bluuebunny/crossref_metadata_2025 huggingface dataset:
Calcitonin gene-related peptide elevates calcium and polarizes membrane potential in MG-63 cells by both cAMP-independent and -dependent mechanisms
Authors: Burns Douglas M. , Stehno-Bittel Lisa , Kawase Tomoyuki
Published: July 2004

Published data suggest that the neuropeptide calcitonin gene-related peptide (CGRP) can stimulate osteoblastic bone formation; however, interest has focused on activation of cAMP-dependent signaling pathways in osteogenic cells without full consideration of the importance of cAMP-independent signaling. We have now examined the effects of CGRP on intracellular Ca2+ concentration ([Ca2+]int) and membrane potential ( Em) in preosteoblastic human MG-63 cells by single-cell fluorescent confocal analysis using fluo 4-AM-fura red-AM and bis(1,3-dibarbituric acid)-trimethine oxanol [DiBAC4( 3 )] bis-oxonol assays. CGRP produced a two-stage change in [Ca2+]int: a rapid transient peak and a secondary sustained increase. Both responses were dose dependent with an EC50 of ∼0.30 nM, and the maximal effect (initially ∼3-fold over basal levels) was observed at 20 nM. The initial phase was sensitive to inhibition of Ca2+ mobilization with thapsigargin, whereas the secondary phase was eliminated only by blocking transmembrane Ca2+ influx with verapamil or inhibiting cAMP-dependent signaling with the Rp isomer of adenosine 3′,5′-cyclic monophosphorothioate (Rp-cAMPS). These data suggest that CGRP initially stimulates Ca2+ discharge from intracellular stores by a cAMP-independent mechanism and subsequently stimulates Ca2+ influx through L-type voltage-dependent Ca2+ channels by a cAMP-dependent mechanism. In addition, CGRP dose-dependently polarized cellular Em, with maximal effect at 20 nM and an EC50 of 0.30 nM. This effect was attenuated with charybdotoxin (−20%) or glyburide (glibenclamide; −80%), suggesting that Em hyperpolarization is induced by both Ca2+-activated and ATP-sensitive K+ channels. Thus CGRP signals strongly by both cAMP-dependent and cAMP-independent signaling pathways in preosteoblastic human MG-63 cells.
5-Lipoxygenase and cyclooxygenase regulate wound closure in NIH/3T3 fibroblast monolayers
Authors: Green J. Angelo , Stockton Rebecca A. , Johnson Christopher , Jacobson Bruce S.
Published: July 2004

Wound healing involves multiple cell signaling pathways, including those regulating cell-extracellular matrix adhesion. Previous work demonstrated that arachidonate oxidation to leukotriene B4 (LTB4) by 5-lipoxygenase (5-LOX) signals fibroblast spreading on fibronectin, whereas cyclooxygenase-2 (COX-2)-catalyzed prostaglandin E2 (PGE2) formation facilitates subsequent cell migration. We investigated arachidonate metabolite signaling in wound closure of perturbed NIH/3T3 fibroblast monolayers. We found that during initial stages of wound closure (0–120 min), all wound margin cells spread into the wound gap perpendicularly to the wound long axis. At regular intervals, between 120 and 300 min, some cells elongated to project across the wound and meet cells from the opposite margin, forming distinct cell bridges spanning the wound that act as foci for later wound-directed cell migration and resulting closure. 5-LOX inhibition by AA861 demonstrated a required LTB4 signal for initial marginal cell spreading and bridge formation, both of which must precede wound-directed cell migration. 5-LOX inhibition effects were reversible by exogenous LTB4. Conversely, COX inhibition by indomethacin reduced directed migration into the wound but enhanced early cell spreading and bridge formation. Exogenous PGE2 reversed this effect and increased cell migration into the wound. The differential effects of arachidonic acid metabolites produced by LOX and COX were further confirmed with NIH/3T3 fibroblast cell lines constitutively over- and underexpressing the 5-LOX and COX-2 enzymes. These data suggest that two competing oxidative enzymes in arachidonate metabolism, LOX and COX, differentially regulate sequential aspects of fibroblast wound closure in vitro.
Redox signaling: thiol chemistry defines which reactive oxygen and nitrogen species can act as second messengers
Authors: Forman Henry Jay , Fukuto Jon M. , Torres Martine
Published: July 2004

Except for the role of NO in the activation of guanylate cyclase, which is well established, the involvement of reactive oxygen species (ROS) and reactive nitrogen species (RNS) in signal transduction remains controversial, despite a large body of evidence suggestive of their participation in a variety of signaling pathways. Several problems have limited their acceptance as signaling molecules, with the major one being the difficulty in identifying the specific targets for each pathway and the chemical reactions supporting reversible oxidation of these signaling components, consistent with a second messenger role for ROS and RNS. Nevertheless, it has become clear that cysteine residues in the thiolate (i.e., ionized) form that are found in some proteins can be specific targets for reaction with H2O2 and RNS. This review focuses on the chemistry of the reversible oxidation of those thiolates, with a particular emphasis on the critical thiolate found in protein tyrosine phosphatases as an example.
Twisted quantum doubles
Authors: Fukuda Daijiro , Kuga Ken′ichi
Published: July 2004

Using diagrammatic pictures of tensor contractions, we consider a Hopf algebra twisted by an element ℛλ ∈ A* ⊗ Aop
corresponding to a Hopf algebra morphism λ : A → A. We show that this Hopf algebra is quasitriangular with the universal R‐matrix coming from ℛλ when λ2 = idA, generalizing the quantum double construction which corresponds to the case λ = idA.
A third‐order nonlocal problem with nonlocal conditions
Authors: Bougoffa Lazhar
Published: July 2004

We study an equation with dominated lower‐order terms and nonlocal conditions. Using the Riesz representation theorem and the Schauder fixed‐point theorem, we prove the existence and uniqueness of a generalized solution.
An extension of the Clark‐Ocone formula
Authors: Ngobi Said , Stan Aurel
Published: July 2004

A white noise proof of the classical Clark‐Ocone formula is first provided. This formula is proven for functions in a Sobolev space which is a subset of the space of square‐integrable functions over a white noise space. Later, the formula is generalized to a larger class of operators.
Nitric Oxide Agents and Apomorphine-Induced Rat Behaviors
Authors: Zarrindast Mohammad-Reza , Nojoomi Katayoon , Sharifzadeh Mohammad , Mokri Azarakhsh
Published: July 2004

Background: Nitric oxide (NO) may alter dopamine release in the brain. Activation of D2-dopamine receptors may suppress NO synthase, and inhibition of NO synthase prevents behaviors induced by psychostimulants. We have investigated the modulatory actions of the precursor of NO synthesis (L-arginine) and the broad-spectrum NO synthesis inhibitor NG-nitro-L-arginine methyl ester (L-NAME) on apomorphine-induced behaviors in the rat. Methods: Apomorphine was injected subcutaneously, and behaviors induced by the drug were examined in the presence or absence of intracerebroventricular administration of L-arginine and L-NAME. Results: Our data indicate that L-arginine or L-NAME treatment decreased licking and yawning, but not penile erection induced by apomorphine. Conclusion: Apomorphine-induced behaviors may be modulated by NO levels.
Antiallergic Activity of Hesperidin Is Activated by Intestinal Microflora
Authors: Lee Neung-Kee , Choi Seung-Hoon , Park Sung-Hwan , Park Eun-Kyung , Kim Dong-Hyun
Published: July 2004

When hesperidin isolated from pericarpium of Citrus unshiu (family Rutaceae) was incubated with human intestinal microflora, its main metabolite was hesperetin, which was a main metabolite in urine of orally hesperidin-administered rats. The antiallergic activity of hesperidin and its metabolite hesperetin were investigated. Hesperidin did not inhibit the histamine release from RBL-2H3 cells induced by IgE. However, its metabolite hesperetin potently inhibited the histamine release from RBL-2H3 cells induced by IgE and the PCA reaction. The inhibitory activity of hesperetin was found to be comparable with azelastine, a commercially available antiallergic drug, and to potently inhibit prostaglandin E2 production in lipopolysaccharide-stimulated RAW 264.7 cells. Hesperetin weakly inhibits cyclooxygenase 2 enzyme activities. These results suggest that hesperidin may be a prodrug, which is metabolized to hesperetin by intestinal bacteria.
S-Adenosylmethionine Protects against Acetaminophen-Induced Hepatotoxicity in Mice
Authors: Song Zhenyuan , McClain Craig J. , Chen Theresa
Published: July 2004

An overdose of acetaminophen (APAP) is the most frequent cause of fulminant liver failure in the United States. Increasing evidence demonstrates that oxidative stress plays an important etiologic role in APAP-induced liver injury. S-Adenosylmethionine (SAMe) is a key intermediate in the hepatic trans-sulfuration pathway and serves as a precursor for glutathione (GSH) as well as the methyl donor in most transmethylation reactions. In the present study, we investigated effects of SAMe on liver injury induced by APAP administration in male C57BL/6 mice. Two related studies were performed. In the first experiment, SAMe (1g/kg BW) was injected intraperitoneally 4 h before APAP (600 mg/kg BW) administration. In the second experiment, SAMe was injected intraperitoneally 1 h after APAP administration. Our results showed that APAP administration induced changes typical of confluent centrilobular necrosis by histological examination and a marked elevation in serum alanine aminotransferase (ALT) activity. APAP administration induced significant decreases in both hepatic and blood SAMe concentrations. In addition, APAP decreased intracellular (both cytosolic and mitochondrial) GSH concentrations along with increased lipid peroxidation in conjunction with mitochondrial dysfunction as documented by Ca2+-induced mitochondrial permeability transition. SAMe treatment (both before and after APAP) significantly attenuated the liver injury. Exogenous SAMe prevented the decrease in liver and blood SAMe concentrations. Moreover, SAMe treatment attenuated both cytosolic and mitochondrial GSH depletion as well as mitochondrial dysfunction. We conclude that SAMe at least in part protects the liver from APAP-induced injury by preventing intracellular GSH depletion and mitochondrial dysfunction.
The initiation of homologous chromosome synapsis in mouse fetal oocytes is not directly driven by centromere and telomere clustering in the bouquet
Authors: Tankimanova M. , Hultén M.A. , Tease C.
Published: July 2004

We investigated the behaviour of centromeres and distal telomeres during the initial phases of female meiosis in mice. In particular, we wished to determine whether clustering of centromeres and telomeres (bouquet formation) played the same crucial role in homologous chromosome pairing in female meiosis as it does in the male. We found that synapsis (intimate homologous chromosome pairing) is most frequently initiated in the interstitial regions of homologous chromosomes, apparently ahead of the distal regions. The proximal ends of the chromosomes appear to be disfavoured for synaptic initiation. Moreover, initiation of synapsis occurred in oocytes that showed little or no evidence of bouquet formation. A bouquet was present in a substantial proportion of cells at mid to late zygotene, and was still present in some pachytene oocytes. This pattern of bouquet formation and pairing initiation is in stark contrast to that previously described in the male mouse. We propose that although dynamic movements of centromeres and telomeres to form clusters may facilitate alignment of homologues or homologous chromosome segments during zygotene, in the female mouse positional control of synaptic initiation is dependent on some other mechanism.
Mouse zona pellucida genes and glycoproteins
Authors: Wassarman P.M. , Jovine L. , Litscher E.S.
Published: July 2004

The zona pellucida (ZP) is a thick extracellular coat that surrounds all mammalian eggs. The ZP plays important roles during oogenesis, fertilization, and preimplantation development. The mouse ZP consists of only three glycoproteins, called ZP1, ZP2, and ZP3. All three glycoproteins are essential structural components of the ZP. Additionally, ZP3 serves as a primary sperm receptor and acrosome reaction-inducer, and ZP2 serves as a secondary sperm receptor during fertilization. ZP1, ZP2, and ZP3 are encoded by single-copy genes present on three different chromosomes. The genes are expressed exclusively by mouse oocytes as they grow and the cellular specificity can be ascribed to cis-acting sequences close to the site of transcription initiation and to certain trans-acting factors. Concomitantly, ZP polypeptides are synthesized, modified with N- and O-linked oligosaccharides, secreted, and assembled into crosslinked filaments that exhibit a structural repeat. Nascent ZP glycoproteins are incorporated into large secretory vesicles that fuse with the oocyte plasma membrane and deposit nascent ZP glycoproteins into the innermost layer of the thickening ZP. Each ZP polypeptide possesses several characteristic features, including an N-terminal signal sequence, a ZP domain, a consensus furin cleavage site, and a C-terminal transmembrane domain. The latter is required for assembly of nascent ZP polypeptides into a ZP, cleavage at the consensus furin cleavage site is required for secretion, and the ZP domain supports protein:protein interactions during ZP assembly. At ovulation, when meiotic maturation of oocytes occurs and chromosomes condense into bivalents, expression of the three ZP genes ceases. Using “knockout mice”, in the absence of either ZP2 or ZP3 expression, a ZP fails to assemble around growing oocytes and females are infertile. There is no effect on males. In the absence of ZP1 expression, a disorganized ZP assembles around growing oocytes and females exhibit reduced fertility. These observations are consistent with the current model for ZP structure in which ZP2 and ZP3 form long Z filaments crosslinked by ZP1.
Systems biology of the 2-cell mouse embryo
Authors: Evsikov A.V. , de Vries W.N. , Peaston A.E. , Radford E.E. , Fancher K.S. , Chen F.H. , Blake J.A. , Bult C.J. , Latham K.E. , Solter D. , Knowles B.B.
Published: July 2004

The transcriptome of the 2-cell mouse embryo was analyzed to provide insight into the molecular networks at play during nuclear reprogramming and embryonic genome activation. Analysis of ESTs from a 2-cell cDNA library identified nearly 4,000 genes, over half of which have not been previously studied. Transcripts of mobile elements, especially those of LTR retrotransposons, are abundantly represented in 2-cell embryos, suggesting their possible role in introducing genomic variation, and epigenetic restructuring of the embryonic genome. Analysis of Gene Ontology of the 2-cell-stage expressed genes outlines the major biological processes that guide the oocyte-to-embryo transition. These results provide a foundation for understanding molecular control at the onset of mammalian development.
Expression of the proliferation marker Ki-67 during early mouse development
Authors: Winking H. , Gerdes J. , Traut W.
Published: July 2004

In somatic tissues, the mouse Ki-67 protein (pKi-67) is expressed in proliferating cells only. Depending on the stage of the cell cycle, pKi-67 is associated with different nuclear domains: with euchromatin as part of the perichromosomal layer, with centromeric heterochromatin, and with the nucleolus. In gametes, sex-specific expression is evident. Mature MII oocytes contain pKi-67, whereas pKi-67 is not detectable in mature sperm. We investigated the re-establishment of the cell cycle-dependent distribution of pKi-67 during early mouse development. After fertilization, male and female pronuclei exhibited very little or no pKi-67, while polar bodies were pKi-67 positive. Towards the end of the first cell cycle, prophase chromosomes of male and female pronuclei simultaneously got decorated with pKi-67. In 2-cell embryos, the distribution pattern changed, presumably depending on the progress of development of the embryo, from a distribution all over the nucleus to a preferential location in the nucleolus precursor bodies (NPBs). From the 4-cell stage onwards, pKi-67 showed the regular nuclear relocations known from somatic tissues: during mitosis the protein was found covering the chromosome arms as a constituent of the perichromosomal layer, in early G1 it was distributed in the whole nucleus, and for the rest of the cell cycle it was associated with NPBs or with the nucleolus.
ATP levels in clone mouse embryos
Authors: Boiani M. , Gambles V. , Schöler H.R.
Published: July 2004

The transfer of a somatic cell nucleus into an oocyte results in a dramatic change of the transcriptional profile. Although the underlying process of chromatin remodeling after nuclear transfer so far has not been defined at the molecular level, adenosine triphosphate (ATP) is considered a crucial component. In our study, clones were cultured in six media (M16, CZB, KSOM(aa), α-MEM, D-MEM, G1/G2) and energy levels compared to fertilized embryos. Our data indicate that nuclear transfer into an oocyte does not cause a significant change of ATP content subsequent to chromatin remodeling and pronucleus-like nucleus formation. During cleavage, while ATP levels of normal embryos were kept within narrow limits, they were less restricted in clones. ATP variability was eminent until the clones reached the blastocyst stage. This profile is consistent with the emerging representation of cleavage-stage clone embryos as mosaics, whereby intra-embryo variations compound inter-embryo variations. The issue of energy in embryos remains a complex one. The existence of multiple and integrated pathways governing the physiology, metabolism and consequently the ATP level of a cell contrasts the single gene readout situation exemplified by Oct4. Such principal differences may explain why Oct4 is a prognostic marker for clones whereas ATP is not.
Maternal and environmental factors in early cloned embryo development
Authors: Gao S. , Latham K.E.
Published: July 2004

Cloning by somatic cell nuclear transfer (SCNT) in mammals has revealed the remarkable ability of an oocyte to reprogram somatic cell nuclei and induce them to recapitulate the developmental program. Despite the success, cloning remains very inefficient. This review summarizes recent observations from cloning in mice that reveal some of the likely causes for the present inefficiency. One cause appears to be the slow pace of reprogramming combined with the early onset of genome transcription, which together cause cloned embryos to elaborate many somatic cell characteristics even before the first cleavage division. The altered phenotypes of cloned embryos render standard embryo culture conditions grossly sub-optimum. Another cause appears to be a hitherto unappreciated contribution of spindle-associated factors to early embryo development. As current procedures remove the spindle and associated factors, cloned embryos lack these factors. These observations are providing new insight into basic mammalian embryology. They also reveal possible changes to protocols that could improve the overall success of cloning.
Spatial genome organization during T-cell differentiation
Authors: Kim S.H. , McQueen P.G. , Lichtman M.K. , Shevach E.M. , Parada L.A. , Misteli T.
Published: July 2004

The spatial organization of genomes within the mammalian cell nucleus is non-random. The functional relevance of spatial genome organization might be in influencing gene expression programs as cells undergo changes during development and differentiation. To gain insight into the plasticity of genomes in space and time and to correlate the activity of specific genes with their nuclear position, we systematically analyzed the spatial genome organization in differentiating mouse T-cells. We find significant global reorganization of centromeres, chromosomes and gene loci during the differentiation process. Centromeres were repositioned from a preferentially internal distribution in undifferentiated cells to a preferentially peripheral position in differentiated CD4+ and CD8+ cells. Chromosome 6, containing the differentially expressed T-cell markers CD4 and CD8, underwent differential changes in position depending on whether cells differentiated into CD4+ or CD8+ thymocytes. Similarly, the two marker loci CD4 and CD8 showed distinct behavior in their position relative to the chromosome 6 centromere at various stages of differentiation. Our results demonstrate that significant spatial genome reorganization occurs during differentiation and indicate that the relationship between dynamic genome topology and single gene regulation is highly complex.
Positional changes of pericentromeric heterochromatin and nucleoli in postmitotic Purkinje cells during murine cerebellum development
Authors: Solovei I. , Grandi N. , Knoth R. , Volk B. , Cremer T.
Published: July 2004

Previous studies revealed changes of pericentromeric heterochromatin arrangements in postmitotic Purkinje cells (PCs) during postnatal development in the mouse cerebellum (Manuelidis, 1985; Martou and De Boni, 2000). Here, we performed vibratome sections of mouse cerebellum (vermis) at P0 (day of birth), at various stages of the postnatal development (P2–P21), as well as in very young (P28) and 17-months-old adults. FISH was carried out on these sections with major mouse satellite DNA in combination with immunostaining of the nucleolar protein B23 (nucleophosmin). Laser confocal microscopy, 3D reconstructions and quantitative image analysis were employed to describe changes in the number and topology of chromocenters and nucleoli. At all stages of postnatal PC development heterochromatin clusters were typically associated either with nucleoli or with the nuclear periphery, while non-associated clusters were rare (<1% at P0 to P21 and about 3% in adult stages). At P0, about 2–4 nucleoli and 7–8 pericentromeric heterochromatin clusters were variably located within PC nuclei. The relative volume of heterochromatin clusters associated with the nucleoli (about 50%) was roughly equal to the volume of clusters associated with the nuclear periphery. Positional changes of both nucleoli and centromeres towards the nuclear center occurred between P0 and P6. At P6 the average number of chromocenters per PC nucleus had decreased to about five. In agreement with previous studies, one or occasionally two nucleoli were noted at the nuclear center surrounded by major perinucleolar heterochromatin clusters. The relative volume of these perinucleolar clusters increased to about 84%, while the volume of clusters in the nuclear periphery decreased to about 15%. At subsequent postnatal stages, the arrangement of most pericentromeric heterochromatin around a central nucleolus was maintained. In adult animals, however, we observed a partial redistribution of heterochromatin towards the nuclear periphery. The average total number of pericentromeric heterochromatin signals increased again to about ten. The volume of heterochromatin associated with the nuclear periphery roughly doubled (30%), while the volume of the perinucleolar heterochromatin decreased correspondingly.
DNA methylation profiles of CpG islands for cellular differentiation and development in mammals
Authors: Shiota K.
Published: July 2004

DNA methylation has been implicated in mammalian development. Transcription units contain CpG islands, but expression of CpG island associated genes in normal tissues was not believed to be controlled by DNA methylation. There are, however, numerous CpG islands containing tissue-dependent and differentially methylated regions (T-DMR), which are potential methylation sites in normal cells and tissues. Genomic scanning which focused on T-DMRs in CpG islands revealed that the DNA methylation profile of each cell/tissue is more complicated than previously considered. Differentiation of cells is associated with both methylation and demethylation, which occur at multiple loci. The epigenetic system characterized by DNA methylation requires cells to memorize gene expression patterns, thus, standardizing cellular phenotypes.
Identification and properties of imprinted genes and their control elements
Authors: Smith R.J. , Arnaud P. , Kelsey G.
Published: July 2004

Imprinted genes have the unusual characteristic that the copy from one parent is destined to remain inactive. Though few in number they nonetheless constitute a functionally important part of the mammalian genome. With their memory of parental origin, imprinted genes represent an important model for the epigenetic regulation of gene function and will provide invaluable paradigms to test whether we can predict epigenetic state from DNA sequence. Since their first discovery, systematic screens and some good fortune have led to identification of over seventy imprinted genes in the mouse and human: recent microarray analysis may reveal many more. With a significant number of imprinted genes now identified and completion of key mammalian genome sequences, we are able systematically to examine the organization of imprinted loci, properties of their control elements and begin to recognize common themes in imprinted gene regulation.
Endogenous reverse transcriptase: a mediator of cell proliferation and differentiation
Authors: Spadafora C.
Published: July 2004

Endogenous, non-telomeric Reverse Transcriptase (RT) is encoded by two classes of repeated genomic elements, retrotransposons and endogenous retroviruses, and is an essential component of the retrotransposition machinery of both types of elements. Expression of RT-coding genes is generally repressed in non-pathological, terminally differentiated cells, but is active in early embryos, germ cells, embryo and tumor tissues, all of which have a high proliferative potential. To clarify whether reverse transcription is functionally implicated in control of cell growth, differentiation and in embryogenesis, recent experiments have been undertaken to inactivate the endogenous RT activity. RT was inhibited in normal and transformed cell lines by exposure to nevirapine, a non-nucleosidic RT inhibitor. The endogenous RT was also blocked in murine embryos by microinjection of an anti-RT antibody. Both experimental approaches yielded a dramatic inhibition of proliferation. Murine embryos arrested at pre-implantation stages. Transformed cell lines underwent a significant reduction in the rate of cell growth, concomitant with the induction of differentiation. In addition, RT inhibition induced an extensive reprogramming of the gene expression profile both in cultured cell lines and in preimplantation embryos. From these studies, endogenous RT begins to emerge as a key function with a driving role in normal and pathological developmental processes.
Factors regulating endogenous retroviral sequences in human and mouse
Authors: Taruscio D. , Mantovani A.
Published: July 2004

Endogenous retroviruses (ERVs) are stably integrated in the genome of vertebrates and inherited as Mendelian genes. The several human ERV (HERV) families and related elements represent up to 5–8% of the DNA of our species. ERVs may be involved in the regulation of adjacent genomic loci, especially promoting the tissue-specific expression of genes; some HERVs may have functional roles, e.g., coding for the placental fusogenic protein, syncytin. This paper reviews the growing evidence about factors that may modulate ERVs, including: cell and tissue types (with special attention to placenta and germ cells), processes related to differentiation and aging, cytokines, agents that disrupt cell functions (e.g., DNA hypomethylating agents) and steroids. Special attention is given to HERVs, due to their possible involvement in autoimmunity and reproduction, as well as altered expression in some cancer types; moreover, different HERV families may deserve specific attention, due to remarkable differences concerning, e.g., expression in tissues. A comparison with factors interacting with murine ERV-related sequences indicates that the mouse may be a useful model for studying some patterns of HERV regulation. Overall, the available evidence identifies the diverse, potential interactions with endogenous or exogenous factors as a promising field for investigating the roles of ERVs in physiology and disease.
An integrative genomics approach to the reconstruction of gene networks in segregating populations
Authors: Zhu J. , Lum P.Y. , Lamb J. , GuhaThakurta D. , Edwards S.W. , Thieringer R. , Berger J.P. , Wu M.S. , Thompson J. , Sachs A.B. , Schadt E.E.
Published: July 2004

The reconstruction of genetic networks in mammalian systems is one of the primary goals in biological research, especially as such reconstructions relate to elucidating not only common, polygenic human diseases, but living systems more generally. Here we propose a novel gene network reconstruction algorithm, derived from classic Bayesian network methods, that utilizes naturally occurring genetic variations as a source of perturbations to elucidate the network. This algorithm incorporates relative transcript abundance and genotypic data from segregating populations by employing a generalized scoring function of maximum likelihood commonly used in Bayesian network reconstruction problems. The utility of this novel algorithm is demonstrated via application to liver gene expression data from a segregating mouse population. We demonstrate that the network derived from these data using our novel network reconstruction algorithm is able to capture causal associations between genes that result in increased predictive power, compared to more classically reconstructed networks derived from the same data.
Chromosomes and speciation in Mus musculus domesticus
Authors: Capanna E. , Castiglia R.
Published: July 2004

Thirty years after its identification, the model of chromosomal speciation in Mus musculus domesticus is reevaluated using the methods of population biology, molecular cytogenetics and functional genomics. Three main points are considered: (1) the structural predisposition of M. m. domesticus chromosomes to Robertsonian fusion; (2) the impediment of structural heterozygosity to gene flow between populations of mice with karyotypes rearranged by Robertsonian fusion and between them and populations with the standard all-acrocentric 40-chromosome karyotype; (3) the selective advantage of chromosomal novelty, essential for the attainment of homozygosis and the rapid fixation of the new karyotype in the population.
Mouse biodiversity in the genomic era
Authors: Galtier N. , Bonhomme F. , Moulia C. , Belkhir K. , Caminade P. , Desmarais E. , Duquesne J.J. , Orth A. , Dod B. , Boursot P.
Published: July 2004

Comparative genomics has developed by comparison of distantly related genomes, for which the link between the reported evolutionary changes and species development/physiology/ecology is not obvious. It is argued that the mouse (genus Mus) is an optimal model for microevolutionary genomics in vertebrates. This is because the mouse genome sequence, physical and genetic map have been completed, because mouse genetics, morpho-anatomy, pathology, behavior and ecology are well-studied, and because the Mus genus is a diverse, well- documented taxon, allowing comparative studies at the level of individual, population, subspecies, and species. The potential of the interaction between mouse genome and mouse biodiversity is illustrated by recent studies of speciation in the house mouse Mus musculus, and studies about the evolution of isochores, the peculiar pattern of GC-content variation across mammalian genomes.
The tobacco mouse and its relatives: a “tail” of coat colors, chromosomes, hybridization and speciation
Authors: Hauffe H.C. , Panithanarak T. , Dallas J.F. , Piálek J. , Gündüz İ. , Searle J.B.
Published: July 2004

The article reviews over 30 years’ study of the chromosomal variation of the western house mice (Mus musculus domesticus) from the neighboring valleys of Poschiavo and Valtellina on the Swiss-Italian border. This is done in the context of the social and political history of this area, on the grounds that mice, as commensals, are influenced by human history. The chromosomal study of mice in this area was initiated because their unusual black coat color led a 19th century naturalist to describe the “tobacco mice” from Val Poschiavo as a separate species (Mus poschiavinus). The special coloration of the Val Poschiavo mice is matched by their chromosomes: they have 26 chromosomes instead of the usual 40. The Val Poschiavo mice are not a separate species according to the Biological Species Concept; instead they constitute a chromosome race (the “Poschiavo”, POS) that is related to other races with reduced chromosome numbers that occur in N Italy (of which only those races in Val Poschiavo and Upper Valtellina have black coats). A phylogenetic analysis of mitochondrial DNA sequences suggests that the lineage of chromosome races found in N Italy was not formed during an extreme population bottleneck, although such bottlenecks have apparently occurred during the origin of individual races and certainly have influenced single populations. In one small, isolated population in Valtellina (Migiondo), two chromosome races (the POS and the “Upper Valtellina”, UV, 2n = 24) became reproductively isolated from each other. In another small population (Sernio) bottlenecking led to fixation of a hybrid form with the UV karyotype and coat color, but with allozyme and microsatellite alleles characteristic of mice with the standard 40-chromosome karyotype. Two of the chromosome races in Valtellina (the UV and the “Mid Valtellina”, MV, 2n = 24) also appear to be the product of hybridization. The dynamic history and patchy distribution of the house mouse chromosome races in Val Poschiavo and Valtellina in part reflects extinction-recolonization events; the formation of the UV and MV races and the introduction of the pale brown Standard race mice are believed to reflect such events. Dynamism in the chromosomal constitution of single populations is also evident from 25 years of data on the population in Migiondo. Due to change in agricultural practices, house mice in Valtellina and Val Poschiavo are becoming rarer, which is likely to have further impacts on the distribution and characteristics of the chromosome races in this area.
RNAi knock-down mice: an emerging technology for post-genomic functional genetics
Authors: Prawitt D. , Brixel L. , Spangenberg C. , Eshkind L. , Heck R. , Oesch F. , Zabel B. , Bockamp E.
Published: July 2004

RNA interference (RNAi) has been extensively used for sequence-specific silencing of gene function in mammalian cells. The latest major breakthrough in the application of RNAi technology came from experiments demonstrating RNAi-mediated gene repression in mice and rats. After more than two decades of functional mouse research aimed at developing and continuously improving transgenic and knock-out technology, the advent of RNAi knock-down mice represents a valuable new alternative for studying gene function in vivo. In this review we provide some basic insight as to how RNAi can induce gene silencing to then focus on recent findings concerning the applicability of RNAi for regulating gene function in the mouse. Reviewed topics will include delivery methods for RNAi-mediating molecules, a comparison between traditional knock-out and innovative transgenic RNAi technology and the generation of graded RNAi knock-down phenotypes. Apart from the exciting possibilities RNAi provides for studying gene function in mice, we discuss several caveats and limitations to be considered. Finally, we present prospective strategies as to how RNAi technology might be applied for generating conditional and tissue-restricted knock-down mice.
Long dsRNA and silent genes strike back:RNAi in mouse oocytes and early embryos
Authors: Svoboda P.
Published: July 2004

RNA interference (RNAi) refers to the selective degradation of mRNA induced by double-stranded RNA (dsRNA), first discovered in Caenorhabditis elegans. Homology-dependent silencing phenomena related to RNAi have been observed in many species from all eukaryotic kingdoms. RNAi and related mechanisms share several conserved components. The hallmark of these phenomena is the presence of short dsRNA molecules (21–25 bp long), termed short interfering RNA (siRNA), which are generated from dsRNA by the activity of Dicer, a specific type III RNAse. These molecules serve as a template for the recognition and cleavage of the cognate mRNA. As it is beyond the scope of a single review to cover all aspects of RNAi, this review will focus on certain steps of the pathway relevant to mammals and on the use of long dsRNA to specifically silence genes in mammalian cells permissive to this technique, such as oocytes and early embryos.
Sequence-specific modification of mouse genomic DNA mediated by gene targeting techniques
Authors: Sangiuolo F. , Novelli G.
Published: July 2004

The major impact of the human genome sequence is the understanding of disease etiology with deduced therapy. The completion of this project has shifted the interest from the sequencing and identification of genes to the exploration of gene function, signalling the beginning of the post-genomic era. Contrasting with the spectacular progress in the identification of many morbid genes, today therapeutic progress is still lagging behind. The goal of all gene therapy protocols is to repair the precise genetic defect without additional modification of the genome. The main strategy has traditionally been focused on the introduction of an expression system designed to express a specific protein, defective in the transfected cell. But the numerous deficiencies associated with gene augmentation have resulted in the development of alternative approaches to treat inherited and acquired genetic disorders. Among these one is represented by gene repair based on homologous recombination (HR). Simply stated, the process involves targeting the mutation in situ for gene correction and for restoration of a normal gene function. Homologous recombination is an efficient means for genomic manipulation of prokaryotes, yeast and some lower eukaryotes. By contrast, in higher eukaryotes it is less efficient than in the prokaryotic system, with non-homologous recombination being 10–50 fold higher. However, recent advances in gene targeting and novel strategies have led to the suggestion that gene correction based on HR might be used as clinical therapy for genetic disease. This site-specific gene repair approach could represent an alternative gene therapy strategy in respect to those involving the use of retroviral or lentiviral vectors to introduce therapeutic genes and linked regulatory sequences into random sites within the target cell genome. In fact, gene therapy approaches involving addition of a gene by viral or nonviral vectors often give a short duration of gene expression and are difficult to target to specific populations of cells. The purpose of this paper is to review oligonucleotide-based gene targeting technologies and their applications on modifying the mouse genome.
Genetic modifiers in mice: the example of the fragile X mouse model
Authors: Errijgers V. , Kooy R.F.
Published: July 2004

Modifiers play an important role in most, if not all human diseases, and mouse models. For some disease models, such as the cystic fibrosis knockout mouse model, the effect of genetic factors other than the causative mutation has been well established and a modifier gene has been mapped. For other mouse models, including those of the fragile X syndrome, a common form of inherited mental retardation, controversies between test results obtained in different laboratories have been well recognized. Yet, the possibility that modifiers could at least explain part of the discrepancies is only scarcely mentioned. In this review we compare the test results obtained in different laboratories and provide evidence that modifiers may affect disease severity in the fragile X knockout mouse.
The role of replicative senescence in cancer and human ageing: utility (or otherwise) of murine models
Authors: Smith S.K. , Kipling D.
Published: July 2004

Replicative senescence has the potential both to act as an anti-tumour mechanism, and to contribute to age-related changes in tissue function. Studies on human cells have revealed much, both about the nature of cell division counters, some of which utilize the gradual erosion of chromosomal telomeres, and the downstream signalling pathways that initiate and maintain growth arrest in senescence. A powerful test of the hypothesis that senescence is linked to either ageing or tumour prevention now requires a suitable animal model system. Here we overview the current understanding of replicative senescence in human cells, and address to what extent the senescence of murine cells in culture mirrors this phenomenon. We also discuss whether examples of telomere-independent senescence, such as those seen in mouse embryonic fibroblasts (MEFs) and several human cells types, should be viewed not as a consequence of “inadequate growth conditions”, but rather as a powerful potential model system to dissect the selective pressures that occur in the early stages of tumour development, ones that we speculate lead to the observed high frequency of abrogation of p16INK4a function in human cancer.
Telomere length measurement in mouse chromosomes by a modified Q-FISH method
Authors: Wong H.-P. , Slijepcevic P.
Published: July 2004

Telomeres are physical ends of mammalian chromosomes that dynamically change during the lifetime of a cell or organism. In order to understand mechanisms responsible for telomere dynamics, it is necessary to develop methods for accurate telomere length measurement. The most sensitive method for measuring telomere length in mouse chromosomes is quantitative fluorescence in situ hybridization (Q-FISH). The usual protocol for Q-FISH requires plasmids with variable numbers of telomeric repeats and fluorescence beads as calibration standards. Here, we describe a Q-FISH protocol in which two mouse lymphoma cell lines with well-defined telomere lengths are used as calibration standards. Using this protocol we demonstrate that reproducible results can be obtained in a set of four different mouse cell lines. This method can be adapted so that any pair of mammalian cell lines can serve as an internal calibration standard.
Manipulating mouse telomeres: models of tumorigenesis and aging
Authors: Xin Z. , Broccoli D.
Published: July 2004

Telomeres are capping structures at the ends of chromosomes, composed of a repetitive DNA sequence and associated proteins. Both a minimal length of telomeric repeats and telomere-associated binding proteins are necessary for proper telomere function. Functional telomeres are essential for maintaining the integrity and stability of eukaryotic genomes. The capping structure enables cells to distinguish chromosome ends from double strand breaks (DSBs) in the genome. Uncapped chromosome ends are at great risk for degradation, recombination, or chromosome fusion by cellular DNA repair systems. Dysfunctional telomeres have been proposed to contribute to tumorigenesis and some aging phenotypes. The analysis of mice deficient in telomerase activity and other telomere-associated proteins has allowed the roles of dysfunctional telomeres in tumorigenesis and aging to be directly tested. Here we will focus on the analysis of different mouse models disrupted for proteins that are important for telomere functions and discuss known and proposed consequences of telomere dysfunction in tumorigenesis and aging.
Sequences and Timing of Dental Eruption in Semi-Free-Ranging Mandrills (Mandrillus sphinx)
Authors: Setchell Joanna M. , Jean Wickings E.
Published: July 2004

The chronology of tooth emergence is often used to examine the growth and development of individuals and to compare life histories across species. Emergence patterns are also used to age animals and to infer life history influences for extinct species. However, comparative studies of primates are hindered by a lack of dental development data for many species. Here we describe the sequences and timing of tooth emergence for a large sample of semi-free-ranging mandrills (Mandrillus sphinx) and compare this with other life history variables for this species. Deciduous dentition emerged in the sequence i1 i2 c p3 p4. The augmented sequence (including information about variability in emergence sequence) was i1 i2 [c p3] p4 for the female maxilla and the male mandible, and i1 i2 c p3 p4 for the female mandible and the male maxilla. Deciduous dentition was complete by 5.0 months in females and 6.4 months in males. The permanent dentition began to emerge at 26 months, and complete adult dentition had emerged by 68 months for males and 85 months for females. Sex differences occurred in the augmented eruption sequences: females M1 I1 I2 [M2 C] P3 P4 M3, males M1 I1 [I2 M2] [P4 = P3 = C] M3. The order of tooth eruption and the occurrence of sequence polymorphisms were very similar to those observed for baboons and macaques. Comparison with life history variables showed that mandrills have complete deciduous dentition at weaning, females possess both adult incisors and M1 when they first reproduce, but still have deciduous canines and premolars, and that both sexes have full adult dentition before they attain their full adult stature and mass.
Footfall Patterns, Stride Length and Speed of Vertical Climbing in Spider Monkeys (Ateles fusciceps robustus) and Woolly Monkeys (Lagothrix lagotricha)
Authors: Isler Karin
Published: July 2004

Vertical climbing is central to theories surrounding the locomotor specialisations of large primates. In this paper, we present spatiotemporal gait parameters obtained from video recordings of captive spider monkeys (Ateles fusciceps robustus) and woolly monkeys (Lagothrix lagotricha) in semi-natural enclosures, with the aim of discovering the influence of body weight and differences in general locomotor behaviour on vertical climbing kinematics on various substrates. Results show that there are only few differences between gait parameters of climbing on thin trees, vertical and oblique ropes, while climbing on large-diameter trees differs considerably, reflecting the higher costs of locomotion on the latter. At the same speed, Ateles takes longer strides and the support phase takes a smaller percentage of cycle duration than in Lagothrix. Footfall patterns are more diverse in Ateles and include a higher proportion of ipsilateral limb coupling. Compared to other primates, the gait characteristics of vertical climbing of atelines most closely resemble those of African apes.