bluuebunny/crossref_metadata_2025_split huggingface dataset:
YACs and the C. elegans genome
Authors: Coulson Alan , Kozono Yoko , Lutterbach Bart , Shownkeen Ratna , Sulston John , Waterston Robert 
Published: February 2005

AbstractDuring the past decade, it has become apparent that it is within our grasp to understand fully the development and functioning of complex organisms. It is widely accepted that this undertaking must include the elucidation of the genetic blueprint – the genome sequence – of a number of model organisms. As a prelude to the determination of these sequences, clonebased physical maps of the genomes of a number of multicellular animals and plants are being constructed. Yeast artificial chromosome (YAC) vectors, by virtue of their relatively unbiased cloning capabilities and capacity to carry large inserts, have come to play a central role in the construction of these maps. The application of YACs to the physical map of the Caenorhabditis elegans genome has enabled cosmid clone ‘islands’ to be linked together in an efficient manner. The long‐range continuity has improved the linkage between the genetic and physical maps, greatly increasing its utility. Since the genome can be represented by a relatively small number of YACs, it has been possible to make replica filters of genomically ordered YACs available to the community at large.
Inositol tetrakisphosphate as a second messenger: Confusions, contradictions, and a potential resolution
Authors: Irvine Robin F. 
Published: February 2005

AbstractThe second messenger function of inositol 1,4,5‐ trisphosphate (InsP3) is now well‐defined – it mobilizes Ca2+ from intracellular stores so that cytosolic Ca2+ increases. However, the function of inositol 1,3,4,5‐ tetrakisphosphate (InsP4) has proved much more difficult to fathom, as it has been reported to exert a wide variety of effects in a collection of experimental systems. In this review, a proposed molecular mechanism for InsP4 actions is discussed; it is suggested that InsP4 is the second messenger that controls Ca2+ entry into cells, and that it does so by binding to a receptor which itself interacts, directly or Indirectly, with the receptor for InsP3 It is proposed that this is InsP4's true physiological function, but the mechanism by which it exerts this function has led to confusing data concerning its action, and also to some misconceptions about how inositol phosphates control Ca2+ entry.
Alternative splicing of fibronectin: Three variants, three functions
Authors: Schwarzbauer Jean E. 
Published: February 2005

AbstractFibronectin (FN) is a multi‐functional extracellular matrix protein required for cell adhesion and migration, blood clotting, wound healing, and oncogenic transformation. The functional complexity is paralleled by structural diversity in that multiple forms of FN are generated by cell type‐specific alternative splicing. In the rat, up to 12 different combinations of the three alternatively spliced segments (EIIIA, EIIIB, and the V region) are produced. What effects do these segments have on FN function? Recently, progress has been made in the identification of specific activities for the three Variants of the V region, V120, V95, and V0. FN‐mediated cell adhesion, FN synthesis and secretion, and incorporation into blood clots are differentially affected by these isoforms. These results suggest that cellular behavior is modulated by environmental cues provided by different types and proportions of alternatively spliced FN variants.
Chromatin replication
Authors: Gruss Claudia , Sogo Josém. 
Published: February 2005

AbstractJust as the faithful replication of DNA is an essential process for the cell, chromatin structures of active and inactive genes have to be copied accurately. Under certain circumstances, however, the activity pattern has to be changed in specific ways. Although analysis of specific aspects of these complex processes, by means of model systems, has led to their further elucidation, the mechanisms of chromatin replication in vivo are still controversial and far from being understood completely. Progress has been achieved in understanding: 1. The initiation of chromatin replication, indicating that a nucleosome‐free origin is necessary for the initiation of replication; 2. The segregation of the parental nucleosomes, where convincing data support the model of random distribution of the parental nucleosomes to the daughter strands; and 3. The assembly of histones on the newly synthesized strands, where growing evidence is emerging for a two‐step mechanism of nucleosome assembly, starting with the deposition of H3/H4 tetramers onto the DNA, followed by H2A/H2B dimers.
The function of melanin or six blind people examine an elephant
Authors: Hill Helene Z. 
Published: February 2005

AbstractThe pigment melanin is found in all living kingdoms and in many different structures and forms. When its various functions are examined separately, its behaviors seem disparate and conflicting. It has a clear role in camouflage and sexual display. Other major roles are examined critically. It can act as a sun screen but is not a very effective one. It can also scavenge active chemical species, but this, too, is not done very effectively. It produces active radicals that can damage DNA. It binds to drugs in ways that are either beneficial or deleterious. Aside from camouflage, its other roles can be brought together by a unifying hypothesis as first proposed by Proctor and McGinness nearly 20 years ago. Melanin is envisaged as an energy transducer with the properties of an amorphous semiconductor. It can absorb many different types of energy and dissipate them in the form of heat. However, if the energy input is too great, the output can be expressed in the form of activated chemical species that can damage cellular macromolecules resulting in cell death, mutations and cancer. The protective aspect of melanin in dark skin is seen as resulting from its high concentration and its confinement to ellipsoidal and densely packed organelles that can effectively shield the nucleus. In light skin, its radical nature is seen as potentially participating in the carcinogenic process, particularly when overwhelmed by intense episodes of sunburn.
Role of macrophages in peripheral nerve degeneration and repair
Authors: Perry V. H. , Brown M. C. 
Published: February 2005

AbstractA cut or crush injury to a peripheral nerve results in the degeneration of that portion of the axon isolated from the cell body. The rapid degeneration of this distal segment was for many years believed to be a process intrinsic to the nerve. It was believed that Schwann cells both phagocytosed degenerating axons and myelin sheaths and also provided growth factors to promote regeneration of the damaged axons. In recent years, it has become apparent that the degenerating distal segment is invaded by monocytes from the blood. We will review the evidence that these recruited macrophages play a role in both degeneration and regeneration of peripheral nerve axons after injury and consider whether the slow degeneration and poor monocyte recruitment in the central nervous system may contribute to the poor regeneration there.
Retinoic acid and development of the central nervous system
Authors: Maden Malcolm , Holder Nigel 
Published: February 2005

AbstractWe consider the evidence that RA†, the vitamin A metabolite, is involved in three fundamental aspects of the development of the CNS: (1) the stimulation of axon outgrowth in particular neuronal sub‐types; (2) the migration of the neural crest; and (3) the specification of rostrocaudal position in the developing CNS (forebrain, midbrain, hindbrain, spinal cord). The evidence we discuss involves RA‐induction of neurites in cell cultures and explants of neural tissue; the teratological effects of RA on the embryo's nervous system; the observation that RA can be detected endogenously in the spinal cord; and the fact that the receptors and binding proteins for RA are expressed in precise domains and neuronal cell types within the nervous system.
The plant hormone auxin: Insight in sight
Authors: Estelle Mark 
Published: February 2005

AbstractPhysiological experiments conducted over the last 60 years indicate that the plant hormone auxin regulates a diverse set of developmental processes via changes in cell division, cell elongation and cell differentiation. Recent studies using transgenic plants with altered auxin levels support these conclusions and promise to provide more detailed information on the role of auxin during plant development. Although it is possible that all auxin responses are mediated by the same primary biochemical events, the studies described in this review are more consistent with multiple modes of auxin action. The development of molecular and genetic approaches to the study of hormone action should resolve this issue. The accelerated rate of progress in this field suggests that real insight into the mechanism of auxin action may be forthcoming.
Roots. Use of the HPRT gene and the HAT selection technique in DNA‐mediated transformation of mammalian cells: First steps toward developing hybridoma techniques and gene therapy
Authors: Szybalski Waclaw 
Published: February 2005

AbstractIn 1956, I decided to apply my experience in microbial genetics to developing analogous systems for human cell lines, including the selection of mutants with either a loss or gain of a biochemical function. For instance, mutants resistant to azahypoxanthine showed a loss of the HPRT enzyme (hypoxanthine phosphoribosyl transferase), whereas gain of the same enzyme was accomplished by blocking de novo purine biosynthesis with aminopterin, while supplying hypoxanthine and thymine (HAT selection). Using HAT selection, we: (i) genetically transformed HPRT− mutant cells to HPRT+ wild type by using DNA extracted from HPRT+ cells, and (ii) selected HPRT+ hybrid cells by fusing HPRT− D98/AH2 cells with skin cells. These approaches, which we dubbed in 1962 as a [first step toward gene therapy], contributed to the later development of (i) cell fusion techniques, (ii) the development of monoclonal antibodies, (iii) routine transformation of mammalian cells with cloned genes, and (iv) methods for creating transgenic organisms.
Myelin Po‐protein, more than just a structural protein?
Authors: Filbin Marie T. , Tennekoon Gihan I. 
Published: February 2005

AbstractThe protein Po has long been proposed to be responsible for the compact nature of peripheral myelin through interactions of both its extracellular and cytoplasmic domains. Recent studies support such a role for Po's extracellular region while more precise mapping of its adhesive domains are ongoing. As Po is a member of the immunoglobulin gene superfamily and perhaps bears the closest similarity to the ancestral molecule of this whole family, these studies may also have more general implications for adhesive interactions. In addition, although long believed to be purely an inert, structural molecule, Po has been reported to promote neurite outgrowth, which suggests a more dynamic role for this interesting molecule.
The biology of hepatocyte growth factor/scatter factor
Authors: Furlong Robert A. 
Published: February 2005

AbstractHepatocyte growth factor, a potent mitogen for epithelial and other cell types, and scatter factor, a stimulant of epithelial cell motility are identical. In addition to these mitogenic and motogenic functions, the factor has been shown to be an epithelial morphogen and also has antiproliferative effects in some cancer cell lines. The membrane receptor for hepatocyte growth factor/scatter factor has been identified as the c‐met proto‐oncogene product.
Problems and paradigns. Evolution of mitochondrial genomes and the genetic code
Authors: Kurland C. G. 
Published: February 2005

AbstractMitochondrial genomes are clearly marked by a strong tendency towards reductive evolution. This tendency has been facilitated by the transfer of most of the essential genes for mitochondrial propogation and function to the nuclear genome. The most extreme examples of genomic simplification are seen in animal mitochondria, where there also are the greatest tendencies to codon reassignment. The reassignment of codons to amino acids different from those designated in the so called universal code is seen in part as an expression of the reduction of the number of genes used by these genomes to code for tRNA species. The driving force for the reductive evolution of mitochondrial genomes is identifed with two population genetic effects which may also be operating on populations of parasites.
Mitochondrial DNA and genetic disease
Authors: Poulton Jo 
Published: February 2005

AbstractSince the human mitochondrial genome was characterised and sequenced in 1981(1), it has been viewed as the likely site of genetic diseases showing a maternal inheritance pattern and associated with defects of the respiratory chain, such as the mitochondrial myopathies (MMs)†(2). The properties that make it a candidate for the source of such conditions are that it encodes polypeptides involved in electron transport(3,4) and that it is maternally inherited(5). However, several of the mtDNA diseases only fulfill one or other of these criteria: the first group of mtDNA diseases showed Only sporadic deletions(6,7), and the first point mutation in Leber's Hereditary Optic Neuropathy(8) (LHON) is not associated with a clear biochemical defect. Furthermore, it is now clear that both autosomal dominant(9) and probably recessive(10) nuclear genes can cause abnormalities of mtDNA. Each of these major groups will be considered in turn.
DNA triple‐helix formation: An approach to artificial gene repressors?
Authors: Maher L. James 
Published: February 2005

AbstractCertain sequences of double‐helical DNA can be recognized and tightly bound by oligonucleotides. The effects of such triple‐helical structures on DNA binding proteins have been studied. Stabilities of DNA triple‐helices at or near physiological conditions are sufficient to inhibit DNA binding proteins directed to overlapping sites. Such proteins include restriction endonucleases, methylases, transcription factors, and RNA polymerases. These and Other results suggest that oligonucleotide‐directed triple‐helix formation could provide the basis for designing artificial gene repressors. The general question of whether biological systems employ RNA molecules for recognition and regulation of double‐helical DNA is discussed.
Sex‐chromosome pairing and activity during mammalian meiosis
Authors: Handel Mary Ann , Hunt Patricia A. 
Published: February 2005

AbstractMammalian sex chromosomes exhibit marked sexual dimorphism in behavior during gametogenesis. During oogenesis, the X chromosomes pair and participate in unrestricted recombination; both are transcriptionally active. However, during spermatogenesis the X and Y chromosomes experience spatial restriction of pairing and recombination, are transcriptionally inactive, and form a chromatin domain that is markedly different from that of the autosomes. Thus the male germ cell has to contend with the potential loss of X‐encoded gene products, and it appears that coping strategies have evolved. Genetic control of sex‐chromosome inactivation during spermatogenesis does not involve pairing or the presence of the Y chromosome or an intact X chromosome, and may therefore be under exogenous control by the gonad. Sex‐chromosome reactivation during oogenesis and inactivation during spermatogenesis probably reflect specific meiotic events such as recombination. Understanding these phenomena may help explain other sex‐related differences in genetic recombination.
Mouse albino‐deletions: From genetics to genes in development
Authors: Holdener‐Kenny Bernadette , Sharan Shyam K. , Magnuson Terry 
Published: February 2005

AbstractSix essential genes located near the mouse albino locus have been identified as required during specific periods of development. Amongst these six, each is required either during the preimplantation stages of development, at specific times during gastrulation, within 12 hrs after birth or during juvenile development. These genes were identified as a result of extensive genetic complementation analysis using embryos homozygous for the albino deletions. Although, in principal, the associated developmental abnormalities could result from loss of multiple genes, the deletion phenotype in one case is identical to that induced by chemical mutagenesis. These results indicate that the abnormalities observed in deletion homozygotes may result from single gene loss. The deletions have proven useful not only as genetic tools to localize the position of the genes, but also as molecular entry points to the regions containing these genes. The current methodology being used to isolate candidate genes from the albino region is also reviewed here.
Bending of DNA by transcription factors
Authors: van der Vliet Peter C. , Verrijzer C. Peter 
Published: February 2005

AbstractAn increasing number of transcription factors both from prokaryotic and eukaryotic sources are found to bend the DNA upon binding to their recognition site. Bending can easily be detected by the anomalous electrophoretic behaviour of the DNA‐protein complex or by increased cyclization of DNA fragments containing the protein‐induced bend. Induction of DNA bending by transcription factors could regulate transcription in various ways. Bending may bring distantly bound transcription factors closer together by facilitating DNA‐looping or it could mediate the interaction between transcription factors and the general transcription machinery by formation of large nucleoprotein structures in which the DNA is wrapped around the protein complex. Alternatively, the energy stored in a protein‐induced bend could be used to favour formation of an open transcription complex or to dissociate the RNA polymerase in the transition from initiation to elongation. Modification of the bend angles and bending centers, caused by homodimerization or heterodimerization of transcription factors, may well turn out to be an important way to enlarge the range of interactions required for regulation of gene expression.
Interaction of rhodopsin with the G‐protein, transducin
Authors: Hargrave Paul A. , Hamm Heidi E. , Hofmann K. P. 
Published: February 2005

AbstractRhodopsin, upon activation by light, transduces the photon signal by activation of the G‐protein, transducin. The well‐studied rhodopsin/transducin system serves as a model for the understanding of signal transduction by the large class of G‐protein‐coupled receptors. The interactive form of rhodopsin, R*, is conformationally similar or identical to rhodopsin's photolysis intermediate Metarhodopsin II (MII). Formation of MII requires deprotonation of rhodopsin's protonated Schiff base which appears to facilitate some opening of the rhodopsin structure. This allows a change in conformation at rhodopsin's cytoplasmic surface that provides binding sites for transducin. Rhodopsin's 2nd, 3rd and putative 4th cytoplasmic loops bind transducin at sites including transducin's 5 kDa carboxyl‐terminal region. Site‐specific mutagenesis of rhodopsin is being used to distinguish sites on rhodopsin's surface that are important in binding transducin from those that function in activating transducin. These observations are consistent with and extend studies on the action of other G‐protein‐coupled receptors and their interactions with their respective G proteins.
Mechanism of action of the Escherichia coli UvrABC nuclease: Clues to the damage recognition problem
Authors: Van Houten Ben , Snowden Amanda 
Published: February 2005

AbstractDuring the process of E. coli nucleotide excision repair, DNA damage recognition and processing are achieved by the action of the uvrA, uvrB, and uvrC gene products. The availability of highly purified proteins has lead to a detailed molecular description of E. coli nucleotide excision repair that serves as a model for similar processes in eukaryotes. An interesting aspect of this repair system is the protein complex's ability to work on a vast array of DNA lesions that differ widely in their chemical composition and molecular architecture. Here we propose a model for damage recognition in which the UvrB protein serves as the component that confers enhanced specificity to a preincision complex. We hypothesize that one major determinant for the formation of a stable preincision complex appears to be the disruption of base stacking interactions by DNA lesions.
Challenges: The pharmacological manipulation of members of the transforming growth factor beta family in the chemoprevention of breast cancer
Authors: Dickens Tracey‐Anne , Colletta Anthony A. 
Published: February 2005

AbstractThe transforming growth factors beta are a family of peptides which are involved in the regulation of cell growth and differentiation. It has been suggested that the loss of sensitivity to growth inhibition by endogenous TGF‐β may contribute to the process of carcinogenesis in epithelial systems. However, many breast cancer cells remain sensitive to the growth inhibitory effects of these peptides, suggesting that the local induction of TGF‐β could provide a pharmacological approach to chemoprevention. Triphenylethylene anti‐oestrogens, synthetic progestins and retinoids all offer potential as chemopreventative agents. A common feature of their mechanism of action is the ability to locally increase the production of the transforming growth factors beta.
What the papers say: Cellular dedifferentiation and spore germination in Dictyostelium may utilize similar regulatory pathways
Authors: Powell‐Coffman Jo Anne , Firtel Richard A. 
Published: February 2005

AbstractCellular dedifferentiation is an important developmental response to perturbations in morphogenesis. In the cellular slime mold Dictyostelium discoideum this process gives cells the flexibility, when multicellular development is disrupted, to respond to nutrients and reinitiate vegetative growth. Recent studies in D. discoideum described by Soll and colleagues(1) show that genes previously thought to be expressed only during spore germination are also expressed during induced dedifferentiation, suggesting that similar molecular mechanisms are involved in these two developmental processes. It should now be possible to determine whether the developmental programs that control dedifferentiation during spore germination also control conversion of cell types in the multicellular organism.
Protein trafficking along the exocytotic pathway
Authors: Hong Wanjin , Tang Bor Luen 
Published: February 2005

AbstractProteins of the exocytotic (secretory) pathway are initially targeted to the endoplasmic reticulum (ER) and then translocated across and/or inserted into the membrane of the ER. During their anterograde transport with the bulk of the membrane flow along the exocytotic pathway, some proteins are selectively retained in various intracellular compartments, while others are sorted to different branches of the pathway. The signals or structural motifs that are involved in these selective targeting processes are being revealed and investigations into the mechanistic nature of these processes are actively underway.