bluuebunny/crossref_metadata_2025_split huggingface dataset:
TKO'ed: Lox, stock and barrel
Authors: Chambers Cynthia A. 
Published: February 2005

AbstractThe generation of panels of mutant mice by homologous recombination has greatly increased the ability to assess the function of particular gene products in vivo. The ability to control the developmental stage, the tissue and the nature of the mutation would be an important innovation. A recent report(1) demonstrates that the conservative site‐specific recombination of bacteriophage P1, namely Cre‐lox, can be used successfuly in combination with homologous recombination to generate temporal‐and cell‐restricted mutations in vivo. The technical advance allows a greater flexibility in gene targeting and will have a significant impact on how complex gene functions are studied in vivo.
Morphogens in vertebrate development: How do they work?
Authors: Cooke Jonathan 
Published: February 2005

AbstractThe idea that concentration gradients of crucial substances might control the pattern of development, even in the embryos of complex organisms, has been around for a long time, but mostly in obscure forms. Twenty five years ago clear, experimentally testable ideas about how such gradients might work were enunciated, and more recently the morphogen gradient principle was shown to underlie the beginnings of patterning in Drosophila. Is it also central to vertebrate development? Four recent papers raise experimentation to a new level(1–4), while showing how difficult it might be to pin down the precise form of the mechanism.
Cell‐cell signalling, microtubule organization and RNA localization: Is PKA a link?
Authors: Lasko Paul 
Published: February 2005

AbstractSpecification of the anterior‐posterior axis of the Drosophila embryo is brought about by the asymmetric localization of specific maternally expressed RNAs and proteins within the oocyte. While many of these localized molecules have been identified and progress has been made towards understanding their functions, how the localization process is instigated remains unclear. A recent paper reports that protein kinase A (PKA) activity is essential for many of these RNA localizations and for the correct polarization of the microtubule cytoskeleton(1). These and other results support a model for anterior‐posterior axis establishment which involves intercellular signalling between the oocyte and certain neighbouring somatic cells.
Phagocytosis
Authors: Brown Eric J. 
Published: February 2005

AbstractPhagocytosis is the process of recognition and engulfment of microorganisms or tissue debris that accumulate during infection, inflammation or wound repair. This ingestion, which is performed most efficiently by migrating, bone marrow‐derived cells called ‘professional phagocytes’, is essential for successful host defense. Ingestion results when an invading microorganism is recognized by specific receptors on the phagocyte surface and requires multiple, successive interactions between the phagocyte and the target. Each of these interactions results in a signal transduction event, which is confined to the membrane and cytoskeleton around the ligated receptor and which is required for successful phagocytosis. Many molecules found at sites of inflammation or infection stimulate phagocytosis, so that efficient ingestion is confined to the site of infection or inflammation, which in turn limits the proinflammatory and tissue‐destructive processes that accompany phagocytosis. This review summarizes current understanding of this critical component of host defense and of its regulation.
Root gravitropism
Authors: Masson Patrick H. 
Published: February 2005

AbstractWhen a plant root is reoriented within the gravity field, it responds by initiating a curvature which eventually results in vertical growth. Gravity sensing occurs primarily in the root tip. It may involve amyloplast sedimentation in the columella cells of the root cap, or the detection of forces exerted by the mass of the protoplast on opposite sides of its cell wall. Gravisensing activates a signal transduction cascade which results in the asymmetric redistribution of auxin and apoplastic Ca2+across the root tip, with accumulation at the bottom side. The resulting lateral asymmetry in Ca2+and auxin concentration is probably transmitted to the elongation zone where differential cellular elongation occurs until the tip resumes vertical growth. The Cholodny‐Went theory proposes that gravity‐induced auxin redistribution across a gravistimulated plant organ is responsible for the gravitropic response. However, recent data indicate that the gravity‐induced reorientation is more complex, involving both auxin gradient‐dependent and auxin gradient‐independent events.
Genetic control of intrachromosomal recombination
Authors: Klein Hannah L. 
Published: February 2005

AbstractIntrachromosomal recombination between direct repeats can occur either as gene conversion events, which maintain exactly the number of repeat units, or as deletions, which reduce the number of repeat units. Gene conversions are classical recombination events that utilize the standard chromosome recombination machinery. Spontaneous deletions between direct repeats are generally recA‐independent in E. coli and RAD52‐independent in S. cerevisiae. This independence from the major recombination genes does not mean that deletions form through a nonrecombinational process. Deletions have been suggested to result from sister chromatid exchange at the replication fork in a recA‐independent process. The same type of exchange is proposed to be RAD52‐independent in Saccharomyces cerevisiae. RAD52‐dependent events encompass all events that involve the initial steps of a recombination reaction, which include strand invasion to form a heteroduplex intermediate.
Synaptic vesicle recycling intermediates revealed
Authors: Vijayraghavan K. 
Published: February 2005

AbstractNeurotransmitter release takes place by the exocytosis of loaded synaptic vesicles. The vesicles then fuse to the presynaptic membrane and are recycled by an endocytotic mechanism. A quantitative optical assay that detects uptake and release of a fluorescent dye during presynaptic activity was recently developed and used on the frog neauromuscular junction. I discuss a report(1) that demonstrates the effective application of this method to a Drosophila preparation. The authors use the shibire mutation and a spider venom to identify two intermediates in vesicle recycling. Their report, along with other recent studies, demonstrates the power and promise of the genetic approach for the understanding of mechanisms of synapse function and development.
Compartments and appendage development in Drosophila
Authors: Blair Seth S. 
Published: February 2005

AbstractThe appendages of Drosophila develop from the imaginal discs. During the extensive growth of these discs cell lineages are for the most part unfixed, suggesting a strong role for cell‐cell interactions in controlling the final pattern of differentiation. However, during early and middle stages of development, discs are subdivided by strict lineage restrictions into a small number of spatially distinct compartments. These compartments appear to be maintained by stably inheriting states of gene expression; the compartmentspecific expression of two such ‘selector’ ‐ like genes, engrailed and apterous, are critical for anterior‐posterior and dorso‐ventral compartmentalization, respectively. Recent work suggests that one purpose of compartmentalization is to establish regions of specialized cells near compartment boundaries via intercompartmental induction, using molecules like the hedgehog protein. Thus, compartments can act as organizing centers for patterning within compartments. Evidence for non‐compartmental patterning mechanisms will also be discussed.
Does Flo flow? Cell layer interactions during floral development
Authors: Szymkowiak Eugene J. 
Published: February 2005

AbstractHigher plant shoot meristems are multicellular structures that are the site of postembryonic organogenesis. Analysis of chimeric plants has indicated that cells in different regions of the meristem can interact with each other so that their activities are coordinated during developmental processes. Correlations have not been demonstrated between events at a molecular level and the interactions observed at a phenotypic level in chimeras. Two recent papers(1,2) address this problem by reporting that expression of the floricaula gene in one region of chimeric snapdragon meristems is sufficient to promote the transition from inflorescence to floral development and to induce the expression of the downstream organ identity genes deficiens and plena throughout the meristem.
A radical approach to enzyme catalysis
Authors: Marsh E. Neil G. 
Published: February 2005

AbstractFree radicals are generally perceived as highly reactive species which are harmful to biological systems. There are, however, a number of enzymes that use carbon‐based radicals to catalyse a variety of important and unusual reactions. The most prominent example is ribonucleotide reductase, an enzyme which is crucial for the synthesis of DNA. In general, radicals are used to remove hydrogen from unreactive positions in the substrate, and in this way the substrate is activated to undergo chemical transformations that would otherwise be difficult to achieve. Several different mechanisms have evolved which allow enzymes to generate and maintain radicals in increasingly aerobic enviroments. An unexpected finding is the existance of stable protein‐based radicals, residing on a variety of amino‐acid side chains, which serve to link the radical‐generating and catalytic sites and to store the radical between turnovers.
Overview of controls in the Escherichia coli cell cycle
Authors: Vinella Daniel , D'Ari Richard 
Published: February 2005

AbstractThe harmonious growth and cell‐to‐cell uniformity of steady‐state bacterial populations indicate the existence of a well‐regulated cell cycle, responding to a set of internal signals. In Escherichia coli, the key events of this cycle are the initiation of DNA replication, nucleoid segregation and the initiation of cell division. The replication initiator is the DnaA protein. In nucleoid segregation, the MukB protein, required for proper partitioning, may be a member of the myosin‐kinesin superfamily of mechanoenzymes. In cell division, the FtsZ protein has a tubulin motif, is a GTPase and polymerizes in a ring around midcell during septation; the FtsA protein has an actin‐like structure. The nature of the internal signals triggering these events is not known but candidates include cell mass, the superhelical density of the chromosome and the concentration of two regulatory nucleotides, cyclic AMP and ppGpp. The involvement of cytoskeletal‐like proteins in key cycle events encourages the notion of a fundamental biological unity in cell cycle regulation in all organisms.
Cell death suffers a TKO
Authors: Osborne Barbara A. , Schwartz Lawrence M. 
Published: February 2005

AbstractThe cytokine interferon‐γ (IFN‐γ), initiates both cell cycle arrest and cell death in certain cell lines. Through a novel strategy of cell transfection with episomal vectors expressing antisense cDNAs, Deiss et al.(1.2) have demonstrated that it is possible to isolate genes that are required for the initiation of cell death by the cytokine IFN‐γ. This approach, referred to as TKO, for Technical Knock Out, has identified several genes whose activity appears to be essential for the induction of apoptosis by IFN‐γ in HeLa cells. Interestingly, these genes appear to mediate IFN‐γ‐induced apoptosis in HeLa cells, but their inhibition by antisense does not ameliorate the anti‐proliferative effects of IFN‐γ in these cells. The clever strategy employed by these authors holds promise for others who wish to isolate genes required for other differentiative processes in cultured cell lines.
Alkylation of DNA and its aftermath
Authors: Lawley P. D. 
Published: February 2005

AbstractCurrent pharmacopoeias invariably refer to a category of ‘alkylating drugs’, still among the most widely used in cancer chemotherapy. They are described as acting through their ability to damage DNA, thus interfering with cell replication. Unfortunately, this mode of action implicates these drugs as carcinogens. Thus the early studies recalled in this essay proved to be relevant to our understanding of both the main problems with which cancer research concerns itself: the causation of cancer and possible methods of treatment of this group of diseases.
The significances of bacterial colony patterns
Authors: Shapiro James A. 
Published: February 2005

AbstractBacteria do many things as organized populations. We have recently learned much about the molecular basis of intercellular communication among prokaryotes. Colonies display bacterial capacities for multicellular coordination which can be useful in nature where bacteria predominantly grow as films, chains, mats and colonies. E. coli colonies are organized into differentiated non‐clonal populations and undergo complex morphogenesis. Multicellularity regulates many aspects of bacterial physiology, including DNA rearrangement systems. In some bacterial species, colony development involves swarming (active migration of cell groups). Swarm colony development displays precise geometrical controls and periodic phenomena. Motile E. coli cells in semi‐solid media form organized patterns due to chemotactic autoaggregation. On poor media, B. subtilis forms branched colonies using group motility and longrange chemical signalling. The significances of bacterial colony patterns thus reside in a deeper understanding of prokaryotic biology and evolution and in experimental systems for studying self‐organization and morphogenesis.
Transcriptional silencing of homeotic genes in drosophila
Authors: Bienz Mariann , Müller Jürg 
Published: February 2005

AbstractHomeotic genes are subject to transcriptional silencing, which prevents their expression in inappropriate body regions. Here, we shall focus on Drosophila, as little is known about this process in other organisms. Evidence is accumulating that silencing of Drosophila homeotic genes is conferred by two types of cis‐regulatory sequences: initiation (SIL‐I) and maintenance (SIL‐M) elements. The former contain target sites for transient repressors with a highly localised distribution in the early embryo and the latter for constitutive repressors that are likely to be present in all cells. We discuss how SIL‐I elements may cooperate with SIL‐M elements to promote formation of a silencing complex. We propose that this complex consists of specific non‐histone proteins, the so‐called Polycomb group proteins, and that it is anchored at SIL‐M elements and at the promoter.
The genetics of lantibiotic biosynthesis
Authors: Jack Ralph , Bierbaum Gabriele , Heidrich Christoph , Sahl Hans‐Georg 
Published: February 2005

AbstractThe lantibiotics are a rapidly expanding group of biologically active peptides produced by a variety of Gram‐positive bacteria, and are so‐called because of their content of the thioether amino acids lanthionine and β‐methyllanthionine. These amino acids, and indeed a number of other unusual amino acids found in the lantibiotics, arise following post‐translational modification of a ribosomally synthesised precursor peptide. A number of genes involved in the biosynthesis of these highly modified peptides have been identified, including genes encoding the precursor peptide, enzymes responsible for specific amino acid modifications, proteases able to remove the leader peptide, ABC‐superfamily transport proteins involved in lantibiotic translocation, regulatory proteins controlling lantibiotic biosynthesis and proteins that protect the producing strain from the action of its own lantibiotic. Analysis of these genes and their products is allowing greater understanding of the complex mechanism(s) of the biosynthesis of these unique peptides.
Dual mechanisms of lymphocytemediated cytotoxicity serve to control and deliver the immune response
Authors: Smyth Mark J. 
Published: February 2005

AbstractCytotoxic lymphocytes play a central role in immune inflammatory responses against tumour cells, viruses and cells transplanted or infected with intracellular bacteria. The pivotal importance of lymphocytes in each of these immune responses has justified our continued interest in their cytotoxic function. Recent studies of cytotoxic lymphocytes have involved the characterisation of recognition structures on cytotoxic lymphocytes and the definition of two mechanisms of cytotoxicity. In contrast to normal cell death, which occurs during embryonic development and the formation and death of hematopoietic cell lineages, lymphocyte‐mediated cytotoxicity occurs in the context of an inflammatory response and the dying cells are lysed into the surroundings rather than phagocytosed. The roles of the two different forms of lymphocyte‐mediated cytotoxicity are quite distinct; however they both involve induction of an endogenous pathway of apoptosis in the targeted cell, and they do share features with all other forms of physiological cell death.
Transparent things: Cell fates and cell movements during early embryogenesis of zebrafish
Authors: Solnica‐Krezel Lilianna , Stemple Derek L. , Driever Wolfgang 
Published: February 2005

AbstractDevelopment of an animal embryo involves the coordination of cell divisions, a variety of inductive interactions and extensive cellular rearrangements. One of the biggest challenges in developmental biology is to explain the relationships between these processes and the mechanisms that regulate them. Teleost embryos provide an ideal subject for the study of these issues. Their optical lucidity combined with modern techniques for the marking and observation of individual living cells allow high resolution investigations of specific morphogenetic movements and the construction of detailed fate maps. In this review we describe the patterns of cell divisions, cellular movements and other morphogenetic events during zebrafish early development and discuss how these events relate to the formation of restricted lineages.
The macrophage
Authors: Gordon Siamon 
Published: February 2005

AbstractThe macrophage plays an important role in host development and physiology, and in pathogenesis of many infectious, immunologic and degenerative disease processes. It displays marked heterogeneity of phenotype in different tissues, reflecting local interactions with other cell types, and contributes to host homeostasis through a varied repertoire of plasma membrane and secretory molecules. Upon isolation from the body it continues to express special, as well as general, features of cellular organisation and function, which make it a delight to study in cell culture.
DNA packaging and cutting by phage terminases: Control in phage T4 by a synaptic mechanism
Authors: Black Lindsay W. 
Published: February 2005

AbstractPhage DNA packaging occurs by DNA translocation into a prohead. Terminases are enzymes which initiate DNA packaging by cutting the DNA concatemer, and they are closely fitted structurally to the portal vertex of the prohead to form a ‘packasome’. Analysis among a number of phages supports an active role of the terminases in coupling ATP hydrolysis to DNA translocation through the portal. In phage T4 the small terminase subunit promotes a sequence‐specific terminase gene amplification within the chromosome. This link between recombination and packaging suggests a DNA synapsis mechanism by the terminase to control packaging initiation, formally homologous to eukaryotic chromosome segregation.
Developmental regulation of αβ T cell antigen receptor assembly in immature CD4+CD8+ thymocytes
Authors: Kearse Kelly P. , Roberts Joseph P. , Wiest David L. , Singer Alfred 
Published: February 2005

AbstractMost lymphocytes of the T cell lineage develop along the CD4/CD8 pathway and express antigen receptors on their surfaces consisting of clonotypic αβ chains associated with invariant CD3‐γδε components and ζ chains, collectively referred to as the T cell antigen receptor complex (TCR). Expression of the TCR complex is dynamically regulated during T cell development, with immature CD4+CD8+ thymocytes expressing only 10% of the number of αβ TCR complexes on their surfaces expressed by mature CD4+ and CD8+ T cells. Recent evidence demonstrates that low surface TCR density on CD4+CD8+ thymocytes results from the limited survival of a single TCR component within the ER, the TCRα chain, which has a half life of only 15 minutes in immature thymocytes, compared to >75 minutes in mature T cells. Instability of TCRα proteins in immature CD4+CD8+ thymocytes represents a novel mechanism by which expression of the multisubunit TCR complex is quantitatively regulated during T cell development. In the current review we discuss our recent findings concerning the assembly, intracellular transport, and expression of αβ TCR complexes in CD4+CD8+ thymocytes and comment on the functional significance of TCRα instability during T cell development.
The pleckstrin homology domain: An intriguing multifunctional protein module
Authors: Shaw Gerry 
Published: February 2005

AbstractPleckstrin homology (PH) domains are a family of compact protein modules defined by sequences of roughly 100 amino acids. These domains are common in vertebrate, Drosophila, C. elegans and yeast proteins, suggesting an early origin and fundamental importance to eukaryotic biology. Many enzymes which have important regulatory functions contain PH domains, and mutant forms of several such proteins are implicated in oncogenesis and developmental disorders. Numerous recent studies show that PH domains bind various proteins and inositolphosphates. Here I discuss PH domains in detail and conclude that they form a versatile family of membrane binding and protein localization modules.
Drosophila Sgs genes: Stage and tissue specificity of hormone responsiveness
Authors: Lehmann Michael 
Published: February 2005

AbstractThe up‐ and down‐regulation of the salivary gland secretion protein (Sgs) genes during the third larval instar of Drosophila melanogaster are controlled by fluctuations of the titre of the steroid hormone 20‐hydroxyecdysone (20E). Induction of these genes by a low hormone titre is a secondary response to 20E mediated by products of 20E‐induced ‘early’ genes. Surprisingly, in the case of the Sgs‐4 gene this response also requires a direct contribution of the 20E‐receptor complex. A model is presented which proposes that the Sgs genes, and other 20E‐regulated genes with similar temporal expression profiles, are regulated by complex hormone response units. The hormonal signal is effectively transmitted by these response units only after binding of additional factors, e.g. secretion enhancer binding proteins, which act together in a synergistic manner with the 20E receptor and early gene products to establish a stage‐ and tissuespecific expression pattern.