Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Terminal Repeat Sequences”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,207 records · Page 67Linked to original sources
PubMed1992

Further analyses of the orthopoxviruses volepox virus and raccoon poxvirus.

Volepox virus (VPX) from skin lesions on a vole and a piñon mouse caught in California and raccoon poxvirus (RCN) from raccoons trapped in Maryland were examined to begin elucidating their relationship to other orthopoxviruses, most of which are not known to be indigenous to the Americas. VPX and RCN produced pinpoint, nonhemorrhagic pocks on chick embryo chorioallantoic membranes. In cell cultures both viruses produced 1-mm diameter, irregular plaques, A-type inclusions (ATIs), and despite production of hemagglutinin, both viruses caused syncytia formation. Considerable cross-hybridization was seen between VPX and RCN DNA and the DNAs of other orthopoxviruses; however, HindIII cleavage site maps showed marked central and terminal region differences between VPX (222.8 kbp) and RCN (224.8 kbp) DNA and mapped DNAs of other orthopoxviruses. Cognate DNAs of the ATI 160-kDa protein and 38-kDa serine protease inhibitor homologue of cowpox virus (CPV) and the 14-kDa fusion protein of vaccinia virus (VAC) were present within the right end of VPX and RCN DNA, matching their location in CPV and VAC. VPX and RCN, respectively, expressed a 150- and a 155-kDa ATI major protein and a 20- and an 18-kDa fusion protein. Low stringency annealing suggested that cognate DNAs for the VAC growth factor and the alpha-amanitin target protein were present within the left end of VPX and RCN DNA, matching their location in VAC. Terminal tandem repeat sequences of VAC and RCN did not cross-hybridize with each other or with VPX DNA end fragments. Together, the data suggested that VPX and RCN are phylogenetically rather distant from orthopoxviruses not indigenous to the Americas, although genetic information is arranged as in other examined orthopoxviruses.

Animals↗
PubMed1991

Eliminating PCR contamination: is UV irradiation the answer?

The sensitivity of the polymerase chain reaction (PCR) can mean that even very low levels of contamination with the target DNA will result in a positive signal. At present this aspect is a major limitation in the use of PCR as a routine diagnostic method. By exposing PCR reagents to UV light, contaminating DNA can be inactivated, thus providing an opportunity to eradicate false positive reactions. UV irradiation was applied to PCR systems used for the detection of human cytomegalovirus (CMV) and human immunodeficiency virus (HIV) and shown to be effective in eradicating both laboratory encountered contamination and plasmid DNA (below 100 pg) added to PCR systems prior to UV exposure. The sensitivity of a PCR system to amplify the long terminal repeat (LTR) sequence of HIV-1 was not affected by the irradiation procedure; however, the ultimate sensitivity of a PCR system for the amplification of an early gene promotor sequence of the CMV genome was reduced 1000-fold. UV irradiation did not affect the size of the PCR product as determined by strand separating polyacrylamide gel electrophoresis of a 32P-labelled amplimer. Thus, a simple pre-exposure to UV light would seem a worthwhile step to incorporate into PCR protocols provided that the effects on sensitivity have been determined empirically for each PCR system.

Base Sequence↗
PubMedDate not supplied

Electric field-mediated gene transfer (electroporation) into mouse Friend and human K562 erythroleukemic cells.

Electroporation, the technique of electric field mediated gene transfer, was evaluated as a means of introducing and expressing genes into mouse Friend and human K562 erythroleukemic cells. Long-term (stable) gene expression in both Friend and K562 cells was measured using the recombinant plasmid Homer 6, which carries the aminoglycoside phosphotransferase (aph) gene as a selectable marker under the transcriptional control of the Moloney murine sarcoma virus long terminal repeat promoter/enhancer sequences. Parameters such as the DNA concentration, the initial field strength, the concentration of recipient cells, and the preselection expression time were examined to obtain optimal transfection frequencies. Short-term (transient) expression was also examined using the plasmid pLW4, which carries the chloramphenicol acetyltransferase gene under the transcriptional control of herpes simplex virus immediate early 5 gene promoter/enhancer sequences. Conditions that gave maximal stable transformation frequency were similar to those giving highest transient gene expression in the mouse and human erythroleukemic cell lines. Under optimal conditions, electroporation gave about ten times higher transfection frequencies and levels of transient expression for both types of cells when compared with the calcium phosphate technique. Because both Friend and K562 cells can be induced to differentiate in vitro, measurement of transient or stable expression levels for genes introduced into these cells may prove to be useful in the study of developmental regulation of genes from the erythroid pathway.

Animals↗
PubMed2004

Expression cloning of functional receptor used by SARS coronavirus.

We have expressed a series of truncated spike (S) glycoproteins of SARS-CoV and found that the N-terminus 14-502 residuals were sufficient to bind to SARS-CoV susceptible Vero E6 cells. With this soluble S protein fragment as an affinity ligand, we screened HeLa cells transduced with retroviral cDNA library from Vero E6 cells and obtained a HeLa cell clone which could bind with the S protein. This cell clone was susceptible to HIV/SARS pseudovirus infection and the presence of a functional receptor for S protein in this cell clone was confirmed by the cell-cell fusion assay. Further studies showed the susceptibility of this cell was due to the expression of endogenous angiotensin-converting enzyme 2 (ACE2) which was activated by inserted LTR from retroviral vector used for expression cloning. When human ACE2 cDNA was transduced into NIH3T3 cells, the ACE2 expressing NIH3T3 cells could be infected with HIV/SARS pseudovirus. These data clearly demonstrated that ACE2 was the functional receptor for SARS-CoV.

Angiotensin-Converting Enzyme 2↗
PubMed2005

Herpes virus proteins ICP0 and BICP0 can activate NF-kappaB by catalyzing IkappaBalpha ubiquitination.

The immediate early proteins ICP0 and BICP0 from Herpes virus are promiscuous activators of both viral and cellular genes and play a critical role in virus life cycle. Here we report that ICP0 and BICP0 could induce NF-kappaB translocation from cytoplasm into nucleus and strongly activate NF-kappaB responsive genes specifically. This process was dependent on the RING domain of both proteins. In addition, ICP0 interacted specifically with IkappaBalpha and its activating effect was attenuated by Ubch5A(C85A) and MG132, but not by IkappaBalpha(S32A/S36A). Remarkably, IkappaBalpha was poly-ubiquitinated by both ICP0 and BICP0, in vitro and in vivo. These data indicate that ICP0 and BICP0, functioning as ubiquitin ligases, are bona fide activators of NF-kappaB signaling pathway. Our study identifies a new way ICP0 and BICP0 explore to regulate gene expression.

Animals↗
PubMed2006

Androgen receptor and vitamin D receptor gene polymorphisms and prostate cancer risk.

We study the CAG repeat region in exon 1 of the androgen receptor (AR) and the TaqI polymorphism in exon 9 of the vitamin D receptor (VDR) and the association with prostate cancer. 137 incidentally discovered, histologically verified prostate cancers were analysed for CAG repeat length in AR and genotype at the TaqI site of the VDR. 124 control subjects were analysed to determine the CAG repeat length and TaqI genotype determined for 176 control subjects. An unpaired t-test shows that the mean CAG repeat length was significantly (p<0.001) shorter among cases (20.1 repeats) compared with controls (22.5 repeats). Dividing the prostate cohort and controls into tertiles (< or = 19, 20-22, > or = 23 repeats) shows that short repeats are significantly more common among cases (odds ratio (OR) 4.45, p=0.00003). Genotype frequencies for the TaqI polymorphism reveals no significant differences between cases and controls. We conclude that men with a short CAG repeat in the androgen receptor gene have an increased risk of developing prostate cancer.

Aged↗
PubMed2005

The 5alpha-reductase type II A49T and V89L high-activity allelic variants are more common in men with prostate cancer compared with the general population.

OBJECTIVES: To compare men with prostate disease with those from the general population regarding polymorphisms in the androgen receptor gene and in the 5alpha-reductase II (SRD5A2) gene. MATERIALS AND METHODS: The SRD5A2 polymorphisms A49T, V89L and R227Q, the androgen receptor CAG and GGN repeats and sex hormone status was investigated in men with prostate cancer (CaP) (n=89), benign prostate hyperplasia (n=45) and healthy military conscripts (n=223). RESULTS: The SRD5A2 high-activity allele variants A49T AT and V89L LL were more frequent in CaP-patients compared to general population, p=0.026 and p=0.05, respectively. CaP progression was, however, independent of SRD5A2 variants. In contrary, men with GGN<23 had a higher risk of dying from the disease than their counterparts with longer repeats. CONCLUSIONS: Men with CaP were more often genetically predisposed to a higher enzymatic activity in the turn over from T to DHT compared to the general population. In our population, androgen receptor genotype affected CaP outcome.

3-Oxo-5-alpha-Steroid 4-Dehydrogenase↗
PubMed2005

Transcription of two human genes from a bidirectional endogenous retrovirus promoter.

Eight percent of the human genome is derived from endogenous retrovirus (ERV) insertions. ERV long terminal repeats (LTRs) contain strong promoters that are known to contribute to the transcriptional regulation of certain human genes. While some LTRs are known to possess bidirectional promoter activity in vitro, only sense orientation LTR promoters have previously been shown to regulate human gene expression. Here we demonstrate that an ERV1 LTR acts as a bidirectional promoter for the human Down syndrome critical region 4 (DSCR4) and DSCR8 genes. We show that while DSCR4 and DSCR8 are essentially co-expressed, their shared LTR promoter is more active in the sense than the antisense orientation. Through deletion analysis of the LTR we have identified positive and negative regulatory elements, and defined a core region of the promoter that is required for transcriptional activity in both orientations. Finally, we show that the ERV LTR also exists in the genomes of several non-human primates, and present evidence that potential transcription factor binding sites in the core region have been maintained throughout primate evolution.

Antigens, Neoplasm↗
PubMedDate not supplied

Natural cases of visna in sheep with myelitis as the sole lesion in the central nervous system.

Of 118 sheep with visna, 12 showed myelitis as the only nervous lesion. They were ovine lentivirus (OvLV)-seropositive and provirus DNA was demonstrated by LTR-PCR in all the samples with lesions. Clinically, all showed hindlimb paralysis and some were completely recumbent. Grossly, a swollen and discoloured area was identified in the white matter in 10 sheep. Microscopical changes consisted of a wedge-shaped area of non-suppurative leucomyelitis with mononuclear perivascular cuffing, demyelination and white matter degeneration. Except for two samples, grey matter was affected adjacent to severe white matter lesions. Three different microscopical patterns of lesion were identified, all having in common the presence of perivascular inflammation: the so-called vascular pattern was characterized by perivascular cuffs with minimal lesions in the adjacent neuroparenchyma; the malacic pattern, which was the commonest type, was characterized by severe white matter destruction and small numbers of macrophages; and the infiltrative pattern was characterized by a severe infiltrate of histiocytes in the parenchyma. Maedi-visna virus antigen was detected immunohistochemically only in areas with lesions, and the degree of immunolabelling was unrelated to the severity of the damage. Diagnosticians should bear in mind that a considerable number of visna cases show only spinal cord lesions. Examination of paraffin wax-embedded samples by LTR-PCR and immunohistochemistry would seem useful in confirming a histopathological diagnosis of visna from spinal cord samples.

Animals↗
PubMed2005

Experimental characterization of the folding kinetics of the notch ankyrin domain.

Proteins constructed from linear arrays of tandem repeats provide a simplified architecture for understanding protein folding. Here, we examine the folding kinetics of the ankyrin repeat domain from the Drosophila Notch receptor, which consists of six folded ankyrin modules and a seventh partly disordered N-terminal ankyrin repeat sequence. Both the refolding and unfolding kinetics are best described as a sum of two exponential phases. The slow, minor refolding phase is limited by prolyl isomerization in the denatured state (D). The minor unfolding phase, which appears as a lag during fluorescence-detected unfolding, is consistent with an on-pathway intermediate (I). This intermediate, although not directly detected during refolding, is shown to be populated by interrupted refolding experiments. When plotted against urea, the rate constants for the major unfolding and refolding phases define a single non-linear v-shaped chevron, as does the minor unfolding phase. These two chevrons, along with unfolding amplitudes, are well-fitted by a sequential three-state model, which yields rate constants for the individual steps in folding and unfolding. Based on these fitted parameters, the D to I step is rate-limiting, and closely matches the major observed refolding phase at low denaturant concentrations. I appears to be midway between N and D in folding free energy and denaturant sensitivity, but has Trp fluorescence properties close to N. Although the Notch ankyrin domain has a simple architecture, folding is slow, with the limiting refolding rate constant as much as seven orders of magnitude smaller than expected from topological predictions.

Animals↗
PubMed2005

Construction and characterization of deltaretrovirus indicator cell lines.

The deltaretroviruses, which include bovine leukemia virus (BLV) and human T-cell leukemia virus types 1 and 2 (HTLV-1 and HTLV-2), replicate poorly in culture and the molecular details of their life cycles are limited. To facilitate the analysis of virus replication, mammalian cell lines were created with the long terminal repeats (LTRs) of each virus driving expression of the enhanced green fluorescent protein gene (egfp). The BLGFP, H1GFP and H2GFP cell lines detect virus infection by the expression of GFP via the transactivation of the LTR via the Tax protein of BLV, HTLV-1 or HTLV-2, respectively. GFP expression was measured by flow cytometry, yielding sensitive and rapid detection of virus infectivity. Interestingly, we observed that the Tax proteins of HTLV-1 and HTLV-2 could transactivate the BLV LTR at levels that were comparable to that of BLV Tax. In contrast, the BLV Tax showed low levels of transactivation in H1GFP and H2GFP cells. HTLV-1 and HTLV-2 Tax proteins efficiently transactivated both the HTLV-1 and HTLV-2 LTRs. Finally, spinoculation of BLV resulted in only a two-fold increase in viral titer.

Animals↗
PubMed2005

Quantitation of feline leukaemia virus viral and proviral loads by TaqMan real-time polymerase chain reaction.

Feline leukaemia virus (FeLV) infection in cats is not only of veterinary importance but also a well-acknowledged animal model for studying the pathogenesis of retroviral disease. After virus exposure, different courses and outcomes of FeLV infection may prevail; they have been associated with cellular and humoral immune responses and the FeLV proviral load in peripheral blood. We hypothesized that the plasma viral RNA load might be an additional relevant indicator for the infection outcome. To quantify these loads, a real-time reverse transcriptase (RT) polymerase chain reaction (PCR) assay was developed. The assay amplifies FeLV-A, -B, and -C as some naturally infected cats could not be identified with a FeLV-A-based assay previously. The assay was applied to determine plasma FeLV RNA loads in cats infected both naturally and experimentally with FeLV. In addition, an improved real-time PCR assay for quantitation of FeLV proviral loads is described. The assays developed were more sensitive than ELISA and virus isolation in the early phase of infection. In addition, PCR allows the identification of provirus carriers that have overcome antigenaemia. Thus, for most effective detection of FeLV exposure and characterization of the infection in a cat, PCR assays are recommended as diagnostic tools.

Animals↗
PubMed2006

Both the 5' and 3' LTRs of FIV contain minor RNA encapsidation determinants compared to the two core packaging determinants within the 5' untranslated region and gag.

This study was undertaken to address the role of feline immunodeficiency virus (FIV) long terminal repeats (LTR) as potential packaging determinants. A number of studies in the recent past have clearly demonstrated that the core packaging determinants of FIV reside within at least two distinct regions at the 5' end of the viral genome, from R in the 5' LTR to approximately 150 bp within the 5' untranslated region (5' UTR) and within the first 100 bp of gag; however, there have been conflicting observations as to the role of the LTR regions in packaging and whether they contain the principal packaging determinants of FIV. Using a semi-quantitative RT-PCR approach on heterologous non-viral vector RNAs in an in vivo packaging assay, this study demonstrates that the principal packaging determinants of FIV reside within the first 150 bp of 5' UTR and 100 bp of gag (the two core regions) and not the viral 5' LTR. Furthermore, it shows that in addition to the 5' LTR, the 3' LTR also contains packaging determinants, but of a less significant nature compared to the core packaging determinants. This study defines the relative contribution of the various regions implicated in FIV genomic RNA packaging, and reveals that like other primate lentiviruses, the packaging determinants of FIV are multipartite and spread out, an observation that has implications for safer and more streamlined design of FIV-based gene transfer vectors.

3' Untranslated Regions↗
PubMed2006

Determinants for dephosphorylation of the RNA polymerase II C-terminal domain by Scp1.

Phosphorylation and dephosphorylation of the C-terminal domain (CTD) of RNA polymerase II (Pol II) represent a critical regulatory checkpoint for transcription. Transcription initiation requires Fcp1/Scp1-mediated dephosphorylation of phospho-CTD. Fcp1 and Scp1 belong to a family of Mg2+ -dependent phosphoserine (P.Ser)/phosphothreonine (P.Thr)-specific phosphatases. We recently showed that Scp1 is an evolutionarily conserved regulator of neuronal gene silencing. Here, we present the X-ray crystal structures of a dominant-negative form of human Scp1 (D96N mutant) bound to mono- and diphosphorylated peptides encompassing the CTD heptad repeat (Y1S2P3T4S5P6S7). Moreover, kinetic and thermodynamic analyses of Scp1-phospho-CTD peptide complexes support the structures determined. This combined structure-function analysis discloses the residues in Scp1 involved in CTD binding and its preferential dephosphorylation of P.Ser5 of the CTD heptad repeat. Moreover, these results provide a template for the design of specific inhibitors of Scp1 for the study of neuronal stem cell development.

Crystallography, X-Ray↗
PubMed2024

Enhanced transgene expression from single-stranded AAV vectors in human cells in&#xa0;vitro and in murine hepatocytes in&#xa0;vivo.

We identified that distal 10 nucleotides in the D-sequence in AAV2 inverted terminal repeat (ITR) share partial sequence homology to 1/2 binding site of glucocorticoid receptor-binding element (GRE). Here, we describe that (1) purified GR binds to AAV2 D-sequence, and the D-sequence competes with GR binding to its cognate binding site; (2) dexamethasone-mediated activation of GR pathway significantly increases the transduction efficiency of AAV2 vectors in human cells; (3) human osteosarcoma cells, U2OS, which lack expression of GR, are poorly transduced by AAV2 vectors, but stable transfection with a GR expression plasmid restores vector-mediated transgene expression; (4) replacement of the distal 10 nucleotides in the D-sequence of the AAV2 ITR with a full-length GRE consensus sequence significantly enhances transgene expression in human cells in&#xa0;vitro and in murine hepatocytes in&#xa0;vivo; and (5) none of the ITRs in AAV1, AAV3, AAV4, AAV5, and AAV6 genomes contains the GRE 1/2 binding site, and insertion of a full-length GRE consensus sequence in the AAV6-ITR also significantly enhances transgene expression from AAV6 vectors, both in&#xa0;vitro and in&#xa0;vivo. These novel vectors, termed generation Y AAV vectors, which are serotype, transgene, or promoter agnostic, should be useful in human gene therapy.

AAV vectors↗
PubMed2005

In vitro selective suppression of feline myeloid colony formation is attributable to molecularly cloned strain of feline leukemia virus with unique long terminal repeat.

Molecularly cloned feline leukemia virus (FeLV)-clone 33 (C-33), derived from a cat with acute myelocytic leukemia (AML), was examined to assess its relation to the pathogenesis of AML and myelodysplastic syndrome (MDS). To evaluate in vitro pathogenicity of FeLV C-33, bone marrow colony-forming assay was performed on marrow cells infected with FeLV C-33 or an FeLV subgroup A strain (61E, a molecularly cloned strain with minimal pathogenicity). The myeloid colony-forming activity of feline bone marrow mononuclear cells infected with FeLV C-33 was significantly lower than that of cells infected with 61E. This suggests that FeLV C-33 has myeloid lineage-specific pathogenicity for cats, and that FeLV C-33 infection is useful as an experimental model for investigating pathogenesis of MDS and AML.

Animals↗
PubMed2004

Comparative functional characterization of the feline foamy virus transactivator reveals its species specificity.

Foamy virus (FV) Bel1/Tas transactivators act as key regulators of gene expression and directly bind DNA Bel1 response elements (BREs) in both the internal (IP) and 5'LTR promoters. Here, we report the mapping and the virus species specificity of the nonhomologous feline foamy virus (FFV) BREs in both promoters. The data indicate that FFV Bel1 did not bind the primate FV IP.BRE and that primate FV Bel1 was not capable of binding the FFV IP.BRE. In addition, we show that the C-terminal activation domain of FFV Bel1 does not contribute to DNA binding because a C-terminal trans-dominant negative FFV Bel1 mutant was still able to bind to both promoters.

5' Untranslated Regions↗