bluuebunny/crossref_metadata_2025 huggingface dataset:
MOLYBDENUM-COFACTOR–CONTAINING ENZYMES: Structure and Mechanism
Authors: Kisker Caroline , Schindelin Hermann , Rees Douglas C.
Published: July 2002

Molybdenum-containing enzymes catalyze basic metabolic reactions in the nitrogen, sulfur, and carbon cycles. With the exception of the nitrogenase cofactor, molybdenum is incorporated into proteins as the molybdenum cofactor that contains a mononuclear molybdenum atom coordinated to the sulfur atoms of a pterin derivative named molybdopterin. Certain microorganisms can also utilize tungsten in a similar fashion. Molybdenum-cofactor–containing enzymes catalyze the transfer of an oxygen atom, ultimately derived from or incorporated into water, to or from a substrate in a two-electron redox reaction. On the basis of sequence alignments and spectroscopic properties, four families of molybdenum-cofactor–containing enzymes have been identified. The available crystallographic structures for members of these families are discussed within the framework of the active site structure and catalytic mechanisms of molybdenum-cofactor–containing enzymes. Although the function of the molybdopterin ligand has not yet been conclusively established, interactions of this ligand with the coordinated metal are sensitive to the oxidation state, indicating that the molybdopterin may be directly involved in the enzymatic mechanism.
DYNAMIC O-LINKED GLYCOSYLATION OF NUCLEAR AND CYTOSKELETAL PROTEINS
Authors: Hart Gerald W.
Published: July 2002

Modification of Ser and Thr residues by attachment of O-linked N-acetylglucosamine [Ser(Thr)-O-GlcNAcylation] to eukaryotic nuclear and cytosolic proteins is as dynamic and possibly as abundant as Ser(Thr) phosphorylation. Known O-GlcNAcylated proteins include cytoskeletal proteins and their regulatory proteins; viral proteins; nuclear-pore, heat-shock, tumor-suppressor, and nuclear-oncogene proteins; RNA polymerase II catalytic subunit; and a multitude of transcription factors. Although functionally diverse, all of these proteins are also phosphoproteins. Most O-GlcNAcylated proteins form highly regulated multimeric associations that are dependent upon their posttranslational modifications. Evidence is mounting that O-GlcNAcylation is an important regulatory modification that may have a reciprocal relationship with O-phosphorylation and may modulate many biological processes in eukaryotes.
THE CAVEOLAE MEMBRANE SYSTEM
Authors: Anderson Richard G. W.
Published: July 2002

The cell biology of caveolae is a rapidly growing area of biomedical research. Caveolae are known primarily for their ability to transport molecules across endothelial cells, but modern cellular techniques have dramatically extended our view of caveolae. They form a unique endocytic and exocytic compartment at the surface of most cells and are capable of importing molecules and delivering them to specific locations within the cell, exporting molecules to extracellular space, and compartmentalizing a variety of signaling activities. They are not simply an endocytic device with a peculiar membrane shape but constitute an entire membrane system with multiple functions essential for the cell. Specific diseases attack this system: Pathogens have been identified that use it as a means of gaining entrance to the cell. Trying to understand the full range of functions of caveolae challenges our basic instincts about the cell.
In Vitro Selection of Functional Nucleic Acids
Authors: Wilson David S. , Szostak Jack W.
Published: July 2002

▪ Abstract  In vitro selection allows rare functional RNA or DNA molecules to be isolated from pools of over 1015different sequences. This approach has been used to identify RNA and DNA ligands for numerous small molecules, and recent three-dimensional structure solutions have revealed the basis for ligand recognition in several cases. By selecting high-affinity and -specificity nucleic acid ligands for proteins, promising new therapeutic and diagnostic reagents have been identified. Selection experiments have also been carried out to identify ribozymes that catalyze a variety of chemical transformations, including RNA cleavage, ligation, and synthesis, as well as alkylation and acyl-transfer reactions and N-glycosidic and peptide bond formation. The existence of such RNA enzymes supports the notion that ribozymes could have directed a primitive metabolism before the evolution of protein synthesis. New in vitro protein selection techniques should allow for a direct comparison of the frequency of ligand binding and catalytic structures in pools of random sequence polynucleotides versus polypeptides.
eIF4 Initiation Factors: Effectors of mRNA Recruitment to Ribosomes and Regulators of Translation
Authors: Gingras Anne-Claude , Raught Brian , Sonenberg Nahum
Published: July 2002

▪ Abstract  Eukaryotic translation initiation factor 4F (eIF4F) is a protein complex that mediates recruitment of ribosomes to mRNA. This event is the rate-limiting step for translation under most circumstances and a primary target for translational control. Functions of the constituent proteins of eIF4F include recognition of the mRNA 5′ cap structure (eIF4E), delivery of an RNA helicase to the 5′ region (eIF4A), bridging of the mRNA and the ribosome (eIF4G), and circularization of the mRNA via interaction with poly(A)-binding protein (eIF4G). eIF4 activity is regulated by transcription, phosphorylation, inhibitory proteins, and proteolytic cleavage. Extracellular stimuli evoke changes in phosphorylation that influence eIF4F activity, especially through the phosphoinositide 3-kinase (PI3K) and Ras signaling pathways. Viral infection and cellular stresses also affect eIF4F function. The recent determination of the structure of eIF4E at atomic resolution has provided insight about how translation is initiated and regulated. Evidence suggests that eIF4F is also implicated in malignancy and apoptosis.
Aminoacyl-tRNA Synthesis
Authors: Ibba Michael , Söll Dieter
Published: July 2002

▪ Abstract  Aminoacyl-tRNAs are substrates for translation and are pivotal in determining how the genetic code is interpreted as amino acids. The function of aminoacyl-tRNA synthesis is to precisely match amino acids with tRNAs containing the corresponding anticodon. This is primarily achieved by the direct attachment of an amino acid to the corresponding tRNA by an aminoacyl-tRNA synthetase, although intrinsic proofreading and extrinsic editing are also essential in several cases. Recent studies of aminoacyl-tRNA synthesis, mainly prompted by the advent of whole genome sequencing and the availability of a vast body of structural data, have led to an expanded and more detailed picture of how aminoacyl-tRNAs are synthesized. This article reviews current knowledge of the biochemical, structural, and evolutionary facets of aminoacyl-tRNA synthesis.
DNA Topoisomerases: Structure, Function, and Mechanism
Authors: Champoux James J.
Published: July 2002

▪ Abstract  DNA topoisomerases solve the topological problems associated with DNA replication, transcription, recombination, and chromatin remodeling by introducing temporary single- or double-strand breaks in the DNA. In addition, these enzymes fine-tune the steady-state level of DNA supercoiling both to facilitate protein interactions with the DNA and to prevent excessive supercoiling that is deleterious. In recent years, the crystal structures of a number of topoisomerase fragments, representing nearly all the known classes of enzymes, have been solved. These structures provide remarkable insights into the mechanisms of these enzymes and complement previous conclusions based on biochemical analyses. Surprisingly, despite little or no sequence homology, both type IA and type IIA topoisomerases from prokaryotes and the type IIA enzymes from eukaryotes share structural folds that appear to reflect functional motifs within critical regions of the enzymes. The type IB enzymes are structurally distinct from all other known topoisomerases but are similar to a class of enzymes referred to as tyrosine recombinases. The structural themes common to all topoisomerases include hinged clamps that open and close to bind DNA, the presence of DNA binding cavities for temporary storage of DNA segments, and the coupling of protein conformational changes to DNA rotation or DNA movement. For the type II topoisomerases, the binding and hydrolysis of ATP further modulate conformational changes in the enzymes to effect changes in DNA topology.
Physicochemical Foundations and Structural Design of Hydrogels in Medicine and Biology
Authors: Peppas N. A. , Huang Y. , Torres-Lugo M. , Ward J. H. , Zhang J.
Published: July 2002

▪ Abstract  Hydrogels are cross-linked hydrophilic polymers that can imbibe water or biological fluids. Their biomedical and pharmaceutical applications include a very wide range of systems and processes that utilize several molecular design characteristics. This review discusses the molecular structure, dynamic behavior, and structural modifications of hydrogels as well as the various applications of these biohydrogels.

Recent advances in the preparation of three-dimensional structures with exact chain conformations, as well as tethering of functional groups, allow for the preparation of promising new hydrogels. Meanwhile, intelligent biohydrogels with pH- or temperature-sensitivity continue to be important materials in medical applications.
ASSEMBLY AND ENLARGEMENT OF THE PRIMARY CELL WALL IN PLANTS
Authors: Cosgrove Daniel J.
Published: July 2002

▪ Abstract  Growing plant cells are shaped by an extensible wall that is a complex amalgam of cellulose microfibrils bonded noncovalently to a matrix of hemicelluloses, pectins, and structural proteins. Cellulose is synthesized by complexes in the plasma membrane and is extruded as a self-assembling microfibril, whereas the matrix polymers are secreted by the Golgi apparatus and become integrated into the wall network by poorly understood mechanisms. The growing wall is under high tensile stress from cell turgor and is able to enlarge by a combination of stress relaxation and polymer creep. A pH-dependent mechanism of wall loosening, known as acid growth, is characteristic of growing walls and is mediated by a group of unusual wall proteins called expansins. Expansins appear to disrupt the noncovalent bonding of matrix hemicelluloses to the microfibril, thereby allowing the wall to yield to the mechanical forces generated by cell turgor. Other wall enzymes, such as (1 → 4) β-glucanases and pectinases, may make the wall more responsive to expansin-mediated wall creep, whereas pectin methylesterases and peroxidases may alter the wall so as to make it resistant to expansin-mediated creep.
NEURAL CELL ADHESION MOLECULES OF THE IMMUNOGLOBULIN SUPERFAMILY: Role in Axon Growth and Guidance
Authors: Walsh Frank S. , Doherty Patrick
Published: July 2002

▪ 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.
[PSI+]: An Epigenetic Modulator of Translation Termination Efficiency
Authors: Serio Tricia R. , Lindquist Susan L.
Published: July 2002

▪ 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.
Patterning Mechanisms Controlling Vertebrate Limb Development
Authors: Capdevila Javier , Belmonte Juan Carlos Izpisúa
Published: July 2002

▪ Abstract  Vertebrate limb buds are embryonic structures for which much molecular and cellular data are known regarding the mechanisms that control pattern formation during development. Specialized regions of the developing limb bud, such as the zone of polarizing activity (ZPA), the apical ectodermal ridge (AER), and the non-ridge ectoderm, direct and coordinate the development of the limb bud along the anterior-posterior (AP), dorsal-ventral (DV), and proximal-distal (PD) axes, giving rise to a stereotyped pattern of elements well conserved among tetrapods. In recent years, specific gene functions have been shown to mediate the organizing and patterning activities of the ZPA, the AER, and the non-ridge ectoderm. The analysis of these gene functions has revealed the existence of complex interactions between signaling pathways operated by secreted factors of the HH, TGF-β/BMP, WNT, and FGF superfamilies, which interact with many other genetic networks to control limb positioning, outgrowth, and patterning. The study of limb development has helped to establish paradigms for the analysis of pattern formation in many other embryonic structures and organs.
TURKIC-TYPE OROGENY AND ITS ROLE IN THE MAKING OF THE CONTINENTAL CRUST
Authors: Sengör A. M. Celâl , Natal'in Boris A.
Published: July 2002

▪ Abstract  Turkic-type orogeny is a class of collisional mountain building, in which the precollision history of one, or both, of the colliding continents involves the growth of very large, subcontinent-size subduction-accretion complexes, into which magmatic arc axes commonly migrate and thus enlarge the continent to which they are attached. A review of the evolution of two Phanerozoic (Altaids, Nipponides), one Neoproterozoic (East African), and one Archean (Yilgarn) Turkic-type orogens shows that this type of orogeny may have been the principal builder of the continental crust through recorded Earth history. The total juvenile material added to Turkic-type orogens at any one time in the Phanerozoic seems close to 1 km3/year, which about equals the amount of material annually fed into the mantle at subduction zones. As some 0.02 to 0.03% of that material is generally agreed to return to the crust by arc magmatism, these figures provide a minimum net growth rate for the continental crust during the Phanerozoic.
ECOLOGICAL ASPECTS OF THE CRETACEOUS FLOWERING PLANT RADIATION
Authors: Wing Scott L. , Boucher Lisa D.
Published: July 2002

▪ Abstract  The first flowering plant fossils occur as rare, undiverse pollen grains in the Early Cretaceous (Valanginian-Hauterivian). Angiosperms diversified slowly during the Barremian-Aptian but rapidly during the Albian-Cenomanian. By the end of the Cretaceous, at least half of the living angiosperm orders were present, and angiosperms were greater than 70% of terrestrial plant species globally. The rapid diversification of the group, and its dominance in modern vegetation, has led to the idea that the Cretaceous radiation of angiosperms also represents their rise to vegetational dominance.

Paleoecological data cast a different light on the Cretaceous radiation of angiosperms. Analyses of sedimentary environments indicate that angiosperms not only originated in unstable habitats but remained centered there through most of the Cretaceous. Morphology of leaves, seeds, and wood is consistent with the status of most Cretaceous angiosperms as herbs to small trees with early successional strategy. The diversification of flowering plants in the Cretaceous represents the evolution of a highly speciose clade of weeds but not necessarily a major change in global vegetation.
FISSION TRACK ANALYSIS AND ITS APPLICATIONS TO GEOLOGICAL PROBLEMS
Authors: Gallagher Kerry , Brown Roderick , Johnson Christopher
Published: July 2002

▪ Abstract  Fission track analysis as a geological dating tool was first proposed in the early 1960s. The past 10 years has seen a major expansion in application to more general geological problems. This reflects advances in understanding the temperature dependence of fission track annealing and of the information contained in fission track length distributions. Fission track analysis provides detailed information on the low-temperature thermal histories of rocks, below ∼120°C for tracks in apatite and below ∼350°C for zircon. Fission track analysis has been applied to a variety of geological problems, including sedimentary provenance, thermal history modeling of sedimentary basins, structural evolution of orogenic belts, and long-term continental denudation.
Heterogeneity of the Lowermost Mantle
Authors: Garnero Edward J.
Published: July 2002

Strong heterogeneity at a variety of scale lengths has been imaged in the lowermost mantle using different forward and inverse methods. Coherent patterns in differential travel times of waves that sample the base of the mantle—such as diffracted shear waves (Sdiff) and compressional waves (Pdiff)—are readily apparent, and are compared with results from tomographic studies. Travel time and waveform modeling studies have demonstrated the presence of intense lateral variations in a variety of mapped features, such as a regionally detected high velocity D″ layer, ultra-low velocity zones, D″ anisotropy, strong scattering and heterogeneity. Such short-wavelength variations currently preclude confident mapping of D″ structure at smaller scales. Issues of seismic resolution and uncertainties are emphasized here, as well as the limitations of one-dimensional modeling/averaging in highly heterogeneous environments.
Response of Late Carboniferous and Early Permian Plant Communities to Climate Change
Authors: DiMichele William A , Pfefferkorn Hermann W , Gastaldo Robert A
Published: July 2002

▪ Abstract  Late Carboniferous and Early Permian strata record the transition from a cold interval in Earth history, characterized by the repeated periods of glaciation and deglaciation of the southern pole, to a warm-climate interval. Consequently, this time period is the best available analogue to the Recent in which to study patterns of vegetational response, both to glacial-interglacial oscillation and to the appearance of warm climate. Carboniferous wetland ecosystems were dominated by spore-producing plants and early gymnospermous seed plants. Global climate changes, largely drying, forced vegetational changes, resulting in a change to a seed plant–dominated world, beginning first at high latitudes during the Carboniferous, reaching the tropics near the Permo-Carboniferous boundary. For most of this time plant assemblages were very conservative in their composition. Change in the dominant vegetation was generally a rapid process, which suggests that environmental thresholds were crossed, and involved little mixing of elements from the wet and dry floras.
Male and Female Alternative Reproductive Behaviors in Fishes: A New Approach Using Intersexual Dynamics
Authors: Henson S. A. , Warner R. R.
Published: July 2002

The study of alternative reproductive behaviors in fishes has contributed to our general understanding of reproductive strategies and mating systems. Despite extensive research on the mechanisms and patterns of alternatives, two important factors have not been addressed, and both may strongly influence the evolution of alternative reproductive behaviors. First, alternative female reproductive behaviors exist and should be considered in theoretical and empirical work. Second, interactions between the sexes will influence the evolution of alternative reproductive behaviors. In this review, we explore these two points and suggest the development of a more comprehensive theory of alternatives that will increase our ability to make predictions regarding the existence and expression of alternative reproductive behaviors in both sexes.
CARBON AND CARBONATE METABOLISM IN COASTAL AQUATIC ECOSYSTEMS
Authors: Gattuso J.-P. , Frankignoulle M. , Wollast R.
Published: July 2002

▪ Abstract  The coastal zone is where land, ocean, and atmosphere interact. It exhibits a wide diversity of geomorphological types and ecosystems, each one displaying great variability in terms of physical and biogeochemical forcings. Despite its relatively modest surface area, the coastal zone plays a considerable role in the biogeochemical cycles because it receives massive inputs of terrestrial organic matter and nutrients, is among the most geochemically and biologically active areas of the biosphere, and exchanges large amounts of matter and energy with the open ocean. Coastal ecosystems have therefore attracted much attention recently and are the focus of several current national and international research programs (e.g. LOICZ, ELOISE). The primary production, respiration, calcification, carbon burial and exchange with adjacent systems, including the atmosphere, are reviewed for the major coastal ecosystems (estuaries, macrophyte communities, mangroves, coral reefs, and the remaining continental shelf). All ecosystems examined, except estuaries, are net autotrophic. The contribution of the coastal zone to the global carbon cycle both during pristine times and at present is difficult to assess due to the limited metabolic data available as well as because of major uncertainties concerning the magnitude of processes such as respiration, exchanges at the open ocean boundary, and air-sea fluxes of biogases.
BACTERIAL GROWTH EFFICIENCY IN NATURAL AQUATIC SYSTEMS
Authors: del Giorgio Paul A. , Cole Jonathan J.
Published: July 2002

▪ Abstract  Heterotrophic bacteria perform two major functions in the transformation of organic matter: They produce new bacterial biomass (bacterial secondary production [BP]), and they respire organic C to inorganic C (bacterial respiration [BR]). For planktonic bacteria, a great deal has been learned about BP and its regulation during the past several decades but far less has been learned about BR. Our lack of knowledge about BR limits our ability to understand the role of bacteria in the carbon cycle of aquatic ecosystems. Bacterial growth efficiency (BGE) is the amount of new bacterial biomass produced per unit of organic C substrate assimilated and is a way to relate BP and BR: BGE = (BP)/(BP + BR). Estimates of BGE for natural planktonic bacteria range from <0.05 to as high as 0.6, but little is known about what might regulate this enormous range. In this paper we review the physiological and ecological bases of the regulation of BGE. Further, we assemble the literature of the past 30 years for which both BP and BR were measured in natural planktonic ecosystems and explore the relationship between BGE and BP. Although the relationship is variable, BGE varies systematically with BP and the trophic richness of the ecosystem. In the most dilute, oligotrophic systems, BGE is as low as 0.01; in the most eutrophic systems, it plateaus near 0.5. Planktonic bacteria appear to maximize carbon utilization rather than BGE. A consequence of this strategy is that maintenance energy costs (and therefore maintenance respiration) seems to be highest in oligotrophic systems.
The Ecology and Physiology of Viviparous and Recalcitrant Seeds
Authors: Farnsworth Elizabeth
Published: July 2002

▪ Abstract  Understanding seed physiology is central to reconstructing how angiosperms have evolved, to characterizing dormancy and germination regimes shared by suites of species, and to devising sound strategies for seed bank conservation, agriculture, and forestry. While species with dormant seeds have received the lion's share of attention, hundreds of plant species exhibit no seed dormancy and germinate either viviparously on the parent plant or shortly after release. Embryos of these recalcitrant and viviparous species cannot tolerate the maturation drying that is usually prerequisite to dormancy; such desiccation intolerance creates challenges for storing and preserving such embryos. I review the physiology, morphology, and ecology of these desiccation-intolerant, nondormant lineages. Differences in the production and function of plant hormones are implicated in the occurrence of recalcitrance and vivipary in plant families. Plant hormones are key regulators of seed physiology and simultaneously coordinate responses of the seedling and mature plant to their environment. Desiccation-intolerant embryos occur most commonly among species of wet or flooded environments and have evolved multiple times in disparate lineages. Natural selection in wetland environments simply may not eliminate these seed types or may select for changes in hormone physiology that simultaneously affect both maternal and embryonic tissues. Integrative data from ecological, genetic, and physiological studies are needed to elucidate evolutionary origins and maintenance of reproductive strategies in organisms.
The Ecology of Tropical Asian Rivers and Streams in Relation to Biodiversity Conservation
Authors: Dudgeon David
Published: July 2002

▪ Abstract  Tropical Asian rivers support a rich but incompletely known biota, including a host of fishes, a diverse array of benthic invertebrates, and an assemblage of mammals adapted to riverine wetlands. River ecology is dominated by flow seasonality imposed by monsoonal rains with profound consequences for fishes and zoobenthos. Information on life histories, feeding, and the trophic base of production of these animals is summarized. Widespread use of allochthonous foods by fishes and zoobenthos is apparent. Migration by fishes is often associated with breeding and results in seasonal occupation of different habitats. Riverine biodiversity is threatened by habitat degradation (pollution, deforestation of drainage basins), dams and flow regulation, as well as over-harvesting. Conservation efforts in tropical Asia are constrained by a variety of factors, including lack of ecological information, but the extent of public awareness and political commitment to environmental protection are likely determinants of the future of riverine biodiversity.
Sex Chromosome Meiotic Drive
Authors: Jaenike John
Published: July 2002

▪ Abstract  Sex chromosome drive refers to the unequal transmission of X and Y chromosomes from individuals of the heterogametic sex, resulting in biased sex ratios among progeny and within populations. The presence of driving sex chromosomes can reduce mean fitness within a population, bring about intragenomic conflict between the X chromosome, the Y, and the autosomes, and alter the intensity or mode of sexual selection within species. Sex chromosome drive, or its genetic equivalent, is known in plants, mammals, and flies. Many species harboring driving X chromosomes have evolved Y-linked and autosomal suppressors of drive. If a drive polymorphism is not stable, then driving chromosomes may spread to fixation and cause the extinction of a species. Certain characteristics of species, such as population density and female mating rate, may affect the probability of fixation of driving chromosomes. Thus, sex chromosome drive could be an agent of species-level selection.
The Physiology of Life History Trade-Offs in Animals
Authors: Zera Anthony J. , Harshman Lawrence G.
Published: July 2002

▪ Abstract  The functional causes of life history trade-offs have been a topic of interest to evolutionary biologists for over six decades. Our review of life history trade-offs discusses conceptual issues associated with physiological aspects of trade-offs, and it describes recent advances on this topic. We focus on studies of four model systems: wing polymorphic insects, Drosophila, lizards, and birds. The most significant recent advances have been: (a) incorporation of genetics in physiological studies of trade-offs, (b) integration of investigations of nutrient input with nutrient allocation, (c) development of more sophisticated models of resource acquisition and allocation, (d) a shift to more integrated, multidisciplinary studies of intraspecific trade-offs, and (e) the first detailed investigations of the endocrine regulation of life history trade-offs.
DENSITY-DEPENDENT PHYSIOLOGICAL PHASE IN INSECTS
Authors: Applebaum S. W. , Heifetz Y.
Published: July 2002

▪ Abstract  Insects respond to crowding in a variety of ways that are usually exemplified by rapid changes in behavior and culminate in enduring long-term morphological and/or chromatic responses. A common feature of both short-term and long-term effects is that they are graded, dependent not only on density but also on the duration and on phase history of the maternal generation. Because of their exoskeletons, which are persistent for the duration of each instar and endure throughout adult life, overt changes in morphology or coloration are restricted to the molting period and shortly afterward, when cuticular hardening and pigmentation are expressed. Changes in internal organs or metabolism elicited by population density, being independent of integumental constraints, are not restricted to the molting period, but the temporal difference between internal and external responses is not of fundamental significance. Intraspecific responses to the presence of sibling insects are of apparent ecological significance and often involve directional movement and/or migration. They are mediated via the sensory system, involve signal transduction, and elicit downstream biochemical and physiological changes.
MANAGEMENT OF PLANT VIRAL DISEASES THROUGH CHEMICAL CONTROL OF INSECT VECTORS
Authors: Perring Thomas M. , Gruenhagen Ned M. , Farrar Charles A.
Published: July 2002

▪ Abstract  In this article we consider the role of epidemiological factors and transmission processes of insect-vectored viruses on the effectiveness of insecticides in a disease management program. We also discuss the use of insecticides within the broader framework of the chemical environment surrounding vectors, and how chemical-induced alterations in the behavior of vectors can influence transmission. Our analysis confirms the belief of Heathcote, who stated in 1973, that “no one method of control is likely to keep crops entirely free from virus infection and as many preventative measures should be taken as are economically justified.”
Evolutionary Ecology of Progeny Size in Arthropods
Authors: Fox Charles W. , Czesak Mary Ellen
Published: July 2002

▪ Abstract  Most models of optimal progeny size assume that there is a trade-off between progeny size and number, and that progeny fitness increases with increasing investment per young. We find that both assumptions are supported by empirical studies but that the trade-off is less apparent when organisms are iteroparous, use adult-acquired resources for reproduction, or provide parental care. We then review patterns of variation in progeny size among species, among populations within species, among individuals within populations, and among progeny produced by a single female. We argue that much of the variation in progeny size among species, and among populations within species, is likely due to variation in natural selection. However, few studies have manipulated progeny environments and demonstrated that the relationship between progeny size and fitness actually differs among environments, and fewer still have demonstrated why selection favors different sized progeny in different environments. We argue that much of the variation in progeny size among females within populations, and among progeny produced by a single female, is probably nonadaptive. However, some species of arthropods exhibit plasticity in progeny size in response to several environmental factors, and much of this plasticity is likely adaptive. We conclude that advances in theory have substantially outpaced empirical data. We hope that this review will stimulate researchers to examine the specific factors that result in variation in selection on progeny size within and among populations, and how this variation in selection influences the evolution of the patterns we observe.
Chemical Ecology and Social Parasitism in Ants
Authors: Lenoir A. , D'Ettorre P. , Errard C. , Hefetz A.
Published: July 2002

▪ Abstract  The chemical strategies by which parasites manage to break into the social fortresses of ants offer a fascinating theme in chemical ecology. Semiochemicals used for interindividual nestmate recognition are also involved in the mechanisms of tolerance and association between the species, and social parasites exploit these mechanisms. The obligate parasites are odorless (“chemical insignificance”) at the time of usurpation, like all other callow ants, and this “invisibility” enables their entry into the host colony. By chemical mimicry (sensu lato), they later integrate the gestalt odor of this colony (“chemical integration”). We hypothesize that host and parasite are likely to be related chemically, thereby facilitating the necessary mimicry to permit bypassing the colony odor barrier. We also review the plethora of chemical weapons used by social parasites (propaganda, appeasement, and/or repellent substances), particularly during the usurpation period, when the young mated parasite queen synthesizes these chemicals before usurpation and ceases such biosynthesis afterwards. We discuss evolutionary trends that may have led to social parasitism, focusing on the question of whether slave-making ants and their host species are expected to engage in a coevolutionary arms race.
Short, Long, and Beyond: Molecular and Embryological Approaches to Insect Segmentation
Authors: Davis Gregory K. , Patel Nipam H.
Published: July 2002

▪ Abstract  Over the past dozen years, studies comparing the expression of orthologues of the Drosophila segmentation genes among various insects have served to broaden our view of the ways in which insects make segments. The molecular data suggest that, although the overall genetic mechanisms of segmentation during embryogenesis have been conserved, the details of this process vary both within and between various insect orders. Here we summarize comparative gene expression data relevant to segmentation with an emphasis on understanding the extent of molecular patterning prior to gastrulation. These results are discussed in embryological context with an eye toward understanding the evolution of segmentation within insects.
AIRCRAFT LAMINAR FLOW CONTROL
Authors: Joslin Ronald D.
Published: July 2002

▪ Abstract  Aircraft laminar flow control (LFC) from the 1930s through the 1990s is reviewed and the current status of the technology is assessed. Examples are provided to demonstrate the benefits of LFC for subsonic and supersonic aircraft. Early studies related to the laminar boundary-layer flow physics, manufacturing tolerances for laminar flow, and insect-contamination avoidance are discussed. LFC concept studies in wind-tunnel and flight experiments are the major focus of the paper. LFC design tools are briefly outlined for completeness.
SYNTHETIC JETS
Authors: Glezer Ari , Amitay Michael
Published: July 2002

▪ Abstract  The evolution of a synthetic (zero-net mass flux) jet and the flow mechanisms of its interaction with a cross flow are reviewed. An isolated synthetic jet is produced by the interactions of a train of vortices that are typically formed by alternating momentary ejection and suction of fluid across an orifice such that the net mass flux is zero. A unique feature of these jets is that they are formed entirely from the working fluid of the flow system in which they are deployed and, thus, can transfer linear momentum to the flow system without net mass injection across the flow boundary. Synthetic jets can be produced over a broad range of length and timescale, and their unique attributes make them attractive fluidic actuators for a number of flow control applications. The interaction of synthetic jets with an external cross flow over the surface in which they are mounted can displace the local streamlines and induce an apparent or virtual change in the shape of the surface, thereby effecting flow changes on length scales that are one to two orders of magnitude larger than the characteristic scale of the jets. This control approach emphasizes an actuation frequency that is high enough so that the interaction domain between the actuator and the cross flow is virtually invariant on the global timescale of the flow, and therefore, global effects such as changes in aerodynamic forces are effectively decoupled from the operating frequency of the actuators.
PARALOGOUS HOX GENES: Function and Regulation
Authors: Maconochie Mark , Nonchev Stefan , Morrison Alastair , Krumlauf Robb
Published: July 2002

▪ Abstract  The Hox homeobox gene family plays a pivotal role in regulating patterning and axial morphogenesis in vertebrates. Molecular characterization of the four Hox clusters has shown that they are evolutionarily related with respect to sequence, organization, and expression, suggesting they arose by duplication and divergence. Transgenic analysis has clearly demonstrated the functional roles of individual genes in a broad range of embryonic tissues, and in compound mutants has addressed the issues of cooperativity and redundancy. There is an emerging picture of the cis-regulatory elements underlying Hox expression, and for the 3′ members of the clusters there is a considerable degree of conservation between paralogous genes with respect to their functional roles and regulatory control.
GENETIC AND MOLECULAR ANALYSIS OF CIRCADIAN RHYTHMS
Authors: Dunlap Jay C.
Published: July 2002

▪ Abstract  The first part of this review summarizes the two best understood aspects of the two best understood circadian systems, the feedback oscillators of Neurospora and Drosophila, concentrating on what we know about the frequency (frq), period (per), and timeless (tim) genes. In the second part, the general circadian genetic and molecular literature is surveyed, with an eye to describing what is known from a variety of systems about input to the oscillator (entrainment), and how the oscillator might work and be temperature compensated, in emerging systems including Synechococcus, Gonyaulax, Arabidopsis, hamsters, and mice. Finally, the conservation of the molecular components of clocks is analyzed: both frq and per are widely conserved in their respective phylogenetic classes. Pharmacological data suggest that most other organisms use a day-phased oscillator of the type seen in Neurospora rather than a night-phased oscillator such as in Drosophila.
THE LEPTOTENE-ZYGOTENE TRANSITION OF MEIOSIS
Authors: Zickler D. , Kleckner N.
Published: July 2002

▪ Abstract  The leptotene/zygotene transition of meiosis, as defined by classical cytological studies, is the period when homologous chromosomes, already being discernible individualized entities, begin to be close together or touching over portions of their lengths. This period also includes the bouquet stage: Chromosome ends, which have already become integral components of the inner nuclear membrane, move into a polarized configuration, along with other nuclear envelope components. Chromosome movements, active or passive, also occur. The detailed nature of interhomologue interactions during this period, with special emphasis on the involvement of chromosome ends, and the overall role for meiosis and recombination of chromosome movement and, especially, the bouquet stage are discussed.
Meiotic Chromosomes: Integrating Structure and Function
Authors: Zickler D. , Kleckner N.
Published: July 2002

▪ Abstract  Meiotic chromosomes have been studied for many years, in part because of the fundamental life processes they represent, but also because meiosis involves the formation of homolog pairs, a feature which greatly facilitates the study of chromosome behavior. The complex events involved in homolog juxtaposition necessitate prolongation of prophase, thus permitting resolution of events that are temporally compressed in the mitotic cycle. Furthermore, once homologs are paired, the chromosomes are connected by a specific structure: the synaptonemal complex. Finally, interaction of homologs includes recombination at the DNA level, which is intimately linked to structural features of the chromosomes. In consequence, recombination-related events report on diverse aspects of chromosome morphogenesis, notably relationships between sisters, development of axial structure, and variations in chromatin status. The current article reviews recent information on these topics in an historical context. This juxtaposition has suggested new relationships between structure and function. Additional issues were addressed in a previous chapter ( 551 ).
DNA MISMATCH REPAIR AND GENETIC INSTABILITY
Authors: Harfe Brian D , Jinks-Robertson Sue
Published: July 2002

▪ Abstract  Mismatch repair (MMR) systems play a central role in promoting genetic stability by repairing DNA replication errors, inhibiting recombination between non-identical DNA sequences and participating in responses to DNA damage. The discovery of a link between human cancer and MMR defects has led to an explosion of research on eukaryotic MMR. The key proteins in MMR are highly conserved from bacteria to mammals, and this conservation has been critical for defining the components of eukaryotic MMR systems. In eukaryotes, there are multiple homologs of the key bacterial MutS and MutL MMR proteins, and these homologs form heterodimers that have discrete roles in MMR-related processes. This review describes the genetic and biochemical approaches used to study MMR, and summarizes the diverse roles that MMR proteins play in maintaining genetic stability.
Recombinational DNA Repair of Damaged Replication Forks inEscherichia coli: Questions
Authors: Cox Michael M.
Published: July 2002

▪ Abstract  It has recently become clear that the recombinational repair of stalled replication forks is the primary function of homologous recombination systems in bacteria. In spite of the rapid progress in many related lines of inquiry that have converged to support this view, much remains to be done. This review focuses on several key gaps in understanding. Insufficient data currently exists on: (a) the levels and types of DNA damage present as a function of growth conditions, (b) which types of damage and other barriers actually halt replication, (c) the structures of the stalled/collapsed replication forks, (d) the number of recombinational repair paths available and their mechanistic details, (e) the enzymology of some of the key reactions required for repair, (f) the role of certain recombination proteins that have not yet been studied, and (g) the molecular origin of certain in vivo observations associated with recombinational DNA repair during the SOS response. The current status of each of these topics is reviewed.
Early T Lymphocyte Progenitors
Authors: Shortman Ken , Wu Li
Published: July 2002

The earliest steps along the pathway leading to T cells in mice and humans are reviewed. These are the steps between the multipotent hemopoietic stem cell (HSC) and the fully committed precursors undergoing T cell receptor (TCR) gene rearrangement. At this level significant differences between adult and fetal lymphopoiesis have been demonstrated. The extent of lymphoid commitment of precursors within bone marrow is still unresolved, although HSCs clearly undergo developmental changes before migration to the thymus. Both multipotent and T-restricted precursors have now been isolated from fetal blood, suggesting both may seed the thymus. Within the thymus, several minute but discrete populations of T precursors precede the stage of TCR gene rearrangement. They include precursors that are not exclusively T-lineage committed, although they are distinct from HSCs. These precursors have a potential to form NK cells, B cells, dendritic cells, and sometimes other myeloid cells. Some factors that control early lymphoid development are discussed, including IL-7 and the Ikaros transcription factors. These will eventually help to clarify the process of T-lineage commitment.
gp130 AND THE INTERLEUKIN-6 FAMILY OF CYTOKINES
Authors: Taga Tetsuya , Kishimoto Tadamitsu
Published: July 2002

▪ Abstract  Receptors for most interleukins and cytokines that regulate immune and hematopoietic systems belong to the class I cytokine receptor family. These molecules form multichain receptor complexes in order to exhibit high-affinity binding to, and mediate biological functions of, their respective cytokines. In most cases, these functional receptor complexes share common signal transducing receptor components that are also in the class I cytokine receptor family, i.e. gp130, common β, and common γ molecules. Interleukin-6 and related cytokines, interleukin-11, leukemia inhibitory factor, oncostatin M, ciliary neurotrophic factor, and cardiotrophin-1 are all pleiotropic and exhibit overlapping biological functions. Functional receptor complexes for this interleukin-6 family of cytokines share gp130 as a component critical for signal transduction. Unlike cytokines sharing common β and common γ chains that mainly function in hematopoietic and lymphoid cell systems, the interleukin-6 family of cytokines function extensively outside these systems as well, e.g. from the cardiovascular to the nervous system, owing to ubiquitously expressed gp130. Stimulation of cells with the interleukin-6 family of cytokines triggers homo- or hetero-dimerization of gp130. Although gp130 and its dimer partners possess no intrinsic tyrosine kinase domain, the dimerization of gp130 leads to activation of associated cytoplasmic tyrosine kinases and subsequent modification of transcription factors. This paper reviews recent progress in the study of the interleukin-6 family of cytokines and gp130.
The Role of Chemokine Receptors in Primary, Effector, and Memory Immune Responses
Authors: Sallusto Federica , Mackay Charles R. , Lanzavecchia Antonio
Published: July 2002

The immune system is composed of single cells, and its function is entirely dependent on the capacity of these cells to traffic, localize within tissues, and interact with each other in a precisely coordinated fashion. There is growing evidence that the large families of chemokines and chemokine receptors provide a flexible code for regulating cell traffic and positioning in both homeostatic and inflammatory conditions. The regulation of chemokine receptor expression during development and following cell activation explains the complex migratory pathways taken by dendritic cells, T and B lymphocytes, providing new insights into the mechanisms that control priming, effector function, and memory responses.