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Expression of mouse metallothionein genes in tobacco  

SciTech Connect

We have expressed a mouse metallothionein (NT) gene in tobacco under control of the cauliflower mosaic virus (CaMV) 35S promoter and a pea ribulose-1,5-bisphosphate carboxylase small subunit (rbcS) gene promoter. Seedlings in which MT gene expression is driven by the 35S promoter are resistant to toxic levels of cadmium. Mature plants carrying the 35S-MT gene accumulate less Cd in their leaves when exposed to low levels of Cd in laboratory growth conditions. Plants with the rbcS-MT construction express this gene in a light-regulated and tissue-specific manner, as expected. Moreover, the MT levels in leaves in these plants are about 20% of those seen in 35S-MT plants. These plants are currently being tested for Cd resistance. In addition, a small field evaluation of 35S-MT lines for Cd levels is being evaluated. These experiments will address the possibility of using MTs to alter Cd levels in crop species.

Maiti, I.B.; Yeargan, R.; Wagner, G.J.; Hunt, A.G. (Univ. of Kentucky, Lexington (USA))



Cloning and characterization of the metallothionein-I gene from mouse LMTK cells.  


A clone of about 14 kb containing the metallothionein MT-I gene and three repetitive sequences, was isolated from a genomic library of mouse LMTK DNA. The MT-I gene was functional. Transfected cells became cadmium resistant. Two of the three repetitive sequences were moderately repetitive while the other was closely related to the R family. PMID:2824133

Brzezinski, R; Smorawinska, M; Vézina, G; Thibodeau, J; Thirion, J P



New mouse somatic cell mutants resistant to cadmium affected in the expression of their metallothionein genes.  


Fluctuation tests à la Luria and Delbruck were performed with mouse LMTK cells, and the results indicate that the appearance of variants resistant to cadmium is due to random spontaneous mutations and not to epigenetic events. The rate of spontaneous mutations leading to cadmium resistance was calculated to be 0.92 x 10(-6) per cell per generation. This rate increased 14-fold on treatment with ethyl methane sulfonate. Several stable mutant cell lines resistant to cadmium were selected and characterized with respect to metallothionein (MT) induction. Based on the copy number of mt+ genes and the levels of MT proteins and mRNA, the mutants could be divided into two classes, A and B. Although group A mutants have the same number of mt1+ and mt2+ genes as wild-type cells, upon induction with cadmium, the amount of MT proteins and mRNA in the mutants are greatly increased over wild-type levels. This observation strongly suggests a mutation that regulates MT gene transcription in these cells. In group B mutants, the mt+ genes are amplified about three- to fourfold, and their MT protein and mRNA basal levels are, as expected, much higher than in the wild-type cells, under uninduced and induced conditions. PMID:2303527

Chopra, A; Thibodeau, J; Tam, Y C; Marengo, C; Mbikay, M; Thirion, J P



Immunological characterization of metallothioneins in mouse LMTK cells and in a variant resistant to cadmium  

SciTech Connect

A cadmium-resistant variant isolated from mouse fibroblast LMTK cells can grow in the presence of 40 Cd/sup 2 +/. This variant retained its properties in the absence of selecting agent. Induction of metallothionein was measured in cell extracts by radioimmunoassay. The maximum amount of metallothioneins in the cells was reached after 36 hours. The cadmium resistant variant produced two times more metallothionein than the wild-type when exposed to 10-20 2 +/. By Ouchterlony double diffusion, the metallothioneins from cultured cells formed a line of partial identity with the mouse liver serotype and a line of complete identity with one of the two mouse kidney serotypes. These observations raise the possibility of a tissue-specific expression of metallothionein genes.

Maiti; I.; Mbikay, M.; Marengo, C.; Thirion, J.-P.



Immunological characterization of metallothioneins in mouse LMTK cells and in a variant resistant to cadmium.  


A cadmium-resistant variant isolated from mouse fibroblast LMTK cells can grow in the presence of 40 muM Cd2+. This variant retained its properties in the absence of selecting agent. Induction of metallothionein was measured in cell extracts by radioimmunoassay. The maximum amount of metallothioneins in the cells was reached after 36 hours. The cadmium resistant variant produced two times more metallothionein than the wild-type when exposed to 10-20 muM Cd2+. By Ouchterlony double diffusion, the metallothioneins from cultured cells formed a line of partial identity with the mouse liver serotype and a line of complete identity with one of the two mouse kidney serotypes. These observations raise the possibility of a tissue-specific expression of metallothionein genes. PMID:6809772

Maiti, I; Mbikay, M; Marengo, C; Thirion, J P



Human metallothionein genes are clustered on chromosome 16  

SciTech Connect

The metallothioneins are a family of heavy-metal binding proteins of low molecular weight. They function in the regulation of trace metal metabolism and in the protection against toxic heavy metal ions. In man, the metallothioneins are encoded by at least 10-12 genes separated into two groups, MT-I and MT-II. To understand the genomic organization of these genes and their involvement in hereditary disorders of trace metal metabolism, we have determined their chromosomal location. Using human-mouse cell hybrids and hybridization probes derived from cloned and functional human MT1 and MT2 genes, we show that the functional human genes are clustered on human chromosome 16. Analysis of RNA from somatic cell hybrids indicated that hybrids that contained human chromosome 16 expressed both human MT1 and MT2 mRNA, and this expression is regulated by both heavy metal ions and glucocorticoid hormones. 27 references, 4 figures, 2 tables.

Karin, M.; Eddy, R.L.; Henry, W.M.; Haley, L.L.; Byers, M.G.; Shows, T.B.



Exercise induces metallothioneins in mouse spinal cord.  


Regular exercise has displayed a beneficial effect on the progression of amyotrophic lateral sclerosis (ALS). However, the mechanism is poorly understood. We here present that regular exercise on a treadmill induces metallothioneins (MTs: MT-1, MT-2, and MT-3) in spinal cords of mice. As MTs are strong scavengers of reactive oxygen species and have some neurotrophic activities, exercise may have some beneficial effects on spinal motor neurons in patients with ALS owing to the induction of MTs. The running exercise on a treadmill for 30 min/day increased the mRNA expression levels of MT-1, MT-2, and MT-3 up to 193%, 298%, and 196%, respectively, of the control value 12 h after the start of exercise. After two weeks of daily exercise, Western blotting of the MTs proteins showed that the expression levels of MT-1/2 and MT-3 reached 173% and 146%, respectively, compared with those in sedentary mice. Running exercise on a treadmill for 2 weeks led to the gradual accumulation of MT proteins in the spinal cords of the mice. In addition, MT-1/2 and MT-3 immunoreactivities were enhanced in astrocytes particularly in the gray matter of the spinal cord. We revealed that regular exercise induced transient increases in the expression levels of MT mRNAs and resulted in accumulation of MT proteins in the spinal cords of the normal mice. PMID:19490933

Hashimoto, K; Hayashi, Y; Inuzuka, T; Hozumi, I



Drosophila melanogaster metallothionein genes: Selection for duplications  

SciTech Connect

The metallothionein genes of Drosophila melanogaster, Mtn and Mto, may play an important role in heavy-metal detoxification. In order to investigate the possibility of increased selection for duplications of these genes in natural populations exposed to high levels of heavy metals, I compared the frequencies of such duplications among flies collected from metal-contaminated and non-contaminated orchards in Pennsylvania, Tennessee, and Georgia. Contaminated of collection sites and of local flies was confirmed by atomic absorption spectrosphotometry. Six-nucleotide-recognizing restriction enzyme analysis was used to screen 1666 wild third chromosomes for Mtn duplications. A subset (327) of these lines was screened for Mto duplications: none were found. Cadmium tolerance test performed on F{sub 2} progeny of wild females failed to detect a difference in tolerance levels between flies from contaminated orchards and flies from control orchards. Estimates of sequence diversity among a subsample (92) of the chromosomes used in the duplication survey, including all 27 Mtn duplication chromosomes, were obtained using four-nucleotide-recognizing restriction enzyme analysis.

Lange, B.W.



Metallothionein gene expression in renal cell carcinoma  

PubMed Central

Introduction: Metallothioneins (MTs) are a group of low-molecular weight, cysteine-rich proteins. In general, MT is known to modulate three fundamental processes: (1) the release of gaseous mediators such as hydroxyl radical or nitric oxide, (2) apoptosis and (3) the binding and exchange of heavy metals such as zinc, cadmium or copper. Previous studies have shown a positive correlation between the expression of MT with invasion, metastasis and poor prognosis in various cancers. Most of the previous studies primarily used immunohistochemistry to analyze localization of MT in renal cell carcinoma (RCC). No information is available on the gene expression of MT2A isoform in different types and grades of RCC. Materials and Methods: In the present study, total RNA was isolated from 38 histopathologically confirmed cases of RCC of different types and grades. Corresponding adjacent normal renal parenchyma was taken as control. Real-time polymerase chain reaction (RT PCR) analysis was done for the MT2A gene expression using ?-actin as an internal control. All statistical calculations were performed using SPSS software. Results: The MT2A gene expression was found to be significantly increased (P < 0.01) in clear cell RCC in comparison with the adjacent normal renal parenchyma. The expression of MT2A was two to three-fold higher in sarcomatoid RCC, whereas there was no change in papillary and collecting duct RCC. MT2A gene expression was significantly higher in lower grade (grades I and II, P < 0.05), while no change was observed in high-grade tumor (grade III and IV) in comparison to adjacent normal renal tissue. Conclusion: The first report of the expression of MT2A in different types and grades of RCC and also these data further support the role of MT2A in tumorigenesis. PMID:25097305

Pal, Deeksha; Sharma, Ujjawal; Singh, Shrawan Kumar; Mandal, Arup Kumar; Prasad, Rajendra



A novel metallothionein gene from a mangrove plant Kandelia candel.  


A new metallothionein (MT) gene was cloned from Kandelia candel, a mangrove plant with constitutional tolerance to heavy metals, by rapid amplification of cDNA ends and named KMT, which is composed of two exons and one intron. The full length of KMT cDNA was 728 bp including 121 bp 5' noncoding domain, 240 bp open reading frame and 384 bp 3' termination. The coding region of KMT represented a putative 79 amino acid protein with a molecular weight of 7.75 kDa. At each of the amino- and carboxy-terminal of the putative protein, cysteine residues were arranged in Cys-Cys, Cys-X-Cys and Cys-X-X-Cys, indicating that the putative protein was a novel type 2 MT. Sequence and homology analysis showed the KMT protein sequence shared more than 60 % homology with other plant type 2 MT-like protein genes. At amino acid level, the KMT was shown homology with the MT of Quercus suber (83 %), of Ricinus communis (81 %) and of Arabidopsis thaliana (64 %). Function studies using protease-deficient Escherichia coli strain BL21 Star ™(DE3) confirmed the functional nature of this KMT gene in sequestering both essential (Zn) and non-essential metals (Cd and Hg) and the E. coli BL21 with KMT can live in 1,000 ?mol/L Zn, 120 ?mol/L Hg, and 2,000 ?mol/L Cd. The information could provide more details of the causative molecular and biochemical mechanisms (including heavy metal sequestration) of the KMT in K. candel or a scientific basis for marine heavy-metal environment remediation with K. candel. This study also provides a great significance of protecting mangrove species and mangrove ecosystem. PMID:22711547

Zhang, Feng-Qin; Wang, You-Shao; Sun, Cui-Ci; Lou, Zhi-Ping; Dong, Jun-De



Characterization of DNA sequences through which cadmium and glucocorticoid hormones induce human metallothionein-IIA gene  

Microsoft Academic Search

Deletion experiments have defined two stretches of DNA (genetic elements), lying close to the promoter for a human gene for metallothionein, that separately mediate the induction of the gene by heavy metal ions, particularly cadmium, and by glucocorticoid hormones. The element responsible for induction by cadmium is duplicated, yet a single copy is fully functional; the element responsible for induction

Michael Karin; Alois Haslinger; Heidi Holtgreve; Robert I. Richards; Paul Krauter; Hannes M. Westphal; Miguel Beato



Mouse Genetics: Determining gene function  

E-print Network

Mouse Genetics: Determining gene function An International Centre for Mouse Genetics Mammalian Genetics Unit #12;Determining gene function · Mutagenesis approaches · Gene-driven, phenotype for Mouse Genetics Mammalian Genetics Unit #12;An International Centre for Mouse Genetics Mammalian Genetics

Goldschmidt, Christina


Metallothionein gene expression differs in earthworm populations with different exposure history.  


Metals are persistent pollutants in soils that can harm soil organisms and decrease species diversity. Animals can cope with metal contamination with the help of metallothioneins, small metal-binding proteins involved in homeostasis and detoxification of metals. We studied the expression of metallothionein with qPCR in a small, epigeic earthworm, Dendrobaena octaedra. We compared expression patterns and metal body content in earthworms collected from two sites with different metal contamination histories: Harjavalta, contaminated by a Cu-Ni smelter operational for over 50 years, and Jyväskylä, an uncontaminated site. Earthworms from both sites were also experimentally exposed to different concentrations of Cu (control, 50, 100 or 200 mg/kg) or Zn (control, 75, 150 or 300 mg/kg) for 7, 14 or 28 days to determine if there is a time related dose-response in gene expression. Population comparison showed that metallothionein expression was higher in earthworms from the contaminated site. In the exposure experiment, exposure time affected expression, but only in the earthworms from the uncontaminated site, suggesting that there is a delay in the metallothionein response of earthworms in this population. In contrast, earthworms from the contaminated site showed higher and constant levels of metallothionein expression at all exposure concentrations and durations. The constant metallothionein expression in earthworms from the contaminated site suggests that inducibility of metallothionein response could be lost in earthworms with metal exposure history. Adaptation of D. octaedra to metal exposure could explain the differences between the populations and explain the persistence of this species in contaminated forest soils. PMID:25179588

Mustonen, M; Haimi, J; Väisänen, A; Knott, K E



Gene Expression of Metallothioneins in Barley during Senescence and Heavy Metal Treatment  

Microsoft Academic Search

Despite their ubiquitous distribution, the exact functions of metallothioneins (MTs) are still not known. We analyzed the expression of four novel barley (Hordeum vulgare L.) genes cod- ing for MTs, comparing two different situations: (i) leaf senescence, and (ii) heavy metal stress. Physiological analysis of chlorophyll content and photosystem II effi ciency revealed simi- lar stress response during natural leaf

Jan Heise; Sebastian Krejci; Jürgen Miersch; Gerd-Joachim Krauss; Klaus Humbeck



Influence of arbuscular mycorrhiza on the growth and cadmium uptake of tobacco with inserted metallothionein gene  

Microsoft Academic Search

The effect of arbuscular mycorrhiza (AM) on the growth and cadmium (Cd) uptake of transgenic tobacco with increased ability to accumulate Cd was assessed. The transgenic tobacco bearing yeast metallothionein gene combined with a polyhistidine cluster was compared to non-transgenic tobacco in two pot experiments with different substrates – soil and river sand – amended or unamended with Cd.The development

M. Janoušková; D. Pavlíková; T. Macek; M. Vosátka



Copper accumulation and compartmentalization in mouse fibroblast lacking metallothionein and copper chaperone, Atox1  

SciTech Connect

Copper (Cu) is the active center of some enzymes because of its redox-active property, although that property could have harmful effects. Because of this, cells have strict regulation/detoxification systems for this metal. In this study, multi-disciplinary approaches, such as speciation and elemental imaging of Cu, were applied to reveal the detoxification mechanisms for Cu in cells bearing a defect in Cu-regulating genes. Although Cu concentration in metallothionein (MT)-knockout cells was increased by the knockdown of the Cu chaperone, Atox1, the concentrations of the Cu influx pump, Ctr1, and another Cu chaperone, Ccs, were paradoxically increased; namely, the cells responded to the Cu deficiency despite the fact that cellular Cu concentration was actually increased. Cu imaging showed that the elevated Cu was compartmentalized in cytoplasmic vesicles. Together, the results point to the novel roles of MT and cytoplasmic vesicles in the detoxification of Cu in mammalian cells.

Miyayama, Takamitsu [Graduate School of Pharmaceutical Sciences, Chiba University, Chuo, Chiba 260-8675 (Japan); Laboratory of Chemical Toxicology and Environmental Health, Showa Pharmaceutical University, Machida, Tokyo 194-8543 (Japan); Suzuki, Kazuo T. [Graduate School of Pharmaceutical Sciences, Chiba University, Chuo, Chiba 260-8675 (Japan); Ogra, Yasumitsu [Graduate School of Pharmaceutical Sciences, Chiba University, Chuo, Chiba 260-8675 (Japan); Laboratory of Chemical Toxicology and Environmental Health, Showa Pharmaceutical University, Machida, Tokyo 194-8543 (Japan)], E-mail:



Efficient expression of truncated recombinant cadmium-metallothionein gene of a ciliate, Tetrahymena tropicalis lahorensis in Escherichia coli.  


Truncated recombinant metallothionein GST-fusion protein has been successfully expressed in Escherichia coli. The previously identified novel Cd-inducible metallothionein (TMCd1) gene from the locally isolated ciliate, Tetrahymena tropicalis lahorensis, was inserted into a pET-41a vector, in frame with a sequence encoding an N-terminal glutathione-S-transferase (GST) tail. Truncated recombinant GST fusion protein has been purified by affinity column chromatography using glutathione sepharose. After enzymatic cleavage of GST tail with enterokinase, the truncated TMCd1 MT shows molecular weight of 11.5 kDa, corresponding to the expected value. This is the first successful report of expression of cadmium metallothionein gene of a ciliate, T. t. lahorensis, reported from this part of the world, in E. coli. This study will further help in characterization of metallothionein protein of this ciliate. PMID:24197693

Shuja, Rukhsana Nighat; Taimuri, Shuja Uddin Ahmad; Shakoori, Farah Rauf; Shakoori, Abdul Rauf



Expression response of duplicated metallothionein 3 gene to copper stress in Silene vulgaris ecotypes.  


Metallothioneins (MTs) were identified as important players in metal metabolism. MT3 gene presents a key metallothionein controlling copper homeostasis in plants. We have selected one cupricolous and one non-cupricolous ecotype to isolate and analyse the MT3 gene in Silene vulgaris. For expression data comparison, we have also included other metal-tolerant ecotypes. Based on a S. vulgaris BAC library screening, we have identified and sequenced a genomic clone containing MT3 gene (SvMT3). We found that SvMT3 gene has been locally duplicated in a tandem arrangement. Expression analysis and complementation studies using yeast mutants showed that both copies of the SvMT3 gene were functional. Moreover, we examined the expression of MT3 gene(s) in selected ecotypes under different copper treatments to show the tissue-specific expression response to copper stress. We demonstrated that higher copper concentrations specifically affected MT3 expression among ecotypes. Our analysis shows that MT3a has similar expression pattern in cupricolous ecotypes while MT3b has common expression features shared by all metallophyte S. vulgaris ecotypes. Our data indicate that down-regulation of MT3b root expression in higher copper concentrations is associated with copper stress. We propose that there might be a specific regulation of SvMT3s transcription depending on the type of heavy metal tolerance. PMID:24748066

Nevrtalova, Eva; Baloun, Jiri; Hudzieczek, Vojtech; Cegan, Radim; Vyskot, Boris; Dolezel, Jaroslav; Safar, Jan; Milde, David; Hobza, Roman



Induction of metallothionein in mouse cerebellum and cerebrum with low-dose thimerosal injection.  


Thimerosal, an ethyl mercury compound, is used worldwide as a vaccine preservative. We previously observed that the mercury concentration in mouse brains did not increase with the clinical dose of thimerosal injection, but the concentration increased in the brain after the injection of thimerosal with lipopolysaccharide, even if a low dose of thimerosal was administered. Thimerosal may penetrate the brain, but is undetectable when a clinical dose of thimerosal is injected; therefore, the induction of metallothionein (MT) messenger RNA (mRNA) and protein was observed in the cerebellum and cerebrum of mice after thimerosal injection, as MT is an inducible protein. MT-1 mRNA was expressed at 6 and 9 h in both the cerebrum and cerebellum, but MT-1 mRNA expression in the cerebellum was three times higher than that in the cerebrum after the injection of 12 microg/kg thimerosal. MT-2 mRNA was not expressed until 24 h in both organs. MT-3 mRNA was expressed in the cerebellum from 6 to 15 h after the injection, but not in the cerebrum until 24 h. MT-1 and MT-3 mRNAs were expressed in the cerebellum in a dose-dependent manner. Furthermore, MT-1 protein was detected from 6 to 72 h in the cerebellum after 12 microg/kg of thimerosal was injected and peaked at 10 h. MT-2 was detected in the cerebellum only at 10 h. In the cerebrum, little MT-1 protein was detected at 10 and 24 h, and there were no peaks of MT-2 protein in the cerebrum. In conclusion, MT-1 and MT-3 mRNAs but not MT-2 mRNA are easily expressed in the cerebellum rather than in the cerebrum by the injection of low-dose thimerosal. It is thought that the cerebellum is a sensitive organ against thimerosal. As a result of the present findings, in combination with the brain pathology observed in patients diagnosed with autism, the present study helps to support the possible biological plausibility for how low-dose exposure to mercury from thimerosal-containing vaccines may be associated with autism. PMID:19357975

Minami, Takeshi; Miyata, Eriko; Sakamoto, Yamato; Yamazaki, Hideo; Ichida, Seiji




EPA Science Inventory

Metallothionein is a cysteine rich, low molecular weight, metal binding protein. Basal levels of endogenous metallothioneins (MT) have been reported in all eucaryotes. MT has been shown to play an essential role in regulating physiological requirements of essential metals such a...


Occurrence of metallothionein gene smtA in synechococcus Tx-20 and other blue-green algae  

SciTech Connect

Blue-green algae are often abundant at Zn- and Cd-contaminated sites. In order to understand the mechanisms associated with Zn- and Cd-tolerance, we have isolated a metallothionein gene, designated smtA, in Synechococcus Tx-20 (- Pcc 6301 - Anacystis nidulans), a strain apparently obtained from an unpolluted site. The gene was cloned and sequenced, and its expression investigated in a range of heavy-metal-tolerant strains of the same organism obtained by stepwise adaptation. The polymerase chain reaction was used to probe for the possible presence of the homologous gene in a range of other strains (especially Synechococcus) isolated from sites without and with heavy metal contamination.

Robinson, N.J.; Gupta, A.; Huckle, J.W.; Jackson, P.; Whitton, B.A. (Univ. of Durham (England))



Transcription patterns of genes encoding four metallothionein homologs in Daphnia pulex exposed to copper and cadmium are time- and homolog- dependent  

PubMed Central

Metallothioneins are proteins that play an essential role in metal homeostasis and detoxification in nearly all organisms studied to date. Yet discrepancies between outcomes of chronic and acute exposure experiments hamper the understanding of the regulatory mechanisms of their isoforms following metal exposure. Here, we investigated transcriptional differences among four identified homologs (mt1–mt4) in Daphnia pulex exposed across time to copper and cadmium relative to a control. Transcriptional upregulation of mt1 and mt3 was detected on day four following exposure to cadmium, whereas that of mt2 and mt4 was detected on day two and day eight following exposure to copper. These results confirm temporal and metal-specific differences in the transcriptional induction of genes encoding metallothionein homologs upon metal exposure which should be considered in ecotoxicological monitoring programs of metal-contaminated water bodies. Indeed, the mRNA expression patterns observed here illustrate the complex regulatory system associated with metallothioneins, as these patterns are not only dependent on the metal, but also on exposure time and the homolog studied. Further phylogenetic analysis and analysis of regulatory elements in upstream promoter regions revealed a high degree of similarity between metallothionein genes of Daphnia pulex and Daphnia magna, a species belonging to the same genus. These findings, combined with a limited amount of available expression data for D. magna metallothionein genes, tentatively suggest a potential generalization of the metallothionein response system between these Daphnia species. PMID:24113165

Asselman, Jana; Shaw, Joseph R.; Glaholt, Stephen P.; Colbourne, John K.; De Schamphelaere, Karel AC.



Structure of an ectodermally expressed sea urchin metallothionein gene and characterization of its metal-responsive region.  

PubMed Central

The metallothionein-A gene in the metallothionein gene family of the sea urchin Strongylocentrotus purpuratus (SpMTA gene) was sequenced and found to contain three coding exons plus a 3' entirely noncoding exon. Putative alpha and beta MT domains were encoded, by its exons 2 and 3, respectively, in reverse of the order in vertebrate metallothionein genes. The SpMTA promoter was characterized through the expression of recombinant constructs containing various portions of the proximal 678-base-pair (bp) 5'-flanking region of the SpMTA gene. Zygotes injected with constructs were cultured to the blastula stage in the presence of a heavy-metal chelator and then incubated in the presence or absence of cadmium. The longest constructs were expressed only when heavy-metal ion was present. Two putative metal-responsive elements (MREs a and b) within 240 bp of the transcription start site resembled mammalian MREs in their critical 8-bp cores (TGCRCNCS) and in their locations relative to each other and to the TATA box. Elimination of activity by site-specific mutations in MREs a and b, separately or in both, identified them as metal regulatory elements. Thus, MRE recognition in this invertebrate resembles that in vertebrates. Upstream sites with single-mismatched MREs neither acted as MREs nor amplified the activity of MREs a and b. The SpMTA, Spec1, and CyIIIa actin genes, which have the same ectodermal specificity, have common DNA elements at relatively similar locations in their promoter regions; however, these elements are insufficient in themselves to promote gene expression. Images PMID:2586524

Harlow, P; Watkins, E; Thornton, R D; Nemer, M



The Mouse Gene Expression Database (GXD)  

Microsoft Academic Search

The Gene Expression Database (GXD) is a community resource of gene expression information for the laboratory mouse. By combining the different types of expression data, GXD aims to provide increasingly complete information about the expression profiles of genes in different mouse strains and mutants, thus enabling valuable insights into the molecular networks that underlie normal development and disease. GXD is

Martin Ringwald; Janan T. Eppig; Dale A. Begley; John P. Corradi; Ingeborg J. Mccright; Terry F. Hayamizu; David P. Hill; James A. Kadin; Joel E. Richardson



Gene expression variation between mouse inbred strains  

Microsoft Academic Search

BACKGROUND: In this study, we investigated the effect of genetic background on expression profiles. We analysed the transcriptome of mouse hindlimb muscle of five frequently used mouse inbred strains using spotted oligonucleotide microarrays. RESULTS: Through ANOVA analysis with a false discovery rate of 10%, we show that 1.4% of the analysed genes is significantly differentially expressed between these mouse strains.

Rolf Turk; Peter AC't Hoen; Ellen Sterrenburg; Renée X de Menezes; Emile J de Meijer; Judith M Boer; Gert-Jan B van Ommen; Johan T den Dunnen



Structure, organization, and regulation of human metallothionein IF gene: differential and cell-type-specific expression in response to heavy metals and glucocorticoids.  


We describe a human genomic clone containing the metallothionein (MT) IF and MT IG genes. Southern blot analysis and partial DNA sequence determinations show that these genes are organized in a head-to-head fashion and are located approximately 7.0 kilobases apart from each other. Sequence analysis shows that the MT IF gene contains three exons separated by two introns. All of the intron-exon junctions are defined by the GT-AG rule. The 5' flanking region shows the presence of a duplicated metal regulatory element (TGCGC CCGGCCC) important in heavy-metal induction of this gene and a sequence for its basal level expression (GCGGGGCGGGTGCAAAG). The 5' flanking region is also highly G + C rich (approximately 75%) and contains several GC boxes (GGGCGG), probably important in the binding of transcription factors. The TATAA box and the AATAAA sequence are represented by their variants, the TATCAA box and the AATTAA sequence, respectively. This gene is functional and inducible by heavy metals but not by dexamethasone in mouse LMTK- cells after its transfer on a plasmid containing the herpes simplex virus thymidine kinase gene. Further studies on various human cell lines show that this gene is not expressed in a splenic lymphoblastoid cell line (WI-L2) but is expressed in two hepatoma cell lines (Hep 3B2 and Hep G2) in response to cadmium, zinc, and copper. Dexamethasone appears to have no significant effect on its expression. The studies suggest that the MT IF gene shows cell-type-specific expression and is differentially regulated by heavy metals and glucocorticoids. PMID:3023827

Varshney, U; Jahroudi, N; Foster, R; Gedamu, L



Zinc rescue of Akt2 gene deletion-linked murine cardiac dysfunction and pathological changes is metallothionein-dependent.  


We have demonstrated that zinc supplementation provides cardiac protection from diabetes in mice, but its underlying mechanism remains unclear. Since zinc mimics the function of insulin, it may provide benefit to the heart via stimulating Akt-mediated glucose metabolism. Akt2 plays an important role in cardiac glucose metabolism and mice with Akt2 gene deletion (Akt2-KO) exhibit a type 2 diabetes phenotype; therefore, we assumed that no cardiac protection by zinc supplementation from diabetes would be observed in Akt2-KO mice. Surprisingly, despite Akt2 gene deletion, zinc supplementation provided protection against cardiac dysfunction and other pathological changes in Akt2-KO mice, which were accompanied by significant decreases in Akt and GSK-3? phosphorylation. Correspondingly, glycogen synthase phosphorylation and hexokinase II and PGC-1? expression, all involved in the regulation of glucose metabolism, were significantly altered in diabetic hearts, along with a significantly increased expression of Akt negative regulators: PTEN, PTP1B, and TRB3. All these molecular, pathological, and functional changes were significantly prevented by 3-month zinc supplementation. Furthermore, the stimulation of Akt-mediated glucose metabolic kinases or enzymes by zinc treatment was metallothionein-dependent since it could not be observed in metallothionein-knockout mice. These results suggest that zinc preserves cardiac function and structure in Akt2-KO mice presumably due to its insulin mimetic effect on cardiac glucose-metabolism. The cardioprotective effects of zinc are metallothionein-dependent. This is very important since zinc supplementation may be required for patients with Akt2 gene deficiency or insulin resistance. PMID:24819347

Sun, Weixia; Miao, Xiao; Zhou, Shanshan; Zhang, Li; Epstein, Paul N; Mellen, Nicholas; Zheng, Yang; Fu, Yaowen; Wang, Yuehui; Cai, Lu



Overexpression of vasopressin in the rat transgenic for the metallothionein-vasopressin fusion gene.  


Arginine vasopressin (AVP) is a major antidiuretic hormone, the overproduction of which causes diluting hyponatremia in humans and is called the syndrome of inappropriate antidiuresis (SIAD). To study physiological changes resulting from AVP overproduction and to develop an animal model of hyponatremia, the human AVP gene was expressed under the control of the metallothionein promoter in transgenic (Tg) rats. Analyses of AVP immunoreactivity (irAVP) in the tissues revealed that the transgene is expressed mainly in the central nervous system. Gel filtration showed that irAVP in the brain and plasma was properly processed AVP. AVP purified from the brains of both Tg and control rats also exerted equal bioactivity to generate cAMP in LLC-PK1 cells. The founder rats did not show any physical or anatomical abnormalities. Under basal conditions, Tg rats had high plasma AVP levels (Tg 13.8 +/- 2.5 pg/ml; control 2.7 +/- 1.2 pg/ml; n=6 in both groups; means +/- S.E.M.), decreased urine volume, and normal plasma [Na(+)]. Hypertonic saline injected i.p. did not affect AVP secretion in Tg rats. In response to a zinc-supplemented liquid diet, plasma AVP decreased in control rats, but increased in Tg rats (Tg 32.7 +/- 2.7 pg/ml; control 1.0+/-0.1 pg/ml; n=6), resulting in hyponatremia (Tg 135.2 +/- 2.5 mEq/l; control 140.8 +/- 0.4 mEq/l; n=6). To our knowledge, this is the first transgenic animal to show diluting hyponatremia. This transgenic rat may therefore provide a useful model in which to investigate various physiological alterations resulting from the oversecretion of AVP which involve SIAD, stress response, behavior, and blood pressure. PMID:11927382

Nagasaki, H; Yokoi, H; Arima, H; Hirabayashi, M; Ishizaki, S; Tachikawa, K; Murase, T; Miura, Y; Oiso, Y



Molecular Evolution of the Metallothionein Gene Mtn in the Melanogaster Species Group: Results from Drosophila Ananassae  

PubMed Central

Three distinctly different alleles of the metallothionein gene Mtn have been identified in natural Drosophila melanogaster populations: Mtn(.3), Mtn(1), and Dp(Mtn(1)), where the latter designates a tandem duplication of Mtn(1). In Drosophila simulans, only Mtn(.3)-type alleles have been found. It has been suggested that Mtn(.3) is the ancestral allele and demonstrated that a presumed two-step transition from Mtn(.3) to Mtn(1) to Dp(Mtn(1)) is accompanied by an approximate 5-fold increase in RNA levels. We analyzed the evolutionary genetics of the Mtn locus of Drosophila ananassae, a distant relative of D. melanogaster and D. simulans within the melanogaster species group. The Mtn gene of D. ananassae is most similar to Mtn(.3). (i) it is identical with Mtn(.3) at the amino acid level, but differs from Mtn(1) in its terminal codon; (ii) its 3' UTR contains a characteristic extra DNA segment of about 50 bp which is present in Mtn(.3), but lacking in Mtn(1); (iii) duplications of Mtn were not found in a worldwide sample of 110 wild D. ananassae chromosomes. However, the intron of the Mtn gene in D. ananassae is only 69 bp long, whereas the length of the Mtn(.3) and Mtn(1) introns is 265 bp; and it lacks a polypyrimidine stretch upstream of the 3' splice site in contrast to the much greater pyrimidine-richness found in the Mtn(.3) and Mtn(1) introns. A short intron (67 bp) was also identified in a D. pseudoobscura Mtn allele, suggesting that the short intron is the ancestral form and that the transition from the short to the long intron occurred within the melanogaster species group. We discuss the significance of this observation with regard to the recently proposed classification of D. melanogaster introns into two groups: short introns (<90 bp) which tend to lack polypyrimidine stretches, and longer ones which have strong 3' splice signals similar to mammalian introns. A database search revealed that this length dimorphism is an evolutionarily conserved feature of Drosophila introns; transitions from one size class to the other appear to be rare between closely related species (e.g., within the melanogaster subgroup). PMID:8001781

Stephan, W.; Rodriguez, V. S.; Zhou, B.; Parsch, J.



Two Metallothionein Genes in Oxya chinensis: Molecular Characteristics, Expression Patterns and Roles in Heavy Metal Stress  

PubMed Central

Metallothioneins (MTs) are small, cysteine-rich, heavy metal-binding proteins involved in metal homeostasis and detoxification in living organisms. In the present study, we cloned two MT genes (OcMT1 and OcMT2) from Oxya chinensis, analyzed the expression patterns of the OcMT transcripts in different tissues and at varying developmental stages using real-time quantitative PCR (RT-qPCR), evaluated the functions of these two MTs using RNAi and recombinant proteins in an E. coli expression system. The full-length cDNAs of OcMT1 and OcMT2 encoded 40 and 64 amino acid residues, respectively. We found Cys-Cys, Cys-X-Cys and Cys-X-Y-Z-Cys motifs in OcMT1 and OcMT2. These motifs might serve as primary chelating sites, as in other organisms. These characteristics suggest that OcMT1 and OcMT2 may be involved in heavy metal detoxification by capturing the metals. Two OcMT were expressed at all developmental stages, and the highest levels were found in the eggs. Both transcripts were expressed in all eleven tissues examined, with the highest levels observed in the brain and optic lobes, followed by the fat body. The expression of OcMT2 was also relatively high in the ovaries. The functions of OcMT1 and OcMT2 were explored using RNA interference (RNAi) and different concentrations and treatment times for the three heavy metals. Our results indicated that mortality increased significantly from 8.5% to 16.7%, and this increase was both time- and dose-dependent. To evaluate the abilities of these two MT proteins to confer heavy metal tolerance to E. coli, the bacterial cells were transformed with pET-28a plasmids containing the OcMT genes. The optical densities of both the MT-expressing and control cells decreased with increasing concentrations of CdCl2. Nevertheless, the survival rates of the MT-overexpressing cells were higher than those of the controls. Our results suggest that these two genes play important roles in heavy metal detoxification in O. chinensis. PMID:25391131

Liu, Yaoming; Wu, Haihua; Kou, Lihua; Liu, Xiaojian; Zhang, Jianzhen; Guo, Yaping; Ma, Enbo



Connectionist Approaches for Predicting Mouse Gene Function from Gene Expression  

E-print Network

Therapy. Identifying gene function based on gene expression data is much easier in prokaryotes than ways, especially in Gene Therapy [5]. Identifying gene function in prokaryotes is much easier thanConnectionist Approaches for Predicting Mouse Gene Function from Gene Expression Emad Andrews

Bonner, Anthony


Intracellular sequestration of zinc, cadmium and silver in Hebeloma mesophaeum and characterization of its metallothionein genes.  


Sequestration of intracellular heavy metals in eukaryotes involves compartmentalization and binding with cytosolic, cysteine-rich metallothionein (MT) peptides. We examined the roles of these processes in handling of zinc (Zn), cadmium (Cd) and silver (Ag) in sporocarps and a metal-exposed extraradical mycelium of Hebeloma mesophaeum, the Zn-accumulating ectomycorrhizal (EM) species frequently associated with metal disturbed sites. Size exclusion chromatography revealed that the majority of Zn and Cd in the sporocarps and mycelium was contained in a low molecular mass fraction attributable to compartmentalized metal. The staining of hyphal cells with the Zn-specific Zinquin and Cd-specific Leadmium fluorescent tracers labeled Zn and Cd in small, punctuated vesicles and vacuoles, respectively. By contrast, the sporocarp and mycelium Ag was associated with cysteine-rich, 5-kDa peptides. The peptides of the same size were also identified in minor Zn and Cd complexes from the metal-exposed mycelium. We have further isolated and characterized HmMT1, HmMT2 and HmMT3 genes coding for different 5-kDa MTs of H. mesophaeum collected at a lead smelter site. Heterologous complementation assays in metal-sensitive yeast mutants indicated that HmMTs encode functional, metal-specific peptides: only HmMT1 was able to complement sensitivity to Zn; HmMT1 conferred higher tolerance to Cd and Cu than HmMT2 or HmMT3; and both HmMT2 and HmMT3, but not HmMT1, conferred increased tolerance to Ag. The presence of HmMT1 and HmMT3, but not HmMT2, was also confirmed in a H. mesophaeum isolate from an unpolluted site. Gene expression analysis in the extraradical mycelium of this isolate revealed that the transcription of HmMT1 was preferentially induced in the presence of Zn and Cd, while Ag was a stronger inducer of HmMT3. Altogether, these results improve our understanding of the handling of intracellular Zn, Cd and Ag in Hebeloma and represent the first evidence suggesting involvement of MTs in sequestration of Zn in EM fungi. PMID:24674773

Sácký, Jan; Leonhardt, Tereza; Borovi?ka, Jan; Gryndler, Milan; Briksí, Aleš; Kotrba, Pavel



Differences in metallothionein gene expression in primary cultures of rainbow trout hepatocytes and the RTH-149 cell line.  


Primary cultures of rainbow trout, Salmo gairdneri, hepatocytes were used to study the expression of metallothionein (MT) genes in response to steroid hormone treatment. The expression pattern was compared to that of an immortal cell line (RTH-149). MT mRNA accumulated in both cell cultures after exposure to zinc while 17 beta-oestradiol had no effect in either system. Treatment with cortisol and corticosterone resulted in a 2-fold increase of metallothionein mRNA levels in the primary cultures but had no effect in the RTH-149 cell culture. Primary cultures that were exposed to zinc or cortisol showed a high temporal correlation (r = 0.974) between MT mRNA and MT protein levels. The basal level expression was 3-4-fold higher in primary cultures than in RTH-149 cells. The present study demonstrates the inducibility of rainbow trout MT genes in response to glucocorticoids. It further indicates that primary cultures are to be preferred to immortal cell lines when investigating the inducibility of MT mRNA. PMID:2357467

Olsson, P E; Hyllner, S J; Zafarullah, M; Andersson, T; Gedamu, L



Activation of Metallothionein Gene Expression by Hypoxia Involves Metal Response Elements and Metal Transcription Factor11  

Microsoft Academic Search

Metallothioneins (MTs) are a family of stress-induced proteins with diverse physiological functions, including protection against metal toxicity and oxidants. They may also contribute to the regulation of cellular proliferation, apoptosis, and malignant progression. We reported previ- ously that the human (h)MT-IIA isoform is induced in carcinoma cells (A431, SiHa, and HT29) exposed to low oxygen, conditions commonly found in solid

Brian J. Murphy; Glen K. Andrews; Doug Bittel; Daryl J. Discher; Jesica McCue; Christopher J. Green; Marianna Yanovsky; Amato Giaccia; Robert M. Sutherland; Keith R. Laderoute; Keith A. Webster



Transgenic Brassica napus and tobacco plants harboring human metallothionein gene are resistant to toxic levels of heavy metals  

SciTech Connect

A chimeric gene containing a cloned human metallothionein-II (MT-II) processed gene was introduced into Brassica napus and tobacco cells on a disarmed Ti plasmid of Agrobacterium tumefaciens. Transformants expressed MT protein as a nuclear trait, and in a constitutive manner. Seeds from self-fertilized transgenic plants were germinated on media containing toxic levels of cadmium and scored for tolerance/susceptibility to this heavy metal. The growth of root and shoot of transformed seedlings was unaffected by up to 100{mu}M CdCl{sub 2}, whereas, control seedlings showed severe inhibition of root and shoot growth and chlorosis of leaves. The results of these experiments indicate that agriculturally important plants such a B. napus can be genetically engineered for heavy metals tolerance/sequestration and eventually for partitioning of heavy metals in non-consumed plant tissues.

Misra, S. (Univ. of Victoria, British Columbia (Canada))



Enhanced metallothionein gene expression is associated with protection from cadmium-induced genotoxity in cultured rat liver cells  

SciTech Connect

Metallothioneins (MTs) are low-molecular-weight, cysteine-rich proteins that appear to play an important role in the cellular defense system against cadmium toxicity. Although substantial evidence exists demonstrating a reduction in cadmium toxicity concomitant with MT induction, little is known about the possible effects of stimulation of MT synthesis on cadmium-induced genotoxicity. Thus, the alkaline elution technique was used to assess single-strand DNA damage (SSD) in TRL-1215 cells, a liver-derived cell line shown to have inducible MT Gene expression. The SSD accumulated over a 2-h time period in a time-dependent manner following exposure to 500 [mu]M CdCl[sub 2]. Low concentration cadmium pretreatment (10 [mu]M CdCl[sub 2], 24 h) provided protection against the genotoxicity of high-concentration cadmium (500 [mu]M CdCl[sub 2], 2 h). A 2-h exposure to 500 [mu]M CdCl[sub 2], had no effect on viability, as assessed using a tetrazolium-dye based assay, in cells from either the pretreated or nonpretreated group. Metallothionein was induced in a time-dependent manner by low-concentration cadmium pretreatment: Exposure for 24 and 48 h resulted in 3.3- and 6.4-fold increases, respectively. In addition, a 24-h exposure to low-concentration cadmium resulted in an increase in MT-I gene expression. Cadmium accumulation was 2.6-fold greater in low-concentration cadmium-pretreated cells as compared to non-pretreated cells. These data demonstrate that low-concentration cadmium pretreatment provides protection against cadmium-induced single-strand DNA damage and support the hypothesis that this protection is due to stimulation of MT gene expression. 38 refs., 6 figs.

Coogan, T.P.; Bare, R.M.; Bjornson, E.J.; Waalkes, M.P. (National Cancer Institute, Frederick, MD (United States))



cDNA sequence encoding metallothionein protein from Aegiceras corniculatum and its gene expression induced by Pb²? and Cd²? stresses.  


Constructing various green wetland examples for mangrove wetland systems is a useful way to use natural power to remediate the polluted wetlands at intertidal zones. Metallothioneins (MT) are involved in heavy metal tolerance, homeostasis, and detoxification of intracellular metal ions in plants. In order to understand the mechanism of heavy metal uptake in Aegiceras corniculatum, we isolated its metallothionein gene and studied the MT gene expression in response to heavy metals contamination. Here, we report the isolation and characterization of MT2 genes from young stem tissues of A. corniculatum growing in the cadmium (Cd) and lead (Pb) polluted wetlands of Quanzhou Bay, southeast of China. The obtained cDNA sequence of MT is 512 bp in length, and it has an open reading frame encoding 79 amino acid residues with a molecular weight of 7.92 kDa and the theoretical isoelectric point of 4.55. The amino acids include 14 cysteine residues and 14 glycine residues. It is a non-transmembrane hydrophilic protein. Sequence and homology analysis showed the MT protein sequence shared more than 60% homology with other plant type 2 MT-like protein genes. The results suggested that the expression level of MT gene of A. corniculatum young stems induced by a certain range concentration of Cd(2+) and Pb(2+) stresses (0.2 mmol L(-1) Pb(2+), 1 mmol L(-1) Pb(2+), 0.2 mmol L(-1) Pb(2+), and 40 ?mmol L(-1) Cd(2+); 1 mmol L(-1) Pb(2+) and 40 ?mol L(-1) Cd(2+)) compared with control might show an adaptive protection. The expression levels of MT gene at 20 h stress treatment were higher than those at 480 h stress treatment. The expression levels of MT gene with 0.2 mmol L(-1) Pb(2+) stress treatment were higher than those with 0.2 mmol L(-1) Pb(2+) and 40 ?mol L(-1) Cd(2+) stress treatment, and the MT gene expression levels with 1 mmol L(-1) Pb(2+) treatment were higher than those with 1 mmol L(-1) Pb(2+) and 40 ?mol L(-1) Cd(2+) treatment. There exists an antagonistic action between Pb(2+) and Cd(2+) in the MT metabolization of A. corniculatum. PMID:23856811

Yuhong, Li; Atagana, Harrison I; Jingchun, Liu; Wenlin, Wu; Shijun, Wu



Enhanced Copper Tolerance in Silene vulgaris (Moench) Garcke Populations from Copper Mines Is Associated with Increased Transcript Levels of a 2b-Type Metallothionein Gene1  

Microsoft Academic Search

Silene vulgaris (Moench) Garcke has evolved populations with extremely high levels of copper tolerance. To evaluate the role of metallothioneins (MTs) in copper tolerance in S. vulgaris, we screened a cDNA library derived from a highly copper- tolerant population using Arabidopsis-based MT probes and identified an MT2b-like gene. When expressed in yeast, this gene, SvMT2b, restored cadmium and copper tolerance

Nathalie A. L. M. van Hoof; Viivi H. Hassinen; Henk W. J. Hakvoort; Koos F. Ballintijn; Henk Schat; Jos A. C. Verkleij; Wilfried H. O. Ernst; Sirpa O. Karenlampi; Arja I. Tervahauta


A cadmium metallothionein gene of ridgetail white prawn Exopalaemon carinicauda (Holthuis, 1950) and its expression  

NASA Astrophysics Data System (ADS)

Metallothioneins (MTs) are a group of low molecular weight cysteine-rich proteins capable of binding heavy metal ions. A cadmium metallothionein ( EcMT — Cd) cDNA with a 189 bp open reading frame (ORF) that encoded a 62 amino acid protein was obtained from Exopalaemon carinicauda. Seventeen cysteines were in the deduced amino acid sequence, and the cysteine (Cys)-rich characteristic was revealed in different metallothioneins in other species. In addition, the deduced amino acid sequence did not contain any aromatic amino acid residues, such as tyrosine (Tyr), tryptophan (Trp), and phenylalanine (Phe). EcMT—Cd mRNA was expressed in all tested tissues (the ovary, muscle, stomach, and hepatopancreas), and its expression profiles in the hepatopancreas were very different when shrimps were exposed to seawater containing either 50 ?mol/L CuSO4 or 2.5 ?mol/L CdCl 2. The expression of EcMT-Cd was significantly up-regulated in shrimp exposed to CuSO4 for 12 h and down-regulated in shrimps exposed to CdCl2 for 12 h. After 24 h exposure to both metals, its expression was down-regulated. By contrast, at 48 h the EcMT-Cd was up-regulated in test shrimps exposed to CdCl2. The transcript of EcMT-Cd was very low or even absent before the zoea stage, and the expression of EcMT-Cd was detected from mysis larvae-I, then its expression began to rise. In conclusion, a cadmium MT exists in E. carinicauda that is expressed in different tissues and during different developmental stages, and responds to the challenge with heavy metal ions, which provides a clue to understanding the function of cadmium MT.

Zhang, Jiquan; Wang, Jing; Xiang, Jianhai



Predicting the Proportion of Essential Genes in Mouse Duplicates Based on Biased Mouse Knockout Genes  

E-print Network

Predicting the Proportion of Essential Genes in Mouse Duplicates Based on Biased Mouse Knockout+Business Media, LLC 2008 Abstract In the yeast or nematode, the proportion of essential genes in duplicates developed a simple bias-cor- recting procedure and shown that the bias-corrected proportion of essential

Gu, Xun


Metallothionein and bZIP Transcription Factor Genes from Velvetleaf and Their Differential Expression Following Colletotrichum coccodes Infection.  


ABSTRACT Colletotrichum coccodes is a biocontrol agent of velvetleaf (Abutilon theophrasti), a noxious weed of corn and soybean. Metallothioneins (MTs) and basic region/leucine zipper motif (bZIP) are heavy-metal-binding proteins and transcription factors, respectively, that have been related to several plant processes, including the responses of plants to pathogen attack. Previous investigation of the determinants involved in the velvet-leaf-C. coccodes interaction had shed light on particular plant and fungal genes expressed in this pathosystem. Here, we report on the temporal expression patterns of two distinct types (2 and 3) of MT and bZIP transcription factor genes in velvetleaf leaves following infection with C. coccodes using quantitative reverse-transcription polymerase chain reaction. Gene expression ratios were significantly upregulated 1 day after infection (DAI), a time at which velvetleaf leaves appeared symptomless. At 2 DAI, bZIP and type 3 MT expression ratios dropped to levels significantly lower than those estimated for noninfected plants. Necrotic symptoms appeared 5 DAI and increased with time, during which gene expression levels were maintained either below or at levels observed in the control. These findings indicate that C. coccodes altered the expression of type 2 and 3 MT and bZIP genes. In addition, this is the first report on induction of a type 3 MT in plants in response to a pathogen attack. PMID:18943500

Dauch, Amélie L; Jabaji-Hare, Suha H



Partial structure of the mouse glucokinase gene  

SciTech Connect

A complementary DNA for glucokinase (GK) was cloned from mouse liver total RNA by a combination of the polymerase chain reaction (PCR) and mouse liver cDNA library screening. Liver- and {beta}-cell-specific exons 1 were isolated by PCR using mouse and rat genomic DNAs. These clones were then used to screen a mouse genomic library; three genomic clones were isolated and characterized. The mouse GK gene spans over 20 kb, containing 11 exons including a liver- or {beta}-cell-specific exon 1, which encodes a tissue-specific 15-aa peptide at the N-terminus of the protein. Both types of GK contain 465 amino acid residues. The predicted amino acid sequence of mouse {beta}-cell-specific GK showed 98 and 96% identity to the rat and human enzymes, respectively; the corresponding values are 98 and 95% respectively, for the liver-specific GK. Several transcription factor-binding consensus sequences are identified in the 5{prime} flanking region of the mouse GK gene. 21 refs., 1 fig.

Ishimura-Oka, Kazumi; Chu, Mei-Jin; Sullivan, M.; Oka, Kazuhiro [Baylor College of Medicine, Houston, TX (United States)



Differential Gene-Expression of Metallothionein 1M and 1G in Response to Zinc in Sertoli TM4 Cells  

PubMed Central

Background: Zinc (Zn) as an important trace element is essential for testicular development and spermatogenesis. Molecular mechanism of Zn action in the reproductive system may be related to metal binding low-molecular weight proteins, metallothioneins (MT). Our objective was to determine the effect of Zn on two important isoforms of MT, MT1M and MT1G genes expression on testicular sertoli cells. Methods: Cultured sertoli TM4 cells were exposed to different concentrations of Zn at different time points. Cellular uptake of Zn was tested using flame atomic absorption spectrometry. The cellular viability and gene expression were assessed by MTT and real-time PCR methods, respectively. Results: The treated cells resulted in higher Zn concentration and cellular viability. The expression of MT1M and MT1G genes in the treated cells were greater than those of the untreated cells (P<0.05). In the high dosage treated group (100 and 500 ?M), Zn concentration and expression of MT1M and MT1G genes increased three h after treatment; MT1G gene expression increased more at sixth h. At 18th h of treatment, the expression of both genes especially MT1G, increased dramatically while Zn concentration decreased. Conclusion: Since the increase of MT1G mRNA was coincident with cellular Zn level, it seems that MT1G has a more prominent role than MT1M in the homeostasis of Zn. In addition, Zn at dosage of 50 ?M (pharmacologic concentration) may protect cells by increasing the expression of MT genes at longer periods. PMID:20683493

Kheradmand, Fatemeh; Nourmohammadi, Issa; Modarressi, Mohammad Hossein; Firoozrai, Mohsen; Ahmadi Faghih, Mohammad Amin



The mouse Gene Expression Database (GXD): updates and enhancements  

Microsoft Academic Search

The Gene Expression Database (GXD) is a com- munity resource for gene expression information in the laboratory mouse. By collecting and integrating different types of expression data, GXD provides information about expression profiles in different mouse strains and mutants. Participation in the Gene Ontology (GO) project classifies genes and gene products with regard to molecular functions, biological processes, and cellular

David P. Hill; Dale A. Begley; Jacqueline H. Finger; Terry F. Hayamizu; Ingeborg J. Mccright; Constance M. Smith; Jon S. Beal; Lori E. Corbani; Judith A. Blake; Janan T. Eppig; James A. Kadin; Joel E. Richardson; Martin Ringwald



Effect of cadmium on glutathione S-transferase and metallothionein gene expression in coho salmon liver, gill and olfactory tissues  

PubMed Central

The glutathione S-transferases (GSTs) are a multifunctional family of phase II enzymes that detoxify a variety of environmental chemicals, reactive intermediates, and secondary products of oxidative damage. GST mRNA expression and catalytic activity have been used as biomarkers of exposure to environmental chemicals. However, factors such as species differences in induction, partial analyses of multiple GST isoforms, and lack of understanding of fish GST gene regulation, have confounded the use of GST as markers of pollutant exposure. In the present study, we examined the effect of exposure to cadmium (Cd), a prototypical environmental contaminant and inducer of mammalian GST, on GST mRNA expression in coho salmon (Oncorhynchus kisutch) liver, gill, and olfactory tissues. GST expression data were compared to those for metallothionein (MT), a prototypical biomarker of metal exposure. Data mining of genomic databases led to the development of quantitative real-time PCR (qPCR) assays for salmon GST isoforms encompassing 9 subfamilies, including alpha, mu, pi, theta, omega, kappa, rho, zeta and microsomal GST. In vivo acute (8-48 hr) exposures to low (3.7 ppb) and high (347 ppb) levels of Cd relevant to environmental scenarios elicited a variety of transient, albeit minor changes (<2.5-fold) in tissue GST profiles, including some reductions in GST mRNA expression. In general, olfactory GSTs were the earliest to respond to cadmium, whereas, more pronounced effects in olfactory and gill GST expression were observed at 48 hr relative to earlier time points. Although evaluation of GSTs reflected a cadmium-associated oxidative stress response, there was no clear GST isoform in any tissue that could serve as a reliable biomarker of acute cadmium exposure. By contrast, metallothionein (MT) mRNA was consistently and markedly induced in all three tissues by cadmium, and among the tissues examined, olfactory MT was the most sensitive marker of cadmium exposures. In summary, coho salmon exhibit a complex GST tissue profile consisting of at least 9 isoforms, all of which are present in the peripheral olfactory system. Short-term exposure to environmental levels of Cd causes transient changes in salmon GST consistent with oxidative stress, and in some cases, includes a loss of GST. In a biomarker context, however, monitoring of tissue MT mRNA expression, especially in the peripheral olfactory system, may be of greater utility for assessing short-term environmental exposures to cadmium. PMID:22257444

Espinoza, Herbert M.; Williams, Chase R.; Gallagher, Evan P.



The association of metallothionein-4 gene polymorphism and renal function in long-term lead-exposed workers.  


The goal of this study is to investigate if metallothionein (MT) gene polymorphism affects the susceptibility to lead as well as renal function parameters and blood pressures (BP) in workers exposed to lead for extended period of time. By means of real-time polymerase chain reaction, the MT4-216 A/G genotypes classified as rs396230 in the single nucleotide polymorphism database of the National Center for Biotechnology Information (database) were analyzed on 113 workers of a lead battery-recycling factory. Workers with G (mutant) allele were more susceptible to the toxic effects of lead on their systolic BP and serum renal function parameters. Their BP was 10 mmHg higher than those with wild-type (AA type) allele. Among subjects with the 3-genome, the GG mutant type subjects appear to be more susceptible to lead. Regression models of serum creatinine and BUN showed significant differences between the GG and GA types compared to AA type subjects. This cross-sectional study shows that workers with different MT-4 genotypes have different lead-induced adverse health effects. Those with the G allele have the greater susceptibility to lead so their exposure should be reduced. PMID:19921116

Chen, Hsin-I; Chiu, Yu-Wen; Hsu, Yu Kuei; Li, Wan-Fen; Chen, Yi-Chun; Chuang, Hung-Yi



Differential Expression of a Metallothionein Gene during the Presymbiotic versus the Symbiotic Phase of an Arbuscular Mycorrhizal Fungus1  

PubMed Central

A full-length cDNA encoding a metallothionein (MT)-like polypeptide, designated GmarMT1, was identified in an expressed sequence tag collection from germinated spores of the arbuscular mycorrhizal fungus Gigaspora margarita (BEG34). The GmarMT1 gene is composed of two exons separated by an 81-bp intron. It codes for a 65-amino acid polypeptide comprising a plant type 1 MT-like N-terminal domain and a C-terminal domain that is most closely related to an as-yet-uncharacterized fungal MT. As revealed by heterologous complementation assays in yeast, GmarMT1 encodes a functional polypeptide capable of conferring increased tolerance against Cd and Cu. The GmarMT1 RNA is expressed in both presymbiotic spores and symbiotic mycelia, even in the absence of metal exposure, but is significantly less abundant in the latter stage. An opposite pattern was observed upon Cu exposure, which up-regulated GmarMT1 expression in symbiotic mycelia but not in germinated spores. Together, these data provide the first evidence, to our knowledge, for the occurrence in an arbuscular mycorrhizal fungus of a structurally novel MT that is modulated in a metal and life cycle stage-dependent manner and may afford protection against heavy metals (and other types of stress) to both partners of the endomycorrhizal symbiosis. PMID:12226486

Lanfranco, Luisa; Bolchi, Angelo; Ros, Emanuele Cesale; Ottonello, Simone; Bonfante, Paola



Identification of two metallothionein genes and their roles in stress responses of Musca domestica toward hyperthermy and cadmium tolerance.  


Stress proteins such as metallothioneins (MTs) play a key role in cellular protection against environmental stressors. In nature, insects such as houseflies (Musca domestica) are commonly exposed to multiple stressors including heavy metals (e.g. Cadmium, Cd) and high temperatures. In this paper, we identify two novel MT genes from the cDNAs of M. domestica, MdMT1 and MdMT2, which putatively encode 40 and 42 amino acid residues respectively. Expression of the two MTs' mRNAs, which are examined in the fat body, gut, hemocyte, and the epidermis. From our study, we saw that the expression of MdMT1 and MdMT2 are enhanced by Cd and thermal stress. Levels of expression are highest at 10 mM Cd(2+) within a 24-h period, and expressions increase significantly with exposure to 10 mM Cd for 12h. Levels of the mRNAs are up-regulated after heat shock and that of MdMT2 reaches its maximum peak faster than MdMT1. Both of the MT genes might be involved in a transient systemic tolerance response to stressors and they may play important roles in heavy metal and high temperature tolerance in the housefly. To detect whether or not the MTs bind heavy metals, the target genes are cloned into the prokaryotic expression vector pET-DsbA to obtain fusion protein expressed in Escherichia coli BL21 (DE3). Recombinant DsbA-MdMT1 significantly increases tolerance of the host bacteria to Cd(2+), but DsbA-MdMT2 is absent. These differential characteristics will facilitate future investigations into the physiological functions of MTs. PMID:21762786

Tang, Ting; Huang, Da-wei; Zhang, Di; Wu, Yin-jian; Murphy, Robert W; Liu, Feng-song



Gene response profiles for Daphnia pulex exposed to the environmental stressor cadmium reveals novel crustacean metallothioneins  

Microsoft Academic Search

BACKGROUND: Genomic research tools such as microarrays are proving to be important resources to study the complex regulation of genes that respond to environmental perturbations. A first generation cDNA microarray was developed for the environmental indicator species Daphnia pulex, to identify genes whose regulation is modulated following exposure to the metal stressor cadmium. Our experiments revealed interesting changes in gene

Joseph R Shaw; John K Colbourne; Jennifer C Davey; Stephen P Glaholt; Thomas H Hampton; Celia Y Chen; Carol L Folt; Joshua W Hamilton



Characterization of the mouse Prox1 gene.  


Prox1, a vertebrate homologue of Drosophila prospero, encodes a divergent homeodomain protein. We have isolated and characterized full length mouse Prox1 cDNA and genomic clones. Mouse Prox1 gene mapped to position 106.3 cM from the centromere of Chromosome 1, which is very close to the retinal degeneration mutation, rd3. Although the coding sequence and exon-intron junctions of the Prox1 genes of wild type and rd3 mutant mice are identical, Northern blot analysis indicated that the ratio of the short (2.3 kb) and long (8 kb) forms of Prox1 mRNA is different in RNA isolated from wild type and rd3 retinas. Immunostaining of the eyes from wild type and rd3 animals also revealed differences in the distribution of Prox1 protein in the retina and lens. These data suggest that the rd3 mutation affects expression of the mouse Prox1 gene. PMID:9703987

Tomarev, S I; Zinovieva, R D; Chang, B; Hawes, N L



Metallothionein is a crucial protective factor against Helicobacter pylori-induced gastric erosive lesions in a mouse model.  


Infection with the gastric pathogen Helicobacter pylori (H. pylori) causes chronic gastritis, peptic ulcer, and gastric adenocarcinoma. These diseases are associated with production of reactive oxygen species (ROS) from infiltrated macrophages and neutrophiles in inflammatory sites. Metallothionein (MT) is a low-molecular-weight, cysteine-rich protein that can act not only as a metal-binding protein, but also as a ROS scavenger. In the present study, we examined the role of MT in the protection against H. pylori-induced gastric injury using MT-null mice. Female MT-null and wild-type mice were challenged with H. pylori SS1 strain, and then histological changes were evaluated with the updated Sydney grading system at 17 and 21 wk after challenge. Although the colonization efficiency of H. pylori was essentially the same for MT-null and wild-type mice, the scores of activity of inflammatory cells were significantly higher in MT-null mice than in wild-type mice at 17 wk after challenge. Histopathological examination revealed erosive lesions accompanied by infiltration of inflammatory cells in the infected MT-null mice but not in wild-type mice. Furthermore, activation of NF-kappaB and expression of NF-kappaB-mediated chemokines such as macrophage inflammatory protein-1alpha and monocytes chemoattractant protein-1 in gastric cells were markedly higher in MT-null mice than in wild-type mice. These results suggest that MT in the gastric mucosa might play an important role in the protection against H. pylori-induced gastric ulceration. PMID:18239062

Mita, Masaharu; Satoh, Masahiko; Shimada, Akinori; Okajima, Mina; Azuma, Sadahiro; Suzuki, Junko S; Sakabe, Kou; Hara, Shuntaro; Himeno, Seiichiro



[The relationship between mouse fertilization antigen 1 gene and the human counterpart gene].  


The cloning of human fertilization antigen 1 gene(FA1) ,the supposed counterpart gene of mouse fertilization antigen 1 gene (FA1),was performed using the PCR and PCR products cloned sequencing methods. The result shows that there might be two mistakes in the mouse FA1 gene open reading frame (ORF),and human OTK27 gene and mouse FA1 gene might be homogeneous genes in the two species. PMID:16135423

Li, Jian-ping; Zhang, Si-zhong; Xia, Qing-jie



Analysis of gene expression in the developing mouse retina  

E-print Network

Analysis of gene expression in the developing mouse retina Elva Di´az*, Yee Hwa Yang , Todd in the developing retina. We assayed gene expression in nasal (anterior), temporal (posterior), dorsal, and ventral embryonic mouse retina. We used a statistical method to estimate gene expression between different retina

Yang, Yee Hwa


Structural and functional characterization of the mouse Hlx homeobox gene  

Microsoft Academic Search

.  \\u000a Hlx is a mesenchymally expressed homeobox transcription factor gene that is essential for normal intestinal and hepatic development\\u000a in the mouse. Here we report further characterization of the mouse Hlx gene, including an additional 3.7 kb of 5? sequence as well as the sequence of the three introns. Comparison of the sequence\\u000a of the mouse Hlx gene 5? to

Michael D. Bates; Lynn C. Schatzman; Thierry Lints; Philip E. Hamlin; Richard P. Harvey; S. Steven Potter



The biology of novel animal genes: Mouse APEX gene knockout  

SciTech Connect

This is the final report of a one-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). The controlled breeding of novel genes into mice, including the gene knockout (KO), or conversely by adding back transgenes provide powerful genetic technologies that together suffice to determine in large part the biological role(s) of novel genes. Inbred mouse remains the best understood and most useful mammalian experimental system available for tackling the biology of novel genes. The major mammalian apurinic/apyrimidinic (AP) endonuclease (APE), is involved in a key step in the repair of spontaneous and induced AP sites in DNA. Efficient repair of these lesions is imperative to prevent the stable incorporation of mutations into the cellular genome which may lead to cell death or transformation. Loss or modulation of base excison repair activity in vivo may elevate the spontaneous mutation rate in cells, and may lead to a substantial increase in the incidence of cancer. Despite extensive biochemical analysis, however, the significance of these individual APE functions in vivo has not been elucidated. Mouse embryonic stem (ES) cells heterozygous for a deletion mutation in APE have been generated and whole animals containing the APE mutation have been derived from these ES cells. Animals homozygous for the APE null mutation die early in gestation, underscoring the biological significance of this DNA repair gene.

MacInnes, M.; Altherr, M.R.; Ludwig, D. [Los Alamos National Lab., NM (United States); Pedersen, R.; Mold, C. [Univ. of California, San Francisco, CA (United States)



The Mouse Genome Database (MGD): from genes to mice--a community resource for mouse biology  

PubMed Central

The Mouse Genome Database (MGD) forms the core of the Mouse Genome Informatics (MGI) system (, a model organism database resource for the laboratory mouse. MGD provides essential integration of experimental knowledge for the mouse system with information annotated from both literature and online sources. MGD curates and presents consensus and experimental data representations of genotype (sequence) through phenotype information, including highly detailed reports about genes and gene products. Primary foci of integration are through representations of relationships among genes, sequences and phenotypes. MGD collaborates with other bioinformatics groups to curate a definitive set of information about the laboratory mouse and to build and implement the data and semantic standards that are essential for comparative genome analysis. Recent improvements in MGD discussed here include the enhancement of phenotype resources, the re-development of the International Mouse Strain Resource, IMSR, the update of mammalian orthology datasets and the electronic publication of classic books in mouse genetics. PMID:15608240

Eppig, Janan T.; Bult, Carol J.; Kadin, James A.; Richardson, Joel E.; Blake, Judith A.



Effects of heavy metals on the expression of a zinc-inducible metallothionein-III gene and antioxidant enzyme activities in Crassostrea gigas.  


Sequestration by metallothioneins and antioxidant defense are two kinds of important defense mechanisms employed by mollusks to minimize adverse effects caused by heavy metal contaminants in marine environment. In the present study, a novel metallothionein gene, CgMT-III, was cloned from Crassostrea gigas, consisting of eighteen conserved cysteine residues and encoding a MT III-like protein with two tandem ? domains. The expression level of CgMT-III transcript induced by zinc was much higher than that induced by cadmium exposure. It suggested that CgMT-III was perhaps mainly involved in homeostatic control of zinc metabolism, which was distinct from previously identified MTs in C. gigas. Among the tested antioxidant enzymes including superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GPx), SOD and GPx showed varying up-regulations in a tissue-specific manner, while CAT activities were inhibited in both gill and hepatopancreas from C. gigas exposed to heavy metals. It can be inferred that CgMT-III was mainly involved in zinc homeostasis, and CgMT-III gene together with CAT enzyme could be potential biomarkers to indicate heavy metal, especially zinc pollution in marine organisms. PMID:22614035

Cong, Ming; Wu, Huifeng; Liu, Xiaoli; Zhao, Jianmin; Wang, Xuan; Lv, Jiasen; Hou, Lin



Characterization and expression of a metallothionein gene in the aquatic fern Azolla filiculoides under heavy metal stress  

Microsoft Academic Search

A cDNA encoding a type 2 metallothionein (MT) was isolated from Azolla filiculoides, termed AzMT2, accession no. AF482470. The AzMT2 transcript was expressed in sterile A. filiculoides that were free of the cyanobiont Anabaena azollae after erythromycin treatment, proving that AzMT2 is encoded by the fern genome. AzMT2 RNA expression was enhanced by the addition of Cd+2, Cu+2, Zn+2 and

Tamar Schor-Fumbarov; Peter B. Goldsbrough; Zach Adam; Elisha Tel-Or



Housekeeping and tissue-specific genes in mouse tissues  

Microsoft Academic Search

BACKGROUND: This study aims to characterize the housekeeping and tissue-specific genes in 15 mouse tissues by using the serial analysis of gene expression (SAGE) strategy which indicates the relative level of expression for each transcript matched to the tag. RESULTS: Here, we identified constantly expressed housekeeping genes, such as eukaryotic translation elongation factor 2, which is expressed in all tissues

Kouame E Kouadjo; Yuichiro Nishida; Jean F Cadrin-Girard; Mayumi Yoshioka; Jonny St-Amand



Web-based digital gene expression atlases for the mouse.  


Over the past 15 years the publicly available mouse gene expression data determined by in situ hybridization have dramatically increased in scope and spatiotemporal resolution. As a consequence of resources and tools available in the post-genomic era, full transcriptomes in the mouse brain and in the mouse embryo can be studied. Here we introduce and discuss seven current databases (MAMEP, EMBRYS, GenePaint, EURExpress, EuReGene, BGEM, and GENSAT) that grant access to large collections of expression data in mouse. We review the experimental focus, coverage, data assessment, and annotation for each of these databases and the implementation of analytic tools and links to other relevant databases. We provide a user-oriented summary of how to interrogate each database. PMID:22936000

Geffers, Lars; Herrmann, Bernhard; Eichele, Gregor



Tryphostin AG879, a tyrosine kinase inhibitor: prevention of transcriptional activation of the electrophile and the aromatic hydrocarbon response elements 1 1 Abbreviations: EPRE, electrophile response element; AHRE, aromatic hydrocarbon response element; MRE, metal response element; Nqo1 and NQO1, mouse NAD(P)H:quinone oxidoreductase [also called NMO1, quinone reductase, DT-diaphorase] gene and mRNA; Cyp1a1 and CYP1A1, mouse cytochrome P450 1A1 gene and mRNA; Mt1 and MT1, mouse metallothionein-1 gene and mRNA; Sod, mouse Cu,Zn-superoxide dismutase gene; SOD, rat Cu,Zn-superoxide dismutase gene; SOD, mouse and rat Cu,Zn-superoxide dismutase mRNA and protein; Luc and LUC, firefly luciferase gene and enzyme; BGAL, ?-galactosidase enzyme activity; tBHQ, tert-butylhydroquinone; dioxin (also TCDD), 2,3,7,8-tetrahydro chlorodibenzo- p-dioxin; SSC, standard sodium citrate; and SET, sodium ethylenediamine tetraacetic acid (EDTA) Tris buffer  

Microsoft Academic Search

To investigate a possible role of phosphorylation in the signal transduction pathways responsible for transcriptional regulation of drug-metabolizing enzymes, we tested seven specific tyrosine kinase inhibitors (tyrphostins) for their effects on NAD(P)H:quinone oxidoreductase-1 (NQO1) mRNA levels in mouse hepatoma Hepa-1c1c7 (Hepa-1) cells and chose to study AG879 further. The potent electrophile tert-butylhydroquinone (tBHQ) is known to activate NQO1 gene transcription

Matthew Z Dieter; Sarah L Freshwater; Willy A Solis; Daniel W Nebert; Timothy P Dalton



Database for exchangeable gene trap clones: pathway and gene ontology analysis of exchangeable gene trap clone mouse lines.  


Gene trapping in embryonic stem (ES) cells is a proven method for large-scale random insertional mutagenesis in the mouse genome. We have established an exchangeable gene trap system, in which a reporter gene can be exchanged for any other DNA of interest through Cre/mutant lox-mediated recombination. We isolated trap clones, analyzed trapped genes, and constructed the database for Exchangeable Gene Trap Clones (EGTC) []. The number of registered ES cell lines was 1162 on 31 August 2013. We also established 454 mouse lines from trap ES clones and deposited them in the mouse embryo bank at the Center for Animal Resources and Development, Kumamoto University, Japan. The EGTC database is the most extensive academic resource for gene-trap mouse lines. Because we used a promoter-trap strategy, all trapped genes were expressed in ES cells. To understand the general characteristics of the trapped genes in the EGTC library, we used Kyoto Encyclopedia of Genes and Genomes (KEGG) for pathway analysis and found that the EGTC ES clones covered a broad range of pathways. We also used Gene Ontology (GO) classification data provided by Mouse Genome Informatics (MGI) to compare the functional distribution of genes in each GO term between trapped genes in the EGTC mouse lines and total genes annotated in MGI. We found the functional distributions for the trapped genes in the EGTC mouse lines and for the RefSeq genes for the whole mouse genome were similar, indicating that the EGTC mouse lines had trapped a wide range of mouse genes. PMID:24444128

Araki, Masatake; Nakahara, Mai; Muta, Mayumi; Itou, Miharu; Yanai, Chika; Yamazoe, Fumika; Miyake, Mikiko; Morita, Ayaka; Araki, Miyuki; Okamoto, Yoshiyuki; Nakagata, Naomi; Yoshinobu, Kumiko; Yamamura, Ken-ichi; Araki, Kimi



The mouse Gene Expression Database (GXD): 2007 update  

Microsoft Academic Search

The Gene Expression Database (GXD) provides the scientific community with an extensive and easily searchable database of gene expression information about the mouse. Its primary emphasis is on deve- lopmental studies. By integrating different types of expression data, GXD aims to provide comprehen- sive information about expression patterns of tran- scripts and proteins in wild-type and mutant mice. Integration with

Constance M. Smith; Jacqueline H. Finger; Terry F. Hayamizu; Ingeborg J. Mccright; Janan T. Eppig; James A. Kadin; Joel E. Richardson; Martin Ringwald



Mouse Lysozyme M Gene: Isolation, Characterization, and Expression Studies  

Microsoft Academic Search

We have isolated and characterized both cDNA and genomic DNA of the mouse lysozyme M gene. Derivation of the amino acid sequence from the nucleotide sequences revealed six positions in the carboxyl terminus that differ from partial sequences previously published. The differential detection of specific mRNAs from the closely related lysozyme M and P genes has revealed different but overlapping

Michael Cross; Inge Mangelsdorf; Angela Wedel; Rainer Renkawitz



The mammalian gene function resource: the International Knockout Mouse Consortium.  


In 2007, the International Knockout Mouse Consortium (IKMC) made the ambitious promise to generate mutations in virtually every protein-coding gene of the mouse genome in a concerted worldwide action. Now, 5 years later, the IKMC members have developed high-throughput gene trapping and, in particular, gene-targeting pipelines and generated more than 17,400 mutant murine embryonic stem (ES) cell clones and more than 1,700 mutant mouse strains, most of them conditional. A common IKMC web portal ( has been established, allowing easy access to this unparalleled biological resource. The IKMC materials considerably enhance functional gene annotation of the mammalian genome and will have a major impact on future biomedical research. PMID:22968824

Bradley, Allan; Anastassiadis, Konstantinos; Ayadi, Abdelkader; Battey, James F; Bell, Cindy; Birling, Marie-Christine; Bottomley, Joanna; Brown, Steve D; Bürger, Antje; Bult, Carol J; Bushell, Wendy; Collins, Francis S; Desaintes, Christian; Doe, Brendan; Economides, Aris; Eppig, Janan T; Finnell, Richard H; Fletcher, Colin; Fray, Martin; Frendewey, David; Friedel, Roland H; Grosveld, Frank G; Hansen, Jens; Hérault, Yann; Hicks, Geoffrey; Hörlein, Andreas; Houghton, Richard; Hrabé de Angelis, Martin; Huylebroeck, Danny; Iyer, Vivek; de Jong, Pieter J; Kadin, James A; Kaloff, Cornelia; Kennedy, Karen; Koutsourakis, Manousos; Lloyd, K C Kent; Marschall, Susan; Mason, Jeremy; McKerlie, Colin; McLeod, Michael P; von Melchner, Harald; Moore, Mark; Mujica, Alejandro O; Nagy, Andras; Nefedov, Mikhail; Nutter, Lauryl M; Pavlovic, Guillaume; Peterson, Jane L; Pollock, Jonathan; Ramirez-Solis, Ramiro; Rancourt, Derrick E; Raspa, Marcello; Remacle, Jacques E; Ringwald, Martin; Rosen, Barry; Rosenthal, Nadia; Rossant, Janet; Ruiz Noppinger, Patricia; Ryder, Ed; Schick, Joel Zupicich; Schnütgen, Frank; Schofield, Paul; Seisenberger, Claudia; Selloum, Mohammed; Simpson, Elizabeth M; Skarnes, William C; Smedley, Damian; Stanford, William L; Stewart, A Francis; Stone, Kevin; Swan, Kate; Tadepally, Hamsa; Teboul, Lydia; Tocchini-Valentini, Glauco P; Valenzuela, David; West, Anthony P; Yamamura, Ken-ichi; Yoshinaga, Yuko; Wurst, Wolfgang



Metallothionein and the Biology of Aging  

PubMed Central

Metallothionein (MT) is a low molecular weight protein with anti-apoptotic properties that has been demonstrated to scavenge free radicals in vitro. MT has not been extensively investigated within the context of aging biology. The purpose of this review, therefore, is to discuss findings on MT that are relevant to basic aging mechanisms and to draw attention to the possible role of MT in pro-longevity interventions. MT is one of just a handful of proteins that, when overexpressed, has been demonstrated to increase mouse lifespan. MT also protects against development of obesity in mice provided a high fat diet as well as diet-induced oxidative stress damage. Abundance of MT is responsive to caloric restriction (CR) and inhibition of the insulin / insulin-like signaling (IIS) pathway, and elevated MT gene expression has been observed in tissues from fasted and CR-fed mice, long-lived dwarf mice, worms maintained under CR conditions, and long-lived daf-2 mutant worms. The dysregulation of MT in these systems is likely to have tissue-specific effects on aging outcomes. Further investigation will therefore be needed to understand how MT contributes to the response of invertebrates and mice to CR and the endocrine mutations studied by aging researchers. PMID:20933613

Swindell, William R.



Cdx gene deficiency compromises embryonic hematopoiesis in the mouse  

Microsoft Academic Search

Cdx genes (Cdx1, Cdx2, and Cdx4) encode a family of caudal-related transcription factors that mediate anterior-posterior patterning during embryogenesis through Hox gene regulation. Homologues in the zebrafish have been shown to play key roles in blood formation. To define the role of Cdx genes during embryonic hematopoiesis in a mammalian system, we examined the hematopoietic potential of Cdx-deficient mouse embryonic

Yuan Wang; Akiko Yabuuchi; Shannon McKinney-Freeman; Danica M. K. Ducharme; Manas K. Ray; Kallayanee Chawengsaksophak; Trevor K. Archer; George Q. Daley



Expression of two novel mouse Iroquois homeobox genes during neurogenesis  

Microsoft Academic Search

Members of the DrosophilaIroquois homeobox gene family are implicated in the development of peripheral nervous system and the regionalization of wing and eye imaginal discs. Recent studies suggest that XenopusIroquois homeobox (Irx) genes are also involved in neurogenesis. Three mouse Irx genes, Irx1, Irx2 and Irx3, have been previously identified and are expressed with distinct spatio-temporal patterns during neurogenesis. We

Dana R. Cohen; Chi Wa Cheng; Shuk Han Cheng; Chi-chung Hui



Characterization and expression of a metallothionein gene in the aquatic fern Azolla filiculoides under heavy metal stress.  


A cDNA encoding a type 2 metallothionein (MT) was isolated from Azolla filiculoides, termed AzMT2, accession no. AF482470. The AzMT2 transcript was expressed in sterile A. filiculoides that were free of the cyanobiont Anabaena azollae after erythromycin treatment, proving that AzMT2 is encoded by the fern genome. AzMT2 RNA expression was enhanced by the addition of Cd(+2), Cu(+2), Zn(+2) and Ni(+2) to the growth medium. The transcript level of AzMT2 correlated with the metal content in the plants. Temporal analysis of AzMT2 expression demonstrated that Cd(2+) and Ni(2+) induction of AzMT2 RNA expression occurred within 48 h. AzMT2-enhanced expression responded more intensely to the toxic Cd and Ni ions in A. filiculoides suggesting that AzMT2 may participate in detoxification mechanism. The more moderate response of AzMT2 to Zn and Cu ions, which are essential micronutrients, suggest a role for AzMT2 in metal homeostasis. PMID:16133213

Schor-Fumbarov, Tamar; Goldsbrough, Peter B; Adam, Zach; Tel-Or, Elisha



Enhanced copper tolerance in Silene vulgaris (Moench) Garcke populations from copper mines is associated with increased transcript levels of a 2b-type metallothionein gene.  


Silene vulgaris (Moench) Garcke has evolved populations with extremely high levels of copper tolerance. To evaluate the role of metallothioneins (MTs) in copper tolerance in S. vulgaris, we screened a cDNA library derived from a highly copper-tolerant population using Arabidopsis-based MT probes and identified an MT2b-like gene. When expressed in yeast, this gene, SvMT2b, restored cadmium and copper tolerance in different hypersensitive strains. Northern-blot analysis and quantitative reverse transcriptase-PCR showed that plants from the copper-tolerant S. vulgaris populations had significantly higher transcript levels of SvMT2b than plants from the copper-sensitive populations, both in roots and shoots and with and without copper exposure. Southern-blot analysis suggested that the higher expression of the latter allele was caused by gene amplification. Segregating families of crosses between copper-sensitive and copper-tolerant plants exhibited a 1 to 3 segregation for SvMT2b expression. Allele-specific PCR showed that low-expression F(3) plants were homozygous for the allele inherited from the copper-sensitive parent, whereas high-expression plants possessed at least one allele from the tolerant parent. SvMT2b expression did not cosegregate with copper tolerance in crosses between sensitive and tolerant plants. However, a significant cosegregation with copper tolerance did occur in families derived from crosses between moderately tolerant F(3) plants with different SvMT2b genotypes. Thus, overexpression of SvMT2b conferred copper tolerance although only within the genetic background of a copper tolerant plant. PMID:11500550

van Hoof, N A; Hassinen, V H; Hakvoort, H W; Ballintijn, K F; Schat, H; Verkleij, J A; Ernst, W H; Karenlampi, S O; Tervahauta, A I



Bi-allelic gene targeting in mouse embryonic stem cells.  


The EUCOMM and KOMP programs have generated targeted conditional alleles in mouse embryonic stem cells for nearly 10,000 genes. The availability of these stem cell resources will greatly accelerate the functional analysis of genes in mice and in cultured cells. We present a method for conditional ablation of genes in ES cells using vectors and targeted clones from the EUCOMM and KOMP conditional resources. Inducible homozygous cells described here provide a precisely controlled experimental system to study gene function in a model cell. PMID:21288739

Tate, Peri H; Skarnes, William C



Overlapping genes in the human and mouse genomes  

PubMed Central

Background Increasing evidence suggests that overlapping genes are much more common in eukaryotic genomes than previously thought. In this study we identified and characterized the overlapping genes in a set of 13,484 pairs of human-mouse orthologous genes. Results About 10% of the genes under study are overlapping genes, the majority of which are different-strand overlaps. The majority of the same-strand overlaps are embedded forms, whereas most different-strand overlaps are not embedded and in the convergent transcription orientation. Most of the same-strand overlapping gene pairs show at least a tenfold difference in length, much larger than the length difference between non-overlapping neighboring gene pairs. The length difference between the two different-strand overlapping genes is less dramatic. Over 27% of the different-strand-overlap relationships are shared between human and mouse, compared to only ~8% conservation for same-strand-overlap relationships. More than 96% of the same-strand and different-strand overlaps that are not shared between human and mouse have both genes located on the same chromosomes in the species that does not show the overlap. We examined the causes of transition between the overlapping and non-overlapping states in the two species and found that 3' UTR change plays an important role in the transition. Conclusion Our study contributes to the understanding of the evolutionary transition between overlapping genes and non-overlapping genes and demonstrates the high rates of evolutionary changes in the un-translated regions. PMID:18410680

Sanna, Chaitanya R; Li, Wen-Hsiung; Zhang, Liqing



Genes and gene expression modules associated with caloric restriction and aging in the laboratory mouse  

Microsoft Academic Search

BACKGROUND: Caloric restriction (CR) counters deleterious effects of aging and, for most mouse genotypes, increases mean and maximum lifespan. Previous analyses of microarray data have identified gene expression responses to CR that are shared among multiple mouse tissues, including the activation of anti-oxidant, tumor suppressor and anti-inflammatory pathways. These analyses have provided useful research directions, but have been restricted to

William R Swindell



A biphasic pattern of gene expression during mouse retina development  

PubMed Central

Background Between embryonic day 12 and postnatal day 21, six major neuronal and one glia cell type are generated from multipotential progenitors in a characteristic sequence during mouse retina development. We investigated expression patterns of retina transcripts during the major embryonic and postnatal developmental stages to provide a systematic view of normal mouse retina development, Results A tissue-specific cDNA microarray was generated using a set of sequence non-redundant EST clones collected from mouse retina. Eleven stages of mouse retina, from embryonic day 12.5 (El2.5) to postnatal day 21 (PN21), were collected for RNA isolation. Non-amplified RNAs were labeled for microarray experiments and three sets of data were analyzed for significance, hierarchical relationships, and functional clustering. Six individual gene expression clusters were identified based on expression patterns of transcripts through retina development. Two developmental phases were clearly divided with postnatal day 5 (PN5) as a separate cluster. Among 4,180 transcripts that changed significantly during development, approximately 2/3 of the genes were expressed at high levels up until PN5 and then declined whereas the other 1/3 of the genes increased expression from PN5 and remained at the higher levels until at least PN21. Less than 1% of the genes observed showed a peak of expression between the two phases. Among the later increased population, only about 40% genes are correlated with rod photoreceptors, indicating that multiple cell types contributed to gene expression in this phase. Within the same functional classes, however, different gene populations were expressed in distinct developmental phases. A correlation coefficient analysis of gene expression during retina development between previous SAGE studies and this study was also carried out. Conclusion This study provides a complementary genome-wide view of common gene dynamics and a broad molecular classification of mouse retina development. Different genes in the same functional clusters are expressed in the different developmental stages, suggesting that cells might change gene expression profiles from differentiation to maturation stages. We propose that large-scale changes in gene regulation during development are necessary for the final maturation and function of the retina. PMID:17044933

Zhang, Samuel Shao-Min; Xu, Xuming; Liu, Mu-Gen; Zhao, Hongyu; Soares, Marcelo Bento; Barnstable, Colin J; Fu, Xin-Yuan



Weighted gene coexpression network analysis strategies applied to mouse weight.  


Systems-oriented genetic approaches that incorporate gene expression and genotype data are valuable in the quest for genetic regulatory loci underlying complex traits. Gene coexpression network analysis lends itself to identification of entire groups of differentially regulated genes-a highly relevant endeavor in finding the underpinnings of complex traits that are, by definition, polygenic in nature. Here we describe one such approach based on liver gene expression and genotype data from an F(2) mouse inter-cross utilizing weighted gene coexpression network analysis (WGCNA) of gene expression data to identify physiologically relevant modules. We describe two strategies: single-network analysis and differential network analysis. Single-network analysis reveals the presence of a physiologically interesting module that can be found in two distinct mouse crosses. Module quantitative trait loci (mQTLs) that perturb this module were discovered. In addition, we report a list of genetic drivers for this module. Differential network analysis reveals differences in connectivity and module structure between two networks based on the liver expression data of lean and obese mice. Functional annotation of these genes suggests a biological pathway involving epidermal growth factor (EGF). Our results demonstrate the utility of WGCNA in identifying genetic drivers and in finding genetic pathways represented by gene modules. These examples provide evidence that integration of network properties may well help chart the path across the gene-trait chasm. PMID:17668265

Fuller, Tova F; Ghazalpour, Anatole; Aten, Jason E; Drake, Thomas A; Lusis, Aldons J; Horvath, Steve



The chromosomal location of the mouse mammary tumor gene Int6 and related pseudogenes in the mouse genome  

SciTech Connect

The Int6 gene is a common insertion site for the mouse mammary tumor virus (MMTV) in mouse mammary tumors. We have determined that this gene is located centromeric of the Myc protooncogene on mouse chromosome 15. In the mouse genome there are several other Int6-reactive restriction fragments that are located on mouse chromosomes 6, 11, 14, 17, and 18. Nucleotide sequence analysis of four of six of these additional Int6 fragments showed that they contain processed Int6 pseudogenes. Comparisons between the Int6 genes of the inbred mouse laboratory strains and the wild mouse species Mus spretus and Mus mus musculus indicate that some pseudogenes were present before divergence of these species and others were acquired since their separation. 27 refs., 2 figs., 1 tab.

Miyazaki, S.; Buttitta, F.; Gallahan, D. [National Cancer Institute, Bethesda, MD (United States)] [and others] [National Cancer Institute, Bethesda, MD (United States); and others



Tissue- and cell-specific expression of metallothionein genes in cadmium- and copper-exposed mussels analyzed by in situ hybridization and RT-PCR  

SciTech Connect

Metallothioneins (MTs) are metal-inducible proteins that can be used as biomarkers of metal exposure. In mussels two families of MT isoforms (MT10 and MT20) have been characterized. In this study, mussels (Mytilus galloprovincialis) were exposed to 200 ppb Cd and 40 ppb Cu for 2 and 9 days to characterize the tissue and isoform specificity of metal-induced MT expression. Non-radioactive in situ hybridization demonstrated that both MT isoforms were mainly transcribed in digestive tubule epithelial cells, especially in basophilic cells. Weaker MT expression was detected in non-ciliated duct cells, stomach and gill epithelial cells, haemocytes, adipogranular cells, spermatic follicles and oocytes. RT-PCR resulted in cloning of a novel M. galloprovincialis isoform homologous to recently cloned Mytilus edulis intron-less MT10B isoform. In gills, Cd only affected MT10 gene expression after 2 days of exposure while increases in MT protein levels occurred at day 9. In the digestive gland, a marked increase of both isoforms, but especially of MT20, was accompanied by increased levels of MT proteins and basophilic cell volume density (Vv{sub BAS}) after 2 and 9 days and of intralysosomal metal accumulation in digestive cells after 9 days. Conversely, although metal was accumulated in digestive cells lysosomes and the Vv{sub BAS} increased in Cu-exposed mussels, Cu exposure did not produce an increase of MT gene expression or MT protein levels. These data suggest that MTs are expressed in a tissue-, cell- and isoform-specific way in response to different metals.

Zorita, I. [Lab. Cell Biology and Histology, Dept. Zoology and Animal Cell Biology, University of the Basque Country, PO Box 644, E-48080 Bilbao, Basque Country (Spain); Bilbao, E. [Lab. Cell Biology and Histology, Dept. Zoology and Animal Cell Biology, University of the Basque Country, PO Box 644, E-48080 Bilbao, Basque Country (Spain); Schad, A. [Institute of Pathology, Johannes Gutenberg University, 55101, Mainz (Germany); Cancio, I. [Lab. Cell Biology and Histology, Dept. Zoology and Animal Cell Biology, University of the Basque Country, PO Box 644, E-48080 Bilbao, Basque Country (Spain); Soto, M. [Lab. Cell Biology and Histology, Dept. Zoology and Animal Cell Biology, University of the Basque Country, PO Box 644, E-48080 Bilbao, Basque Country (Spain); Cajaraville, M.P. [Lab. Cell Biology and Histology, Dept. Zoology and Animal Cell Biology, University of the Basque Country, PO Box 644, E-48080 Bilbao, Basque Country (Spain)]. E-mail:



Automatically identifying and annotating mouse embryo gene expression patterns  

PubMed Central

Motivation: Deciphering the regulatory and developmental mechanisms for multicellular organisms requires detailed knowledge of gene interactions and gene expressions. The availability of large datasets with both spatial and ontological annotation of the spatio-temporal patterns of gene expression in mouse embryo provides a powerful resource to discover the biological function of embryo organization. Ontological annotation of gene expressions consists of labelling images with terms from the anatomy ontology for mouse development. If the spatial genes of an anatomical component are expressed in an image, the image is then tagged with a term of that anatomical component. The current annotation is done manually by domain experts, which is both time consuming and costly. In addition, the level of detail is variable, and inevitably errors arise from the tedious nature of the task. In this article, we present a new method to automatically identify and annotate gene expression patterns in the mouse embryo with anatomical terms. Results: The method takes images from in situ hybridization studies and the ontology for the developing mouse embryo, it then combines machine learning and image processing techniques to produce classifiers that automatically identify and annotate gene expression patterns in these images. We evaluate our method on image data from the EURExpress study, where we use it to automatically classify nine anatomical terms: humerus, handplate, fibula, tibia, femur, ribs, petrous part, scapula and head mesenchyme. The accuracy of our method lies between 70% and 80% with few exceptions. We show that other known methods have lower classification performance than ours. We have investigated the images misclassified by our method and found several cases where the original annotation was not correct. This shows our method is robust against this kind of noise. Availability: The annotation result and the experimental dataset in the article can be freely accessed at Contact: Supplementary Information: Supplementary data are available at Bioinformatics online. PMID:21357576

Han, Liangxiu; van Hemert, Jano I.; Baldock, Richard A.



Activation of genes involved in xenobiotic metabolism is a shared signature of mouse models with extended lifespan.  


Xenobiotic metabolism has been proposed to play a role in modulating the rate of aging. Xenobiotic metabolizing enzymes (XME) are expressed at higher levels in calorically restricted mice (CR) and in GH/IGF-I-deficient, long-lived mutant mice. In this study, we show that many phase I XME genes are similarly upregulated in additional long-lived mouse models, including "crowded litter" (CL) mice, whose lifespan has been increased by food restriction limited to the first 3 wk of life, and in mice treated with rapamycin. Induction in the CL mice lasts at least through 22 mo of age, but induction by rapamycin is transient for many of the mRNAs. Cytochrome P-450s, flavin monooxygenases, hydroxyacid oxidase, and metallothioneins were found to be significantly elevated in similar proportions in each of the models of delayed aging tested, whether these were based on mutation, diet, drug treatment, or transient early intervention. The same pattern of mRNA elevation could be induced by 2 wk of treatment with tert-butylhydroquinone, an oxidative toxin known to activate Nrf2-dependent target genes. These results suggest that elevation of phase I XMEs is a hallmark of long-lived mice and may facilitate screens for agents worth testing in intervention-based lifespan studies. PMID:22693205

Steinbaugh, Michael J; Sun, Liou Y; Bartke, Andrzej; Miller, Richard A



The functional landscape of mouse gene expression  

Microsoft Academic Search

ABSTRACT: BACKGROUND: Large-scale quantitative analysis of transcriptional co-expression has been used to dissect regulatory networks and to predict the functions of new genes discovered by genome sequencing in model organisms such as yeast. Although the idea that tissue-specific expression is indicative of gene function in mammals is widely accepted, it has not been objectively tested nor compared with the related

Wen Zhang; Quaid D Morris; Richard Chang; Ofer Shai; Malina A Bakowski; Nicholas Mitsakakis; Naveed Mohammad; Mark D Robinson; Ralph Zirngibl; Eszter Somogyi; Nancy Laurin; Eftekhar Eftekharpour; Eric Sat; Jörg Grigull; Qun Pan; Wen-Tao Peng; Nevan Krogan; Jack Greenblatt; Michael Fehlings; Derek van der Kooy; Jane Aubin; Benoit G Bruneau; Janet Rossant; Benjamin J Blencowe; Brendan J Frey; Timothy R Hughes



Jackson Laboratory - Mouse Genome Informatics: The Gene Expression Database  

NSDL National Science Digital Library

A very unique biomedical research institution, "The Jackson Laboratory, a non-profit institution, is the world's largest mammalian genetic research facility." As such, Jackson provides universities and hospitals worldwide with millions of mice -- representing more than 2,500 varieties -- each year. This website offering from Jackson Laboratory, located in Bar Harbor, Maine, allows visitors to solicit valuable information on the mouse genome. "The Gene Expression Database (GXD) is a community resource for gene expression information from the laboratory mouse. GXD stores and integrates different types of expression data and makes these data freely available in formats appropriate for comprehensive analysis." At the site, visitors can learn about how to acquire data and search for via the Gene Expression Query Forms. Also of interest are the sections devoted to Who's Who in GXD and links to Selected Publications.


Lentiviral gene transduction in human and mouse NK cell lines.  


Natural killer (NK) cells play a vital role in the control of cancer and microbial infections. A major hinderance in studying NK cells is the resistance of these cells to gene transfer. Considering over-expression and gene knockdown studies are crucial tools to study the biology of cells, technologies suitable for transferring genes into NK cells are invaluable. Among various technologies available for gene transfer, lentiviral-mediated transduction has been successful in introducing genes into NK cells. We have standardized methods of lentiviral infection in human and mouse NK cell lines. We obtain transduction efficiencies of 15% in the NK-92 cell line and 30-40% in LNK, YT, and DERL7 cell lines. This method allows efficient and stable introduction of genes and shRNAs into NK cell lines. PMID:20033643

Savan, Ram; Chan, Tim; Young, Howard A



Ptaquiloside reduces NK cell activities by enhancing metallothionein expression, which is prevented by selenium.  


Pteridium aquilinum, one of the most important poisonous plants in the world, is known to be carcinogenic to animals and humans. Moreover, our previous studies showed that the immunosuppressive effects of ptaquiloside, its main toxic agent, were prevented by selenium in mouse natural killer (NK) cells. We also verified that this immunosuppression facilitated development of cancer. Here, we performed gene expression microarray analysis in splenic NK cells from mice treated for 14 days with ptaquiloside (5.3 mg/kg) and/or selenium (1.3 mg/kg) to identify gene transcripts altered by ptaquiloside that could be linked to the immunosuppression and that would be prevented by selenium. Transcriptome analysis of ptaquiloside samples revealed that 872 transcripts were expressed differentially (fold change>2 and p<0.05), including 77 up-regulated and 795 down-regulated transcripts. Gene ontology analysis mapped these up-regulated transcripts to three main biological processes (cellular ion homeostasis, negative regulation of apoptosis and regulation of transcription). Considering the immunosuppressive effect of ptaquiloside, we hypothesized that two genes involved in cellular ion homeostasis, metallothionein 1 (Mt1) and metallothionein 2 (Mt2), could be implicated because Mt1 and Mt2 are responsible for zinc homeostasis, and a reduction of free intracellular zinc impairs NK functions. We confirm these hypotheses and show increased expression of metallothionein in splenic NK cells and reduction in free intracellular zinc following treatment with ptaquiloside that were completely prevented by selenium co-treatment. These findings could help avoid the higher susceptibility to cancer that is induced by P. aquilinum-mediated immunosuppressive effects. PMID:23274088

Latorre, Andreia O; Caniceiro, Beatriz D; Fukumasu, Heidge; Gardner, Dale R; Lopes, Fabricio M; Wysochi, Harry L; da Silva, Tereza C; Haraguchi, Mitsue; Bressan, Fabiana F; Górniak, Silvana L



Tetrahymena Metallothioneins Fall into Two Discrete Subfamilies  

PubMed Central

Background Metallothioneins are ubiquitous small, cysteine-rich, multifunctional proteins which can bind heavy metals. Methodology/Principal Findings We report the results of phylogenetic and gene expression analyses that include two new Tetrahymena thermophila metallothionein genes (MTT3 and MTT5). Sequence alignments of all known Tetrahymena metallothioneins have allowed us to rationalize the structure of these proteins. We now formally subdivide the known metallothioneins from the ciliate genus Tetrahymena into two well defined subfamilies, 7a and 7b, based on phylogenetic analysis, on the pattern of clustering of Cys residues, and on the pattern of inducibility by the heavy metals Cd and Cu. Sequence alignment also reveals a remarkably regular, conserved and hierarchical modular structure of all five subfamily 7a MTs, which include MTT3 and MTT5. The former has three modules, while the latter has only two. Induction levels of the three T. thermophila genes were determined using quantitative real time RT-PCR. Various stressors (including heavy metals) brought about dramatically different fold-inductions for each gene; MTT5 showed the highest fold-induction. Conserved DNA motifs with potential regulatory significance were identified, in an unbiased way, upstream of the start codons of subfamily 7a MTs. EST evidence for alternative splicing in the 3? UTR of the MTT5 mRNA with potential regulatory activity is reported. Conclusion/Significance The small number and remarkably regular structure of Tetrahymena MTs, coupled with the experimental tractability of this model organism for studies of in vivo function, make it an attractive system for the experimental dissection of the roles, structure/function relationships, regulation of gene expression, and adaptive evolution of these proteins, as well as for the development of biotechnological applications for the environmental monitoring of toxic substances. PMID:17356700

Campos, Virginia; Benitez, Laura; Martin-Gonzalez, Ana; Hamilton, Eileen P.; Orias, Eduardo; Gutierrez, Juan C.



Conditional gene expression in the mouse using a Sleeping Beauty gene-trap transposon  

PubMed Central

Background Insertional mutagenesis techniques with transposable elements have been popular among geneticists studying model organisms from E. coli to Drosophila and, more recently, the mouse. One such element is the Sleeping Beauty (SB) transposon that has been shown in several studies to be an effective insertional mutagen in the mouse germline. SB transposon vector studies have employed different functional elements and reporter molecules to disrupt and report the expression of endogenous mouse genes. We sought to generate a transposon system that would be capable of reporting the expression pattern of a mouse gene while allowing for conditional expression of a gene of interest in a tissue- or temporal-specific pattern. Results Here we report the systematic development and testing of a transposon-based gene-trap system incorporating the doxycycline-repressible Tet-Off (tTA) system that is capable of activating the expression of genes under control of a Tet response element (TRE) promoter. We demonstrate that the gene trap system is fully functional in vitro by introducing the "gene-trap tTA" vector into human cells by transposition and identifying clones that activate expression of a TRE-luciferase transgene in a doxycycline-dependent manner. In transgenic mice, we mobilize gene-trap tTA vectors, discover parameters that can affect germline mobilization rates, and identify candidate gene insertions to demonstrate the in vivo functionality of the vector system. We further demonstrate that the gene-trap can act as a reporter of endogenous gene expression and it can be coupled with bioluminescent imaging to identify genes with tissue-specific expression patterns. Conclusion Akin to the GAL4/UAS system used in the fly, we have made progress developing a tool for mutating and revealing the expression of mouse genes by generating the tTA transactivator in the presence of a secondary TRE-regulated reporter molecule. A vector like the gene-trap tTA could provide a means for both annotating mouse genes and creating a resource of mice that express a regulable transcription factor in temporally- and tissue-specific patterns for conditional gene expression studies. These mice would be a valuable resource to the mouse genetics community for purpose of dissecting mammalian gene function. PMID:16800892

Geurts, Aron M; Wilber, Andrew; Carlson, Corey M; Lobitz, Paul D; Clark, Karl J; Hackett, Perry B; McIvor, R Scott; Largaespada, David A



EMAGE mouse embryo spatial gene expression database: 2014 update  

PubMed Central

EMAGE ( is a freely available database of in situ gene expression patterns that allows users to perform online queries of mouse developmental gene expression. EMAGE is unique in providing both text-based descriptions of gene expression plus spatial maps of gene expression patterns. This mapping allows spatial queries to be accomplished alongside more traditional text-based queries. Here, we describe our recent progress in spatial mapping and data integration. EMAGE has developed a method of spatially mapping 3D embryo images captured using optical projection tomography, and through the use of an IIP3D viewer allows users to view arbitrary sections of raw and mapped 3D image data in the context of a web browser. EMAGE now includes enhancer data, and we have spatially mapped images from a comprehensive screen of transgenic reporter mice that detail the expression of mouse non-coding genomic DNA fragments with enhancer activity. We have integrated the eMouseAtlas anatomical atlas and the EMAGE database so that a user of the atlas can query the EMAGE database easily. In addition, we have extended the atlas framework to enable EMAGE to spatially cross-index EMBRYS whole mount in situ hybridization data. We additionally report on recent developments to the EMAGE web interface, including new query and analysis capabilities. PMID:24265223

Richardson, Lorna; Venkataraman, Shanmugasundaram; Stevenson, Peter; Yang, Yiya; Moss, Julie; Graham, Liz; Burton, Nicholas; Hill, Bill; Rao, Jianguo; Baldock, Richard A.; Armit, Chris



EMAGE mouse embryo spatial gene expression database: 2014 update.  


EMAGE ( is a freely available database of in situ gene expression patterns that allows users to perform online queries of mouse developmental gene expression. EMAGE is unique in providing both text-based descriptions of gene expression plus spatial maps of gene expression patterns. This mapping allows spatial queries to be accomplished alongside more traditional text-based queries. Here, we describe our recent progress in spatial mapping and data integration. EMAGE has developed a method of spatially mapping 3D embryo images captured using optical projection tomography, and through the use of an IIP3D viewer allows users to view arbitrary sections of raw and mapped 3D image data in the context of a web browser. EMAGE now includes enhancer data, and we have spatially mapped images from a comprehensive screen of transgenic reporter mice that detail the expression of mouse non-coding genomic DNA fragments with enhancer activity. We have integrated the eMouseAtlas anatomical atlas and the EMAGE database so that a user of the atlas can query the EMAGE database easily. In addition, we have extended the atlas framework to enable EMAGE to spatially cross-index EMBRYS whole mount in situ hybridization data. We additionally report on recent developments to the EMAGE web interface, including new query and analysis capabilities. PMID:24265223

Richardson, Lorna; Venkataraman, Shanmugasundaram; Stevenson, Peter; Yang, Yiya; Moss, Julie; Graham, Liz; Burton, Nicholas; Hill, Bill; Rao, Jianguo; Baldock, Richard A; Armit, Chris



The functional significance of brain metallothioneins  

Microsoft Academic Search

Metallothioneins (MTs) are ubiquitous low molecular weight proteins characterized by their abundant content of cysteines. Two MT isoforms, MT-I and MT-lI, are expressed coordinately in all mammalian tissues. In the CNS, MT-I and MT-I! are conspicuously absent from neuronal populations, yet abundant in fibrous and protoplasmic astrocytes. A newly identified brain-specific MT gene, MT-Ill, is predominantly expressed in zinc-containing neurons



Carbonic anhydrase II gene expression in mouse pancreatic duct cells.  


Our goal is to create a transgenic mouse model for human pancreatic duct cell adenocarcinoma using the promoter/enhancer region of the carbonic anhydrase (CA) II gene to drive the expression of SV-40 T-antigen in pancreatic duct cells. This requires that the CA II gene be expressed in mouse pancreatic duct cells and not in other pancreatic cells, as has already been shown to be the case in the human and guinea pig pancreas. We have shown with an enzyme histochemical assay that mouse pancreatic duct cells contain CA activity in both intact pancreas and cultured interlobular duct epithelium. In addition, CA activity was detected with a biochemical assay in homogenates of cultured duct epithelium. The specific activity of duct cells was 2.75-fold greater than in whole pancreas, suggesting that a substantial amount of total pancreatic CA activity is contributed by duct cells. At least some of the CA in cultured duct cells was inferred to be CA II by Northern blot analysis of RNA extracted from the cells. The concentration of CA II mRNA in the cultured duct cells was substantially greater than in whole pancreas and would appear to account for the majority, if not all, of the CA II in the mouse pancreas. PMID:1381098

Githens, S; Schexnayder, J A; Frazier, M L



Insights from spatially mapped gene expression in the mouse brain.  


The growing number of publicly available databases of murine gene expression arising from genomic-scale transcriptome/proteome profiling projects allows open access to information about genes potentially involved in diseases and disorders of the brain. The use of various methodologies by myriad projects provides complementary types of information, ranging from easily quantifiable microarray data for gross brain regions, to transcript tag analysis and proteomic characterization. One mode of gene expression analysis that has recently been widely adopted is the utilization of colorimetric in situ hybridization. This approach is adaptable for high throughput production, and provides a reproducible, scaleable platform for large datasets. The Allen Brain Atlas in particular has utilized this technology to produce a genomic-scale anatomical digital atlas of gene expression in the adult male mouse brain. The availability of global datasets with cellular level spatial resolution, which can be easily parsed due to accessible informatics-derived image analysis tools, can provide both high level and detailed insights into gene regulation. This article reviews various gene expression profiling projects in the mouse brain, how these data sets are increasingly used to complement other studies and applications of these datasets to further understanding of neurological disease. PMID:17911164

Sunkin, Susan M; Hohmann, John G



Effects of perinatal exposure to low doses of cadmium or methylmercury on thyroid hormone metabolism in metallothionein-deficient mouse neonates.  


Perinatal exposure to cadmium (Cd) or methylmercury (MeHg) results in impaired neurodevelopment. Thyroid hormone is essential for normal brain development. However, the issue whether Cd or MeHg, especially at low doses, interrupts thyroid hormone action remains to be investigated. In the present study, effects of perinatal exposure to low levels of Cd or MeHg on thyroid hormone metabolism were examined using metallothionein I and II (MT-I/II) null or wild-type neonatal mice. Dams were exposed to 10 mg/L water of Cd or 5 mg/kg chow of MeHg from gestational day 0 to post-natal day 10 (PND 10). Sera, livers and brains were collected from neonates on PND 10. Iodothyronine deiodinase activities and serum thyroxine (T4) concentrations were measured. MeHg exposure failed to induce changes in serum T4 levels and liver type 1 deiodinase (D1) and brain type 2 deiodinase (D2) activities regardless of the MT genotype. However, exposure to MeHg resulted in a decrease in brain type 3 deiodinase (D3) activity in MT-I/II null and wild-type neonates. In contrast, exposure to Cd resulted in a decrease in serum T4 levels in MT-I/II null neonates. Consistently, brain D2 activity was increased in Cd-exposed MT-I/II null neonates. No significant changes in liver D1 and brain D3 activities were induced by Cd administration. Our study demonstrates that perinatal exposure to low doses of Cd or MeHg can induce changes in brain deiodinase activities in the neonates, suggesting that thyroid hormone metabolism in fetuses and neonates might be a potential target of Cd and MeHg. PMID:16982123

Mori, Kouki; Yoshida, Katsumi; Hoshikawa, Saeko; Ito, Sadayoshi; Yoshida, Minoru; Satoh, Masahiko; Watanabe, Chiho



Sex-specific gene expression in the BXD mouse liver  

PubMed Central

Differences in clinical phenotypes between the sexes are well documented and have their roots in differential gene expression. While sex has a major effect on gene expression, transcription is also influenced by complex interactions between individual genetic variation and environmental stimuli. In this study, we sought to understand how genetic variation affects sex-related differences in liver gene expression by performing genetic mapping of genomewide liver mRNA expression data in a genetically defined population of naive male and female mice from C57BL/6J, DBA/2J, B6D2F1, and 37 C57BL/6J × DBA/2J (BXD) recombinant inbred strains. As expected, we found that many genes important to xenobiotic metabolism and other important pathways exhibit sexually dimorphic expression. We also performed gene expression quantitative trait locus mapping in this panel and report that the most significant loci that appear to regulate a larger number of genes than expected by chance are largely sex independent. Importantly, we found that the degree of correlation within gene expression networks differs substantially between the sexes. Finally, we compare our results to a recently released human liver gene expression data set and report on important similarities in sexually dimorphic liver gene expression between mouse and human. This study enhances our understanding of sex differences at the genome level and between species, as well as increasing our knowledge of the molecular underpinnings of sex differences in responses to xenobiotics. PMID:20551147

Gatti, Daniel M.; Zhao, Ni; Chesler, Elissa J.; Bradford, Blair U.; Shabalin, Andrey A.; Yordanova, Roumyana; Lu, Lu




EPA Science Inventory

The objectives of these studies were two-fold: (1) to determine efficacy of low and high expression hMT gene constructs by assessing accumulation of Cu in shoots of parental and transgenic plants of alfalfa (Medicago varia L.) exposed to different concentrations of CuSO4 by addit...


Update of the human and mouse SERPIN gene superfamily  

PubMed Central

The serpin family comprises a structurally similar, yet functionally diverse, set of proteins. Named originally for their function as serine proteinase inhibitors, many of its members are not inhibitors but rather chaperones, involved in storage, transport, and other roles. Serpins are found in genomes of all kingdoms, with 36 human protein-coding genes and five pseudogenes. The mouse has 60 Serpin functional genes, many of which are orthologous to human SERPIN genes and some of which have expanded into multiple paralogous genes. Serpins are found in tissues throughout the body; whereas most are extracellular, there is a class of intracellular serpins. Serpins appear to have roles in inflammation, immune function, tumorigenesis, blood clotting, dementia, and cancer metastasis. Further characterization of these proteins will likely reveal potential biomarkers and therapeutic targets for disease. PMID:24172014



The mouse angiogenin gene family: Structures of an angiogenin-related protein gene and two pseudogenes  

SciTech Connect

Angiogenin, a homologue of pancreatic ribonuclease, is a potent inducer of blood vessel formation. As an initial step toward investigating the in vivo functional role of this protein via gene disruption, we undertook the isolation of the angiogenin gene (Ang) from the 129 strain mouse, which will be used for generating targeting constructs. Unexpectedly, screening of a genomic library with an Ang gene probe obtained previously from the BALB/c strain yielded two new genes closely similar to Ang rather than Ang itself. One of these encodes a protein with 78% sequence identity to angiogenin and is designated {open_quotes}Angrp{close_quotes} for {open_quotes}angiogenin-related protein.{close_quotes} The ribonucleolytic active site of angiogenin, which is critical for angiogenic activity, is completely conserved in Angrp, whereas a second essential site, thought to bind cellular receptors, is considerably different. Thus, the Angrp product may have a function distinct from that of angiogenin. The second gene obtained by library screening is a pseudogene, designated {open_quotes}Ang-ps1,{close_quotes} that contains a frame shift mutation in the early part of the coding region. Although the Ang gene was not isolated from this library, it was possible to amplify this gene from 129 mouse genomic DNA by the polymerase chain reaction (PCR). Sequence analysis showed that the 129 strain Ang gene is identical to the BALB/c gene throughout the coding region. PCR cloning also yielded a second Ang-like pseudogene, designated {open_quotes}Ang-ps2.{close_quotes} Southern blotting of genomic DNA confirmed the presence of Ang, Angrp, and at least one of the pseudogenes in an individual mouse and suggested that the mouse Ang gene family may contain more than the four members identified here. 31 refs., 4 figs., 1 tab.

Brown, W.E.; Nobile, V.; Shapiro, R. [Harvard Medical School, Boston, MA (United States)] [and others] [Harvard Medical School, Boston, MA (United States); and others



Molecular cloning and characterisation of metallothionein type 2a gene from Jatropha curcas L., a promising biofuel plant.  


In the present study, we have cloned a gene encoding JcMT2a protein from Jatropha curcas L., a promising biofuel tree species. Full length sequence of JcMT2a gene was isolated using RACE PCR. Heterologous expression of JcMT2a in Escherichia coli and its purification has shown distinct bands corresponding to the GST and GST-fused JcMT2a protein. Significant tolerance was observed in E. coli cells expressing recombinant GST-JcMT2a for zinc, copper and cadmium metals compared to cells expressing GST alone. JcMT2a also restored Cu and Cd tolerance in the metal sensitive yeast mutants. Quantitative real time PCR showed a significant increase in JcMT2a transcripts with Cu and Cd in the leaf compared to root tissue. Our Scanning electron microscopy and energy dispersive X-ray spectroscopy analysis clearly demonstrates that J. curcas L. could be a potential candidate for phytoremediation to clean heavy metals from the environment, in addition to its non-edible oil seed yields for biodiesel production. PMID:24190491

Mudalkar, Shalini; Golla, Ramesh; Sengupta, Debashree; Ghatty, Sreenivas; Reddy, Attipalli Ramachandra



Fibrillin genes map to regions of conserved mouse/human synteny on mouse chromosomes 2 and 18.  


Fibrillin proteins are major structural components of the 10-nm microfibrils found in elastic and nonelastic connective tissues. Previous studies have mapped the human genes for two fibrillins to chromosome bands 15q21 (FBN1) and 5q23-q31 (FBN2) and have demonstrated that FBN1 mutations are associated with Marfan syndrome, while FBN2 is linked to the gene for congenital contractural arachnodactyly. Here, we report the isolation of genomic clones of the corresponding mouse fibrillin genes (Fbn-1 and Fbn-2). By analyzing a mapping panel of mouse x rodent somatic hybrid cell lines, we have assigned the Fbn-1 gene to mouse chromosome 2 and the Fbn-2 gene to mouse chromosome 18. We then sublocalized the fibrillin genes to bands 2F (Fbn-1) and 18D-E1 (Fbn-2) by fluorescence in situ hybridization. These regions are known to exhibit conserved synteny with the regions on human chromosomes 15 and 5 that carry the homologous human fibrillin genes. In addition, the Fbn-1 gene maps in the vicinity of the gene for a connective tissue disorder on mouse chromosome 2 called Tight-skin (Tsk). PMID:8307578

Li, X; Pereira, L; Zhang, H; Sanguineti, C; Ramirez, F; Bonadio, J; Francke, U



Cotransfer of two linked human genes into cultured mouse cells.  


Two linked human genes which code for the expression of cytosol thymidine kinase (ATP:thymidine 5'-phosphotransferase, EC and galactokinase (ATP:D-galactose 1-phosphotransferase, EC have been cotransferred via purified metaphase chromosomes from the human lymphoblastoid cell line WI-L2a, into mouse L-cells [B82 and LM(TK-)]. Both genes have previously been shown to be closely linked on the human chromosome E17, band q21-22. Coexpression of both human enzyme markers was detected in two out of eight gene transfer clones, whilst the remaining six clones contained only human cytosol thymidine kinase, as shown by electrophoretic techniques. A further 23 human enzyme markers corresponding to 15 different human chromosomes were found to be absent in these gene transfer clones. No human chromosome or chromosomal fragment could be detected by karyotype analyses. Some of the gene transfer clones rapidly lost the transferred donor material when grown in nonselective medium, whereas others expressed a stable phenotype under these conditions. Prolonged maintenance in selective medium favors the survival of gene transfer cells expressing a stable phenotype. Possibly these cells harbor the donor genes integrated into a recipient chromosome. PMID:177984

Willecke, K; Lange, R; Krüger, A; Reber, T



The mouse Gene Expression Database (GXD): 2014 update  

PubMed Central

The Gene Expression Database (GXD; is an extensive and well-curated community resource of mouse developmental expression information. GXD collects different types of expression data from studies of wild-type and mutant mice, covering all developmental stages and including data from RNA in situ hybridization, immunohistochemistry, RT-PCR, northern blot and western blot experiments. The data are acquired from the scientific literature and from researchers, including groups doing large-scale expression studies. Integration with the other data in Mouse Genome Informatics (MGI) and interconnections with other databases places GXD’s gene expression information in the larger biological and biomedical context. Since the last report, the utility of GXD has been greatly enhanced by the addition of new data and by the implementation of more powerful and versatile search and display features. Web interface enhancements include the capability to search for expression data for genes associated with specific phenotypes and/or human diseases; new, more interactive data summaries; easy downloading of data; direct searches of expression images via associated metadata; and new displays that combine image data and their associated annotations. At present, GXD includes >1.4 million expression results and 250 000 images that are accessible to our search tools. PMID:24163257

Smith, Constance M.; Finger, Jacqueline H.; Hayamizu, Terry F.; McCright, Ingeborg J.; Xu, Jingxia; Berghout, Joanne; Campbell, Jeff; Corbani, Lori E.; Forthofer, Kim L.; Frost, Pete J.; Miers, Dave; Shaw, David R.; Stone, Kevin R.; Eppig, Janan T.; Kadin, James A.; Richardson, Joel E.; Ringwald, Martin


100 an atlas of gene expression patterns in the mouse embryo  

PubMed Central

High-throughput instruments were recently developed to determine gene expression patterns on tissue sections by RNA in situ hybridization. The resulting images of gene expression patterns, chiefly of E14.5 mouse embryos, are accessible to the public at This relational database is searchable for gene identifiers and RNA probe sequences. Moreover, patterns and intensity of expression in ?100 different embryonic tissues are annotated and can be searched using a standardized catalog of anatomical structures. A virtual microscope tool, the Zoom Image Server, was implemented in and permits interactive zooming and panning across ?15 000 high-resolution images. PMID:14681479

Visel, Axel; Thaller, Christina; Eichele, Gregor



Effects of light on the accumulation of abscisic acid and expression of an early cysteine-labeled metallothionein gene in microspores of Triticum aestivum during induced embryogenic development  

Microsoft Academic Search

A cloned cDNA to the wheat (Triticum aestivum) early cysteine-labeled metallothionein has many characteristics of a molecular marker for pollen embryogenesis in this plant. This transcript was not detected in uninucleate microspores at the time of culture or in pollen at any stage during normal ontogeny; its mRNA did begin to increase in embryogenic microspores within 6 h of culture,

T. L. Reynolds; R. L. Crawford



Cadmium-inducible BgMT2, a type 2 metallothionein gene from mangrove species ( Bruguiera gymnorrhiza), its encoding protein shows metal-binding ability  

Microsoft Academic Search

Metallothioneins (MTs) are a family of low-molecular-weight Cys-rich proteins and are thought to play possible role in metal metabolism or detoxification. To shed light on the role of type 2 MT in Bruguiera gymnorrhiza (BgMT2) under heavy metal stress, B. gymnorrhiza seedlings were exposed to different concentrations of CdCl2 (2?M, 10?M, 20?M or 40?M) for 3, 7 and 11d. Real-time

Guo-Yong Huang; You-Shao Wang; Guang-Guo Ying



Mouse models of gene-environment interactions in schizophrenia  

PubMed Central

Gene-environment interactions (GEI) likely play significant roles in the pathogenesis of schizophrenia and underlie differences in pathological, behavioral, and clinical presentations of the disease. Findings from epidemiology and psychiatric genetics have assisted in the generation of animal models of GEI relevant to schizophrenia. These models may provide a foundation for elucidating the molecular, cellular, and circuitry mechanisms that mediate GEI in schizophrenia. Here we critically review current mouse models of GEI related to schizophrenia, describe directions for their improvement, and propose endophenotypes provide a more tangible basis for molecular studies of pathways of GEI and facilitate the identification of novel therapeutic targets. PMID:23748077

Kannan, Geetha; Sawa, Akira; Pletnikov, Mikhail V.



Mouse Genetic Nomenclature: Standardization of Strain, Gene, and Protein Symbols  

PubMed Central

The use of standard nomenclatures for describing the strains, genes, and proteins of species is vital for the interpretation, archiving, analysis, and recovery of experimental data on the laboratory mouse. At a time when sharing of data and meta- analysis of experimental results is becoming a dominant mode of scientific investigation, failure to respect formal nomenclatures can cause confusion, errors, and in some cases contribute to poor science. Here we present the basic nomenclature rules for laboratory mice and explain how these rules should be applied to complex genetic manipulations and crosses. PMID:20685919

Sundberg, John P.; Schofield, Paul N



Characterization of the p16 gene in the mouse: Evidence for a large gene family  

SciTech Connect

The p16 gene product is an inhibitor of the cyclin-dependent kinase 4 (CDK4)/cyclin D complex. When uninhibited, the CDK4/cyclin D complex participates in the phosphorylation of the retinoblastoma (RB) protein and renders it inactive. Upon inactivation of the RB protein, transition from the G{sub 1} to the S phase of mitosis occurs and results in cellular proliferation. Thus, p16 is presumed to act as a negative regulator of cell growth by preventing the phosphorylation, and thereby subsequent inactivation, of RB by CDK4/cyclin D. Recently, the p16 gene (also known as the multiple tumor suppressor 1 (MTS1) gene) has been mapped to chromosome 9p21 and found to be deleted or mutated in a number of tumor cell lines. These findings support the role of p16 as a growth inhibitor or tumor suppressor gene and suggest that the mutation of this gene may have global implications in carcinogenesis. We have chosen to test the functional significance of p16 mutations in vivo through the generation of a mouse mutant for p16. In preparation for this undertaking, eight apparently independent (as judged by restriction enzyme digestion and differential hybridization) mouse genomic embryonic stem cell clones have been identified using exon 2 from the human p16 gene as a probe. The identification of these multiple nonoverlapping clones was not entirely surprising since the reduced stringency hybridization of a zoo blot with the same probe also revealed 10-15 positive EcoRI fragments in all species tested, including human, monkey, cow, dog, cat, rabbit, hamster, mouse, chicken and D. melanogaster. Taken together, these findings suggest that the p16 gene is a member of a large gene family. The location of these genomic clones, as well as their potential expression in the mouse, is currently under investigation.

Fountain, J.W.; Giendening, J.M.; Flores, J.F. [Univ. of Southern California, Los Angeles, CA (United States)] [and others



Genetic Mapping of Four Mouse bHLH Genes Related to DrosophilaProneural Gene atonal  

Microsoft Academic Search

It has been shown that mammalian neurogenesis is partly controlled by multiple basic helix–loop–helix (bHLH) genes, as inDrosophila.Recently, mouse homologs ofDrosophila atonal,a proneural gene encoding a bHLH protein required for chordotonal organ and photoreceptor development, have been characterized to obtain further insights into the molecular nature of mammalian neurogenesis. Here, to assess their potential involvement in genetic neural disorders, we

Fumiaki Isaka; Chikara Shimizu; Shigetada Nakanishi; Ryoichiro Kageyama



Identify lymphatic metastasis-associated genes in mouse hepatocarcinoma cell lines using gene chip  

Microsoft Academic Search

Abstract Abstract Abstract Abstract Abstract AIM: In order to obtain ,lymphogenous ,metastasis- associated genes, we compared the transcriptional profiles of mouse hepatocarcinoma,cell lines Hca-F with highly lymphatic,metastasis ,potential ,and ,Hca-P with low lymphatic metastasis potential. METHODS:T otal RNA was isolated from Hca-F and Hca-P

Bo Song; Jian-Wu Tang; Bo Wang; Xiao-Nan Cui; Lu Sun; Li-Min Mao; Chun-Hui Zhou; Yue Du; Li-Hui Wang; Hua-Xin Wang; Ren-Shu Zheng; Lei Sun



Mouse NGF promoter upstream sequences do not affect gene expression in mouse fibroblasts.  


The expression of nerve growth factor (NGF) is tightly controlled in a tissue-specific manner during development and in response to injury. In fibroblasts and in other cell types, expression of NGF is regulated at the transcriptional level. In order to elucidate the mechanism of this regulation, we have undertaken the analysis of the mouse NGF promoter in a mouse fibroblast cell line (LTA), using transient transfection of NGF promoter-human growth hormone (hGH) reporter gene plasmids. We find that sequences between +8bp and +120bp, containing an AP-1 site, confer increased levels of expression from the full length and truncated NGF promoters. When this region is deleted, a significant decrease in expression is observed from both the full length promoter and truncated versions thereof. A gradual increase in expression is observed with successive 5' deletions of both the AP-1 containing and AP-1 deleted promoters; this effect results from the juxtapositioning of adjacent plasmid sequences closer to the transcription initiation site and not from deletion of promoter sequences as was previously reported. When the NGF promoter is analyzed using a luciferase reporter plasmid, these 5' promoter deletions have no significant effect on reporter gene expression in fibroblasts. Thus, sequences downstream of the transcription start site influence NGF promoter activity in fibroblasts, but sequences upstream of the TATA box fail to affect promoter activity in these cells. PMID:7877455

Cowie, A; Ivanco, T L; Fahnestock, M



Gene expression profiles and transcriptional regulatory pathways underlying mouse tissue macrophage identity and diversity  

E-print Network

We assessed gene expression in tissue macrophages from various mouse organs. The diversity in gene expression among different populations of macrophages was considerable. Only a few hundred mRNA transcripts were selectively ...

Regev, Aviv


Diesel exhaust particles disturb gene expression in mouse testis.  


Inhalation of diesel exhaust particles (DEP) has been found to reduce sperm production. There is a possibility that DEP exposure elicits changes in gene expression in testis. To identify the alteration of gene expression resulting from DEP exposure, we constructed subtracted cDNA libraries from mouse testis using the suppression subtractive hybridization method. We isolated 16 candidate clones whose expression levels changed after exposure. Some of these candidates were highly similar to known testis-specific genes. Some of the clones also seemed to correlate with spermatogenesis. Northern blot analysis revealed that DEP exposure changed the expression levels of several clones in a dose-dependent manner. For example, the expression of clone R8, which was very similar to human XRRA1, increased by 2.3-fold in testis after DEP exposure. On the other hand, the expressions of long-chain acyl-CoA synthetase 6 (Acsl6) and serine/threonine kinase 35 reduced by 0.3-fold. These results indicated that some constituents of DEP alter gene expression in the testis. PMID:17295261

Mori, Tetsuya; Watanuki, Taro; Kashiwagura, Tadashi



Gene Targeting of Mouse Tardbp Negatively Affects Masp2 Expression  

PubMed Central

Amyotrophic Lateral Sclerosis (ALS) is a devastating adult onset neurodegenerative disease affecting both upper and lower motor neurons. TDP-43, encoded by the TARDBP gene, was identified as a component of motor neuron cytoplasmic inclusions in both familial and sporadic ALS and has become a pathological signature of the disease. TDP-43 is a nuclear protein involved in RNA metabolism, however in ALS, TDP-43 is mislocalized to the cytoplasm of affected motor neurons, suggesting that disease might be caused by TDP-43 loss of function. To investigate this hypothesis, we attempted to generate a mouse conditional knockout of the Tardbp gene using the classical Cre-loxP technology. Even though heterozygote mice for the targeted allele were successfully generated, we were unable to obtain homozygotes. Here we show that although the targeting vector was specifically designed to not overlap with Tardbp adjacent genes, the homologous recombination event affected the expression of a downstream gene, Masp2. This may explain the inability to obtain homozygote mice with targeted Tardbp. PMID:24740308

Dib, Samar; Xiao, Shangxi; Miletic, Denise; Robertson, Janice



Gene Expression and Functional Annotation of the Human and Mouse Choroid Plexus Epithelium  

PubMed Central

Background The choroid plexus epithelium (CPE) is a lobed neuro-epithelial structure that forms the outer blood-brain barrier. The CPE protrudes into the brain ventricles and produces the cerebrospinal fluid (CSF), which is crucial for brain homeostasis. Malfunction of the CPE is possibly implicated in disorders like Alzheimer disease, hydrocephalus or glaucoma. To study human genetic diseases and potential new therapies, mouse models are widely used. This requires a detailed knowledge of similarities and differences in gene expression and functional annotation between the species. The aim of this study is to analyze and compare gene expression and functional annotation of healthy human and mouse CPE. Methods We performed 44k Agilent microarray hybridizations with RNA derived from laser dissected healthy human and mouse CPE cells. We functionally annotated and compared the gene expression data of human and mouse CPE using the knowledge database Ingenuity. We searched for common and species specific gene expression patterns and function between human and mouse CPE. We also made a comparison with previously published CPE human and mouse gene expression data. Results Overall, the human and mouse CPE transcriptomes are very similar. Their major functionalities included epithelial junctions, transport, energy production, neuro-endocrine signaling, as well as immunological, neurological and hematological functions and disorders. The mouse CPE presented two additional functions not found in the human CPE: carbohydrate metabolism and a more extensive list of (neural) developmental functions. We found three genes specifically expressed in the mouse CPE compared to human CPE, being ACE, PON1 and TRIM3 and no human specifically expressed CPE genes compared to mouse CPE. Conclusion Human and mouse CPE transcriptomes are very similar, and display many common functionalities. Nonetheless, we also identified a few genes and pathways which suggest that the CPE between mouse and man differ with respect to transport and metabolic functions. PMID:24391755

Janssen, Sarah F.; van der Spek, Sophie J. F.; ten Brink, Jacoline B.; Essing, Anke H. W.; Gorgels, Theo G. M. F.; van der Spek, Peter J.; Jansonius, Nomdo M.; Bergen, Arthur A. B.



Microarray and comparative genomics-based identification of genes and gene regulatory regions of the mouse immune system  

Microsoft Academic Search

BACKGROUND: In this study we have built and mined a gene expression database composed of 65 diverse mouse tissues for genes preferentially expressed in immune tissues and cell types. Using expression pattern criteria, we identified 360 genes with preferential expression in thymus, spleen, peripheral blood mononuclear cells, lymph nodes (unstimulated or stimulated), or in vitro activated T-cells. RESULTS: Gene clusters,

John J Hutton; Anil G Jegga; Sue Kong; Ashima Gupta; Catherine Ebert; Sarah Williams; Jonathan D Katz; Bruce J Aronow



Brain Gene Expression of a Sporadic (icv-STZ Mouse) and a Familial Mouse Model (3xTg-AD Mouse) of Alzheimer’s Disease  

PubMed Central

Alzheimer’s disease (AD) can be divided into sporadic AD (SAD) and familial AD (FAD). Most AD cases are sporadic and may result from multiple etiologic factors, including environmental, genetic and metabolic factors, whereas FAD is caused by mutations of presenilins or amyloid-? (A?) precursor protein (APP). A commonly used mouse model for AD is 3xTg-AD mouse, which is generated by over-expression of mutated presenilin 1, APP and tau in the brain and thus represents a mouse model of FAD. A mouse model generated by intracerebroventricular (icv) administration of streptozocin (STZ), icv-STZ mouse, shows many aspects of SAD. Despite the wide use of these two models for AD research, differences in gene expression between them are not known. Here, we compared the expression of 84 AD-related genes in the hippocampus and the cerebral cortex between icv-STZ mice and 3xTg-AD mice using a custom-designed qPCR array. These genes are involved in APP processing, tau/cytoskeleton, synapse function, apoptosis and autophagy, AD-related protein kinases, glucose metabolism, insulin signaling, and mTOR pathway. We found altered expression of around 20 genes in both mouse models, which affected each of above categories. Many of these gene alterations were consistent with what was observed in AD brain previously. The expression of most of these altered genes was decreased or tended to be decreased in the hippocampus of both mouse models. Significant diversity in gene expression was found in the cerebral cortex between these two AD mouse models. More genes related to synaptic function were dysregulated in the 3xTg-AD mice, whereas more genes related to insulin signaling and glucose metabolism were down-regulated in the icv-STZ mice. The present study provides important fundamental knowledge of these two AD mouse models and will help guide future studies using these two mouse models for the development of AD drugs. PMID:23236499

Liang, Zhihou; Sun, Shenggang; Dai, Chun-ling; Lee, Moon H.; LaFerla, Frank M.; Grundke-Iqbal, Inge; Iqbal, Khalid; Liu, Fei; Gong, Cheng-Xin



Genes and gene expression modules associated with caloric restriction and aging in the laboratory mouse  

PubMed Central

Background Caloric restriction (CR) counters deleterious effects of aging and, for most mouse genotypes, increases mean and maximum lifespan. Previous analyses of microarray data have identified gene expression responses to CR that are shared among multiple mouse tissues, including the activation of anti-oxidant, tumor suppressor and anti-inflammatory pathways. These analyses have provided useful research directions, but have been restricted to a limited number of tissues, and have focused on individual genes, rather than whole-genome transcriptional networks. Furthermore, CR is thought to oppose age-associated gene expression patterns, but detailed statistical investigations of this hypothesis have not been carried out. Results Systemic effects of CR and aging were identified by examining transcriptional responses to CR in 17 mouse tissue types, as well as responses to aging in 22 tissues. CR broadly induced the expression of genes known to inhibit oxidative stress (e.g., Mt1, Mt2), inflammation (e.g., Nfkbia, Timp3) and tumorigenesis (e.g., Txnip, Zbtb16). Additionally, a network-based investigation revealed that CR regulates a large co-expression module containing genes associated with the metabolism and splicing of mRNA (e.g., Cpsf6, Sfpq, Sfrs18). The effects of aging were, to a considerable degree, similar among groups of co-expressed genes. Age-related gene expression patterns characteristic of most mouse tissues were identified, including up regulation of granulin (Grn) and secreted phosphoprotein 1 (Spp1). The transcriptional association between CR and aging varied at different levels of analysis. With respect to gene subsets associated with certain biological processes (e.g., immunity and inflammation), CR opposed age-associated expression patterns. However, among all genes, global transcriptional effects of CR were only weakly related to those of aging. Conclusion The study of aging, and of interventions thought to combat aging, has much to gain from data-driven and unbiased genomic investigations. Expression patterns identified in this analysis characterize a generalized response of mammalian cells to CR and/or aging. These patterns may be of importance in determining effects of CR on overall lifespan, or as factors that underlie age-related disease. The association between CR and aging warrants further study, but most evidence indicates that CR does not induce a genome-wide "reversal" of age-associated gene expression patterns. PMID:19968875



Identification of a set of genes showing regionally enriched expression in the mouse brain  

PubMed Central

Background The Pleiades Promoter Project aims to improve gene therapy by designing human mini-promoters (< 4 kb) that drive gene expression in specific brain regions or cell-types of therapeutic interest. Our goal was to first identify genes displaying regionally enriched expression in the mouse brain so that promoters designed from orthologous human genes can then be tested to drive reporter expression in a similar pattern in the mouse brain. Results We have utilized LongSAGE to identify regionally enriched transcripts in the adult mouse brain. As supplemental strategies, we also performed a meta-analysis of published literature and inspected the Allen Brain Atlas in situ hybridization data. From a set of approximately 30,000 mouse genes, 237 were identified as showing specific or enriched expression in 30 target regions of the mouse brain. GO term over-representation among these genes revealed co-involvement in various aspects of central nervous system development and physiology. Conclusion Using a multi-faceted expression validation approach, we have identified mouse genes whose human orthologs are good candidates for design of mini-promoters. These mouse genes represent molecular markers in several discrete brain regions/cell-types, which could potentially provide a mechanistic explanation of unique functions performed by each region. This set of markers may also serve as a resource for further studies of gene regulatory elements influencing brain expression. PMID:18625066

D'Souza, Cletus A; Chopra, Vikramjit; Varhol, Richard; Xie, Yuan-Yun; Bohacec, Slavita; Zhao, Yongjun; Lee, Lisa LC; Bilenky, Mikhail; Portales-Casamar, Elodie; He, An; Wasserman, Wyeth W; Goldowitz, Daniel; Marra, Marco A; Holt, Robert A; Simpson, Elizabeth M; Jones, Steven JM



Gene silencing by RNAi in mouse Sertoli cells  

PubMed Central

Background RNA interference (RNAi) is a valuable tool in the investigation of gene function. The purpose of this study was to examine the availability, target cell types and efficiency of RNAi in the mouse seminiferous epithelium. Methods The experimental model was based on transgenic mice expressing EGFP (enhanced green fluorescent protein). RNAi was induced by in vivo transfection of plasmid vectors encoding for short hairpin RNAs (shRNAs) targeting EGFP. shRNAs were transfected in vivo by microinjection into the seminiferous tubules via the rete testis followed by square wave electroporation. As a transfection reporter, expression of red fluorescent protein (HcRed 1) was used. Cell types, the efficiency of both transfections and RNAi were all evaluated. Results Sertoli cells were the main transfected cells. A reduction of about 40% in the level of EGFP protein was detected in cells successfully transfected both in vivo and in vitro. However, the efficiency of in vivo transfection was low. Conclusion In adult seminiferous epithelial cells, in vivo post-transcriptional gene silencing mediated by RNAi via shRNA is efficient in Sertoli cells. Similar levels of RNAi were detected both in vivo and in vitro. This also indicates that Sertoli cells have the necessary silencing machinery to repress the expression of endogenous genes via RNAi. PMID:18620581

Gonzalez-Gonzalez, Emilio; Lopez-Casas, Pedro P; del Mazo, Jesus



Targeted disruption of the mouse Lipoma Preferred Partner gene  

SciTech Connect

LPP (Lipoma Preferred Partner) is a zyxin-related cell adhesion protein that is involved in the regulation of cell migration. We generated mice with a targeted disruption of the Lpp gene and analysed the importance of Lpp for embryonic development and adult functions. Aberrant Mendelian inheritance in heterozygous crosses suggested partial embryonic lethality of Lpp{sup -/-} females. Fertility of Lpp{sup -/-} males was proven to be normal, however, females from Lpp{sup -/-} x Lpp{sup -/-} crosses produced a strongly reduced number of offspring, probably due to a combination of female embryonic lethality and aberrant pregnancies. Apart from these developmental and reproductive abnormalities, Lpp{sup -/-} mice that were born reached adulthood without displaying any additional macroscopic defects. On the other hand, Lpp{sup -/-} mouse embryonic fibroblasts exhibited reduced migration capacity, reduced viability, and reduced expression of some Lpp interaction partners. Finally, we discovered a short nuclear form of Lpp, expressed mainly in testis via an alternative promoter.

Vervenne, Hilke B.V.K.; Crombez, Koen R.M.O.; Delvaux, Els L. [Laboratory for Molecular Oncology, Department of Human Genetics, Herestraat 49, Box 602, K.U.Leuven, Leuven (Belgium); Janssens, Veerle [Protein Phosphorylation and Proteomics Laboratory, Department of Molecular Cell Biology, K.U.Leuven, Leuven (Belgium); Ven, Wim J.M. van de [Laboratory for Molecular Oncology, Department of Human Genetics, Herestraat 49, Box 602, K.U.Leuven, Leuven (Belgium)], E-mail:; Petit, Marleen M.R. [Laboratory for Molecular Oncology, Department of Human Genetics, Herestraat 49, Box 602, K.U.Leuven, Leuven (Belgium)



Genomic cloning of mouse MIF (macrophage inhibitory factor) and genetic mapping of the human and mouse expressed gene and nine mouse pseudogenes  

SciTech Connect

The single functional mouse gene for MIF (macrophage migration inhibitory factor) has been cloned from a P1 library, and its exon/intron structure determined and shown to resemble that of the human gene. The gene was mapped to chromosome 10 using two multilocus crosses between laboratory strains and either Mus musculus or Mus spretus. Nine additional loci containing related sequences, apparently all processed pseudogenes, were also mapped to chromosomes 1, 2, 3, 7, 8, 9, 12, 17, and 19. While most of these pseudogenes were also found in inbred mice and M. spretus, some are species specific. This suggests that there have been active phases of pseudogene formation in Mus both before and after the separation of musculus and spretus. The human gene contains no pseudogene; we assigned the human gene to chromosome 19, consistent with the location of mouse and human functional genes for MIF in a region of conserved linkage. 43 refs., 4 figs., 1 tab.

Kozak, C.A.; Adamson, M.C.; Buckler, C.E. [National Institute of Allergy and Infectious Diseases, Bethesda, MD (United States)] [and others] [National Institute of Allergy and Infectious Diseases, Bethesda, MD (United States); and others



The mouse homologue of the polycystic kidney disease gene (Pkd1) is a single-copy gene  

SciTech Connect

The mouse homologue of the polycystic kidney disease 1 gene (PKD1) was mapped to chromosome 17 using somatic cell hybrid, BXD recombinant inbred strains, and FISH. The gene is located within a previously defined conserved synteny group that includes the mouse homologue of tuberous sclerosis 2 (TSC2) and is linked to the {alpha} globin pseudogene Hba-ps4. Although the human genome contains multiple copies of genes related to PKD1, there is no evidence for more than one copy in the mouse genome. Like their human counterparts, the mouse Tsc2 and Pkd1 genes are arranged in a tail-to-tail orientation with a distance of only 63 bp between the polyadenylation signals of the two genes. 17 refs., 3 figs.

Olsson, P.G.; Loehning, C.; Frischauf, A.M. [Imperial Cancer Research Fund, London (United Kingdom)] [and others] [Imperial Cancer Research Fund, London (United Kingdom); and others



Organization and evolution of D region class I genes in the mouse major histocompatibility complex  

PubMed Central

Chromosome walking has been used to study the organization of the class I genes in the D and Qa regions of the MHC of the BALB/c mouse and in the D region of the AKR mouse. Five and eight class I genes are found in the D and Qa regions of the BALB/c mouse, respectively, while the AKR mouse contains only a single class I D region gene that has been identified by transfection as the Dk gene. Restriction map homologies and crosshybridization experiments suggest that the multiple class I genes in the D region of the BALB/c mouse have been generated by unequal crossing-over involving class I genes from the Qa region. The expanded D region of BALB/c and other H-2d haplotype mouse strains appears to be metastable, since evidence for gene contraction in the Dd region has been found in two mutant strains. Thus the D region and also the Qa region class I genes are in a dynamic state, evolving by gene expansion and contraction. PMID:3701254



DG-CST (Disease Gene Conserved Sequence Tags), a database of human-mouse conserved elements associated to disease genes  

Microsoft Academic Search

The identification and study of evolutionarily con- served genomic sequences that surround disease- related genes is a valuable tool to gain insight into the functional role of these genes and to better eluci- date the pathogenetic mechanisms of disease. We created the DG-CST (Disease Gene Conserved Sequence Tags) database for the identification and detailed annotation of human-mouse conserved genomic sequences

Angelo Boccia; Mauro Petrillo; Diego Di Bernardo; Alessandro Guffanti; Flavio Mignone; Stefano Confalonieri; Lucilla Luzi; Graziano Pesole; Giovanni Paolella; Andrea Ballabio; Sandro Banfi



Differential Divergence of Three Human Pseudoautosomal Genes and Their Mouse Homologs: Implications for Sex Chromosome Evolution  

PubMed Central

The human pseudoautosomal region 1 (PAR1) is essential for meiotic pairing and recombination, and its deletion causes male sterility. Comparative studies of human and mouse pseudoautosomal genes are valuable in charting the evolution of this interesting region, but have been limited by the paucity of genes conserved between the two species. We have cloned a novel human PAR1 gene, DHRSXY, encoding an oxidoreductase of the short-chain dehydrogenase/reductase family, and isolated a mouse ortholog Dhrsxy. We also searched for mouse homologs of recently reported PGPL and TRAMP genes that flank it within PAR1. We recovered a highly conserved mouse ortholog of PGPL by cross-hybridization, but found no mouse homolog of TRAMP. Like Csf2ra and Il3ra, both mouse homologs are autosomal; Pgpl on chromosome 5, and Dhrsxy subtelomeric on chromosome 4. TRAMP, like the human genes within or near PAR1, is probably very divergent or absent in the mouse genome. We interpret the rapid divergence and loss of pseudoautosomal genes in terms of a model of selection for the concentration of repetitive recombinogenic sequences that predispose to high recombination and translocation. [The sequence data described in this paper have been submitted to the EMBL data library under accession nos. AJ293620, AJ296079, and AJ293619.] PMID:11731500

Gianfrancesco, Fernando; Sanges, Remo; Esposito, Teresa; Tempesta, Sergio; Rao, Ercole; Rappold, Gudrun; Archidiacono, Nicoletta; Graves, Jennifer A.M.; Forabosco, Antonino; D'Urso, Michele



Differential divergence of three human pseudoautosomal genes and their mouse homologs: implications for sex chromosome evolution.  


The human pseudoautosomal region 1 (PAR1) is essential for meiotic pairing and recombination, and its deletion causes male sterility. Comparative studies of human and mouse pseudoautosomal genes are valuable in charting the evolution of this interesting region, but have been limited by the paucity of genes conserved between the two species. We have cloned a novel human PAR1 gene, DHRSXY, encoding an oxidoreductase of the short-chain dehydrogenase/reductase family, and isolated a mouse ortholog Dhrsxy. We also searched for mouse homologs of recently reported PGPL and TRAMP genes that flank it within PAR1. We recovered a highly conserved mouse ortholog of PGPL by cross-hybridization, but found no mouse homolog of TRAMP. Like Csf2ra and Il3ra, both mouse homologs are autosomal; Pgpl on chromosome 5, and Dhrsxy subtelomeric on chromosome 4. TRAMP, like the human genes within or near PAR1, is probably very divergent or absent in the mouse genome. We interpret the rapid divergence and loss of pseudoautosomal genes in terms of a model of selection for the concentration of repetitive recombinogenic sequences that predispose to high recombination and translocation. PMID:11731500

Gianfrancesco, F; Sanges, R; Esposito, T; Tempesta, S; Rao, E; Rappold, G; Archidiacono, N; Graves, J A; Forabosco, A; D'Urso, M



Genetic Incorporation of Human Metallothionein into the Adenovirus Protein IX for Non-Invasive SPECT Imaging  

PubMed Central

As the limits of existing treatments for cancer are recognized, clearly novel therapies must be considered for successful treatment; cancer therapy using adenovirus vectors is a promising strategy. However tracking the biodistribution of adenovirus vectors in vivo is limited to invasive procedures such as biopsies, which are error prone, non-quantitative, and do not give a full representation of the pharmacokinetics involved. Current non-invasive imaging strategies using reporter gene expression have been applied to analyze adenoviral vectors. The major drawback to approaches that tag viruses with reporter genes is that these systems require initial viral infection and subsequent cellular expression of a reporter gene to allow non-invasive imaging. As an alternative to conventional vector detection techniques, we developed a specific genetic labeling system whereby an adenoviral vector incorporates a fusion between capsid protein IX and human metallothionein. Our study herein clearly demonstrates our ability to rescue viable adenoviral particles that display functional metallothionein (MT) as a component of their capsid surface. We demonstrate the feasibility of 99mTc binding in vitro to the pIX-MT fusion on the capsid of adenovirus virions using a simple transchelation reaction. SPECT imaging of a mouse after administration of a 99mTc-radiolabeled virus showed clear localization of radioactivity to the liver. This result strongly supports imaging using pIX-MT, visualizing the normal biodistribution of Ad primarily to the liver upon injection into mice. The ability we have developed to view real-time biodistribution in their physiological milieu represents a significant tool to study adenovirus biology in vivo. PMID:21347423

Mathis, J. Michael; Bhatia, Shilpa; Khandelwal, Alok; Kovesdi, Imre; Lokitz, Stephen J.; Odaka, Yoshi; Takalkar, Amol M.; Terry, Tracee; Curiel, David T.



Cloning, structure, and chromosome localization of the mouse glutaryl-CoA dehydrogenase gene  

SciTech Connect

Glutaryl-CoA dehydrogenase (GCDH) is a nuclear-encoded, mitochondrial matrix enzyme. In humans, deficiency of GCDH leads to glutaric acidemia type I, and inherited disorder of amino acid metabolism characterized by a progressive neurodegenerative disease. In this report we describe the cloning and structure of the mouse GCDH (Gcdh) gene and cDNA and its chromosomal localization. The mouse Gcdh cDNA is 1.75 kb long and contains and open reading frame of 438 amino acids. The amino acid sequences of mouse, human, and pig GCDH are highly conserved. The mouse Gcdh gene contains 11 exons and spans 7 kb of genomic DNA. Gcdh was mapped by backcross analysis to mouse chromosome 8 within a region that is homologous to a region of human chromosome 19, where the human gene was previously mapped. 14 refs., 3 figs.

Koeller, D.M.; DiGiulio, A.; Frerman, F.E. [Univ. of Colorado Health Sciences Center, Denver, CO (United States)] [and others] [Univ. of Colorado Health Sciences Center, Denver, CO (United States); and others



Mouse models of Down syndrome: how useful can they be? Comparison of the gene content of human chromosome 21 with orthologous mouse genomic regions.  


With an incidence of approximately 1 in 700 live births, Down syndrome (DS) remains the most common genetic cause of mental retardation. The phenotype is assumed to be due to overexpression of some number of the >300 genes encoded by human chromosome 21. Mouse models, in particular the chromosome 16 segmental trisomies, Ts65Dn and Ts1Cje, are indispensable for DS-related studies of gene-phenotype correlations. Here we compare the updated gene content of the finished sequence of human chromosome 21 (364 genes and putative genes) with the gene content of the homologous mouse genomic regions (291 genes and putative genes) obtained from annotation of the public sector C57Bl/6 draft sequence. Annotated genes fall into one of three classes. First, there are 170 highly conserved, human/mouse orthologues. Second, there are 83 minimally conserved, possible orthologues. Included among the conserved and minimally conserved genes are 31 antisense transcripts. Third, there are species-specific genes: 111 spliced human transcripts show no orthologues in the syntenic mouse regions although 13 have homologous sequences elsewhere in the mouse genomic sequence, and 38 spliced mouse transcripts show no identifiable human orthologues. While these species-specific genes are largely based solely on spliced EST data, a majority can be verified in RNA expression experiments. In addition, preliminary data suggest that many human-specific transcripts may represent a novel class of primate-specific genes. Lastly, updated functional annotation of orthologous genes indicates genes encoding components of several cellular pathways are dispersed throughout the orthologous mouse chromosomal regions and are not completely represented in the Down syndrome segmental mouse models. Together, these data point out the potential for existing mouse models to produce extraneous phenotypes and to fail to produce DS-relevant phenotypes. PMID:14585506

Gardiner, Katheleen; Fortna, Andrew; Bechtel, Lawrence; Davisson, Muriel T



Using the mouse to identify genes involved in human disease Jenny Murdoch  

E-print Network

Lab, School of Biological Sciences, Royal Holloway-University of London, Egham, TW20 0EX ABSTRACT: Allows us to identify the genetic defect that causes the disease Mouse mutant with severe spina bifidaUsing the mouse to identify genes involved in human disease Jenny Murdoch Neural Tube Development

Royal Holloway, University of London


Genomic structure and chromosomal assignment of the mouse Ku70 gene  

SciTech Connect

DNA-dependent protein kinase (DNA-PK) consists of three polypeptide subunits: Ku70, Ku80, and the DNA-PK catalytic subunit (DNA-PKcs). Mammalian mutants deficient in either Ku80 or DNA-PKcs function have been shown to be lacking in DNA double-strand break repair and V(D)J recombination, respectively. The precise role of the Ku70 gene in this process has not yet been determined, in part because no cell lines, animals, or human diseases involved with deficiencies in this gene have yet been identified. Both the human and the mouse Ku70 cDNAs have been cloned, and the human gene has been mapped to chromosome 22q13. The original mouse cDNA clones, however, lacked a complete 5{prime}-region, and none of the mammalian Ku70 genomic sequences have been characterized. This report contains an analysis of the 5{prime}-region of the mouse cDNA sequence, a characterization of the mouse Ku70 genomic structure, and fluorescence in situ hybridization data that map the mouse gene to chromosome 15. The deduced amino acid sequence of the mouse gene consists of 608 amino acids compared to 609 for the human gene. The genomic sequence is 24 kb and consists of 13 exons, including an untranslated first exon. Sequences form the upstream region of exon 1 revealed four consensus GC box sequences and a strong transcription initiation site at a reasonable location. The assignment of the mouse Ku70 gene to chromosome 15 is consistent with the syntenic relationship of this gene in human (chromosome 22q13) and mouse and adds to the comparative mapping data for the genes involved in the SCID phenotype. 39 refs., 3 figs.

Takiguchi, Yuichi [Los Alamos National Lab., NM (United States)] [Los Alamos National Lab., NM (United States); [Medical School of Chiba Univ., Chuo-ku (Japan); Kurimasa, Akihiro; Chen, Fanqing [Los Alamos National Lab., NM (United States)] [and others] [Los Alamos National Lab., NM (United States); and others



Dispersion of alpha-like globin genes of the mouse to three different chromosomes  

Microsoft Academic Search

The three active alpha-globin genes of the mouse are physically linked at a locus little more than 25 kilobases long. These genes form a part of an unexpectedly large and dispersed multigene family, including at least two pseudogenes located on two different chromosomes. This finding suggests that related gene sequences can be dispersed from their primary loci and that their

Aya Leder; David Swan; Frank Ruddle; Peter D'Eustachio; Philip Leder



The mouse snail gene encodes a key regulator of the epithelial-mesenchymal transition  

Microsoft Academic Search

Snail family genes encode DNA binding zinc finger proteins that act as transcriptional repressors. Mouse embryos deficient for the Snail (Sna) gene exhibit defects in the formation of the mesoderm germ layer. In Sna(-\\/-) mutant embryos, a mesoderm layer forms and mesodermal marker genes are induced but the mutant mesoderm is morphologically abnormal. Lacunae form within the mesoderm layer of




Otx2 Gene Deletion in Adult Mouse Retina Induces Rapid RPE Dystrophy and Slow Photoreceptor Degeneration  

Microsoft Academic Search

BackgroundMany developmental genes are still active in specific tissues after development is completed. This is the case for the homeobox gene Otx2, an essential actor of forebrain and head development. In adult mouse, Otx2 is strongly expressed in the retina. Mutations of this gene in humans have been linked to severe ocular malformation and retinal diseases. It is, therefore, important

Francis Béby; Michael Housset; Nicolas Fossat; Coralie Le Greneur; Frédéric Flamant; Pierre Godement; Thomas Lamonerie; Thomas A. Reh



Otitis Media Impacts Hundreds of Mouse Middle and Inner Ear Genes  

PubMed Central

Objective Otitis media is known to alter expression of cytokine and other genes in the mouse middle ear and inner ear. However, whole mouse genome studies of gene expression in otitis media have not previously been undertaken. Ninety-nine percent of mouse genes are shared in the human, so these studies are relevant to the human condition. Methods To assess inflammation-driven processes in the mouse ear, gene chip analyses were conducted on mice treated with trans-tympanic heat-killed Hemophilus influenza using untreated mice as controls. Middle and inner ear tissues were separately harvested at 6 hours, RNA extracted, and samples for each treatment processed on the Affymetrix 430 2.0 Gene Chip for expression of its 34,000 genes. Results Statistical analysis of gene expression compared to control mice showed significant alteration of gene expression in 2,355 genes, 11% of the genes tested and 8% of the mouse genome. Significant middle and inner ear upregulation (fold change >1.5, p<0.05) was seen in 1,081 and 599 genes respectively. Significant middle and inner ear downregulation (fold change <0.67, p<0.05) was seen in 978 and 287 genes respectively. While otitis media is widely believed to be an exclusively middle ear process with little impact on the inner ear, the inner ear changes noted in this study were numerous and discrete from the middle ear responses. This suggests that the inner ear does indeed respond to otitis media and that its response is a distinctive process. Numerous new genes, previously not studied, are found to be affected by inflammation in the ear. Conclusion Whole genome analysis via gene chip allows simultaneous examination of expression of hundreds of gene families influenced by inflammation in the middle ear. Discovery of new gene families affected by inflammation may lead to new approaches to the study and treatment of otitis media. PMID:24124478

MacArthur, Carol J.; Hausman, Fran; Kempton, J. Beth; Choi, Dongseok; Trune, Dennis R.



Mammalian metallothioneins: properties and functions.  


Metallothioneins (MT) are a family of ubiquitous proteins, whose role is still discussed in numerous papers, but their affinity to some metal ions is undisputable. These cysteine-rich proteins are connected with antioxidant activity and protective effects on biomolecules against free radicals, especially reactive oxygen species. In this review, the connection between zinc(II) ions, reactive oxygen species, heavy metal ions and metallothioneins is demonstrated with respect to effect of these proteins on cell proliferation and a possible negative role in resistance to heavy metal-based and non-heavy metal-based drugs. PMID:22791193

Babula, Petr; Masarik, Michal; Adam, Vojtech; Eckschlager, Tomas; Stiborova, Marie; Trnkova, Libuse; Skutkova, Helena; Provaznik, Ivo; Hubalek, Jaromir; Kizek, Rene



Cloning, analysis, and chromosomal localization of myoxin (MYH12), the human homologue to the mouse dilute gene  

SciTech Connect

The mouse dilute gene encodes a novel type of non-muscle myosin that structurally combines elements from both nonmuscle myosin type I and nonmuscle myosin type II. Phenotypically, mutations in the mouse dilute gene result not only in the lightening of coat color, but also in the onset of severe neurological defects shortly after birth. This may indicate that the mouse dilute gene is important in maintaining the normal neuronal function in the mouse. The authors report the isolation and sequencing of [open quotes]myoxin[close quotes] (MYH12), the human homologue of the mouse dilute gene, and its assignment to human chromosome 15. 35 refs., 6 figs.

Engle, L.J.; Kennett, R.H. (Univ. of Pennsylvania School of Medicine, Philadelphia, PA (United States))



Positive-negative selection gene targeting with the diphtheria toxin A-chain gene in mouse embryonic stem cells  

Microsoft Academic Search

The diphtheria toxin A-chain gene was used in a positive-negative selection gene targeting vector to alter the CD4 gene which is transcriptionally silent in mouse embryonic stem cells. Expression of the toxin gene was driven by a constitutively active enhancer, yet the targeting construct exhibited only minimal transient toxicity while enriching for targeted clones 9- to 29-fold. Germline transmissiion of

James W. McCarrick; Jane R. Parnes; Rho H. Seong; Davor Solter; Barbara B. Knowles



Assignment of the mouse tartrate-resistant acid phosphatase gene (Acp5) to chromosome 9  

SciTech Connect

Tartrate-resistant acid phosphatase is a marker enzyme for osteoclasts, the multinucleated cell responsible for bone resorption. Interspecific somatic whole cell hybrids and karyotypically simple microcell hybrids were used to map the gene encoding tartrate-resistant acid phosphatse (acp5) to mouse Chromosome 9. Acp5 is therefore a member of a syntenic family of genes that map to human chromosome 19p13.1-p13.3 and mouse Chromosome 9. 8 refs., 1 fig., 1 tab.

Grimes, R.; Reddy, S.V.; Leach, R.J.; Scarcez, T.; Sakaguchi, A.Y. (Univ. of Texas Health Science Center, San Antonio (United States)); Roodman, G.D. (Univ. of Texas Health Science Center, San Antonio (United States) Audie Murphy Veterans Administration Hospital, San Antonio, TX (United States)); Lalley, P.A. (Wayne State Univ. of School of Medicine, Detroit, MI (United States)); Windle, J.J. (Cancer Therapy and Research Center, San Antonio, TX (United States))



Lgn1, a gene that determines susceptibility to Legionella pneumophila, maps to mouse chromosome 13  

SciTech Connect

The intracellular pathogen Legionella pneumophila is unable to replicate in macrophages derived from most inbred mouse strains. Here, we report the mapping of a gene, called Lgn1, that determines whether mouse macrophages are permissive for the intracellular replication of L. pneumophila. Although Lgn1 has been previously reported to map to mouse chromosome 15, we show here that it actually maps to chromosome 13, between D13Mit128 and D13Mit70. In the absence of any regional candidates for Lgn1, this map position will facilitate positional cloning attempts directed at this gene. 22 refs., 2 figs., 2 tabs.

Dietrich, W.F.; Damron, D.M.; Lander, E.S. [Whitehead Institute/MIT Genome Center, Cambridge, MA (United States)] [and others] [Whitehead Institute/MIT Genome Center, Cambridge, MA (United States); and others



Gene Array and Expression of Mouse Retina Guanylate Cyclase Activating Proteins 1 and 2  

Microsoft Academic Search

RESULTS. In this study, the mouse GCAP1 and GCAP2 gene array, its chromosomal localization, RNA transcripts, and immunolocalization of the gene products were fully characterized. The GCAP tail-to-tail array is located at the D band of chromosome 17. Each gene is transcribed into a single transcript of 0.8 kb (GCAP1) and 2 kb (GCAP2). Immunocytochemistry showed that both GCAP genes

Kim Howes; J. Darin Bronson; Yan Li Dang; Ning Li; Kai Zhang; Claudia Ruiz; Bharati Helekar; Muriel Lee; Iswari Subbaraya; Helga Kolb; Jeannie Chen; Wolfgang Baehr



Precise and in situ genetic humanization of 6 Mb of mouse immunoglobulin genes  

PubMed Central

Genetic humanization, which involves replacing mouse genes with their human counterparts, can create powerful animal models for the study of human genes and diseases. One important example of genetic humanization involves mice humanized for their Ig genes, allowing for human antibody responses within a mouse background (HumAb mice) and also providing a valuable platform for the generation of fully human antibodies as therapeutics. However, existing HumAb mice do not have fully functional immune systems, perhaps because of the manner in which they were genetically humanized. Heretofore, most genetic humanizations have involved disruption of the endogenous mouse gene with simultaneous introduction of a human transgene at a new and random location (so-called KO-plus-transgenic humanization). More recent efforts have attempted to replace mouse genes with their human counterparts at the same genetic location (in situ humanization), but such efforts involved laborious procedures and were limited in size and precision. We describe a general and efficient method for very large, in situ, and precise genetic humanization using large compound bacterial artificial chromosome–based targeting vectors introduced into mouse ES cells. We applied this method to genetically humanize 3-Mb segments of both the mouse heavy and ? light chain Ig loci, by far the largest genetic humanizations ever described. This paper provides a detailed description of our genetic humanization approach, and the companion paper reports that the humoral immune systems of mice bearing these genetically humanized loci function as efficiently as those of WT mice. PMID:24706858

Macdonald, Lynn E.; Karow, Margaret; Stevens, Sean; Auerbach, Wojtek; Poueymirou, William T.; Yasenchak, Jason; Frendewey, David; Valenzuela, David M.; Giallourakis, Cosmas C.; Alt, Frederick W.; Yancopoulos, George D.; Murphy, Andrew J.



Arbuscular mycorrhizal fungi restore normal growth in a white poplar clone grown on heavy metal-contaminated soil, and this is associated with upregulation of foliar metallothionein and polyamine biosynthetic gene expression  

PubMed Central

Background and Aims It is increasingly evident that plant tolerance to stress is improved by mycorrhiza. Thus, suitable plant–fungus combinations may also contribute to the success of phytoremediation of heavy metal (HM)-polluted soil. Metallothioneins (MTs) and polyamines (PAs) are implicated in the response to HM stress in several plant species, but whether the response is modulated by arbuscular mycorrhizal fungi (AMF) remains to be clarified. The aim of the present study was to check whether colonization by AMF could modify growth, metal uptake/translocation, and MT and PA gene expression levels in white poplar cuttings grown on HM-contaminated soil, and to compare this with plants grown on non-contaminated soil. Methods In this greenhouse study, plants of a Populus alba clone were pre-inoculated, or not, with either Glomus mosseae or G. intraradices and then grown in pots containing either soil collected from a multimetal- (Cu and Zn) polluted site or non-polluted soil. The expression of MT and PA biosynthetic genes was analysed in leaves using quantitative reverse transcription–PCR. Free and conjugated foliar PA concentrations were determined in parallel. Results On polluted soil, AMF restored plant biomass despite higher Cu and Zn accumulation in plant organs, especially roots. Inoculation with the AMF caused an overall induction of PaMT1, PaMT2, PaMT3, PaSPDS1, PaSPDS2 and PaADC gene expression, together with increased free and conjugated PA levels, in plants grown on polluted soil, but not in those grown on non-polluted soil. Conclusions Mycorrhizal plants of P. alba clone AL35 exhibit increased capacity for stabilization of soil HMs, together with improved growth. Their enhanced stress tolerance may derive from the transcriptional upregulation of several stress-related genes, and the protective role of PAs. PMID:20810743

Cicatelli, Angela; Lingua, Guido; Todeschini, Valeria; Biondi, Stefania; Torrigiani, Patrizia; Castiglione, Stefano



A survey for novel imprinted genes in the mouse placenta by mRNA-seq.  


Many questions about the regulation, functional specialization, computational prediction, and evolution of genomic imprinting would be better addressed by having an exhaustive genome-wide catalog of genes that display parent-of-origin differential expression. As a first-pass scan for novel imprinted genes, we performed mRNA-seq experiments on embryonic day 17.5 (E17.5) mouse placenta cDNA samples from reciprocal cross F1 progeny of AKR and PWD mouse strains and quantified the allele-specific expression and the degree of parent-of-origin allelic imbalance. We confirmed the imprinting status of 23 known imprinted genes in the placenta and found that 12 genes reported previously to be imprinted in other tissues are also imprinted in mouse placenta. Through a well-replicated design using an orthogonal allelic-expression technology, we verified 5 novel imprinted genes that were not previously known to be imprinted in mouse (Pde10, Phf17, Phactr2, Zfp64, and Htra3). Our data suggest that most of the strongly imprinted genes have already been identified, at least in the placenta, and that evidence supports perhaps 100 additional weakly imprinted genes. Despite previous appearance that the placenta tends to display an excess of maternally expressed imprinted genes, with the addition of our validated set of placenta-imprinted genes, this maternal bias has disappeared. PMID:21705755

Wang, Xu; Soloway, Paul D; Clark, Andrew G



A Survey for Novel Imprinted Genes in the Mouse Placenta by mRNA-seq  

PubMed Central

Many questions about the regulation, functional specialization, computational prediction, and evolution of genomic imprinting would be better addressed by having an exhaustive genome-wide catalog of genes that display parent-of-origin differential expression. As a first-pass scan for novel imprinted genes, we performed mRNA-seq experiments on embryonic day 17.5 (E17.5) mouse placenta cDNA samples from reciprocal cross F1 progeny of AKR and PWD mouse strains and quantified the allele-specific expression and the degree of parent-of-origin allelic imbalance. We confirmed the imprinting status of 23 known imprinted genes in the placenta and found that 12 genes reported previously to be imprinted in other tissues are also imprinted in mouse placenta. Through a well-replicated design using an orthogonal allelic-expression technology, we verified 5 novel imprinted genes that were not previously known to be imprinted in mouse (Pde10, Phf17, Phactr2, Zfp64, and Htra3). Our data suggest that most of the strongly imprinted genes have already been identified, at least in the placenta, and that evidence supports perhaps 100 additional weakly imprinted genes. Despite previous appearance that the placenta tends to display an excess of maternally expressed imprinted genes, with the addition of our validated set of placenta-imprinted genes, this maternal bias has disappeared. PMID:21705755

Wang, Xu; Soloway, Paul D.; Clark, Andrew G.



METALLOTHIONEIN: An Intracellular Protein to Protect Against Cadmium Toxicity  

Microsoft Academic Search

Metallothioneins (MT) are low-molecular-weight, cysteine-rich, metal-binding proteins. MT genes are readily induced by various physiologic and toxicologic stimuli. Because the cysteines in MT are absolutely conserved across species, it was suspected that the cysteines are necessary for function and MT is essential for life. In attempts to determine the function(s) of MT, studies have been performed using four different experimental

Curtis D. Klaassen; Jie Liu; Supratim Choudhuri



Efficient isolation of novel mouse genes differentially expressed in early postimplantation embryos  

SciTech Connect

Most genes with regulatory functions in embryogenesis are expressed in highly specific patterns, suggesting that expression patterns can serve as criteria to define potential candidates for developmentally relevant genes. To isolate such genes, we selected and partially sequenced 80 cDNA clones from a 10.5-day mouse embryo library. Forty-one clones that represented novel mouse genes were analyzed for expression in embryos of the same stage by whole-mount in situ hybridization. A high proportion (24%) of these genes, including a homologue of the Drosophila Delta gene, were expressed in specific spatially restricted patterns, suggesting that selection based on expression patterns is a useful strategy to isolate novel genes that may play pivotal roles in mammalian development. 24 refs., 1 fig., 1 tab.

Bettenhausen, B.; Gossler, A. [Max-Delbrueck-Laboratorium in der MPG, Cologne (Germany)] [Max-Delbrueck-Laboratorium in der MPG, Cologne (Germany)



A gene mapping to the sex-determining region of the mouse Y chromosome is a member of a novel family of embryonically expressed genes  

Microsoft Academic Search

A gene mapping to the sex-determining region of the mouse Y chromosome is deleted in a line of XY female mice mutant for Tdy, and is expressed at a stage during male gonadal development consistent with its having a role in testis determination. This gene is a member of a new family of at least five mouse genes, related by

John Gubbay; Jérôme Collignon; Peter Koopman; Blanche Capel; Androulla Economou; Andrea Münsterberg; Nigel Vivian; Peter Goodfellow; Robin Lovell-Badge



Comparative analysis of sequence characteristics of imprinted genes in human, mouse, and cattle  

PubMed Central

Genomic imprinting is an epigenetic mechanism that results in monoallelic expression of genes depending on parent-of-origin of the allele. Although the conservation of genomic imprinting among mammalian species has been widely reported for many genes, there is accumulating evidence that some genes escape this conservation. Most known imprinted genes have been identified in the mouse and human, with few imprinted genes reported in cattle. Comparative analysis of genomic imprinting across mammalian species would provide a powerful tool for elucidating the mechanisms regulating the unique expression of imprinted genes. In this study we analyzed the imprinting of 22 genes in human, mouse, and cattle and found that in only 11 was imprinting conserved across the three species. In addition, we analyzed the occurrence of the sequence elements CpG islands, C + G content, tandem repeats, and retrotransposable elements in imprinted and in nonimprinted (control) cattle genes. We found that imprinted genes have a higher G + C content and more CpG islands and tandem repeats. Short interspersed nuclear elements (SINEs) were notably fewer in number in imprinted cattle genes compared to control genes, which is in agreement with previous reports for human and mouse imprinted regions. Long interspersed nuclear elements (LINEs) and long terminal repeats (LTRs) were found to be significantly underrepresented in imprinted genes compared to control genes, contrary to reports on human and mouse. Of considerable significance was the finding of highly conserved tandem repeats in nine of the genes imprinted in all three species. Electronic supplementary material The online version of this article (doi: 10.1007/s00335-007-9039-z) contains supplementary material, which is available to authorized users. PMID:17653590

Zaitoun, Ismail; Kim, Eui-Soo



Positional cloning of the mouse obese gene and its human homologue  

Microsoft Academic Search

The mechanisms that balance food intake and energy expenditure determine who will be obese and who will be lean. One of the molecules that regulates energy balance in the mouse is the obese (ob) gene. Mutation ofobresults in profound obesity and type II diabetes as part of a syndrome that resembles morbid obesity in humans. The ob gene product may

Yiying Zhang; Ricardo Proenca; Margherita Maffei; Marisa Barone; Lori Leopold; Jeffrey M. Friedman



Inducible Cre transgenic mouse strain for skeletal muscle-specific gene targeting  

PubMed Central

Background The use of the Cre/loxP system for gene targeting has been proven to be a powerful tool for understanding gene function. The purpose of this study was to create and characterize an inducible, skeletal muscle-specific Cre transgenic mouse strain. Methods To achieve skeletal muscle-specific expression, the human ?-skeletal actin promoter was used to drive expression of a chimeric Cre recombinase containing two mutated estrogen receptor ligand-binding domains. Results Western blot analysis, PCR and ?-galactosidase staining confirmed that Cre-mediated recombination was restricted to limb and craniofacial skeletal muscles only after tamoxifen administration. Conclusions A transgenic mouse was created that allows inducible, gene targeting of floxed genes in adult skeletal muscle of different developmental origins. This new mouse will be of great utility to the skeletal muscle community. PMID:22564549



Gene amplification in methotrexate-resistant mouse cells  

Microsoft Academic Search

Wild-type mouse LtAp20 cells were treated with calcium phosphate-precipitated DNA or chromosomes from two highly Methotrexate (MTX)-resistant mouse lymphoma cell lines — EL4\\/8 and EL4\\/11. Transfections with purified MTX-resistant DNA produced colonies of LtAp20 cells resistant to 3×10-8M MTX, at about eight times the frequency with which resistant colonies arose in control transfections. DNA transfectants contained multiple copies of the

Christopher J. Bostock; Elizabeth M. Clark



The neuronal nicotinic acetylcholine receptor {alpha}7 subunit gene: Cloning, mapping, structure, and targeting in mouse  

SciTech Connect

The neuronal nicotinic acetylcholine receptor {alpha}7 subunit is a member of a family of ligand-gated ion channels, and is the only subunit know to bind {alpha}-bungarotoxin in mammalian brain. {alpha}-Bungarotoxin binding sites are known to be more abundant in the hippocampus of mouse strains that are particularly sensitive to nicotine-induced seizures. The {alpha}7 receptor is highly permeable to calcium, which could suggest a role in synaptic plasticity in the nervous system. Auditory gating deficiency, an abnormal response to a second auditory stimulus, is characteristic of schizophrenia. Mouse strains that exhibit a similar gating deficit have reduced hippocampal expression of the {alpha}7 subunit. We have cloned and sequenced the full length cDNA for the mouse {alpha}7 gene (Acra-7) and characterized its gene structure. The murine {alpha}7 shares amino acid identity of 99% and 93% with the rat and human {alpha}7 subunits, respectively. Using an interspecies backcross panel, the murine gene was mapped to chromosome 7 near the p locus, a region syntenic with human chromosome 15; the human gene (CHRNA7) was confirmed to map to 15q13-q14 by FISH. To generate a mouse {alpha}7 mutant by homologous recombination, we have constructed a replacement vector which will delete transmembrane domains II-IV and the cytoplasmic domain from the gene product. Recombinant embryonic stem (ES) cell clones were selected and used to develop mouse chimeras that are currently being bred to obtain germline transmission.

Orr-Urtreger, A.; Baldini, A.; Beaudet, A.L. [Howard Hughes Medical Institute, Houston, TX (United States)] [and others



Sequencing the mouse y chromosome reveals convergent gene acquisition and amplification on both sex chromosomes.  


We sequenced the MSY (male-specific region of the Y chromosome) of the C57BL/6J strain of the laboratory mouse Mus musculus. In contrast to theories that Y chromosomes are heterochromatic and gene poor, the mouse MSY is 99.9% euchromatic and contains about 700 protein-coding genes. Only 2% of the MSY derives from the ancestral autosomes that gave rise to the mammalian sex chromosomes. Instead, all but 45 of the MSY's genes belong to three acquired, massively amplified gene families that have no homologs on primate MSYs but do have acquired, amplified homologs on the mouse X chromosome. The complete mouse MSY sequence brings to light dramatic forces in sex chromosome evolution: lineage-specific convergent acquisition and amplification of X-Y gene families, possibly fueled by antagonism between acquired X-Y homologs. The mouse MSY sequence presents opportunities for experimental studies of a sex-specific chromosome in its entirety, in a genetically tractable model organism. PMID:25417157

Soh, Y Q Shirleen; Alföldi, Jessica; Pyntikova, Tatyana; Brown, Laura G; Graves, Tina; Minx, Patrick J; Fulton, Robert S; Kremitzki, Colin; Koutseva, Natalia; Mueller, Jacob L; Rozen, Steve; Hughes, Jennifer F; Owens, Elaine; Womack, James E; Murphy, William J; Cao, Qing; de Jong, Pieter; Warren, Wesley C; Wilson, Richard K; Skaletsky, Helen; Page, David C



Chromosomal mapping of the structural gene coding for the mouse cell adhesion molecule uvomorulin  

SciTech Connect

The gene coding for the mouse cell adhesion molecule uvomorulin has been mapped to chromosome 8. Uvomorulin cDNA clone F5H3 identified restriction fragment length polymorphisms in Southern blots of genomic DNA from mouse species Mus musculus domesticus and Mus spretus. By analyzing the segregation pattern of the gene in 75 offspring from an interspecific backcross a single genetic locus, Um, was defined on chromosome 8. Recombination frequency between Um and the co-segregating loci serum esterase 1 (Es-1) and tyrosine aminotransferase (Tat) places Um about 14 centimorgan (cM) distal to Es-1, and 5 cM proximal to Tat. In situ hybridization of uvomorulin ({sup 3}H)cDNA to mouse metaphase chromosomes located the Um locus close to the distal end of chromosome 8 (bands C3-E1). Since uvomorulin is evolutionarily highly conserved, its chromosomal assignment adds an important marker to the mouse genetic map.

Eistetter, H.R.; Adolph, S.; Ringwald, M.; Simon-Chazottes, D.; Schuh, R.; Guenet, J.L.; Kemler, R. (Max-Planck-Gesellschaft, Tuebingen (West Germany))



Six members of the mouse forkhead gene family are developmentally regulated.  

PubMed Central

The 110-aa forkhead domain defines a class of transcription factors that have been shown to be developmentally regulated in Drosophila melanogaster and Xenopus laevis. The forkhead domain is necessary and sufficient for target DNA binding as shown for the rat hepatic nuclear factor 3 (HNF3) gene family. We have cloned six forkhead gene family members from a mouse genomic library in addition to the mouse equivalents of the genes for HNF3 alpha, -beta, and -gamma. The six genes, termed fkh-1 to fkh-6, share a high degree of similarity with the Drosophila forkhead gene, having 57-67% amino acid identity within the forkhead domain. fkh-1 seems to be the mammalian homologue of the Drosophila FD1 gene, as the sequences are 86% identical. fkh-1 to fkh-6 show distinct spatial patterns of expression in adult tissues and are expressed during embryogenesis. Images Fig. 2 Fig. 3 PMID:7689224

Kaestner, K H; Lee, K H; Schlondorff, J; Hiemisch, H; Monaghan, A P; Schutz, G



Mfrp, a gene encoding a frizzled related protein, is mutated in the mouse retinal degeneration 6  

Microsoft Academic Search

The autosomal recessive mouse mutation retinal degeneration 6 (rd6 ) causes small, white retinal spots and progressive photoreceptor degeneration similar to that observed in human flecked retinal diseases. Using a positional cloning approach, we determined that rd6 mice carry a splice donor mutation in the mouse homolog of the human membrane-type frizzled-related protein (Mfrp) gene that results in the skipping

Shuhei Kameya; Norman L. Hawes; Bo Chang; John R. Heckenlively; J urgen K. Naggert; Patsy M. Nishina



A gene atlas of the mouse and human protein-encoding transcriptomes  

Microsoft Academic Search

The tissue-specific pattern of mRNA expression can indicate important clues about gene function. High-density oligonucleotide arrays offer the opportunity to examine patterns of gene expression on a genome scale. Toward this end, we have designed custom arrays that interrogate the expression of the vast majority of protein-encoding human and mouse genes and have used them to profile a panel of

Andrew I. Su; Tim Wiltshire; Serge Batalov; Hilmar Lapp; Keith A. Ching; David Block; Jie Zhang; Richard Soden; Mimi Hayakawa; Gabriel Kreiman; Michael P. Cooke; John R. Walker; John B. Hogenesch



The Human and Mouse Receptors for Hyaluronan-Mediated Motility, RHAMM, Genes ( HMMR) Map to Human Chromosome 5q33.2–qter and Mouse Chromosome 11  

Microsoft Academic Search

The gene for the receptor for hyaluronan-mediated motility, RHAMM (designated hyaluronan-mediated motility receptor,HMMR(human) andHmmr(mouse), for mapping purposes), was localized to human chromosome 5q33.2–qter by somatic cell and radiation hybrid analyses. Investigation of two interspecific backcrosses localized the mouse RHAMM (Hmmr) locus 18 cM from the centromere of mouse chromosome 11 within a region of synteny homology with human chromosome 5q23–q35




Zeptomole Electrochemical Detection of Metallothioneins  

Microsoft Academic Search

BackgroundThiol-rich peptides and proteins possess a large number of biological activities and may serve as markers for numerous health problems including cancer. Metallothionein (MT), a small molecular mass protein rich in cysteine, may be considered as one of the promising tumour markers. The aim of this paper was to employ chronopotentiometric stripping analysis (CPSA) for highly sensitive detection of MT.Methodology\\/Principal

Vojtech Adam; Jitka Petrlova; Joseph Wang; Tomas Eckschlager; Libuse Trnkova; Rene Kizek; Yann Astier



Redox biochemistry of mammalian metallothioneins  

Microsoft Academic Search

Metallothionein (MT) is a generic name for certain families of structurally rather variable metal-binding proteins. While\\u000a purely chemical or biological approaches failed to establish a single physiologic function for MTs in any species, a combination\\u000a of chemical and biological approaches and recent progress in defining the low but significant concentrations of cytosolic\\u000a free zinc(II) ions have demonstrated that mammalian MTs

Wolfgang Maret


The mouse lysosomal membrane protein 1 gene as a candidate for the motorneuron degeneration (mnd) locus  

SciTech Connect

The motorneuron degeneration (mnd) mutation causes one of the few late-onset progressive neurodegenerations in mice; therefore, the mnd mouse is a valuable paradigm for studying neurodegenerative biology. The mnd mutation may also model human neuronal ceroid lipofuscinosis (NCL) or Batten disease. Mnd maps to the centromeric region of mouse chromosome 8, which likely corresponds to portions of human chromosomes 13,8, or 19; we note that the chromosome 13 portion maps close to a region thought to contain the human Type V NCL locus. We have identified candidate genes for the mnd locus from human chromosomes 13, 8, and 19, and we are mapping these genes in the mouse to determine their proximity to the mutated locus and to refine the comparative human-mouse map in this area. A candidate gene from human chromosome 13 is LAMP1, which encodes lysosomal membrane protein 1. We found that Lamp1 in the mouse lies within the region of the mnd mutation. Therefore, we sequenced Lamp1 cDNAs from homozygous mnd mice and unrelated wildtype C57BL/6 mice. We find no differences between the two cDNA species in the regions examined, and expression analysis shows a similar LAMP1 protein distribution in wildtype and mutant mice, suggesting that an abnormal accumulation of material within normal lysosome structures is unlikely to be the pathogenetic mechanism in the mnd mouse. 19 refs., 3 figs.

Bermingham, N.A.; Martin, J.E.; Fisher, E.M.C. [Imperial College of Medicine at St. Mary`s, London (United Kingdom)] [Imperial College of Medicine at St. Mary`s, London (United Kingdom)



Mapping of the mouse actin capping protein {alpha} subunit genes and pseudogenes  

SciTech Connect

Capping protein (CP), a heterodimer of {alpha} and {beta} subunits, is found in all eukaryotes. CP binds to the barbed ends of actin filaments in vitro and controls actin assembly and cell motility in vivo. Vertebrates have three {alpha} isoforms ({alpha}1, {alpha}2, {alpha}3) produced from different genes, whereas lower organisms have only one gene and one isoform. We isolated genomic clones corresponding to the a subunits of mouse CP and found three {alpha}1 genes, two of which are pseudogenes, and a single gene for both {alpha}2 and {alpha}3. Their chromosomal locations were identified by interspecies backcross mapping. The {alpha}1 gene (Cappa1) mapped to Chromosome 3 between D3Mit11 and D3Mit13. The {alpha}1 pseudogenes (Cappa1-ps1 and Cappa1-ps2) mapped to Chromosomes 1 and 9, respectively. The {alpha}2 gene (Cappa2) mapped to Chromosome 6 near Ptn. The {alpha}3 gene (Cappa3) also mapped to Chromosome 6, approximately 68 cM distal from Cappa2 near Kras2. One mouse mutation, de, maps in the vicinity of the {alpha}1 gene. No known mouse mutations map to regions near the {alpha}2 or {alpha}3 genes. 29 refs., 3 figs., 1 tab.

Hart, M.C.; Korshunova, Y.O.; Cooper, J.A. [Washington Univ. School of Medicine, St. Louis, MO (United States)] [Washington Univ. School of Medicine, St. Louis, MO (United States)



The expression and chromatin structure of the chicken glyceraldehyde-3-phosphate dehydrogenase gene in mouse cells.  


Chicken glyceraldehyde-3-phosphate dehydrogenase gene (GAPD) and thymidine kinase gene (TK) were co-transfected into mouse LMTK- cells by the calcium phosphate precipitation technique. Four of the eight hypoxanthine/aminopterin/thymidine-containing medium-resistant, TK+ transfectants were shown to produce different amounts of chicken glyceraldehyde-3-phosphate dehydrogenase by zymogram analysis. Subcloning and further analysis revealed that the chicken GAPD was stably inherited and that its enzyme subunits randomly combined with mouse subunits in heterotetramers. Although the contribution of chicken enzyme varied from approximately 30 to approximately 90% of the total glyceraldehyde-3-phosphate dehydrogenase activity with a proportional increase in total activity in the different subclones, it did not appear to affect the expression of mouse endogenous glycolytic enzymes since there was no distinct change in the levels of either mouse glyceraldehyde-3-phosphate dehydrogenase mRNA nor mouse phosphoglycerate kinase enzyme activity. The levels of chicken GAPD copy number, mRNA, and enzyme apparently were generally correlated in the different subclones, suggesting that the chicken GAPD in the mouse cells were expressed constitutively. In situ hybridization revealed that the transfected genes were integrated into mouse chromosomes in one cluster, and the locations of these clusters were different in different clones. Chromatin structure analyses of the chicken GAPD in four different transfectants revealed three DNase I-hypersensitive sites located around 0.2, 2.0, and 3.4 kilobases upstream from the 5' side of the gene. These sites are also present in the same locations in chicken lymphoblastoid cells (Kuo, M. T., Iyer, B., and Schwartz, R. J. (1982) Nucleic Acids Res 10, 4565-4579), indicating the dominant transmission of DNase I-hypersensitive cleavage sites in the transfected gene. PMID:3972817

Sen, S; Siciliano, M J; Johnston, D A; Schwartz, R J; Kuo, T



Comparison of Human Chromosome 6p25 with Mouse Chromosome 13 Reveals a Greatly Expanded Ov-Serpin Gene Repertoire in the Mouse  

Microsoft Academic Search

Ov-serpins are intracellular proteinase inhibitors implicated in the regulation of tumor progression, inflammation, and cell death. The 13 human ov-serpin genes are clustered at 6p25 (3 genes) and 18q21 (10 genes), and share common structures. We show here that a 1-Mb region on mouse chromosome 13 contains at least 15 ov-serpin genes compared with the three ov-serpin genes within 0.35

Dion Kaiserman; Susan Knaggs; Katrina L Scarff; Anneliese Gillard; Ghazala Mirza; Matthew Cadman; Richard McKeone; Paul Denny; Jessica Cooley; Charaf Benarafa; Eileen Remold-O'Donnell; Jiannis Ragoussis; Phillip I Bird



Structure and polymorphism of the mouse myelin/oligodendrocyte glycoprotein gene  

SciTech Connect

The authors have isolated and characterized genomic clones containing the mouse myelin/oligodendrocyte glycoprotein (MOG) gene. It spans a region of 12.5 kb and consists of eight exons. Its exon-intron structure differs from that of classical MHC-class I genes, with which it is linked in the mouse genome. Nucleotide sequencing of the 5{prime} flanking region revelas that it contains several putative protein-binding sites, some of them in common with other myelin gene promoters. One intragenic polymorphism has been identified: it consists of a GA repeat, defining at least three alleles in mouse inbred strains, and is easily detectable using the polymerase chain reaction method.

Daubas, P.; Pham-Dinh, D.; Dautigny, A. [Universite Paris VI (France)] [Universite Paris VI (France)



Effect of ICSI on gene expression and development of mouse preimplantation embryos  

PubMed Central

BACKGROUND In vitro culture (IVC) and IVF of preimplantation mouse embryos are associated with changes in gene expression. It is however not known whether ICSI has additional effects on the transcriptome of mouse blastocysts. METHODS We compared gene expression and development of mouse blastocysts produced by ICSI and cultured in Whitten's medium (ICSIWM) or KSOM medium with amino acids (ICSIKSOMaa) with control blastocysts flushed out of the uterus on post coital Day 3.5 (in vivo). In addition, we compared gene expression in embryos generated by IVF or ICSI using WM. Global pattern of gene expression was assessed using the Affymetrix 430 2.0 chip. RESULTS Blastocysts from ICSI fertilization have a reduction in the number of trophoblastic and inner cell mass cells compared with embryos generated in vivo. Approximately 1000 genes are differentially expressed between ICSI blastocyst and in vivo blastocysts; proliferation, apoptosis and morphogenetic pathways are the most common pathways altered after IVC. Unexpectedly, expression of only 41 genes was significantly different between embryo cultured in suboptimal conditions (WM) or optimal conditions (KSOMaa). CONCLUSIONS Our results suggest that fertilization by ICSI may play a more important role in shaping the transcriptome of the developing mouse embryo than the culture media used. PMID:20889529

Giritharan, G.; Li, M.W.; De Sebastiano, F.; Esteban, F.J.; Horcajadas, J.A.; Lloyd, K.C.K.; Donjacour, A.; Maltepe, E.; Rinaudo, P.F.



Construction of a mouse model of factor VIII deficiency by gene targeting  

SciTech Connect

To develop a small animal model of hemophilia A for gene therapy experiments, we set out to construct a mouse model for factor VIII deficiency by gene targeting. First, we screened a mouse liver cDNA library using a human FVIII cDNA probe. We cloned a 2.6 Kb partial mouse factor VIII cDNA which extends from 800 base pairs of the 3{prime} end of exon 14 to the 5{prime} end of exon 26. A mouse genomic library made from strain 129 was then screened to obtain genomic fragments covering the exons desired for homologous recombination. Two genomic clones were obtained, and one covering exon 15 through 22 was used for gene targeting. To make gene targeting constructs, a 5.8 Kb genomic DNA fragment covering exons 15 to 19 of the mouse FVIII gene was subcloned, and the neo expression cassette was inserted into exons 16 and 17 separately by different strategies. These two constructs were named MFVIIIC-16 and MFVIIIC-17. The constructs were linearized and transfected into strain 129 mouse ES cells by electroporation. Factor VIII gene-knockout ES cell lines were selected by G-418 and screened by genomic Southern blots. Eight exon 16 targeted cell lines and five exon 17 targeted cell lines were obtained. Three cell lines from each construct were injected into blastocysts and surgically transferred into foster mothers. Multiple chimeric mice with 70-90% hair color derived from the ES-cell genotype were seen with both constructs. Germ line transmission of the ES-cell genotype has been obtained for the MFVIIIC-16 construct, and multiple hemophilia A carrier females have been identified. Factor VIII-deficient males will be conceived soon.

Bi, L.; Lawler, A.; Gearhart, J. [Univ. of Pennsylvania School of Medicine, Philadelphia, PA (United States)] [and others



The murine gap junction gene connexin36 is highly expressed in mouse retina and regulated during brain development  

Microsoft Academic Search

A new gap junction gene isolated from rat brain cDNA, mouse retina cDNA and mouse genomic DNA is called connexin36, since it codes for a connexin protein of 321 amino acids corresponding to the theoretical molecular mass of 36?045 kDa (rat) and 36?084 kDa (mouse). Only one amino acid residue differs between rat and mouse connexin36. In the single murine

Goran Söhl; Joachim Degen; Barbara Teubner; Klaus Willecke



Physical mapping of the retinoid X receptor B gene in mouse and human  

SciTech Connect

Retinoid X receptors (RXRs) are zinc finger-containing nuclear transcription factors. They belong to the nuclear receptor superfamily that contains retinoid receptors, vitamin D receptors, thyroid hormone receptors, and steroid hormone receptors as well as the so-called orphan receptors. We previously mapped all three RXR genes on mouse chromosomes, using a panel of Mus spretus-Mus musculus interspecific backcross mice: namely, the RXRA-gene (Rxra) on Chr 2 near the centromere, the RXRB gene (Rxrb) on Chr 17 in the H2 region, and the RXRG gene (Rxrg) on distal Chr 1. Using cosmid clones that cover the major histocompatibility complex (MHC) region, we determined the precise physical map positions of the gene encoding mouse and human RXRB, respectively. The mouse gene (Rxrb) maps between H2-Ke4 and H2-Ke5: namely, immediately telomeric to H2-Ke4 which encodes a histidine-rich transmembrane protein, and 12 kilobases centromeric to H2-Ke5 which is expressed in lymphoid tissues, Rxrb and H2-Ke4 are transcribed into opposite directions from a CpG-rich promoter of about 250 base pairs. This gene organization is well conserved also in the human genome at the HLA-DP subregion of Chr 6p, underscoring the strong conservation of the gene organization in the MHC region between the two mammals. 54 refs., 4 figs.

Nagata, T.; Kitagawa, K.; Taketo, M. [Banyu Tsukuba Research Institute, Tsukuba (Japan); Weiss, E.H. [Ludwig-Maximilians-Univ., Munich (Germany); Abe, K. [Kumamoto Univ. School of Medicine, Kumamoto (Japan); Ando, A.; Yara-Kikuti, Y.; Inoko, H. [Tokai Univ. School of Medicine, Isehara (Japan); Seldin, M.F. [Duke Univ. Medical Center, Durham, NC (United States); Ozato, K. [National Institutes of Health, Bethesda, MD (United States)



A mouse embryonic stem cell bank for inducible overexpression of human chromosome 21 genes  

Microsoft Academic Search

Background  Dosage imbalance is responsible for several genetic diseases, among which Down syndrome is caused by the trisomy of human\\u000a chromosome 21.\\u000a \\u000a \\u000a \\u000a \\u000a Results  To elucidate the extent to which the dosage imbalance of specific human chromosome 21 genes perturb distinct molecular pathways,\\u000a we developed the first mouse embryonic stem (ES) cell bank of human chromosome 21 genes. The human chromosome 21-mouse ES

Rossella De Cegli; Antonio Romito; Simona Iacobacci; Lei Mao; Mario Lauria; Anthony O Fedele; Joachim Klose; Christelle Borel; Patrick Descombes; Stylianos E Antonarakis; Diego di Bernardo; Sandro Banfi; Andrea Ballabio; Gilda Cobellis



Night-time restricted feeding normalises clock genes and Pai-1 gene expression in the db\\/db mouse liver  

Microsoft Academic Search

Aims\\/hypothesis  An increase in PAI-1 activity is thought to be a key factor underlying myocardial infarction. Mouse Pai-1 (mPai-1) activity shows a daily rhythm in vivo, and its transcription seems to be controlled not only by clock genes but also by humoral factors such as insulin and triglycerides. Thus, we investigated daily clock genes and mPai-1 mRNA expression in the liver

T. Kudo; M. Akiyama; K. Kuriyama; M. Sudo; T. Moriya; S. Shibata



Metallothionein labeling for CLEM method for identification of protein subunits.  


CLEM (correlative light and electron microscopy) is one of the powerful techniques to elucidate the localization and structure of the target proteins or their complexes in cell. First, target proteins labeled fluorescently can be searched using a fluorescence microscope, i.e., due to its low resolution (200nm), it is used as rough searching of target proteins. After rough detection of the localization of target proteins, they can be easily observed by electron microscopy with a high resolution and processed into fine structure, especially 3D structure. On the other hand, in the case of only electron microscopy, it is difficult for researchers to detect their localization due to a narrow range of views and no labeling of them.Thus, CLEM normally needs fluorescent labels for fluorescence microscopy but a label for electron microscopy is also expectedly for easier detection. Thus we focused on metallothionein. Metallothionein binds to cadmium ions, i.e., heavy atoms with strong density in electron microscopy [1]; in addition, cadmium ions and selenium ions are known to form Qdot-like nanoparticles induced by metallothionein [2]. These are 2 ? 5nm in size, fluorescent wavelength changes depending on the size of nanoparticles. Thus, target proteins fused with metallothionein could be observed by both of fluorescence microscopy and electron microscopy.We here used Chlamydomonas reinhardtii, single cell green algae with two flagella. Flagella are used for bending motion and motility. Flagella contain FAP20 (Flagellar Asociate Protein 20) and PACRG (PArkin Co-Regulated gene), which are related to composing axoneme architecture. If Chlamydomonas reinhardtii doesn't have FAP20 or PACRG, they can't generate bending motion. It is considered that FAP20 and PACRG locate on the root of the radial spoke. Recently the location of FAP20 was reported by Yanagisawa et al.[3]. First, we also focus on detecting localization of FAP20 and then will do so on that of PACKRG.We could observe fluorescence of metallothionein fused with FAP20 to form nanoparticle. We are now trying to observe larger electron density from metallothionein with cadmium for CLEM. PMID:25359836

Yamanaka, Ryutaro; Hirasaka, Yuka; Jin, Mingyue; Yanagisawa, Haruaki; Yasunaga, Takuo



A mouse atlas of gene expression: Large-scale digital gene-expression profiles from precisely defined developing C57BL/6J mouse tissues and cells  

PubMed Central

We analyzed 8.55 million LongSAGE tags generated from 72 libraries. Each LongSAGE library was prepared from a different mouse tissue. Analysis of the data revealed extensive overlap with existing gene data sets and evidence for the existence of ?24,000 previously undescribed genomic loci. The visual cortex, pancreas, mammary gland, preimplantation embryo, and placenta contain the largest number of differentially expressed transcripts, 25% of which are previously undescribed loci. PMID:16352711

Siddiqui, Asim S.; Khattra, Jaswinder; Delaney, Allen D.; Zhao, Yongjun; Astell, Caroline; Asano, Jennifer; Babakaiff, Ryan; Barber, Sarah; Beland, Jaclyn; Bohacec, Slavita; Brown-John, Mabel; Chand, Steve; Charest, David; Charters, Anita M.; Cullum, Rebecca; Dhalla, Noreen; Featherstone, Ruth; Gerhard, Daniela S.; Hoffman, Brad; Holt, Robert A.; Hou, Juan; Kuo, Byron Y.-L.; Lee, Lisa L. C.; Lee, Stephanie; Leung, Derek; Ma, Kevin; Matsuo, Corey; Mayo, Michael; McDonald, Helen; Prabhu, Anna-liisa; Pandoh, Pawan; Riggins, Gregory J.; de Algara, Teresa Ruiz; Rupert, James L.; Smailus, Duane; Stott, Jeff; Tsai, Miranda; Varhol, Richard; Vrljicak, Pavle; Wong, David; Wu, Mona K.; Xie, Yuan-Yun; Yang, George; Zhang, Ida; Hirst, Martin; Jones, Steven J. M.; Helgason, Cheryl D.; Simpson, Elizabeth M.; Hoodless, Pamela A.; Marra, Marco A.




NSDL National Science Digital Library

Based in New York City, the MOUSE organization works to empower "underserved students to provide technology support and leadership in their schools, supporting their academic and career success." On their homepage, visitors can learn about their programs, learn about supporting the MOUSE organization, and read up on their resources. In the "Resources" area, visitors can learn about their outreach activities in New York City, Chicago, and California. Visitors working in educational outreach will appreciate the information offered here, including materials on how different groups can receive assistance from the MOUSE organization. Also, visitors can look over the "News" updates to learn about their new programs, their educational seminars, and their outreach activities.


Manual Gene Ontology annotation workflow at the Mouse Genome Informatics Database  

PubMed Central

The Mouse Genome Database, the Gene Expression Database and the Mouse Tumor Biology database are integrated components of the Mouse Genome Informatics (MGI) resource ( The MGI system presents both a consensus view and an experimental view of the knowledge concerning the genetics and genomics of the laboratory mouse. From genotype to phenotype, this information resource integrates information about genes, sequences, maps, expression analyses, alleles, strains and mutant phenotypes. Comparative mammalian data are also presented particularly in regards to the use of the mouse as a model for the investigation of molecular and genetic components of human diseases. These data are collected from literature curation as well as downloads of large datasets (SwissProt, LocusLink, etc.). MGI is one of the founding members of the Gene Ontology (GO) and uses the GO for functional annotation of genes. Here, we discuss the workflow associated with manual GO annotation at MGI, from literature collection to display of the annotations. Peer-reviewed literature is collected mostly from a set of journals available electronically. Selected articles are entered into a master bibliography and indexed to one of eight areas of interest such as ‘GO’ or ‘homology’ or ‘phenotype’. Each article is then either indexed to a gene already contained in the database or funneled through a separate nomenclature database to add genes. The master bibliography and associated indexing provide information for various curator-reports such as ‘papers selected for GO that refer to genes with NO GO annotation’. Once indexed, curators who have expertise in appropriate disciplines enter pertinent information. MGI makes use of several controlled vocabularies that ensure uniform data encoding, enable robust analysis and support the construction of complex queries. These vocabularies range from pick-lists to structured vocabularies such as the GO. All data associations are supported with statements of evidence as well as access to source publications. PMID:23110975

Drabkin, Harold J.; Blake, Judith A.



The Rab protein family: Genetic mapping of six Rab genes in the mouse  

SciTech Connect

Rab proteins constitute a family of GTP-binding proteins that are located in distinct intracellular compartments and play a role in the regulation of vesicular trafficking. Yeast mutations in Rab gene homologs cause defects in vesicular transport similar to those observed in beige (bg) mice. To investigate Rab genes as candidates for mouse mutations characterized by defects in vesicular trafficking, we utilized an intersubspecific backcross [C57BL/6J-bg{sup J} X (C57BL/6J-bg{sup J} X CAST/Ei)F{sub 1}] segregating for the bg locus. Restriction fragment length polymorphisms (RFLPs) were obtained through Southern hybridization of F{sub 1} and C57BL/6J chromosomal DNA with the coding sequences of Rab genes. These RFLPs and 12 polymorphic microsatellites were used to determine the segregation of the Rab genes in 93 backcross mice. Rab4a, Rab4b, Rab7, Rab10, Rab22, and Rab24 were localized on mouse chromosomes 8, 7, 9, 12, 2, and 13, respectively. Although the results exclude these loci as candidates for bg, they demonstrate a wide dispersion of Rab genes throughout the mouse genome and reveal that Rab4b and Rab24 are possible candidates for the mouse mutations reduced pigmentation (rp) and purkinje cell degeneration (pcd), respectively. 31 refs., 3 figs., 2 tabs.

Barbosa, M.D.F.S.; Gutierrez, M.J.; Kingsmore, S.F. [Univ. of Florida, Gainesville (United States)] [and others] [Univ. of Florida, Gainesville (United States); and others



Co-expression Profiling of Autism Genes in the Mouse Brain  

PubMed Central

Autism spectrum disorder (ASD) is one of the most prevalent and highly heritable neurodevelopmental disorders in humans. There is significant evidence that the onset and severity of ASD is governed in part by complex genetic mechanisms affecting the normal development of the brain. To date, a number of genes have been associated with ASD. However, the temporal and spatial co-expression of these genes in the brain remain unclear. To address this issue, we examined the co-expression network of 26 autism genes from AutDB (, in the framework of 3,041 genes whose expression energies have the highest correlation between the coronal and sagittal images from the Allen Mouse Brain Atlas database ( These data were derived from in situ hybridization experiments conducted on male, 56-day old C57BL/6J mice co-registered to the Allen Reference Atlas, and were used to generate a normalized co-expression matrix indicating the cosine similarity between expression vectors of genes in this database. The network formed by the autism-associated genes showed a higher degree of co-expression connectivity than seen for the other genes in this dataset (Kolmogorov–Smirnov P?=?5×10?28). Using Monte Carlo simulations, we identified two cliques of co-expressed genes that were significantly enriched with autism genes (A Bonferroni corrected P<0.05). Genes in both these cliques were significantly over-expressed in the cerebellar cortex (P?=?1×10?5) suggesting possible implication of this brain region in autism. In conclusion, our study provides a detailed profiling of co-expression patterns of autism genes in the mouse brain, and suggests specific brain regions and new candidate genes that could be involved in autism etiology. PMID:23935468

Larsen, Eric C.; Banerjee-Basu, Sharmila; Mitra, Partha P.



Expression Profiling of the Solute Carrier Gene Family in the Mouse BrainS?  

PubMed Central

The solute carrier (Slc) superfamily is a major group of membrane transport proteins present in mammalian cells. Although Slc transporters play essential and diverse roles in the central nervous system, the localization and function of the vast majority of Slc genes in the mammalian brain are largely unknown. Using high-throughput in situ hybridization data generated by the Allen Brain Atlas, we systematically and quantitatively analyzed the spatial and cellular distribution of 307 Slc genes, which represent nearly 90% of presently known mouse Slc genes, in the adult C57BL/6J mouse brain. Our analysis showed that 252 (82%) of the 307 Slc genes are present in the brain, and a large proportion of these genes were detected at low to moderate expression levels. Evaluation of 20 anatomical brain subdivisions demonstrated a comparable level of Slc gene complexity but significant difference in transcript enrichment. The distribution of the expressed Slc genes was diverse, ranging from near-ubiquitous to highly localized. Functional annotation in 20 brain regions, including the blood-brain and blood-cerebral spinal fluid (CSF) barriers, suggests major roles of Slc transporters in supporting brain energy utilization, neurotransmission, nutrient supply, and CSF production. Furthermore, hierarchical cluster analysis revealed intricate Slc expression patterns associated with neuroanatomical organization. Our studies also revealed Slc genes present within defined brain microstructures and described the putative cell types expressing individual Slc genes. These results provide a useful resource for investigators to explore the roles of Slc genes in neurophysiological and pathological processes. PMID:19179540

Dahlin, Amber; Royall, Josh; Hohmann, John G.; Wang, Joanne



Glucocorticoid regulation of mouse mammary tumor virus gene expression.  


Glucocorticoid hormones act rapidly and specifically to stimulate the synthesis of mouse mammary tumor virus RNA in a variety of mouse mammary tumor cells and infected heterologous cells. The increase in viral RNA production appears to be mediated by receptor proteins and requires the presence of basal levels of viral RNA. Infection of heterologous cells with MMTV may alter host cell responses to glucocorticoids; in addition, production of unintegrated viral DNA in these cells has provided reagents required for studying the structure and function of the viral DNA itself. The advent of new techniques for genetic manipulation of eukaryotic cells and for isolation of large amounts of specific DNA sequences should now permit detailed analyses of steroid hormone action in this system. PMID:229906

Ringold, G M



Gene expression profiling of mouse p53-deficient epidermal carcinoma defines molecular determinants of human cancer malignancy  

PubMed Central

Background The epidermal specific ablation of Trp53 gene leads to the spontaneous development of aggressive tumors in mice through a process that is accelerated by the simultaneous ablation of Rb gene. Since alterations of p53-dependent pathway are common hallmarks of aggressive, poor prognostic human cancers, these mouse models can recapitulate the molecular features of some of these human malignancies. Results To evaluate this possibility, gene expression microarray analysis was performed in mouse samples. The mouse tumors display increased expression of cell cycle and chromosomal instability associated genes. Remarkably, they are also enriched in human embryonic stem cell gene signatures, a characteristic feature of human aggressive tumors. Using cross-species comparison and meta-analytical approaches, we also observed that spontaneous mouse tumors display robust similarities with gene expression profiles of human tumors bearing mutated TP53, or displaying poor prognostic outcome, from multiple body tissues. We have obtained a 20-gene signature whose genes are overexpressed in mouse tumors and can identify human tumors with poor outcome from breast cancer, astrocytoma and multiple myeloma. This signature was consistently overexpressed in additional mouse tumors using microarray analysis. Two of the genes of this signature, AURKA and UBE2C, were validated in human breast and cervical cancer as potential biomarkers of malignancy. Conclusions Our analyses demonstrate that these mouse models are promising preclinical tools aimed to search for malignancy biomarkers and to test targeted therapies of prospective use in human aggressive tumors and/or with p53 mutation or inactivation. PMID:20630075



Weighted gene coexpression network analysis strategies applied to mouse weight  

Microsoft Academic Search

Systems-oriented genetic approaches that incorporate gene expression and genotype data are valuable in the quest for genetic\\u000a regulatory loci underlying complex traits. Gene coexpression network analysis lends itself to identification of entire groups\\u000a of differentially regulated genes—a highly relevant endeavor in finding the underpinnings of complex traits that are, by definition,\\u000a polygenic in nature. Here we describe one such approach

Tova F. Fuller; Anatole Ghazalpour; Jason E. Aten; Thomas A. Drake; Aldons J. Lusis; Steve Horvath



Mouse Studies Identify Gene that May Influence Metastasis Risk in Breast Cancer

Researchers have identified a pattern of gene activity in mice that may help to predict individual risk for breast cancer metastasis and survival in humans. A single gene called bromodomain 4 (Brd4) regulates the expression of this pattern, also called a signature. The researchers found that one result of this Brd4 regulation is the suppression of tumor growth and metastasis in a mouse model of cancer.


Identification of Genes and Networks Driving Cardiovascular and Metabolic Phenotypes in a Mouse F2 Intercross  

Microsoft Academic Search

To identify the genes and pathways that underlie cardiovascular and metabolic phenotypes we performed an integrated analysis of a mouse C57BL\\/6J x A\\/J F2 (B6AF2) cross by relating genome-wide gene expression data from adipose, kidney, and liver tissues to physiological endpoints measured in the population. We have identified a large number of trait QTLs including loci driving variation in cardiac

Jonathan M. J. Derry; Hua Zhong; Cliona Molony; Doug MacNeil; Debraj Guhathakurta; Bin Zhang; John Mudgett; Kersten Small; Lahcen El Fertak; Alain Guimond; Mohammed Selloum; Wenqing Zhao; Marie France Champy; Laurent Monassier; Tom Vogt; Doris Cully; Andrew Kasarskis; Eric E. Schadt; Gregory S. Barsh



Can we generate new hypotheses about Dent's disease from gene analysis of a mouse model?  


In humans, Dent's disease, an X-linked renal tubular disorder, is characterized by low molecular weight proteinuria, aminoaciduria, glycosuria, hyperphosphaturia, hypercalciuria, nephrolithiasis, progressive renal failure and sometimes rickets or osteomalacia. The aetiology of X-linked Dent's disease is established to be caused by mutations of the CLCN5 gene. The protein product of this gene is the voltage-gated chloride-proton exchanger CLC-5. Previous studies by the Johns Hopkins group (Guggino) and the Hamburg group (Jentsch) have established that the Clcn5 knockout mouse recapitulates the renal attributes of Dent's disease. In order to understand the changes in kidney function that accompany the knockout of the Clcn5 gene, we examined gene expression profiles from dissected proximal segment 1 (S1) and segment 2 (S2) tubules of mouse kidneys. Overall, 725 genes are expressed differentially in the proximal tubules of the Dent Clcn5 knockout mouse model compared with those of control wild-type mice. A major finding is the change in the cholesterol synthesis pathway. Some interesting changes also occur in genes encoding transport proteins. One of these transport proteins, the sodium bile cotransporter gene, Slc10a2, has transcripts increased by 17-fold in the Clcn5 knockout mouse. The Clc-3 protein encoded by Clcn3, a chloride-proton exchanger related to Clc-5, has a 1.9-fold increase in transcripts. The Npt2c protein, a proximal tubule sodium phosphate cotransporter encoded by Slc34a3, has a 0.6-fold decrease in the number of transcripts. The sodium-proton exchanger-like protein, Nhe10/sperm, encoded by Slc9a10, has a 0.5-fold decrease in transcript number. These genes are discussed with regard to the possible physiological outcomes of their transcript or protein changes. PMID:18931044

Guggino, Sandra E



Phenotypes of major immediate-early gene mutants of mouse cytomegalovirus  

Microsoft Academic Search

Immediate-early (IE) genes are the first genes to be transcribed during the lytic replication cycle of cytomegaloviruses (CMV),\\u000a and encode nonstructural proteins, which are assumed to have mainly regulatory functions. The IE proteins may play important\\u000a roles in the pathogenesis of CMV in vivo, for instance during the establishment of latency and during reactivation. We constructed\\u000a mouse CMV mutants with

Andreas Busche; Ana Angulo; Penelope Kay-Jackson; Peter Ghazal; Martin Messerle



Effects of the steel gene product on mouse primordial germ cells in culture  

Microsoft Academic Search

MUTATIONS at the steel (si) and dominant white spotting (W) loci in the mouse affect primordial germ cells (PGC), melanoblasts and haemopoietic stem cells1. The W gene encodes a cell-surface receptor of the tyrosine kinase family2,3, the proto-oncogene c-kit. In situ analysis has shown c-kitmessenger RNA expression in PGC in the early genital ridges4. The SI gene encodes the ligand

I. Godin; R. Deed; J. Cooke; K. Zsebo; M. Dexter; C. C. Wylie



Regulation of human protein C gene expression by the mouse WAP promoter  

Microsoft Academic Search

A 4.1 kb mouse whey acidic protein (mWAP) promoter was cloned from a C57BL\\/6 cosmid library. The tissue-specific and developmental pattern of expression of a hybrid gene comprised of the mWAP promoter fragment and the human protein C (HPC) gene was analysed in transgenic mice. The corresponding RNA was detected mainly in the mammary gland, with ‘leakage’ of expression in

Rekha K. Paleyanda; Da-Wei Zhang; Lothar Hennighausen; Robert A. McKnight; Henryk Lubon



Structural Organization and Chromosomal Assignment of the Mouse Embryonic TEA Domain-Containing Factor (ETF) Gene  

Microsoft Academic Search

Embryonic TEA domain-containing factor (ETF) belongs to the family of proteins structurally related to transcriptional enhancer factor-1 (TEF-1) and is implicated in neural development. Isolation and characterization of the cosmid clones encoding the mouse ETF gene (Etdf) revealed thatEtdfspans approximately 17.9 kb and consists of 12 exons. The exon–intron structure ofEtdfclosely resembles that of theDrosophila scallopedgene, indicating that these genes

Kazuo Suzuki; Michio Yasunami; Yoichi Matsuda; Takako Maeda; Hironori Kobayashi; Hidenori Terasaki; Hiroaki Ohkubo



Patterning the Embryonic Heart: Identification of Five Mouse Iroquois Homeobox Genes in the Developing Heart  

Microsoft Academic Search

We isolated cDNAs of mouse Iroquois-related homeobox genes Irx1, -2, -3, -4, and -5 and characterized their patterns of expression in the developing heart. Irx1 and Irx2 were found to be expressed specifically in the ventricular septum from the onset of its formation onward. In fetal stages, the expression of both genes appeared to gradually become confined to the myocardium

Vincent M. Christoffels; Astrid G. M. Keijser; Arjan C. Houweling; Danielle E. W. Clout; Antoon F. M. Moorman



Characterization of the genomic structure of the mouse APLP1 gene  

SciTech Connect

This article reports on the organization of the mouse APLP1 gene, an evolutionarily conserved amyloid precursor-like protein. The amyloid beta protein, important in Alzheimer diseases, is derived from these precursor proteins. By investigating the expression and structure of this murine gene, it is hoped that more will be learned about the function and regulation of the human homologue. 27 refs., 2 figs.

Zhong, Sue; Wu, Kuo; Black, I.B.; Schaar, D.G. [State Univ. of New Jersey, Piscataway, NJ (United States)] [State Univ. of New Jersey, Piscataway, NJ (United States)



Effects of Methylmercury Contained in a Diet Mimicking the Wayana Amerindians Contamination through Fish Consumption: Mercury Accumulation, Metallothionein Induction, Gene Expression Variations, and Role of the Chemokine CCL2  

PubMed Central

Methylmercury (MeHg) is a potent neurotoxin, and human beings are mainly exposed to this pollutant through fish consumption. We addressed the question of whether a diet mimicking the fish consumption of Wayanas Amerindians from French Guiana could result in observable adverse effects in mice. Wayanas adult men are subjected to a mean mercurial dose of 7 g Hg/week/kg of body weight. We decided to supplement a vegetarian-based mice diet with 0.1% of lyophilized Hoplias aimara fish, which Wayanas are fond of and equivalent to the same dose as that afflicting the Wayanas Amerindians. Total mercury contents were 1.4 ± 0.2 and 5.4 ± 0.5 ng Hg/g of food pellets for the control and aimara diets, respectively. After 14 months of exposure, the body parts and tissues displaying the highest mercury concentration on a dry weight (dw) basis were hair (733 ng/g) and kidney (511 ng/g), followed by the liver (77 ng/g). Surprisingly, despite the fact that MeHg is a neurotoxic compound, the brain accumulated low levels of mercury (35 ng/g in the cortex). The metallothionein (MT) protein concentration only increased in those tissues (kidney, muscles) in which MeHg demethylation had occurred. This can be taken as a molecular sign of divalent mercurial contamination since only Hg2+ has been reported yet to induce MT accumulation in contaminated tissues. The suppression of the synthesis of the chemokine CCL2 in the corresponding knockout (KO) mice resulted in important changes in gene expression patterns in the liver and brain. After three months of exposure to an aimara-containing diet, eight of 10 genes selected (Sdhb, Cytb, Cox1, Sod1, Sod2, Mt2, Mdr1a and Bax) were repressed in wild-type mice liver whereas none presented a differential expression in KO Ccl2?/? mice. In the wild-type mice brain, six of 12 genes selected (Cytb, Cox1, Sod1, Sod2, Mdr1a and Bax) presented a stimulated expression, whereas all remained at the basal level of expression in KO Ccl2?/? mice. In the liver of aimara-fed mice, histological alterations were observed for an accumulated mercury concentration as low as 32 ng/g, dw, and metal deposits were observed within the cytoplasm of hepatic cells. PMID:22837723

Bourdineaud, Jean-Paul; Laclau, Muriel; Maury-Brachet, Regine; Gonzalez, Patrice; Baudrimont, Magalie; Mesmer-Dudons, Nathalie; Fujimura, Masatake; Marighetto, Aline; Godefroy, David; Rostene, William; Brethes, Daniel



Dissecting Epigenetic Silencing Complexity in the Mouse Lung Cancer Suppressor Gene Cadm1  

Microsoft Academic Search

Disease-oriented functional analysis of epigenetic factors and their regulatory mechanisms in aberrant silencing is a prerequisite for better diagnostics and therapy. Yet, the precise mechanisms are still unclear and complex, involving the interplay of several effectors including nucleosome positioning, DNA methylation, histone variants and histone modifications. We investigated the epigenetic silencing complexity in the tumor suppressor gene Cadm1 in mouse

Stella Marie Reamon-Buettner; Juergen Borlak



A Complex Oscillating Network of Signaling Genes Underlies the Mouse Segmentation Clock  

Microsoft Academic Search

The segmental pattern of the spine is established early in development, when the vertebral precursors, the somites, are rhythmically produced from the presomitic mesoderm. Microarray studies of the mouse presomitic mesoderm transcriptome reveal that the oscillator associated with this process, the segmentation clock, drives the periodic expression of a large network of cyclic genes involved in cell signaling. Mutually exclusive

Mary-Lee Dequéant; Earl Glynn; Karin Gaudenz; Matthias Wahl; Jie Chen; Arcady Mushegian; Olivier Pourquié



Aberrant alternative splicing and extracellular matrix gene expression in mouse models of myotonic dystrophy.  

E-print Network

Aberrant alternative splicing and extracellular matrix gene expression in mouse models of myotonic , and Manuel Ares, Jr.1 * 1 RNA Center, Department of Molecular, Cell and Developmental Biology, Sinsheimer Labs, University of California, Santa Cruz, California 95064 USA 2 Neuromuscular Disease Center

Ares Jr., Manny


Delivery and Inhibition of Reporter Genes by Small Interfering RNAs in a Mouse Skin Model  

Microsoft Academic Search

RNA interference offers the potential of a novel therapeutic approach for treating skin disorders. To this end, we investigated delivery of nucleic acids, including a plasmid expressing the reporter gene luciferase, to mouse skin by intradermal injection into footpads using in vivo bioluminescence imaging over multiple time points. In order to evaluate the ability of RNA interference to inhibit skin

Qian Wang; Heini Ilves; Pauline Chu; Christopher H. Contag; Devin Leake; Brian H. Johnston; Roger L. Kaspar



The characterization of mouse carboxypeptidase N small subunit gene structure and presence in developing embryos  

Microsoft Academic Search

Carboxypeptidase N (CPN) is a plasma zinc metalloprotease, which consists of two enzymatically active small subunits and two large subunits that protect the protein from degradation. CPN cleaves carboxy-terminal arginines and lysines from peptides found in the bloodstream such as complement anaphylatoxins, kinins, and creatine kinase MM. In this study, the mouse CPN small subunit (CPN1) coding region, gene structure,

Kirstin Renee Watts Matthews



Mouse cytosolic and mitochondrial deoxyribonucleotidases: cDNA cloning of the mitochondrial enzyme, gene structures, chromosomal  

E-print Network

Mouse cytosolic and mitochondrial deoxyribonucleotidases: cDNA cloning of the mitochondrial enzyme, gene structures, chromosomal mapping and comparison with the human orthologsq Chiara Rampazzoa , Maria is a cytoplasmic enzyme (dNT-1), the other occurs in mitochondria (dNT-2). The human mitochondrial enzyme, recently

Bianchi, Vera


Enhanced gene expression in mouse lung by prolonging the retention time of intravenously injected plasmid DNA  

Microsoft Academic Search

The effect of retention time of plasmid DNA in mouse lung on the level of transgene expression after intravenous administration was examined. Using CMV driven expression system with luciferase gene as a reporter and preinjection of free cationic liposomes into the animal as means of manipulating the retention time of plasmid DNA, we demonstrated that naked plasmid DNA is effective

YK Song; F Liu; D Liu



Reference gene selection for real-time RT-PCR in regenerating mouse livers  

SciTech Connect

The liver has an intrinsic ability to undergo active proliferation and recover functional liver mass in response to an injury response. This regenerative process involves a complex yet well orchestrated change in the gene expression profile. To produce accurate and reliable gene expression of target genes during various stages of liver regeneration, the determination of internal control housekeeping genes (HKGs) those are uniformly expressed is required. In the present study, the gene expression of 8 commonly used HKGs, including GAPDH, ACTB, HPRT1, GUSB, PPIA, TBP, TFRC, and RPL4, were studied using mouse livers that were quiescent and actively regenerating induced by partial hepatectomy. The amplification of the HKGs was statistically analyzed by two different mathematical algorithms, geNorm and NormFinder. Using this method, PPIA and TBP gene expression found to be relatively stable regardless of the stages of liver regeneration and would be ideal for normalization to target gene expression.

Tatsumi, Kohei [Department of Pediatrics, Nara Medical University, 840 Shijo-cho, Kashihara, Nara 634-8522 (Japan); Ohashi, Kazuo [Institute of Advanced Biomedical Engineering and Science, Tokyo Women's Medical University, 8-1 Kawada-cho, Shinjuku-ku, Tokyo 162-8666 (Japan)], E-mail:; Taminishi, Sanae [Department of Pediatrics, Nara Medical University, 840 Shijo-cho, Kashihara, Nara 634-8522 (Japan); Okano, Teruo [Institute of Advanced Biomedical Engineering and Science, Tokyo Women's Medical University, 8-1 Kawada-cho, Shinjuku-ku, Tokyo 162-8666 (Japan); Yoshioka, Akira; Shima, Midori [Department of Pediatrics, Nara Medical University, 840 Shijo-cho, Kashihara, Nara 634-8522 (Japan)



Number of CpG islands and genes in human and mouse  

SciTech Connect

Estimation of gene number in mammals is difficult due to the high proportion of noncoding DNA within the nucleus. In this study, the authors provide a direct measurement of the number of genes in human and mouse. They have taken advantage of the fact that many mammalian genes are associated with CpG islands whose distinctive properties allow their physical separation from bulk DNA. The results suggest that there are [approx]45,000 CpG islands per haploid genome in humans and 37,000 in the mouse. Sequence comparison confirms that about 20% of the human CpG islands are absent from the homologous mouse genes. Analysis of a selection of germ line followed by CpG loss through mutation. This process appears to be more rapid in rodents. Combining the number of CpG islands with the proportion of island-associated genes, the authors estimate that the total number of genes per haploid genome is [approx]80,000 in both organisms.

Antequera, F.; Bird, A. (Univ. of Edinburgh (United Kingdom))



Chromosome localizations of genes for five cAMP-specific phosphodiesterases in man and mouse  

SciTech Connect

Cyclic nucleotides are important second messengers that mediate a number of cellular responses to external signals. Cyclic nucleotide phosphodiesterases play a role in signal transduction by regulating the cellular concentrations of these messengers. Here, the authors have applied Southern analyses of somatic cell hybrid lines and of recombinant inbred (RI) mouse strains as well as fluorescence chromosomal in situ hybridization (FISH) to chromosomally localize five cAMP-specific nucleotide phosphodiesterase genes in human and mouse. Genes DPDE1, DPDE2, DPDE3, and DPDE4 that share sequence homology with the Drosophila dunce gene were assigned to human chromosomes 19 (DPDE1 and DPDE2), ga12 (DPDE3), and 1p31 (DPDE4) and to mouse chromosomes 8, 9, 13, and 4, respectively. The high-affinity cAMP-specific phosphodiesterase gene (HCP1) was mapped to human chromosome 8q13-q22. Since these genes are potential candidates for involvement in psychiatric or behavioral disorders, knowledge of their chromosomal localizations will facilitate the discovery of their association with disease genes as they are being mapped by linkage studies.

Milatovich, A.; Francke, U. (Stanford Univ. Medical Center, CA (United States)); Bolger, G.; Michaeli, T. (Cold Spring Harbor Lab., NY (United States))



Genetics of gene expression surveyed in maize, mouse and man  

Microsoft Academic Search

Treating messenger RNA transcript abundances as quantitative traits and mapping gene expression quantitative trait loci for these traits has been pursued in gene-specific ways. Transcript abundances often serve as a surrogate for classical quantitative traits in that the levels of expression are significantly correlated with the classical traits across members of a segregating population. The correlation structure between transcript abundances

Eric E. Schadt; Stephanie A. Monks; Thomas A. Drake; Aldons J. Lusis; Nam Che; Veronica Colinayo; Thomas G. Ruff; Stephen B. Milligan; John R. Lamb; Guy Cavet; Peter S. Linsley; Mao Mao; Roland B. Stoughton; Stephen H. Friend



Human chromosome 21 gene expression atlas in the mouse  

Microsoft Academic Search

Genome-wide expression analyses have a crucial role in functional genomics. High resolution methods, such as RNA in situ hybridization provide an accurate description of the spatiotemporal distribution of transcripts as well as a three-dimensional `in vivo' gene expression overview. We set out to analyse systematically the expression patterns of genes from an entire chromosome. We chose human chromosome 21 because

Alexandre Reymond; Valeria Marigo; Murat B. Yaylaoglu; Antonio Leoni; Catherine Ucla; Nathalie Scamuffa; Cristina Caccioppoli; Emmanouil T. Dermitzakis; Robert Lyle; Sandro Banfi; Gregor Eichele; Stylianos E. Antonarakis; Andrea Ballabio



From Mouse to Human: Evolutionary Genomics Analysis of Human Orthologs of Essential Genes  

PubMed Central

Understanding the core set of genes that are necessary for basic developmental functions is one of the central goals in biology. Studies in model organisms identified a significant fraction of essential genes through the analysis of null-mutations that lead to lethality. Recent large-scale next-generation sequencing efforts have provided unprecedented data on genetic variation in human. However, evolutionary and genomic characteristics of human essential genes have never been directly studied on a genome-wide scale. Here we use detailed phenotypic resources available for the mouse and deep genomics sequencing data from human populations to characterize patterns of genetic variation and mutational burden in a set of 2,472 human orthologs of known essential genes in the mouse. Consistent with the action of strong, purifying selection, these genes exhibit comparatively reduced levels of sequence variation, skew in allele frequency towards more rare, and exhibit increased conservation across the primate and rodent lineages relative to the remainder of genes in the genome. In individual genomes we observed ?12 rare mutations within essential genes predicted to be damaging. Consistent with the hypothesis that mutations in essential genes are risk factors for neurodevelopmental disease, we show that de novo variants in patients with Autism Spectrum Disorder are more likely to occur in this collection of genes. While incomplete, our set of human orthologs shows characteristics fully consistent with essential function in human and thus provides a resource to inform and facilitate interpretation of sequence data in studies of human disease. PMID:23675308

Georgi, Benjamin; Voight, Benjamin F.; Bucan, Maja



T lymphomagenesis is determined by a dominant host gene thymic lymphoma susceptible mouse-1 (TLSM-1) in mouse models  

PubMed Central

Susceptibility to T lymphomas in mice is determined by a number of viral and host genetic factors. We analyzed the types and latent period of lymphomas spontaneously occurring in crosses between AKR/Ms, a T lymphoma-prone mouse strain, and SL/Kh, a pre-B lymphoma-prone strain. The incidence of T lymphomas in the F1 hybrids backcross to SL/Kh as well as F2 generation mice indicated that a dominant host gene thymic lymphoma susceptible mouse-1 (Tlsm-1) of AKR/Ms determined the type of lymphomas to be thymic. Linkage analysis with microsatellite markers assigned Tlsm-1 to the map position 61 cM from centromere of the chromosome 7. Close scrutiny of this region of AKXD recombinant inbred strains for spontaneous T lymphomas revealed the presence of Tlsm-1- like gene most likely between D7MIT71 (map position 62) and D7MIT13 (map position 70). On the other hand, a SL/Kh-derived recessive allele at a major histocompatibility complex (MHC)-linked locus accelerated development of both T and B lymphomas. PMID:7964490



Structural characterization and chromosomal location of the mouse macrophage migration inhibitory factor gene and pseudogenes  

SciTech Connect

Macrophage migration inhibitory factor, MIF, is a cytokine released by T-lymphocytes, macrophages, and the pituitary gland that serves to integrate peripheral and central inflammatory responses. Ubiquitous expression and developmental regulation suggest that MIF may have additional roles outside of the immune system. Here we report the structure and chromosomal location of the mouse Mif gene and the partial characterization of five Mif pseudogenes. The mouse Mif gene spans less than 0.7 kb of chromosomal DNA and is composed of three exons. A comparison between the mouse and the human genes shows a similar gene structure and common regulatory elements in both promoter regions. The mouse Mif gene maps to the middle region of chromosome 10, between Bcr and S100b, which have been mapped to human chromosomes 22q11 and 21q22.3, respectively. The entire sequence of two pseudogenes demonstrates the absence of introns, the presence of the 5{prime} untranslated region of the cDNA, a 3{prime} poly(A) tail, and the lack of sequence similarity with untranscribed regions of the gene. The five pseudogenes are highly homologous to the cDNA, but contain a variable number of mutations that would produce mutated or truncated MIF-like proteins. Phylogenetic analyses of MIF genes and pseudogenes indicate several independent genetic events that can account for multiple genomic integrations. Three of the Mif pseudogenes were also mapped by interspecific backcross to chromosomes 1, 9, and 17. These results suggest that Mif pseudogenes originated by retrotransposition. 46 refs., 5 figs., 1 tab.

Bozza, M.; Gerard, C.; Kolakowski, L.F. Jr. [Children`s Hospital, Boston, MA (United States)] [and others] [Children`s Hospital, Boston, MA (United States); and others



Developmental regulation of myosin gene expression in mouse cardiac muscle  

Microsoft Academic Search

Expression of the two isoforms of cardiac myosin heavy chain (MHC), MHCot and MHC\\/3, in mammals is regulated postnatally by a variety of stim- uli, including serum hormone levels. Less is known about the factors that regulate myosin gene expression in rapidly growing cardiac muscle in embryos. Using isoform-specific 35S-labeled cRNA probes correspond- ing to the two MHC genes and

Gary E. Lyons; Stefano Schiaflino; David Sassoon; Paul Barton; Margaret Buckingham



Impact of cigarette smoke on the human and mouse lungs: a gene-expression comparison study.  


Cigarette smoke is well known for its adverse effects on human health, especially on the lungs. Basic research is essential to identify the mechanisms involved in the development of cigarette smoke-related diseases, but translation of new findings from pre-clinical models to the clinic remains difficult. In the present study, we aimed at comparing the gene expression signature between the lungs of human smokers and mice exposed to cigarette smoke to identify the similarities and differences. Using human and mouse whole-genome gene expression arrays, changes in gene expression, signaling pathways and biological functions were assessed. We found that genes significantly modulated by cigarette smoke in humans were enriched for genes modulated by cigarette smoke in mice, suggesting a similar response of both species. Sixteen smoking-induced genes were in common between humans and mice including six newly reported to be modulated by cigarette smoke. In addition, we identified a new conserved pulmonary response to cigarette smoke in the induction of phospholipid metabolism/degradation pathways. Finally, the majority of biological functions modulated by cigarette smoke in humans were also affected in mice. Altogether, the present study provides information on similarities and differences in lung gene expression response to cigarette smoke that exist between human and mouse. Our results foster the idea that animal models should be used to study the involvement of pathways rather than single genes in human diseases. PMID:24663285

Morissette, Mathieu C; Lamontagne, Maxime; Bérubé, Jean-Christophe; Gaschler, Gordon; Williams, Andrew; Yauk, Carole; Couture, Christian; Laviolette, Michel; Hogg, James C; Timens, Wim; Halappanavar, Sabina; Stampfli, Martin R; Bossé, Yohan



Molecular Characterization of J558 Genes Encoding Tight-Skin Mouse Autoantibodies: Identical Heavy-Chain Variable Genes Code for Antibodies with Different Specificities  

Microsoft Academic Search

Tight-skin mouse, a mutant strain with a single gene defect, develops cutaneous hyperplasia and specific autoantibodies, like humans affected by scleroderma. The autoantibodies produced in the tight-skin mouse are encoded primarily by heavy-chain variable (V_H) genes from the J558 family. To understand the genetic basis of production of autoantibodies, we have analyzed the structure of J558 genes encoding these autoantibodies.

Kuppuswamy N. Kasturi; Xian Y. Yio; Constantin A. Bona



Network statistics of genetically-driven gene co-expression modules in mouse crosses  

PubMed Central

In biology, networks are used in different contexts as ways to represent relationships between entities, such as for instance interactions between genes, proteins or metabolites. Despite progress in the analysis of such networks and their potential to better understand the collective impact of genes on complex traits, one remaining challenge is to establish the biologic validity of gene co-expression networks and to determine what governs their organization. We used WGCNA to construct and analyze seven gene expression datasets from several tissues of mouse recombinant inbred strains (RIS). For six out of the 7 networks, we found that linkage to “module QTLs” (mQTLs) could be established for 29.3% of gene co-expression modules detected in the several mouse RIS. For about 74.6% of such genetically-linked modules, the mQTL was on the same chromosome as the one contributing most genes to the module, with genes originating from that chromosome showing higher connectivity than other genes in the modules. Such modules (that we considered as “genetically-driven”) had network statistic properties (density and centralization) that set them apart from other modules in the network. Altogether, a sizeable portion of gene co-expression modules detected in mouse RIS panels had genetic determinants as their main organizing principle. In addition to providing a biologic interpretation validation for these modules, these genetic determinants imparted on them particular properties that set them apart from other modules in the network, to the point that they can be predicted to a large extent on the basis of their network statistics. PMID:24421784

Scott-Boyer, Marie-Pier; Haibe-Kains, Benjamin; Deschepper, Christian F.



Network statistics of genetically-driven gene co-expression modules in mouse crosses.  


In biology, networks are used in different contexts as ways to represent relationships between entities, such as for instance interactions between genes, proteins or metabolites. Despite progress in the analysis of such networks and their potential to better understand the collective impact of genes on complex traits, one remaining challenge is to establish the biologic validity of gene co-expression networks and to determine what governs their organization. We used WGCNA to construct and analyze seven gene expression datasets from several tissues of mouse recombinant inbred strains (RIS). For six out of the 7 networks, we found that linkage to "module QTLs" (mQTLs) could be established for 29.3% of gene co-expression modules detected in the several mouse RIS. For about 74.6% of such genetically-linked modules, the mQTL was on the same chromosome as the one contributing most genes to the module, with genes originating from that chromosome showing higher connectivity than other genes in the modules. Such modules (that we considered as "genetically-driven") had network statistic properties (density and centralization) that set them apart from other modules in the network. Altogether, a sizeable portion of gene co-expression modules detected in mouse RIS panels had genetic determinants as their main organizing principle. In addition to providing a biologic interpretation validation for these modules, these genetic determinants imparted on them particular properties that set them apart from other modules in the network, to the point that they can be predicted to a large extent on the basis of their network statistics. PMID:24421784

Scott-Boyer, Marie-Pier; Haibe-Kains, Benjamin; Deschepper, Christian F



Extraordinary Sequence Divergence at Tsga8, an X-linked Gene Involved in Mouse Spermiogenesis  

PubMed Central

The X chromosome plays an important role in both adaptive evolution and speciation. We used a molecular evolutionary screen of X-linked genes potentially involved in reproductive isolation in mice to identify putative targets of recurrent positive selection. We then sequenced five very rapidly evolving genes within and between several closely related species of mice in the genus Mus. All five genes were involved in male reproduction and four of the genes showed evidence of recurrent positive selection. The most remarkable evolutionary patterns were found at Testis-specific gene a8 (Tsga8), a spermatogenesis-specific gene expressed during postmeiotic chromatin condensation and nuclear transformation. Tsga8 was characterized by extremely high levels of insertion–deletion variation of an alanine-rich repetitive motif in natural populations of Mus domesticus and M. musculus, differing in length from the reference mouse genome by up to 89 amino acids (27% of the total protein length). This population-level variation was coupled with striking divergence in protein sequence and length between closely related mouse species. Although no clear orthologs had previously been described for Tsga8 in other mammalian species, we have identified a highly divergent hypothetical gene on the rat X chromosome that shares clear orthology with the 5? and 3? ends of Tsga8. Further inspection of this ortholog verified that it is expressed in rat testis and shares remarkable similarity with mouse Tsga8 across several general features of the protein sequence despite no conservation of nucleotide sequence across over 60% of the rat-coding domain. Overall, Tsga8 appears to be one of the most rapidly evolving genes to have been described in rodents. We discuss the potential evolutionary causes and functional implications of this extraordinary divergence and the possible contribution of Tsga8 and the other four genes we examined to reproductive isolation in mice. PMID:21186189

Good, Jeffrey M.; Vanderpool, Dan; Smith, Kimberly L.; Nachman, Michael W.



High-efficiency and heritable gene targeting in mouse by transcription activator-like effector nucleases  

PubMed Central

Transcription activator-like effector nucleases (TALENs) are a powerful new approach for targeted gene disruption in various animal models, but little is known about their activities in Mus musculus, the widely used mammalian model organism. Here, we report that direct injection of in vitro transcribed messenger RNA of TALEN pairs into mouse zygotes induced somatic mutations, which were stably passed to the next generation through germ-line transmission. With one TALEN pair constructed for each of 10 target genes, mutant F0 mice for each gene were obtained with the mutation rate ranged from 13 to 67% and an average of ?40% of total healthy newborns with no significant differences between C57BL/6 and FVB/N genetic background. One TALEN pair with single mismatch to their intended target sequence in each side failed to yield any mutation. Furthermore, highly efficient germ-line transmission was obtained, as all the F0 founders tested transmitted the mutations to F1 mice. In addition, we also observed that one bi-allele mutant founder of Lepr gene, encoding Leptin receptor, had similar diabetic phenotype as db/db mouse. Together, our results suggest that TALENs are an effective genetic tool for rapid gene disruption with high efficiency and heritability in mouse with distinct genetic background. PMID:23630316

Qiu, Zhongwei; Liu, Meizhen; Chen, Zhaohua; Shao, Yanjiao; Pan, Hongjie; Wei, Gaigai; Yu, Chao; Zhang, Long; Li, Xia; Wang, Ping; Fan, Heng-Yu; Du, Bing; Liu, Bin; Liu, Mingyao; Li, Dali



Mouse hepatitis virus gene 5b protein is a new virion envelope protein.  


Highly purified radiolabeled mouse hepatitis virus (MHV) A59 contained a previously overlooked protein which coelectrophoreses with the gene 5b product immunoprecipitated from infected cells. The gene 5b protein is post-translationally acylated. Rabbit antibody raised against a recombinant gene 5b protein expressed in Escherichia coli neutralized viral infectivity in the presence of complement, although not in the absence of complement. Immunofluorescent staining of MHV-infected cells with two anti-peptide antibodies revealed that the gene 5b product is membrane-associated and is transported to the cell surface, findings consistent with the prediction of a membrane-spanning segment in the gene 5b polypeptide. These results suggest strongly that the gene 5b polypeptide represents a new MHV virion envelope protein which is homologous to the TGEV ORF 4 and IBV 3c proteins. PMID:8030202

Yu, X; Bi, W; Weiss, S R; Leibowitz, J L



Gene Entropy-Fractal Dimension Informatics with Application to Mouse-Human Translational Medicine  

PubMed Central

DNA informatics represented by Shannon entropy and fractal dimension have been used to form 2D maps of related genes in various mammals. The distance between points on these maps for corresponding mRNA sequences in different species is used to study evolution. By quantifying the similarity of genes between species, this distance might be indicated when studies on one species (mouse) would tend to be valid in the other (human). The hypothesis that a small distance from mouse to human could facilitate mouse to human translational medicine success is supported by the studied ESR-1, LMNA, Myc, and RNF4 sequences. ID1 and PLCZ1 have larger separation. The collinearity of displacement vectors is further analyzed with a regression model, and the ID1 result suggests a mouse-chimp-human translational medicine approach. Further inference was found in the tumor suppression gene, p53, with a new hypothesis of including the bovine PKM2 pathways for targeting the glycolysis preference in many types of cancerous cells, consistent with quantum metabolism models. The distance between mRNA and protein coding CDS is proposed as a measure of the pressure associated with noncoding processes. The Y-chromosome DYS14 in fetal micro chimerism that could offer protection from Alzheimer's disease is given as an example. PMID:23586047

Holden, T.; Cheung, E.; Dehipawala, S.; Ye, J.; Tremberger, G.; Lieberman, D.; Cheung, T.



An ENU mutagenesis screen identifies novel and known genes involved in epigenetic processes in the mouse  

PubMed Central

Background We have used a sensitized ENU mutagenesis screen to produce mouse lines that carry mutations in genes required for epigenetic regulation. We call these lines Modifiers of murine metastable epialleles (Mommes). Results We report a basic molecular and phenotypic characterization for twenty of the Momme mouse lines, and in each case we also identify the causative mutation. Three of the lines carry a mutation in a novel epigenetic modifier, Rearranged L-myc fusion (Rlf), and one gene, Rap-interacting factor 1 (Rif1), has not previously been reported to be involved in transcriptional regulation in mammals. Many of the other lines are novel alleles of known epigenetic regulators. For two genes, Rlf and Widely-interspaced zinc finger (Wiz), we describe the first mouse mutants. All of the Momme mutants show some degree of homozygous embryonic lethality, emphasizing the importance of epigenetic processes. The penetrance of lethality is incomplete in a number of cases. Similarly, abnormalities in phenotype seen in the heterozygous individuals of some lines occur with incomplete penetrance. Conclusions Recent advances in sequencing enhance the power of sensitized mutagenesis screens to identify the function of previously uncharacterized factors and to discover additional functions for previously characterized proteins. The observation of incomplete penetrance of phenotypes in these inbred mutant mice, at various stages of development, is of interest. Overall, the Momme collection of mouse mutants provides a valuable resource for researchers across many disciplines. PMID:24025402



Gene entropy-fractal dimension informatics with application to mouse-human translational medicine.  


DNA informatics represented by Shannon entropy and fractal dimension have been used to form 2D maps of related genes in various mammals. The distance between points on these maps for corresponding mRNA sequences in different species is used to study evolution. By quantifying the similarity of genes between species, this distance might be indicated when studies on one species (mouse) would tend to be valid in the other (human). The hypothesis that a small distance from mouse to human could facilitate mouse to human translational medicine success is supported by the studied ESR-1, LMNA, Myc, and RNF4 sequences. ID1 and PLCZ1 have larger separation. The collinearity of displacement vectors is further analyzed with a regression model, and the ID1 result suggests a mouse-chimp-human translational medicine approach. Further inference was found in the tumor suppression gene, p53, with a new hypothesis of including the bovine PKM2 pathways for targeting the glycolysis preference in many types of cancerous cells, consistent with quantum metabolism models. The distance between mRNA and protein coding CDS is proposed as a measure of the pressure associated with noncoding processes. The Y-chromosome DYS14 in fetal micro chimerism that could offer protection from Alzheimer's disease is given as an example. PMID:23586047

Holden, T; Cheung, E; Dehipawala, S; Ye, J; Tremberger, G; Lieberman, D; Cheung, T



Changes in gene expression associated with retinal degeneration in the rd3 mouse  

PubMed Central

Purpose To identify and characterize changes in gene expression associated with photoreceptor degeneration in the rd3 mouse model of Leber congenital amaurosis (LCA) type 12. Methods Global genome expression profiling using microarray technology was performed on total RNA extracts from rd3 and wild-type control mouse retinas at postnatal day 21. Quantitative PCR analysis of selected transcripts was performed to validate the microarray results. Results Functional annotation of differentially regulated genes in the rd3 mouse defined key canonical pathways, including phototransduction, glycerophospholipid metabolism, tumor necrosis factor receptor 1 signaling, and endothelin signaling. Overall, 1,140 of approximately 55,800 transcripts were differentially represented. In particular, a large percentage of the upregulated transcripts encode proteins involved in the immune response; whereas the downregulated transcripts encode proteins involved in phototransduction and lipid metabolism. Conclusions This analysis has elucidated several candidate genes and pathways, thus providing insight into the pathogenic mechanisms underlying the photoreceptor degeneration in the rd3 mouse retina and indicating directions for future studies. PMID:23687432

Cheng, Christiana L.



Regulation of mouse mammary tumor virus gene expression by glucocorticoid hormones.  


Several laboratories have documented that glucocorticoid hormones markedly stimulate the expression of mouse mammary tumor virus genes in a variety of mouse mammary tumor cells and in infected heterologous cells. The effect of the hormone appears to be a rapid and specific augmentation of the synthesis of viral RNA, mediated by interaction with glucocorticoid receptor proteins. The availability of virus-specific reagents and recent developments in the molecular biology of RNA tumor viruses now permit a highly refined analysis of hormonal regulation in this experimental system. PMID:226870

Varmus, H E; Ringold, G; Yamamoto, K R



A transgenic mouse strain expressing four drug-selectable marker genes.  

PubMed Central

Murine embryonic stem (ES) cells are commonly cultured on feeder layers of primary murine embryonic fibroblasts (MEFs). Because gene targeting experiments often involve sequential selection for multiple-drug resistance in single ES cell lines, we have developed a new mouse strain which represents an economical donor for the production of multiple-drug resistant MEFs. MEFs prepared from the DR-4 mouse strain displayed resistance to concentrations of the drugs G418, 6-thioguanine, puromycin and hygromycin well above those used normally for the selection of drug-resistant ES cells. PMID:9278500

Tucker, K L; Wang, Y; Dausman, J; Jaenisch, R



Time course of gene expression during mouse skeletal muscle hypertrophy  

PubMed Central

The purpose of this study was to perform a comprehensive transcriptome analysis during skeletal muscle hypertrophy to identify signaling pathways that are operative throughout the hypertrophic response. Global gene expression patterns were determined from microarray results on days 1, 3, 5, 7, 10, and 14 during plantaris muscle hypertrophy induced by synergist ablation in adult mice. Principal component analysis and the number of differentially expressed genes (cutoffs ?2-fold increase or ?50% decrease compared with control muscle) revealed three gene expression patterns during overload-induced hypertrophy: early (1 day), intermediate (3, 5, and 7 days), and late (10 and 14 days) patterns. Based on the robust changes in total RNA content and in the number of differentially expressed genes, we focused our attention on the intermediate gene expression pattern. Ingenuity Pathway Analysis revealed a downregulation of genes encoding components of the branched-chain amino acid degradation pathway during hypertrophy. Among these genes, five were predicted by Ingenuity Pathway Analysis or previously shown to be regulated by the transcription factor Kruppel-like factor-15, which was also downregulated during hypertrophy. Moreover, the integrin-linked kinase signaling pathway was activated during hypertrophy, and the downregulation of muscle-specific micro-RNA-1 correlated with the upregulation of five predicted targets associated with the integrin-linked kinase pathway. In conclusion, we identified two novel pathways that may be involved in muscle hypertrophy, as well as two upstream regulators (Kruppel-like factor-15 and micro-RNA-1) that provide targets for future studies investigating the importance of these pathways in muscle hypertrophy. PMID:23869057

Lee, Jonah D.; England, Jonathan H.; Esser, Karyn A.; McCarthy, John J.



Yeast and Mammalian Metallothioneins Functionally Substitute for Yeast Copper-Zinc Superoxide Dismutase  

NASA Astrophysics Data System (ADS)

Copper-zinc superoxide dismutase catalyzes the disproportionation of superoxide anion to hydrogen peroxide and dioxygen and is thought to play an important role in protecting cells from oxygen toxicity. Saccharomyces cerevisiae strains lacking copper-zinc superoxide dismutase, which is encoded by the SOD1 gene, are sensitive to oxidative stress and exhibit a variety of growth defects including hypersensitivity to dioxygen and to superoxide-generating drugs such as paraquat. We have found that in addition to these known phenotypes, SOD1-deletion strains fail to grow on agar containing the respiratory carbon source lactate. We demonstrate here that expression of the yeast or monkey metallothionein proteins in the presence of copper suppresses the lactate growth defect and some other phenotypes associated with SOD1-deletion strains, indicating that copper metallothioneins substitute for copper-zinc superoxide dismutase in vivo to protect cells from oxygen toxicity. Consistent with these results, we show that yeast metallothionein mRNA levels are dramatically elevated under conditions of oxidative stress. Furthermore, in vitro assays demonstrate that yeast metallothionein, purified or from whole-cell extracts, exhibits copper-dependent antioxidant activity. Taken together, these data suggest that both yeast and mammalian metallothioneins may play a direct role in the cellular defense against oxidative stress by functioning as antioxidants.

Tamai, Katherine T.; Gralla, Edith B.; Ellerby, Lisa M.; Valentine, Joan S.; Thiele, Dennis J.



Birth defects caused by mutations in human GLI3 and mouse Gli3 genes.  


ABSTRACT GLI3 is the gene responsible for Greig cephalopolysyndactyly syndrome (GCPS), Pallister-Hall syndrome (PHS) and Postaxial polydactyly type-A (PAP-A). Genetic polydactyly mice such as Pdn/Pdn (Polydactyly Nagoya), Xt(H)/Xt(H) (Extra toes) and Xt(J)/Xt(J) (Extra toes Jackson) are the mouse homolog of GCPS, and Gli3(tmlUrtt)/Gli3(tmlUrt) is produced as the mouse homolog of PHS. In the present review, relationships between mutation points of GLI3 and Gli3, and resulting phenotypes in humans and mice are described. It has been confirmed that mutation in the upstream or within the zinc finger domain of the GLI3 gene induces GCPS; that in the post-zinc finger region including the protease cleavage site induces PHS; and that in the downstream of the GLI3 gene induces PAP-A. A mimicking phenomenon was observed in the mouse homolog. Therefore, human GLI3 and mouse Gli3 genes have a common structure, and it is suggested here that mutations in the same functional regions produce similar phenotypes in human and mice. The most important issue might be that GCPS and PHS exhibit an autosomal dominant trait, but mouse homologs, such as Pdn/Pdn, Xt(H)/Xt(H), Xt(J)/Xt(J) and Gli3(tmlUrt)/Gli3(tmlUrt), are autosomal recessive traits in the manifestation of similar phenotypes to human diseases. It is discussed here how the reduced amounts of the GLI3 protein, or truncated mutant GLI3 protein, disrupt development of the limbs, head and face. PMID:20201963

Naruse, Ichiro; Ueta, Etsuko; Sumino, Yoshiki; Ogawa, Masaya; Ishikiriyama, Satoshi



Assignment of genes to regions of mouse chromosomes.  

PubMed Central

A genetic mapping procedure, called the duplication-deficiency method, is described. This method permits the genetic location of a translocation to be determined within a linkage group without the use of recombination. By utilizing the duplication-deficiency method to define the genetic breakpoints for a series of translocations involving a given chromosome and integrating this information with their cytological breakpoints, obtained by Giemsa banding, a genetic map of the chromosomes is constructed whereby groups of loci are assigned to banded regions. Duplication-deficiency mapping and Giemsa banding analysis of the T(X;7)1Ct and T(7;19)145H translocations together with information from the c25H deletion have permitted mouse chromosome 7 to be divided into six and chromosome 19 into two definable genetic regions. Images PMID:273256

Eicher, E M; Washburn, L L



Activation of the rainbow trout metallothionein-A promoter by silver and zinc  

Microsoft Academic Search

In fish, the synthesis of metallothionein (MT) is increased by a number of heavy metals. The rainbow trout MT-A gene promoter region contains six known metal responsive elements (MREs), that mediate promoter activation by metals. In the present study, two fish cell lines differing in their ability to produce MT, RTG-2 (produce MT protein) and CHSE-214 (produce no detectable MT

Gregory D Mayer; Allan Leach; Peter Kling; Per-Erik Olsson; Christer Hogstrand



Effect of microgravity on gene expression in mouse brain  

PubMed Central

Changes in gravitational force such as that experienced by astronauts during space flight induce a redistribution of fluids from the caudad to the cephalad portion of the body together with an elimination of normal head-to-foot hydrostatic pressure gradients. To assess brain gene profile changes associated with microgravity and fluid shift, a large-scale analysis of mRNA expression levels was performed in the brains of 2-week control and hindlimb-unloaded (HU) mice using cDNA microarrays. Although to different extents, all functional categories displayed significantly regulated genes indicating that considerable transcriptomic alterations are induced by HU. Interestingly, the TIC class (transport of small molecules and ions into the cells) had the highest percentage of up-regulated genes, while the most down-regulated genes were those of the JAE class (cell junction, adhesion, extracellular matrix). TIC genes comprised 16% of those whose expression was altered, including sodium channel, nonvoltage-gated 1 beta (Scnn1b), glutamate receptor (Grin1), voltage-dependent anion channel 1 (Vdac1), calcium channel beta 3 subunit (Cacnb3) and others. The analysis performed by Gene-MAPP revealed several altered protein classes and functional pathways such as blood coagulation and immune response, learning and memory, ion channels and cell junction. In particular, data indicate that HU causes an alteration in hemostasis which resolves in a shift toward a more hyper-coagulative state with an increased risk of venous thrombosis. Furthermore, HU treatment seems to impact on key steps of synaptic plasticity and learning processes. PMID:18704384

Iacobas, Dumitru A.; Iacobas, Sanda; Nicchia, Grazia Paola; Desaphy, Jean Francois; Camerino, Diana Conte; Svelto, Maria; Spray, David C.



Effect of light on global gene expression in the neuroglobin-deficient mouse retina  

PubMed Central

Several previous studies have raised controversy over the functional role of neuroglobin (Ngb) in the retina. Certain studies indicate a significant impact of Ngb on retinal physiology, whereas others are conflicting. The present is an observational study that tested the effect of Ngb deficiency on gene expression in dark- and light-adapted mouse retinas. Large-scale gene expression profiling was performed using GeneChip® Mouse Exon 1.0 ST arrays and the results were compared to publicly available data sets. The lack of Ngb was found to have a minor effect on the light-induced retinal gene expression response. In addition, there was no increase in the expression of marker genes associated with hypoxia, endoplasmic reticulum-stress and oxidative stress in the Ngb-deficient retina. By contrast, several genes were identified that appeared to be differentially expressed between the genotypes when the effect of light was ignored. The present study indicates that Ngb deficiency does not lead to major alternations in light-dependent gene expression response, but leads to subtle systemic differences of a currently unknown functional significance. PMID:25279145




Mapping of the Sca1 and pcd genes on mouse chromosome 13 provides evidence that they are different genes  

SciTech Connect

It is well established that large chromosomal segments have remained intact during the evolution of different mammalian species. Thus, mapping information for a gene in mammalian species facilitates mapping the same gene in another mammalian species. In addition, phenotypically similar diseases that map to linkage conserved regions in two species may be caused by mutations in the same gene. Spinocerebellar ataxia type 1 (SCA1) is a dominantly inherited human disorder characterized by progressive ataxia, dysarthria, and dysmetria. SCA1 maps to the short arm of human chromosome (Chr) 6 in the 6p23-p22 region. SCA1 is caused by the expansion of an unstable CAG repeat located within the coding region of a novel protein, ataxin-1, Purkinje cell degeneration (pcd) is a recessively inherited mouse disorder characterized by a moderate ataxia, usually noted by 3-4 weeks of age. Progressive degeneration of Purkinje cells is the underlying pathogenesis in this disorder. The pcd gene was assigned to mouse Chr 13 because it showed linkage to extra toes (Xt) and pearl (pe). Some doubt about this assignment existed, however, because the calculated genetic distance between pcd and Xt was 32 cM and that between pcd and pe was 18 cM. If pcd is located in Chr 13, its placement relative to Xt and pe suggests that it would be located in the region that shares linkage homology with the region that shares linkage homology with the region of human Chr 6 that contains SCA1. Here, we present data that confirm the assignment of pcd to Chr 13, map the mouse Sca1 gene to Chr 13, and eliminate Sca1 as a candidate gene for pcd. 11 refs., 1 tab.

Servadio, A.; McCall, A.; Zoghbi, H. [Baylor College of Medicine, Houston, TX (United States)] [Baylor College of Medicine, Houston, TX (United States); Eicher, E.M. [Jackson Laboratory, Bar Harbor, ME (United States)] [Jackson Laboratory, Bar Harbor, ME (United States)



Global gene expression profile progression in Gaucher disease mouse models  

PubMed Central

Background Gaucher disease is caused by defective glucocerebrosidase activity and the consequent accumulation of glucosylceramide. The pathogenic pathways resulting from lipid laden macrophages (Gaucher cells) in visceral organs and their abnormal functions are obscure. Results To elucidate this pathogenic pathway, developmental global gene expression analyses were conducted in distinct Gba1 point-mutated mice (V394L/V394L and D409 V/null). About 0.9 to 3% of genes had altered expression patterns (? ± 1.8 fold change), representing several categories, but particularly macrophage activation and immune response genes. Time course analyses (12 to 28 wk) of INF?-regulated pro-inflammatory (13) and IL-4-regulated anti-inflammatory (11) cytokine/mediator networks showed tissue differential profiles in the lung and liver of the Gba1 mutant mice, implying that the lipid-storage macrophages were not functionally inert. The time course alterations of the INF? and IL-4 pathways were similar, but varied in degree in these tissues and with the Gba1 mutation. Conclusions Biochemical and pathological analyses demonstrated direct relationships between the degree of tissue glucosylceramides and the gene expression profile alterations. These analyses implicate IFN?-regulated pro-inflammatory and IL-4-regulated anti-inflammatory networks in differential disease progression with implications for understanding the Gaucher disease course and pathophysiology. PMID:21223590



Extracellular matrix gene expression in the developing mouse aorta  

E-print Network

strength and elastic modulus bear most of the stressing force at and above physiologic blood pressure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84 3.1. Collagens . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86 3.2. Elastic fiber . . . . . . . . . . . . . . . . . . . . 100 4.4. Group D: Genes that decrease at birth . . . . . . . . . . . . . . . 112 5. Conclusions

Mecham, Robert


Activin Regulates Estrogen Receptor Gene Expression in the Mouse Ovary*  

E-print Network

demonstrated that estrogen suppresses activin gene expression, suggesting a feedback rela- tionship between activin signaling through Smad2, and small inter- fering RNAs targeting Smad2 or Smad3 suppressed ER pro- ulating gonadotropin release, activin and inhibin have been shown to play an important role in regulating

Mayo, Kelly E.


Bioaccumulation of Arsenic in recombinant Escherichia coli expressing human metallothionein  

Microsoft Academic Search

The recombinant Escherichia coli (E. coli) expressing human hepatic metallothionein_IA (hMT_IA) was constructed for bioaccumulation of Arsenic (As). The gene sequence\\u000a of hMT_IA was modified for codon preference of E. coli and synthesized using chemical method. The vector of pGEX_4T_1 was used and hMT_IA was expressed as the fusion protein with\\u000a glutathione S-transferase (GST) tag. The bioaccumulation capability of arsenite

Yu-Jie Su; Jian-Qun Lin; Jian-Qiang Lin; Dong-Hui Hao



Mapping of the insulin promoter factor 1 gene (Ipf1) to distal mouse chromosome 5  

SciTech Connect

We have identified sequence variants in the 3{prime} untranslated region of the insulin promoter factor 1 (Ipf1) cDNA sequence in mice and used a PCR-based oligonucleotide hybridization assay to map the Ipf1 gene to distal mouse chromosome (Chr) 5. An identical 12-bp insertion in the 3{prime} untranslated region of the mouse Ipf1 gene sequence is present in Mus spretus and Mus m. musculus Czech II mice, two feral strains used for meiotic mapping by backcross analysis. The human IPF1 gene homolog would be expected to map to either chromosome 13q12-q14 or 7pter-q21 based on homology of synteny of other loci in this region of mouse Chr 5. Given its genetic map position, the Ipf1 gene may be part of a cassette of homeodomain-containing transcription factors involved in the development of the pancreas and other foregut-derived organs. 19 refs., 3 figs.

Fiedorek, F.T. Jr.; Kay, E.S. [Univ. of North Carolina School of Medicine, Chapel Hill, NC (United States)] [Univ. of North Carolina School of Medicine, Chapel Hill, NC (United States)



Positions of pluripotency genes and hepatocyte-specific genes in the nucleus before and after mouse ES cell differentiation.  


Spatial positioning of genes in the cell nucleus plays an important role in the regulation of genomic functions. Evidence for changes in gene positioning associated with transcriptional activity has been reported. However, our understanding of this phenomenon is still quite limited. We examined how pluripotency genes and hepatocyte-specific genes behave during the differentiation of mouse embryonic stem (ES) cells into hepatocytes, by targeting the loci of the Klf4, Nanog, Oct4, Sox2, Cyp7?1, Pck1, Tat, and Tdo2 genes, and using three-dimensional fluorescence in situ hybridization analyses. We found that each gene has a distinctly inherent localization profile in the ES cell nucleus. During differentiation, the Klf4, Nanog, Oct4, Cyp7?1, Pck1, and Tat loci shifted toward the nuclear center, while the Sox2 and Tdo2 loci shifted toward the periphery. The Klf4, Nanog, Oct4, and Tdo2 seem to prefer the outer regions, rather than the inner regions, when they are active. We also found that the radial positioning of the focused genes in the hepatocyte cell nucleus was highly correlated with the local GC content and the gene density of the surrounding region, but not with gene activity. PMID:24737423

Udagawa, K; Ohyama, T



A synthetic small molecule for rapid induction of multiple pluripotency genes in mouse embryonic fibroblasts  

NASA Astrophysics Data System (ADS)

Cellular reprogramming involves profound alterations in genome-wide gene expression that is precisely controlled by a hypothetical epigenetic code. Small molecules have been shown to artificially induce epigenetic modifications in a sequence independent manner. Recently, we showed that specific DNA binding hairpin pyrrole-imidazole polyamides (PIPs) could be conjugated with chromatin modifying histone deacetylase inhibitors like SAHA to epigenetically activate certain pluripotent genes in mouse fibroblasts. In our steadfast progress to improve the efficiency of SAHA-PIPs, we identified a novel compound termed, ? that could dramatically induce the endogenous expression of Oct-3/4 and Nanog. Genome-wide gene analysis suggests that in just 24 h and at nM concentration, ? induced multiple pluripotency-associated genes including Rex1 and Cdh1 by more than ten-fold. ? treated MEFs also rapidly overcame the rate-limiting step of epithelial transition in cellular reprogramming by switching ``'' the complex transcriptional gene network.

Pandian, Ganesh N.; Nakano, Yusuke; Sato, Shinsuke; Morinaga, Hironobu; Bando, Toshikazu; Nagase, Hiroki; Sugiyama, Hiroshi



Double replacement gene targeting for the production of a series of mouse strains with different prion protein gene alterations  

SciTech Connect

We have developed a double replacement gene targeting strategy which enables the production of a series of mouse strains bearing different subtle alterations to endogenous genes. This is a two-step process in which a region of the gene of interest is first replaced with a selectable marker to produce an inactivated allele, which is then re-targeted with a second vector to reconstruct the inactivated allele, concomitantly introducing an engineered mutation. Five independent embryonic stem cell lines have been produced bearing different targeted alterations to the prion protein gene, including one which raises the level of expression. We have constructed mice bearing the codon 101 proline to leucine substitution linked to the human familial prion disease, Gerstmann-Straussler-Scheinker syndrome. We anticipate that this procedure will have applications to the study of human inherited diseases and the development of therapies. 43 refs., 6 figs., 1 tab.

Moore, R.C.; Redhead, N.J.; Selfridge, J. [Univ. of Edinburgh (United Kingdom)] [and others] [Univ. of Edinburgh (United Kingdom); and others



Metallothionein polymorphisms in pathological processes.  


Metallothioneins (MTs) are a class of metal-binding proteins characterized by a high cysteine content and low molecular weight. MTs play an important role in metal metabolism and protect cells against the toxic effects of radiation, alkylating agents and oxygen free radicals. The evidence that individual genetic characteristics of MTs play an important role in physiological and pathological processes associated with antioxidant defense and detoxification inspired targeted studies of genetic polymorphisms in a clinical context. In recent years, common MT polymorphisms were identified and associated with, particularly, western lifestyle diseases such as cancer, complications of atherosclerosis, and type 2 diabetes mellitus along with related complications. This review summarizes all evidence regarding MT polymorphisms of major human MTs (MT1, MT2, MT3 and MT4), their relation to pathological processes, and outlines specific applications of MTs as a set of genetic markers for certain pathologies. PMID:24068159

Raudenska, Martina; Gumulec, Jaromir; Podlaha, Ondrej; Sztalmachova, Marketa; Babula, Petr; Eckschlager, Tomas; Adam, Vojtech; Kizek, Rene; Masarik, Michal



Gene expression profiling in a mouse model for African trypanosomiasis  

Microsoft Academic Search

This study aimed to provide the foundation for an integrative approach to the identification of the mechanisms underlying the response to infection with Trypanosoma congolense, and to identify pathways that have previously been overlooked. We undertook a large-scale gene expression analysis study comparing susceptible A\\/J and more tolerant C57BL\\/6 mice. In an initial time course experiment, we monitored the development

S Kierstein; H Noyes; J Naessens; Y Nakamura; C Pritchard; J Gibson; S Kemp; A Brass



Immunoprophylaxis in fish by injection of mouse antibody genes  

Microsoft Academic Search

Antibodies are a crucial part of the body's specific defense against infectious diseases and have considerable potential as therapeutic and prophylactic agents in humans and animals. The development of recombinant single-chain antibodies allows a genetic application strategy for prevention of infectious diseases. To test this in a fish model, a gene construct encoding a neutralizing single-chain antibody to the fish-pathogenic

Pauline M. Cupit; Katja Einer-Jensen; Ellen Lorenzen; Peter Ahrens; Christopher J. Secombes; Charles Cunningham; Niels Lorenzen



Akt1 mediates the posterior Hoxc gene expression through epigenetic modifications in mouse embryonic fibroblasts.  


The evolutionarily conserved Hox genes are organized in clusters and expressed colinearly to specify body patterning during embryonic development. Previously, Akt1 has been identified as a putative Hox gene regulator through in silico analysis. Substantial upregulation of consecutive 5' Hoxc genes has been observed when Akt1 is absent in mouse embryonic fibroblast (MEF) cells. In this study, we provide evidence that Akt1 regulates the 5' Hoxc gene expression by epigenetic modifications. Enrichment of histone H3K9 acetylation and a low level of the H3K27me3 mark were detected at the posterior 5' Hoxc loci when Akt1 is absent. A histone deacetylase (HDAC) inhibitor de-repressed 5' Hoxc gene expression when Akt1 is present, and a DNA demethylating reagent synergistically upregulated HDAC-induced 5' Hoxc gene expression. A knockdown study revealed that Hdac6 is mediated in the Hoxc12 repression through direct binding to the transcription start site (TSS) in the presence of Akt1. Co-immunoprecipitation analysis revealed that endogenous Akt1 directly interacted with Hdac6. Furthermore, exogenous Akt1 was enriched at the promoter region of the posterior Hoxc genes such as Hoxc11 and Hoxc12, not the Akt1-independent Hoxc5 and Hoxd10 loci. The regulation of the H3K27me3 mark by Ezh2 and Kdm6b at the 5' Hoxc gene promoter turned out to be Akt1 dependent. Taken together, these results suggest that Akt1 mediates the posterior 5' Hoxc gene expression through epigenetic modification such as histone methylation and acetylation, and partly through a direct binding to the promoter region of the 5' Hoxc genes and/or Hdac6 in mouse embryonic fibroblast cells. PMID:24955524

Kong, Kyoung-Ah; Lee, Ji-Yeon; Oh, Ji Hoon; Lee, Youra; Kim, Myoung Hee



Gene order is conserved within the human chromosome 21 linkage group on mouse chromosome 10  

SciTech Connect

One hundred progeny from each of two intersubspecific mouse backcrosses were used to construct a comparative genetic map of a region of mouse chromosome 10 (MMU10) that is homologous to the distal tip of the long arm of human chromosome 21 (HSA21). The analysis included five genes and three simple sequence repeat markers, two of which flanked the HSA21-homologous cluster on either side. Analysis of 200 backcross progeny detected at least one crossover between each pair of adjacent genes and demonstrated that the proximal to distal orientation of the cluster was reversed between human and mouse. The order was determined to be Fyn-1-D10Mit20-S100b-Col6a1-Itgb2-Pfk1/D10Mit7-D10Mit11. Comparative mapping supports the order of corresponding markers on HSA21 determined using pulsed-field gel electrophoresis and radiation hybrid line data. However, sequence tagged site content mapping of human yeast artificial chromosomes (YACs) yielded conflicting data on the relative positions of human COL6A1 and S100B on HSA21. This discrepancy was resolved here by demonstrating that several key YACs used in the human contig analysis were mistyped for S100B. The murine map reported here provides a scaffold for construction of physical maps and yeast artificial chromosome contigs that will be useful in the development of mouse models for the study of Down syndrome. 28 refs., 4 figs., 2 tabs.

Irving, N.G.; Cabin, D.E.; Swanson, D.A.; Reeves, R.H. (Johns Hopkins Univ. School of Medicine, Baltimore, MD (United States))



Systems Biology-Based Identification of Mycobacterium tuberculosis Persistence Genes in Mouse Lungs  

PubMed Central

ABSTRACT Identifying Mycobacterium tuberculosis persistence genes is important for developing novel drugs to shorten the duration of tuberculosis (TB) treatment. We developed computational algorithms that predict M. tuberculosis genes required for long-term survival in mouse lungs. As the input, we used high-throughput M. tuberculosis mutant library screen data, mycobacterial global transcriptional profiles in mice and macrophages, and functional interaction networks. We selected 57 unique, genetically defined mutants (18 previously tested and 39 untested) to assess the predictive power of this approach in the murine model of TB infection. We observed a 6-fold enrichment in the predicted set of M. tuberculosis genes required for persistence in mouse lungs relative to randomly selected mutant pools. Our results also allowed us to reclassify several genes as required for M. tuberculosis persistence in vivo. Finally, the new results implicated additional high-priority candidate genes for testing. Experimental validation of computational predictions demonstrates the power of this systems biology approach for elucidating M. tuberculosis persistence genes. PMID:24549847

Dutta, Noton K.; Bandyopadhyay, Nirmalya; Veeramani, Balaji; Lamichhane, Gyanu; Karakousis, Petros C.; Bader, Joel S.



Analysis of key genes and pathways involved in acute lung injury in a mouse model.  


A mouse model of acute lung injury (ALI) was chosen in this study to explore the key genes and pathways involved in the process of ALI with microarray technology. Gene expression microarray data were downloaded from the Gene Expression Omnibus database. Mice from the experimental group were further divided into 6 subgroups, which received octadecenoate treatments for 1, 1.5, 3, 4, 18, and 24 h. Differentially co-expressed genes were screened to uncover the pathogenesis of ALI. Almost all of the differentially co-expressed genes were identified at two times: 1.5 and 3 h. Functional analysis revealed that several inflammation-related pathways were significantly enriched. Ubiquitin-mediated proteolysis, hematopoietic cell lineage, and leukocyte transendothelial migration were enriched at 1.5 h. The B cell receptor signaling pathway, T cell receptor signaling pathway, natural killer cell-mediated cytotoxicity, Fc epsilon RI signaling pathway, and ubiquitin-mediated proteolysis were significantly enriched at 3 h. It could be inferred that ALI initiated at 1.5 h and lasted through 3 h. However, co-expression patterns were not found from 4 h onward. In conclusion, several key genes and pathways implicated in the development of ALI were found in this study using the mouse model, among which ubiquitin-mediated proteolysis appears to play an important role in the process. PMID:25036508

Han, Q H; Han, N; Liu, Y Z; Jin, Q H; Lu, Q Y; Li, Z C



Subretinal injection of gene therapy vectors and stem cells in the perinatal mouse eye.  


The loss of sight affects approximately 3.4 million people in the United States and is expected to increase in the upcoming years.(1) Recently, gene therapy and stem cell transplantations have become key therapeutic tools for treating blindness resulting from retinal degenerative diseases. Several forms of autologous transplantation for age-related macular degeneration (AMD), such as iris pigment epithelial cell transplantation, have generated encouraging results, and human clinical trials have begun for other forms of gene and stem cell therapies.(2) These include RPE65 gene replacement therapy in patients with Leber's congenital amaurosis and an RPE cell transplantation using human embryonic stem (ES) cells in Stargardt's disease.(3-4) Now that there are gene therapy vectors and stem cells available for treating patients with retinal diseases, it is important to verify these potential therapies in animal models before applying them in human studies. The mouse has become an important scientific model for testing the therapeutic efficacy of gene therapy vectors and stem cell transplantation in the eye.(5-8) In this video article, we present a technique to inject gene therapy vectors or stem cells into the subretinal space of the mouse eye while minimizing damage to the surrounding tissue. PMID:23207897

Wert, Katherine J; Skeie, Jessica M; Davis, Richard J; Tsang, Stephen H; Mahajan, Vinit B



Meta-Analysis of Differentiating Mouse Embryonic Stem Cell Gene Expression Kinetics Reveals Early Change of a Small Gene Set  

PubMed Central

Stem cell differentiation involves critical changes in gene expression. Identification of these should provide endpoints useful for optimizing stem cell propagation as well as potential clues about mechanisms governing stem cell maintenance. Here we describe the results of a new meta-analysis methodology applied to multiple gene expression datasets from three mouse embryonic stem cell (ESC) lines obtained at specific time points during the course of their differentiation into various lineages. We developed methods to identify genes with expression changes that correlated with the altered frequency of functionally defined, undifferentiated ESC in culture. In each dataset, we computed a novel statistical confidence measure for every gene which captured the certainty that a particular gene exhibited an expression pattern of interest within that dataset. This permitted a joint analysis of the datasets, despite the different experimental designs. Using a ranking scheme that favored genes exhibiting patterns of interest, we focused on the top 88 genes whose expression was consistently changed when ESC were induced to differentiate. Seven of these (103728_at, 8430410A17Rik, Klf2, Nr0b1, Sox2, Tcl1, and Zfp42) showed a rapid decrease in expression concurrent with a decrease in frequency of undifferentiated cells and remained predictive when evaluated in additional maintenance and differentiating protocols. Through a novel meta-analysis, this study identifies a small set of genes whose expression is useful for identifying changes in stem cell frequencies in cultures of mouse ESC. The methods and findings have broader applicability to understanding the regulation of self-renewal of other stem cell types. PMID:17121458

Glover, Clive H; Marin, Michael; Eaves, Connie J; Helgason, Cheryl D; Piret, James M; Bryan, Jennifer



Mouse in utero electroporation: controlled spatiotemporal gene transfection.  


In order to understand the function of genes expressed in specific region of the developing brain, including signaling molecules and axon guidance molecules, local gene transfer or knock- out is required. Gene targeting knock-in or knock-out into local regions is possible to perform with combination with a specific CRE line, which is laborious, costly, and time consuming. Therefore, a simple transfection method, an in utero electroporation technique, which can be performed with short time, will be handy to test the possible function of candidate genes prior to the generation of transgenic animals. In addition to this, in utero electroporation targets areas of the brain where no specific CRE line exists, and will limit embryonic lethality. Here, we present a method of in utero electroporation combining two different types of electrodes for simple and convenient gene transfer into target areas of the developing brain. First, a unique holding method of embryos using an optic fiber optic light cable will make small embryos (from E9.5) visible for targeted DNA solution injection into ventricles and needle type electrodes insertion to the targeted brain area. The patterning of the brain such as cortical area occur at early embryonic stage, therefore, these early electroporation from E9.5 make a big contribution to understand entire area patterning event. Second, the precise shape of a capillary prevents uterine damage by making holes by insertion of the capillary. Furthermore, the precise shape of the needle electrodes are created with tungsten and platinum wire and sharpened using sand paper and insulated with nail polish, a method which is described in great detail in this protocol. This unique technique allows transfection of plasmid DNA into restricted areas of the brain and will enable small embryos to be electroporated. This will help to, open a new window for many scientists who are working on cell differentiation, cell migration, axon guidance in very early embryonic stage. Moreover, this technique will allow scientists to transfect plasmid DNA into deep parts of the developing brain such as thalamus and hypothalamus, where not many region-specific CRE lines exist for gain of function (GOF) or loss of function (LOF) analyses. PMID:21860382

Matsui, Asuka; Yoshida, Aya C; Kubota, Mayumi; Ogawa, Masaharu; Shimogori, Tomomi



Transcriptome-Wide Identification of Novel Imprinted Genes in Neonatal Mouse Brain  

PubMed Central

Imprinted genes display differential allelic expression in a manner that depends on the sex of the transmitting parent. The degree of imprinting is often tissue-specific and/or developmental stage-specific, and may be altered in some diseases including cancer. Here we applied Illumina/Solexa sequencing of the transcriptomes of reciprocal F1 mouse neonatal brains and identified 26 genes with parent-of-origin dependent differential allelic expression. Allele-specific Pyrosequencing verified 17 of them, including three novel imprinted genes. The known and novel imprinted genes all are found in proximity to previously reported differentially methylated regions (DMRs). Ten genes known to be imprinted in placenta had sufficient expression levels to attain a read depth that provided statistical power to detect imprinting, and yet all were consistent with non-imprinting in our transcript count data for neonatal brain. Three closely linked and reciprocally imprinted gene pairs were also discovered, and their pattern of expression suggests transcriptional interference. Despite the coverage of more than 5000 genes, this scan only identified three novel imprinted refseq genes in neonatal brain, suggesting that this tissue is nearly exhaustively characterized. This approach has the potential to yield an complete catalog of imprinted genes after application to multiple tissues and developmental stages, shedding light on the mechanism, bioinformatic prediction, and evolution of imprinted genes and diseases associated with genomic imprinting. PMID:19052635

Wang, Xu; Sun, Qi; McGrath, Sean D.; Mardis, Elaine R.; Soloway, Paul D.; Clark, Andrew G.



From zebrafish heart jogging genes to mouse and human orthologs: using Gene Ontology to investigate mammalian heart development.  

PubMed Central

For the majority of organs in developing vertebrate embryos, left-right asymmetry is controlled by a ciliated region; the left-right organizer node in the mouse and human, and the Kuppfer’s vesicle in the zebrafish. In the zebrafish, laterality cues from the Kuppfer’s vesicle determine asymmetry in the developing heart, the direction of ‘heart jogging’ and the direction of ‘heart looping’.  ‘Heart jogging’ is the term given to the process by which the symmetrical zebrafish heart tube is displaced relative to the dorsal midline, with a leftward ‘jog’. Heart jogging is not considered to occur in mammals, although a leftward shift of the developing mouse caudal heart does occur prior to looping, which may be analogous to zebrafish heart jogging. Previous studies have characterized 30 genes involved in zebrafish heart jogging, the majority of which have well defined orthologs in mouse and human and many of these orthologs have been associated with early mammalian heart development.    We undertook manual curation of a specific set of genes associated with heart development and we describe the use of Gene Ontology term enrichment analyses to examine the cellular processes associated with heart jogging.  We found that the human, mouse and zebrafish ‘heart jogging orthologs’ are involved in similar organ developmental processes across the three species, such as heart, kidney and nervous system development, as well as more specific cellular processes such as cilium development and function. The results of these analyses are consistent with a role for cilia in the determination of left-right asymmetry of many internal organs, in addition to their known role in zebrafish heart jogging.    This study highlights the importance of model organisms in the study of human heart development, and emphasises both the conservation and divergence of developmental processes across vertebrates, as well as the limitations of this approach. PMID:24627794

Lovering, Ruth C



Linking susceptibility genes and pathogenesis mechanisms using mouse models of systemic lupus erythematosus  

PubMed Central

Systemic lupus erythematosus (SLE) represents a challenging autoimmune disease from a clinical perspective because of its varied forms of presentation. Although broad-spectrum steroids remain the standard treatment for SLE, they have many side effects and only provide temporary relief from the symptoms of the disease. Thus, gaining a deeper understanding of the genetic traits and biological pathways that confer susceptibility to SLE will help in the design of more targeted and effective therapeutics. Both human genome-wide association studies (GWAS) and investigations using a variety of mouse models of SLE have been valuable for the identification of the genes and pathways involved in pathogenesis. In this Review, we link human susceptibility genes for SLE with biological pathways characterized in mouse models of lupus, and discuss how the mechanistic insights gained could advance drug discovery for the disease. PMID:25147296

Crampton, Steve P.; Morawski, Peter A.; Bolland, Silvia



Sequence analysis of the ERCC2 gene regions in human, mouse, and hamster reveals three linked genes  

SciTech Connect

The ERCC2 (excision repair cross-complementing rodent repair group 2) gene product is involved in transcription-coupled repair as an integral member of the basal transcription factor BTF2/TFIIH complex. Defects in this gene can result in three distinct human disorders, namely the cancer-prone syndrome xeroderma pigmentosum complementation group D, trichothiodystrophy, and Cockayne syndrome. We report the comparative analysis of 91.6 kb of new sequence including 54.3 kb encompassing the human ERCC2 locus, the syntenic region in the mouse (32.6 kb), and a further 4.7 kb of sequence 3{prime} of the previously reported ERCC2 region in the hamster. In addition to ERCC2, our analysis revealed the presence of two previously undescribed genes in all three species. The first is centromeric (in the human) to ERCC2 and is most similar to the kinesin light chain gene in sea urchin. The second gene is telomeric (in the human) to ERCC2 and contains a motif found in ankyrins, some cell proteins, and transcription factors. Multiple EST matches to this putative new gene indicate that it is expressed in several human tissues, including breast. The identification and description of two new genes provides potential candidate genes for disorders mapping to this region of 19q13.2. 42 refs., 6 figs., 3 tabs.

Lamerdin, J.E.; Stilwagen, S.A.; Ramirez, M.H. [Lawrence Livermore National Lab., CA (United States)] [and others] [Lawrence Livermore National Lab., CA (United States); and others



The Consensus Coding Sequence (Ccds) Project: Identifying a Common Protein-Coding Gene Set for the Human and Mouse Genomes  

E-print Network

Effective use of the human and mouse genomes requires reliable identification of genes and their products. Although multiple public resources provide annotation, different methods are used that can result in similar but ...

Kellis, Manolis


Mouse Small eye results from mutations in a paired-like homeobox-containing gene  

Microsoft Academic Search

SMALL eye (Sey) in mouse is a semidominant mutation which in the homozygous condition results in the complete lack of eyes and nasal primordia. On the basis of comparative mapping studies and on phenotypic similarities, Sey has been suggested to be homologous to congenital aniridia (lack of iris) in human1,2. A candidate gene for the aniridia (AN) locus at 11p13

Robert E. Hill; Jack Favor; Brigid L. M. Hogan; Carl C. T. Ton; Grady F. Saunders; Isabel M. Hanson; Jane Prosser; Tim Jordan; Nicholas D. Hastie; Veronica Van Heyningen



Transcript Annotation in FANTOM3: Mouse Gene Catalog Based on Physical cDNAs  

Microsoft Academic Search

The international FANTOM consortium aims to produce a comprehensive picture of the mammalian transcriptome, based upon an extensive cDNA collection and functional annotation of full-length enriched cDNAs. The previous dataset, FANTOM2, comprised 60,770 full-length enriched cDNAs. Functional annotation revealed that this cDNA dataset contained only about half of the estimated number of mouse protein-coding genes, indicating that a number of

Norihiro Maeda; Takeya Kasukawaa; Rieko Oyama; Julian Gough; Martin Frith; Pär G. Engström; Boris Lenhard; Rajith N. Aturaliya; Serge Batalov; Kirk W. Beisel; Carol J. Bult; Colin F. Fletcher; Alistair R. R. Forrest; Masaaki Furuno; David Hill; Masayoshi Itoh; Mutsumi Kanamori-Katayama; Shintaro Katayama; Masaru Katoh; Tsugumi Kawashima; John Quackenbushb; Timothy Ravasi; Brian Z. Ring; Kazuhiro Shibata; Koji Sugiura; Yoichi Takenaka; Rohan D. Teasdale; Christine A. Wells; Yunxia Zhu; Chikatoshi Kai; Jun Kawai; David A. Hume; Piero Carninci; Yoshihide Hayashizaki



Expression of gap junction genes, connexin40 and connexin43, during fetal mouse development  

Microsoft Academic Search

The expression patterns of the gap junction genes connexin40 and connexin43 have been analyzed during late mouse fetal development, i.e., at embryonic days 14.5 and 16.5, by in situ hybridization and immunofluorescence. Connexin40 was found in endothelial cells of vessels, cardiomyocytes and in developing myoblasts and myotubes. Expression of connexin40 in developing muscle fibers was strong in the back muscles

E. Dahl; E. Winterhager; O. Traub; K. Willecke



Differential display and cloning of the hippocampal gene mRNAs in senescence accelerated mouse  

Microsoft Academic Search

Identification of genes that are specifically expressed in the hippocampus of senescence accelerated mouse (SAM) is important for understanding the molecular basis of the pathological changes in the brain and of the deterioration of learning and memory in SAM-prone\\/8 (SAMP8), a substrain of SAM. The differential display technique was applied to compare mRNAs expression between SAMP8 and SAM-resistance 1 (SAMR1),

Xiaolong Wei; Yongxiang Zhang; Jinhuang Zhou



Resolving candidate genes of mouse skeletal muscle QTL via RNA-Seq and expression network analyses  

PubMed Central

Background We have recently identified a number of Quantitative Trait Loci (QTL) contributing to the 2-fold muscle weight difference between the LG/J and SM/J mouse strains and refined their confidence intervals. To facilitate nomination of the candidate genes responsible for these differences we examined the transcriptome of the tibialis anterior (TA) muscle of each strain by RNA-Seq. Results 13,726 genes were expressed in mouse skeletal muscle. Intersection of a set of 1061 differentially expressed transcripts with a mouse muscle Bayesian Network identified a coherent set of differentially expressed genes that we term the LG/J and SM/J Regulatory Network (LSRN). The integration of the QTL, transcriptome and the network analyses identified eight key drivers of the LSRN (Kdr, Plbd1, Mgp, Fah, Prss23, 2310014F06Rik, Grtp1, Stk10) residing within five QTL regions, which were either polymorphic or differentially expressed between the two strains and are strong candidates for quantitative trait genes (QTGs) underlying muscle mass. The insight gained from network analysis including the ability to make testable predictions is illustrated by annotating the LSRN with knowledge-based signatures and showing that the SM/J state of the network corresponds to a more oxidative state. We validated this prediction by NADH tetrazolium reductase staining in the TA muscle revealing higher oxidative potential of the SM/J compared to the LG/J strain (p<0.03). Conclusion Thus, integration of fine resolution QTL mapping, RNA-Seq transcriptome information and mouse muscle Bayesian Network analysis provides a novel and unbiased strategy for nomination of muscle QTGs. PMID:23126637



Cumulus-specific genes are transcriptionally silent following somatic cell nuclear transfer in a mouse model  

Microsoft Academic Search

This study investigated whether four cumulus-specific genes: follicular stimulating hormone receptor (FSHr), hyaluronan synthase\\u000a 2 (Has2), prostaglandin synthase 2 (Ptgs2) and steroidogenic acute regulator protein (Star), were correctly reprogrammed to\\u000a be transcriptionally silent following somatic cell nuclear transfer (SCNT) in a murine model. Cumulus cells of C57×CBAF1 female\\u000a mouse were injected into enucleated oocytes, followed by activation in 10 ?mol\\/L

Guo-qing Tong; Boon-chin Heng; Soon-chye Ng



Manipulation of iron transporter genes results in the suppression of human and mouse mammary adenocarcinomas.  


Since malignant cells often have a high demand for iron, we hypothesize that breast cancer cells may alter the expression of iron transporter genes including iron importers [transferrin receptor (TFRC) and solute carrier family 11 (proton-coupled divalent metal ion transporters), member 2 (SLC11A2)] and the iron exporter SLC40A1 (ferroportin), and additionally that the growth of breast cancer can be inhibited by manipulating iron transporter gene expression. To test our hypothesis, reverse transcription polymerase chain reaction (RT-PCR) was used to determine mRNA expression of iron transporter genes in normal human mammary epithelial MCF-12A cells and human breast cancer MCF-7 cells. Antisense oligonucleotides were employed to suppress the expression of TFRC gene in the 4T1 mammary adenocarcinoma in both cell culture and a mouse tumor model. We found the following: i) the MCF-7 cells have higher expression of TFRC and SLC11A2 compared with MCF-12A epithelia; ii) SLC40A1 was only expressed in MCF-12A epithelia but not in MCF-7 cells; iii) iron increased mRNA levels of the SLC11A2 gene in both MCF-12A and MCF-7 cells; iv) TFRC antisense oligonucleotides reduced TFRC mRNA levels and intracellular total iron, and inhibited the proliferation of the 4T1 cells in cell culture; v) TFRC antisense oligonucleotide inhibited tumor growth and lung metastases in the 4T1 mammary adenocarcinoma mouse model. In conclusion, breast cancer cells up-regulate the expression of iron importer genes and down-regulate the expression of iron exporter SLC40A1 to satisfy their increased demand for iron. Suppression of transferrin receptor by antisense results in inhibition of tumor growth and lung metastasis in the 4T1 mammary adenocarcinoma mouse model. PMID:20392994

Jiang, Xian P; Elliott, Robert L; Head, Jonathan F



A High-Resolution Anatomical Framework of the Neonatal Mouse Brain for Managing Gene Expression Data  

PubMed Central

This study aims to provide a high-resolution atlas and use it as an anatomical framework to localize the gene expression data for mouse brain on postnatal day 0 (P0). A color Nissl-stained volume with a resolution of 13.3?×?50?×?13.3??3 was constructed and co-registered to a standard anatomical space defined by an averaged geometry of C57BL/6J P0 mouse brains. A 145 anatomical structures were delineated based on the histological images. Anatomical relationships of delineated structures were established based on the hierarchical relations defined in the atlas of adult mouse brain (MacKenzie-Graham et al., 2004) so the P0 atlas can be related to the database associated with the adult atlas. The co-registered multimodal atlas as well as the original anatomical delineations is available for download at The region-specific anatomical framework based on the neonatal atlas allows for the analysis of gene activity within a high-resolution anatomical space at an early developmental stage. We demonstrated the potential application of this framework by incorporating gene expression data generated using in situ hybridization to the atlas space. By normalizing the gene expression patterns revealed by different images, experimental results from separate studies can be compared and summarized in an anatomical context. Co-displaying multiple registered datasets in the atlas space allows for 3D reconstruction of the co-expression patterns of the different genes in the atlas space, hence providing better insight into the relationship between the differentiated distribution pattern of gene products and specific anatomical systems. PMID:18974801

Lee, Erh-Fang; Boline, Jyl; Toga, Arthur W.



Cloning and characterization of the gene for mouse macrophage migration inhibitory factor (MIF)  

SciTech Connect

An emerging body of data indicates that the protein mediator described originally as macrophage migration inhibitory factor (MIF) exerts a central and wide ranging role in host inflammatory responses. MIF is a major constituent of corticotrophic cells within the anterior pituitary gland and is secreted into the circulation in a hormone-like fashion. MIF also exists preformed in monocytes/macrophages and is a pivotal mediator in the host response to endotoxic shock. To gain further insight into the biologic expression of this protein that encompasses components of both the immune and the endocrine systems, we have cloned the mouse MIF gene and identified potential regulatory sequences present within the 5{prime}-proximal promoter region. The gene for mouse MIF is located on chromosome 10, spans approximately 1 kb, and shares a high degree of structural homology with its human counterpart. Of note, the consensus enhancer/promoter motifs identified include both inflammatory/growth factor-related elements and sites associated with the genes for certain peptide hormones. We also report the structures of two MIF pseudogenes that account for early observations suggesting that mouse MIF is encoded by a highly homologous multigene family. 38 refs., 5 figs., 1 tab.

Mitchell, R.; Bacher, M.; Bernhagen, J. [Picower Institute for Medical Research, Manhasset, NY (United States)] [and others



Characterization and mapping of the gene encoding mouse proteasome subunit DELTA (Lmp19)  

SciTech Connect

The proteasome subunit DELTA is unusually closely related to the major histocompatibility complex (MHC)-linked proteasome subunit, LMP2. The sequence of a mouse cDNA for DELTA confirms that this 22 100 M{sub r} proteasome subunit is highly conserved across species. Sequence analysis of the mouse gene encoding DELTA, designated Lmp19, indicates that it consists of six exons and five introns, similar to the Lmp2 gene. The 5{prime} upstream region lacks a TATA regulatory sequence, which is also absent from proteasome genes isolated from Drosophila. BXD recombinant inbred (RI) mice were used to map the potential chromosomal location of Lmp19, and revealed that the DELTA subunit has related sequences present on two different mouse chromosomes, chromosomes 1 and 11. Typing of 89 progeny from a C57BL/6J X Mus spretus DNA backcross panel (BSS) confirmed the chromosome 1 assignment. Southern hybridization with a polymerase chain reaction-generated Lmp19 intron 2-specific probe indicates that the Lmp19 genomic clone corresponds to the sequence on chromosome 11, and further suggests that the chromosome 1 copy represents a processed pseudogene (Lmp19-ps1). 39 refs., 6 figs., 2 tabs.

Woodward, E.C. [Virginia Commonwealth Univ., Richmond, VA (United States); Monaco, J.J. [Univ. of Cincinnati, OH (United States)



The Construction of Transgenic and Gene Knockout/Knockin Mouse Models of Human Disease  

PubMed Central

The genetic and physiological similarities between mice and humans have focused considerable attention on rodents as potential models of human health and disease. Together with the wealth of resources, knowledge, and technologies surrounding the mouse as a model system, these similarities have propelled this species to the forefront of biomedical research. The advent of genomic manipulation has quickly led to the creation and use of genetically engineered mice as powerful tools for cutting edge studies of human disease research, including the discovery, refinement, and utility of many currently available therapeutic regimes. In particular, the creation of genetically modified mice as models of human disease has remarkably changed our ability to understand the molecular mechanisms and cellular pathways underlying disease states. Moreover, the mouse models resulting from gene transfer technologies have been important components correlating an individual’s gene expression profile to the development of disease pathologies. The objective of this review is to provide physician-scientists with an expansive historical and logistical overview of the creation of mouse models of human disease through gene transfer technologies. Our expectation is that this will facilitate on-going disease research studies and may initiate new areas of translational research leading to enhanced patient care. PMID:21800101

Doyle, Alfred; McGarry, Michael P.; Lee, Nancy A.; Lee, James J.



Transposon mutagenesis identifies genes driving hepatocellular carcinoma in a chronic hepatitis B mouse model.  


The most common risk factor for developing hepatocellular carcinoma (HCC) is chronic infection with hepatitis B virus (HBV). To better understand the evolutionary forces driving HCC, we performed a near-saturating transposon mutagenesis screen in a mouse HBV model of HCC. This screen identified 21 candidate early stage drivers and a very large number (2,860) of candidate later stage drivers that were enriched for genes that are mutated, deregulated or functioning in signaling pathways important for human HCC, with a striking 1,199 genes being linked to cellular metabolic processes. Our study provides a comprehensive overview of the genetic landscape of HCC. PMID:24316982

Bard-Chapeau, Emilie A; Nguyen, Anh-Tuan; Rust, Alistair G; Sayadi, Ahmed; Lee, Philip; Chua, Belinda Q; New, Lee-Sun; de Jong, Johann; Ward, Jerrold M; Chin, Christopher K Y; Chew, Valerie; Toh, Han Chong; Abastado, Jean-Pierre; Benoukraf, Touati; Soong, Richie; Bard, Frederic A; Dupuy, Adam J; Johnson, Randy L; Radda, George K; Chan, Eric Chun Yong; Wessels, Lodewyk F A; Adams, David J; Jenkins, Nancy A; Copeland, Neal G



Transposon mutagenesis identifies genes driving hepatocellular carcinoma in a chronic hepatitis B mouse model  

PubMed Central

The most common risk factor for developing hepatocellular carcinoma (HCC) is chronic infection with hepatitis B virus (HBV). To better understand the evolutionary forces driving HCC we performed a near saturating transposon mutagenesis screen in a mouse HBV model of HCC. This screen identified 21 candidate early stage drivers, and a bewildering number (2860) of candidate later stage drivers, that were enriched for genes mutated, deregulated, or that function in signaling pathways important for human HCC, with a striking 1199 genes linked to cellular metabolic processes. Our study provides a comprehensive overview of the genetic landscape of HCC. PMID:24316982

Bard-Chapeau, Emilie A.; Nguyen, Anh-Tuan; Rust, Alistair G.; Sayadi, Ahmed; Lee, Philip; Chua, Belinda Q; New, Lee-Sun; de Jong, Johann; Ward, Jerrold M.; Chin, Christopher KY.; Chew, Valerie; Toh, Han Chong; Abastado, Jean-Pierre; Benoukraf, Touati; Soong, Richie; Bard, Frederic A.; Dupuy, Adam J.; Johnson, Randy L.; Radda, George K.; Chan, Eric CY.; Wessels, Lodewyk FA.; Adams, David J.



Genetic and Molecular Basis of QTL of Diabetes in Mouse: Genes and Polymorphisms  

PubMed Central

A systematic study has been conducted of all available reports in PubMed and OMIM (Online Mendelian Inheritance in Man) to examine the genetic and molecular basis of quantitative genetic loci (QTL) of diabetes with the main focus on genes and polymorphisms. The major question is, What can the QTL tell us? Specifically, we want to know whether those genome regions differ from other regions in terms of genes relevant to diabetes. Which genes are within those QTL regions, and, among them, which genes have already been linked to diabetes? whether more polymorphisms have been associated with diabetes in the QTL regions than in the non-QTL regions. Our search revealed a total of 9038 genes from 26 type 1 diabetes QTL, which cover 667,096,006 bp of the mouse genomic sequence. On one hand, a large number of candidate genes are in each of these QTL; on the other hand, we found that some obvious candidate genes of QTL have not yet been investigated. Thus, the comprehensive search of candidate genes for known QTL may provide unexpected benefit for identifying QTL genes for diabetes. PMID:19471607

Gao, Peng; Jiao, Yan; Xiong, Qing; Wang, Cong-Yi; Gerling, Ivan; Gu, Weikuan



Gene expression profiling in C57BL\\/6J and A\\/J mouse inbred strains reveals gene networks specific for brain regions independent of genetic background  

Microsoft Academic Search

BACKGROUND: We performed gene expression profiling of the amygdala and hippocampus taken from inbred mouse strains C57BL\\/6J and A\\/J. The selected brain areas are implicated in neurobehavioral traits while these mouse strains are known to differ widely in behavior. Consequently, we hypothesized that comparing gene expression profiles for specific brain regions in these strains might provide insight into the molecular

Simone de Jong; Tova F Fuller; Esther Janson; Eric Strengman; Steve Horvath; Martien JH Kas; Roel A Ophoff



Integration of gene chip and topological network techniques to screen a candidate biomarker gene (CBG) for predication of the source water carcinogenesis risks on mouse Mus musculus  

Microsoft Academic Search

Screening of a candidate biomarker gene (CBG) to predicate the carcinogenesis risks in the Yangtze River source of drinking\\u000a water in Nanjing area (YZR-SDW-NJ) on mouse (Mus musculus) was conducted in this research. The effects of YZR-SDW-NJ on the genomic transcriptional expression levels were measured\\u000a by the GeneChip® Mouse Genome and data treated by the GO database analysis. The 298

Jie Sun; Shupei Cheng; Aimin Li; Rui Zhang; Bing Wu; Yan Zhang; Xuxiang Zhang



Characterization and transcriptional analysis of the mouse Chromosome 16 cytokine receptor gene cluster.  


The class II cytokine receptor (CIICR) genes Il10r2 and Ifnar1 are localized on mouse Chr 16 in a cluster that also contains the CIICR genes Ifnar2 and Ifngr2. The structure of the Il10r2 gene was deduced and consisted of 7 exons and 6 introns arrayed in an organization similar to its human ortholog. We also present a revised Il10r2 cDNA sequence with a total of 100 bp of additional nucleotide sequence in the 5' and 3' untranslated regions, and report the first extensive profiles of Il10r2 and Ifnar1 mRNA developmental stage and adult tissue expression. Promoter-luciferase reporter constructs were used to define the major region (-108 to +67) that conferred basal expression of the Il10r2 gene. Long-range comparative genomic sequence analysis between the mouse and the orthologous human CIICR genomic loci revealed several conserved non-coding regions. The most proximal conserved non-coding sequence was a 204-bp element located 1.6 kb upstream of the transcriptional start site of Ifnar2 that had repressor-like activity in transient transfection assays with an SV40 promoter-luciferase reporter construct. The identification of multiple conserved non-coding sequences will provide the basis for further investigations to elucidate CIICR gene regulation. PMID:12584606

Hardy, Matthew P; Sanij, Elaine P; Hertzog, Paul J; Owczarek, Catherine M



Retroviral-mediated gene transfer and expression of human phenylalanine hydroxylase in primary mouse hepatocytes  

SciTech Connect

Genetic therapy for phenylketonuria (severe phenylalanine hydroxylase deficiency) may require introduction of a normal phenylalanine hydroxylase gene into hepatic cells of patients. The authors report development of a recombinant retrovirus based on the N2 vector for gene transfer and expression of human phenylalanine hydroxylase cDNA in primary mouse hepatocytes. This construct contains an internal promoter of the human {alpha}{sub 1}-antitrypsin gene driving transcription of the phenylalanine hydroxylase cDNA. Primary mouse hepatocytes were isolated from newborn mice, infected with the recombinant virus, and selected for expression of the neomycin-resistance gene. Hepatocytes transformed with the recombinant virus contained high levels of human phenylalanine hydroxylase mRNA transcripts originating from the retroviral and internal promoters. These results demonstrate that the transcriptional regulatory elements of the {alpha}{sub 1} antitrypsin gene retain their tissue-specific function in the recombinant provirus and establish a method for efficient transfer and high-level expression of human phenylalanine hydroxylase in primary hepatocytes.

Peng, H.; Armentano, D.; Mackenzie-Graham, L.; Shen, R.F.; Darlington, G.; Ledley, F.D.; Woo, S.L.C. (Baylor College of Medicine, Houston, TX (USA))



Electroacupuncture suppresses myostatin gene expression: cell proliferative reaction in mouse skeletal muscle.  


Complementary and alternative medicine (CAM) may provide patients with an alternative to traditional medicine, but an assessment of its efficacy is required. One CAM method, electroacupuncture (EA) treatment, is a maneuver that utilizes stimulation of acupuncture needles with a low-frequency microcurrent. To study the effect of short-term EA, we evaluated the differential expression of genes induced by EA in mouse skeletal muscle for up to 24 h. We then used RT-PCR to confirm the expression patterns of six differentially expressed genes. Bioinformatics analysis of their transcription control regions showed that EA-inducible genes have numerous common binding motifs that are related to cell differentiation, cell proliferation, muscle repair, and hyperplasia. These results suggested that EA treatment may induce cell proliferation in skeletal muscle. To verify this possibility, we used EA to stimulate mouse skeletal muscle daily for up to 1 mo and examined the long-term effects. Immunohistochemical analysis showed that nuclei of muscle cells treated with EA for 1 mo, especially nuclei of satellite cells, reacted with anti-human PCNA. Also, expression of the gene encoding myostatin, which is a growth repressor in muscle satellite cells, was suppressed by daily EA treatment for 1 wk; EA treatment for 1 mo resulted in more marked suppression of the gene. These molecular findings constitute strong evidence that EA treatment suppresses myostatin expression, which leads to a satellite cell-related proliferative reaction and repair in skeletal muscle. PMID:17341691

Takaoka, Yutaka; Ohta, Mika; Ito, Akihiko; Takamatsu, Kunihiko; Sugano, Aki; Funakoshi, Kotaro; Takaoka, Nobuo; Sato, Nobuko; Yokozaki, Hiroshi; Arizono, Naoki; Goto, Shuji; Maeda, Eiichi



Localization of a human homolog of the mouse pericentrin gene (PCNT) to chromosome 21qter  

SciTech Connect

Exon trapping was used to identify portions of genes from cosmid DNA of a human chromosome 21-specific library LL21NC02-Q. More than 650 potential exons have been cloned and characterized to date. Among these, 3 trapped {open_quotes}exons{close_quotes} showed strong homology to different regions of the cDNA for the mouse pericentrin (Pcnt) gene, indicating that these 3 exons are portions of a human homolog of the mouse pericentrin gene. With PCR amplification, Southern blot analysis, and FISH, we have mapped this presumed human pericentrin gene (PCNT) to the long arm of chromosome 21 between marker PFKL and 21qter. Pericentrin is a conserved protein component of the filamentous matrix of the centrosome involved in the initial establishment of the organized microtubule array. No candidate hereditary disorder for pericentrin deficiency/abnormality has yet been mapped in the most distal region of 21q; in addition the role of triplication of the pericentrin gene in the pathophysiology or etiology of trisomy 21 is currently unknown. 16 refs., 3 figs.

Chen, Haiming [Univ. of Geneva Medical School (Switzerland)] [Univ. of Geneva Medical School (Switzerland); Gos, A.; Morris, M.A. [Cantonal Hospital, Geneva (Switzerland)] [and others] [Cantonal Hospital, Geneva (Switzerland); and others



Cloning and characterization of the mouse glucokinase gene locus and identification of distal liver-specific DNase I hypersensitive sites  

SciTech Connect

We cloned and characterized an 83-kb fragment of mouse genomic DNA containing the entire glucokinase (GK) gene. The 11 exons of the gene span a total distance of 49 kb, with exons 1{beta} and 1L being separated by 35 kb. A total of 25,266 bp of DNA sequence information was determined: from {approximately}-9.2 to {approximately}+15 kb (24,195 bp), relative to the hepatocyte transcription start site, and from -335 to -736 bp (1071 bp), relative to the transcription start site in {beta} cells. These sequences revealed that mouse GK is >94% identical to rat and human GK. Mouse hepatic GK mRNA is regulated by fasting and refeeding, as also occurs in the rat. Alignment of the upstream and downstream promoter regions of the mouse, rat, and human genes revealed several evolutionarily conserved regions that may contribute to transcriptional regulation. However, fusion gene studies in transgenic mice indicate that the conserved regions near the transcription start site in hepatocytes are themselves not sufficient for position-independent expression in liver. Analysis of the chromatin structure of a 48-kb region of the mouse gene using DNase I revealed eight liver-specific hypersensitive sites whose locations ranged from 0.1 to 36 kb upstream of the liver transcription start site. The availability of a single, contiguous DNA fragment containing the entire mouse GK gene should allow further studies of cell-specific expression of GK to be performed. 46 refs., 8 figs.

Postic, C.; Niswender, K.D.; Shelton, K.D.; Pettepher, C.C.; Granner, D.K.; Magnuson, M.A. [Vanderbilt Univ., Nashville, TN (United States)] [and others



Selection-Independent Generation of Gene Knockout Mouse Embryonic Stem Cells Using Zinc-Finger Nucleases  

PubMed Central

Gene knockout in murine embryonic stem cells (ESCs) has been an invaluable tool to study gene function in vitro or to generate animal models with altered phenotypes. Gene targeting using standard techniques, however, is rather inefficient and typically does not exceed frequencies of 10?6. In consequence, the usage of complex positive/negative selection strategies to isolate targeted clones has been necessary. Here, we present a rapid single-step approach to generate a gene knockout in mouse ESCs using engineered zinc-finger nucleases (ZFNs). Upon transient expression of ZFNs, the target gene is cleaved by the designer nucleases and then repaired by non-homologous end-joining, an error-prone DNA repair process that introduces insertions/deletions at the break site and therefore leads to functional null mutations. To explore and quantify the potential of ZFNs to generate a gene knockout in pluripotent stem cells, we generated a mouse ESC line containing an X-chromosomally integrated EGFP marker gene. Applying optimized conditions, the EGFP locus was disrupted in up to 8% of ESCs after transfection of the ZFN expression vectors, thus obviating the need of selection markers to identify targeted cells, which may impede or complicate downstream applications. Both activity and ZFN-associated cytotoxicity was dependent on vector dose and the architecture of the nuclease domain. Importantly, teratoma formation assays of selected ESC clones confirmed that ZFN-treated ESCs maintained pluripotency. In conclusion, the described ZFN-based approach represents a fast strategy for generating gene knockouts in ESCs in a selection-independent fashion that should be easily transferrable to other pluripotent stem cells. PMID:22194948

Osiak, Anna; Radecke, Frank; Guhl, Eva; Radecke, Sarah; Dannemann, Nadine; Lutge, Fabienne; Glage, Silke; Rudolph, Cornelia; Cantz, Tobias; Schwarz, Klaus; Heilbronn, Regine; Cathomen, Toni



Gene expression profile of mouse fibroblasts exposed to a biodegradable iron alloy for stents.  


Iron-based materials could constitute an interesting option for cardiovascular biodegradable stent applications due to their superior ductility compared to their counterparts - magnesium alloys. Since the predicted degradation rate of pure iron is considered slow, manganese (35% w/w), an alloying element for iron, was explored to counteract this problem through the powder metallurgy process (Fe-35 Mn). However, manganese presents a high cytotoxic potential; thus its effect on cells must first be established. Here, we established the gene expression profile of mouse 3T3 fibroblasts exposed to Fe-35 Mn degradation products in order to better understand cell response to potentially cytotoxic degradable metallic material (DMM). Mouse 3T3 cells were exposed to degradation products eluting through tissue culture insert filter (3 ?m pore size) containing cytostatic amounts of 3.25 mg ml(-1) of Fe-35 Mn powder, 0.25 mg ml(-1) of pure Mn powder or 5 mg ml(-1) of pure iron powder for 24 h. We then conducted a gene expression profiling study from these cells. Exposure of 3T3 cells to Fe-35 Mn was associated with the up-regulation of 75 genes and down-regulation of 59 genes, while 126 were up-regulated and 76 down-regulated genes in the presence of manganese. No genes were found regulated for the iron powder. When comparing the GEP of 3T3 fibroblasts in the presence of Fe-35 Mn and Mn, 68 up-regulated and 54 down-regulated genes were common. These results were confirmed by quantitative RT-PCR for a subset of these genes. This GEP study could provide clues about the mechanism behind degradation products effects on cells of the Fe-35 Mn alloy and may help in the appraisal of its potential for DMM applications. PMID:23499988

Purnama, Agung; Hermawan, Hendra; Champetier, Serge; Mantovani, Diego; Couet, Jacques



BMD Regulation on Mouse Distal Chromosome 1, Candidate Genes, and Response to Ovariectomy or Dietary Fat  

PubMed Central

The distal end of mouse chromosome 1 (Chr 1) harbors quantitative trait loci (QTLs) that regulate bone mineral density (BMD) and share conserved synteny with human chromosome 1q. The objective of this article was to map this mouse distal Chr 1 region and identify gene(s) responsible for BMD regulation in females. We used X-ray densitometry [ie, dual-energy X-ray Absorptiometry (DXA), micro–computed tomography (µCT), and peripheral quantitative computed tomography (pQCT)] to phenotype a set of nested congenic strains constructed from C57BL/6BmJ (B6/Bm) and C3H/HeJ (C3H) mice to map the region associated with the BMD QTL. The critical region has been reduced to an interval of 0.152 Mb that contributes to increased BMD when C3H alleles are present. Histomorphometry and osteoblast cultures indicated that increased osteoblast activity was associated with increased BMD in mouse strains with C3H alleles in this critical region. This region contains two genes, Aim2, which binds with cytoplasmic dsDNA and results in apoptosis, and AC084073.22, a predicted gene of unknown function. Ovariectomy induced bone loss in the B6/Bm progenitor and the three congenic strains regardless of the alleles present in the critical BMD region. High dietary fat treatment (thought to suppress distal Chr 1 QTL for BMD in mice) did not induce bone loss in the congenics carrying C3H alleles in the critical 0.152 Mb carrying the AIM2 and AC084073.22 genes. Gene expression studies in whole bone of key congenics showed differential expression of AC084073.22 for strains carrying B6/Bm versus C3H alleles but not for Aim2. In conclusion, our data suggest that osteoblasts are the cellular target of gene action and that AC084073.22 is the best candidate for female BMD regulation in the distal region of mouse Chr 1. © 2011 American Society for Bone and Mineral Research. PMID:20687154

Beamer, Wesley G; Shultz, Kathryn L; Coombs, Harold F; DeMambro, Victoria E; Reinholdt, Laura G; Ackert-Bicknell, Cheryl L; Canalis, Ernesto; Rosen, Clifford J; Donahue, Leah Rae



Genetic-Genomic Replication to Identify Candidate Mouse Atherosclerosis Modifier Genes  

PubMed Central

Objective Genetics plays a large role in atherosclerosis susceptibility in humans and mice. We attempted to confirm previously determined mouse atherosclerosis?associated loci and use bioinformatics and transcriptomics to create a catalog of candidate atherosclerosis modifier genes at these loci. Methods and Results A strain intercross was performed between AKR and DBA/2 mice on the apoE?/? background generating 166 F2 progeny. Using the phenotype log10 of the aortic root lesion area, we identified 3 suggestive atherosclerosis quantitative trait loci (Ath QTLs). When combined with our prior strain intercross, we confirmed 3 significant Ath QTLs on chromosomes 2, 15, and 17, with combined logarithm of odds scores of 5.9, 5.3, and 5.6, respectively, which each met the genome?wide 5% false discovery rate threshold. We identified all of the protein coding differences between these 2 mouse strains within the Ath QTL intervals. Microarray gene expression profiling was performed on macrophages and endothelial cells from this intercross to identify expression QTLs (eQTLs), the loci that are associated with variation in the expression levels of specific transcripts. Cross tissue eQTLs and macrophage eQTLs that replicated from a prior strain intercross were identified. These bioinformatic and eQTL analyses produced a comprehensive list of candidate genes that may be responsible for the Ath QTLs. Conclusions Replication studies for clinical traits as well as gene expression traits are worthwhile in identifying true versus false genetic associations. We have replicated 3 loci on mouse chromosomes 2, 15, and 17 that are associated with atherosclerosis. We have also identified protein coding differences and multiple replicated eQTLs, which may be useful in the identification of atherosclerosis modifier genes. PMID:23525445

Hsu, Jeffrey; Smith, Jonathan D.



Modeling the mouse lymphoma forward mutational assay: the Gene-Tox program database.  


An SAR model of the induction of mutations at the tk(+/-) locus of L5178Y mouse lymphoma cells (MLA, for mouse lymphoma assay) was derived based upon a re-evaluation of experimental results reported by a Gene-Tox (GT) working group [A.D. Mitchell, A.E. Auletta, D. Clive, P.E. Kirby, M.M. Moore, B.C. Myhr, The L5178Y/tk(+/-) mouse lymphoma specific gene and chromosomal mutation assay. A phase III report of the U.S. Environmental Protection Agency Gene-Tox Program, Mutation Res. 394 (1997) 177-303.]. The predictive performance of the GT MLA SAR model was similar to that of a Salmonella mutagenicity model containing the same number of chemicals. However, the structural determinants (biophores) derived from the GT MLA SAR model include both electrophilic as well as non-electrophilic moieties, suggesting that the induction of mutations in the MLA may occur by both direct interaction with DNA and by non-DNA-related mechanisms. This was confirmed by the observation that the set of biophores associated with MLA overlapped significantly with those associated with phenomena related to loss of heterozygosity, chromosomal rearrangements and aneuploidy. The MLA SAR model derived from the GT data evaluation was significantly more predictive than an SAR model previously derived from MLA data reported by the US National Toxicology Program [B. Henry, S.G. Grant, G. Klopman, H.S. Rosenkranz, Induction of forward mutations at the thymidine kinase locus of mouse lymphoma cells: evidence for electrophilic and non-electrophilic mechanisms, Mutation Res. 397 (1998) 331-335.]. Moreover, the latter model appeared to be more complex than the former, suggesting that the GT induction data was both simpler mechanistically and more homogeneous than that of the NTP. PMID:10708987

Grant, S G; Zhang, Y P; Klopman, G; Rosenkranz, H S



Computational promoter analysis of mouse, rat and human antimicrobial peptide-coding genes  

PubMed Central

Background Mammalian antimicrobial peptides (AMPs) are effectors of the innate immune response. A multitude of signals coming from pathways of mammalian pathogen/pattern recognition receptors and other proteins affect the expression of AMP-coding genes (AMPcgs). For many AMPcgs the promoter elements and transcription factors that control their tissue cell-specific expression have yet to be fully identified and characterized. Results Based upon the RIKEN full-length cDNA and public sequence data derived from human, mouse and rat, we identified 178 candidate AMP transcripts derived from 61 genes belonging to 29 AMP families. However, only for 31 mouse genes belonging to 22 AMP families we were able to determine true orthologous relationships with 30 human and 15 rat sequences. We screened the promoter regions of AMPcgs in the three species for motifs by an ab initio motif finding method and analyzed the derived promoter characteristics. Promoter models were developed for alpha-defensins, penk and zap AMP families. The results suggest a core set of transcription factors (TFs) that regulate the transcription of AMPcg families in mouse, rat and human. The three most frequent core TFs groups include liver-, nervous system-specific and nuclear hormone receptors (NHRs). Out of 440 motifs analyzed, we found that three represent potentially novel TF-binding motifs enriched in promoters of AMPcgs, while the other four motifs appear to be species-specific. Conclusion Our large-scale computational analysis of promoters of 22 families of AMPcgs across three mammalian species suggests that their key transcriptional regulators are likely to be TFs of the liver-, nervous system-specific and NHR groups. The computationally inferred promoter elements and potential TF binding motifs provide a rich resource for targeted experimental validation of TF binding and signaling studies that aim at the regulation of mouse, rat or human AMPcgs. PMID:17254313

Brahmachary, Manisha; Schonbach, Christian; Yang, Liang; Huang, Enli; Tan, Sin Lam; Chowdhary, Rajesh; Krishnan, SPT; Lin, Chin-Yo; Hume, David A; Kai, Chikatoshi; Kawai, Jun; Carninci, Piero; Hayashizaki, Yoshihide; Bajic, Vladimir B



Identifying aging-related genes in mouse hippocampus using gateway nodes  

PubMed Central

Background High-throughput studies continue to produce volumes of metadata representing valuable sources of information to better guide biological research. With a stronger focus on data generation, analysis models that can readily identify actual signals have not received the same level of attention. This is due in part to high levels of noise and data heterogeneity, along with a lack of sophisticated algorithms for mining useful information. Networks have emerged as a powerful tool for modeling high-throughput data because they are capable of representing not only individual biological elements but also different types of relationships en masse. Moreover, well-established graph theoretic methodology can be applied to network models to increase efficiency and speed of analysis. In this project, we propose a network model that examines temporal data from mouse hippocampus at the transcriptional level via correlation of gene expression. Using this model, we formally define the concept of “gateway” nodes, loosely defined as nodes representing genes co-expressed in multiple states. We show that the proposed network model allows us to identify target genes implicated in hippocampal aging-related processes. Results By mining gateway genes related to hippocampal aging from networks made from gene expression in young and middle-aged mice, we provide a proof-of-concept of existence and importance of gateway nodes. Additionally, these results highlight how network analysis can act as a supplement to traditional statistical analysis of differentially expressed genes. Finally, we use the gateway nodes identified by our method as well as functional databases and literature to propose new targets for study of aging in the mouse hippocampus. Conclusions This research highlights the need for methods of temporal comparison using network models and provides a systems biology approach to extract information from correlation networks of gene expression. Our results identify a number of genes previously implicated in the aging mouse hippocampus related to synaptic plasticity and apoptosis. Additionally, this model identifies a novel set of aging genes previously uncharacterized in the hippocampus. This research can be viewed as a first-step for identifying the processes behind comparative experiments in aging that is applicable to any type of temporal multi-state network. PMID:24886704



667. Lentiviral Gene Transfer of RPE65 cDNA in Knock-Out Mouse Models of Leber Congenital Amaurosis  

Microsoft Academic Search

Gene transfer is a promising approach for single gene defect in several retinal degeneration disorders. Among them, 10-15% of Leber congenital amaurosis (LCA) cases, a severe retinal degeneration of early childhood, bear a mutation in the RPE65 gene, the function of which is essential for the visual cycle. AAV-mediated gene therapy was already described in dog and mouse models of

Corinne Kostic; Alexis-Pierre Bemelmans; Muriel Jaquet; Dana Hornfeld; William W. Hauswirth; Janis Lem; Zhongyan Wang; Daniel F. Schorderet; Francis L. Munier; Andreas Wenzel; Yvan Arsenijevic



Mapping of the gene for high-density lipoprotein binding protein (Hdlbp) to proximal mouse Chromosome 1  

SciTech Connect

HDL binding protein (HBP) is a 150-kDa glycoprotein that is processed to smaller forms (105-110 kDa) that bind HDL. In vitro studies have shown that HBP protein mass and mRNA levels increase in cells overloaded with cholesterol, suggesting that this protein plays a role in HDL-mediated removal of cholesterol from cells, a process that may underlie the anti-atherogenic effects of HDL. The cDNA for human HBP has been identified and the gene (HDLBP) localized to chromosome 2q37. To test whether the HDL binding protein gene underlies any mutations in the mouse or whether it contributes to multigenic variations contributing to lipoprotein metabolism between inbred mouse strains, we report the chromosomal mapping in mouse for the mouse HBP gene (Hdlbp).

LeBoeuf, R.C.; Oram, J.F. [Univ. of Washington, Seattle, WA (United States)] [Univ. of Washington, Seattle, WA (United States); Xia, Y.R.; Lusis, A.J. [Univ. of California, Los Angeles, CA (United States)] [Univ. of California, Los Angeles, CA (United States)



The human and mouse receptors of hyaluronan-mediated motility, RHAMM, genes (HMMR) map to human chromosome 5q33.2-qter and mouse chromosome 11  

SciTech Connect

The gene for the receptor for hyaluronan-mediated motility, RHAAM (designated hyaluronan-mediated motility receptor, HMMR (human) and Hmmr (mouse), for mapping purposes), was localized to human chromosome 5q33.2-qter by somatic cell and radiation hybrid analyses. Investigation of two interspecific back-crosses localized the mouse RHAMM (Hmmr) locus 18 cM from the centromere of mouse chromosome 11 within a region of synteny homology with human chromosome 5q23-q35 genes. The map position of the human RHAMM gene places it in a region comparatively rich in disease-associated genes, including those for low-frequency hearing loss, dominant limb-girdle muscular dystrophy, diastrophic dysplasia, Treacher Collins syndrome, and myeloid disorders associated with the 5q-syndrome. The RHAMM gene location and its ability to transform cells when overexpressed implicate RHAMM as a possible candidate gene in the pathogenesis of the recently described t(5;14)(q33-q34;q11) acute lymphoblastic leukemias. 18 refs., 1 fig.

Spicer, A.P.; McDonald, J.A. [Mayo Clinic Scottsdale, AZ (United States); Roller, M.L.; Camper, S.A. [Univ. of Michigan Medical School, Ann Arbor, MI (United States)] [and others



The human and mouse receptors for hyaluronan-mediated motility, RHAMM, genes (HMMR) map to human chromosome 5q33.2-qter and mouse chromosome 11.  


The gene for the receptor for hyaluronan-mediated motility, RHAMM (designated hyaluronan-mediated motility receptor, HMMR (human) and Hmmr (mouse), for mapping purposes), was localized to human chromosome 5q33.2-qter by somatic cell and radiation hybrid analyses. Investigation of two interspecific backcrosses localized the mouse RHAMM (Hmmr) locus 18 cM from the centromere of mouse chromosome 11 within a region of synteny homology with human chromosome 5q23-q35 genes. The map position of the human RHAMM gene places it in a region comparatively rich in disease-associated genes, including those for low-frequency hearing loss, dominant limb-girdle muscular dystrophy, diastrophic dysplasia, Treacher Collins syndrome, and myeloid disorders associated with the 5q- syndrome. The RHAMM gene location and its ability to transform cells when overexpressed implicate RHAMM as a possible candidate gene in the pathogenesis of the recently described t(5;14)(q33-q34;q11) acute lymphoblastic leukemias. PMID:8595891

Spicer, A P; Roller, M L; Camper, S A; McPherson, J D; Wasmuth, J J; Hakim, S; Wang, C; Turley, E A; McDonald, J A



Restricted immunoglobulin variable region (Ig V) gene expression accompanies secondary rearrangements of light chain Ig V genes in mouse plasmacytomas.  


The many binding studies of monoclonal immunoglobulin (Ig) produced by plasmacytomas have found no universally common binding properties, but instead, groups of plasmacytomas with specific antigen-binding activities to haptens such as phosphorylcholine, dextrans, fructofuranans, or dinitrophenyl. Subsequently, it was found that plasmacytomas with similar binding chain specificities not only expressed the same idiotype, but rearranged the same light (V(L)) and heavy (V(H)) variable region genes to express a characteristic monoclonal antibody. In this study, we have examined by enzyme-linked immunosorbent assay five antibodies secreted by silicone-induced mouse plasmacytomas using a broader panel of antigens including actin, myosin, tubulin, single-stranded DNA, and double-stranded DNA. We have determined the Ig heavy and light chain V gene usage in these same plasmacytomas at the DNA and RNA level. Our studies reveal: (a) antibodies secreted by plasmacytomas bind to different antigens in a manner similar to that observed for natural autoantibodies; (b) the expressed Ig heavy genes are restricted in V gene usage to the V(H)-J558 family; and (c) secondary rearrangements occur at the light chain level with at least three plasmacytomas expressing both kappa and lambda light chain genes. These results suggest that plasmacytomas use a restricted population of B cells that may still be undergoing rearrangement, thereby bypassing the allelic exclusion normally associated with expression of antibody genes. PMID:10562316

Diaw, L; Siwarski, D; Coleman, A; Kim, J; Jones, G M; Dighiero, G; Huppi, K



A genomic reservoir for Tnfrsf genes is developmentally regulated and imprinted in the mouse  

PubMed Central

Tumor necrosis factor receptor superfamily is composed of at least 26 members in the mouse, three of which exist as a cluster within the imprinted Kcnq1 domain on chromosome 7. Tnfrsf22, 23 and 26 contain typical cystein-rich domains and Tnfrsf22 and 23 can bind ligands but have no signaling capacity. Thus, they are assumed to be decoy receptors. The developmental expression profile of these genes is unknown and knowledge of their imprinting patterns is incomplete and controversial. We found that all three genes are expressed during mouse embryonic development, and that they have a strong maternal bias, indicating that they may be affected by the KvDMR, the Kcnq1 imprinting control region. We found expression of an antisense non-coding RNA, AK155734, in embryos and some neonatal tissues. This RNA overlaps the Tnfrsf22 and possibly the Tnfrsf23 coding regions and is also expressed with a maternal bias. We were interested in exploring the evolutionary origins of the three Tnfrsf genes, because they are absent in the orthologous human Kcnq1 domain. To determine whether the genes were deleted from humans or acquired in the rodent lineage, we performed phylogenetic analyses. Our data suggest that TNFRSF sequences were duplicated and/or degenerated or eliminated from the KCNQ1 region several times during the evolution of mammals. In humans, multiple mutations (point mutations and/or deletions) have accumulated on the ancestral TNFRSF, leaving a single short non-functional sequence. PMID:22595876

Esperon, Elena de la Casa; Cordier, Gaelle; Engel, Nora



PCR detection of retinoblastoma gene deletions in radiation-induced mouse lung adenocarcinomas  

SciTech Connect

From 1971--1986, Argonne National Laboratory conducted a series of large-scale studies of tumor incidence in 40,000 BCF{sub 1} mice irradiated with {sup 60}Co {gamma}-rays or JANUS fission-spectrum neutrons. Polymerase chain reaction (PCR) technique was used to detect deletions in the mouse retinoblastoma (mRb) gene. Six mRb gene exon fragments were amplified in a 40-cycle, 3-temperature PCR protocol. Absence of any of these fragments on a Southern blot indicated a deletion of that portion of the mRb gene. Tumors chosen for analysis were lung adenocarcinomas that were judged to be the cause of death in post-mortem analyses. Spontaneous tumors as well as those from irradiated mice were analyzed for mRb deletions. In all normal mouse tissues studies all six mRb exon fragments were present on Southern blots. Tumors in six neutron-irradiated mice also had no mRb deletions. However, 1 of 6 tumors from {gamma}-irradiated mice and 6 of 18 spontaneous tumors from unirradiated mice showed a deletion in one or both mRb alleles. All deletions detected were in the 5{prime} region of the mRb gene.

Churchill, M.E.; Gemmell, M.A.; Woloschak, G.E.



A short upstream promoter region mediates transcriptional regulation of the mouse doublecortin gene in differentiating neurons  

PubMed Central

Background Doublecortin (Dcx), a MAP (Microtubule-Associated Protein), is transiently expressed in migrating and differentiating neurons and thereby characterizes neuronal precursors and neurogenesis in developing and adult neurogenesis. In addition, reduced Dcx expression during development has been related to appearance of brain pathologies. Here, we attempt to unveil the molecular mechanisms controlling Dcx gene expression by studying its transcriptional regulation during neuronal differentiation. Results To determine and analyze important regulatory sequences of the Dcx promoter, we studied a putative regulatory region upstream from the mouse Dcx coding region (pdcx2kb) and several deletions thereof. These different fragments were used in vitro and in vivo to drive reporter gene expression. We demonstrated, using transient expression experiments, that pdcx2kb is sufficient to control specific reporter gene expression in cerebellar cells and in the developing brain (E14.5). We determined the temporal profile of Dcx promoter activity during neuronal differentiation of mouse embryonic stem cells (mESC) and found that transcriptional activation of the Dcx gene varies along with neuronal differentiation of mESC. Deletion experiments and sequence comparison of Dcx promoters across rodents, human and chicken revealed the importance of a highly conserved sequence in the proximal region of the promoter required for specific and strong expression in neuronal precursors and young neuronal cells. Further analyses revealed the presence in this short sequence of several conserved, putative transcription factor binding sites: LEF/TCF (Lymphoid Enhancer Factor/T-Cell Factor) which are effectors of the canonical Wnt pathway; HNF6/OC2 (Hepatocyte Nuclear Factor-6/Oncecut-2) members of the ONECUT family and NF-Y/CAAT (Nuclear Factor-Y). Conclusions Studies of Dcx gene regulatory sequences using native, deleted and mutated constructs suggest that fragments located upstream of the Dcx coding sequence are sufficient to induce specific Dcx expression in vitro: in heterogeneous differentiated neurons from mESC, in primary mouse cerebellar neurons (PND3) and in organotypic slice cultures. Furthermore, a region in the 3'-end region of the Dcx promoter is highly conserved across several species and exerts positive control on Dcx transcriptional activation. Together, these results indicate that the proximal 3'-end region of the mouse Dcx regulatory sequence is essential for Dcx gene expression during differentiation of neuronal precursors. PMID:20509865



Transcriptional Regulation of Mouse PXR Gene: An Interplay of Transregulatory Factors  

PubMed Central

Pregnane X Receptor (PXR) is an important ligand-activated nuclear receptor functioning as a ‘master regulator’ of expression of phase I, phase II drug metabolizing enzymes, and members of the drug transporters. PXR is primarily expressed in hepatic tissues and to lesser extent in other non-hepatic tissues both in human and in mice. Although its expression profile is well studied but little is known about the regulatory mechanisms that govern PXR gene expression in these cells. In the present study, we have cloned and characterized over 5 kb (?4963 to +54) region lying upstream of mouse PXR transcription start site. Promoter-reporter assays revealed that the proximal promoter region of up to 1 kb is sufficient to support the expression of PXR in the mouse liver cell lines. It was evident that the 500 bp proximal promoter region contains active binding sites for Ets, Tcf, Ikarose and nuclear factor families of transcription factors. Electrophoretic mobility shift assays demonstrated that the minimal region of 134 bp PXR promoter was able to bind Ets-1 and ?-catenin proteins. This result was further confirmed by chromatin immunoprecipitation analysis. In summary, the present study identified a promoter region of mouse PXR gene and the transregulatory factors responsible for PXR promoter activity. The results presented herein are expected to provide important cues to gain further insight into the regulatory mechanisms of PXR function. PMID:22952895

Kumari, Sangeeta; Mukhopadhyay, Gauranga; Tyagi, Rakesh K.



Acat1 knockdown gene therapy decreases amyloid-? in a mouse model of Alzheimer's disease.  


Both genetic inactivation and pharmacological inhibition of the cholesteryl ester synthetic enzyme acyl-CoA:cholesterol acyltransferase 1 (ACAT1) have shown benefit in mouse models of Alzheimer's disease (AD). In this study, we aimed to test the potential therapeutic applications of adeno-associated virus (AAV)-mediated Acat1 gene knockdown in AD mice. We constructed recombinant AAVs expressing artificial microRNA (miRNA) sequences, which targeted Acat1 for knockdown. We demonstrated that our AAVs could infect cultured mouse neurons and glia and effectively knockdown ACAT activity in vitro. We next delivered the AAVs to mouse brains neurosurgically, and demonstrated that Acat1-targeting AAVs could express viral proteins and effectively diminish ACAT activity in vivo, without inducing appreciable inflammation. We delivered the AAVs to the brains of 10-month-old AD mice and analyzed the effects on the AD phenotype at 12 months of age. Acat1-targeting AAV delivered to the brains of AD mice decreased the levels of brain amyloid-? and full-length human amyloid precursor protein (hAPP), to levels similar to complete genetic ablation of Acat1. This study provides support for the potential therapeutic use of Acat1 knockdown gene therapy in AD. PMID:23774792

Murphy, Stephanie R; Chang, Catherine Cy; Dogbevia, Godwin; Bryleva, Elena Y; Bowen, Zachary; Hasan, Mazahir T; Chang, Ta-Yuan



Using mouse models of autism spectrum disorders to study the neurotoxicology of gene-environment interactions.  


To better study the role of genetics in autism, mouse models have been developed which mimic the genetics of specific autism spectrum and related disorders. These models have facilitated research on the role genetic susceptibility factors in the pathogenesis of autism in the absence of environmental factors. Inbred mouse strains have been similarly studied to assess the role of environmental agents on neurodevelopment, typically without the complications of genetic heterogeneity of the human population. What has not been as actively pursued, however, is the methodical study of the interaction between these factors (e.g., gene and environmental interactions in neurodevelopment). This review suggests that a genetic predisposition paired with exposure to environmental toxicants plays an important role in the etiology of neurodevelopmental disorders including autism, and may contribute to the largely unexplained rise in the number of children diagnosed with autism worldwide. Specifically, descriptions of the major mouse models of autism and toxic mechanisms of prevalent environmental chemicals are provided followed by a discussion of current and future research strategies to evaluate the role of gene and environment interactions in neurodevelopmental disorders. PMID:23010509

Schwartzer, Jared J; Koenig, Claire M; Berman, Robert F



The Mmachc gene is required for pre-implantation embryogenesis in the mouse.  


Patients with mutations in MMACHC have the autosomal recessive disease of cobalamin metabolism known as cblC. These patients are unable to convert cobalamin into the two active forms, methylcobalamin and adenosylcobalamin and consequently have elevated homocysteine and methylmalonic acid in blood and urine. In addition, some cblC patients have structural abnormalities, including congenital heart defects. MMACHC is conserved in the mouse and shows tissue and stage-specific expression pattern in midgestation stage embryos. To create a mouse model of cblC we generated a line of mice with a gene-trap insertion in intron 1 of the Mmachc gene, (Mmachc(Gt(AZ0348)Wtsi)). Heterozygous mice show a 50% reduction of MMACHC protein, and have significantly higher levels of homocysteine and methylmalonic acid in their blood. The Mmachc(Gt) allele was inherited with a transmission ratio distortion in matings with heterozygous animals. Furthermore, homozygous Mmachc(Gt) embryos were not found after embryonic day 3.5 and these embryos were unable to generate giant cells in outgrowth assays. Our findings confirm that cblC is modeled in mice with reduced levels of Mmachc and suggest an early requirement for Mmachc in mouse development. PMID:24889031

Moreno-Garcia, Maira A; Pupavac, Mihaela; Rosenblatt, David S; Tremblay, Michel L; Jerome-Majewska, Loydie A



Using mouse models of autism spectrum disorders to study the neurotoxicology of gene-environment interactions  

PubMed Central

To better study the role of genetics in autism, mouse models have been developed which mimic the genetics of specific autism spectrum and related disorders. These models have facilitated research on the role genetic susceptibility factors in the pathogenesis of autism in the absence of environmental factors. Inbred mouse strains have been similarly studied to assess the role of environmental agents on neurodevelopment, typically without the complications of genetic heterogeneity of the human population. What has not been as actively pursued, however, is the methodical study of the interaction between these factors (e.g., gene and environmental interactions in neurodevelopment). This review suggests that a genetic predisposition paired with exposure to environmental toxicants play an important role in the etiology of neurodevelopmental disorders including autism, and may contribute to the largely unexplained rise in the number of children diagnosed with autism worldwide. Specifically, descriptions of the major mouse models of autism and toxic mechanisms of prevalent environmental chemicals are provided followed by a discussion of current and future research strategies to evaluate the role of gene and environment interactions in neurodevelopmental disorders. PMID:23010509

Schwartzer, Jared J.; Koenig, Claire M.; Berman, Robert F



Molecular characterization of a mouse prostaglandin D receptor and functional expression of the cloned gene.  

PubMed Central

Prostanoid receptors belong to the family of G protein-coupled receptors with seven transmembrane domains. By taking advantage of nucleotide sequence homology among the prostanoid receptors, we have isolated and identified a cDNA fragment and its gene encoding a mouse prostaglandin (PG) D receptor by reverse transcription polymerase chain reaction and gene cloning. This gene codes for a polypeptide of 357 amino acids, with a calculated molecular weight of 40,012. The deduced amino acid sequence has a high degree of similarity with the mouse PGI receptor and the EP2 subtype of the PGE receptor, which together form a subgroup of the prostanoid receptors. Chinese hamster ovary cells stably expressing the gene showed a single class of binding sites for [#H]PGD2 with a Kd of 40 nM. This binding was displaced by unlabeled ligands in the following order: PGD2 > BW 245C (a PGD agonist) > BW A868C (a PGD antagonist) > STA2 (a thromboxane A2 agonist). PGE2, PGF2 alpha, and iloprost showed little displacement activity at concentrations up to 10 microM. PGD2 and BW 245C also increased cAMP levels in Chinese hamster ovary cells expressing the receptor, in a concentration-dependent manner. BW A868C showed a partial agonist activity in the cAMP assay. Northern blotting analysis with mouse poly(A)+ RNA identified a major mRNA species of 3.5 kb that was most abundantly expressed in the ileum, followed by lung, stomach, and uterus. Images PMID:7972033

Hirata, M; Kakizuka, A; Aizawa, M; Ushikubi, F; Narumiya, S



PCR detection of retinoblastoma gene deletions in radiation-induced mouse lung adenocarcinomas  

SciTech Connect

From 1971 to 1986, Argonne National Laboratory conducted a series of large-scale studies of tumor incidence in 40,000 BCF{sub 1} mice irradiated with {sup 60}Co {gamma} rays or JANUS fission-spectrum neutrons; normal and tumor tissues from mice in these studies were preserved in paraffin blocks. A polymerase chain reaction (PCR) technique has been developed to detect deletions in the mouse retinoblastoma (mRb) gene in the paraffin-embedded tissues. Microtomed sections were used as the DNA source in PCR reaction mixtures. Six mRb gene exon fragments were amplified in a 40-cycle, 3-temperature PCR protocol. The absence of any of these fragments (relative to control PCR products) on a Southern blot indicated a deletion of that portion of the mRb gene. The tumors chosen for analysis were lung adenocarcinomas that were judged to be the cause of death in post-mortem analyses. Spontaneous tumors as well as those from irradiated mice (569 cGy of {sup 60}Co {gamma} rays or 60 cGy of JANUS neutrons, doses that have been found to have approximately equal biological effectiveness in the BCF, mouse) were analyzed for mRb deletions. In all normal mouse tissues studies, all six mRb exon fragments were present on Southem blots. Tumors in six neutron-irradiated mice also had no mRb deletions. However, I of 6 tumors from {gamma}-irradiated mice and 6 of 18 spontaneous tumors from unirradiated mice had a deletion in one or both mRb alleles. All deletions detected were in the 5{prime} region of the mRb gene.

Churchill, M.E.; Gemmell, M.A.; Woloschak, G.E.



Maternal infection leads to abnormal gene regulation and brain atrophy in mouse offspring  

PubMed Central

Prenatal viral infection has been associated with development of schizophrenia and autism. Our laboratory has previously shown that viral infection causes deleterious effects on brain structure and function in mouse offspring following late first trimester (E9) administration of influenza virus. We hypothesized that late second trimester infection (E18) in mice may lead to a different pattern of brain gene expression and structural defects in the developing offspring. C57BL6J mice were infected on E18 with a sublethal dose of human influenza virus or sham-infected using vehicle solution. Male offsping of the infected mice were collected at P0, P14, P35 and P56, their brains removed and prefrontal cortex, hippocampus and cerebellum dissected and flash frozen. Microarray, qRT-PCR, DTI and MRI scanning, western blotting and neurochemical analysis were performed to detect differences in gene expression and brain atrophy. Expression of several genes associated with schizophrenia or autism including Sema3a, Trfr2 and Vldlr were found to be altered as were protein levels of Foxp2. E18 infection of C57BL6J mice with a sublethal dose of human influenza virus led to significant gene alterations in frontal, hippocampal and cerebellar cortices of developing mouse progeny. Brain imaging revealed significant atrophy in several brain areas and white matter thinning in corpus callosum. Finally, neurochemical analysis revealed significantly altered levels of serotonin (P14, P35), 5-Hydroxyindoleacetic acid (P14) and taurine (P35). We propose that maternal infection in mouse provides an heuristic animal model for studying the environmental contributions to genesis of schizophrenia and autism, two important examples of neurodevelopmental disorders. PMID:18248790

Fatemi, S. Hossein; Reutiman, Teri J.; Folsom, Timothy D.; Huang, Hao; Oishi, Kenichi; Mori, Susumu; Smee, Donald F.; Pearce, David A.; Winter, Christine; Sohr, Reinhard; Juckel, Georg




PubMed Central

Pretreatment of mice with the peroxisome proliferator clofibrate (CFB) protects against acetaminophen (APAP)-induced hepatotoxicity. Previous studies have shown that activation of the nuclear peroxisome proliferator activated receptor ? (PPAR?) is required for this effect. The present study utilizes gene expression profile analysis to identify potential pathways contributing to PPAR?-mediated hepatoprotection. Gene expression profiles were compared between wild type and PPAR?-null mice pretreated with vehicle or CFB (500mg/kg, i.p., daily for 10 days) and then challenged with APAP (400mg/kg, p.o.). Total hepatic RNA was isolated 4 h after APAP treatment and hybridized to Affymetrix Mouse Genome MGU74v2.0 GeneChips. Gene expression analysis was performed utilizing GeneSpring ® software. Our analysis identified 53 genes of interest including vanin-1, cell-cycle regulators, lipid-metabolizing enzymes, and aldehyde dehydrogenase 2, an acetaminophen binding protein. Vanin-1 could be important for CFB-mediated hepatoprotection because this protein is involved in the synthesis of cysteamine and cystamine. These are potent antioxidants capable of ameliorating APAP toxicity in rodents and humans. HPLC-ESI/MS/MS analysis of liver extracts indicates that enhanced vanin-1 gene expression results in elevated cystamine levels, which could be mechanistically associated with CFB-mediated hepatoprotection. PMID:17585979

Moffit, Jeffrey S; Koza-Taylor, Petra H; Holland, Ricky D; Thibodeau, Michael S; Beger, Richard D; Lawton, Michael P; Manautou, José E



Common responses in gene expression by Ephedra herba in brain and heart of mouse.  


The physiological activities of Ephedra herba have been investigated extensively, particularly in the cardiovascular and cerebrovascular systems. However, the molecular mechanisms underlying the effects of Ephedra herba on the brain and heart have yet to be thoroughly elucidated at the whole genome level. Therefore, the present study focused on the identification of the regulatory pattern of gene expression occurring in response to Ephedra herba, using microarray assays in three mouse organs - namely, the brain, heart and liver. Interestingly, the brain and heart exhibited a similar reciprocal pattern of gene expression during the early stages after the administration of Ephedra herba, whereas the liver evidenced a different gene expression profile. Moreover, pathways analysis showed that genes regulated reciprocally by Ephedra herba were associated with neural disease-related functions, such as the Parkinson's disease pathway, in both the brain and the heart. Promoter sequence analysis demonstrated that reciprocally regulated genes could be classified into subgroups on the basis of the similarity of their transcription factor binding sequences, in which temporally up-regulated genes were clustered as distinctive subgroups. In conclusion, the brain and heart responded commonly to Ephedra herba with a temporally reciprocal pattern of gene expression. PMID:21953708

Kim, Bu-Yeo; Cao, Li Hua; Kim, Jong Yeol



The mouse Fau gene: Genomic structure, chromosomal localization, and characterization of two retropseudogenes  

SciTech Connect

The Fau gene is the cellular homolog of the fox sequence of the Finkel-Biskis-Reilly murine sarcoma virus (FBR-MuSV). FBR-MuSV acquired the Fau gene by transduction in a transcriptional orientation opposite to that of the genomic Fau gene. The genomic structure of the mouse Fau gene (MMFAU) and its upstream elements have been determined and are similar to those of the human FAU gene. The gene consists of five exons and is located on chromosome 19. The first exon is not translated. The promoter region has no well-defined TATA box but contains the polypyrimidine initiator flanked by regions of high GC content (65%) and shows all of the characteristics of a housekeeping gene. The 5{prime} end of the mRNA transcript was determined by 5{prime} RACE analysis and is located, as expected, in the polypyrimidine initiator site. Furthermore, the sequences of two retropseudogenes (Fau-ps1 and Fau-ps2) are reported. Both pseudogenes are approximately 75% identical to the Fau cDNA, but both are shorter due to a deletion at the 5{prime} end and do not encode a functional protein. Fau-prs is interrupted by an AG-rich region of about 350 bp within the S30 region of the Fau cDNA. Fau-ps1 was localized on chromosome 1 and Fau-ps2 on chromosome 7. 17 refs., 1 fig., 1 tab.

Casteels, D.; Merregaert, J. [Univ. of Antwerp, Wilrijk (Belgium)] [and others] [Univ. of Antwerp, Wilrijk (Belgium); and others



Effect of Chronic Valproic Acid Treatment on Hepatic Gene Expression Profile in Wfs1 Knockout Mouse  

PubMed Central

Valproic acid (VPA) is a widely used anticonvulsant and mood-stabilizing drug whose use is often associated with drug-induced weight gain. Treatment with VPA has been shown to upregulate Wfs1 expression in vitro. Aim of the present study was to compare the effect of chronic VPA treatment in wild type (WT) and Wfs1 knockout (KO) mice on hepatic gene expression profile. Wild type, Wfs1 heterozygous, and homozygous mice were treated with VPA for three months (300?mg/kg i.p. daily) and gene expression profiles in liver were evaluated using Affymetrix Mouse GeneChip 1.0?ST array. We identified 42 genes affected by Wfs1 genotype, 10 genes regulated by VPA treatment, and 9 genes whose regulation by VPA was dependent on genotype. Among the genes that were regulated differentially by VPA depending on genotype was peroxisome proliferator-activated receptor delta (Ppard), whose expression was upregulated in response to VPA treatment in WT, but not in Wfs1 KO mice. Thus, regulation of Ppard by VPA is dependent on Wfs1 genotype. PMID:24799886

Sütt, Silva; Kõks, Sulev; Schalkwyk, Leonard C.; Fernandes, Catherine; Vasar, Eero



Chromosomal locations of the human and mouse genes for precursors of epidermal growth factor and the. beta. subunit of nerve growth factor  

SciTech Connect

DNA probes for pre-pro-epidermal growth factor (EGF) and the precursor of the ..beta.. subunit of nerve growth factor (NGF) were used to chromosomally map human and mouse EGF and NGF genes in panels of human-mouse and mouse-Chinese hamster somatic cell hybrids. The EGF and NGF genes were mapped to human chromosomes 4 and 1, respectively, by using human-mouse cell hybrids. A combination of regional mapping using a chromosome 1 translocation and comparative gene mapping suggests that the human NGF gene is in the p21-p22.1 region of chromosome 1. In mouse-Chinese hamster cell hybrids, both genes were assigned to mouse chromosome 3. A knowledge of the chromosomal assignment of these genes should help in our understanding of their regulation and role in development and disease.

Zabel, B.U.; Eddy, R.L.; Lalley, P.A.; Scott, J.; Bell, G.I.; Shows, T.B.



Gene Expression Analysis of Mouse Embryonic Stem Cells Following Levitation in an Ultrasound Standing Wave Trap  

PubMed Central

In the present paper, gene expression analysis of mouse embryonic stem (ES) cells levitated in a novel ultrasound standing wave trap (USWT) (Bazou et al. 2005a) at variable acoustic pressures (0.08–0.85 MPa) and times (5–60 min) was performed. Our results showed that levitation of ES cells at the highest employed acoustic pressure for 60 min does not modify gene expression and cells maintain their pluripotency. Embryoid bodies (EBs) also expressed the early and late neural differentiation markers, which were also unaffected by the acoustic field. Our results suggest that the ultrasound trap microenvironment is minimally invasive as the biologic consequences of ES cell replication and EB differentiation proceed without significantly affecting gene expression. The technique holds great promise in safe cell manipulation techniques for a variety of applications including tissue engineering and regenerative medicine. (E-mail: PMID:21208732

Bazou, Despina; Kearney, Roisin; Mansergh, Fiona; Bourdon, Celine; Farrar, Jane; Wride, Michael



Identification of peroxisome-proliferator responsive element in the mouse HSL gene  

SciTech Connect

Hormone-sensitive lipase (HSL) catalyzes the rate-limiting step of lipolysis in adipose tissue. Several studies suggest that protein phosphorylation regulates the HSL enzymatic activity. On the other hand, the precise mechanism of the transcriptional regulation of the HSL gene remains to be elucidated. Here, we identified a functional peroxisome-proliferator responsive element (PPRE) in the mouse HSL promoter by reporter assay in CV-1 cells using serial deletion and point mutants of the 5'-flanking region. Chromatin immunoprecipitation (ChIP) analysis revealed that both peroxisome-proliferator activated receptor (PPAR{gamma}) and retinoid X receptor (RXR{alpha}) interacted with the region. Binding of the PPAR{gamma}/RXR{alpha} heterodimer to the PPRE sequence was also confirmed by electrophoretic mobility shift assay. These results indicate that the HSL gene is transcriptionally regulated by PPAR{gamma}/RXR{alpha} heterodimer, and suggest that a cis-acting element regulates the HSL gene expression.

Yajima, Hiroaki [Central Laboratories for Frontier Technology, Kirin Brewery Co., Ltd., Kanazawa-ku Fukuura 1-13-5, Yokohama 236-0004 (Japan)]. E-mail:; Kobayashi, Yumie [Central Laboratories for Frontier Technology, Kirin Brewery Co., Ltd., Kanazawa-ku Fukuura 1-13-5, Yokohama 236-0004 (Japan); Kanaya, Tomoka [Central Laboratories for Frontier Technology, Kirin Brewery Co., Ltd., Kanazawa-ku Fukuura 1-13-5, Yokohama 236-0004 (Japan); Horino, Yoko [Central Laboratories for Frontier Technology, Kirin Brewery Co., Ltd., Kanazawa-ku Fukuura 1-13-5, Yokohama 236-0004 (Japan)



Stereotaxic injection of a viral vector for conditional gene manipulation in the mouse spinal cord.  


Intraparenchymal injection of a viral vector enables conditional gene manipulation in distinct populations of neurons or particular regions of the central nervous system. We demonstrate a stereotaxic injection technique that allows targeted gene expression or silencing in the dorsal horn of the mouse spinal cord. The surgical procedure is brief. It requires laminectomy of a single vertebra, providing for quick recovery of the animal and unimpaired motility of the spine. Controlled injection of a small vector suspension volume at low speed and use of a microsyringe with beveled glass cannula minimize the tissue lesion. The local immune response to the vector depends on the intrinsic properties of the virus employed; in our experience, it is minor and short-lived when a recombinant adeno-associated virus is used. A reporter gene such as enhanced green fluorescent protein facilitates monitoring spatial distribution of the vector, and the efficacy and cellular specificity of the transfection. PMID:23542888

Inquimbert, Perrine; Moll, Martin; Kohno, Tatsuro; Scholz, Joachim



A change of expression in the conserved signaling gene MKK7 is associated with a selective sweep in the western house mouse Mus  

E-print Network

in the western house mouse Mus musculus domesticus B. HARR,* C. VOOLSTRA,* T. J. A. J. HEINEN,* J. F. BAINES,* R an analysis of gene expression differences between subspe- cies of the house mouse Mus musculus: adaptation; gene expression; microarray; mus musculus; selective sweep. Abstract Changes in gene expression

Nachman, Michael


HER2/neu DNA vaccination by intradermal gene delivery in a mouse tumor model  

PubMed Central

DNA vaccines are potential tools for the induction of immune responses against both infectious disease and cancer. The dermal application of DNA vaccines is of particular interest since the epidermal and dermal layers of the skin are characterized by an abundance of antigen-presenting cells (APCs). The aim of our study was to compare tumor protection as obtained by two different methods of intradermal DNA delivery (gene gun and jet injector) in a well-established HER2/neu mouse tumor model. BALB/c mice were immunized twice with a HER2/neu-coding plasmid by gene gun or jet injector. Mice were then subcutaneously challenged with HER2/neu+ syngeneic D2F2/E2 tumor cells. Protection against subsequent challenges with tumor cells as well as humoral and T-cell immune responses induced by the vaccine were monitored. Gene gun immunization was far superior to jet injector both in terms of tumor protection and induction of HER2/neu-specific immune responses. After gene gun immunization, 60% of the mice remained tumor-free until day 140 as compared with 25% after jet injector immunization. Furthermore, gene gun vaccination was able to induce both a strong TH1-polarized T-cell response with detectable cytotoxic T-lymphocyte (CTL) activity and a humoral immune response against HER2/neu, whereas the jet injector was not. Although the disadvantages that were associated with the use of the jet injector in our model may be overcome with methodological modifications and/or in larger animals, which exhibit a thicker skin and/or subcutaneous muscle tissue, we conclude that gene gun delivery constitutes the method of choice for intradermal DNA delivery in preclinical mouse models and possibly also for the clinical development of DNA-based vaccines. PMID:23264900

Nguyen-Hoai, Tam; Kobelt, Dennis; Hohn, Oliver; Vu, Minh D.; Schlag, Peter M.; Dorken, Bernd; Norley, Steven; Lipp, Martin; Walther, Wolfgang; Pezzutto, Antonio; Westermann, Jorg



Of mice and Marfan: genetic linkage analyses of the fibrillin genes, Fbn1 and Fbn2 , in the mouse genome  

Microsoft Academic Search

The fibrillin genes, FBN1 and FBN2, encode large extracellular matrix glycoproteins involved in the structure and function of microfibrils. Mutations in FBN1 are found in patients with Marfan syndrome, a heritable connective tissue disease that primarily affects the cardiovascular, ocular, and skeletal systems. We extended the studies of these genes by determining their chromosomal position in the mouse genome. Restriction

C. Goldstein; P. Liaw; S. A. Jimenez; A. M. Buchberg; L. D. Siracusa



Transcriptional activation of mouse cytosolic chaperonin CCT subunit genes by heat shock factors HSF1 and HSF2  

Microsoft Academic Search

The chaperonin containing TCP-1 (CCT) is a eukaryotic molecular chaperone consisting of eight subunit species and assists in the folding of cytosolic proteins. We show here that all eight mouse CCT subunit genes contain sequences called heat shock elements for binding heat shock transcription factors (HSFs) by electrophoretic mobility shift assays and that these genes are transcriptionally activated by HSFs

Hiroshi Kubota; Shuji Matsumoto; Shin-ichi Yokota; Hideki Yanagi; Takashi Yura



Multi-stage analysis of gene expression and transcription regulation in C57/B6 mouse liver development  

E-print Network

Multi-stage analysis of gene expression and transcription regulation in C57/B6 mouse liver history: Received 7 August 2008 Accepted 12 October 2008 Available online 10 December 2008 Keywords: Liver development Microarray Gene expression Function Transcriptional regulation The liver performs a number


Gene Expression Profile Change and Associated Physiological and Pathological Effects in Mouse Liver Induced by Fasting and Refeeding  

Microsoft Academic Search

Food availability regulates basal metabolism and progression of many diseases, and liver plays an important role in these processes. The effects of food availability on digital gene expression profile, physiological and pathological functions in liver are yet to be further elucidated. In this study, we applied high-throughput sequencing technology to detect digital gene expression profile of mouse liver in fed,

Fang Zhang; Xiang Xu; Ben Zhou; Zhishui He; Qiwei Zhai



Gene Expression in Mouse Ovarian Follicle Development In Vivo versus an Ex Vivo Alginate Culture System  

PubMed Central

Ovarian follicle maturation results from a complex interplay of endocrine, paracrine, and direct cell-cell interactions. This study compared the dynamic expression of key developmental genes during folliculogenesis in vivo and during in vitro culture in a three-dimensional alginate hydrogel system. Candidate gene expression profiles were measured within mouse two-layered secondary follicles (2LS), multi-layered secondary follicles (MLS), and cumulus-oocyte complexes (COCs). The expression of 20 genes involved in endocrine communication, growth signaling, and oocyte development was investigated by real-time PCR. Gene product levels were compared between i) follicles of similar stage and ii) COCs derived either in vivo or by in vitro culture. For follicles cultured for 4 days, the expression pattern and the expression level of 12 genes was the same in vivo and in vitro. Some endocrine (Cyp19a1, Inh?a) and growth related genes (Bmp15, Kitl, Tgf?r2) were down-regulated relative to in vivo follicles. For COCs obtained from cultured follicles, endocrine related genes (Inh? and Inh?a) had increased expression relative to in vivo counterparts, whereas growth related genes (Bmp15, Gdf9, Kit) and zona pellucida genes were decreased. However, most of the oocyte specific genes (e.g., Figl?, Jag1, Mater) were expressed in vitro at the same level and with the same pattern as in vivo-derived follicles. These studies establish the similarities and differences between in vivo and in vitro cultured follicles, guiding the creation of environments that maximize follicle development and oocyte quality. PMID:21610168

Parrish, Elizabeth M.; Siletz, Anaar; Xu, Min; Woodruff, Teresa K.; Shea, Lonnie D.



Transfer of nonselectable genes into mouse teratocarcinoma cells and transcription of the transferred human. beta. -globin gene  

SciTech Connect

Teratocarcinoma (TCC) stem cells can function as vehicles for the introduction of specific recombinant genes into mice. Because most genes do not code for a selectable marker, the authors investigated the transformation efficiency of vectors with a linked selectable gene. In one series, TCC cells first selected for thymidine kinase deficiency were treated with DNA from the plasmid vector PtkH..beta..1 containing the human genomic ..beta..-globin gene and the thymidine kinase gene of herpes simplex virus. A high transformation frequency was obtained after selection in hypoxanthine-aminopterin-thymidine medium. Hybridization tests revealed that the majority of transformants had intact copies of the human gene among three to six total copies per cell. These were associated with cellular DNA sequences as judged from the presence of additional new restriction fragments and from stability of the sequences in tumors produced by injecting the cells subcutaneously. Total polyadenylate-containing RNA from cell cultures of two out of four transformants examined showed hybridization to the human gene probe: one RNA species resembled mature human ..beta..-globin mRNA transcripts; the others were of larger size. In differentiating tumors, various tissues, including hematopoietic cells of TCC provenance could be found. In a second model set of experiments, wild-type TCC cells were used to test a dominant-selection scheme with pSV-gpt vectors. Numerous transformants were isolated, and their transfected DNA was apparently stably integrated. Thus, any gene of choice can be transferred into TCC stem cells even without mutagenesis of the cells, and selected cell clones can be characterized. Cells of interest may then be introduced into early embryos to produce new mouse strains with predetermined genetic changes.

Wagner, E.F.; Mintz, B.



Microarray analysis of gene expression in mouse (strain 129) embryonic stem cells after typical synthetic musk exposure.  


Synthetic musks are widely used in personal-care products and can readily accumulate in the adipose tissue, breast milk, and blood of humans. In this study, the Affymetrix Mouse Genome GeneChip was used to identify alterations in gene expression of embryonic stem cells from the 129 strain of the laboratory mouse after treatment with the synthetic musk tonalide (AHTN). Among the 45,037 transcripts in the microarray, 2,879 genes were differentially expressed. According to the microarray analysis, the potential influence of AHTN on the development to embryo should be of concern, and the toxicological effects of it and related musk compounds should be studied further. PMID:23099888

Shi, Jiachen; Li, Ming; Jiao, Zhihao; Zhang, Jing; Feng, Yixing; Shao, Bing



Vertebrate caudal gene expression gradients investigated by use of chick cdx-A\\/ lacZ and mouse cdx-1\\/ lacZ reporters in transgenic mouse embryos: evidence for an intron enhancer  

Microsoft Academic Search

The vertebrate caudal proteins, being upstream regulators of the Hox genes, play a role in establishment of the body plan. We describe analysis of two orthologous caudal genes (chick cdx-A and mouse cdx-1) by use of lacZ reporters expressed in transgenic mouse embryos. The expression patterns show many similarities to the expression of endogenous mouse cdx-1. At 8.7 days, cdx\\/lacZ

Stephen J. Gaunt; Deborah Drage; Adam Cockley



DNA methylation map of mouse and human brain identifies target genes in Alzheimer's disease  

PubMed Central

The central nervous system has a pattern of gene expression that is closely regulated with respect to functional and anatomical regions. DNA methylation is a major regulator of transcriptional activity, and aberrations in the distribution of this epigenetic mark may be involved in many neurological disorders, such as Alzheimer’s disease. Herein, we have analysed 12 distinct mouse brain regions according to their CpG 5’-end gene methylation patterns and observed their unique epigenetic landscapes. The DNA methylomes obtained from the cerebral cortex were used to identify aberrant DNA methylation changes that occurred in two mouse models of Alzheimer’s disease. We were able to translate these findings to patients with Alzheimer’s disease, identifying DNA methylation-associated silencing of three targets genes: thromboxane A2 receptor (TBXA2R), sorbin and SH3 domain containing 3 (SORBS3) and spectrin beta 4 (SPTBN4). These hypermethylation targets indicate that the cyclic AMP response element-binding protein (CREB) activation pathway and the axon initial segment could contribute to the disease. PMID:24030951

Sanchez-Mut, Jose V.; Aso, Ester; Panayotis, Nicolas; Lott, Ira; Dierssen, Mara; Rabano, Alberto; Urdinguio, Rocio G.; Fernandez, Agustin F.; Astudillo, Aurora; Martin-Subero, Jose I.; Balint, Balazs; Fraga, Mario F.; Gomez, Antonio; Gurnot, Cecile; Roux, Jean-Christophe; Avila, Jesus; Hensch, Takao K.; Ferrer, Isidre



Activation of transgene-specific T cells following lentivirus-mediated gene delivery to mouse lung.  


Integrating lentiviral vectors based on the human immunodeficiency virus type-1 (HIV-1) can transduce quiescent cells, which in lung account for almost 95% of the epithelial cell population. Pseudotyping lentiviral vectors with the envelope glycoprotein from the Ebola Zaire virus, the lymphocytic choriomeningitis virus (LCMV), the Mokola virus, and the vesicular stomatitis virus (VSV-G) resulted in transduction of mouse alveolar epithelium, but gene expression in the lung of C57BL/6 and BALB/c mice waned within 90 days of vector injection. Intratracheal delivery of the four pseudotyped lentiviral vectors resulted in transgene-specific T-cell activation in both mouse strains, albeit lower than that achieved by intramuscular injection of the vectors. We performed an adoptive transfer of luciferase-specific T cells, isolated from spleen or lung of donor mice injected with VSV-G-pseudotyped lentivirus vector expressing luciferase into the muscle or lung, respectively, into recipient recombination-activating gene (RAG)-deficient mice transduced in lung with adenovirus expressing firefly luciferase (ffluc2). Gene expression declined within 7 days of adoptive transfer approaching background levels by day 36. Taken together, our results suggest that the loss of transduced cells in lung is due to VSV-G.HIV vector-mediated activation of transgene-specific T cells rather than as result of normal turnover of airway cells. PMID:19724265

Limberis, Maria P; Bell, Christie L; Heath, Jack; Wilson, James M



Identification of candidate lung cancer susceptibility genes in mouse using oligonucleotide arrays  

PubMed Central

We applied microarray gene expression profiling to lungs from mouse strains having variable susceptibility to lung tumour development as a means to identify, within known quantitative trait loci (QTLs), candidate genes responsible for susceptibility or resistance to lung cancer. At least eight chromosomal regions of mice have been mapped and verified to be linked with lung tumour susceptibility or resistance. In this study, high density oligonucleotide arrays were used to measure the relative expression levels of >36 000 genes and ESTs in lung tissues of A/J, BALB/cJ, SM/J, C3H/HeJ, and C57BL/6J mice. A number of differentially expressed genes were found in each of the lung cancer susceptibility QTLs. Bioinformatic analysis of the differentially expressed genes located within QTLs produced 28 susceptibility candidates and 22 resistance candidates. These candidates may be extremely helpful in the ultimate identification of the precise genes responsible for lung tumour susceptibility or resistance in mice and, through follow up, humans. Complete data sets are available at PMID:12205107

Lemon, W; Bernert, H; Sun, H; Wang, Y; You, M



Analysis of metabolic and gene expression changes after hydrodynamic DNA injection into mouse liver.  


The hydrodynamic injection in mice tail vein of a plasmid (40 µg DNA) bearing the human ?1-antitrypsin gene mediates: a) good liver gene transfer resulting in therapeutic plasma levels of human protein (1 mg/ml, approximately) from days 1-10 after injection; b) low liver injury as demonstrated by a poor and transient increase of aspartate aminotransferase (AST) and alanine transaminase (ALT) in mouse plasma; 3) limited expression and metabolic changes in host liver genes and metabolites as evaluated on days 2 and 10 after injection. Groups of three mice were uninjected (control) or hydrodynamically injected with saline or plasmid DNA and then sacrificed on days 2 and 10 after injection. The results of principal component analysis (PCA) show, both in expression microarray and metabolomic analysis, that changes between control and hydrodynamically injected groups are not dramatic and tend to normalize after 10 d. The differences are even smaller between DNA and saline hydrodynamically injected mice. Hydrodynamic injection induces a complex but limited gene expression and metabolic change which includes variations in molecules related to energy metabolism and stress response. The results contribute to support that hydrodynamic method is a safe procedure of liver gene transfer but the long-term effect of hydrodynamic gene transfer procedure, remains to be studied. PMID:21212539

Herrero, Maria Jose; Monleon, Daniel; Morales, Jose Manuel; Mata, Manuel; Serna, Eva; Aliño, Salvador Francisco



Dominant Cone-Rod Dystrophy: A Mouse Model Generated by Gene Targeting of the GCAP1/Guca1a Gene  

PubMed Central

Cone dystrophy 3 (COD3) is a severe dominantly inherited retinal degeneration caused by missense mutations in GUCA1A, the gene encoding Guanylate Cyclase Activating Protein 1 (GCAP1). The role of GCAP1 in controlling cyclic nucleotide levels in photoreceptors has largely been elucidated using knock-out mice, but the disease pathology in these mice cannot be extrapolated directly to COD3 as this involves altered, rather than loss of, GCAP1 function. Therefore, in order to evaluate the pathology of this dominant disorder, we have introduced a point mutation into the murine Guca1a gene that causes an E155G amino acid substitution; this is one of the disease-causing mutations found in COD3 patients. Disease progression in this novel mouse model of cone dystrophy was determined by a variety of techniques including electroretinography (ERG), retinal histology, immunohistochemistry and measurement of cGMP levels. It was established that although retinal development was normal up to 3 months of age, there was a subsequent progressive decline in retinal function, with a far greater alteration in cone than rod responses, associated with a corresponding loss of photoreceptors. In addition, we have demonstrated that accumulation of cyclic GMP precedes the observed retinal degeneration and is likely to contribute to the disease mechanism. Importantly, this knock-in mutant mouse has many features in common with the human disease, thereby making it an excellent model to further probe disease pathogenesis and investigate therapeutic interventions. PMID:21464903

Buch, Prateek K.; Mihelec, Marija; Cottrill, Phillippa; Wilkie, Susan E.; Pearson, Rachael A.; Duran, Yanai; West, Emma L.; Michaelides, Michel; Ali, Robin R.; Hunt, David M.



Spatial and Temporal Analysis of Gene Expression during Growth and Fusion of the Mouse Facial Prominences  

PubMed Central

Orofacial malformations resulting from genetic and/or environmental causes are frequent human birth defects yet their etiology is often unclear because of insufficient information concerning the molecular, cellular and morphogenetic processes responsible for normal facial development. We have, therefore, derived a comprehensive expression dataset for mouse orofacial development, interrogating three distinct regions – the mandibular, maxillary and frontonasal prominences. To capture the dynamic changes in the transcriptome during face formation, we sampled five time points between E10.5–E12.5, spanning the developmental period from establishment of the prominences to their fusion to form the mature facial platform. Seven independent biological replicates were used for each sample ensuring robustness and quality of the dataset. Here, we provide a general overview of the dataset, characterizing aspects of gene expression changes at both the spatial and temporal level. Considerable coordinate regulation occurs across the three prominences during this period of facial growth and morphogenesis, with a switch from expression of genes involved in cell proliferation to those associated with differentiation. An accompanying shift in the expression of polycomb and trithorax genes presumably maintains appropriate patterns of gene expression in precursor or differentiated cells, respectively. Superimposed on the many coordinated changes are prominence-specific differences in the expression of genes encoding transcription factors, extracellular matrix components, and signaling molecules. Thus, the elaboration of each prominence will be driven by particular combinations of transcription factors coupled with specific cell:cell and cell:matrix interactions. The dataset also reveals several prominence-specific genes not previously associated with orofacial development, a subset of which we externally validate. Several of these latter genes are components of bidirectional transcription units that likely share cis-acting sequences with well-characterized genes. Overall, our studies provide a valuable resource for probing orofacial development and a robust dataset for bioinformatic analysis of spatial and temporal gene expression changes during embryogenesis. PMID:20016822

Feng, Weiguo; Leach, Sonia M.; Tipney, Hannah; Phang, Tzulip; Geraci, Mark; Spritz, Richard A.; Hunter, Lawrence E.; Williams, Trevor



The mifepristone-inducible gene regulatory system in mouse models of disease and gene therapy.  


The mifepristone (Mfp)-inducible gene regulatory system is designed to allow control of the spatiotemporal expression of transgenes in vivo in a ligand-dependent manner. This regulatory system is composed of two components: (1) a chimeric transactivator protein that activates transgene transcription only in the presence of the progesterone antagonist Mfp, and (2) a target transgene placed in the context of a promoter which is responsive only to the Mfp-bound chimeric transactivator. Incorporation of the components of the Mfp-inducible gene regulatory system into transgenic mice has resulted in the establishment of several novel, Mfp-dependent models of disease. Similarly, adaptation of the Mfp-inducible system for use in gene knockout models has resulted in the development of new gene ablation technology which is both tissue-specific and Mfp-dependent. Additionally, the Mfp-inducible gene regulatory system has been used in animal experiments involving somatic gene therapy, where it has shown considerable promise in the regulation of both reporter and therapeutic gene expression. This review focuses on recent application of the Mfp-inducible system to transgenic models, gene knockout models, and somatic gene therapy experiments. In so doing, it demonstrates the considerable promise that future use of this system holds for better understanding and treatment of human disease. PMID:12240599

Ngan, Elly S W; Schillinger, Kurt; DeMayo, Francesco; Tsai, Sophia Y



Genetic mapping of the adenine nucleotide translocase-2 gene (Ant2) to the mouse proximal X chromosome  

SciTech Connect

Adenine nucleotide translocases are mitochondrial membrane proteins encoded by a small dispersed multigene family. We have previously cloned cDNAs derived from the mouse adenine nucleotide translocase-1 and -2 genes (Ant1 and Ant2) and assigned to the loci to mouse chromosomes 8 and X, respectively. Here we describe the genomic organization of the Ant2 gene and its regional map position on the X chromosome, which was determined through linkage analysis using an interspecific backcross between Mus musculus and Mus spretus inbred strains. Ant2 cosegregates with DXMit49 and DXMit50 and lies distal to Agtr2 in the proximal region of the mouse X chromosome. This map assignment further defines a region of conserved synteny between human Xq22-q25 and the mouse proximal X chromosome. 11 refs., 2 figs.

Ellison, J.W.; Salido, E.C.; Shapiro, L.J. [Univ. of California, San Francisco, CA (United States)] [Univ. of California, San Francisco, CA (United States)



Metallothionein Protection of Cadmium Toxicity  

PubMed Central

The discovery of the cadmium (Cd)-binding protein from horse kidney in 1957 marked the birth of research on this low-molecular weight, cysteine-rich protein called metallothionein (MT) in Cd toxicology. MT plays minimal roles in the gastrointestinal absorption of Cd, but MT plays important roles in Cd retention in tissues and dramatically decreases billiary excretion of Cd. Cd-bound to MT is responsible for Cd accumulation in tissues and the long biological half-life of Cd in the body. Induction of MT protects against acute Cd-induced lethality, as well as acute toxicity to the liver and lung. Intracellular MT also plays important roles in ameliorating Cd toxicity following prolonged exposures, particularly chronic Cd-induced nephrotoxicity, osteotoxicity, and toxicity to the lung, liver, and immune system. There is an association between human and rodent Cd exposure and prostate cancers, especially in the portions where MT is poorly expressed. MT expression in Cd-induced tumors varies depending on the type and the stage of tumor development. For instance, high levels of MT are detected in Cd-induced sarcomas at the injection site, whereas the sarcoma metastases were devoid of MT. The use of MT-transgenic and MT-null mice has greatly helped define the role of MT in Cd toxicology, with the MT-null mice being hypersensitive and MT-transgenic mice resistant to Cd toxicity. Thus, MT is critical for protecting human health from Cd toxicity. There are large individual variations in MT expression, which might in turn predispose some people to Cd toxicity. PMID:19362100

Klaassen, Curtis D.; Liu, Jie; Diwan, Bhalchandra A.



Metallothionein protection of cadmium toxicity  

SciTech Connect

The discovery of the cadmium (Cd)-binding protein from horse kidney in 1957 marked the birth of research on this low-molecular weight, cysteine-rich protein called metallothionein (MT) in Cd toxicology. MT plays minimal roles in the gastrointestinal absorption of Cd, but MT plays important roles in Cd retention in tissues and dramatically decreases biliary excretion of Cd. Cd-bound to MT is responsible for Cd accumulation in tissues and the long biological half-life of Cd in the body. Induction of MT protects against acute Cd-induced lethality, as well as acute toxicity to the liver and lung. Intracellular MT also plays important roles in ameliorating Cd toxicity following prolonged exposures, particularly chronic Cd-induced nephrotoxicity, osteotoxicity, and toxicity to the lung, liver, and immune system. There is an association between human and rodent Cd exposure and prostate cancers, especially in the portions where MT is poorly expressed. MT expression in Cd-induced tumors varies depending on the type and the stage of tumor development. For instance, high levels of MT are detected in Cd-induced sarcomas at the injection site, whereas the sarcoma metastases are devoid of MT. The use of MT-transgenic and MT-null mice has greatly helped define the role of MT in Cd toxicology, with the MT-null mice being hypersensitive and MT-transgenic mice resistant to Cd toxicity. Thus, MT is critical for protecting human health from Cd toxicity. There are large individual variations in MT expression, which might in turn predispose some people to Cd toxicity.

Klaassen, Curtis D. [Department of Pharmacology, Toxicology and Therapeutics, University of Kansas Medical Center, Kansas City, KS 66160-7417 (United States)], E-mail:; Liu, Jie [Inorganic Carcinogenesis Section, Laboratory of Comparative Carcinogenesis, National Cancer Institute at NIEHS, Research Triangle Park, NC 27709 (United States); Diwan, Bhalchandra A. [Basic Science Program, SAIC-Frederick, Inc., NCI Frederick, MD (United States)



Exposure to ionizing radiation induced persistent gene expression changes in mouse mammary gland  

PubMed Central

Background Breast tissue is among the most sensitive tissues to the carcinogenic actions of ionizing radiation and epidemiological studies have linked radiation exposure to breast cancer. Currently, molecular understanding of radiation carcinogenesis in mammary gland is hindered due to the scarcity of in vivo long-term follow up data. We undertook this study to delineate radiation-induced persistent alterations in gene expression in mouse mammary glands 2-month after radiation exposure. Methods Six to eight week old female C57BL/6J mice were exposed to 2 Gy of whole body ? radiation and mammary glands were surgically removed 2-month after radiation. RNA was isolated and microarray hybridization performed for gene expression analysis. Ingenuity Pathway Analysis (IPA) was used for biological interpretation of microarray data. Real time quantitative PCR was performed on selected genes to confirm the microarray data. Results Compared to untreated controls, the mRNA levels of a total of 737 genes were significantly (p<0.05) perturbed above 2-fold of control. More genes (493 genes; 67%) were upregulated than the number of downregulated genes (244 genes; 33%). Functional analysis of the upregulated genes mapped to cell proliferation and cancer related canonical pathways such as ‘ERK/MAPK signaling’, ‘CDK5 signaling’, and ‘14-3-3-mediated signaling’. We also observed upregulation of breast cancer related canonical pathways such as ‘breast cancer regulation by Stathmin1’, and ‘HER-2 signaling in breast cancer’ in IPA. Interestingly, the downregulated genes mapped to fewer canonical pathways involved in cell proliferation. We also observed that a number of genes with tumor suppressor function (GPRC5A, ELF1, NAB2, Sema4D, ACPP, MAP2, RUNX1) persistently remained downregulated in response to radiation exposure. Results from qRT-PCR on five selected differentially expressed genes confirmed microarray data. The PCR data on PPP4c, ELF1, MAPK12, PLCG1, and E2F6 showed similar trend in up and downregulation as has been observed with the microarray. Conclusions Exposure to a clinically relevant radiation dose led to long-term activation of mammary gland genes involved in proliferative and metabolic pathways, which are known to have roles in carcinogenesis. When considered along with downregulation of a number of tumor suppressor genes, our study has implications for breast cancer initiation and progression after therapeutic radiation exposure. PMID:23216862



Altered brain gene expression but not steroid biochemistry in a genetic mouse model of neurodevelopmental disorder  

PubMed Central

Background The 39,XY*O mouse, which lacks the orthologues of the ADHD and autism candidate genes STS (steroid sulphatase) and ASMT (acetylserotonin O-methyltransferase), exhibits behavioural phenotypes relevant to developmental disorders. The neurobiology underlying these phenotypes is unclear, although there is evidence for serotonergic abnormalities in the striatum and hippocampus. Methods Using microarray and quantitative gene expression analyses, and gas chromatography–mass spectrometry, we compared brain gene expression and steroid biochemistry in wildtype (40,XY) and 39,XY*O adult mice to identify non-obvious genetic and endocrine candidates for between-group differences in behaviour and neurochemistry. We also tested whether acute STS inhibition by COUMATE in wildtype (40,XY) adult male mice recapitulated any significant gene expression or biochemical findings from the genetic comparison. Data were analysed by unpaired t-test or Mann Whitney U-test depending on normality, with a single factor of KARYOTYPE. Results Microarray analysis indicated seven robust gene expression differences between the two groups (Vmn2r86, Sfi1, Pisd-ps1, Tagap1, C1qc, Metap1d, Erdr1); Erdr1 and C1qc expression was significantly reduced in the 39,XY*O striatum and hippocampus, whilst the expression of Dhcr7 (encoding 7-dehydrocholesterol reductase, a modulator of serotonin system development), was only reduced in the 39,XY*O hippocampus. None of the confirmed gene expression changes could be recapitulated by COUMATE administration. We detected ten free, and two sulphated steroids in 40,XY and 39,XY*O brain; surprisingly, the concentrations of all of these were equivalent between groups. Conclusions Our data demonstrate that the mutation in 39,XY*O mice: i) directly disrupts expression of the adjacent Erdr1 gene, ii) induces a remarkably limited suite of downstream gene expression changes developmentally, with several of relevance to associated neurobehavioural phenotypes and iii) does not elicit large changes in brain steroid biochemistry. It is possible that individuals with STS/ASMT deficiency exhibit a similarly specific pattern of gene expression changes to the 39,XY*O mouse, and that these contribute towards their abnormal neurobiology. Future work may focus on whether complement pathway function, mitochondrial metabolism and cholesterol biosynthesis pathways are perturbed in such subjects. PMID:24602487



Glutamate–cysteine ligase modifier subunit: mouse Gclm gene structure and regulation by agents that cause oxidative stress  

Microsoft Academic Search

Glutamate–cysteine ligase is a heterodimer comprising a modifier (GCLM) and a catalytic (GCLC) subunit. In mouse Hepa-1c1c7 hepatoma cell cultures, we found that tert-butylhydroquinone (tBHQ; 50?M) induces the GCLM and GCLC mRNAs ?10- and ?2-fold, respectively, and that these increases primarily reflect de novo transcription. We determined that the mouse Gclm gene has seven exons, spanning 22.3kb; all exons, intron–exon

Willy A. Solis; Timothy P. Dalton; Matthew Z. Dieter; Sarah Freshwater; Judy M. Harrer; Lei He; Howard G. Shertzer; Daniel W. Nebert



Bisulfite Sequencing in Preimplantation Embryos: DNA Methylation Profile of the Upstream Region of the Mouse Imprinted H19Gene  

Microsoft Academic Search

In this study we describe a modification of the bisulfite genomic sequencing protocol that enables detection of methylation from as few as five diploid cells from preimplantation mouse embryos. We have used bisulfite genomic sequencing to study the methylation profile of the putative imprinting element upstream of the mouseH19gene at several stages of embryonic development, including fertilized oocytes and two-cell

Peter M. Warnecke; Jeffrey R. Mann; Marianne Frommer; Susan J. Clark



Assignment of the gene governing cellular ouabain resistance to Mus musculus chromosome 3 using human\\/mouse microcell hybrids  

Microsoft Academic Search

Human\\/mouse microcell hybrids were used to establish the assignment of the gene governing resistance to the cardiac glycoside ouabain (Oua-1) to Mus musculus chromosome 3. Microcells were prepared from primary mouse embryo fibroblasts and fused with HeLa S3 cells, and microcell hybrids were isolated and maintained in medium containing 10-6m ouabain. Resistance to ouabain was not expressed concordantly with any

C. A. Kozak; R. E. K. Fournier; L. A. Leinwand; F. H. Ruddle



In Vivo Gene Therapy with Interleukin12 Inhibits Primary Vascular Tumor Growth and Induces Apoptosis in a Mouse Model1  

Microsoft Academic Search

Interleukin-12 is proposed to have anti-neoplastic activity on the basis of both its anti-angiogenic and immunologic effects. Gene gun therapy with interleukin-12 cDNA into the peritumoral area of immunocompetent 129\\/J mice with life-threatening primary vascular tumors reduced tumor volume 7.5-fold and almost tripled the duration of mouse survival, in contrast with luciferase-bombarded control mice. Epidermal expression of mouse interleukin-12 elevated

Chong Wang; M. Eugenia Quevedo; Brian J. Lannutti; Kenneth B. Gordon; Danqing Guo; Wenn Sun; Amy S. Paller



Coexpression of FBN1 with mesenchyme-specific genes in mouse cell lines: implications for phenotypic variability in Marfan syndrome  

Microsoft Academic Search

Mutations in the human FBN1 gene cause Marfan syndrome, a complex disease affecting connective tissues but with a highly variable phenotype. To identify genes that might participate in epistatic interactions with FBN1, and could therefore explain the observed phenotypic variability, we have looked for genes that are co-expressed with Fbn1 in the mouse. Microarray expression data derived from a range

Kim M Summers; Sobia Raza; Erik van Nimwegen; Thomas C Freeman; David A Hume



Investigation of Mcp1 as a Quantitative Trait Gene for Prion Disease Incubation Time in Mouse  

PubMed Central

The genetic basis of prion disease incubation time is principally determined by polymorphisms in the prion protein gene, Prnp. However, it is now known that other genetic factors are important. Several quantitative trait loci (QTL) have been identified across the genome including a broad region of linkage on Mmu11. Monocyte chemoattractant protein 1 (MCP-1) maps to this region and has been associated with microglial activation and reduced survival in the ME7 mouse scrapie model of prion disease. We have identified 10 polymorphisms, 3 of which are nonsynonomous, in Mcp1 between “long” (CAST) and “short” (SJL or NZW) incubation-time mouse strains. Crosses between these strains and Mcp1?/? mice inoculated with the Chandler/RML mouse scrapie prion strain formed the basis of a quantitative complementation test. In these models loss of Mcp1 did not show an increase in incubation time suggesting that the effects of Mcp1 may be specific to the ME7 prion strain and that Mcp1 does not contribute to the QTL described on Mmu11. PMID:18716327

O'Shea, Marie; Maytham, Emma G.; Linehan, Jackie M.; Brandner, Sebastian; Collinge, John; Lloyd, Sarah E.



Constitutive expression of human keratin 14 gene in mouse lung induces premalignant lesions and squamous differentiation  

PubMed Central

Squamous cell carcinoma accounts for 20% of all human lung cancers and is strongly linked to cigarette smoking. It develops through premalignant changes that are characterized by high levels of keratin 14 (K14) expression in the airway epithelium and evolve through basal cell hyperplasia, squamous metaplasia and dysplasia to carcinoma in situ and invasive carcinoma. In order to explore the impact of K14 in the pulmonary epithelium that normally lacks both squamous differentiation and K14 expression, human keratin 14 gene hK14 was constitutively expressed in mouse airway progenitor cells using a mouse Clara cell specific 10 kDa protein (CC10) promoter. While the lungs of CC10-hK14 transgenic mice developed normally, we detected increased expression of K14 and the molecular markers of squamous differentiation program such as involucrin, loricrin, small proline-rich protein 1A, transglutaminase 1 and cholesterol sulfotransferase 2B1. In contrast, wild-type lungs were negative. Aging CC10-hK14 mice revealed multifocal airway cell hyperplasia, occasional squamous metaplasia and their lung tumors displayed evidence for multidirectional differentiation. We conclude that constitutive expression of hK14 initiates squamous differentiation program in the mouse lung, but fails to promote squamous maturation. Our study provides a novel model for assessing the mechanisms of premalignant lesions in vivo by modifying differentiation and proliferation of airway progenitor cells. PMID:18701433

Habib Dakir, EL; Feigenbaum, Lionel; Linnoila, R. Ilona



Constitutive expression of human keratin 14 gene in mouse lung induces premalignant lesions and squamous differentiation.  


Squamous cell carcinoma accounts for 20% of all human lung cancers and is strongly linked to cigarette smoking. It develops through premalignant changes that are characterized by high levels of keratin 14 (K14) expression in the airway epithelium and evolve through basal cell hyperplasia, squamous metaplasia and dysplasia to carcinoma in situ and invasive carcinoma. In order to explore the impact of K14 in the pulmonary epithelium that normally lacks both squamous differentiation and K14 expression, human keratin 14 gene hK14 was constitutively expressed in mouse airway progenitor cells using a mouse Clara cell specific 10 kDa protein (CC10) promoter. While the lungs of CC10-hK14 transgenic mice developed normally, we detected increased expression of K14 and the molecular markers of squamous differentiation program such as involucrin, loricrin, small proline-rich protein 1A, transglutaminase 1 and cholesterol sulfotransferase 2B1. In contrast, wild-type lungs were negative. Aging CC10-hK14 mice revealed multifocal airway cell hyperplasia, occasional squamous metaplasia and their lung tumors displayed evidence for multidirectional differentiation. We conclude that constitutive expression of hK14 initiates squamous differentiation program in the mouse lung, but fails to promote squamous maturation. Our study provides a novel model for assessing the mechanisms of premalignant lesions in vivo by modifying differentiation and proliferation of airway progenitor cells. PMID:18701433

Dakir, E L Habib; Feigenbaum, Lionel; Linnoila, R Ilona



Msg1 and Mrg1, founding members of a gene family, show distinct patterns of gene expression during mouse embryogenesis.  


Msg1 and Mrg1 are founding members of a gene family which exhibit distinct patterns of gene expression during mouse embryogenesis. Sequence analysis reveals that these genes are unlike any other gene identified to date, but they share two near-identical sequence domains. The Msg1 and Mrg1 expression profiles during early development are distinct from each other. Msg1 is predominantly expressed in nascent mesoderm, the heart tube, limb bud and sclerotome. Intriguingly, Msg1 expression is restricted, within these developing mesodermal sites, to posterior domains. Mrg1 is expressed prior to gastrulation in the anterior visceral endoderm. Expression is maintained in the endoderm once gastrulation has begun and commences in the rostralmost embryonic mesoderm which underlies the anterior visceral endoderm. Mrg1 expression persists in this rostral mesoderm as it is translocated caudalwards during the invagination of the foregut and the formation of the heart. Later Mrg1 expression predominates in the septum transversum caudal to the heart. This expression pattern suggests that the septum transversum originates from the rostralmost embryonic mesoderm which first expressed Mrg1 at the late primitive streak stage. PMID:9533950

Dunwoodie, S L; Rodriguez, T A; Beddington, R S



Ducky Mouse Phenotype of Epilepsy and Ataxia Is Associated with Mutations in the Cacna2d2 Gene and Decreased Calcium Channel  

E-print Network

Ducky Mouse Phenotype of Epilepsy and Ataxia Is Associated with Mutations in the Cacna2d2 Gene, Virginia 22908-0735 The mouse mutant ducky, a model for absence epilepsy, is characterized by spike of ataxia and epilepsy in the mouse. Key words: epilepsy; ataxia; calcium channel; subunit; Pur- kinje cell

Dolphin, Annette C.


Zinc and low-dose of cadmium protect sertoli cells against toxic-dose of cadmium: The role of metallothionein  

PubMed Central

Background: The impact of cadmium (Cd) on male infertility may be related to the interaction with metal-binding proteins known as metallothioneins (Mts). Trace elements like zinc (Zn) have protective effects on testicular damage induced by Cd. Objective: We determined the effect of Zn and low-dose Cd pre-treatment on the expression of Mt1 and Mt2 genes on testicular Sertoli cells. Materials and Methods: The cultured TM4 mouse sertoli cells were treated with 50 ?M ZnSO4 (Zn pre-treated group; ZnPG), 2 ?M CdCl2 (Cd pre-treated group; CdPG), or distilled water (DW pre-treated group; DWPG). After 18 hour, all of these groups were exposed to 100 ?M CdCl2 for different periods of time (1, 2, 3, and 6 hours). There was also a control group for all three groups, which was treated only with distilled water (without Cd or Zn pre-treatment). Cellular viability, Zn and Cd concentrations and gene expression were assessed by MTT, atomic absorption spectrometry and real time PCR methods, respectively. Results: The expression of Mt1 and Mt2 genes in ZnPG, CdPG, and DWPG was greater than the control group (p=0.02 and p=0.01, respectively). Cd concentrations in CdPG and DWPG were greater than the control group (p=0.00). Expression of both genes in ZnPG and CdPG increased after 3 hours of treatment and Cd concentration decreased simultaneously, which was more obvious in ZnPG. Conclusion: Zn and short term low-dose Cd pre-treatment might reduce the adverse effects of Cd by increasing expression of Mts genes in Sertoli cells. The protective effect of Zn was stronger than Cd. PMID:24639783

Kheradmand, Fatemeh; Nourmohammadi, Issa; Ahmadi-Faghih, Mohamad Amin; Firoozrai, Mohsen; Modarressi, Mohammad Hossein



The mouse homologue of the tuberin gene (TSC2) maps to a conserved synteny group between mouse chromosome 17 and human 16p13.3  

SciTech Connect

The tuberous sclerosis gene (TSC2) on human chromosome 16p13.3 has recently been identified. Several markers from this region have previously been shown to be members of a conserved synteny group, in the mouse located on chromosome 17. The mouse region includes markers D17Lon1, D17Lon2, D17Lon3, and D17Lon4, which are linked to the {alpha}-globin pseudogene Hba-ps4 on chromosome 17, while the corresponding human markers, NK12, NK92, sazD, and KM17, are linked to the functional {alpha}-globin locus near the tip of chromosome 16p. Since the human TSC2 maps in close proximity to NK12, we wanted to investigate whether a mouse gene, homologous to TSC2, was present on mouse chromosome 17 and thus included in the conserved synteny group. During the characterization of transcripts from the human PKD1 region on human chromosome 16p13.3, we isolated three short clones encoding fragments of TSC2 from a human fetal brain cDNA library enriched for transcripts from the PKD1 region. These TSC2 clones were used as probes to screen a mouse teratocarcinoma (PCC4) cDNA library (Stratagene), at a final stringency of 0.3 x SSC, 0.1% SDS at 65{degrees}C. One of the positive clones isolated, mTS-1, had a 2.8-kb insert. Two hundred bases from each end of the insert were sequenced, showing 88 and 83.5% identity to the human tuberin nucleotide sequence, with the 5{prime} end of the clone starting at position 2351 and the 3{prime} end ending at position 5265. The high degree of homology to the human tuberin sequence suggests that clone mTS-1 is indeed derived from the mouse homologue of TSC2. 11 refs., 1 fig.

Olsson, P.G.; Sutherland, H.F.; Nowicka, U. [Lincoln`s Inn Fields, London (United Kingdom)] [and others] [Lincoln`s Inn Fields, London (United Kingdom); and others



Differential gene expression in mouse primary hepatocytes exposed to the peroxisome proliferator-activated receptor ? agonists  

PubMed Central

Background Fibrates are a unique hypolipidemic drugs that lower plasma triglyceride and cholesterol levels through their action as peroxisome proliferator-activated receptor alpha (PPAR?) agonists. The activation of PPAR? leads to a cascade of events that result in the pharmacological (hypolipidemic) and adverse (carcinogenic) effects in rodent liver. Results To understand the molecular mechanisms responsible for the pleiotropic effects of PPAR? agonists, we treated mouse primary hepatocytes with three PPAR? agonists (bezafibrate, fenofibrate, and WY-14,643) at multiple concentrations (0, 10, 30, and 100 ?M) for 24 hours. When primary hepatocytes were exposed to these agents, transactivation of PPAR? was elevated as measured by luciferase assay. Global gene expression profiles in response to PPAR? agonists were obtained by microarray analysis. Among differentially expressed genes (DEGs), there were 4, 8, and 21 genes commonly regulated by bezafibrate, fenofibrate, and WY-14,643 treatments across 3 doses, respectively, in a dose-dependent manner. Treatments with 100 ?M of bezafibrate, fenofibrate, and WY-14,643 resulted in 151, 149, and 145 genes altered, respectively. Among them, 121 genes were commonly regulated by at least two drugs. Many genes are involved in fatty acid metabolism including oxidative reaction. Some of the gene changes were associated with production of reactive oxygen species, cell proliferation of peroxisomes, and hepatic disorders. In addition, 11 genes related to the development of liver cancer were observed. Conclusion Our results suggest that treatment of PPAR? agonists results in the production of oxidative stress and increased peroxisome proliferation, thus providing a better understanding of mechanisms underlying PPAR? agonist-induced hepatic disorders and hepatocarcinomas. PMID:17118139

Guo, Lei; Fang, Hong; Collins, Jim; Fan, Xiao-hui; Dial, Stacey; Wong, Alex; Mehta, Kshama; Blann, Ernice; Shi, Leming; Tong, Weida; Dragan, Yvonne P



Dosage Compensation in the Mouse Balances Up-Regulation and Silencing of X-Linked Genes  

PubMed Central

Dosage compensation in mammals involves silencing of one X chromosome in XX females and requires expression, in cis, of Xist RNA. The X to be inactivated is randomly chosen in cells of the inner cell mass (ICM) at the blastocyst stage of development. Embryonic stem (ES) cells derived from the ICM of female mice have two active X chromosomes, one of which is inactivated as the cells differentiate in culture, providing a powerful model system to study the dynamics of X inactivation. Using microarrays to assay expression of X-linked genes in undifferentiated female and male mouse ES cells, we detect global up-regulation of expression (1.4- to 1.6-fold) from the active X chromosomes, relative to autosomes. We show a similar up-regulation in ICM from male blastocysts grown in culture. In male ES cells, up-regulation reaches 2-fold after 2–3 weeks of differentiation, thereby balancing expression between the single X and the diploid autosomes. We show that silencing of X-linked genes in female ES cells occurs on a gene-by-gene basis throughout differentiation, with some genes inactivating early, others late, and some escaping altogether. Surprisingly, by allele-specific analysis in hybrid ES cells, we also identified a subgroup of genes that are silenced in undifferentiated cells. We propose that X-linked genes are silenced in female ES cells by spreading of Xist RNA through the X chromosome territory as the cells differentiate, with silencing times for individual genes dependent on their proximity to the Xist locus. PMID:18076287

Lin, Hong; Gupta, Vibhor; VerMilyea, Matthew D; Falciani, Francesco; Lee, Jeannie T; O'Neill, Laura P; Turner, Bryan M



Integration of gene chip and topological network techniques to screen a candidate biomarker gene (CBG) for predication of the source water carcinogenesis risks on mouse Mus musculus.  


Screening of a candidate biomarker gene (CBG) to predicate the carcinogenesis risks in the Yangtze River source of drinking water in Nanjing area (YZR-SDW-NJ) on mouse (Mus musculus) was conducted in this research. The effects of YZR-SDW-NJ on the genomic transcriptional expression levels were measured by the GeneChip(®) Mouse Genome and data treated by the GO database analysis. The 298 genes discovered as the differently expressed genes (DEGs) were down-regulated and their values were ?-1.5-fold. Of the 298 DEGs, 25 were cancer-related genes selected as the seed genes to build a topological network map with Genes2Networks software, only 7 of them occurred at the constructed map. Smad2 gene was at the constructed map center and could be identified as a candidate biomarker gene (CBG) primarily which involves the genesis and development of colorectal, leukemia, lung and prostate cancers directly. Analysis of the gene signal pathway further approved that smad2 gene had the relationships closely to other 16 cancer-related genes and could be used as a CBG to indicate the carcinogenic risks in YZR-SDW-NJ. The data suggest that integration of gene chip and network techniques may be a way effectively to screen a CBG. And the parameter values for further judgment of the CBG through signal pathway relationship analysis also will be discussed. PMID:21541659

Sun, Jie; Cheng, Shupei; Li, Aimin; Zhang, Rui; Wu, Bing; Zhang, Yan; Zhang, Xuxiang



Ex vivo magnetofection: A novel strategy for the study of gene function in mouse organogenesis  

PubMed Central

Gene function during mouse development is often studied through the production and analysis of transgenic and knock-out models. However, these techniques are time- and resource-consuming, and require specialized equipment and expertise. We have established a new protocol for functional studies that combines organ culture of explanted fetal tissues with micro-injection and magnetically-induced transfection (“magnetofection”) of gene expression constructs. As proof-of-principle, we magnetofected cDNA constructs into genital ridge tissue as a means of gain-of-function analysis, and shRNA constructs for loss-of-function analysis. Ectopic expression of Sry induced female-to-male sex-reversal, whereas knockdown of Sox9 expression caused male-to-female sex-reversal, consistent with the known functions of these genes. Further, ectopic expression of Tmem184a, a gene of unknown function, in female genital ridges, resulted in failure of gonocytes to enter meiosis. This technique will likely be applicable to the study of gene function in a broader range of developing organs and tissues. PMID:19301396

Svingen, Terje; Wilhelm, Dagmar; Combes, Alexander N.; Hosking, Brett; Harley, Vincent R.; Sinclair, Andrew H.; Koopman, Peter



Altered gene expression and spongiotrophoblast differentiation in placenta from a mouse model of diabetes in pregnancy  

PubMed Central

Aims/hypothesis Pregnancies complicated by diabetes have a higher risk of adverse outcomes for mothers and children, including predisposition to disease later in life, e.g. metabolic syndrome and hypertension. We hypothesised that adverse outcomes from diabetic pregnancies may be linked to compromised placental function, and sought to identify cellular and molecular abnormalities in diabetic placenta. Methods Using a mouse model of diabetic pregnancy, placental gene expression was assayed at mid-gestation and cellular composition analysed at various stages. Genome-wide expression profiling was validated by quantitative PCR and tissue localisation studies were performed to identify cellular correlates of altered gene expression in diabetic placenta. Results We detected significantly altered gene expression in diabetic placenta for genes expressed in the maternal and those expressed in the embryonic compartments. We also found altered cellular composition of the decidual compartment. In addition, the junctional and labyrinth layers were reduced in diabetic placenta, accompanied by aberrant differentiation of spongiotrophoblast cells. Conclusions/interpretation Diabetes during pregnancy alters transcriptional profiles in the murine placenta, affecting cells of embryonic and maternal origin, and involving several genes not previously implicated in diabetic pregnancies. The molecular changes and abnormal differentiation of multiple cell types precede impaired growth of junctional zone and labyrinth, and of placenta overall. Regardless of whether these changes represent direct responses to hyperglycaemia or are physiological adaptations, they are likely to play a role in pregnancy complications and outcomes, and to have implications for developmental origins of adult disease. PMID:21491160

Salbaum, J. M.; Kruger, C.; Zhang, X.; Delahaye, N. Arbour; Pavlinkova, G.; Burk, D. H.; Kappen, C.



Global Characterization of Differential Gene Expression Profiles in Mouse V?1+ and V?4+ ?? T Cells  

PubMed Central

Peripheral ?? T cells in mice are classified into two major subpopulations, V?1+ and V?4+, based on the composition of T cell receptors. However, their intrinsic differences remain unclear. In this study, we analyzed gene expression profiles of the two subsets using Illumina HiSeq 2000 Sequencer. We identified 1995 transcripts related to the activation of V?1+ ?? T cells, and 2158 transcripts related to the activation of V?4+ ?? T cells. We identified 24 transcripts differentially expressed between the two subsets in resting condition, and 20 after PMA/Ionomycin treatment. We found that both cell types maintained phenotypes producing IFN-?, TNF-?, TGF-? and IL-10. However, V?1+ ?? T cells produced more Th2 type cytokines, such as IL-4 and IL-5, while V?4+ ?? T cells preferentially produced IL-17. Our study provides a comprehensive gene expression profile of mouse peripheral V?1+ and V?4+ ?? T cells that describes the inherent differences between them. PMID:25405356

Dong, Peng; Zhang, Siya; Cai, Menghua; Kang, Ning; Hu, Yu; Cui, Lianxian; Zhang, Jianmin; He, Wei



Cloning and characterization of the mouse JDP2 gene promoter reveal negative regulation by p53.  


Jun dimerization protein 2 (JDP2) is a repressor of transcription factor AP-1. To investigate the transcriptional regulation of the JDP2 gene, we cloned the 5'-flanking region of the mouse JDP2 gene. Primer extension analysis revealed a new transcription start site (+1). Promoter analysis showed that the region from nt -343 to nt +177 contains basal transcriptional activity. Interestingly, the tumor suppressor p53 significantly repressed the transcriptional activity of the JDP2 promoter. Given that JDP2 inhibits expression of p53, our results suggest a negative feedback loop between JDP2 and p53, and a direct link between JDP2 and a key oncogenic pathway. PMID:25026555

Xu, Yuanhong; Jin, Chunyuan; Liu, Zhe; Pan, Jianzhi; Li, Hongjie; Zhang, Zhongbo; Bi, Shulong; Yokoyama, Kazunari K



Dissecting the heterogeneity of gene expressions in mouse embryonic stem cells  

NASA Astrophysics Data System (ADS)

A population of genetically identical cells, of the same nominal cell type, and cultured in the same petri dish, will nevertheless often exhibit varying patterns of gene expression. Taking mouse embryonic stem (ES) cells as a model system, we use immunofluorescence and flow cytometry to examine in detail the distribution of expression levels for various transcription factors key to the maintenance of the ES cell identity. We find the population-level distribution of many proteins, once rescaled by the average expression level, have very similar shapes. This suggest the largest component of observed heterogeneity comes from a single source. More subtly, we find the expression many of genes appears to modulate with the cell cycle. This may suggest that the program for maintaining ES cell identity is tightly coupled to the cell cycle machinery.

Zou, Ling-Nan; Thomson, Matt; Liu, S. John; Ramanathan, Sharad



Global gene expression of methicillin-resistant Staphylococcus aureus USA300 during human and mouse infection.  


Little is known about the expression of methicillin-resistant Staphylococcus aureus (MRSA) genes during infection conditions. Here, we described the transcriptome of the clinical MRSA strain USA300 derived from human cutaneous abscesses, and compared it with USA300 bacteria derived from infected kidneys in a mouse model. Remarkable similarity between the transcriptomes allowed us to identify genes encoding multiple proteases and toxins, and iron- and peptide-transporter molecules, which are upregulated in both infections and are likely important for establishment of infection. We also showed that disruption of the global transcriptional regulators agr and sae prevents in vivo upregulation of many toxins and proteases, protecting mice from lethal infection dose, and hinting at the role of these transcriptional regulators in the pathology of MRSA infection. PMID:24286981

Date, Shailesh V; Modrusan, Zora; Lawrence, Michael; Morisaki, J Hiroshi; Toy, Karen; Shah, Ishita M; Kim, Janice; Park, Summer; Xu, Min; Basuino, Li; Chan, Liana; Zeitschel, Deborah; Chambers, Henry F; Tan, Man-Wah; Brown, Eric J; Diep, Binh An; Hazenbos, Wouter L W



Effect of melatonin and tetrapeptide on gene expression in mouse brain.  


A microchip technique was used to study expression of 16,897 clones from a cDNA library in the brain of mice receiving melatonin or tetrapeptide Epithalon (Ala-Glu-Asp-Gly). Expression of 53 transcripts in mouse brain underwent significant changes after treatment with the preparations. Melatonin and Epithalon modified expression of 38 and 22 transcripts, respectively. These preparations produced similar changes in the expression of 6 transcripts. Expression of 1 transcript (Rp119) was inhibited by melatonin, but induced by Epithalon. The target genes are physiologically related to the cell cycle, apoptosis, biosynthesis, processing, and transport of nucleic acids. Comparative study of gene expression in the brain and heart of CBA mice receiving melatonin and Epithalon suggest that these preparations have a tissue-specific biological effect. PMID:15723138

Anisimov, S V; Khavinson, V Kh; Anisimov, V N



A Mutation in the Mouse Ttc26 Gene Leads to Impaired Hedgehog Signaling  

PubMed Central

The phenotype of the spontaneous mutant mouse hop-sterile (hop) is characterized by a hopping gait, polydactyly, hydrocephalus, and male sterility. Previous analyses of the hop mouse revealed a deficiency of inner dynein arms in motile cilia and a lack of sperm flagella, potentially accounting for the hydrocephalus and male sterility. The etiology of the other phenotypes and the location of the hop mutation remained unexplored. Here we show that the hop mutation is located in the Ttc26 gene and impairs Hedgehog (Hh) signaling. Expression analysis showed that this mutation led to dramatically reduced levels of the Ttc26 protein, and protein-protein interaction assays demonstrated that wild-type Ttc26 binds directly to the Ift46 subunit of Intraflagellar Transport (IFT) complex B. Although IFT is required for ciliogenesis, the Ttc26 defect did not result in a decrease in the number or length of primary cilia. Nevertheless, Hh signaling was reduced in the hop mouse, as revealed by impaired activation of Gli transcription factors in embryonic fibroblasts and abnormal patterning of the neural tube. Unlike the previously characterized mutations that affect IFT complex B, hop did not interfere with Hh-induced accumulation of Gli at the tip of the primary cilium, but rather with the subsequent dissociation of Gli from its negative regulator, Sufu. Our analysis of the hop mouse line provides novel insights into Hh signaling, demonstrating that Ttc26 is necessary for efficient coupling between the accumulation of Gli at the ciliary tip and its dissociation from Sufu. PMID:25340710

Swiderski, Ruth E.; Nakano, Yoko; Mullins, Robert F.; Seo, Seongjin; Banfi, Botond



Multi-walled carbon nanotube-induced gene expression in the mouse lung: Association with lung pathology  

SciTech Connect

Due to the fibrous shape and durability of multi-walled carbon nanotubes (MWCNT), concerns regarding their potential for producing environmental and human health risks, including carcinogenesis, have been raised. This study sought to investigate how previously identified lung cancer prognostic biomarkers and the related cancer signaling pathways are affected in the mouse lung following pharyngeal aspiration of well-dispersed MWCNT. A total of 63 identified lung cancer prognostic biomarker genes and major signaling biomarker genes were analyzed in mouse lungs (n = 80) exposed to 0, 10, 20, 40, or 80 {mu}g of MWCNT by pharyngeal aspiration at 7 and 56 days post-exposure using quantitative PCR assays. At 7 and 56 days post-exposure, a set of 7 genes and a set of 11 genes, respectively, showed differential expression in the lungs of mice exposed to MWCNT vs. the control group. Additionally, these significant genes could separate the control group from the treated group over the time series in a hierarchical gene clustering analysis. Furthermore, 4 genes from these two sets of significant genes, coiled-coil domain containing-99 (Ccdc99), muscle segment homeobox gene-2 (Msx2), nitric oxide synthase-2 (Nos2), and wingless-type inhibitory factor-1 (Wif1), showed significant mRNA expression perturbations at both time points. It was also found that the expression changes of these 4 overlapping genes at 7 days post-exposure were attenuated at 56 days post-exposure. Ingenuity Pathway Analysis (IPA) found that several carcinogenic-related signaling pathways and carcinogenesis itself were associated with both the 7 and 11 gene signatures. Taken together, this study identifies that MWCNT exposure affects a subset of lung cancer biomarkers in mouse lungs. - Research Highlights: > Multi-Walled Carbon Nanotubes affect lung cancer biomarkers in mouse lungs. > The results suggest potentially harmful effects of MWCNT exposure on human lungs. > The results could potentially be used for the medical surveillance of workers.

Pacurari, M. [Mary Babb Randolph Cancer Center, West Virginia University, Morgantown, WV 26506-9300 (United States); Qian, Y., E-mail: [Pathology and Physiology Research Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV 26505 (United States); Porter, D.W.; Wolfarth, M. [Pathology and Physiology Research Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV 26505 (United States); Wan, Y.; Luo, D. [Mary Babb Randolph Cancer Center, West Virginia University, Morgantown, WV 26506-9300 (United States); Ding, M. [Pathology and Physiology Research Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV 26505 (United States); Castranova, V. [Mary Babb Randolph Cancer Center, West Virginia University, Morgantown, WV 26506-9300 (United States); Pathology and Physiology Research Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV 26505 (United States); Guo, N.L., E-mail: [Mary Babb Randolph Cancer Center, West Virginia University, Morgantown, WV 26506-9300 (United States); Department of Community Medicine, School of Medicine, West Virginia University, Morgantown, WV 26506-9190 (United States)



Selection of reference genes for normalization of quantitative polymerase chain reaction data in mouse models of heart failure.  


The accurate measurement of mRNA expression levels is crucially dependent on the use of relevant reference genes for the normalization of data. Currently, heart failure is a serious and widespread disease, and multiple mouse models are utilized for the study of this complex disease. Although mouse models are commonly used to study cardiovascular disease, various studies have not employed the appropriate selection strategies. The present study investigated the expression stability of eight candidate reference genes (GAPDH, ACTB, B2M, CycA, TBP, PBGD, HTRP 1 and 18S) in two mouse models of heart failure, including the transverse aortic arch constriction (TAC) model and the myocardial infarction (MI) model, using GeNorm software. The expression of BNP was normalized using different reference gene strategies, and it was demonstrated that its induction following heart failure was most profound with the optimal reference gene combination. The most stable genes were identified as follows: TBP and CycA in the MI model, and PBGD and GAPDH in the TAC model. The present study provides important information for reference gene selection in mouse models of heart failure, and will aid further investigations of the transcriptome in cardiovascular research. PMID:25338732

Li, Qiaoling; Hu, Tingting; Chen, Liang; Sun, Jiayin; Xie, Jun; Li, Rang; Xu, Biao



Molecular cloning and functional characterization of a mouse gene upregulated by lipopolysaccharide treatment reveals alternative splicing  

SciTech Connect

Treatment of mouse cells with lipopolysaccharide (LPS) potently initiates an inflammatory response, but the underlying mechanisms are unclear. We therefore sought to characterize cDNA sequences of a new mouse LPS-responsive gene, and to evaluate the effects of MLrg. Full-length cDNAs were obtained from LPS-treated NIH3T3 cells. We report that the MLrg gene produces two alternative splice products (GenBank Accession Nos. (DQ316984) and (DQ320011)), respectively, encoding MLrgW and MLrgS polypeptides. Both proteins contain zinc finger and leucine zipper domains and are thus potential regulators of transcription. Expression of MLrgW and MLrgS were robustly upregulated following LPS treatment, and the proteins were localized predominantly in the nuclear membrane and cytoplasm. In stable transfectants over-expressing MLrgW the proportion of cells in G1 phase was significantly reduced, while in cells over-expressing MLrgS the proportion of cells in G2 was significantly increased; both proteins are thus potential regulators of cell cycle progression. Upregulation of MLrgW and MLrgS may be an important component of the LPS inflammatory pathway and of the host response to infection with GNB.

Du, Kejun; Chen, Yaoming; Dai, Zongming; Bi, Yuan; Cai, Tongjian [Department of Occupational and Environmental Health, Fourth Military Medical University, Xi'an 710032, Shaanxi Province (China)] [Department of Occupational and Environmental Health, Fourth Military Medical University, Xi'an 710032, Shaanxi Province (China); Hou, Lichao [Department of Anesthesiology, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, Shaanxi Province (China)] [Department of Anesthesiology, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, Shaanxi Province (China); Chai, Yubo; Song, Qinghe; Chen, Sumin [Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an 710032, Shaanxi Province (China)] [Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an 710032, Shaanxi Province (China); Luo, Wenjing, E-mail: [Department of Occupational and Environmental Health, Fourth Military Medical University, Xi'an 710032, Shaanxi Province (China)] [Department of Occupational and Environmental Health, Fourth Military Medical University, Xi'an 710032, Shaanxi Province (China); Chen, Jingyuan, E-mail: [Department of Occupational and Environmental Health, Fourth Military Medical University, Xi'an 710032, Shaanxi Province (China)] [Department of Occupational and Environmental Health, Fourth Military Medical University, Xi'an 710032, Shaanxi Province (China)



Increased gene expression of glucose transporters in the mouse brain after treatment with fluoxetine and pergolide.  


Glucose transporters play key roles in the homeostatic control of brain functions. In the present study, we examined the effect of fluoxetine, a selective serotonin reuptake inhibitor, and pergolide, a dopamine D receptor agonist, on the gene expression levels of glucose transporters in the mouse brain. mRNAs for 8 sodium-independent glucose transporters (GLUTs), other than GLUT4 and GLUT9, and sodium-dependent glucose transporter 1 (SGLT1) were confirmed to be expressed in brain tissue. Fluoxetine and pergolide significantly increased the expression levels of mRNAs for GLUT1 and GLUT10 in the brain. Furthermore, the expression of GLUT6 in tissue was increased by administering pergolide to mice. On the other hand, fluoxetine and pergolide had no effect on the expression levels of mRNAs for the other GLUTs and SGLT1. Therefore, we concluded that the gene expression of several GLUT isoforms in the mouse brain was affected by the treatment with fluoxetine and pergolide. PMID:24227476

Nagai, K; Inoue, T; Konishi, H



Genetic mapping of a mouse modifier gene that can prevent ALS onset.  


Mutations in the cytoplasmic Cu/Zn superoxide dismutase (SOD1) gene on human chromosome 21q22.1 cause 10-20% of familial amyotrophic lateral sclerosis (ALS) cases. The expression of the ALS phenotype in mice carrying the murine G86R SOD1 mutation is highly dependent upon the mouse genetic background. This is similar to the phenotypic variation observed in ALS patients containing identical SOD1 mutations. In the FVB/N background, mice expressing mG86R SOD1 develop an ALS phenotype at approximately 100 days. However, when these mice were bred into a mixed background of C57Bl6/129Sv, the onset of the ALS phenotype was delayed (143 days to >2 years). Using 129 polymorphic autosomal markers in a whole genome scan, we have identified a major genetic modifier locus with a maximum lod score of 5.07 on mouse chromosome 13 between D13mit36 and D13mit76. This 5- to 8-cM interval contains the spinal muscular atrophy (SMA)-associated gene Smn (survival motor neuron) and seven copies of Naip (neuronal apoptosis inhibitory protein), suggesting a potential link between SMA and ALS. PMID:11112346

Kunst, C B; Messer, L; Gordon, J; Haines, J; Patterson, D



Evidence for the evolutionary origin of human chromosome 21 from comparative gene mapping in the cow and mouse  

SciTech Connect

To determine the extent of conservation between bovine syntenic group U10, human chromosome 21 (HSA 21), and mouse chromosome 16(MMU 16), 11 genes were physically mapped by segregation analysis in a bovine-hamster hybrid somatic cell panel. The genes chosen for study span MMU 16 and represent virtually the entire q arm of HSA 21. Because the somatostatin gene (SST), an HSA 3/MMU 16 locus, was previously shown to be in U10, the transferrin gene (TF), an HSA 3/MMU 9 marker, was also mapped to determine whether U10 contains any HSA 3 genes not represented on MMU 16. With the exception of the protamine gene PRM1 (HSA 16/MMU 16), all of the genes studies were syntenic on bovine U10. Thus, all homologous loci from HSA 21 that have been studied in the cow are on a single chromosome. The bovine homolog of HSA 21 also carries several HSA 3 genes, two of which have homologous loci on MMU 16. The syntenic association of genes from the q arm of HSA 3 with HSAS 21 genes in two mammalian species, the mouse and the cow, indicates that HSA 21 may have evolved from a larger ancestral mammalian chromosome that contained genes now residing on HSA 3. Additionally, the syntenic association of TF with SST in the cow permits the prediction that the rhodopsin gene (RHO) is proximal to TF on HSA 3q.

Threadgill, D.S.; Womack, J.E. (Texas A and M Univ., College Station (United States)); Kraus, J.P. (Univ. of Colorado Health Sciences Center, Denver (United States)); Krawetz, S.A. (Wayne State Univ., Detroit, MI (United States))



Genes affected by mouse mammary tumor virus (MMTV) proviral insertions in mouse mammary tumors are deregulated or mutated in primary human mammary tumors  

PubMed Central

The accumulation of mutations is a contributing factor in the initiation of premalignant mammary lesions and their progression to malignancy and metastasis. We have used a mouse model in which the carcinogen is the mouse mammary tumor virus (MMTV) which induces clonal premalignant mammary lesions and malignant mammary tumors by insertional mutagenesis. Identification of the genes and signaling pathways affected in MMTV-induced mouse mammary lesions provides a rationale for determining whether genetic alteration of the human orthologues of these genes/pathways may contribute to human breast carcinogenesis. A high-throughput platform for inverse PCR to identify MMTV-host junction fragments and their nucleotide sequences in a large panel of MMTV-induced lesions was developed. Validation of the genes affected by MMTV-insertion was carried out by microarray analysis. Common integration site (CIS) means that the gene was altered by an MMTV proviral insertion in at least two independent lesions arising in different hosts. Three of the new genes identified as CIS for MMTV were assayed for their capability to confer on HC11 mouse mammary epithelial cells the ability for invasion, anchorage independent growth and tumor development in nude mice. Analysis of MMTV induced mammary premalignant hyperplastic outgrowth (HOG) lines and mammary tumors led to the identification of CIS restricted to 35 loci. Within these loci members of the Wnt, Fgf and Rspo gene families plus two linked genes (Npm3 and Ddn) were frequently activated in tumors induced by MMTV. A second group of 15 CIS occur at a low frequency (2-5 observations) in mammary HOGs or tumors. In this latter group the expression of either Phf19 or Sdc2 was shown to increase HC11 cells invasion capability. Foxl1 expression conferred on HC11 cells the capability for anchorage-independent colony formation in soft agar and tumor development in nude mice. The published transcriptome and nucleotide sequence analysis of gene expression in primary human breast tumors was interrogated. Twenty of the human orthologues of MMTV CIS associated genes are deregulated and/or mutated in human breast tumors. PMID:23131872

Callahan, Robert; Mudunuri, Uma; Bargo, Sharon; Raafat, Ahmed; McCurdy, David; Boulanger, Corinne; Lowther, William; Stephens, Robert; Luke, Brian T.; Stewart, Claudia; Wu, Xiaolin; Munroe, David; Smith, Gilbert H.



Differential transcriptome analysis of diabetes-resistant and -sensitive mouse islets reveals significant overlap with human diabetes susceptibility genes.  


Type 2 diabetes in humans and in obese mice is polygenic. In recent genome-wide association studies, genetic markers explaining a small portion of the genetic contribution to the disease were discovered. However, functional evidence linking these genes with the pathogenesis of diabetes is scarce. We performed RNA sequencing-based transcriptomics of islets from two obese mouse strains, a diabetes-susceptible (NZO) and a diabetes-resistant (B6-ob/ob) mouse, after a short glucose challenge and compared these results with human data. Alignment of 2,328 differentially expressed genes to 106 human diabetes candidate genes revealed an overlap of 20 genes, including TCF7L2, IGFBP2, CDKN2A, CDKN2B, GRB10, and PRC1. The data provide a functional validation of human diabetes candidate genes, including those involved in regulating islet cell recovery and proliferation, and identify additional candidates that could be involved in human ?-cell failure. PMID:25053586

Kluth, Oliver; Matzke, Daniela; Schulze, Gunnar; Schwenk, Robert W; Joost, Hans-Georg; Schürmann, Annette



Automated pipeline for atlas-based annotation of gene expression patterns: application to postnatal day 7 mouse brain.  


Massive amounts of image data have been collected and continue to be generated for representing cellular gene expression throughout the mouse brain. Critical to exploiting this key effort of the post-genomic era is the ability to place these data into a common spatial reference that enables rapid interactive queries, analysis, data sharing, and visualization. In this paper, we present a set of automated protocols for generating and annotating gene expression patterns suitable for the establishment of a database. The steps include imaging tissue slices, detecting cellular gene expression levels, spatial registration with an atlas, and textual annotation. Using high-throughput in situ hybridization to generate serial sets of tissues displaying gene expression, this process was applied toward the establishment of a database representing over 200 genes in the postnatal day 7 mouse brain. These data using this protocol are now well-suited for interactive comparisons, analysis, queries, and visualization. PMID:19698790

Carson, James; Ju, Tao; Bello, Musodiq; Thaller, Christina; Warren, Joe; Kakadiaris, Ioannis A; Chiu, Wah; Eichele, Gregor



Variation and Genetic Control of Gene Expression in Primary Immunocytes across Inbred Mouse Strains.  


To determine the breadth and underpinning of changes in immunocyte gene expression due to genetic variation in mice, we performed, as part of the Immunological Genome Project, gene expression profiling for CD4(+) T cells and neutrophils purified from 39 inbred strains of the Mouse Phenome Database. Considering both cell types, a large number of transcripts showed significant variation across the inbred strains, with 22% of the transcriptome varying by 2-fold or more. These included 119 loci with apparent complete loss of function, where the corresponding transcript was not expressed in some of the strains, representing a useful resource of "natural knockouts." We identified 1222 cis-expression quantitative trait loci (cis-eQTL) that control some of this variation. Most (60%) cis-eQTLs were shared between T cells and neutrophils, but a significant portion uniquely impacted one of the cell types, suggesting cell type-specific regulatory mechanisms. Using a conditional regression algorithm, we predicted regulatory interactions between transcription factors and potential targets, and we demonstrated that these predictions overlap with regulatory interactions inferred from transcriptional changes during immunocyte differentiation. Finally, comparison of these and parallel data from CD4(+) T cells of healthy humans demonstrated intriguing similarities in variability of a gene's expression: the most variable genes tended to be the same in both species, and there was an overlap in genes subject to strong cis-acting genetic variants. We speculate that this "conservation of variation" reflects a differential constraint on intraspecies variation in expression levels of different genes, either through lower pressure for some genes, or by favoring variability for others. PMID:25267973

Mostafavi, Sara; Ortiz-Lopez, Adriana; Bogue, Molly A; Hattori, Kimie; Pop, Cristina; Koller, Daphne; Mathis, Diane; Benoist, Christophe; Blair, David A; Dustin, Michael L; Shinton, Susan A; Hardy, Richard R; Shay, Tal; Regev, Aviv; Cohen, Nadia; Brennan, Patrick; Brenner, Michael; Kim, Francis; Rao, Tata Nageswara; Wagers, Amy; Heng, Tracy; Ericson, Jeffrey; Rothamel, Katherine; Ortiz-Lopez, Adriana; Mathis, Diane; Benoist, Christophe; Kreslavsky, Taras; Fletcher, Anne; Elpek, Kutlu; Bellemare-Pelletier, Angelique; Malhotra, Deepali; Turley, Shannon; Miller, Jennifer; Brown, Brian; Merad, Miriam; Gautier, Emmanuel L; Jakubzick, Claudia; Randolph, Gwendalyn J; Monach, Paul; Best, Adam J; Knell, Jamie; Goldrath, Ananda; Jojic, Vladimir; Koller, Daphne; Laidlaw, David; Collins, Jim; Gazit, Roi; Rossi, Derrick J; Malhotra, Nidhi; Sylvia, Katelyn; Kang, Joonsoo; Bezman, Natalie A; Sun, Joseph C; Min-Oo, Gundula; Kim, Charlie C; Lanier, Lewis L



Subchronic effects of valproic acid on gene expression profiles for lipid metabolism in mouse liver  

SciTech Connect

Valproic acid (VPA) is used clinically to treat epilepsy, however it induces hepatotoxicity such as microvesicular steatosis. Acute hepatotoxicity of VPA has been well documented by biochemical studies and microarray analysis, but little is known about the chronic effects of VPA in the liver. In the present investigation, we profiled gene expression patterns in the mouse liver after subchronic treatment with VPA. VPA was administered orally at a dose of 100 mg/kg/day or 500 mg/kg/day to ICR mice, and the livers were obtained after 1, 2, or 4 weeks. The activities of serum liver enzymes did not change, whereas triglyceride concentration increased significantly. Microarray analysis revealed that 1325 genes of a set of 32,996 individual genes were VPA responsive when examined by two-way ANOVA (P < 0.05) and fold change (> 1.5). Consistent with our previous results obtained using an acute VPA exposure model (Lee et al., Toxicol Appl Pharmacol. 220:45-59, 2007), the most significantly over-represented biological terms for these genes included lipid, fatty acid, and steroid metabolism. Biological pathway analysis suggests that the genes responsible for increased biosynthesis of cholesterol and triglyceride, and for decreased fatty acid {beta}-oxidation contribute to the abnormalities in lipid metabolism induced by subchronic VPA treatment. A comparison of the VPA-responsive genes in the acute and subchronic models extracted 15 commonly altered genes, such as Cyp4a14 and Adpn, which may have predictive power to distinguish the mode of action of hepatotoxicants. Our data provide a better understanding of the molecular mechanisms of VPA-induced hepatotoxicity and useful information to predict steatogenic hepatotoxicity.

Lee, Min-Ho [College of Pharmacy, Seoul National Univ., Seoul 151-742 (Korea, Republic of)]|[Bio-MAX Inst., Seoul National Univ., Seoul 151-742 (Korea, Republic of); Kim, Mingoo [Seoul National Univ. Biomedical Informatics College of Medicine, Seoul National Univ., Seoul 151-742 (Korea, Republic of)]|[Toxicogenomics Research Consortium, Hanyang Univ., Seoul 133-791 (Korea, Republic of); Lee, Byung-Hoon [College of Pharmacy, Seoul National Univ., Seoul 151-742 (Korea, Republic of)]|[Toxicogenomics Research Consortium, Hanyang Univ., Seoul 133-791 (Korea, Republic of); Kim, Ju-Han [Seoul National Univ. Biomedical Informatics College of Medicine, Seoul National Univ., Seoul 151-742 (Korea, Republic of)]|[Toxicogenomics Research Consortium, Hanyang Univ., Seoul 133-791 (Korea, Republic of); Kang, Kyung-Sun [Dept. of Veterinary Public Health College of Veterinary Medicine, Seoul National Univ., Seoul 151-742 (Korea, Republic of)]|[Toxicogenomics Research Consortium, Hanyang Univ., Seoul 133-791 (Korea, Republic of); Kim, Hyung-Lae [Dept. of Biochemistry College of Medicine, Ewha Womans Univ., Seoul 158-710 (Korea, Republic of)]|[Toxicogenomics Research Consortium, Hanyang Univ., Seoul 133-791 (Korea, Republic of); Yoon, Byung-Il [School of Veterinary Medicine, Kangwon National Univ., Kangwon 200-701 (Korea, Republic of)]|[Toxicogenomics Research Consortium, Hanyang Univ., Seoul 133-791 (Korea, Republic of); Chung, Heekyoung; Kong, Gu [Dept. of Pathology College of Medicine, Hanyang Univ., Seoul 133-791 (Korea, Republic of)]|[Toxicogenomics Research Consortium, Hanyang Univ., Seoul 133-791 (Korea, Republic of); Lee, Mi-Ock [College of Pharmacy, Seoul National Univ., Seoul 151-742 (Korea, Republic of)]|[Bio-MAX Inst., Seoul National Univ., Seoul 151-742 (Korea, Republic of)]|[Toxicogenomics Research Consortium, Hanyang Univ., Seoul 133-791 (Korea, Republic of)], E-mail:



Gene expression profiling in mouse lung following polymeric hexamethylene diisocyanate exposure  

SciTech Connect

Isocyanates are a common cause of occupational lung disease. Hexamethylene diisocyanate (HDI), a component of polyurethane spray paints, can induce respiratory symptoms, inflammation, lung function impairment, and isocyanate asthma. The predominant form of HDI in polyurethane paints is a nonvolatile polyisocyanate known as HDI biuret trimer (HDI-BT). Exposure of mice to aerosolized HDI-BT results in pathological effects, including pulmonary edema, lung inflammation, cellular proliferation, and fibrotic lesions, which occur with distinct time courses following exposure. To identify genes that mediate lung pathology in the distinct temporal phases after exposure, gene expression profiles in HDI-BT-exposed C57BL/6J mouse lungs were analyzed. RNase protection assay (RPA) of genes involved in apoptosis, cell survival, and inflammation revealed increased expression of I{kappa}B{alpha}, Fas, Bcl-X{sub L}, TNF{alpha}, KC, MIP-2, IL-6, and GM-CSF following HDI-BT exposure. Microarray analysis of approximately 10 000 genes was performed on lung RNA collected from mice 6, 18, and 90 h after HDI-BT exposure and from unexposed mice. Classes of genes whose expression was increased 6 h after exposure included those involved in stress responses (particularly oxidative stress and thiol redox balance), growth arrest, apoptosis, signal transduction, and inflammation. Types of genes whose expression was increased at 18 h included proteinases, anti-proteinases, cytoskeletal molecules, and inflammatory mediators. Transcripts increased at 90 h included extracellular matrix components, transcription factors, inflammatory mediators, and cell cycle regulators. This characterization of the gene expression profile in lungs exposed to HDI-BT will provide a basis for investigating injury and repair pathways that are operative during isocyanate-induced lung disease.

Lee, C.-T. [Section of Pulmonary Diseases, Critical Care and Environmental Medicine, Department of Medicine, Tulane University Health Sciences Center, New Orleans, LA 70112 (United States); Interdisciplinary Graduate Program in Molecular and Cellular Toxicology, Tulane University Health Sciences Center, New Orleans, LA 70112 (United States); Ylostalo, Joni [Center for Gene Therapy, Tulane University Health Sciences Center, New Orleans, LA 70112 (United States); Friedman, Mitchell [Section of Pulmonary Diseases, Critical Care and Environmental Medicine, Department of Medicine, Tulane University Health Sciences Center, New Orleans, LA 70112 (United States); Hoyle, Gary W. [Section of Pulmonary Diseases, Critical Care and Environmental Medicine, Department of Medicine, Tulane University Health Sciences Center, New Orleans, LA 70112 (United States)]. E-mail:



CRISPR-mediated direct mutation of cancer genes in the mouse liver.  


The study of cancer genes in mouse models has traditionally relied on genetically-engineered strains made via transgenesis or gene targeting in embryonic stem cells. Here we describe a new method of cancer model generation using the CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated proteins) system in vivo in wild-type mice. We used hydrodynamic injection to deliver a CRISPR plasmid DNA expressing Cas9 and single guide RNAs (sgRNAs) to the liver that directly target the tumour suppressor genes Pten (ref. 5) and p53 (also known as TP53 and Trp53) (ref. 6), alone and in combination. CRISPR-mediated Pten mutation led to elevated Akt phosphorylation and lipid accumulation in hepatocytes, phenocopying the effects of deletion of the gene using Cre-LoxP technology. Simultaneous targeting of Pten and p53 induced liver tumours that mimicked those caused by Cre-loxP-mediated deletion of Pten and p53. DNA sequencing of liver and tumour tissue revealed insertion or deletion mutations of the tumour suppressor genes, including bi-allelic mutations of both Pten and p53 in tumours. Furthermore, co-injection of Cas9 plasmids harbouring sgRNAs targeting the ?-catenin gene and a single-stranded DNA oligonucleotide donor carrying activating point mutations led to the generation of hepatocytes with nuclear localization of ?-catenin. This study demonstrates the feasibility of direct mutation of tumour suppressor genes and oncogenes in the liver using the CRISPR/Cas system, which presents a new avenue for rapid development of liver cancer models and functional genomics. PMID:25119044

Xue, Wen; Chen, Sidi; Yin, Hao; Tammela, Tuomas; Papagiannakopoulos, Thales; Joshi, Nikhil S; Cai, Wenxin; Yang, Gillian; Bronson, Roderick; Crowley, Denise G; Zhang, Feng; Anderson, Daniel G; Sharp, Phillip A; Jacks, Tyler



Mouse model of human beta zero thalassemia: targeted deletion of the mouse beta maj- and beta min-globin genes in embryonic stem cells.  

PubMed Central

beta zero-Thalassemia is an inherited disorder characterized by the absence of beta-globin polypeptides derived from the affected allele. The molecular basis for this deficiency is a mutation of the adult beta-globin structural gene or cis regulatory elements that control beta-globin gene expression. A mouse model of this disease would enable the testing of therapeutic regimens designed to correct the defect. Here we report a 16-kb deletion that includes both adult beta-like globin genes, beta maj and beta min, in mouse embryonic stem cells. Heterozygous animals derived from the targeted cells are severely anemic with dramatically reduced hemoglobin levels, abnormal red cell morphology, splenomegaly, and markedly increased reticulocyte counts. Homozygous animals die in utero; however, heterozygous mice are fertile and transmit the deleted allele to progeny. The anemic phenotype is completely rescued in progeny derived from mating beta zero-thalassemic animals with transgenic mice expressing high levels of human hemoglobin A. The beta zero-thalassemic mice can be used to test genetic therapies for beta zero-thalassemia and can be bred with transgenic mice expressing high levels of human hemoglobin HbS to produce an improved mouse model of sickle cell disease. Images Fig. 1 Fig. 2 Fig. 3 Fig. 4 Fig. 5 PMID:7568113

Ciavatta, D J; Ryan, T M; Farmer, S C; Townes, T M



Rapid target gene validation in complex cancer mouse models using re-derived embryonic stem cells  

PubMed Central

Human cancers modeled in Genetically Engineered Mouse Models (GEMMs) can provide important mechanistic insights into the molecular basis of tumor development and enable testing of new intervention strategies. The inherent complexity of these models, with often multiple modified tumor suppressor genes and oncogenes, has hampered their use as preclinical models for validating cancer genes and drug targets. In our newly developed approach for the fast generation of tumor cohorts we have overcome this obstacle, as exemplified for three GEMMs; two lung cancer models and one mesothelioma model. Three elements are central for this system; (i) The efficient derivation of authentic Embryonic Stem Cells (ESCs) from established GEMMs, (ii) the routine introduction of transgenes of choice in these GEMM-ESCs by Flp recombinase-mediated integration and (iii) the direct use of the chimeric animals in tumor cohorts. By applying stringent quality controls, the GEMM-ESC approach proofs to be a reliable and effective method to speed up cancer gene assessment and target validation. As proof-of-principle, we demonstrate that MycL1 is a key driver gene in Small Cell Lung Cancer. PMID:24401838

Huijbers, Ivo J; Bin Ali, Rahmen; Pritchard, Colin; Cozijnsen, Miranda; Kwon, Min-Chul; Proost, Natalie; Song, Ji-Ying; Vries, Hilda; Badhai, Jitendra; Sutherland, Kate; Krimpenfort, Paul; Michalak, Ewa M; Jonkers, Jos; Berns, Anton



Suicide gene-mediated ablation of tumor-initiating mouse pluripotent stem cells.  


Pluripotent stem cells, including embryonic stem (ES) and induced pluripotent stem (iPS) cells, serve as unlimited resources for cell replacement therapy and tissue engineering because such cells are capable of extensive proliferation in vitro and can give rise to lineages that represent any of the three embryonic germ layers. However, in the context of the in vivo behavior of cell transplants, key challenges need to be addressed and essential strategies should be developed before stem cells can be used in clinical practice. In the present study, we modified mouse ES/iPS cells to contain a suicide gene, deltaTK or CodA, under the transcriptional control of the EF1? or Nanog promoter. The suicide gene was introduced via lentivirus transduction without interfering with their self-renewal and pluripotency characteristics. We found that EF1? promoter-controlled deltaTK/CodA expression efficiently eliminated pluripotent stem cells and their derivatives both in vitro and in vivo. When the suicide gene was under the control of the Nanog promoter, tumor-initiating undifferentiated pluripotent stem cells were selectively ablated in vitro after prodrug treatment. These results indicate that modification of pluripotent stem cells with a suicide gene prior to transplantation offers a safe manner by which wayward stem cells, and their progeny, can be controlled in vivo. Our approach will render the clinical application of human pluripotent stem cells increasingly possible. PMID:23218839

Chen, Fei; Cai, Bing; Gao, Yong; Yuan, Xiaofeng; Cheng, Fuyi; Wang, Tao; Jiang, Meihua; Zhou, Yijia; Lahn, Bruce T; Li, Weiqiang; Xiang, Andy Peng



Alternative splicing of the tuberous sclerosis 2 (TSC2) gene in human and mouse tissues  

SciTech Connect

The recently isolated gene for tuberous sclerosis 2 (TSC2) encodes a 5.5.kb transcript that is widely expressed. The TSC2 gene product, named tuberin, is a 1784-amino-acid protein that shows a small stretch of homology to the GTPase activating protein rap1GAP. We have detected a novel variant of the TSC2 mRNA lacking 129 nucleotides, predicting an in-frame deletion of 43 amino acids spanning codons 946-988 of tuberin. This 129-bp deletion precisely corresponds to exon 25 of the TSC2 gene suggesting that alternative splicing leads to production of two forms of transcripts designated isoforms 1 and 2. Further molecular analysis revealed a third isoform exhibiting a deletion of 44 amino acids spanning codons 946-989 of tuberin. Amino acid 989 is a Ser residue encoded by the first codon of exon 26. The two isoforms also exist in newborn and adult mouse tissues, reinforcing the potential functional importance of these alternatively spliced products. These alternative isoforms should have implications for efforts aimed at identifying mutations in TSC patients. The distinct polypeptides encoded by the TSC2 gene may have different targets as well as functions involved in the regulation of cell growth. 26 refs., 4 figs.

Xu, Lin; Sterner, C.; Maheshwar, M.M. [and others] [and others



Rapid target gene validation in complex cancer mouse models using re-derived embryonic stem cells.  


Human cancers modeled in Genetically Engineered Mouse Models (GEMMs) can provide important mechanistic insights into the molecular basis of tumor development and enable testing of new intervention strategies. The inherent complexity of these models, with often multiple modified tumor suppressor genes and oncogenes, has hampered their use as preclinical models for validating cancer genes and drug targets. In our newly developed approach for the fast generation of tumor cohorts we have overcome this obstacle, as exemplified for three GEMMs; two lung cancer models and one mesothelioma model. Three elements are central for this system; (i) The efficient derivation of authentic Embryonic Stem Cells (ESCs) from established GEMMs, (ii) the routine introduction of transgenes of choice in these GEMM-ESCs by Flp recombinase-mediated integration and (iii) the direct use of the chimeric animals in tumor cohorts. By applying stringent quality controls, the GEMM-ESC approach proofs to be a reliable and effective method to speed up cancer gene assessment and target validation. As proof-of-principle, we demonstrate that MycL1 is a key driver gene in Small Cell Lung Cancer. PMID:24401838

Huijbers, Ivo J; Bin Ali, Rahmen; Pritchard, Colin; Cozijnsen, Miranda; Kwon, Min-Chul; Proost, Natalie; Song, Ji-Ying; de Vries, Hilda; Badhai, Jitendra; Sutherland, Kate; Krimpenfort, Paul; Michalak, Ewa M; Jonkers, Jos; Berns, Anton



A novel mouse model for Down syndrome that harbor a single copy of human artificial chromosome (HAC) carrying a limited number of genes from human chromosome 21.  


Down syndrome (DS), also known as Trisomy 21, is the most common chromosome aneuploidy in live-born children and displays a complicated symptom. To date, several kinds of mouse models have been generated to understand the molecular pathology of DS, yet the gene dosage effects and gene(s)-phenotype(s) correlation are not well understood. In this study, we established a novel method to generate a partial trisomy mice using the mouse ES cells that harbor a single copy of human artificial chromosome (HAC), into which a small human DNA segment containing human chromosome 21 genes cloned in a bacterial artificial chromosome (BAC) was recombined. The produced mice were found to maintain the HAC carrying human genes as a mini-chromosome, hence termed as a Trans-Mini-Chromosomal (TMC) mouse, and HAC was transmitted for more than twenty generations independent from endogenous mouse chromosomes. The three human transgenes including cystathionine ?-synthase, U2 auxiliary factor and crystalline alpha A were expressed in several mouse tissues with various expression levels relative to mouse endogenous genes. The novel system is applicable to any of human and/or mouse BAC clones. Thus, the TMC mouse carrying a HAC with a limited number of genes would provide a novel tool for studying gene dosage effects involved in the DS molecular pathogenesis and the gene(s)-phenotype(s) correlation. PMID:24293126

Miyamoto, Kenichi; Suzuki, Nobutaka; Sakai, Kosuke; Asakawa, Shuichi; Okazaki, Tsuneko; Kudoh, Jun; Ikeno, Masashi; Shimizu, Nobuyoshi



Identification, cloning and expression of the mouse N-acetylglutamate synthase gene.  

PubMed Central

In ureotelic animals, N-acetylglutamate (NAG) is an essential allosteric activator of carbamylphosphate synthetase I (CPSI), the first enzyme in the urea cycle. NAG synthase (NAGS; EC catalyses the formation of NAG from glutamate and acetyl-CoA in liver and intestinal mitochondria. This enzyme is supposed to regulate ureagenesis by producing variable amounts of NAG, thus modulating CPSI activity. Moreover, inherited deficiencies in NAGS have been associated with hyperammonaemia, probably due to the loss of CPSI activity. Although the existence of the NAGS protein in mammals has been known for decades, the gene has remained elusive. We identified the mouse (Mus musculus) and human NAGS genes using their similarity to the respective Neurospora crassa gene. NAGS was cloned from a mouse liver cDNA library and was found to encode a 2.3 kb message, highly expressed in liver and small intestine with lower expression levels in kidney, spleen and testis. The deduced amino acid sequence contains a putative mitochondrial targeting signal at the N-terminus. The cDNA sequence complements an argA (NAGS)-deficient Escherichia coli strain, reversing its arginine auxotrophy. His-tagged versions of the pre-protein and two putative mature proteins were each overexpressed in E. coli, and purified to apparent homogeneity by using a nickel-affinity column. The pre-protein and the two putative mature proteins catalysed the NAGS reaction but one of the putative mature enzymes had significantly higher activity than the pre-protein. The addition of l-arginine increased the catalytic activity of the purified recombinant NAGS enzymes by approx. 2-6-fold. PMID:12049647

Caldovic, Ljubica; Morizono, Hiroki; Yu, Xiaolin; Thompson, Mark; Shi, Dashuang; Gallegos, Rene; Allewell, Norma M; Malamy, Michael H; Tuchman, Mendel



Genomic imprinting variations in the mouse type 3 deiodinase gene between tissues and brain regions.  


The Dio3 gene, which encodes for the type 3 deiodinase (D3), controls thyroid hormone (TH) availability. The lack of D3 in mice results in tissue overexposure to TH and a broad neuroendocrine phenotype. Dio3 is an imprinted gene, preferentially expressed from the paternally inherited allele in the mouse fetus. However, heterozygous mice with paternal inheritance of the inactivating Dio3 mutation exhibit an attenuated phenotype when compared with that of Dio3 null mice. To investigate this milder phenotype, the allelic expression of Dio3 was evaluated in different mouse tissues. Preferential allelic expression of Dio3 from the paternal allele was observed in fetal tissues and neonatal brain regions, whereas the biallelic Dio3 expression occurred in the developing eye, testes, and cerebellum and in the postnatal brain neocortex, which expresses a larger Dio3 mRNA transcript. The newborn hypothalamus manifests the highest degree of Dio3 expression from the paternal allele, compared with other brain regions, and preferential allelic expression of Dio3 in the brain relaxed in late neonatal life. A methylation analysis of two regulatory regions of the Dio3 imprinted domain revealed modest but significant differences between tissues, but these did not consistently correlate with the observed patterns of Dio3 allelic expression. Deletion of the Dio3 gene and promoter did not result in significant changes in the tissue-specific patterns of Dio3 allelic expression. These results suggest the existence of unidentified epigenetic determinants of tissue-specific Dio3 imprinting. The resulting variation in the Dio3 allelic expression between tissues likely explains the phenotypic variation that results from paternal Dio3 haploinsufficiency. PMID:25232934

Martinez, M Elena; Charalambous, Marika; Saferali, Aabida; Fiering, Steven; Naumova, Anna K; St Germain, Donald; Ferguson-Smith, Anne C; Hernandez, Arturo



Gene expression profiles of a mouse congenic strain carrying an obesity susceptibility QTL under obesigenic diets  

PubMed Central

Genetic factors are strongly involved in the development of obesity, likely through the interactions of susceptibility genes with obesigenic environments, such as high-fat, high-sucrose (HFS) diets. Previously, we have established a mouse congenic strain on C57BL/6 J background, carrying an obesity quantitative trait locus (QTL), tabw2, derived from obese diabetic TALLYHO/JngJ mice. The tabw2 congenic mice exhibit increased adiposity and hyperleptinemia, which becomes exacerbated upon feeding HFS diets. In this study, we conducted genome-wide gene expression profiling to evaluate differentially expressed genes between tabw2 and control mice fed HFS diets, which may lead to identification of candidate genes as well as insights into the mechanisms underlying obesity mediated by tabw2. Both tabw2 congenic mice and control mice were fed HFS diets for 10 weeks beginning at 4 weeks of age, and total RNA was isolated from liver and adipose tissue. Whole-genome microarray analysis was performed and verified by real-time quantitative RT–PCR. At False Discovery Rate adjusted P < 0.05, 1026 genes were up-regulated and 308 down-regulated in liver, whereas 393 were up-regulated and 187 down-regulated in adipose tissue in tabw2 congenic mice compared to controls. Within the tabw2 QTL interval, 70 genes exhibited differential expression in either liver or adipose tissue. A comprehensive pathway analysis revealed a number of biological pathways that may be perturbed in the diet-induced obesity mediated by tabw2. PMID:20020228

Kim, Hyoung Yon; Stewart, Taryn P.; Wyatt, Brantley N.; Siriwardhana, Nalin; Saxton, Arnold M.



Gene expression profile of quinacrine-cured prion-infected mouse neuronal cells.  


Prion diseases are transmissible fatal neurodegenerative diseases of humans and animals, characterised by the presence of an abnormal isoform (scrapie prion protein; PrP(Sc)) of the endogenous cellular prion protein (PrP(C)). The pathological mechanisms at the basis of prion diseases remain elusive, although the accumulation of PrP(Sc) has been linked to neurodegeneration. Different genomic approaches have been applied to carry out large-scale expression analysis in prion-infected brains and cell lines, in order to define factors potentially involved in pathogenesis. However, the general lack of overlap between the genes found in these studies prompted us to carry an analysis of gene expression using an alternative approach. Specifically, in order to avoid the complexities of shifting gene expression in a heterogeneous cell population, we used a single clone of GT1 cells that was de novo infected with mouse prion-infected brain homogenate and then treated with quinacrine to clear PrP(Sc). By comparing the gene expression profiles of about 15 000 genes in quinacrine-cured and not cured prion-infected GT1 cells, we investigated the influence of the presence or the absence of PrP(Sc). By real-time PCR, we confirmed that the gene encoding for laminin was down-regulated as a consequence of the elimination of PrP(Sc) by the quinacrine treatment. Thus, we speculate that this protein could be a specific candidate for further analysis of its role in prion infection and pathogenesis. PMID:18036195

Fasano, Carlo; Campana, Vincenza; Griffiths, Beatrice; Kelly, Gavin; Schiavo, Giampietro; Zurzolo, Chiara



Differential deployment of paralogous Wnt genes in the mouse and chick embryo during development  

PubMed Central

SUMMARY Genes encoding Wnt ligands are crucial in body patterning and are highly conserved among metazoans. Given their conservation at the protein-coding level, it is likely that changes in where and when these genes are active are important in generating evolutionary variations. However, we lack detailed knowledge about how their deployment has diverged. Here, we focus on four Wnt subfamilies (Wnt2, Wnt5, Wnt7, and Wnt8) in mammalian and avian species, consisting of a paralogous gene pair in each, believed to have duplicated in the last common ancestor of vertebrates. We use three-dimensional imaging to capture expression patterns in detail and carry out systematic comparisons. We find evidence of greater divergence between these subgroup paralogues than the respective orthologues, consistent with some level of subfunctionalization/neofunctionalization in the common vertebrate ancestor that has been conserved. However, there were exceptions; in the case of chick Wnt2b, individual sites were shared with both mouse Wnt2 and Wnt2b. We also find greater divergence, between paralogues and orthologues, in some subfamilies (Wnt2 and Wnt8) compared to others (Wnt5 and Wnt7) with the more highly similar expression patterns showing more extensive expression in more structures in the embryo. Wnt8 genes were most restricted and most divergent. Major sites of expression for all subfamilies include CNS, limbs, and facial region, and in general there were more similarities in gene deployment in these territories with divergent patterns featuring more in organs such as heart and gut. A detailed comparison of gene expression patterns in the limb showed similarities in overall combined domains across species with notable differences that may relate to lineage-specific morphogenesis. PMID:23017026

Martin, Audrey; Maher, Stephanie; Summerhurst, Kristen; Davidson, Duncan; Murphy, Paula



Influence of Aromatase Absence on the Gene Expression and Histology of the Mouse Meibomian Gland  

PubMed Central

Purpose. We hypothesize that aromatase, an enzyme that controls estrogen biosynthesis, plays a major role in the sex-related differences of the meibomian gland. To begin to test this hypothesis, we examined the influence of aromatase absence, which completely eliminates estrogen production, on glandular gene expression and histology in male and female mice. Methods. Meibomian glands were obtained from adult, age-matched wild-type (WT) and aromatase knockout (ArKO) mice. Tissues were processed for histology or the isolation of total RNA, which was analyzed for differentially expressed mRNAs by using microarrays. Results. Our results show that aromatase significantly influences the expression of more than a thousand genes in the meibomian gland. The nature of this effect is primarily sex-dependent. In addition, the influence of aromatase on sex-related differences in gene expression is predominantly genotype-specific. However, many of the sex-related variations in biological process, molecular function, and cellular component ontologies, as well as in KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways, are remarkably similar between WT and ArKO mice. The loss of aromatase activity has no obvious effect on the histology of meibomian glands in male or female mice. Conclusions. Our findings demonstrate that aromatase has a significant impact on gene expression in the meibomian gland. The nature of this influence is sex-dependent and genotype-specific; however, many of the sex-related variations in gene ontologies and KEGG pathways are similar between WT and ArKO mice. Consequently, it appears that aromatase, and by extension estrogen, do not play a major role in the sex-related differences of the mouse meibomian gland. PMID:23233261

Rahimi Darabad, Raheleh; Suzuki, Tomo; Richards, Stephen M.; Jensen, Roderick V.; Jakobiec, Frederick A.; Zakka, Fouad R.; Liu, Shaohui; Sullivan, David A.



Epigenetic patterns at the mouse prolyl oligopeptidase gene locus suggest the CpG island in the gene body to be a novel regulator for gene expression.  


Prolyl oligopeptidase (POP) is a widely distributed serine peptidase which hydrolyzes small peptides on the carboxyl side of an internal proline residue. While its physiological role has been intensely studied, the regulatory mechanism of the gene expression is poorly understood. This time we assessed the POP mRNA expression in mouse embryos and tissues related to reproduction and development and found that POP mRNA was highly expressed in the ovarian granulosa cell, placental spongiotrophoblast, and blastocyst embryo. To elucidate the mechanism by which POP expression is regulated, we investigated DNA methylation and histone modification patterns of the two CpG islands (CGIs) found at the mouse POP locus. Whereas the CGI including the POP promoter (CGI-1) was completely hypomethylated in all the tissues examined, DNA methylation level of the CGI in the gene body (CGI-2) was lower in the granulosa cell, placenta, and blastocyst than in the liver. Some specific CpGs in CGI-2 were significantly demethylated in the three tissues. An in vitro reporter analysis indicated that CGI-2 enhanced POP promoter activity and its effect was significantly reduced by DNA methylation. Moreover, histone H3 acetylation and H3K4 methylation levels of CGI-2 were higher in the granulosa cell than liver. The results suggest that the CGI-2 region is a cis-element for the POP gene expression. PMID:20600704

Matsubara, Shin; Takahashi, Takayuki; Kimura, Atsushi P



Two structurally distinct {kappa}B sequence motifs cooperatively control LPS-induced KC gene transcription in mouse macrophages  

SciTech Connect

The mouse KC gene is an {alpha}-chemokine gene whose transcription is induced in mononuclear phagocytes by LPS. DNA sequences necessary for transcriptional control of KC by LPS were identified in the region flanking the transcription start site. Transient transfection analysis in macrophages using deletion mutants of a 1.5-kb sequence placed in front of the chloramphenicol acetyl transferase (CAT) gene identified an LPS-responsive region between residues -104 and +30. This region contained two {kappa}B sequence motifs. The first motif (position -70 to -59, {kappa}B1) is highly conserved in all three human GRO genes and in the mouse macrophage inflammatory protein-2 (MIP-2) gene. The second {kappa}B motif (position -89 to -78, {kappa}B2) was conserved only between the mouse and the rat KC genes. Consistent with previous reports, the highly conserved {kappa}B site ({kappa}B1) was essential for LPS inducibility. Surprisingly, the distal {kappa}B site ({kappa}B2) was also necessary for optimal response; mutation of either {kappa}B site markedly reduced sensitivity to LPS in RAW264.7 cells and to TNF-{alpha} in NIH 3T3 fibroblasts. Although both {kappa}B1 and {kappa}B2 sequences were able to bind members of the Rel homology family, including NF{kappa}B1 (P50), RelA (65), and c-Rel, the {kappa}B1 site bound these factors with higher affinity and functioned more effectively than the {kappa}B2 site in a heterologous promoter. These findings demonstrate that transcriptional control of the KC gene requires cooperation between two {kappa}B sites and is thus distinct from that of the three human GRO genes and the mouse MIP-2 gene. 71 refs., 8 figs.

Ohmori, Y.; Fukumoto, S.; Hamilton, T.A. [Cleveland Clinic Foundation, Cleveland, OH (United States)



Differential effects of simvastatin on IL-13-induced cytokine gene expression in primary mouse tracheal epithelial cells  

PubMed Central

Background Asthma causes significant morbidity worldwide in adults and children alike, and incurs large healthcare costs. The statin drugs, which treat hyperlipidemia and cardiovascular diseases, have pleiotropic effects beyond lowering cholesterol, including immunomodulatory, anti-inflammatory, and anti-fibrotic properties which may benefit lung health. Using an allergic mouse model of asthma, we previously demonstrated a benefit of statins in reducing peribronchiolar eosinophilic inflammation, airway hyperreactivity, goblet cell hyperplasia, and lung IL-4 and IL-13 production. Objectives In this study, we evaluated whether simvastatin inhibits IL-13-induced pro-inflammatory gene expression of asthma-related cytokines in well-differentiated primary mouse tracheal epithelial (MTE) cell cultures. We hypothesized that simvastatin reduces the expression of IL-13-inducible genes in MTE cells. Methods We harvested tracheal epithelial cells from naïve BALB/c mice, grew them under air-liquid interface (ALI) cell culture conditions, then assessed IL-13-induced gene expression in MTE cells using a quantitative real-time PCR mouse gene array kit. Results We found that simvastatin had differential effects on IL-13-mediated gene expression (inhibited eotaxin-1; MCP-1,-2,-3; and osteopontin (SPP1), while it induced caspase-1 and CCL20 (MIP-3?)) in MTE cells. For other asthma-relevant genes such as TNF, IL-4, IL-10, CCL12 (MCP-5), CCL5 (RANTES), and CCR3, there were no significant IL-13-inducible or statin effects on gene expression. Conclusions Simvastatin modulates the gene expression of selected IL-13-inducible pro-inflammatory cytokines and chemokines in primary mouse tracheal epithelial cells. The airway epithelium may be a viable target tissue for the statin drugs. Further research is needed to assess the mechanisms of how statins modulate epithelial gene expression. PMID:22583375



Characteristic and expression analysis of a metallothionein gene, OsMT2b, down-regulated by cytokinin suggests functions in root development and seed embryo germination of rice.  


Metallothioneins (MTs) are low molecular mass and cysteine-rich metal-binding proteins known to be mainly involved in maintaining metal homeostasis and stress responses. But, their functions in higher plant development are scarcely studied. Here, we characterized rice (Oryza sativa) METALLOTHIONEIN2b (OsMT2b) molecularly and found that its expression was down-regulated by cytokinins. OsMT2b was preferentially expressed in rice immature panicles, scutellum of germinating embryos, and primordium of lateral roots. In contrast with wild-type plants, OsMT2b-RNA interference (RNAi) transgenic plants had serious handicap in plant growth and root formation, whereas OsMT2b-overexpressing transformants were dwarfed and presented more adventitious roots and big lateral roots. The increased cytokinin levels in RNAi plants and decreased cytokinin levels in overexpressing plants were confirmed by high-performance liquid chromatography quantitative analysis in the roots of wild-type and transgenic plants. In RNAi plants, localization of isopentenyladenosine, a kind of endogenous cytokinin, in roots and germinating embryos expanded to the whole tissues, whereas in overexpressing plants, the isopentenyladenosine signals were very faint in the vascular tissues of roots and scutellum cells of germinating embryos. In vitro culture of embryos could largely resume the reduced germination frequency in RNAi plants but had no obvious change in overexpressing plants. Taken together, these results indicate a possible feedback regulation mechanism of OsMT2b to the level of endogenous cytokinins that is involved in root development and seed embryo germination of rice. PMID:18258694

Yuan, Jing; Chen, Dan; Ren, Yujun; Zhang, Xuelian; Zhao, Jie



Mouse model of congenital polycythemia: Homologous replacement of murine gene by mutant human erythropoietin receptor gene  

Microsoft Academic Search

Mutations causing truncations of the cytoplasmic domain of the human erythropoietin receptor (EPOR) result in a dominantly inherited disorderprimary familial congenital polycythemia. This disorder is characterized by increased numbers of erythrocytes (polycythemia) and by in vitro hypersensitivity of erythroid precursors to erythropoietin. The consequences of EPOR truncation in nonerythroid tissues are unknown. We replaced the murine EPOR gene with a

Vladimir Divoky; Zhiyong Liu; Thomas M. Ryan; Jaroslav F. Prchal; Tim M. Townes; Josef T. Prchal



Isolation of cDNAs for mouse phenol and bilirubin UDP-glucuronosyltransferases and mapping of the mouse gene for phenol UDP-glucuronosyltransferase (Ugtlal) to chromosome 1 by restriction fragment length variations  

SciTech Connect

The mouse gene for phenol UDP-glucuronosyltransferase (UDPGT; Ugtla1) was mapped at 42 cM on chromosome 1, a position identical to that of the gene for bilirubin UDPGT (Ugtla1), from linkage analysis of a three-point cross test with Idh-1, En-1, and Ugtla1 as marker genes. The cDNAs for mouse phenol and bilirubin UDPGTs, isolated after amplification by PCR, shared an identical 3{prime}-half region. Our results strongly suggest that mouse bilirubin and phenol UDPGTs are expressed from a single gene and involve alternative splicing events. We also detect duplication of the gene for phenol UDPGT in all mouse strains examined with the exception of MOL-MIT and SUB-SHH. 15 refs., 3 figs., 1 tab.

Koiwai, O.; Yasui, Y. [Aichi Cancer Center Institute, Nagoya (Japan); Hasada, K. [Institute for Developmental Research, Aichi (Japan)] [and others



Expression of the mouse corticotropin-releasing hormone gene in vivo and targeted inactivation in embryonic stem cells.  

PubMed Central

Corticotropin-releasing hormone (CRH), one of the primary regulators of the hypothalamic-pituitary-adrenal (HPA) axis, exhibits abnormal regulation in pathologic states such as depression and anorexia nervosa. Analysis of the role of CRH in regulation of the HPA axis would be facilitated by the creation of animal models in which CRH gene structure and function could be manipulated. We have determined the DNA sequence of the mouse CRH gene. Using a highly sensitive reverse transcription-polymerase chain reaction method, we have found expression of CRH mRNA in adrenal, ovary, testis, gut, heart, anterior pituitary, lung, and spleen, in addition to cerebral cortex and hypothalamus. Within the spleen, CRH mRNA is localized specifically to T-lymphocytes. We mapped the chromosomal location of mouse CRH via interspecific mouse backcrosses to chromosome 3, which is not the site of any naturally occurring mutations consistent with CRH deficiency. Because of this, we inactivated a CRH allele in mouse embryonic stem (ES) cells by homologous recombination with a mutant mouse CRH gene lacking the entire coding region of preproCRH. Mice chimeric for each of two ES clones with an inactivated CRH allele are being used to generate animals with complete CRH deficiency. Images PMID:8182138

Muglia, L J; Jenkins, N A; Gilbert, D J; Copeland, N G; Majzoub, J A



Abundance of female-biased and paucity of male-biased somatically expressed genes on the mouse X-chromosome  

PubMed Central

Background Empirical evaluations of sexually dimorphic expression of genes on the mammalian X-chromosome are needed to understand the evolutionary forces and the gene-regulatory mechanisms controlling this chromosome. We performed a large-scale sex-bias expression analysis of genes on the X-chromosome in six different somatic tissues from mouse. Results Our results show that the mouse X-chromosome is enriched with female-biased genes and depleted of male-biased genes. This suggests that feminisation as well as de-masculinisation of the X-chromosome has occurred in terms of gene expression in non-reproductive tissues. Several mechanisms may be responsible for the control of female-biased expression on chromosome X, and escape from X-inactivation is a main candidate. We confirmed escape in case of Tmem29 using RNA-FISH analysis. In addition, we identified novel female-biased non-coding transcripts located in the same female-biased cluster as the well-known coding X-inactivation escapee Kdm5c, likely transcribed from the transition-region between active and silenced domains. We also found that previously known escapees only partially explained the overrepresentation of female-biased X-genes, particularly for tissue-specific female-biased genes. Therefore, the gene set we have identified contains tissue-specific escapees and/or genes controlled by other sexually skewed regulatory mechanisms. Analysis of gene age showed that evolutionarily old X-genes (>100 myr, preceding the radiation of placental mammals) are more frequently female-biased than younger genes. Conclusion Altogether, our results have implications for understanding both gene regulation and gene evolution of mammalian X-chromosomes, and suggest that the final result in terms of the X-gene composition (masculinisation versus feminisation) is a compromise between different evolutionary forces acting on reproductive and somatic tissues. PMID:23140559



Gene Expression and Gene Ontology Enrichment Analysis for H3K4me3 and H3K4me1 in Mouse Liver and Mouse Embryonic Stem Cell Using ChIP-Seq and RNA-Seq  

PubMed Central

Recent study has identified the cis-regulatory elements in the mouse genome as well as their genomic localizations. Recent discoveries have shown the enrichment of H3 lysine 4 trimethylation (H3K4me3) binding as an active promoter and the presence of H3 lysine 4 monomethylation (H3K4me1) outside promoter regions as a mark for an enhancer. In this work, we further identified highly expressed genes by H3K4me3 mark or by both H3K4me3 and H3K4me1 marks in mouse liver using ChIP-Seq and RNA-Seq. We found that in mice, the liver carries embryonic stem cell-related functions while the embryonic stem cell also carries liver-related functions. We also identified novel genes in RNA-Seq experiments for mouse liver and for mouse embryonic stem cells. These genes are not currently in the Ensemble gene database at NCBI. PMID:24526835

Tran, Ngoc Tam L.; Huang, Chun-Hsi



Statistical analysis of differential gene expression relative to a fold change threshold on NanoString data of mouse odorant receptor genes  

PubMed Central

Background A challenge in gene expression studies is the reliable identification of differentially expressed genes. In many high-throughput studies, genes are accepted as differentially expressed only if they satisfy simultaneously a p value criterion and a fold change criterion. A statistical method, TREAT, has been developed for microarray data to assess formally if fold changes are significantly higher than a predefined threshold. We have recently applied the NanoString digital platform to study expression of mouse odorant receptor genes, which form with 1,200 members the largest gene family in the mouse genome. Our objectives are, on these data, to decrease false discoveries when formally assessing the genes relative to a fold change threshold, and to provide a guided selection in the choice of this threshold. Results Statistical tests have been developed for microarray data to identify genes that are differentially expressed relative to a fold change threshold. Here we report that another approach, which we refer to as tTREAT, is more appropriate for our NanoString data, where false discoveries lead to costly and time-consuming follow-up experiments. Methods that we refer to as tTREAT2 and the running fold change model improve the performance of the statistical tests by protecting or selecting the fold change threshold more objectively. We show the benefits on simulated and real data. Conclusions Gene-wise statistical analyses of gene expression data, for which the significance relative to a fold change threshold is important, give reproducible and reliable results on NanoString data of mouse odorant receptor genes. Because it can be difficult to set in advance a fold change threshold that is meaningful for the available data, we developed methods that enable a better choice (thus reducing false discoveries and/or missed genes) or avoid this choice altogether. This set of tools may be useful for the analysis of other types of gene expression data. PMID:24495268



Gene delivery in mouse auditory brainstem and hindbrain using in utero electroporation  

PubMed Central

Background Manipulation of gene expression via recombinant viral vectors and creation of transgenic knock-out/in animals has revolutionized our understanding of genes that play critical roles during neuronal development and pathophysiology of neurological disorders. Recently, target-specific genetic manipulations are made possible to perform in combination with specific Cre-lines, albeit costly, labor-intensive and time consuming. Thus, alternative methods of gene manipulations to address important biological questions are highly desirable. In this study, we utilized in utero electroporation technique which involves efficient delivery of hindbrain-specific enhancer/promoter construct, Krox20 into the third ventricle of live mouse embryo to investigate green fluorescent protein (GFP) expression pattern in mouse auditory brainstem and other hindbrain neurons. Results We created a GFP/DNA construct containing a Krox20 B enhancer and ?-globin promoter to drive GFP expression in the hindbrain via injection into the third ventricle of E12 to E13.5 mice. Electrical currents were applied directly to the embryonic hindbrain to allow DNA uptake into the cell. Confocal images were then acquired from fixed brain slices to analyze GFP expression in mouse whole brain at different postnatal stages (P6-P21). By using a cell-type specific enhancer as well as region specific injection and electroporation, robust GFP expression in the cerebellum and auditory brainstem but not in the forebrain was observed. GFP expression in calyx of Held terminals was more robust in P15 mice. In contrast, GFP expression in MNTB neurons was more prevalent in >P15 compared to



The use of carboxymethylcellulose gel to increase non-viral gene transfer in mouse airways  

PubMed Central

We have assessed whether viscoelastic gels known to inhibit mucociliary clearance can increase lipid-mediated gene transfer. Methylcellulose or carboxymethylcellulose (0.25 to 1.5%) were mixed with complexes of the cationic lipid GL67A and plasmids encoding luciferase and perfused onto the nasal epithelium of mice. Survival after perfusion with 1% CMC or1% MC was 90 and 100%, respectively. In contrast 1.5% CMC was uniformly lethal likely due to the viscous solution blocking the airways. Perfusion with 0.5% CMC containing lipid/DNA complexes reproducibly increased gene expression by approximately 3-fold (n= 16, p<0.05). Given this benefit, likely related to increased duration of contact, we also assessed the effect of prolonging contact time of the liposome/DNA complexes by delivering our standard 80 ?g DNA dose over either approximately 22 or 60 min of perfusion. This independently increased gene transfer by 6-fold (n=8, p<0.05) and could be further enhanced by the addition of 0.5% CMC, leading to an overall 25-fold enhancement (n=8, p<0.001) in gene expression. As a result of these interventions CFTR transgene mRNA transgene levels were increased several logs above background. Interestingly, this did not lead to correction of the ion transport defects in the nasal epithelium of cystic fibrosis mice nor for immunohistochemical quantification of CFTR expression. To assess if 0.5% CMC also increased gene transfer in the mouse lung, we used whole body nebulisation chambers. CMC was nebulised for 1 hr immediately before, or simultaneously with GL67A/pCIKLux. The former did not increase gene transfer, whereas co-administration significantly increased gene transfer by 4-fold (p<0.0001, n=18). This study suggests that contact time of non-viral gene transfer agents is a key factor for gene delivery, and suggests two methods which may be translatable for use in man. PMID:20022367

Griesenbach, Uta; Meng, Cuixiang; Farley, Raymond; Wasowicz, Marguerite; Munkonge, Felix M; Chan, Mario; Stoneham, Charlotte; Sumner-Jones, Stephanie; Pringle, Ian A.; Gill, Deborah R.; Hyde, Stephen C.; Stevenson, Barbara; Holder, Emma; Ban, Hiroshi; Hasegawa, Mamoru; Cheng, Seng H; Scheule, Ronald K; Sinn, Patrick L; McCray, Paul B; Alton, Eric WFW



Trehalose Maintains Vitality of Mouse Epididymal Epithelial Cells and Mediates Gene Transfer  

PubMed Central

In the present study, trehalose was utilized to improve primary culture of mouse epididymal epithelial cells in vitro, and to enhance naked DNA delivery in epididymis in vivo. During the six-day culture, the proliferation activity of the cells in the medium with addition of trehalose was higher than that of those cells cultured in absence of trehalose (p<0.01). To determine the optimal concentration for cell proliferation, a series of trehalose concentrations (0, 60, 120, 180 mM) were tested, and the result indicated that the cell in the medium with 120 mM trehalose showed the highest proliferation potential. The epididymis epithelial cells were cultured in the medium containing 120 mM trehalose upon 16th passage, and they continued expressing markers of epididymal epithelial cell, such as rE-RABP, AR and ER-beta. Our study also indicated that trehalose concentrations of 120–240 mM, especially 180 mM, could effectively enhance DNA delivery into the mouse epididymis epithelial cell in vitro. Moreover, trehalose could induce in vivo expression of exogenous DNA in epididymal epithelial cells and help to internalize plasmid into sperm,which did not influence motility of sperm when the mixture of trehalose (180 mM) and DNA was injected into epididymal lumen through efferent tubule. This study suggested that trehalose, as an effective and safer reagent, could be employed potentially to maintain vitality of mouse epididymal epthetial cells during long-term culture in vitro and to mediate in vitro and in vivo gene transfer. PMID:24651491

Shen, Jian; Qin, Jinzhou; Bao, Jianqiang; Hu, Yuan; Zeng, Wenxian; Dong, Wuzi



Apoptosis and gene expression in the developing mouse brain of fusarenon-X-treated pregnant mice.  


Fusarenon-X (FX), a type B trichothecene mycotoxin, is mainly produced by Fusarium crookwellense, which occurs naturally in agricultural commodities, such as wheat and barley. FX has been shown to exert a variety of toxic effects on multiple targets in vitro. However, the embryonic toxicity of FX in vivo remains unclear. In the present study, we investigated FX-induced apoptosis and the relationship between the genetic regulatory mechanisms and FX-induced apoptosis in the developing mouse brain of FX-treated pregnant mice. Pregnant mice were orally administered FX (3.5 mg/kg b.w.) and were assessed at 0, 12, 24 and 48 h after treatment (HAT). Apoptosis in the fetal brain was determined using hematoxylin and eosin staining, the TUNEL method, immunohistochemistry for PCNA and electron microscopy. Gene expressions were evaluated using microarray and real time-reverse transcription polymerase chain reaction (qRT-PCR). Histopathological changes showed that the number of apoptotic cells in the telencephalon of the mouse fetus peaked at 12 HAT and decreased at 24 and 48 HAT. FX induced the up-regulation of Bax, Trp53 and Casp9 and down-regulated Bcl2 but the expression levels of Fas and Casp8 mRNA remained unchanged. These data suggested that FX induces apoptosis in the developing mouse brain in FX-treated dams. Moreover, the genetic regulatory mechanisms of FX-induced apoptosis are regulated by Bax, Bcl2, Trp53 and Casp9 or can be defined via an intrinsic apoptotic pathway. PMID:24983900

Sutjarit, Samak; Nakayama, Shota M M; Ikenaka, Yoshinori; Ishizuka, Mayumi; Banlunara, Wijit; Rerkamnuaychoke, Worawut; Kumagai, Susumu; Poapolathep, Amnart