bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gene expression during metamorphosis: An ideal model for post‐embryonic development
Authors: Tata Jamshed R. 
Published: February 2005

AbstractThe precocious induction in vivo and in culture of insect and amphibian metamorphosis by exogenous ecdysteroids and thyroid hormones, and its retardation or inhibition by juvenile hormone and prolactin, respectively, has allowed the analysis of such diverse processes of post‐embryonic development as morphogenesis, tissue remodelling, functional reorganization, and programmed cell death. Metamorphosis in vertebrates also shares many similarities with mammalian development in the late foetal and perinatal period. This review describes the regulation of expression of some of the ‘adult’ gene products during metamorphosis in invertebrates and vertebrates. Recent studies on metamorphosis have revealed the important role played by auto‐induction of hormone receptor genes, based on which a model will be presented to explain the activation of ‘downstream’ genes which give rise to the adult phenotype. It will also be argued that metamorphosis is an ideal model for analyzing some of the major mechanisms governing post‐embryonic development.
RNA as a catalyst: Natural and designed ribozymes
Authors: Von Ahsen Uwe , Schroeder Renée 
Published: February 2005

AbstractRNA can catalyse chemical reactions through its ability to fold into complex three‐dimensional structures and to specifically bind small molecules and divalent metal ions. The 2′‐hydroxyl groups of the ribose moieties contribute to this exceptional reactivity of RNA, compared to DNA. RNA is not only able to catalyse phosphate ester transfer reactions in ribonucleic acids, but can also show aminoacyl esterase activity, and is probably able to promote peptide bond formation. Bearing its potential for functioning both as a genome and as a gene product, RNA is suitable for in vitro evolution experiments enabling the selection of molecules with new properties. The growing repertoire of RNA catalysed reactions will establish RNA as a primordial molecule in the evolution of life.
Integrins hold Drosophila together
Authors: Brown Nicholas H. 
Published: February 2005

AbstractThe Drosophila position‐specific (PS) integrins are members of the integrin family of cell surface receptors and are thought to be receptors for extracellular matrix components. Each PS integrin consists of an α subunit, αPS1 or αPS2, and a βPS subunit. Mutations in the βPS subunit and the αPS2 subunit have been characterised and reveal that the PS integrins have an essential role in the adhesion of different cell layers to each other. The PS integrins are especially required for the function of the cell‐matrix‐cell junctions, where the muscles attach to the epidermis and where one surface of the developing wing adheres to the other. These junctions are similar to vertebrate focal adhesions and hemidesmosomes, which also contain integrins. Integrin‐mediated cell to cell adhesion via the extracellular matrix provides a way for tissues to adhere to each other without intermingling of their cells.
Molecular mechanisms of segmental patterning in the vertebrate hindbrain and neural crest
Authors: Wilkinson David G. 
Published: February 2005

AbstractRecent work has shown that segmentation underlies the patterning of the vertebrate hindbrain and its neural crest derivatives. Several genes have been identified with segment‐restricted expression, and evidence is now emerging regarding their function and regulatory relationships. The expression patterns of Hox genes and the phenotype of null mutants indicate roles in specifying segment identity. A zinc finger gene Krox‐20 is a segment‐specific regulator of Hox expression, and it seems probable that retinoic acid receptors also regulate Hox genes in the hindbrain. The receptor tyrosine kinase gene Sek may mediate cell‐cell interactions that lead to segmentation. These studies provide a starting point for understanding the molecular basis of segmental patterning in the hindbrain.
The making of a feather: Homeoproteins, retinoids and adhesion molecules
Authors: Chuong Cheng‐Ming 
Published: February 2005

AbstractWe have been using feather development as a model for understanding the molecular basis of pattern formation and to explore the roles of homeoproteins, retinoids and adhesion molecules in this process. Two kinds of homeobox (Hox) protein gradients in the skin have been identified: a ‘microgradient’ within a single feather bud and a ‘macrogradient’ across the feather tract. The asynchronous alignment of different Hox macrogradients establishes a unique repertoire of Hox expression patterns in skin appendages within the integument, designated here as the ‘Hox codes of skin appendages’. It is hypothesized that these Hox codes contribute to the phenotypic determination of skin appendages. High doses of retinoic acid cause a morphological transformation between feather and scale, while low doses of retinoic acid cause an alteration of the axial orientation of skin appendages. We have tested the ability of molecules directly involved in the feather formation process to mediate the action of the Hox codes, and surmise that adhesion molecules are potential candidates. Using specific Fabs to suppress the activity of adhesion molecules, we have found that L‐CAM is involved in the formation of the hexagonal pattern, N‐CAM is involved in mediating dermal condensations, tenascin is involved in feather bud growth and elongation, and integrin β‐1 is essential for epithelial‐mesenchymal interactions. More work is in progress to fully understand the molecular pathways regulating the feather formation process.
A signature for the HMG‐1 box DNA‐binding proteins
Authors: Landsman David , Bustin Michael 
Published: February 2005

AbstractA diverse group of DNA‐binding regulatory proteins share a common structural domain which is homologous to the sequence of a highly conserved and abundant chromosomal protein, HMG‐1. Proteins containing this HMG‐1 box regulate various cellular functions involving DNA binding, suggesting that the target DNA sequences share a common structural element. Members of this protein family exhibit a dual DNA‐binding specificity: each recognizes a unique sequence as well as a common DNA conformation. The highly conserved HMG‐1/‐2 proteins may modulate the binding of other HMG‐1 box proteins to bent DNA. We examine the structural and functional relationships between the proteins, identify their signature† and describe common features of their target DNA elements.
Assembly of intermediate filaments
Authors: Shoeman Robert L. , Traub Peter 
Published: February 2005

AbstractThe assembly of intermediate filaments is a fundamental property of the central rod domain of the individual subunit proteins. This rod domain, with its high propensity for α‐helix formation, is the common and identifying feature of this family of proteins. Assembly occurs in vitro in the absence of other proteins or exogenous sources of energy; in vivo, it appears as if other factors, as yet poorly understood, modulate the assembly of intermediate filaments. Parallel, in‐register dimers form via coiled‐coil interactions of the rod domain. Tetramers may form from staggered arrays of parallel or antiparallel arrangements of dimers. Higher‐order polymerization, which occurs spontaneously if the ionic strength of a mixture of dimers and tetramers is raised, proceeds rapidly through poorly described intermediates to the final 10 nm filament. This process is dependent on and modulated by the non‐α‐helical end domains, as well as those amino acids present at the very beginning and end of the rod domain. The interactions governing tetramer formation are most probably the same ones that are responsible for the lateral and longitudinal associations within intermediate filaments.
Problems and Paradigms: Relating biochemistry to biology: How the recombinational repair function of RecA protein is manifested in its molecular properties
Authors: Cox Michael M. 
Published: February 2005

AbstractThe multiple activities of the RecA protein in DNA metabolism have inspired over a decade of research in dozens of laboratories around the world. This effort has nevertheless failed to yield an understanding of the mechanism of several RecA protein‐mediated processes, the DNA strand exchange reactions prominent among them. The major factors impeding progress are the invalid constraints placed upon the problem by attempting to understand RecA protein‐mediated DNA strand exchange within the context of an inappropriate biological paradigm – namely, homologous genetic recombination as a mechanism for generating genetic diversity. In this essay I summarize genetic and biochemical data demonstrating that RecA protein evolved as the central component of a recombinational DNA repair system, with the generation of genetic diversity being a sometimes useful byproduct, and review the major in vitro activities of RecA protein from a repair perspective. While models proposed for both recombination and recombinational repair often make use of DNA strand cleavage and transfer steps that appear to be quite similar, the molecular and thermodynamic requirements of the two processes are very different. The recombinational repair function provides a much more logical and informative framework for thinking about the biochemical properties of RecA and the strand exchange reactions it facilitates.
The molecular biology of taste transduction
Authors: Margolskee Robert F. 
Published: February 2005

AbstractTaste cells respond to a wide variety of chemical stimuli: certain ions are perceived as salty (Na+) or sour (H+); other small molecules are perceived as sweet (sugars) and bitter (alkaloids). Taste has evolutionary value allowing animals to respond positively (to sweet carhohydrates and salty NaCl) or aversively (to bitter poisons and corrosive acids). Recently, some of the proteins involved in taste transduction have been cloned. Several different G proteins have been identified and cloned from taste tissue: gustducin is a taste cell specific G protein closely related to the transducins. Work is under way to clone additional components of the taste transduction pathways. The combination of electrophysiology, biochemistry and molecular biology is being used to characterize taste receptor cells and their sensory transduction mechanisms.
Protein splicing: Excision of intervening sequences at the protein level
Authors: Cooper Antony A. , Stevens To M. H. 
Published: February 2005

AbstractProtein splicing is an extraordinary post‐translational reaction that removes an intact central “spacer” domain (Sp) from precursor proteins (N‐Sp‐C) while splicing together the N‐ and C‐domains of the precursor, via a peptide bond, to produce a new protein (N‐C). All of the available data on protein splicing fit a model in which these intervening sequences excise at the protein level via a self‐splicing mechanism. Several proteins have recently been discovered that undergo protein splicing, and in two such cases, the excised spacer protein is an endonuclease. Such endonucleases are capable of conferring genetic mobility upon the intervening sequences that encodes them. These intervening sequences define a new family of mobile genetic elements that are translated yet remain phenotypically silent by excising at the protein rather than the RNA level.
Movement of virus and photoassimilate in the phloem: A comparative analysis
Authors: Leisner Scott M. , Turgeon Robert 
Published: February 2005

AbstractRecent progress in the study of short‐distance (cell‐to‐cell) movement of plant virus, facilitated by ‘movement proteins’, has led to a resurgence of interest in long‐distance virus transport in the phloem. Relatively little is known about phloem‐specific barriers to virus movement or about the form in which virus enters, travels within and exits this tissue. Progress in understanding virus and photoassimilate transport is limited by a paucity of information on the substructure and properties of plasmodesmata at specific interfaces. The direction of virus movement, once it has entered the phloem, can be understood by following photoassimilate translocation, a complex and dynamic process influenced by plant growth, development and vascular topology.
Feedback controls and G2 checkpoints: Fission yeast as a model system
Authors: Sheldrick Katherine S. , Carr Antony M. 
Published: February 2005

AbstractDependency relationships within the cell cycle allow cells to arrest the cycle reversibly in response to agents or conditions that interfere with specific aspects of its normal progression. In addition, overlapping pathways exist which also arrest the cell cycle in response to DNA damage. Collectively, these control mechanisms have become known as checkpoints. Analysis of checkpoints is facilitated by the fact that dependency relationships within the cell cycle, such as the dependency of mitosis on the completion of DNA synthesis, and the DNA damage checkpoint can be separated genetically. In fission yeast, Schizosaccharomyces pombe, the dependency of mitosis on prior completion of DNA synthesis is mediated through tyrosine‐15 phosphorylation of the ubiquitous mitotic regulator p34cdc2. In contrast, the arrest of mitosis caused by DNA damage acts through a separate mechanism that appears to be independent of tyrosine‐15 phosphorylation. Despite these distinct interactions with the mitotic machinery, the majority of fission yeast mutants that are deficient in mitotic arrest after DNA damage are also unable to respond to inhibition of DNA synthesis. In this essay we survey the current knowledge concerning feedback controls and checkpoints within fission yeast and relate this to information derived from other systems.
DNA helicases: Enzymes with essential roles in all aspects of DNA metabolism
Authors: Matson Steven W. , Bean Daniel W. , George James W. 
Published: February 2005

AbstractDNA helicases catalyze the disruption of the hydrogen bonds that hold the two strands of double‐stranded DNA together. This energy‐requiring unwinding reaction results in the formation of the single‐stranded DNA required as a template or reaction intermediate in DNA replication, repair and recombination. A combination of biochemical and genetic studies have been used to probe and define the roles of the multiple DNA helicases found in E. coli. This work and similar efforts in eukaryotic cells, although far from complete, have established that DNA helicases are essential components of the machinery that interacts with the DNA molecule.
Convergence and divergence in the evolution of transport proteins
Authors: Saier Milton H. 
Published: February 2005

AbstractDifferent families of transport proteins catalyze transmembrane solute translocation, employing different mechanisms and energy sources. Several of these functionally dissimilar proteins nevertheless exhibit similar strutural units, consisting of six tightly packed α‐helices which may comprise all or part of a transmembrane channel. It is now recognized that some of these families arose independently of each other by convergence, while others arose from common precursors by divergence. The former families apparently arose at different times in evolutionary history, in different groups of organisms, employing different routes.
Why do plants have phosphoinositides?
Authors: Coté Gary G. , Crain Richard C. 
Published: February 2005

AbstractPhosphoinositides are inositol‐containing phospholipids whose hydrolysis is a key step in the rapid responses of animal cells to extracellular signals. Whether they play similar roles in plant cells has not been established, and some have suggested alternative roles as direct modulators of specific proteins. Nonetheless, evidence is accumulating that phosphoinositide hydrolysis mediates transduction of some signal in plants. The evidence is strongest for a role in triggering the shedding of flagella by the unicellular alga Chlamydomonas reinhardtii under acid stress. Rapid kinetic analysis indicates that phosphoinositide hydrolysis occures within half a second and could trigger the rapid loss of flagella. Plant responses to pathogens and osmotic stress, as well as the regulation of turgor changes which underlie stomatal opening and closing and the movement of leaves and flower parts, may also be mediated by phosphoinositide hydrolysis. The evidence thus indicates that at least one reason plants have phosphoinositides is to mediate transduction of environmental signals.
Unusual DNA structures, chromatin and transcription
Authors: van Holde Kensal , Zlatanova Jordanka 
Published: February 2005

AbstractExtensive studies of DNA secondary structure during the past decade have shown that DNA is a dynamic molecule, whose structure depends on the underlying nucleotide sequence and is influenced by the environment and the overall DNA topology. Three major non‐B‐DNA structures have been described (Z‐DNA, triplex DNA and cruciform DNA) which are stabilized by unconstrained negative supercoiling and can be formed under physiological conditions. In this essay we summarize the DNA primary structure features that are pertinent to the formation of these conformers and present data concerning the occurrence of these sequences in the eukaryotic genome. The evidence in favor of the existence of these unusual DNA structures in vivo is discussed. The effect of alternative non‐B‐DNA structures on the way DNA is organized in chromatin is considered, and this is followed by evaluation of the data relating these structures to eukaryotic transcription. Some possible mechanisms by which the effect of non‐B structures on transcription might be exerted are proposed.
Spatial cues play a role in the development of Myxococcus xanthus
Authors: Crawford Eugene W. , Shimkets Lawrence J. 
Published: February 2005

AbstractIntercellular signaling plays an important role in spatially regulated developmental processes. Myxococcus xanthus C signal transmission during fruiting body formation requires motile, densely packed, well aligned cells. tThe fruiting body consists of two domains: an outer domain which has densely packed, well aligned, motile cells: and an inner domain of more loosely packed, non‐motile, sporulating cells. The two domains are characterized by different patterns of C‐dependent gene expression, which begins in the outer domain where C‐signaling is most efficient, and reaches its maximum in the inner domain. These domains may be maintained by a dynamic mechanism which relies on passive transport of the sporulating cells from the outer domain, where sporulation is initiated, to the inner domain by the motile cells in the outer domain.
Neutrophil chemoattractant receptors and the membrane skeleton
Authors: Klotz Karl‐Norbert , Jesaitis Algirdas J. 
Published: February 2005

AbstractSignal transduction via receptors for N‐formylmethionyl peptide chemoattractants (FPR) on human neutrophils is a highly regulated process which involves participation of cytoskeletal elements. Evidence exists suggesting that the cytoskeleton and/or the membrane skeleton controls the distribution of FPR in the plane of the plasma membrane, thus controlling the accessibility of FPR to different proteins in functionally distinct domains. In desensitized cells, FPR are restricted to domains which are depleted of G proteins but enriched in cytoskeletal proteins such as actin and fodrin. Thus, the G protein signal transduction partners of FPR become inaccessible to the agonist‐occupied receptor, preventing cell activation. The mechanism of interaction of FPR with the membrane skeleton is poorly understood but evidence is accumulating that suggests a direct binding of FPR (and other receptors) to cytoskeletal proteins such as actin.
Hypothesis: RNA polymerase: Structural determinat of the chromatin loop and the chromosome
Authors: Cook Peter R. 
Published: February 2005

AbstractCurrent models for RNA synthesis involve an RNA polymerase that tracks along a static template. However, research on chromatin loops suggests that the template slides past a stationary polymerase; individual polymerases tie the chromatin fibre into loops and clusters of polymerases determine the basic structure of the interphase and metaphase chromosome. RNA polymerase is then both a player and a manager of the chromosome loop.
Cysteine strings, calcium channels and synaptic transmission
Authors: Ganetzky Barry 
Published: February 2005

AbstractMultidisciplinary studies have led to the discovery and characterization of cysteine string proteins (csps) in both Drosophila and Torpedo. Phenotypic analysis of csp mutants in Drosophila demonstrates a crucial role for csp in synaptic transmission. Expression studies of Torpedo csp (Tcsp) in Xenopus oocytes suggests that the protein has some role in the function of presynaptic Ca2+ channels. However, biochemical purification of Tcsp indicates that is associated with synaptic vesicles rather than with the plasma membrane of presynaptic terminals where Ca2+ channels reside. These results suggest a model in which csps serve as a link by which docked synaptic vesicles could modulate the activity of presynaptic Ca2+ channels.
Borrowing thy neighbour's genetics: Neural induction and a Brachyury mutant in Xenopus
Authors: Green JeremyB. A. 
Published: February 2005

AbstractA recent article by Rao(1) exemplifies a number of new trends in developmental biology, both of technical strategy and approach to the problem of neural induction. Rao introduced into frog embryos a mutant form of a mesodermal gene, Brachyury, and caused ectopic neural differentiation. This essay traces the route from the original Brachyury mutation in mouse to the most likely conclusion of Rao's experiments — suggested previously(2) — that neural fate is a default pathway.
Butterfly wings: Colour patterns and now gene expression patterns
Authors: French Vernon , Monteiro Antonia 
Published: February 2005

AbstractThe particular fascination of butterfly wings for developmental biologists (and others) lies in their spectacular array of colour patterns. The evolutionary and developmental relationships between these patterns have been analysed and we know something of the cell interactions involved in their formation(1). Now butterfly homologues of Drosophila wing‐patterning genes have been identified, and their expression patterns offer the first clues to the molecular mechanisms which specify wing colour patterns(2).
Mapping in the realm of polyploidy: The wheat model
Authors: Gill Kulvinder S. , Gill Bikram S. 
Published: February 2005

AbstractWheat is an allopolyploid containing three distinct but genetically related (homoeologous) genomes, A, B and D. Because of polyploid inheritance and large genome size (16×1012bp), the wheat genome is thought to be intractable to map‐based cloning of agronomic and other genes of interest. We propose a targeted geneti mapping strategy that combines linkage and physical mapping and may facilitate map‐based cloning. High‐density linkage maps are either generated in wheat or in diploidTriticum tauschii, the donor of the D genome to wheat. Molecular marker‐based chromosome maps are constructed, using an array of deletion lines in wheat. The conventional genetic linkage maps are aligned with chromosome maps to construct cytogenetic ladder maps (CLMs). The CLMs allow region‐specific mapping and convert genetic distances into physical distances. The information from CLMs suggests that many genes in wheat are present in clusters that are highly recombiogenic, small, and may be amenable to cloning by chromosome walking. Therefore, the effective genome size of wheat is relatively small in comparison to the whole genome. The utility of using the smaller genome of rice for mapping and homologous gene cloning is discussed.