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The Mouse SAGE Site: database of public mouse SAGE libraries.

The Mouse SAGE Site is a web-based database of all available public libraries generated by the Serial Analysis of Gene Expression (SAGE) from various mouse tissues and cell lines. The database contains mouse SAGE libraries organized in a uniform way and provides web-based tools for browsing, comparing and searching SAGE data with reliable tag-to-gene identification. A modified approach based on the SAGEmap database is used for reliable tag identification. The Mouse SAGE Site is maintained on an ongoing basis at the Institute of Molecular Genetics, Academy of Sciences of the Czech Republic and is accessible at the internet address http://mouse.biomed.cas.cz/sage/.

Animals↗

The RNA ligands for mouse proline-rich RNA-binding protein (mouse Prrp) contain two consensus sequences in separate loop structure.

Mouse proline-rich RNA-binding protein (mPrrp) is a mouse ortholog of Xenopus Prrp, which binds to a vegetal localization element (VLE) in the 3'-untranslated region (3'-UTR) of Vg1 mRNA and is expected to be involved in the transport and/or localization of Vg1 mRNA to the vegetal cortex of oocytes. In mouse testis, mPrrp protein is abundantly expressed in the nuclei of pachytene spermatocytes and round spermatids, and shifts to the cytoplasm in elongating spermatids. To gain an insight into the function of mPrrp in male germ cells, we performed in vitro RNA selection (SELEX) to determine the RNA ligand sequence of mPrrp. This analysis revealed that many of the selected clones contained both of two conserved elements, AAAUAG and GU1-3AG. RNA-binding study on deletion mutants and secondary structure analyses of the selected RNA revealed that a two-loop structure containing the conserved elements is required for high-affinity binding to mPrrp. Furthermore, we found that the target mRNAs of Xenopus Prrp contain intact AAAUAG and GU1-3AG sequences in the 3'-UTR, suggesting that these binding sequences are shared by Prrps of Xenopus and mouse.

Animals↗

Percoll gradient-centrifuged capacitated mouse sperm have increased fertilizing ability and higher contents of sulfogalactosylglycerolipid and docosahexaenoic acid-containing phosphatidylcholine compared to washed capacitated mouse sperm.

Although Percoll gradient centrifugation has been used routinely to prepare motile human sperm, its use in preparing motile mouse sperm has been limited. Here, we showed that Percoll gradient-centrifuged (PGC) capacitated mouse sperm had markedly higher fertilizing ability (sperm-zona pellucida [ZP] binding and in vitro fertilization) than washed capacitated mouse sperm. We also showed that the lipid profiles of PGC capacitated sperm and washed capacitated sperm differed significantly. The PGC sperm had much lower contents of cholesterol and phospholipids. This resulted in relative enrichment of male germ cell-specific sulfogalactosylglycerolipid (SGG), a ZP-binding ligand, in PGC capacitated sperm, and this would explain, in part, their increased ZP-binding ability compared with that of washed capacitated sperm. Analyses of phospholipid fatty acyl chains revealed that PGC capacitated sperm were enriched in phosphatidylcholine (PC) molecular species containing highly unsaturated fatty acids (HUFAs), with docosahexaenoic acid (DHA; C22: 6n-3) being the predominant HUFA (42% of total hydrocarbon chains of PC). In contrast, the level of PC-HUFAs comprising arachidonic acid (20:4n-6), docosapentaenoic acid (C22:5n-6), and DHA in washed capacitated sperm was only 27%. Having the highest unsaturation degree among all HUFAs in PC, DHA would enhance membrane fluidity to the uppermost. Therefore, membranes of PGC capacitated sperm would undergo fertilization-related fusion events at higher rates than washed capacitated sperm. These results suggested that PGC mouse sperm should be used in fertilization experiments and that SGG and DHA should be considered to be important biomarkers for sperm fertilizing ability.

Animals↗

Studies on the expression of spontaneous and induced interferons in mouse peritoneal macrophages by means of monoclonal antibodies to mouse interferons.

Monoclonal antibodies (MAbs) to mouse interferons (MuIFN) have been used to characterize the interferon-like activities spontaneously expressed in mouse peritoneal macrophages freshly explanted from normal pathogen-free mice. Injection of mice with MAbs to MuIFN-alpha or -beta resulted in a significant increase of vesicular stomatitis virus (VSV) multiplication in peritoneal macrophages. Addition of these MAbs to freshly explanted mouse macrophages accelerated the decay of the antiviral state to VSV during the 'ageing' in vitro of these macrophage cultures. Furthermore, these MAbs to MuIFN-alpha or -beta markedly inhibited the transfer of the antiviral state from freshly explanted peritoneal cells or macrophages to syngeneic macrophages 'aged' in vitro permissive for virus replication. These effects were not observed using a non-neutralizing antibody to MuIFN-alpha, nor with a MAb to MuIFN-gamma. In all experiments sheep polyclonal antibodies to MuIFN-alpha/beta were more effective than the corresponding amount of MAbs to MuIFN-alpha or -beta. A mixture of both these MAbs was more effective than either alone. Interferons produced after stimulation of peritoneal macrophages with Newcastle disease virus (NDV) and of total peritoneal cells with lipopolysaccharides (LPS) have also been characterized by means of MAbs to IFNs. The results of neutralization studies with these antibodies indicated that MuIFN-beta was the major component of peritoneal cell IFN (induced by both NDV and LPS) and MuIFN-alpha was a minor component (13 to 17%). These data indicate that both MuIFN-alpha and -beta, but not MuIFN-gamma, are spontaneously present in/on mouse peritoneal macrophages and are produced after stimulation with NDV or LPS.

Animals↗

Splice variation in mouse full-length cDNAs identified by mapping to the mouse genome.

We mapped the collection of The Institute of Physical and Chemical Research (Japan) (RIKEN) 21,076 full-length mouse cDNA clone sequences and the mouse RefSeq sequences to the recently completed draft of the mouse genome. Using this mapping, we identified 3674 mouse genes with multiple transcripts, of which 1098 have splice variants. All but 532 of 21,076 clones (97.5%) mapped to the genome assembly. Alignments of cDNA clone sequences with proteins show that much of the detected splice variation alters coding regions and affects the translated protein. We developed novel analytical techniques to classify observed splice variation and to assess the relation between splice variation and alternative transcription. This analysis indicates that an alternative choice of transcription start or polyadenylation signal frequently induces splice variation.

Alternative Splicing↗

The development of a highly informative mouse Simple Sequence Length Polymorphism (SSLP) marker set and construction of a mouse family tree using parsimony analysis.

To identify highly informative markers for a large number of commonly employed murine crosses, we selected a subset of the extant mouse simple sequence length polymorphism (SSLP) marker set for further development. Primer pairs for 314 SSLP markers were designed and typed against 54 inbred mouse strains. We designed new PCR primer sequences for the markers selected for multiplexing using the fluorescent dyes FAM, VIC, NED, and ROX. The number of informative markers for C57BL/6J x DBA/2J is 217, with an average spacing of 6.8 centiMorgans (cM). For all other pairs of strains, the mean number of informative markers per cross is 197.0 (SD 37.8) with a mean distance between markers of 6.8 cM (SD 1.1). To confirm map positions of the 224 markers in our set that are polymorphic between Mus musculus and Mus spretus, we used The Jackson Laboratory (TJL) interspecific backcross mapping panel (TJL BSS); 168 (75%) of these markers had not been previously mapped in this cross by other investigators, adding new information to this community map resource. With this large data set, we sought to reconstruct a phylogenetic history of the laboratory mouse using Wagner parsimony analysis. Our results are largely congruent with the known history of inbred mouse strains.

Alleles↗

The synthesis of specific proteins in adult mouse epidermis during phases of proliferation and differentiation induced by the tumor promoter TPA, and in basal and differentiating layers of neonatal mouse epidermis.

Mouse epidermis can be induced to undergo sequential waves of proliferation and keratinization by treatment with the tumor promoter TPA (12-O-tetradecanoyl-phorbol-13-acetate). This model system offers a unique possibility to study the synthesis of differentiation-specific proteins in the epidermis. During these studies it could be shown by sodium dodecyl sulfate-polyacrylamide gel electrophoresis that several previously undetected proteins appear in the epidermis during the phase of differentiation. These have been fractionated according to solubility in 1 M phosphate buffer, pH 7.0, or 0.1 M sodium citrate buffer, pH 2.6. Of the soluble proteins, a band of approximate molecular weight 13,500 (band 1) appears early during the differentiative phase (24 hr after treatment with TPA). Another previously undetected protein of approximate molecular weight 27,000 (band 2) appears in the soluble fraction after 48 hr, at a time when many of the typical manifestations of increased keratinization can be observed. Both of these soluble proteins, although not detectable in normal adult mouse epidermis, are shown to be present in newborn mouse epidermis, which demonstrates histologically a well-developed layer of keratinizing and cornified cells. In addition, by separation of neonatal and TPA-treated adult mouse epidermis into "basal" and "cornified" layers, it could be demonstrated that these two proteins are localized exclusively in the upper layer of the epidermis.

Animals↗

Mouse placental 57-kDa calcium-binding protein: II. Localization of mRNA in mouse and human placentae by in situ cDNA hybridization.

Using a cloned cDNA to the mouse placental calcium-binding protein (MCaBP) [Tuan and Kirwin, preceding paper], mRNA transcripts of the MCaBP have been localized in the mouse placenta by in situ cDNA-RNA hybridization. The procedure involved the use of a nonradioactive, biotinylated cDNA probe. Paraffin sections of the mouse chorioallantoic placenta were processed for in situ hybridization using a procedure modified from that of Lo [8]. The results demonstrated that MCaBP mRNA is localized specifically to the fetal trophoblast of the mouse placenta, and is expressed in a development-dependent manner. The MCaBP cDNA also hybridized strongly in situ to sections of human term placenta, giving rise to signals localized specifically to the syncytiotrophoblastic layer of the chorionic villi.

Animals↗

Interferon production and action in mouse, hamster and somatic hybrid mouse-hamster cells.

A hybrid mouse-hamster cell line was developed from a mouse cell line which produces a high titer of interferon and is sensitive to its action, and a hamster cell line which produces little interferon and is relatively insensitive to its action. Parental cell lines demonstrated complete species specificity with respect to interferon production and action. The hybrid cells produced interferon (or interferons) effective when tested on the mouse cell line and primary hamster cells; the hybrids were sensitive to the action of both mouse and hamster interferons. Hybrid cells produced ten times more hamster interferon than the parent hamster cell line and were eight times more sensitive to hamster interferon than the parent hamster cell line.

Animals↗

Biology of mouse thymic virus, a herpesvirus of mice, and the antigenic relationship to mouse cytomegalovirus.

Mouse thymic virus (TA) is a herpesvirus which produces extensive necrosis of the thymus of newborn mice 7 to 14 days after infection. Infectious virus can be recovered from the thymus for only 10 days after infection, with highest titers occurring between days 5 and 7. In mice 5 days old or less, TA infects thymus cells and produces massive necrosis. TA also infects the salivary glands and persists as a chronic infection. Newborn mice infected with TA have no detectable humoral immune response. Infected adult mice respond, and humoral antibody is detected 7 days after infection. Titers are maintained for months thereafter. Regardless of the age of the mice inoculated with TA, persistent infection was established in the salivary glands, but no evidence for thymus involvement was observed when adults were infected. TA does not cross-react serologically by immunofluorescent, complement fixation, or virus neutralization tests with mouse cytomegalovirus; however, interestingly, the epidemiology of the two herpesviruses are similar. Both mouse cytomegalovirus and TA were isolated from the same animals in populations of laboratory and wild mice. Evidence of infection with mouse cytomegalovirus and TA were most apparent by virus isolations, since humoral antibody responses are rarely observed. All strains of mice tested were susceptible to TA infection. However, in some strains maximum necrosis occurred at 7 days, compared with 10 to 14 days for other strains. The difference in age susceptibility and the target tissue of thymus in newborn mice suggests that TA is a model herpesvirus for studying the effects of viral infections on humoral and cell-mediated immunological functions.

Animals↗

Mouse immunoglobulin antibodies require complement for neutralization of mouse retroviruses.

The addition of guinea pig complement was found to enhance the neutralizing capacity of mouse antibodies directed against the endogenous ecotropic murine leukemia viruses. The same immune sera, when tested without complement, had low or negligible neutralizing capacities, regardless of whether freshly harvested, unfrozen virus was used to preserve virus infectivity. Antibodies in high titers were found in sera from NFS congenic mice carrying the mouse leukemia virus inducing locus Akv-2. These mouse antibodies were type specific and failed to neutralize either Friend or Moloney leukemia virus. The mouse serum immunoglobulin fraction containing the complement-dependent antibodies was tentatively identified as immunoglobulin M.

AKR murine leukemia virus↗

Erythroid differentiation of mouse erythroleukemia cells results in reorganization of protein-DNA complexes in the mouse beta maj globin promoter but not its distal enhancer.

Dimethyl sulfoxide (DMSO) induction of mouse erythroleukemia (MEL) cells represents a well-defined in vitro system of terminal erythroid differentiation. We have studied the molecular mechanisms of transcriptional activation of the mouse beta maj globin gene during MEL cell differentiation by analyzing nuclear factor-DNA interactions in vivo at the gene's upstream promoter and a distal enhancer, 5'HS-2. Genomic footprinting data indicate that three motifs, CAC, NF-E2/AP1, and GATA-1, of the 5'HS-2 enhancer are bound with nuclear factors in MEL cells both prior to and after DMSO induction. No obvious conformational change of these nuclear factor-DNA complexes could be detected upon terminal differentiation of MEL cells. On the other hand, DMSO induction of MEL cells leads to the formation of specific nuclear factor-DNA complexes at several transcriptional regulatory elements of the mouse beta maj globin upstream promoter. Our genomic footprinting data have interesting implications with respect to the molecular mechanisms of transcriptional regulation and chromatin change of the mouse beta maj globin gene during erythroid differentiation.

Animals↗

Plasmids containing mouse rDNA do not recombine with cellular ribosomal genes when introduced into cultured mouse cells.

We have examined the fate of plasmids containing a segment of a mouse rDNA repeat after they were introduced by transfection into cultured mouse cells. In addition to the rDNA segment, the plasmids contained the thymidine kinase gene from herpes simplex virus 1 to allow for selection of the plasmid after transfection into thymidine kinase-deficient mouse cells. Thus far, no cases of homologous recombination between transfected plasmid DNAs and host cell sequences have been documented. We reasoned that the high repetition frequency of the rRNA genes in the mouse genome (200 copies per diploid cell) might create a favorable situation for obtaining homologous recombination events between the plasmids containing rDNA and host cell rDNA sequences. The plasmids were introduced into cells in both the presence and the absence of carrier DNA and both as covalently closed circles and linear molecules. The sites of plasmid integration in the genomes of various cell lines were examined by DNA restriction digests and hybridization, molecular cloning, and nuclear fractionation. In the seven cell lines examined, there was no evidence that the plasmids had integrated into the rRNA gene clusters of the cell. Thus, the apparent absence of site-specific integration of cloned DNAs introduced into mammalian cells does not appear to be due simply to the small target presented by most host cell sequences.

Animals↗

Autonomous replicating sequences from mouse cells which can replicate in mouse cells in vivo and in vitro.

We have already reported that the cloned mouse DNA fragment (pMU65) could replicate in a simian virus 40 T antigen-dependent system in vivo and in vitro (H. Ariga, Z. Tsuchihashi, M. Naruto, and M. Yamada, Mol. Cell. Biol. 5:563-568, 1985). The plasmid p65-tk, containing the thymidine kinase (tk) gene of herpes simplex virus and the BglII-EcoRI region of pMU65 homologous to the simian virus 40 origin of DNA replication, was constructed. The p65-tk persisted episomally in tk+ transformants after the transfection of p65-tk into mouse FM3Atk- cells. The copy numbers of p65-tk in FM3Atk+ cells were 100 to 200 copies per cell. Furthermore, the p65-tk replicated semiconservatively, and the initiation of DNA replication started from the mouse DNA sequences when the replicating activity of p65-tk was tested in the in vitro DNA replication system developed from the FM3A cells. These results show that a 2.5-kilobase fragment of mouse DNA contains the autonomously replicating sequences.

Animals↗

Electrophysiology of retinal ganglion cells in the mouse: a study of a normally pigmented mouse and a congenic hypopigmentation mutant, pearl.

1. The organization of the receptive fields of retinal ganglion cells in te normal mouse was studied qualitatively in recordings from 43 single axons in the optic nerve and optic tract, and the light sensitivity was studied quantitatively in 26 of these cells by measuring incremental sensitivity. 2. The receptive fields of normal animals were elliptical, had concentric center and peripheral subdivisions, and had an antagonistic center/surround organization; the receptive-field centers ranged from 1.95 to 83 degrees in diameter, with a median of 7 degrees. 3. The incremental sensitivity to white light was measured using a criterion response of 10 extra spikes; the most sensitive dark-adapted cell required a stimulus luminance of 3.5 x 10(-3) cd/m2 to generate a criterion response. 4. The action spectrum measured at seven different wavelengths (433-619 nm) from ganglion cells in the normally pigmented mouse resembled the CIE (International Commission on Illumination, CIE 1957 (11)) relative scotopic luminous efficiency function (41) and is consistent with a curve having a peak around 500 nm. 5. On light adaptation with blue light (less than 460 nm), the sensitivity to longer wavelength stimuli increased by 0.2-0.5 log units relative to the sensitivity to the shorter wavelengths; these results are compatible with the presence of a photoreceptor sensitive to long wavelengths in the normally pigmented mouse (C57BL/6J+/+). 6. The organization of the receptive fields of 48 retinal ganglion cells from the hypopigmentation mutant pearl (C57BL/6J-pe) was also studied qualitatively; the receptive field organization was similar to that of the normally pigmented mouse. 7. In 25 cells from dark-adapted pearl mice, the incremental sensitivity to white light was, on the average, 1.6 log units less than that for normal mice. 8. The dark-adapted action spectrum of pearl mice was similar to that of normally pigmented mice. However, a shift in sensitivity to longer wavelengths did not occur on selective light adaptation with the most luminous blue light (less than 460 nm) background that we could produce. 9. We conclude that pearl is one of the mammalian genes that codes for functions that affect dark-adapted retinal sensitivity. The results of this study and past studies suggest that the pearl gene's action on light sensitivity is predominantly within the retina and before (distal to) the ganglion cells.

Adaptation, Physiological↗

Identification of the mouse beta'-COP Golgi component as a spermatocyte autoantigen in scleroderma and mapping of its gene Copb2 to mouse chromosome 9.

In an immunological screening of a mouse testicular cDNA library with a human CREST serum we isolated five overlapping cDNA clones encoding the mouse homolog of a Golgi coatomer complex protein (accession number AF043120), designated beta'-COP in bovine and p102 in humans. We generated antibodies against this protein which specifically recognize the Golgi apparatus of mouse spermatocytes. FISH analyses assigned the beta'-COP gene Copb2 to mouse Chromosome 9, region E3-F1. Our results demonstrate that CREST sera can contain antibody components against Golgi proteins as well as against nuclear proteins.

Animals↗

A functional mouse ornithine decarboxylase gene (Odc) maps to chromosome 12: further evidence of homoeology between mouse chromosome 12 and the short arm of human chromosome 2.

We have used a DNA probe specific for a functional mouse ornithine decarboxylase gene (Odc) in conjunction with a panel of Chinese hamster x mouse somatic cell hybrids to assign Odc to mouse chromosome 12. This assignment provides further evidence of genetic homoeology between a region of mouse chromosome 12 and the distal short arm of human chromosome 2.

Animals↗

Assignment of mouse Gfra1, the homologue of a new human HSCR candidate gene, to the telomeric region of mouse chromosome 19.

Glial cell line-derived neurotrophic factor (Gdnf) and its alpha receptor (Gfra1) interact with the Ret receptor triggering its tyrosine kinase activity. As Gdnf and Ret have been linked to the development of Hirschsprung disease (HSCR), it seems likely that Gfra1 could also be a susceptibility gene for HSCR. A further HSCR candidate gene is represented by the human homologue of the Dom (Dominant megacolon) mouse mutation, mapped to Chr 15, for which the gene has not yet been identified. In order to test if Gfra1 could be the Dom gene or if it represents a new possible HSCR locus we have undertaken the mapping of the mouse Gfra1. Using specific PCR primers on a somatic cell hybrid mapping panel and fluorescence in situ hybridization with an expressed sequence tag (EST) cDNA clone corresponding to the mouse Gfra1, we mapped the gene to mouse chromosome 19D2-D3, a region with known homology with human chromosome 10q24-->q26.

Animals↗