bluuebunny/crossref_metadata_2025 huggingface dataset:
Polarised membrane traffic in hepatocytes
Authors: Wilton Joanne C. , Matthews Glenn M.
Published: February 2005

The liver was used widely in early studies of polarised transport but has been largely overlooked in recent years, mostly because of the development of epithelial cell lines which provide more tractable experimental systems. The majority of membrane proteins and lipids reach the hepatocyte apical membrane by transcytosis and it remains unclear whether there is a direct route for apical targeting, although the pathways present have yet to be fully characterised. The recent development of systems that allow hepatocyte transport processes to be studied in culture and the observation that transcytosis can be significantly stimulated under physiological conditions suggest that hepatocytes have a role to play in future studies of polarised transport. This review discusses the known features of polarised membrane traffic in hepatocytes and contrasts them with the characteristics of vesicular transport in other epithelial cell types.
CAC – the neglected repeat
Authors: Sertedaki Amalia , Lindsay Susan
Published: February 2005

It is becoming increasingly clear that repetitive DNA is of biological significance as well as experimental importance. Here we review the information available about one type of repetitive DNA, the trinucleotide repeat (CAC)n, and briefly compare it with other trinucleotide repeats. Although much work has been done in analysing DNA fingerprinting patterns produced using the synthetic oligonucleotide (CAC)5 as a probe, there is relatively little information about individual (CAC)n‐containing sequences and their abundance, organisation and distribution in mammalian DNA. From the data that is available, it is clear that there are at least two areas that should repay further study: (1) the organisation and generation of long sequences that contain (CAC)n motifs as part of a larger repeating unit (minisatellites) and (2) the distribution of small (CAC)n sequences (microsatellites), in particular their relationship to genes.
Common ground plans in early brain development in mice and flies
Authors: Arendt Detlev , Nübler‐Jung Katharina
Published: February 2005

Comparing expression patterns of orthologous genes between insects and vertebrates, we have recently proposed that the ventral nerve cord in insects may correspond to the dorsal nerve cord in vertebrates. Here we show that the early development of the insect and vertebrate brain anlagen is indeed very similar. Insect and vertebrate brains express similar sets of genes in comparable areas with similar functions in the adult. In addition, early axogenesis establishes surprisingly similar patterns of axonal connectivity in both groups. We therefore propose that insect and vertebrate brains are built according to a common ground plan, and that specific areas of the insect and vertebrate brains be considered as homologous, meaning that these areas already existed, with their specific functions, in their common ancestor.
Antigenic variation in trypansosomes: Secrets surface slowly
Authors: Cross George A. M.
Published: February 2005

Among pathogenic micro‐organisms that evade the mammalian immune responses, Trypanosoma brucei has developed the most elaborate capacity for antigenic variation. Trypanosomes branched early during eukaryotic evolution. They are characterized by many aberrations, ranging from the unusual compartmentation of metabolic pathways to the heresy of RNA editing. The ubiquitous phenomenon of glycosylphosphatidylinositol‐anchoring of eukaryotic plasma membrane proteins and RNA trans‐splicing (trypanosome genes contain no introns), which adds an identical leader sequence to all trypanosome mRNAs, were first defined during studies of antigenic variation. Genetic transformation of trypanosomes and the high efficiency of gene targeting provide new opportunities to investigate the regulation of antigenic variation. There is every reason to expect trypanosomes to provide further surprises and insights into the evolution of genetic regulatory mechanisms.
Holding chromatids together to ensure they go their separate ways
Authors: Bickel Sharon E. , Orr‐Weaver Terry L.
Published: February 2005

Association between sister chromatids is essential for their attachment and segregation to opposite poles of the spindle in mitosis and meiosis II. Sister‐chromatid cohesion is also likely to be involved in linking homologous chromosomes together in meiosis I. Cytological observations provide evidence that attachment between sister chromatids is different in meiosis and mitosis and suggest that cohesion between the chromatid arms may differ mechanistically from that at the centromere. The physical nature of cohesion is addressed, and proteins that are candidates for holding sister chromatids together are discussed. Dissolution of sister‐chromatid cohesion must be regulated precisely, and potential mechanisms to release cohesion are presented.
A case of convergent evolution of nucleic acid binding modules
Authors: Graumann Peter , Marahiel Moharned A.
Published: February 2005

Divergent evolution can explain how many proteins containing structurally similar domains, which perform a variety of related functions, have evolved from a relatively small number of modules or protein domains. However, it cannot explain how protein domains with similar, but distinguishable, functions and similar, but distinguishable, structures have evolved. Examples of this are the RNA‐binding proteins containing the RNA‐binding domain (RBD), and a newly established protein group, the cold‐shock domain (CSD) protein family. Both protein domains contain conserved RNP motifs on similar single‐stranded nucleic acid‐binding surfaces. Apart from the RNP motifs, which have a similar function, the two families show little similarity in topology or amino acid sequence. This can be considered an interesting example of convergent evolution at the molecular level. Previously, a β‐sheet surface was found to interact with RNA in non‐homologous proteins from yeast, phage and man, revealing that this mode of RNA binding may be a widely recurring theme.
Developmental genetics and traditional homology
Authors: Bolker Jessica A. , Raff Rudolf A.
Published: February 2005

The concept of homology arose from classical studies of comprative morphology, and took on a new signficance with the advent of evolutionary theory. It is currentlyl undergoing antoher metamorphosis: many developmental geneticists now dfine homology as shared patterns of gene expression. However, this ne usage conflaes difinition with criteri, and fails to recognize the meaninful asignments of homology must speify a biologcal level. We argue the although developmental genetic data can help identify homologus structures. they are niether necessary nor sufficient, and do not in any case jutify a new definition of homology.
Molecular mechanisms of durg inhibition of DNA gyrase
Authors: Lewis Richard J. , Tsai Francis T. F. , Wigley Dale B.
Published: February 2005

DNA gyrase, an enzyme unique to prokaryotes, has been implicated in almost all processes that involve DNA. Although efficient inhibitors of this protein have been known for more than 20 years, none of them have enjoyed prolonged pharmaceutical success. It is only recently that the mechanisms of inhibition for some of these classes of drugs have been established unequivocally by X‐ray crystallography. It is hoped that this detailed structural information will assist the design of novel, effective inhibitors of DNA gyrase.
Unraveling the late stages of recombinational repair: Metabolism of DNA junctions in Escherichia coli
Authors: Kuzminov Andrei
Published: February 2005

DNA junctions are by‐products of recombinational repair, during which a damaged DNA sequence, assisted by RecA filament, invades an intact homologous DNA to form a joint molecule. The junctions are three‐strand or four‐strand depending on how many single DNA strands participate in joint molecules. In E. coli, at least two independent pathways to remove the junctions are proposed to operate. One is via RuvAB‐promoted migration of four‐strand junctions with their subsequent resolution by RuvC. In vivo, RuvAB and RuvC enzymes might work in a single complex, a resolvasome, to clean DNA from used RecA filaments and to resolve four‐strand junctions. An alternative pathway for junction removal could be via RecG‐promoted branch migration of three‐strand junctions, provided that an as yet uncharacterized endonuclease activity incises one of the strands in the joint molecules.
recA mutants of E. coli K12: A personal turning point
Authors: Clark Alvin J.
Published: February 2005

A first year graduate student, Ann Dee Margulies, changed my research career in 1962 by challenging me to direct her in the isolation of recombination‐deficient mutants of Escherichia coli K‐12. She succeeded in isolating two mutants, which conjugated with donor strains and received the donor DNA, but could not recombine that DNA with their own chromosomes. Ann Dee showed that both mutants were much more sensitive to UV radiation than was the wild type. Furthermore, she showed that one of these mutants carried a single mutation affecting both recombination and resistance. This work, published in 1965, was the first demonstration of the recA gene of E. coli. Subsequent work led to the discovery of many more recombination genes, the phenomenon of post replication‐recombination repair, the invention of the SOS hypothesis and the discovery of genes encoding proteins with similar primary structure and function in all major groups of organisms. This article honors the memory of Ann Dee.
PKC ‐ A pivotal regulator of early development
Authors: Gallicano G. Ian , Yousef Martin C. , Capco David G.
Published: February 2005

Oocytes, eggs and blastomeres of the embryo are special cells that undergo rapid changes in structure and function at developmental transitions. These changes are frequently regulated by cytoplasmic signaling events, particularly at the developmental transition of fertilization, because the genome is largely inactivated at this time. Protein kinase C (PKC) is a signaling agent that acts after the sperm‐induced rise in calcium and has a central role in the remodeling of the structure of the egg into the zygote in many species. PKC also acts during other developmental transitions. This kinase serves as a chronometer, which can choreograph the cell's remodeling events in both space and time. Several technical advancements discussed in this review have permitted a better understanding of the actions of PKC.
Peroxisome biogenesis
Authors: Waterham Hans R. , Cregg James M.
Published: February 2005

Peroxisomes are eukaryotic organelles that are the subcellular location of important metabolic reactions. In humans, defects in the organelle's function are often lethal. Yet, relative to other organelles, little is known about how cells maintain and propagate peroxisomes or how they direct specific sets of newly synthesized proteins to these organelles (peroxisome biogenesis/assembly). In recent years, substantial progress has been made in elucidating aspects of peroxisome biogenesis and in identifying PEX genes whose products, peroxins, are essential for one or more of these processes. The most progress has been made in understanding the mechanism by which peroxisome matrix proteins are imported into the organelles. Signal sequences responsible for targeting proteins to the organelle have been defined. Potential signal receptor proteins, a receptor docking protein and other components of the import machinery have been identified, along with insights into how they operate. These studies indicate that multiple peroxisomal protein‐import mechanisms exist and that these mechanisms are novel, not simply variations of those described for other organelles.
Wnt signalling goes nuclear
Authors: Kühl Michael , Wedlich Doris
Published: February 2005

The Wnt signalling cascade is a highly conserved signalling pathway throughout the animal kingdom. In Xenopus, Wnt signalling functions in mesodermal dorsoventral patterning. Earlier work on deciphering the components of the wnt signalling cascade left a gap between cytosolic β‐catenin, the final member of the cascade, and the nuclear target genes. Several recent papers now reveal how the Wnt signal is transmitted into the nucleus. Surprisingly, β‐catenin directly interacts with the transcription factor LEF‐1/XTCF‐3, and thereby is not only translocated into the nucleus but also modulates the properties of LEF‐1/XTCF‐3 as a transcription factor(1–5).
Signaling through focal adhesion kinase
Authors: Hanks Steven K. , Polte Thomas R.
Published: February 2005

Focal adhesion kinase (FAK) is a nonreceptor protein‐tyrosine kinase implicated in controlling cellular responses to the engagement of cell‐surface integrins, including cell spreading and migration, survival and proliferation. Aberrant FAK signaling may contribute to the process of cell transformation by certain oncoproteins, including v‐Src. Progress toward elucidating the events leading to FAK activation following integrin‐mediated cell adhesion, as well as events downstream of FAK, has come through the identification of FAK phosphorylation sites and interacting proteins. A signaling partnership is formed between FAK and Src‐family kinases, leading to tyrosine phosphorylation of FAK and associated ‘docking’ proteins Cas and paxillin. Subsequent recruitment of proteins containing Src homology 2 domains, including Grb2 and c‐Crk, to the complex is likely to trigger adhesion‐induced cellular responses, including changes to the actin cytoskeleton and activation of the Ras‐MAP kinase pathway.
Mechanism of gene expression by the glucocorticoid receptor: Role of protein‐protein interactions
Authors: McEwan Iain J. , Wright Anthony P. H. , Gustafsson Jan‐Åke
Published: February 2005

The glucocorticoid receptor belongs to an important class of transcription factors that alter the expression of target genes in response to a specific hormone signal. The glucocorticoid receptor can function at least at three levels: (1) recruitment of the general transcription machinery; (2) modulation of transcription factor action, independent of DNA binding, through direct protein‐protein interactions; and (3) modulation of chromatin structure to allow the assembly of other gene regulatory proteins and/or the general transcription machinery on the DNA. This review will focus on the multifaceted nature of protein‐protein interactions involving the glucocorticoid receptor and basal transcription factors, coactivators and other transcription factors, occurring at these different levels of regulation.
On the functions of lithium: The mood stabilizer
Authors: Shastry Barkur S.
Published: February 2005

Lithium, despite its simple structure, has numerous biological effects. It also has a remarkable therapeutic effect in the prophylactic treatment of manic depression, and is finding a role in controlling aggressive and self‐mutilating behavior. The special feature of lithium is that it only acts on overactive systems to bring them back to normal, without affecting the stable system. The mechanisms of action of this simple cation are still largely unknown although the inositol depletion theory is the most widely accepted model. A recent paper(1) described a different molecular mechanism for its effect on development, which may also explain its action in manic depression.
Variable peroxisomal and mitochondrial targeting of alanine: Glyoxylate aminotransferase in mammalian evolution and disease
Authors: Danpure Christopher J.
Published: February 2005

Under the putative influence of dietary selection pressure, the subcellular distribution of alanine:glyoxylate aminotransferase 1 (AGT) has changed on many occasions during the evolution of mammals. Depending on the particular species, AGT can be found either in peroxisomes or mitochondria, or in both peroxisomes and mitochondria. This variable localization depends on the differential expression of N‐terminal mitochondrial and C‐terminal peroxisomal targeting sequences by the use of alternative transcription and translation initiation sites. AGT is peroxisomal in most humans, but it is mistargeted to the mitochondria in a subset of patients suffering from the rare herediatry disease primary hyperoxaluria type 1. Mistargeting is due to the unlikely combination of a normally occurring polymorphism that generates a functionally weak mitochondrial targeting sequence and a disease‐specific mutation which, in combination with the polymorphism, inhibits AGT dimerization. The mechanisms by which AGT can be targeted differentially to peroxisomes and/or mitochondria highlight the different molecular requirements for protein import into these two organelles.
Genetics of phototaxis in a model eukaryote, Dictyostelium discoideum
Authors: Fisher Paul R.
Published: February 2005

The life cycle of Dictyostelium discoideum offers a unique opportunity to study signal transduction in eukaryotic cells at both the unicellular and multicellular levels of organization. Adding to the already extensive knowledge of the unicellular stages, classical and molecular genetics have begun to unravel transduction of signals controlling morphogenesis and behaviour (phototaxis and thermotaxis) in the multicellular ‘slug’ stage of the life cycle. Distributed over all seven genetic linkage groups are probably about 20, but possibly as many as 55, genes of importance for slug behaviour. The encoded proteins appear from pharmacological studies and mutant phenotypes to govern transduction pathways involving the intracellular second messengers cyclic AMP, cyclic GMP, IP3 and Ca2+. Pathways from the photo‐ and thermoreceptors converge first with each other and thence, at the level of the second messengers, with those from extracellular tip activation (cyclic AMP) and inhibition (Slug Turning Factor and/or ammonia and/or adenosine) signals that control slug movement and morphogenesis.
Patterning of the mammalian dentition in development and evolution
Authors: Stock David W. , Weiss Kenneth M. , Zhao Zhiyong
Published: February 2005

The mammalian dentition is a segmented organ system with shape differences among its serially homologous elements (individual teeth). It is believed to have evolved from simpler precursors with greater similarities in shape among teeth, and a wealth of descriptive data exist on changes to the dentition that have occurred within mammals. Recent progress has been made in determining the genetic basis of the processes that form an individual tooth, but patterning of the dentition as a whole (i.e. the number, location and shape of the teeth) is less well understood. In contrast to similarly organized systems, such as the vertebral column and limb, Hox genes are not involved in specifying differences among elements. Nevertheless, recent work on a variety of systems is providing clues to the transcription factors and extracellular signalling molecules involved.
Death substrates come alive
Authors: Porter Alan G. , Ng Patrick , Jänicke Reiner U.
Published: February 2005

Interleukin 1β‐converting enzyme (ICE)‐like proteases (caspases) play an important role in programmed cell death (apoptosis), and elucidating the consequences of their proteolytic activity is central to our understanding of the molecular mechanisms of cell death. Diverse structural and regulatory proteins and enzymes, including protein kinase Cδ, the retinoblastoma protein (a protein involved in cell survival), the DNA repair enzyme DNA‐dependent protein kinase and the nuclear lamins, undergo specific and limited endoproteolytic cleavage by various caspases during apoptosis. Since individual caspases can cleave multiple substrates, the consequences of cleavage of only a single substrate are still poorly understood. Nevertheless, proteolytic activation of protein kinase Cδ may be an important early step in the cell death pathway, and cleavage of the retinoblastoma protein could suppress its cell survival function, whereas proteolytic inactivation of DNA repair enzymes might compromise the ability of the cell to reverse DNA fragmentation. On the other hand, cleavages of nuclear and cytoplasmic structural proteins (e.g. the lamins and Gas2) appear to be required for or contribute to the dramatic rearrangements in cellular architecture that are necessary for the completion of the cell death process. An emerging theme is that parallel and sequential proteolytic activation and inactivation of key protein substrates occurs during the multiple steps of apoptosis.
A hypothesis to explain why translation inhibitors stabilize mRNAs in mammalian cells: mRNA Stability and mitosis
Authors: Ross Jeff
Published: February 2005

Protein synthesis inhibitors prolong the half‐lives of most mRNAs at least fourfold in the somatic cells of higher eukaryotes and in yeast cells. Some mRNAs are stabilized because the inhibitors affect mRNA‐specific regulatory factors; however, hundreds or thousands of other mRNAs are probably stabilized by a common mechanism. We propose that mRNA stabilization in cells treated with a translation inhibitor reflects a physiological process that occurs during each mitosis and is important for cell survival. Transcription and translation rates decline drastically during a 1–2 hour interval of mitosis. We hypothesize that translational repression during this interval somehow inactivates a critical component of the mRNA degradation machinery. As a result, mRNA half‐lives are prolonged during the interval when transcription is repressed. If labile mRNAs were not stabilized during mitosis they, and perhaps also the labile proteins they encode, would be depleted as the cell entered G1 phase, with deleterious consequences. Stabilization during mitosis, or in response to translation inhibitors, thus preserves the capacity of the cell to synthesize essential proteins as it enters G1 or recovers from inhibitor treatment. mRNA stabilization might serve a similar purpose during starvation or any stress negatively affecting translation.
The phytochromes: A biochemical mechanism of signaling in sight?
Authors: Quail Peter H.
Published: February 2005

The biochemical mechanism by which the phytochrome family of plant sensory photoreceptors transmit perceived informational light signals downstream to transduction pathway components is undetermined. The recent sequencing of the entire genome of the cyanobacterium Synechocystis, however, has revealed a protein that has an NH2‐terminal domain with striking sequence similarity to the photosensory NH2‐terminal domain of the phytochromes, and a COOH‐terminal domain strongly related to the transmitter histidine kinase module of bacterial two‐component sensors. The Synechocystis protein is capable of autocatalytic chromophore ligation and exhibits photoreversible light‐absorption changes analogous to the phytochromes, indicating its capacity to function as an informational photoreceptor. Together with earlier observations that the COOH‐terminal domains of the plant phytochromes also have sequence similarity to the histidine kinases, these data suggest that the cyanobacteria utilize photoregulated histidine kinases as a sensory system and that the plant phytochromes may be evolutionary descendants of these photoreceptors.
Transforming growth factor‐β: The breaking open of a black box
Authors: Alevizopoulos Athanassios , Mermod Nicolas
Published: February 2005

Transforming growth factor‐β (TGF‐β) and its related proteins regulate broad aspects of body development, including cell proliferation, differentiation, apoptosis and gene expression, in various organisms. Deregulated TGF‐β function has been causally implicated in the generation of human fibrotic disorders and in tumor progression. Nevertheless, the molecular mechanisms of TGF‐β action remained essentially unknown until recently. Here, we discuss recent progress in our understanding of the mechanism of TGF‐β signal transduction with respect to the regulation of gene expression, the control of cell phenotype and the potential usage TGF‐β for the treatment of human diseases.
Set‐aside cells in maximal indirect development: Evolutionary and developmental significance
Authors: Peterson Kevin J. , Cameron R. Andrew , Davidson Eric H.
Published: February 2005

In the maximal form of indirect development found in many taxa of marine invertebrates, embryonic cell lineages of fixed fate and limited division capacity give rise to the larval structures. The adult arises from set‐aside cells in the larva that are held out from the early embryonic specification processes, and that retain extensive proliferative capacity. We review the locations and fates of set‐aside cells in two protostomes, a lophophorate and a deuterostome. The distinct adult body plans of many phyla develop from homologous set‐aside cells within homologous larvae. We argue that the stocks from which these phyla arose utilized these respective larvae, and the diversity of their adult body plans reflects diverse pattern formation processes executed in their set‐aside cell populations. Chordates and arthropods develop directly, but share adult characters with indirectly developing phyla. Thus the deuterostome and protostome stocks that were ancestral to chordates and arthropods, respectively, also utilized maximal indirect development.
Dueling orphans–interacting nuclear receptors coordinate Drosophila metamorphosis
Authors: Thummel Carl S.
Published: February 2005

At least seven orphan members of the nuclear receptor superfamily are transcriptionally regulated by the steroid hormone ecdysone and expressed during the onset of Drosophila metamorphosis. A recent paper provides functions for two of these receptors, E75B and DHR3, through trans‐regulation and heterodimerization(1). DHR3 appears to function as a switch that defines the transition from a late larva to a prepupa, and E75B functions as a timer that modulates this transition. This study provides a biological function for orphan receptor interactions during development.
The epithelial cell default‐phenotype hypothesis and its implications for cancer
Authors: Frisch Steven M.
Published: February 2005

The expression of epithelial cell adhesion and cytoskeletal genes is orchestrated by an apparently unique set of rules. No tissue‐specific transactivator proteins have been found to drive them; only ubiquitous factors are utilized. In non‐epithelial cells, they are actively repressed. Moreover, it was recently found that a single protein (adenovirus E1a) coordinately represses non‐epithelial genes while inducing epithelial genes. A simple model is offered to explain how epithelial gene expression is coordinated. Under this model, the epithelial cell gene expression program is a transcriptional ‘default’; that is, it occurs in the absence of tissue‐specific transactivation. Conversion to this default requires only that mesenchymal transactivators are not expressed, or that central ‘integrator’ proteins are inactive. In their absence, mesenchymal gene expression cannot occur. Moreover, because the repressors cease to be expressed, the epithelial genes are induced. Oncogenes generally cause the breakdown of the epithelial phenotype ‐ generating carcinomas ‐ so genes such as E1a that cause epithelial conversion may prove useful for both understanding and controlling cancer.
Intrinsic neuronal determinants that promotes axonal sprouting and elongation
Authors: Caroni Pico
Published: February 2005

Nerve processes elongate, branch and form synaptic contacts in a highly regulated and specific manner. Long‐distance axon elongation is restricted to the main phase of axon formation during development, but can be reinduced upon lesions in the adult (regeneration). It correlates with the expression of defined genes, including proteins involved in signalling (e.g. src, NCAM, integrins), transcription factors (e.g. c‐jun) and structural proteins (e.g. actin and tubulin isoforms). Activation of an axon elongation program may require bcl‐2. The formation and growth of local branches (sprouting) is controlled by mechanisms in the target region. In addition, the expression of growth‐associated proteins such as GAP‐43 and CAP‐23 in neurons lowers the threshold for nerve sprouting and potentiates its vigour. Recent studies suggest that nerve sprouting and long‐distance elongation depend on the expression of different intrinsic components in neurons. One implication of these findings is that the differential expression of genes facilitating local branching may affect structural plasticity in the intact adult nervous system.
Physiological electrical fields modify cell behaviour
Authors: McCaig Colin D. , Zhao Min
Published: February 2005

Steady direct current (dc) electric fields exist in many biological systems over many hours. At these times cells are dividing, differentiating, moving to final locations and extending motile processes. Each of these events may be influenced by physiological electric fields in tissue culture and when electric fields are disrupted in vivo, major developmental abnormalities arise. The likelihood of physiological electric fields playing a role in cell behaviours and some potential mechanisms are outlined.
Ion channel targeting in neurons
Authors: Sheng Morgan , Wyszynski Michael
Published: February 2005

Electrical signaling by neurons depends on the precisely ordered distribution of a wide variety of ion channels on the neuronal surface. The mechanisms underlying the targeting of particular classes of ion channels to specific subcellular sites are poorly understood. Recent studies have identified a new class of protein‐protein interaction mediated by PDZ domains, protein binding modules that recognize specific sequences at the C terminus of membrane proteins. The PDZ domains of a family of synaptic cytoskeleton‐associated proteins, typified by PSD‐95, bind to the intracellular C‐terminal tails of NMDA receptors and Shaker‐type K+ channels. This interaction appears to be important in the clustering and localization of these ion channels at synaptic sites. Recognition of specific C‐terminal peptide sequences by different PDZ domain‐containing proteins may be a general mechanism for differential targeting of proteins to a variety of subcellular locations.
Growth and development of the mammalian oocyte
Authors: Gosden Roger , Krapez Jennifer , Briggs David
Published: February 2005

The oocyte is not only the rarest and the largest cell in the body, but it also has one of the most remarkable life histories. Formed in the fetal ovary and suspended at diplotene of meiosis, it may wait for years before beginning to grow, and not until this process is complete can it resume meiosis and undergo fertilisation. Major changes in the number, morphology and distribution of cytoplasmic organelles occur during growth, and a molecular program for embryogenesis is formed. Specific yolk proteins are absent and much of the RNA and some of the protein are degraded by the cleavage stage. The zona pellucida has been intensively studied, but knowledge of oocyte‐specific genes is otherwise surprisingly patchy given the significance of this cell type and the expansion of reproductive technology. Finally, it is now clear that oocytes are not mere passengers which depend on granulosa cells for nutrition and regulation but actively promote the growth and differentiation of their follicles.
Tyrosine phosphorylation and cadherin/catenin function
Authors: Daniel Juliet M. , Reynolds Albert B.
Published: February 2005

Cadherin‐mediated cell‐cell adhesion is perturbed in protein tyrosine kinase (PTK)‐transformed cells. While cadherins themselves appear to be poor PTK substrates, their cytoplasmic binding partners, the Arm catenins, are excellent PTK substrates and therefore good candidates for mediating PTK‐induced changes in cadherin behavior. These proteins, p120ctn, β‐catenin and plakoglobin, bind to the cytoplasmic region of classical cadherins and function to modulate adhesion and/or bridge cadherins to the actin cytoskeleton. In addition, as demonstrated recently for β‐catenin, these proteins also have crucial signaling roles that may or may not be related to their effects on cell‐cell adhesion. Tyrosine phosphorylation of cadherin complexes is well documented and widely believed to modulate cell adhesiveness. The data to date, however, is largely correlative and the mechanism of action remains unresolved. In this review, we discuss the current literature and suggest models whereby tyrosine phosphorylation of Arm catenins contribute to regulation or perturbation of cadherin function.
Hypothesis: Ataxia‐telangiectasia: Is ATM a sensor of oxidative damage and stress?
Authors: Rotman Galit , Shiloh Yosef
Published: February 2005

Ataxia‐telangiectasia (A‐T) is a pleiotropic recessive disorder characterized cerebellar ataxia, immunodeficiency, specific developmental defects, profound predisposition to cancer and acute radiosensitivity. Functional inactivation of single gene product, ATM, accounts for this compound phenotype. We suggest that ATM acts as a sensor of reactive oxygen species and/or oxidative damage cellular macromolecules, including DNA. In turn, ATM induces signalling through multiple pathways, thereby coordinating acute phase stress responses with cell cycle checkpoint control and repair of oxidative damage. Absence of ATM is proposed to limit the repair of insidious oxidative damage that can occur under normal physiological conditions, ultimately leading to apoptosis of particularly sensitive cells, such as neurons and thymocytes.
Morphological control of cell growth and viability
Authors: Price Leo S.
Published: February 2005

Integrin‐mediated cell adhesion and subsequent cell spreading are essential for the growth and survival of many cell types. While integrin engagement is known to activate various signalling pathways, the role that cell spreading plays in the control of growth and survival is not clear. Using a novel technique, however, Chen et al.(1) demonstrate that the effect of cell spreading on growth and survival is not a consequence of increased area of contact with the extracellular matrix, supporting the hypothesis that regulation through changes in cell tension and architecture play a key role.
Genetic approach to neuroethology
Authors: Heisenberg Martin
Published: February 2005

In neuroethology, the nervous system and behavior are analyzed in the context of the animal's natural habitat and evolutionary history. For the last 30 years the influence of genetics on neuroethology has steadily grown, particularly in Drosophila. Genetic variants reveal new properties of neurons; they help to dissect neuronal circuits and complex behavioral systems; genetics provides new methods to visualize certain brain structures and to assign behavioral functions to them; and, finally, genetic variants can be used to test ecological models. While single‐gene mutations can have highly specific behavioral effects, molecular analysis of the corresponding genes reveals that the latter normally have a much broader functional scope. The ‘graininess’ of a functional model of the brain, therefore, is defined by the independent regulatory units of the genes rather than by the genes themselves.
Circadian rhythms: From behaviour to molecules
Authors: Rosato Ezio , Piccin Alberto , Kyriacou Charalambos P.
Published: February 2005

In higher eukaryotes, circadian behaviour patterns have been dissected at the molecular level in Drosophila and, more recently, in the mouse. Considerable progress has been made in identifying some of the molecular components of the clock in the fly, where two genes, period (per) and timeless (tim), are essential for behavioural rhythmicity. The PER and TIM proteins show circadian cycles in abundance, and are part of a negative feedback loop with their own mRNAs. Within the pacemaker neurons, the PER and TIM products are believed to form a complex which allows them to translocate to the nucleus, but how they repress their own transcription is unclear. TIM is rapidly degraded by light, a feature which permits a compelling molecular description of both behavioural light entrainment and phase responses to light pulses. The regulation of per and tim is altered in different Drosophila tissues, however, and comparative analyses of the two genes outside the Diptera reveals further unusual patterns of tissue‐specific regulation. Evolution appears to have modified the way in which the two genes are utilised to generate circadian phenotypes. More recently, the cloning of mouse clock genes, including putative per homologues, opens up exciting possibilities for mammalian molecular chronobiology.
Drosophila learning and memory: Recent progress and new approaches
Authors: Belvin Marcia P. , Yin Jerry C. P.
Published: February 2005

The processes of learning and memory have traditionally been studied in large experimental organisms (Aplysia, mice, rats and humans), where well‐characterized behaviors are easily tested. Although Drosophila is one of the most experimentally tractable organisms, it has only recently joined the others as a model organism for learning and memory. Drosophila behavior has been studied for over 20 years; however, most of the work in the learning and memory field has focused on initial learning, because establishing memory in Drosophila has not been as straightforward as in other organisms. A major recent advance in this field has been the development of a training protocol that induces long‐term memory in flies. This made possible experiments that implicated the Drosophila CREB gene as a critical component in the consolidation of long‐term memory, and paves the way for future experiments utilizing the well developed tools in Drosophila. This review will briefly summarize what is known in the field of Drosophila learning and memory to date, and discuss why the unique aspects of this field make traditional approaches difficult and reward the use of alternative paths of experimentation.
Novel site‐specific systemic delivery of Rapamycin with perfluorobutane gas microbubble carrier reduced neointimal formation in a porcine coronary restenosis model
Authors: Kipshidze Nicholas N. , Porter Thomas R. , Dangas George , Yazdi Hamid , Tio Fermin , Xie Feng , Hellinga David , Wolfram Roswitha , Seabron Rufus , Waksman Ron , Abizaid Alexander , Roubin Gary , Iyer Sriram , Colombo Antonio , Leon Martin B. , Moses Jeffrey W. , Iversen Patrick
Published: February 2005

Earlier studies demonstrated that perfluorobutane gas microbubble carrier (PGMC) adheres to injured arteries and enhances the drug uptake specifically into the cells of the denuded vessel segment. The purpose of this study was to investigate the effect of PGMC‐based systemic delivery of Rapamycin on expression of p27 in vascular tissue and restenosis in porcine coronary arteries after stent implantation. Eight pigs underwent coronary stent implantation (three stents per animal). Five pigs were treated with i.v. injection of PGMC with 2 mg of Rapamycin and three animals served as control. Four hours postprocedure, three pigs were sacrificed and stented segments were analyzed by high‐performance liquid chromatography (HPLC) and Western blot. In chronic experiments, five pigs (15 stent sites) were sacrificed at 28 days following intervention and vessels were perfusion‐fixed. HPLC of the treated arteries demonstrated high drug concentration in the vessel tissue, and Western blot analysis showed elevated expression of p27 at 4 hr postprocedure. Histomorphometry revealed significantly reduced (by 40%) neointimal formation in the PGMC/Rapamycin group compared with controls (1.84 ± 0.84 vs. 4.77 ± 1.71 mm2, respectively; P < 0.001). In the porcine coronary model, site‐specific systemic delivery of Rapamycin utilizing PGMC resulted in overexpression of p27 and a significant reduction of neointimal formation within the stented segments. Catheter Cardiovasc Interv 2005;64:389–394. © 2005 Wiley‐Liss, Inc.
Developmental regulation of neuron‐specific P2X3 receptor expression in the rat cochlea
Authors: Huang Lin‐Chien , Greenwood Denise , Thorne Peter R. , Housley Gary D.
Published: February 2005

ATP‐gated ion channels assembled from P2X3 receptor (P2X3R) subunits contribute to neurotransmission and neurotrophic signaling, associated with neurite development and synaptogenesis, particularly in peripheral sensory neurons. Here, P2X3R expression was characterized in the rat cochlea from embryonic day 16 (E16) to adult (P49–56), using RT‐PCR and immunohistochemistry. P2X3R mRNA was strongly expressed in the cochlea prior to birth, declined to a minimal level at P14, and was absent in adult tissue. P2X3R protein expression was confined to spiral ganglion neurons (SGN) within Rosenthal's canal of the cochlea. At E16, immunolabeling was detected in the SGN neurites, but not the distal neurite projection within the developing sensory epithelium (greater epithelial ridge). From E18, the immunolabeling was observed in the peripheral neurites innervating the inner hair cells but was reduced by P6. However, from P2–8, immunolabeling of the SGN neurites extended to include the outer spiral bundle fiber tract beneath the outer hair cells. This labeling of type II SGN afferent fiber declined after P8. By P14, all synaptic terminal immunolabeling in the organ of Corti was absent, and SGN cell body labeling was minimal. In adult cochlear tissue, P2X3R immunolabeling was not detected. Noise exposure did not induce P2X3R expression in the adult cochlea. These data indicate that ATP‐gated ion channels incorporating P2X3R subunit expression are specifically targeted to the afferent terminals just prior to the onset of hearing, and likely contribute to the neurotrophic signaling which establishes functional auditory neurotransmission. J. Comp. Neurol. 484:133–143, 2005. © 2005 Wiley‐Liss, Inc.
Central inhibitory microcircuits controlling spike propagation into sensory terminals
Authors: Watson Alan , Le Bon‐Jego Morgane , Cattaert Daniel
Published: February 2005

The phenomenon of afferent presynaptic inhibition has been intensively studied in the sensory neurons of the chordotonal organ from the coxobasal joint (CBCO) of the crayfish leg. This has revealed that it has a number of discrete roles in these afferents, mediated by distinct populations of interneurons. Here we examine further the effect of presynaptic inhibition on action potentials in the CBCO afferents and investigate the nature of the synapses that mediate it. In the presence of picrotoxin, the action potential amplitude is increased and its half‐width decreased, and a late depolarizing potential following the spike is increased in amplitude. Ultrastructural examination of the afferent terminals reveals that synaptic contacts on terminal branches are particularly abundant in the neuropil close to the main axon. Many of the presynaptic terminals contain small agranular vesicles, are of large diameter, and are immunoreactive for γ‐aminobutyric acid (GABA). These terminals are sometimes seen to make reciprocal connections with the afferents. Synaptic contacts from processes immunoreactive for glutamate are found on small‐diameter afferent terminals. A few of the presynaptic processes contain numerous large granular vesicles and are immunoreactive for neither GABA nor glutamate. The effect that the observed reciprocal synapses might have was investigated by using a multicompartmental model of the afferent terminal. J. Comp. Neurol. 484:234–248, 2005. © 2005 Wiley‐Liss, Inc.
Run‐time evaluation of opportunities for object inlining in Java
Authors: Lhoták Ondřej , Hendren Laurie
Published: February 2005

Object‐oriented languages, such as Java, encourage the use of many small objects linked together by field references, instead of a few monolithic structures. While this practice is beneficial from a program design perspective, it can slow down program execution by incurring many pointer indirections. One solution to this problem is object inlining: when the compiler can safely do so, it fuses small objects together, thus removing the reads/writes to the removed field, saving the memory needed to store the field and object header, and reducing the number of object allocations. The objective of this paper is to measure the potential for object inlining by studying the run‐time behaviour of a comprehensive set of Java programs. We study the traces of program executions in order to determine which fields behave like inlinable fields. Since we are using dynamic information instead of a static analysis, our results give an upper bound on what could be achieved via a static compiler‐based approach. Our experimental results measure the potential improvements attainable with object inlining, including reductions in the numbers of field reads and writes, and reduced memory usage. Our study shows that some Java programs can benefit significantly from object inlining, with close to a 10% speedup. Somewhat to our surprise, our study found one case, the db benchmark, where the most important inlinable field was the result of unusual program design, and fixing this small flaw led to both better performance and clearer program design. However, the opportunities for object inlining are highly dependent on the individual program being considered, and are in many cases very limited. Furthermore, fields that are inlinable also have properties that make them potential candidates for other optimizations such as removing redundant memory accesses. The memory savings possible through object inlining are moderate. Copyright © 2005 John Wiley & Sons, Ltd.
Two nodal‐responsive enhancers control left–right asymmetric expression of Nodal
Authors: Saijoh Yukio , Oki Shinya , Tanaka Chinatsu , Nakamura Tetsuya , Adachi Hitoshi , Yan Yu‐Ting , Shen Michael M. , Hamada Hiroshi
Published: February 2005

Asymmetric expression of Nodal in the lateral plate mesoderm (LPM) plays the major role in left–right (L‐R) patterning. A Nodal‐responsive enhancer located in the intron 1 (ASE) regulates asymmetric Nodal expression, but it is unknown how Nodal expression is initiated in the left LPM. Here, we have identified a second asymmetric enhancer (left side‐specific enhancer, LSE) in the upstream region of mouse Nodal gene. LSE is also located in the corresponding region of human NODAL. L‐R specificity of LSE is affected by iv and inv mutations. The requirement of a conserved FoxH1‐binding sequence for LSE activity and the dependence of LSE activity on Nodal coreceptor Cryptic indicate that LSE is activated by Nodal signal. However, the mutant mouse lacking LSE does not show obvious L‐R patterning defects. These results suggest that Nodal expression in the left LPM is induced by a combination of two Nodal‐responsive autoregulatory enhancers, ASE and LSE. Developmental Dynamics 232:1031–1036, 2005. © 2005 Wiley‐Liss, Inc.