bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nuclear organization: Uniting replication foci, chromatin domains and chromosome structure
Authors: Jackson Dean A. 
Published: February 2005

AbstractIn higher eukaryotes, ‘replication factories’ coordinate DNA synthesis within local clusters of chromatin domains. Recent experiments(1,2) have confirmed the complexity of these clusters and established that the organization of sites labelled during S phase persists throughout the cell cycle. This implies that domain clusters are critical elements of an hierarchy that is fundamental to both nuclear and chromosome structure.
In vivo biochemistry: Physical monitoring of recombination induced by site‐specific endonucleases
Authors: Haber James E. 
Published: February 2005

AbstractThe recombinational repair of chromosomal double‐strand breaks (DSBs) is of critical importance to all organisms, who devote considerable genetic resources to ensuring such repair is accomplished. In Saccharomyces cerevisiae, DSB‐mediated recombination can be initiated synchronously by the conditional expression of two site‐specific endonucleases, HO or I‐Scel. DNA undergoing recombination can then be extracted at intervals and analyzed. Recombination initiated by meiotic‐specific DSBs can be followed in a similar fashion. This type of ‘in vivo biochemistry’ has been used to describe several discrete steps in two different homologous recombination pathways: gene conversion and single‐strand annealing. The roles of specific proteins during recombination can be established by examining DNA in strains deleted for the corresponding gene. These same approaches are now becoming available for the study of recombination in both higher plants and animals. Physical monitoring can also be used to analyze nonhomologous recombination events, whose mechanisms appear to be conserved from yeast to mammals.
Physiological and pathological interrelationships of amyloid β peptide and the amyloid precursor protein
Authors: Larner Andrew J. 
Published: February 2005

AbstractAmyloid β peptide (βA4) accumulates as plaques in the brains of individuals with Alzheimer's disease and Down's syndrome, and may contribute to the cognitive decline that is a feature of these diseases. βA4 is a normal product of cell metabolism, derived from the amyloid precursor protein (APP), but the biological functions of these molecules are not fully known. A hypothetical, descriptive model of the biological interrelationships between βA4 and APP is presented. APPS, the soluble form of APP, which is released at the neuronal surface, and βA4 are envisaged as physiological ligands which have reciprocal paracrine effects on neuronal growth and neurite extension. Differential expression of these factors, manifest as changes in the APPS:βA4 ratio, may therefore have growth‐promoting or growth‐inhibiting effects on neurons. These effects may be mediated through separate cell‐surface interactions but common intracellular effector systems, such as calcium and protein kinase C. In turn, the intracellular events may control the relative production of each ligand from APP through negative feedback loops. Disturbances of these control mechanisms may permit pathological overproduction, and hence accumulation, of βA4. Such a model may also have therapeutic implications.
Tag team specification of a neural precursor in the Drosophila embryonic central nervous system
Authors: Skeath James B. 
Published: February 2005

AbstractThe development of vertebrate and invertebrate nervous systems requires the production of thousands to millions of uniquely specified neurons from progenitor neural stem cells. A central question focuses on the elucidation of the developmental mechanisms that function within neural stem cell lineages to impart unique identities to neurons. A recent report(1) details the roles that two genes, pdm‐1 and pdm‐2, play within an identified neural stem cell lineage in the Drosophila embryonic central nervous system. The results show that pdm‐1 and pdm‐2 are coexpressed in an identified neural precursor and function redundantly to specify the fate of this cell. As such this report offers an initial view of the genetic programs that create neural diversity.
The anterior‐posterior and dorsalventral axes have a common origin in Drosophila melanogaster
Authors: Munn Kirsteen , Steward Ruth 
Published: February 2005

AbstractThe mechanisms governing anterior‐posterior and dorsal‐ventral polarity in Drosophila melanogaster had previously been considered as independent processes. However, two papers(1,2) now reveal that both axes are initiated during oogenesis by the same pathway, and also clearly demonstrate that one is dependent on the other.
Melanoma formation in xiphophorus: A model system for the role of receptor tyrosine kinases in tumorigenesis
Authors: Malitschek Barbara , Förnzler Dorothee , Schartl Manfred 
Published: February 2005

AbstractCancer is one of the most frequent fatal human diseases. It is a genetic disease, and molecular analysis of the genes involved revealed that they belong to several distinct classes of molecules, one of which is the receptor tyrosine kinases. Neoplastic transformation is regarded as the result of a multistep process and, in most cases, it is hard to evaluate what the initial events in tumor formation are. What makes it difficult to approach this question is the paucity of animal models for tumorigenesis allowing investigation of the mechanisms leading to uncontrolled cell proliferation. Melanoma formation in Xiphophorus is one of these model systems. Here, overexpression and activation of a receptor tyrosine kinase causes neoplastic transformation of pigment cells. Xiphophorus provides all the advantages of a well‐characterised genetic system. In addition, some crucial components of the transformation pathway have been identified at the molecular level. As a vertebrate, Xiphophorus might serve as a model system to aid understanding, in more general terms, of the mechanisms of tumorigenesis in human diseases.
Src and the control of cell division
Authors: Taylor Stephen J. , Shalloway David 
Published: February 2005

AbstractThe finely tuned mechanisms that control cell cycle progression go awry in cancer, pointing to proto‐oncogene products as important players in cell‐cycle regulation. One such proto‐oncoprotein, c‐Src, has previously been directly implicated, based on its requirement for growth factor‐stimulated DNA synthesis. Roche et al.(1) have now shown that c‐Src or its close relatives are also required for cell division to occur. The demonstration of essential functions for the Src family at multiple points in the cell cycle raises important questions about the normal and transforming activities of these and other proto‐oncoproteins.
How do single homeotic genes control multiple segment identities?
Authors: Duncan Ian 
Published: February 2005

AbstractEach of the homeotic genes of the bithorax complex of Drosophila defines the identities of more than one body segment. The mechanisms by which this occurs have been elusive. In a recent report, Castelli‐Gair and Akam(1) analyze in detail the control of parasegment 5 and parasegment 6 identities by the bithorax complex gene Ubx. Their results indicate that differences in the spatial and temporal expression patterns of Ubx are critical in determining differences between these parasegments. However, dose effects observed by others indicate that parasegment‐specific differences in the level of Ubx expression are also important. For the other BX‐C genes, parasegment‐specific expression of protein isoforms, or combinatorial control dependent on the expression patterns of other spatially restricted regulators, may also play a role.
Serial analysis of gene expression: ESTs get smaller
Authors: Adams Mark D. 
Published: February 2005

AbstractMeasuring gene expression on a global scale has been one of the vexing problems of cell biology. Velculescu et al.(1) recently proposed a system for identifying gene expression levels based on very short sequence tags – about nine base pairs – located at a specific site within a gene transcript. By coupling the strategy to current automated sequencing machines and the large expressed sequence tag databases, it should be possible to follow changes in gene expression for large numbers of genes economically and accurately.
Molecular mechanisms of anti‐inflammatory action of glucocorticoids
Authors: Cato Andrew C. B. , Wade Erik 
Published: February 2005

AbstractGlucocorticoid hormones are effective in controlling inflammation, but the mechanisms that confer this action are largely unknown. Recent advances in this field have shown that both positive and negative regulation of gene expression are necessary for this process. The genes whose activity are modulated in the anti‐inflammatory process code for several cytokines, adhesion molecules and enzymes. Most of them do not carry a classical binding site for regulation by a glucocorticoid receptor, but have instead regulatory sequences for transcription factors such as AP‐1 or NF‐κ. This makes them unusual targets for glucocorticoid action and emphasizes the need for novel regulatory mechanisms. Recent studies describe an important contribution by protein‐protein interactions, in which several domains of the receptor participate; these studies provide a better understanding of the action of the receptor and offer opportunities for the design of steroidal compounds that could function more effectively as anti‐inflammatory drugs.
Tadpole competence and tissue‐specific temporal regulation of amphibian metamorphosis: Roles of thyroid hormone and its receptors
Authors: Shi Yun‐Bo , Wong J. , Puzianowska‐Kuznicka M. , Stolow M. A. 
Published: February 2005

AbstractAmphibian metamorphosis is a post‐embryonic process that systematically transforms different tissues in a tadpole. Thyroid hormone plays a causative role in this complex process by inducing a cascade of gene regulation. While natural metamorphosis does not occur until endogenous thyroid hormone has been synthesized, tadpoles are competent to respond to exogenous thyroid hormone shortly after hatching. In addition, even though the metamorphic transitions of individual organs are all controlled by thyroid hormone, each occurs at distinct developmental stages. Recent molecular studies suggest that this competence of premetamorphic tadpoles to respond to the hormone and the developmental stage‐dependent regulation of tissue‐specific transformations are determined in part by the levels of thyroid hormone receptors and the concentrations of cellular free thyroid hormone. In addition, at least two genes, encoding a cytosolic thyroid hormone binding protein and a 5‐deiodinase, respectively, are likely to be critical players in regulating cellular free thyroid hormone concentrations. This review discusses how all of these molecuar components coordinate to induce amphibian metamorphosis in a correct spatial and temporal manner. These studies provde us with general clues as to how and why tissues become competent to respond to hormonal signals.
Segmentation (and eve) in very odd insect embryos
Authors: French Vernon 
Published: February 2005

AbstractThe formation of segments in the Drosophila early embryo is understood in greater detail than any other complex developmental process. Now, by studying other types of insect embryo, we can hope to deduce something of the ancestral mechanism of segmentation and the ways in which it has been modified in evolution. The parasitic wasp, Copidosoma floridanum, is spectacularly atypical of insects in that the small egg cell divides extensively, with no initial syncytial phase, and forms eventually some 2000 embryos(1). This process raises intriguing questions about the control of embryonic polarity and segmentation.
BMP‐1 and the astacin family of metalloproteinases: A potential link between the extracellular matrix, growth factors and pattern formation
Authors: Sarras Michael P. 
Published: February 2005

AbstractMembers of the astacin family of metalloproteinases such as human bone morphogenetic protein 1 (BMP‐1) have previously been linked to cell differentiation and pattern formation during development through a proposed role in the activation of latent growth factors of the TGF‐β superfamily. Recent finding(1) indicate that BMP‐1 is identical to pro‐collagen C‐proteinase, which is a metalloproteinase involved in extracellular matrix (ECM) formation. This observation suggests that a functional link may exist between astacin metalloproteinases, growth factors and cell differentiation and pattern formation during development. Taken together, current studies indicate that BMP‐1 and possibly other astacin metalloproteinases are multifunctional enzymes that act directly on growth factors and the ECM. In combination, these dual actions would have profound effects on developmental processes.
Plant cell enlargement and the action of expansins
Authors: Cosgrove Daniel J. 
Published: February 2005

AbstractPlant cells are caged within a distended polymeric network (the cell wall), which enlarges by a process of stress relaxation and slippage (creep) of the polysaccharides that make up the load‐bearing network of the wall. Protein mediators of wall creep have recently been isolated and characterized. These proteins, called expansins, appear to disrupt the noncovalent adhesion of matrix polysaccharides to cellulose microfibrils, thereby permitting turgor‐driven wall enlargement. Expansin activity is specifically expressed in the growing tissues of dicotyledons and monocotyledons. Sequence analysis of cDNAs indicates that expansins are novel proteins, without previously known functional motifs. Comparison of expansin cDNAs from cucumber, pea, Arabidopsis and rice shows that the proteins are highly conserved in size and amino acid sequence. Phylogenetic analysis of expansin sequences suggests that this multigene family diverged before the evolution of angiosperms. Speculation is presented about the role of this gene family in plant development and evolution.
Molecular analysis of Fanconi anaemia
Authors: Digweed Martin , Sperling Karl 
Published: February 2005

AbstractThe autosomal recessive genetic disease, Fanconi anaemia, is perceived as another manifestation of defective cellular DNA repair, just as in the autosomal recessive disease Xeroderma pigmentosum. The biochemistry and cellular biology of Xeroderma pigmentosum have been convincingly elucidated, but the same has not been true for Fanconi anaemia. In this review we consider the pleiotropic nature of Fanconi anaemia, its clinical and cellular variability and its genetic heterogeneity. We take into account the wealth of experimental findings available and offer a novel hypothesis involving feedback control of DNA replication during S phase of the cell cycle to explain the basic defect in the disease.
Retinoic acid, HOX genes and the anterior‐posterior axis in chordates
Authors: Shimeld Sebastian M. 
Published: February 2005

AbstractIn vertebrate development, the HOX genes act to specify cell identity along much of the anterior‐posterior axis of the embryonic central nervous system. In all vertebrates examined to date, the vitamin A metabolite retinoic acid is implicated in the patterning of the anterior posterior axis and the induction of HOX gene expression. Two recent papers have extended the study of retinoic acid induction of HOX genes to the closest relatives of the vertebrates, amphioxus and tunicates(1,2). In both these species, exogenous retinoic acid is able to induce ectopic expression of HOX 1 genes in the anterior central nervous system. This suggests that retinoic acid control of anterior‐posterior axis formation and HOX induction is not specific to vertebrates. However, in the more distantly related echinoderms and arthropods, retinoic acid does not seem to act in the same way. Thus the role of retinoic acid in anterior‐posterior axis specification may be a chordate innovation, perhaps linked to the evolution of another chordate character, the dorsal neural tube.
Epithelial integrins
Authors: Sheppard Dean 
Published: February 2005

AbstractThe integrin family was originally described as a family of adhesion receptors, utilized by cells for attachment to and migration across components of the extracellular matrix. Epithelial cells in adult tissues are generally stationary cells, but these cells nevertheless express several different integrins. This review will discuss the evidence that integrins on epithelial cells are also likely to function as signaling molecules, allowing these cells to detect attachment or detachment, and changes in the local composition of ligands. Signals initiated by integrins appear to modulate epithelial cell differentiation, proliferation, survival, and gene expression. Because the local concentration of integrin ligands is altered by injury, inflammation, and remodeling, signals initiated through integrins are likely to play important roles in the responses of epithelial cells to each of these processes.
Chromatin architectural proteins and transcription factors: A structural connection
Authors: van Holde Kensal , Zlatanova Jordanka 
Published: February 2005

AbstractIt has long been assumed that the architectural proteins of chromatin (the histones, for example) are unrelated to their functional proteins (transcription factors, polymerases, etc). New studies(1,2)drastically change this perspective. It appears that a portion of the general transcription initiation complex TFIID is made up of proteins that not only carry marked sequence and structural resemblances to the core histones of the nucleosome, but also form an octameric complex similar to the histone octamer. This can now be seen as part of a general pattern of continuity among structural and functional chromatin proteins.
Two is company: The complex travel arrangements of floral homeotic factors
Authors: Davies Brendan 
Published: February 2005

AbstractThe control of floral organ identity has received much attention since the first homeotic genes were isolated five years ago. The homeotic factors may be subject to a bewildering variety of control mechanisms including spatial and temporal transcriptional regulation, autoregulation, mutual protein stabilization, specific heterodimerization, post‐transcriptional modification and interaction with accessory factors. Now another level of complexity has been added by the recent discovery that the ‘B function factors’ depend on each other for nuclear localization(1) and can act non‐cell‐autonomously in a polar fashion(2).
Chloride channels: An emerging molecular picture
Authors: Jentsch Thomas J. , Günther Willy 
Published: February 2005

AbstractChloride channels are probably found in every cell, from bacteria to mammals. Their physiological tasks range from cell volume regulation to stabilization of the membrane potential, signal transduction, transepithelial transport and acidification of intracellular organelles. These different functions require the presence of many distinct chloride channels, which are differentially expressed and regulated by various stimuli. These include various intracellular messengers (like calcium and cyclic AMP), pH, extracellular ligands and transmembrane voltage. Three major structural classes of chloride channels are known to date, but there may be others not yet identified. After an overview of the general functions of chloride channels, this review will focus on these cloned chloride channels: the CLC chloride channel family, which includes voltage‐gated chloride channels, and the cystic fibrosis transmembrane regulator (CFTR), which performs other functions in addition to being a chloride channel. Finally, a short section deals with GABA and glycine receptors. Diseases resulting from chloride channel defects will be specially emphasized, together with the somewhat limited information about how these proteins work at the molecular level.
Transcription factors and head formation in vertebrates
Authors: Bally‐Cuif Laure , Boncinelli Edoardo 
Published: February 2005

AbstractEvidence from Drosophila and also vertebrates predicts that two different sets of instructions may determine the development of the rostral and caudal parts of the body. This implies different cellular and inductive processes during gastrulation, whose genetic requirements remain to be understood. To date, four genes encoding transcription factors expressed in the presumptive vertebrate head during gastrulation have been studied at the functional level: Lim‐1, Otx‐2, HNF‐3β and goosecoid. We discuss here the potential functions of these genes in the formation of rostral head as compared to posterior head and trunk, and in the light of recent fate map and expression analyses in mouse, chick, Xenopus and zebrafish. These data indicate that Lim‐1, Otx‐2 and HNF‐3β may be involved in the same genetic pathway controlling the formation of the prechordal mesendoderm, which is subsequently required for rostral head development. goosecoid may act in a parallel pathway, possibly in conjunction with other, yet unidentified, factors.
The genetics of phototransduction and circadian rhythms in arabidopsis
Authors: Millar Andrew J. , Kay Steve A. 
Published: February 2005

AbstractA wide range of biological processes, in all eukaryotes and in some prokaryotes, are controlled by rhythms with a period close to 24 hours. The circadian oscillator, which is responsible for generating these rhythms, is controlled by light signals that maintain its synchrony with the environmental day/night cycle. Higher plants exhibit many circadian rhythms, including rhythms in the transcription of specific genes. Molecular tools derived from such clock‐controlled genes have led to the identification of several circadian rhythm mutants in the genetic model, Arabidopsis thaliana. The extensive understanding of photoperception in this species will make it a powerful system with which to investigate the light regulation of circadian rhythms. We compare Arabidopsis rhythms to the results from other systems, and discuss these data with respect to the current phototransduction models.
Butterflies in the spotlight
Authors: Pigliucci Massimo 
Published: February 2005

AbstractRecent advances in our understanding of developmental phenomena has come from highly interdisciplinary studies where molecular biology, ecology and evolution converge to elucidate fundamental mechanisms, how they change through time, and what function they actually have in the context of the niche of the organism. A recent study on butterfly eyespots(1) pinpoints the surprisingly simple regulatory cascade controlling such an apparently complex phenotype. The implications go beyond the elucidation of a fascinating developmental pathway, into the mechanisms and tempo of speciation and macroevolution.
DNA turnover and mutation in resting cells
Authors: Bridges Bryn A. 
Published: February 2005

AbstractThere is growing evidence that mutations can arise in non‐dividing cells (both bacterial and mammalian) in the absence of chromosomal replication. The processes that are involved are still largely unknown but may include two separate mechanisms. In the first, DNA lesions resulting from the action of endogenous mutagens may give rise to RNA transcripts with miscoded bases. If these confer the ability to initiate DNA replication, the DNA lesions may have an opportunity to miscode during replication and thus could give rise to apparently ‘adaptive’ mutations. A second mechanism is suggested by recent work in starved bacteria, showing that there is much more turnover of chromosomal DNA than has been previously thought. This could permit polymerase errors to lead to mutations in non‐dividing cells. Such cryptic DNA synthesis, which may essentially replace existing DNA rather than duplicating it, could, in principle, act as an additional source of variability on which selection may act, initially in the absence of cell division. In mammals such processes would undoubtedly have implications for germ cell mutagenesis and carcinogenesis.