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At least 253 records · Page 14Linked to original sources
PubMed1996

A novel gene selectively expressed in the cerebellum.

A cDNA clone encoding a novel protein (Cer-1) was isolated from a mouse cerebellar cDNA library. The deduced amino acid sequence of Cer-1 is not homologous to other sequences in the protein sequence data base. RNA blot analysis suggests that expression of Cer-1 RNA occurs selectively in the adult cerebellum and in purified cultures of cerebellar granule neurons. An increase in its expression correlates with the timing of granule neuron differentiation in the cerebellum. Thus, the expression of Cer-1 may provide a selective marker for terminal differentiation of cerebellar granule neurons.

Amino Acid Sequence↗
PubMed1995

A mutation in the dystrophin gene selectively affecting dystrophin expression in the heart.

We have previously shown in a large X-linked pedigree that a deletion removing the dystrophin muscle promoter, the first muscle exon and part of intron 1 caused a severe dilated cardiomyopathy with no associated muscle weakness. Dystrophin expression was present in the muscle of affected males and transcription studies indicated that this dystrophin originated from the brain and Purkinje cell isoforms, upregulated in this skeletal muscle. We have now studied dystrophin transcription and expression in the heart of one member of this family. In contrast to the skeletal muscle, dystrophin transcription and expression were absent in the heart, with the exception of the distal Dp71 dystrophin isoform, normally present in the heart. The 43- and 50-kD dystrophin-associated proteins were severely reduced in the heart, despite the presence of Dp71, but not in skeletal muscle. The absence of dystrophin and the down-regulation of the dystrophin-associated proteins in the heart accounted for the severe cardiomyopathy in this family. The mutation present in these males selectively affects dystrophin expression in the heart; this could be secondary to the removal of cardiac-specific regulatory sequences. This family may represent the first example of a mutation specifically affecting the cardiac expression of a gene, present physiologically in both the skeletal and cardiac muscles.

Base Sequence↗
PubMed1998

Selective gene transfer into the liver of non-human primates with E1-deleted, E2A-defective, or E1-E4 deleted recombinant adenoviruses.

Preclinical studies were designed to investigate the feasibility and safety of recombinant adenoviruses transduced into the hepatic artery of nonhuman primates. The vectors used are recombinant adenoviruses deleted in E1 and contain either a temperature-sensitive mutation in the E2a gene, which encodes a defective DNA-binding protein at nonpermissive temperatures, or a deletion of the E4 region, including open reading frame (ORF) 6. Six 8- to 10-kg baboons underwent femoral artery cannulation, and angiographic techniques were used to introduce vector selectively into either a portion of the right lobe of the liver via a branch of the right hepatic artery or the common hepatic artery. Necropsies were performed at 4, 29, or 61 days. Serial sequential liver biopsies were performed in the baboons that survived 29 or 61 days. In the 2 baboons with vector transduction into the right hepatic artery, X-Gal histochemical analysis of the liver showed evidence of quantitatively increased gene transfer in the targeted lobe; however, gene transfer was present throughout the liver. Quantitative analysis of histopathology showed that portal inflammation was present throughout both livers transduced with the highest dose of vector. No differences were seen in the level of portal inflammation in targeted and untargeted lobes despite the observed qualitative and quantitative differences in gene expression. Southern blot analysis of total cellular DNA isolated from targeted and nontargeted lobes showed similar levels of viral DNA throughout the liver. Polymerase chain reaction (PCR) analysis was able to detect viral DNA sequence in gonads and brain as well as many other tissues in baboons treated with high-dose vector. In baboons treated with lower doses of an E1-E4 deleted vector expressing the human ornithine transcarbamylase (OTC) gene, DNA was detectable by nested PCR in liver but not gonads at days 29 and 61. The data suggest that intraarterial administration of recombinant adenoviral E1-E4 deleted vector is feasible and safe. At high doses of vector, widespread dissemination of vector DNA is seen. At low doses, hepatic gene transfer is not associated with vector DNA dissemination to gonads.

Adenoviridae↗
PubMed2005

Comparative analysis of selected genes from Diachasmimorpha longicaudata entomopoxvirus and other poxviruses.

The Diachasmimorpha longicaudata entomopoxvirus (DlEPV) is the first symbiotic EPV described from a parasitic wasp. The DlEPV is introduced into the tephritid fruit fly larval host along with the wasp egg at oviposition. We sequenced a shotgun genomic library of the DlEPV DNA and analyzed and compared the predicted protein sequences of eight ORFs with those of selected poxviruses and other organisms. BlastP searches showed that five of these are homologous to poxvirus putative proteins such as metalloprotease, a putative membrane protein, late transcription factor-3, virion surface protein, and poly (A) polymerase (PAP) regulatory small subunit. Three of these are similar to those of other organisms such as the gamma-glutamyltransferase (GGT) of Arabidopsis thaliana, eukaryotic initiation factor 4A (eIF4A) of Caenorhabditis briggsae and lambda phage integrase (lambda-Int) of Enterococcus faecium. Transcription motifs for early (TGA,A/T,XXXXA) or late (TAAATG, TAAT, or TAAAT) gene expression conserved in poxviruses were identified with those ORFs. Phylogenetic analysis of multiple alignments of five ORFs and 20 poxvirus homologous sequences and of a concatenate of multiple alignments suggested that DlEPV probably diverged from the ancestral node between the fowlpox virus and the genus B, lepidopteran and orthopteran EPVs, to which Amsacta moorei and Melanoplus sanguinipes EPV, respectively, belong. The DlEPV putative GGT, eIF4A, and lambda-Int contained many conserved domains that typified these proteins. These homologues may be involved in either viral pathogenicity or enhancing parasitism via the gamma-glutamyl cycle and compensation of eIF4A levels in the parasitized fly, or via the integration of a portion of the viral genome into the wasp and/or parasitized fly.

Amino Acid Motifs↗
PubMed2006

Selective gene delivery for cancer therapy using cationic liposomes: in vivo proof of applicability.

Targeted gene therapy is essential if cancer treatment is to become a reality with this form of therapy. In the past few years, cationic liposomes, discovered 2 decades ago, and at present, the most commonly used class of transfection reagents, have been tested in various clinical trials for diseases not restricted to cancer. They have been shown to be selective for tumour vascular endothelial cells raising hopes for antiangiogenic and antivascular therapies. They are also capable of being selectively delivered to the lungs and liver when administered intravenously. These vesicles are also being targeted to the tumour in various parts of the body by using advanced liposomal systems such as antibody-antigen and ligand-receptor combinations. This review looks at the state of play in this rapidly growing field.

Animals↗
PubMed1997

Borrelia burgdorferi genes selectively expressed in ticks and mammals.

Lyme disease is a tick-borne infection caused by the spirochete Borrelia burgdorferi. Recent studies have focused on how the Lyme disease bacterium overcomes the challenges faced by an organism that depends on a vector-borne life style. These studies indicate that the spirochete expresses different surface proteins at different stages of its life. Here, Aravinda de Silva and Erol Fikrig review the evidence for differential gene expression and discuss the implications of these findings for the Lyme disease vaccine that is currently being tested in human trials.

Journal Article↗
PubMed2000

Molecular cloning and chromosomal mapping of a candidate cytokine gene selectively expressed in human CD34+ cells.

A rare population of human bone marrow (BM) and cord blood (CB) mononuclear cells bearing the CD34 surface marker (CD34+) function as hematopoietic stem/progenitor cells. Cells lacking CD34 expression (CD34-) in BM and CB are largely mature hematopoietic cells of various lineages that are derived from the CD34+ cells. To elucidate molecular mechanisms governing functional differences between CD34+ and CD34- hematopoietic cells, we used representational difference analysis (RDA)-based subtraction to identify genes that are specifically or preferentially expressed in CD34+ cells. Among the 73 RDA fragments initially sequenced, 30% are derived from the CD34 and c-kit genes that are preferentially expressed in CD34+ cells. An additional 27 (37%) are novel or homologous only to entries in expressed sequence tag databases. One (C17) was found four times and is expressed in CD34+ but not in CD34- cell populations from CB or BM. The cloned C17 cDNA encodes a novel polypeptide of 136 amino acids with a signal sequence. No homology to this peptide was found in the public databases. A secondary-structure analysis predicts that the C17 peptide contains four alpha-helices, a characteristic of hematopoietic cytokines and interleukins. This novel gene is mapped to human chromosome 4p15-p16.

Amino Acid Sequence↗
PubMed1991

Mouse NKR-P1. A family of genes selectively coexpressed in adherent lymphokine-activated killer cells.

NK cells are a subpopulation of large granular lymphocytes. They are able to recognize and lyse a wide variety of virally infected or neoplastic target cells without previous sensitization or MHC restriction. The molecules involved in target recognition and subsequent triggering of the killing process are still undefined. Recently, a 30-kDa protein highly expressed on rat NK cells and capable of mediating transmembrane signaling was identified and the gene coding for it cloned and sequenced. To better understand the role of this protein in NK cell-mediated cytotoxicity, we cloned its mouse homologue by cross-hybridization of the rat gene to a cDNA library generated from highly purified mouse lymphokine-activated NK cells. Three messages, differing in size and sequence and encoded by different genes, are specifically cotranscribed in mouse NK cells. The protein products of this gene family express the lectin-like motif characteristic of type II transmembrane molecules. Both the rat and mouse proteins have conserved tyrosine and serine residues in their cytoplasmatic portion that are potential phosphorylation sites. They also share a sequence that could be the binding site of the P56lck tyrosine kinase. These observations are consistent with the signaling function hypothesized for these proteins.

Amino Acid Sequence↗
PubMed1982

Are mitochondrial structural genes selectively amplified during senescence in Podospora anserina?

Genetic and transcriptional maps have been constructed for the mitochondrial genome of the Ascomycete Podospora anserina. These data have been plotted on the restriction maps for Sal I, Xho I, Bam HI, Eco RI, BgI II and Hae III. We have characterized and cloned a new and unique senescent mitochondrial DNA (beta-event senDNA) and have organized all of the recognized senDNAs on the genomic maps. We make the observation that all of the known and characterized senDNAs are derived from specific genes or gene regions of the young mitochondrial genome. We have unambiguously assigned the alpha-event senDNA (the 2.6 kb monomer) to the oxi3 gene locus and the beta-event senDNA to the oxi2 gene locus.

Ascomycota↗
PubMed2002

Engineered viruses to select genes encoding secreted and membrane-bound proteins in mammalian cells.

We have developed a functional genomics tool to identify the subset of cDNAs encoding secreted and membrane-bound proteins within a library (the 'secretome'). A Sindbis virus replicon was engineered such that the envelope protein precursor no longer enters the secretory pathway. cDNA fragments were fused to the mutant precursor and expression screened for their ability to restore membrane localization of envelope proteins. In this way, recombinant replicons were released within infectious viral particles only if the cDNA fragment they contain encodes a secretory signal. By using engineered viral replicons to selectively export cDNAs of interest in the culture medium, the methodology reported here efficiently filters genetic information in mammalian cells without the need to select individual clones. This adaptation of the 'signal trap' strategy is highly sensitive (1/200 000) and efficient. Indeed, of the 2546 inserts that were retrieved after screening various libraries, more than 97% contained a putative signal peptide. These 2473 clones encoded 419 unique cDNAs, of which 77% were previously annotated. Of the 94 cDNAs encoding proteins of unknown function, 24% either had no match in databases or contained a secretory signal that could not be predicted from electronic data.

Animals↗
PubMed1998

Analysis of clonal diversity in mouse immunoglobulin heavy chain genes selected for size of the antigen combining site.

Size-diversity of Ig and T cell receptor antigen binding (CDR3) regions can be visualized by "CDR3 fingerprinting", and provides an estimate of B- or T-cell repertoire complexity. The method does not identify clonal diversity, however, which can only be determined by random sequencing of the CDR3s. In this study we demonstrate that a combination of fingerprinting and single strand conformation polymorphism (SSCP) analysis can be used for a rapid estimation of clonal diversity within mouse Ig antigen binding regions selected for size. This application may be useful in the analysis of clonal expansion within B- and T-cell repertoires.

Amino Acid Sequence↗
PubMed1986

Introduction of a selectable gene into murine T-lymphoblasts by a retroviral vector.

A recombinant retroviral vector with an inserted bacterial neomycin resistance (neo) gene was used to transfer in vitro neomycin resistance (neoR) into murine cytotoxic lymphocyte precursors (CLP). The infection protocol involved co-cultivation of mitogen-activated splenic T-blasts with irradiated cells that produced either the recombinant retrovirus plus a helper virus, or exclusively the recombinant retrovirus. Infected T-blasts were subsequently cultured under limiting dilution (LD) conditions that supported clonal in vitro development of a large fraction of murine CLP. In infected T-blast populations, frequency estimates were obtained for CLP that developed into functional cytotoxic T-lymphocyte (CTL) populations under G418-selected or non-selected conditions; from these frequency estimates, an efficiency of transduction of the neoR phenotype into murine CLP of 2-8% was calculated. Some conditions were defined that influenced transduction efficiency, i.e., the density of the infecting monolayer cells; the presence of interleukin 2-containing conditioned medium and mitogenic lectins during the co-culture period; a delayed onset of G418 selection after infection. It was demonstrated that the neoR phenotype of functional CTL populations derived from infected CLP resulted from expressed recombinant retrovirus.

Animals↗
PubMed2005

Gene selective suppression of nonsense termination using antisense agents.

An estimated one third of all inherited genetic disorders and many forms of cancer are caused by premature (nonsense) termination codons. Aminoglycoside antibiotics are candidate drugs for a large number of such genetic diseases; however, aminoglycosides are toxic, lack specificity and show low efficacy in this application. Because translational termination is an active process, we considered that steric hindrance by antisense sequences could trigger the ribosome's "default mode" of readthrough when positioned near nonsense codons. To test this hypothesis, we performed experiments using plasmids containing a luciferase reporter with amber, ochre and opal nonsense mutations within the luxB gene in Escherichia coli. The nonspecific termination inhibitors gentamicin and paromomycin and six antisense peptide nucleic acids (PNA) spanning the termination region were tested for their potential to suppress the luxB mutation. Gentamicin and paromomycin increased luciferase activity up to 2.5- and 10-fold, respectively. Two of the PNAs increased Lux activity up to 2.5-fold over control levels, with no significant effect on cell growth or mRNA levels. Thus, it is possible to significantly suppress nonsense mutations within target genes using antisense PNAs. The mechanism of suppression likely involves enhanced readthrough, but this requires further investigation. Nonsense termination in human cells may also be susceptible to suppression by antisense agents, providing a new approach to address numerous diseases caused by nonsense mutations.

Anti-Bacterial Agents↗
PubMed2000

Suppression of intestinal polyposis in Apc(delta 716) knockout mice by an additional mutation in the cytosolic phospholipase A(2) gene.

Arachidonic acid is a precursor for biosynthesis of eicosanoids, including prostaglandins, thromboxanes, leukotrienes, and lipoxins. Cytosolic phospholipase A(2) (cPLA(2)) plays a key role in the release of arachidonic acid as the substrate of cyclooxygenase-1 (COX-1) or COX-2. We found that the level of cPLA(2) mRNA was markedly elevated in the polyps and correlated with the polyp size in the small intestine of the Apc(delta)(716) knockout mouse, a model for human familial adenomatous polyposis. To determine the role of cPLA(2) in intestinal tumorigenesis, we then introduced a cPLA(2) gene mutation into Apc(delta)(716) mice. In the compound mutant mice, the size of the small intestinal polyps was reduced significantly, although the numbers remained unchanged. These results provide direct genetic evidence that cPLA(2) plays a key role in the expansion of polyps in the small intestine rather than in the initiation process. In contrast, colonic polyps were not affected in either size or number. Interestingly, group X sPLA(2) was constitutively expressed in the colon at much higher levels than in the small intestine. These results suggest that in the colon, group X sPLA(2) supplies arachidonic acid in both the normal epithelium and the polyps even in the absence of cPLA(2).

Animals↗
PubMed2004

Identification of a mouse cytomegalovirus gene selectively targeting CD86 expression on antigen-presenting cells.

We and others have shown that infection of dendritic cells with murine cytomegalovirus (MCMV) leads to severe functional impairment of these antigen-presenting cells (D. M. Andrews, C. E. Andoniou, F. Granucci, P. Ricciardi-Castagnoli, and M. A. Degli-Esposti, Nat. Immunol. 2:1077-1084, 2001; S. Mathys, T. Schroeder, J. Ellwart, U. H. Koszinowski, M. Messerle, and U. Just, J. Infect. Dis. 187:988-999, 2003). Phenotypically, reduced surface expression of costimulatory molecules and major histocompatibility complex molecules was detected. In order to identify the molecular basis for the observed effects, we generated MCMV mutants with large deletions of nonessential genes. The study was facilitated by the finding that a monocyte-macrophage cell line displayed similar phenotypic alterations after MCMV infection. By analyzing the expression of cell surface molecules on infected cells, we identified a mutant virus which is no longer able to downmodulate the expression of the costimulatory molecule CD86. Additional mutants with smaller deletions allowed us to pin down the responsible gene to a certain genomic region. RNA analysis led to the identification of the spliced gene m147.5, encoding a protein with 145 amino acids. Experiments with an m147.5 mutant revealed that the protein affects CD86 expression only, suggesting that additional MCMV genes are responsible for downmodulation of the other surface molecules. Identification of viral gene products interfering with functionally important proteins of antigen-presenting cells will provide the basis to dissect the complex interaction of CMV with these important cells and to evaluate the biological importance of these viral genes in vivo.

Amino Acid Sequence↗
PubMed2006

Exercise training in normobaric hypoxia in endurance runners. III. Muscular adjustments of selected gene transcripts.

We hypothesized that specific muscular transcript level adaptations participate in the improvement of endurance performances following intermittent hypoxia training in endurance-trained subjects. Fifteen male high-level, long-distance runners integrated a modified living low-training high program comprising two weekly controlled training sessions performed at the second ventilatory threshold for 6 wk into their normal training schedule. The athletes were randomly assigned to either a normoxic (Nor) (inspired O2 fraction = 20.9%, n = 6) or a hypoxic group exercising under normobaric hypoxia (Hyp) (inspired O2 fraction = 14.5%, n = 9). Oxygen uptake and speed at second ventilatory threshold, maximal oxygen uptake (VO2 max), and time to exhaustion (Tlim) at constant load at VO2 max velocity in normoxia and muscular levels of selected mRNAs in biopsies were determined before and after training. VO2 max (+5%) and Tlim (+35%) increased specifically in the Hyp group. At the molecular level, mRNA concentrations of the hypoxia-inducible factor 1alpha (+104%), glucose transporter-4 (+32%), phosphofructokinase (+32%), peroxisome proliferator-activated receptor gamma coactivator 1alpha (+60%), citrate synthase (+28%), cytochrome oxidase 1 (+74%) and 4 (+36%), carbonic anhydrase-3 (+74%), and manganese superoxide dismutase (+44%) were significantly augmented in muscle after exercise training in Hyp only. Significant correlations were noted between muscular mRNA levels of monocarboxylate transporter-1, carbonic anhydrase-3, glucose transporter-4, and Tlim only in the group of athletes who trained in hypoxia (P < 0.05). Accordingly, the addition of short hypoxic stress to the regular endurance training protocol induces transcriptional adaptations in skeletal muscle of athletic subjects. Expressional adaptations involving redox regulation and glucose uptake are being recognized as a potential molecular pathway, resulting in improved endurance performance in hypoxia-trained subjects.

Adaptation, Physiological↗
PubMed1980

Gene deletion and gene duplication within the cluster of human heavy-chain genes. Selective absence of IgG sub-classes.

Individuals with selective absence of IgG1 and IgG2 were discovered by testing for allotypes and isotypes of the respective sub-classes. These individuals were homozygous for sub-class deleted Gm-Am haplotypes, as shown by allotype studies in two families (Gm--;..;g;A2m1/Gm--;n;b;A2m1 and Gm--;n;b;A2m1/Gm--;..;b;A2m1) and by a population study of New Guineans (Gm fa;--;b;A2m2). The individuals with IgG1 sub-class deficiency showed elevation of IgG2, IgG4 and in particular of IgG3. Gene deletion can result from unequal crossing over which renders a complementary chromosome with a duplication of a sub-class gene. In one family, duplication of gamma 3 genes was observed to have happened in one of a twin pair. Quanitation of sub-classes in families with gamma 1- and with gamma 3-duplicated haplotypes did not show increased levels of the gene involved.

Crossing Over, Genetic↗
PubMed2003

Using ANOVA for gene selection from microarray studies of the nervous system.

Methods are presented for detecting differential expression using statistical hypothesis testing methods including analysis of variance (ANOVA). Practicalities of experimental design, power, and sample size are discussed. Methods for multiple testing correction and their application are described. Instructions for running typical analyses are given in the R programming environment. R code and the sample data set used to generate the examples are available at http://microarray.cpmc.columbia.edu/pavlidis/pub/aovmethods/.

Analysis of Variance↗