mediating the fusion of the viral membrane with the host-cell membrane. Structural and biochemical studies of two viral glycoproteins, influenza hemagglutinin and HIV-1 envelope protein, have led to a common model for viral entry. The fusion mechanism involves a transient conformational species that can be targeted by therapeutic strategies. This mechanism of infectivity is likely utilized by a wide variety of enveloped viruses for which similar therapeutic interventions should be possible.
Fluid Mechanics of Vascular Systems, Diseases, and Thrombosis
Authors: Wootton David M. , Ku David N.
Published: July 2002

▪ Abstract  The cardiovascular system is an internal flow loop with multiple branches circulating a complex liquid. The hallmarks of blood flow in arteries are pulsatility and branches, which cause wall stresses to be cyclical and nonuniform. Normal arterial flow is laminar, with secondary flows generated at curves and branches. Arteries can adapt to and modify hemodynamic conditions, and unusual hemodynamic conditions may cause an abnormal biological response. Velocity profile skewing can create pockets in which the wall shear stress is low and oscillates in direction. Atherosclerosis tends to localize to these sites and creates a narrowing of the artery lumen—a stenosis. Plaque rupture or endothelial injury can stimulate thrombosis, which can block blood flow to heart or brain tissues, causing a heart attack or stroke. The small lumen and elevated shear rate in a stenosis create conditions that accelerate platelet accumulation and occlusion. The relationship between thrombosis and fluid mechanics is complex, especially in the post-stenotic flow field. New convection models have been developed to predict clinical occlusion from platelet thrombosis in diseased arteries. Future hemodynamic studies should address the complex mechanics of flow-induced, large-scale wall motion and convection of semisolid particles and cells in flowing blood.
Computer Modeling and Simulation of Human Movement
Authors: Pandy Marcus G.
Published: July 2002

▪ Abstract  Recent interest in using modeling and simulation to study movement is driven by the belief that this approach can provide insight into how the nervous system and muscles interact to produce coordinated motion of the body parts. With the computational resources available today, large-scale models of the body can be used to produce realistic simulations of movement that are an order of magnitude more complex than those produced just 10 years ago. This chapter reviews how the structure of the neuromusculoskeletal system is commonly represented in a multijoint model of movement, how modeling may be combined with optimization theory to simulate the dynamics of a motor task, and how model output can be analyzed to describe and explain muscle function. Some results obtained from simulations of jumping, pedaling, and walking are also reviewed to illustrate the approach.
THE STRUCTURE AND MECHANISM OF PROTEIN PHOSPHATASES: Insights into Catalysis and Regulation
Authors: Barford David , Das Amit K. , Egloff Marie-Pierre
Published: July 2002

▪ Abstract  Eukaryotic protein phosphatases are structurally and functionally diverse enzymes that are represented by three distinct gene families. Two of these, the PPP and PPM families, dephosphorylate phosphoserine and phosphothreonine residues, whereas the protein tyrosine phosphatases (PTPs) dephosphorylate phosphotyrosine amino acids. A subfamily of the PTPs, the dual-specificity phosphatases, dephosphorylate all three phosphoamino acids. Within each family, the catalytic domains are highly conserved, with functional diversity endowed by regulatory domains and subunits. The protein Ser/Thr phosphatases are metalloenzymes and dephosphorylate their substrates in a single reaction step using a metal-activated nucleophilic water molecule. In contrast, the PTPs catalyze dephosphorylation by use of a cysteinyl-phosphate enzyme intermediate. The crystal structures of a number of protein phosphatases have been determined, enabling us to understand their catalytic mechanisms and the basis for substrate recognition and to begin to provide insights into molecular mechanisms of protein phosphatase regulation.
MOLECULAR DYNAMICS SIMULATIONS OF BIOMOLECULES: Long-Range Electrostatic Effects
Authors: Sagui Celeste , Darden Thomas A.
Published: July 2002

▪ 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.
Molecular Mechanisms Controlling Actin Filament Dynamics in Nonmuscle Cells
Authors: Pollard Thomas D. , Blanchoin Laurent , Mullins R. Dyche
Published: July 2002

▪ Abstract  We review how motile cells regulate actin filament assembly at their leading edge. Activation of cell surface receptors generates signals (including activated Rho family GTPases) that converge on integrating proteins of the WASp family (WASp, N-WASP, and Scar/WAVE). WASP family proteins stimulate Arp2/3 complex to nucleate actin filaments, which grow at a fixed 70° angle from the side of pre-existing actin filaments. These filaments push the membrane forward as they grow at their barbed ends. Arp2/3 complex is incorporated into the network, and new filaments are capped rapidly, so that activated Arp2/3 complex must be supplied continuously to keep the network growing. Hydrolysis of ATP bound to polymerized actin followed by phosphate dissociation marks older filaments for depolymerization by ADF/cofilins. Profilin catalyzes exchange of ADP for ATP, recycling actin back to a pool of unpolymerized monomers bound to profilin and thymosin-β4 that is poised for rapid elongation of new barbed ends.
CYTOKINE RECEPTOR SIGNAL TRANSDUCTION AND THE CONTROL OF HEMATOPOIETIC CELL DEVELOPMENT
Authors: Watowich Stephanie S. , Wu Hong , Socolovsky Merav , Klingmuller Ursula , Constantinescu Stefan N. , Lodish Harvey F.
Published: July 2002

▪ Abstract  The cytokine receptor superfamily is characterized by structural motifs in the exoplasmic domain and by the absence of catalytic activity in the cytosolic segment. Activated by ligand-triggered multimerization, these receptors in turn activate a number of cytosolic signal transduction proteins, including protein tyrosine kinases and phosphatases, and affect an array of cellular functions that include proliferation and differentiation. Molecular study of these receptors is revealing the roles they play in the control of normal hematopoiesis and in the development of disease.
CELLULAR FUNCTIONS REGULATED BY SRC FAMILY KINASES
Authors: Thomas Sheila M. , Brugge Joan S.
Published: July 2002

▪ 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.
Thrombospondins: Multifunctional Regulators of Cell Interactions
Authors: Adams Josephine C.
Published: July 2002

▪ Abstract  Thrombospondins are secreted, multidomain macromolecules that act as regulators of cell interactions in vertebrates. Gene knockout mice constructed for two members of this family demonstrate roles in the organization and homeostasis of multiple tissues, with particularly significant activities in the regulation of angiogenesis. This review discusses the functions of thrombospondins with regard to their cellular mechanisms of action and highlights recent advances in understanding how multifactorial molecular interactions, at the cell surface and within extracellular matrix, produce cell-type-specific effects on cell behavior and the organization of matrix and tissues.
Vertebrate Somitogenesis
Authors: Pourquié Olivier
Published: July 2002

▪ Abstract  In vertebrates, the paraxial mesoderm corresponds to the bilateral strips of mesodermal tissue flanking the notochord and neural tube and which are delimited laterally by the intermediate mesoderm and the lateral plate. The paraxial mesoderm comprises the head or cephalic mesoderm anteriorly and the somitic region throughout the trunk and the tail of the vertebrates. Soon after gastrulation, the somitic region of vertebrates starts to become segmented into paired blocks of mesoderm, termed somites. This process lasts until the number of somites characteristic of the species is reached. The somites later give rise to all skeletal muscles of the body, the axial skeleton, and part of the dermis. In this review I discuss the processes involved in the formation of the paraxial mesoderm and its segmentation into somites in vertebrates.
Left-Right Asymmetry Determination in Vertebrates
Authors: Mercola Mark , Levin Michael
Published: July 2002

▪ Abstract  A distinctive and essential feature of the vertebrate body is a pronounced left-right asymmetry of internal organs and the central nervous system. Remarkably, the direction of left-right asymmetry is consistent among all normal individuals in a species and, for many organs, is also conserved across species, despite the normal health of individuals with mirror-image anatomy. The mechanisms that determine stereotypic left-right asymmetry have fascinated biologists for over a century. Only recently, however, has our understanding of the left-right patterning been pushed forward by links to specific genes and proteins. Here we examine the molecular biology of the three principal steps in left-right determination: breaking bilateral symmetry, propagation and reinforcement of pattern, and the translation of pattern into asymmetric organ morphogenesis.
SEISMIC ANISOTROPY BENEATH THE CONTINENTS: Probing the Depths of Geology
Authors: Silver Paul G.
Published: July 2002

▪ Abstract  Seismic anisotropy beneath continents is analyzed from shear-wave splitting recorded at more than 300 continental seismic stations. Anisotropy is found to be a ubiquitous property that is due to mantle deformation from past and present orogenic activity. The observed coherence with crustal deformation implies that the mantle plays a major, if not dominant, role in orogenies. No evidence is found for a continental asthenospheric decoupling zone, suggesting that continents are coupled to general mantle circulation.
THE Re-OsISOTOPE SYSTEM IN COSMOCHEMISTRY AND HIGH-TEMPERATURE GEOCHEMISTRY
Authors: Shirey Steven B. , Walker Richard J.
Published: July 2002

▪ Abstract  The Re-Os isotope sytem, based on the long-lived β−transition of187Re to187Os, has matured to wide use in cosmochemistry and high-temperature geochemistry. The siderophilic/chalcophilic behavior of Re and Os is different from that of the elements that comprise most other long-lived radiogenic isotope systems. Magmatic iron meteorites (IIIAB, IIAB, IVA, and IVB) have Re-Os isochrons that indicate asteroidal core crystallization within the first 10–40 million years of Solar System evolution. Rocks from Earth's convecting mantle show generally chondritic Re/Os evolution throughout Earth history that is explained by the addition of highly siderophile elements to the mantle after core formation via late accretion. Oceanic basalts have Os-isotope systematics that improve the detailed geological interpretation of extant mantle components. Some portions of ancient subcontinental lithospheric mantle are severely depleted in Re and have correspondingly subchondritic187Os/188Os, indicating long-term isolation from the convecting mantle during the Archean-Proterozoic. Magmatic ore deposits have differences in initial Os isotopic composition traceable to the crustal vs mantle sources of the platinum-group elements and base metals.
LINKING THERMAL, HYDROLOGICAL, AND MECHANICAL PROCESSES IN FRACTURED ROCKS
Authors: Tsang Chin-Fu
Published: July 2002

▪ Abstract  In this paper, an overview is presented of coupled processes linking thermo-hydro-mechanical (THM) effects in fractured rocks. A formulation is first presented to show the linkage mathematically, which can be used as a basis for numerical solutions and for further developments. Two simple examples of hydromechanical (HM) and thermo-hydro-mechanical (THM) coupled processes are discussed to convey physical insight into such couplings. Finally, three large-scale, long-term experiments currently under way are described. These are being conducted specifically to study coupled processes in situ.
New Perspectives on Orbitally Forced Stratigraphy
Authors: Hinnov Linda A.
Published: July 2002

This survey of the current status of research into Earth’s orbitally forced paleoclimatic record summarizes recent developments in the theory of Earth’s orbital parameters, and reviews how various techniques of data collection and analysis have fared in the search and recovery of orbital signals in ancient stratigraphy. The emerging significance of the quasi-periodicity of Earth’s orbital variations as a principal tool in the analysis of orbitally forced stratigraphy is discussed in detail. Five case studies are presented that illustrate new directions in research: (a) time series analysis of discontinuous strata; (b) measurement of ultra-high resolution stratigraphic signals; (c) new perspectives on the 100 kyr Pleistocene glaciation problem; (d) stratigraphic evidence for solar system resonance modes; and (e) evaluating Phanerozoic length of day from orbitally forced stratigraphy.
Remote Sensing of Active Volcanoes
Authors: Francis Peter , Rothery David
Published: July 2002

The synoptic coverage offered by satellites provides unparalleled opportunities for monitoring active volcanoes, and opens new avenues of scientific inquiry. Thermal infrared radiation can be used to monitor levels of activity, which is useful for automated eruption detection and for studying the emplacement of lava flows. Satellite radars can observe volcanoes through clouds or at night, and provide high-resolution topographic data. In favorable conditions, radar inteferometery can be used to measure ground deformation associated with eruptive activity on a centimetric scale. Clouds from explosive eruptions present a pressing hazard to aviation; therefore, techniques are being developed to assess eruption cloud height and to discriminate between ash and meterological clouds. The multitude of sensors to be launched on future generations of space platforms promises to greatly enhance volcanological studies, but a satellite dedicated to volcanology is needed to meet requirements of aviation safety and volcano monitoring.
Rusty Relics of Earth History: Iron(III) Oxides, Isotopes, and Surficial Environments
Authors: Yapp Crayton
Published: July 2002

▪ Abstract  The two most common low-temperature iron(III) oxides on Earth are goethite (α-FeOOH) and hematite (α-Fe2O3). The δ18O values of natural goethites range from −15.5‰ to +3.3‰, whereas δ18O values of low-temperature hematites range from −16.7‰ to +4.7‰. Plots of δD against δ18O for continental goethites are approximately parallel to the meteoric water line of Craig ( H Craig. 1961 . Science 133:1702–3). This suggests that goethite-water fractionation factors are systematic over a wide range of surficial environments and may indicate that isotopic equilibrium is commonly attained or closely approached. Several experimental or calculated mineral-water, oxygen isotope fractionation curves have been determined for both goethite and hematite. Although there is not yet a consensus on which of these curves best approximates isotopic fractionation in natural samples, oxygen isotope measurements of both goethite and hematite have provided evidence of significant continental climate change on time scales that range from thousands to millions of years. The concentration and δ13C values of an Fe(CO3)OH component in apparent solid solution in goethite are proxies for the partial pressure and δ13C values, respectively, of CO2 in the environment at the time of goethite crystallization. Biological productivity, CO2 pressures in soil or groundwater, and partial pressures of atmospheric CO2 in ancient environments have been estimated from measurements of the mole fractions and δ13C values of Fe(CO3)OH in goethite.
Prelude to the Cambrian Explosion
Authors: Valentine James W.
Published: July 2002

▪ Abstract  The Prelude began with the origin of Metazoa, perhaps between 720 and 660 million years ago (mya), and ended with the geologically abrupt appearance of crown bilaterian phyla that began between 530 and 520 mya. The origin and early evolution of phyla cannot be tracked by fossils during this interval, but molecular phylogenetics permits reconstruction of their branching topology, whereas molecular developmental evidence supports hypotheses for the evolution of the metzoan genome during the rise of complex bodyplans. A flexible architecture of genetic regulation was in place even before the appearance of crown sponges, permitting increases in gene expression events as bodyplan complexity rose. Neoproterozoic bilaterians were chiefly small-bodied but likely diverse, whereas in the earliest Cambrian, between 543 and approximately 530–520 mya, bodies that were complex by marine invertebrate standards evolved in association with body-size increases.
Petrology of Subducted Slabs
Authors: Poli Stefano , Schmidt Max W.
Published: July 2002

▪ Abstract  The subducted lithosphere is composed of a complex pattern of chemical systems that undergo continuous and discontinuous phase transformation, through pressure and temperature variations. Volatile recycling plays a major geodynamic role in triggering mass transfer, melting, and volcanism. Although buoyancy forces are controlled by modal amounts of the most abundant phases, usually volatile-free, petrogenesis and chemical differentiation are controlled by the occurrence of minor phases, most of them volatile-bearing. Devolatilization of the subducted lithosphere is a continuous process distributed over more than 300 km of the slab-mantle interface. Melting of the subducted crust, if any, along sufficiently hot P-T paths, is governed by fluid-absent reactions, even though the difference between fluid and melt vanishes at pressures above the second critical end point. The density distribution at a depth of 660 km suggests episodic penetration in space and time of subducted slabs into the lower mantle and sinking down to the D″ region at the core-mantle boundary.
Fossil Plants as Indicators of the Phanerozoic Global Carbon Cycle
Authors: Beerling D.J. , Royer D.L.
Published: July 2002

▪ Abstract  Developments in plant physiology since the 1980s have led to the realization that fossil plants archive both the isotopic composition of atmospheric CO2 and its concentration, both critical integrators of carbon cycle processes through geologic time. These two carbon cycle signals can be read by analyzing the stable carbon isotope composition (δ13C) of fossilized terrestrial organic matter and by determining the stomatal characters of well-preserved fossil leaves, respectively. We critically evaluate the use of fossil plants in this way at abrupt climatic boundaries associated with mass extinctions and during times of extreme global warmth. Particular emphasis is placed on evaluating the potential to extract a quantitative estimate of the δ13C of atmospheric CO2 because of the key role it plays in understanding the carbon cycle. We critically discuss the use of stomatal index and stomatal ratios for reconstructing atmospheric CO2 levels, especially the need for adequate replication, and present a newly derived CO2 record for the Mesozoic that supports levels calculated from geochemical modeling of the long-term carbon cycle. Several suggestions for future research using stable carbon isotope analyses of fossil terrestrial organic matter and stomatal measurements are highlighted.
HERBIVORY AND PLANT DEFENSES IN TROPICAL FORESTS
Authors: Coley P. D. , Barone J. A.
Published: July 2002

▪ Abstract  In this review, we discuss the ecological and evolutionary consequences of plant-herbivore interactions in tropical forests. We note first that herbivory rates are higher in tropical forests than in temperate ones and that, in contrast to leaves in temperate forests, most of the damage to tropical leaves occurs when they are young and expanding. Leaves in dry tropical forests also suffer higher rates of damage than in wet forests, and damage is greater in the understory than in the canopy. Insect herbivores, which typically have a narrow host range in the tropics, cause most of the damage to leaves and have selected for a wide variety of chemical, developmental, and phenological defenses in plants. Pathogens are less studied but cause considerable damage and, along with insect herbivores, may contribute to the maintenance of tree diversity. Folivorous mammals do less damage than insects or pathogens but have evolved to cope with the high levels of plant defenses. Leaves in tropical forests are defended by having low nutritional quality, greater toughness, and a wide variety of secondary metabolites, many of which are more common in tropical than temperate forests. Tannins, toughness, and low nutritional quality lengthen insect developmental times, making them more vulnerable to predators and parasitoids. The widespread occurrence of these defenses suggests that natural enemies are key participants in plant defenses and may have influenced the evolution of these traits. To escape damage, leaves may expand rapidly, be flushed synchronously, or be produced during the dry season when herbivores are rare. One strategy virtually limited to tropical forests is for plants to flush leaves but delay “greening” them until the leaves are mature. Many of these defensive traits are correlated within species, due to physiological constraints and tradeoffs. In general, shade-tolerant species invest more in defenses than do gap-requiring ones, and species with long-lived leaves are better defended than those with short-lived leaves.
ADAPTIVE EVOLUTION OF PHOTORECEPTORS AND VISUAL PIGMENTS IN VERTEBRATES
Authors: Yokoyama Shozo , Yokoyama Ruth
Published: July 2002

▪ Abstract  Animals may be camouflaged by a coloration that matches their surroundings or by a combination of color and shape. Some species make themselves conspicuous and rely upon bold and bright coloration as a means of warning off their potential predators. Population biologists have accumulated information on the adaptive significance of coloration for a large number of species. To elucidate the mechanisms underpinning such natural selection events, it is necessary to understand the visual systems of interacting organisms.

Molecular genetic analyses on the human opsin genes by Nathans and his colleagues made it possible to characterize the opsin genes of various vertebrates. A striking level of diversity in the opsin gene sequences reflects adaptive responses of various species to different environments. Comparative analyses of opsins reveal that gene duplications and accumulation of mutations have been important in achieving that diversity. The analyses also identify amino acid changes that are potentially important in controlling wavelength absorption by the photosensitive molecules, the visual pigments. These hypotheses can now be rigorously tested using tissue culture cells. Thanks to the molecular characterization of the opsin genes, it is now possible to study the types of opsins associated with certain environmental conditions. Such surveys will provide important first molecular clues to how animals adapt to their environments with respect to their coloration and behavior.
A Comparison of Alternative Strategies for Estimating Gene Flow from Genetic Markers
Authors: Neigel Joseph E.
Published: July 2002

The estimation of gene flow from the distribution of genetic markers in populations requires an indirect approach. Gene flow parameters are defined by demographic models, and population genetic models provide the link between these parameters and the distributions of genetic markers. Following the introduction of allozyme methods in the 1960s, a standard approach to the estimation of gene flow was developed. Wright's island model of population structure was used to relate the distribution of allozyme alleles in populations to Nem, the product of the effective population size and the rate of migration.

Alternative strategies for the estimation of gene flow have been developed using different genetic markers, different models of demography and population genetics, and different methods of parameter estimation. No alternative strategy now available is clearly superior to the standard approach based on Wright's model and allozyme markers. However, this may soon change as methods are developed that fully utilize the genealogical relationships of DNA sequences. At present, alternative strategies do fill important needs. They can provide independent estimates of gene flow, measure different components of gene flow, and detect historical changes in population structure.
THE CHEMICAL CYCLE AND BIOACCUMULATION OF MERCURY
Authors: Morel François M. M. , Kraepiel Anne M. L. , Amyot Marc
Published: July 2002

▪ Abstract  Because it is very toxic and accumulates in organisms, particularly in fish, mercury is an important pollutant and one of the most studied. Nonetheless we still have an incomplete understanding of the factors that control the bioconcentration of mercury. Elemental mercury is efficiently transported as a gas around the globe, and even remote areas show evidence of mercury pollution originating from industrial sources such as power plants. Besides elemental mercury, the major forms of mercury in water are ionic mercury (which is bound to chloride, sulfide, or organic acids) and organic mercury, particularly methylmercury. Methylmercury rather than inorganic mercury is bioconcentrated because it is better retained by organisms at various levels in the food chain. The key factor determining the concentration of mercury in the biota is the methylmercury concentration in water, which is controlled by the relative efficiency of the methylation and demethylation processes. Anoxic waters and sediments are an important source of methylmercury, apparently as the result of the methylating activity of sulfate-reducing bacteria. In surface waters, methylmercury may originate from anoxic layers or be formed through poorly known biological or chemical processes. Demethylation is effected both photochemically and biologically.
Environmental Influences on Regional Deep-Sea Species Diversity
Authors: Levin Lisa A. , Etter Ron J. , Rex Michael A. , Gooday Andrew J. , Smith Craig R. , Pineda Jesús , Stuart Carol T. , Hessler Robert R. , Pawson David
Published: July 2002

▪ Abstract  Most of our knowledge of biodiversity and its causes in the deep-sea benthos derives from regional-scale sampling studies of the macrofauna. Improved sampling methods and the expansion of investigations into a wide variety of habitats have revolutionized our understanding of the deep sea. Local species diversity shows clear geographic variation on spatial scales of 100–1000 km. Recent sampling programs have revealed unexpected complexity in community structure at the landscape level that is associated with large-scale oceanographic processes and their environmental consequences. We review the relationships between variation in local species diversity and the regional-scale phenomena of boundary constraints, gradients of productivity, sediment heterogeneity, oxygen availability, hydrodynamic regimes, and catastrophic physical disturbance. We present a conceptual model of how these interdependent environmental factors shape regional-scale variation in local diversity. Local communities in the deep sea may be composed of species that exist as metapopulations whose regional distribution depends on a balance among global-scale, landscape-scale, and small-scale dynamics. Environmental gradients may form geographic patterns of diversity by influencing local processes such as predation, resource partitioning, competitive exclusion, and facilitation that determine species coexistence. The measurement of deep-sea species diversity remains a vital issue in comparing geographic patterns and evaluating their potential causes. Recent assessments of diversity using species accumulation curves with randomly pooled samples confirm the often-disputed claim that the deep sea supports higher diversity than the continental shelf. However, more intensive quantitative sampling is required to fully characterize the diversity of deep-sea sediments, the most extensive habitat on Earth. Once considered to be constant, spatially uniform, and isolated, deep-sea sediments are now recognized as a dynamic, richly textured environment that is inextricably linked to the global biosphere. Regional studies of the last two decades provide the empirical background necessary to formulate and test specific hypotheses of causality by controlled sampling designs and experimental approaches.
VISUAL ACUITY IN INSECTS
Authors: Land Michael F.
Published: July 2002

▪ Abstract  The acuity of compound eyes is determined by interommatidial angles, optical quality, and rhabdom dimensions. It is also affected by light levels and speed of movement. In insects, interommatidial angles vary from tens of degrees in Apterygota, to as little as 0.24° in dragonflies. Resolution better than this is not attainable in compound eyes of realistic size. The smaller the interommatidial angle the greater the distance at which objects—prey, predators, or foliage—can be resolved. Insects with different lifestyles have contrasting patterns of interommatidial angle distribution, related to forward flight, capture on the wing, and predation on horizontal surfaces.
NEW INSECTICIDES WITH ECDYSTEROIDAL AND JUVENILE HORMONE ACTIVITY
Authors: Dhadialla Tarlochan S. , Carlson Glenn R. , Le Dat P.
Published: July 2002

▪ Abstract  Agrochemical research over the last two decades has resulted in the discovery of chemically novel insecticides that mimic the action of the two insect growth and developmental hormones, the steroidal 20-hydroxyecdysone (20E) and the sesquiterpenoid juvenile hormone (JH). Bisacylhydrazines are non-steroidal agonists of 20E and exhibit their insecticidal activity via interaction with the ecdysteroid receptor proteins. Interestingly, two of the bisacylhydrazine (tebufenozide and RH-2485) insecticides are very selectively toxic to lepidopteran pests. These insecticides are safe to beneficial insects and have a benign ecotoxicological profile. Aromatic non-terpenoidal insecticides (fenoxycarb and pyriproxyfen) mimic the action of JHs. However, like the JHs, their exact mode of action is not well understood. These insecticides are toxic to a broad spectrum of insects during their embryonic, last larval, or reproductive stages. The insecticidal, ecotoxicological properties and the mode of action of the two groups of insecticides are reviewed in this article.
RECENT ADVANCES IN CASSAVA PEST MANAGEMENT
Authors: Bellotti Anthony C. , Smith Lincoln , Lapointe Stephen L.
Published: July 2002

▪ Abstract  Cassava (Manihot esculenta) occupies a uniquely important position as a food security crop for smallholder farmers in areas of the tropics where climate, soils, or societal stresses constrain production. Given its reliability and productivity, cassava is the most important locally produced food in a third of the world's low-income, food-deficit countries. It is the fourth most important source of carbohydrates for human consumption in the tropics, after rice, sugar, and maize. World production of cassava from 1994–1996 averaged 166 million tons/year grown on 16.6 million hectares (ha), for an average yield of 9.9 tons/ha. Approximately 57% is used for human consumption, 32% for animal feed and industrial purposes, and 11% is waste. Africa accounts for 51.3% of the production; Asia, 29.4%; and Latin America, 19.3%. The area planted to cassava in Africa, Asia, and Latin America is 10.3, 3.7, and 2.6 million ha, respectively.
Applications of Tagging and Mapping Insect Resistance Loci in Plants
Authors: Yencho G.C. , Cohen M.B. , Byrne P.F.
Published: July 2002

▪ Abstract  This review examines how molecular markers can be used to increase our understanding of the mechanisms of plant resistance to insects and develop insect resistant crops. We provide a brief description of the types of molecular markers currently being employed, and describe how they can be applied to identify and track genes of interest in a marker-assisted breeding program. A summary of the work reported in this field of study, with examples in which molecular markers have been applied to increase understanding of the mechanistic and biochemical bases of resistance in potato and maize plant/pest systems, is provided. We also describe how molecular markers can be applied to develop more durable insect-resistant crops. Finally, we identify key areas in molecular genetics that we believe will provide exciting and productive research opportunities for those working to develop insectresistant crops.
Parasitic Mites of Honey Bees: Life History, Implications, and Impact
Authors: Sammataro Diana , Gerson Uri , Needham Glen
Published: July 2002

▪ Abstract  The hive of the honey bee is a suitable habitat for diverse mites (Acari), including nonparasitic, omnivorous, and pollen-feeding species, and parasites. The biology and damage of the three main pest species Acarapis woodi, Varroa jacobsoni, and Tropilaelaps clareae is reviewed, along with detection and control methods. The hypothesis that Acarapis woodi is a recently evolved species is rejected. Mite-associated bee pathologies (mostly viral) also cause increasing losses to apiaries. Future studies on bee mites are beset by three main problems: (a) The recent discovery of several new honey bee species and new bee-parasitizing mite species (along with the probability that several species are masquerading under the name Varroa jacobsoni) may bring about new bee-mite associations and increase damage to beekeeping; (b) methods for studying bee pathologies caused by viruses are still largely lacking; (c) few bee- and consumer-friendly methods for controlling bee mites in large apiaries are available.
Turbulence in Plant Canopies
Authors: Finnigan John
Published: July 2002

▪ Abstract  The single-point statistics of turbulence in the ‘roughness sub-layer’ occupied by the plant canopy and the air layer just above it differ significantly from those in the surface layer. The mean velocity profile is inflected, second moments are strongly inhomogeneous with height, skewnesses are large, and second-moment budgets are far from local equilibrium. Velocity moments scale with single length and time scales throughout the layer rather than depending on height. Large coherent structures control turbulence dynamics. Sweeps rather than ejections dominate eddy fluxes and a typical large eddy consists of a pair of counter-rotating streamwise vortices, the downdraft between the vortex pair generating the sweep. Comparison with the statistics and instability modes of the plane mixing layer shows that the latter rather than the boundary layer is the appropriate model for canopy flow and that the dominant large eddies are the result of an inviscid instability of the inflected mean velocity profile. Aerodynamic drag on the foliage is the cause both of the unstable inflected velocity profile and of a ‘spectral short cut’ mechanism that removes energy from large eddies and diverts it to fine scales, where it is rapidly dissipated, bypassing the inertial eddy-cascade. Total dissipation rates are very large in the canopy as a result of the fine-scale shear layers that develop around the foliage.
Recent Developments in Rayleigh-Bénard Convection
Authors: Bodenschatz Eberhard , Pesch Werner , Ahlers Guenter
Published: July 2002

▪ Abstract  This review summarizes results for Rayleigh-Bénard convection that have been obtained over the past decade or so. It concentrates on convection in compressed gases and gas mixtures with Prandtl numbers near one and smaller. In addition to the classical problem of a horizontal stationary fluid layer heated from below, it also briefly covers convection in such a layer with rotation about a vertical axis, with inclination, and with modulation of the vertical acceleration.
POLYPLOID INCIDENCE AND EVOLUTION
Authors: Otto Sarah P , Whitton Jeannette
Published: July 2002

▪ Abstract  Changes in ploidy occurred early in the diversification of some animal and plant lineages and represent an ongoing phenomenon in others. While the prevalence of polyploid lineages indicates that this phenomenon is a common and successful evolutionary transition, whether polyploidization itself has a significant effect on patterns and rates of diversification remains an open question. Here we review evidence for the creative role of polyploidy in evolution. We present new estimates for the incidence of polyploidy in ferns and flowering plants based on a simple model describing transitions between odd and even base chromosome numbers. These new estimates indicate that ploidy changes may represent from 2 to 4% of speciation events in flowering plants and 7% in ferns. Speciation via polyploidy is likely to be one of the more predominant modes of sympatric speciation in plants, owing to its potentially broad-scale effects on gene regulation and developmental processes, effects that can produce immediate shifts in morphology, breeding system, and ecological tolerances. Theoretical models support the potential for increased adaptability in polyploid lineages. The evidence suggests that polyploidization can produce shifts in genetic systems and phenotypes that have the potential to result in increased evolutionary diversification, yet conclusive evidence that polyploidy has changed rates and patterns of diversification remains elusive.
The Inheritance of Genes in Mitochondria and Chloroplasts: Laws, Mechanisms, and Models
Authors: Birky C. William
Published: July 2002

▪ Abstract  The inheritance of mitochondrial and chloroplast genes differs from that of nuclear genes in showing vegetative segregation, uniparental inheritance, intracellular selection, and reduced recombination. Vegetative segregation and some cases of uniparental inheritance are due to stochastic replication and partitioning of organelle genomes. The rate and pattern of vegetative segregation depend partly on the numbers of genomes and of organelles per cell, but more importantly on the extent to which genomes are shared between organelles, their distribution in the cell, the variance in number of replications per molecule, and the variance in numerical and genotypic partitioning of organelles and genomes. Most of these parameters are unknown for most organisms, but a simple binomial probability model using the effective number of genomes is a useful substitute. Studies using new cytological, molecular, and genetic methods are shedding some light on the processes involved in segregation, and also on the mechanisms of intracellular selection and uniparental inheritance in mammals. But significant issues remain unresolved, notably about the extent of paternal transmission and mitochondrial fusion in mammals.
Regulation of Gene Expression by Cell-to-Cell Communication: Acyl-Homoserine Lactone Quorum Sensing
Authors: Fuqua Clay , Parsek Matthew R. , Greenberg E. Peter
Published: July 2002

▪ Abstract  Quorum sensing is an example of community behavior prevalent among diverse bacterial species. The term “quorum sensing” describes the ability of a microorganism to perceive and respond to microbial population density, usually relying on the production and subsequent response to diffusible signal molecules. A significant number of gram-negative bacteria produce acylated homoserine lactones (acyl-HSLs) as signal molecules that function in quorum sensing. Bacteria that produce acyl-HSLs can respond to the local concentration of the signaling molecules, and high population densities foster the accumulation of inducing levels of acyl-HSLs. Depending upon the bacterial species, the physiological processes regulated by quorum sensing are extremely diverse, ranging from bioluminescence to swarming motility. Acyl-HSL quorum sensing has become a paradigm for intercellular signaling mechanisms. A flurry of research over the past decade has led to significant understanding of many aspects of quorum sensing including the synthesis of acyl-HSLs, the receptors that recognize the acyl-HSL signal and transduce this information to the level of gene expression, and the interaction of these receptors with the transcriptional machinery. Recent studies have begun to integrate acyl-HSL quorum sensing into global regulatory networks and establish its role in developing and maintaining the structure of bacterial communities.
A NEWAPPROACH TODECODINGLIFE: Systems Biology
Authors: Ideker Trey , Galitski Timothy , Hood Leroy
Published: July 2002

▪ Abstract  Systems biology studies biological systems by systematically perturbing them (biologically, genetically, or chemically); monitoring the gene, protein, and informational pathway responses; integrating these data; and ultimately, formulating mathematical models that describe the structure of the system and its response to individual perturbations. The emergence of systems biology is described, as are several examples of specific systems approaches.