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PubMedDate not supplied

[Search for unique segments of the ectromelia virus genome by cross blot hybridization with DNA from other orthopoxviruses].

In order to identify ectromelia virus (EMV) genome regions which may contain genes responsible for the specific pathogenicity of this virus, blot cross-hybridization of EMV DNA with those of other orthopoxviruses was performed. Two hybridization schemes were employed: one of them included hybridization of labelled cloned fragments of EMV with digests of other viral DNAs, the other, reciprocal, consisted in hybridization of labelled total DNAs of various orthopoxviruses with digests of the region of EMV DNA adjacent to the right-terminal inverted repeat. It was demonstrated that the counterpart to an approximately 8-kilobase pair portion of EMV genome flanking the inverted repeat could be detected only in the cowpox virus genome but not in the genomes of vaccinia and rabbitpox viruses. XhoI-O and XhoI-K fragments of EMV DNA contained, along with genes found in other poxviruses, certain genes which appeared to be unique for EMV. It is postulated that some of these genes may determine the specific biological properties of EMV, including its pathogenicity for mice.

DNA, Viral↗
PubMed2004

The Sleeping Beauty transposable element: evolution, regulation and genetic applications.

Members of the Tc1/mariner superfamily of transposable elements isolated from vertebrate species are inactive due to the accumulation of mutations. A representative of a subfamily of fish elements estimated to be last active > 10 million years ago has been reconstructed, and named Sleeping Beauty(SB). This element opened up new avenues for studies on DNA transposition in vertebrates, and for the development of transposon tools for genetic manipulation in important model species and in humans. Multiple transposase binding sites within the terminal inverted repeats, a transpositional enhancer sequence, unequal affinity of the transposase to the binding sites and the activity of the cellular HMGB1 protein all contribute to a highly regulated assembly of SB synaptic complexes, which is likely a requirement for the subsequent catalytic steps. Host proteins involved in double-strand DNA break repair are limiting factors of SB transposition in mammalian cells, underscoring evolutionary, structural and functional links between DNA transposition, retroviral integration and V(D)J recombination. SB catalyzes efficient cut-and-paste transposition in a wide range of vertebrate cells in tissue culture, and in somatic tissues as well as the germline of the mouse and zebrafish in vivo, indicating its usefulness as a vector for transgenesis and insertional mutagenesis.

Animals↗
PubMed1991

A highly repetitive, mariner-like element in the genome of Hyalophora cecropia.

A highly repetitive DNA element, homologous to the mariner transposon of Drosophila mauritiana was found in the intron of the gene for cecropin A, an antibacterial peptide from the Cecropia moth. The mariner-like elements (MLE) represent a homogeneous population with a copy number of about 1000/genome. Sequencing analysis showed it to be 1255 base pairs long, including 38-base pair terminal inverted repeats. The MLE contains a defective reading frame. Nevertheless, the putative product is clearly homologous to the predicted translation product encoded by mariner. In consonance is also the fact that the inverted repeats are highly conserved between the two elements and that the overall DNA homology is 48%. Since the mariner element is present in several Drosophila species closely related to Drosophila melanogaster and since MLE is present in the lepidopteran Cecropia, a route of horizontal transfer is indicated rather than vertical transmission from a common ancestor. This suggests the possible use of mariner for the construction of an interspecies vector.

Amino Acid Sequence↗
PubMed2006

[Complete nucleotide sequence analysis of Bombyx mori Densonucleosis virus type 3 VD2 (China isolate)].

The genome of Bombyx mori densonucleosis virus type 3 (China isolate) contains two kinds different single-stranded linear DNA molecules (VD1, VD2). The VD2 was purified and cloned into the pUC119 vector, and the complete nucleotide sequence of VD2 was determined. Sequence analysis showed that the VD2 genome sequence consisted of 6022 nts, including inverted terminal repeats (ITRs) of 524 nts. In the viral genome, two major open reading frames (ORF1 and ORF2) in the plus strand and one minor ORF (ORF3) in the complementary strand were identified. Computer analysis suggested the plus stand ORF1 and the minus strand ORF3 most likely encode the major nonstructural protein, while the plus stand ORF2 most likely encodes the major structural protein. Comparing the complete genome sequence of BmDNV-3 VD2 with that of BmDNV-2 VD2 (Yamanashi isolate) demonstrated that they shared 97.7% genome sequence in the VD2 region, with substitutions of 132 nucleotides, deletions of 11 nucleotides and insertions of 2 nucleotides in the VD2 region of BmDNV-3. The results suggested that BmDNV-3 is closely related to BmDNV-2, but with some differences, giving a better understanding about the variation of the viruses and providing clues to their evolution.

Animals↗
PubMed1991

Gamma delta transposase. Purification and analysis of its interaction with a transposon end.

gamma delta, a member of the Tn3 family of prokaryotic transposons, encodes a transposase that binds to the 35-base pair (bp) terminal inverted repeats (IRs) which define the transposing DNA segment. The gamma delta transposase has been overexpressed, identified by molecular weight determination and by immunoblotting, and purified to homogeneity. Production of soluble transposase required the presence of Mg2+ prior to cell lysis. Fractions from a Sephacryl S-300 column contained levels of IR-binding activity that parallel the concentration of transposase, indicating that transposase alone is sufficient for binding to the ends of gamma delta. Hydroxyl radical footprinting indicated that transposase binds to one face of the DNA helix. The protected region extends across the IR and up to 17 bp into the flanking DNA. Integration host factor (IHF), which binds adjacent to transposase, also protects one face of the DNA helix and is shifted about 70 degrees around the helical axis from the transposase protection. Analysis of transposase-DNA complexes by electrophoresis on nondenaturing gels indicated that three complexes, two within the gel and one trapped at the well, result from specific interactions with the IR. The complex in the well and one complex in the gel were analyzed by methylation interference experiments. The results indicate that transposase interacts with specific base pairs between positions 10 and 37 of the IR, a region encompassing three consecutive major and minor grooves. Methylated bases at the very end of the transposon (positions 1-9) and in the flanking DNA did not inhibit transposase binding. Thus, although transposase seems to be in intimate contact throughout the IR of gamma delta and 17 bp of flanking DNA, specific base pair recognition needed for binding appears to be determined by the inner three-quarters of the IR.

Binding Sites↗
PubMed1990

In vitro transposition of transposon Tn3.

Transposition of the ampicillin-resistant transposon Tn3 was reproduced in vitro using the Escherichia coli cell extract. In this cell-free system, we used plasmid DNA carrying mini-Tn3 as donor and phage lambda DNA as target and assayed for ampicillin-resistance transducing phages formed by cointegration of these DNA molecules. Ampicillin-resistance transducing phages, which were obtained by in vitro packaging of lambda DNA after the in vitro transposition reaction, were formed only in the presence of Tn3 transposase. The reaction required mini-Tn3 with the proper sequence and orientation of the terminal inverted repeats of Tn3. The reaction also required DNA synthesis but not RNA synthesis by E. coli RNA polymerase.

Ampicillin Resistance↗
PubMed1988

Initiation of adenovirus DNA replication. II. Structural requirements using synthetic oligonucleotide adenovirus templates.

Adenovirus (Ad) virions contain a 55-kDa terminal protein covalently linked to both 5'-ends of the linear duplex DNA genome. The origin of DNA replication is contained within the terminal 50 base pair of the inverted terminal repeats. In the accompanying paper (Kenny, M. K., Balogh, L. A., and Hurwitz, J. (1988) J. Biol. Chem. 263, 9801-9808), it was demonstrated that synthetic oligonucleotide templates which contain the Ad origin, but lack the 55-kDa terminal protein, can serve as templates for the initiation of Ad DNA replication. Partially duplex oligonucleotides that lacked up to 14 nucleotides from the 5'-end of the nontemplate (displaced) strand supported initiation as much as 20-fold more efficiently than fully duplex oligonucleotides. The removal of 18 nucleotides or more from the 5'-end of the displaced strand resulted in a sharp decrease in the ability of the DNA templates to support initiation. The poor template efficiency of certain DNAs could be explained by their inability to bind nuclear factor I. The initiation efficiency observed with other DNAs correlated with their ability to bind the preterminal protein-Ad DNA polymerase complex. At low concentrations of the Ad DNA-binding protein, protein-primed initiation was also observed on single-stranded DNAs. The single-stranded template strand of the Ad origin was at least 5-20-fold better at supporting initiation than other single-stranded DNAs. These findings suggest a model in which the 3'-end of the template strand is rendered single-stranded as a prerequisite for initiation of Ad DNA replication.

Adenosine Triphosphate↗
PubMed1986

Leporine acquired immune deficiency disease.

We have identified a recombinant leporipoxvirus that produces disseminated fibromas and a severe combined immune deficiency disease of sudden onset. The virus is recombinant between the SFV and the MV. MV was identified as a trace contaminant in stocks of SFV (Patuxent strain). Rabbits inoculated with the original uncloned stock of SFV prepared in vitro develop local tumors that subsequently regress. However, tumor extracts prepared from these animals, when injected into a second group of rabbits, produced MV syndrome. Rabbits with MV syndrome develop severe, usually lethal, Pasteurella or Bordetella infections and have disseminated fibroxanthosarcomas more similar to those produced by myxoma virus. The virus that induces this syndrome has been isolated by two cycles of plaque purification. This virus is indistinguishable from SFV using cross-neutralization and electron microscopy. Analyses of restriction enzyme digests of MV and plaque-purified SFV show them to be quite dissimilar and indicate that MV is recombinant between SFV and myxoma virus. This recombinational event resulted in approximately 5.5 kb of myxoma virus DNA within each of the inverted terminal repeats being replaced by a similar amount of DNA derived from the corresponding region of the SFV genome. Thus, MV contains approximately 149 kb of myxoma sequences and 11 kb of SFV sequences. Immunofluorescent studies of spleen and lymph nodes from MV-infected rabbits demonstrate that viral antigens are present predominantly in the sinusoidal lining cells in lymph nodes and in phagocytes in the splenic cords. This contrasts with the distribution of antigen observed in myxoma virus-infected rabbits where myxoma-specific antigens are present in large amounts in hyperplastic epithelium overlying tumors, particularly in the nasal mucosa and in spleen and lymph node cells. MV-infected rabbits essentially lose their lymphocyte proliferative response to T and B cell mitogens and are unable to initiate an antibody response to SRBC, as determined by a modified Jerne plaque assay. In vitro MV severely depresses the mitogen responses of normal B and T lymphocytes after two days of culture. Lymphoid cells and lysates of lymphoid cells from MV-infected rabbits will suppress mitogen- and antigen-induced responses in vitro. MV can grow in lymphocytes, but replication of MV is less efficient in lymphocytes than in RK-13 cells. Thus, MV produces a disseminated viral infection, systemic myxofibromas, and a severe combined immune deficiency in rabbits. The molecular and immunologic basis for these effects is now under study.

Acquired Immunodeficiency Syndrome↗
PubMed1984

Transposable element Mu1 is found in multiple copies only in Robertson's Mutator maize lines.

An approximately 1.4 kb fragment of DNA called Mu1, mutationally inserted into the Adh1 locus of maize in a Robertson's Mutator plant, has been cloned. The instability of the mutation induced by this element, the nature of the Robertson's Mutator system, and terminal inverted repeats indicate that the 1.4 kb insert is a transposable element. All Robertson's Mutator corn lines have Mu1-like elements, at copy numbers of 10-70 per diploid genome. The basic size of these multiple interspersed copies is generally the same. The elements are found on different genomic restriction fragments in closely related individuals, indicating a high degree of mobility. Aside from the one corn line identified by Robertson in the mid-1970s as Mutator, all maize lines tested, plus several near and remote corn relatives, have no detectable DNA which cross-hybridizes strongly with Mu1.

Cloning, Molecular↗
PubMedDate not supplied

Simple method for cDNA amplification starting from small amount of total RNA.

We describe a novel simple PCR-based technique for construction of cDNA libraries starting from the small samples of cells or tissues. This technique is based on the insertion of inverted terminal repeats (ITR) into amplified cDNA which causes a part of molecules to generate "pan"-type structures at each cycle of PCR amplification. This allows to avoid generation of the primer dimmer and makes possible the regulation of an average length of amplified sequences varying in concentration of primers.

Animals↗
PubMed1993

Expression of the cystic fibrosis transmembrane conductance regulator from a novel adeno-associated virus promoter.

Adeno-associated virus type 2 (AAV) vectors have been used for gene expression in respiratory epithelial cells and may be useful in gene therapy for diseases like cystic fibrosis (CF) which affect the airways. The AAV p5 promoter together with the AAV inverted terminal repeat (ITR) forms a 263-base pair cassette which mediated efficient expression in a CF bronchial epithelial cell line. We report here that the ITR itself can mediate gene expression. In stable transfection assays, AAV-CF vectors expressing the full-length cystic fibrosis transmembrane conductance regulator (CFTR) cDNA from either the p5 promoter or the ITR restored cAMP regulation of the chloride efflux characteristic of CFTR function. An AAV-ITR-CF vector deleted for the amino terminus of CFTR was also functional. This vector was packaged into AAV particles and used to transduce cells without selection. Transduced cells also exhibited cAMP-regulated Cl- efflux. The complemented cell lines showed increased levels of CFTR protein immunofluorescence, and the presence of intact AAV-CF vector sequence was confirmed by Southern blot analysis of rescued vector sequences. These studies provide novel insights into AAV gene expression, and this newly described promoter allows for the production of AAV vectors expressing CFTR in those differentiated cells affected in CF.

Base Sequence↗
PubMed1995

Efficient gene transfer with adeno-associated virus-based plasmids complexed to cationic liposomes for gene therapy of human prostate cancer.

We have shown previously that treatment of rats bearing the Dunning R3327 MatLyLu prostatic tumor with human interleukin 2 (IL-2) gene-modified tumor cell preparations induces potent antitumor immunity in the animal. To test the clinical feasibility of using genetically modified tumor vaccines for the treatment of prostate cancer, we have explored the use of a simplified gene delivery system based on liposomes to introduce and express the IL-2 gene in the Dunning rat R3327 MatLyLu prostatic tumor cell line (MatLyLu) and in short-term cultures of primary human prostatic tumor cells. Liposome-DNA complexes containing the adeno-associated virus inverted terminal repeats exhibited 3-10-fold higher levels of gene transfer and IL-2 expression than did liposome complexes with non-adeno-associated virus containing plasmids. Single transfections resulted in IL-2 expression for an extended period of time that exceeded severalfold the amount of IL-2 secreted from retrovirally transduced MatLyLu cells. X-irradiation of cells (4000 rads) prior to transfection did not affect cytokine secretion, indicating that liposome-mediated gene transfer does not depend on cell proliferation. High levels of gene transfer and IL-2 expression were also achieved in short-term cultures of primary human prostatic tumor cells established from tumor specimens obtained following radical prostatectomy of cancer patients. Depending on the type of liposome used, IL-2 levels secreted from the human prostatic tumor cells were comparable to or exceeded the levels of IL-2 secreted from retrovirally transduced MatLyLu cells, which induced antitumor immunity in the rat model. The ability to culture and expand ex vivo human prostatic tumor cells, and the use of a simple and highly efficient gene transfer method to generate genetically modified tumor vaccines, set the stage for clinical exploration of gene-based immunotherapy of prostate cancer.

Animals↗
PubMed1994

Recombinant adeno-associated virus-mediated gene transfer into hematopoietic progenitor cells.

Recombinant adeno-associated viruses (rAAV) containing only the inverted terminal repeats (ITR) from the wild-type virus are capable of stable integration into the host cell genome, and expression of inserted genes in cultured cells. We have now defined the ability of rAAV to introduce genes into primary hematopoietic progenitors. A vector was constructed containing the coding sequences for beta-galactosidase (beta-gal), including a nuclear localization signal, under the control of a strong viral promotor. Infectious vector particles were prepared by cotransfection of the vector plasmid with a second plasmid that contained the coding sequences for AAV proteins into adenovirus-infected human embryonic kidney cells. These vector preparations transferred and expressed the beta-gal gene in human K562 erythroleukemia and Detroit 6 cells. Positive immunoselection yielded a population of enriched CD34+ cells that were transduced with the rAAV beta-gal vector. Nuclear localized enzyme expression was documented in 60% to 70% of infected cells. Progenitor-derived colonies that developed after 2 weeks in clonogenic cultures were shown to have viral-associated DNA at an estimated copy number of 1 to 2 per cell using a semiquantitative polymerase chain reaction (PCR) method. Integration of AAV into hematopoietic progenitors was documented using wild-type virus, as its genome may integrate at a preferred site on chromosome 19. Our data suggest that rAAV will transfer and express genes in primitive hematopoietic progenitors with high frequency, and support the development of this vector system for therapeutic gene transfer.

Adenoviruses, Human↗
PubMed1996

A purified mariner transposase is sufficient to mediate transposition in vitro.

Mariners are a widespread and diverse family of animal transposons. Extremely similar mariners of the irritans subfamily are present in the genomes of three divergent insect host species, which strongly suggests that species-specific host factors are unnecessary for mobility. We tested this hypothesis by examining the activity of a purified transposase from one of these elements (Himar1) present in the horn fly, Haematobia irritans. Himar1 transposase was sufficient to reproduce transposition faithfully in an in vitro inter-plasmid transposition reaction. Further analyses showed that Himar1 transposase binds to the inverted terminal repeat sequences of its cognate transposon and mediates 5' and 3' cleavage of the element termini. Independence of species-specific host factors helps to explain why mariners have such a broad distribution and why they are capable of horizontal transfer between species.

Animals↗
PubMed1996

Autonomous parvovirus transduction of a gene under control of tissue-specific or inducible promoters.

Several classes of viruses are in use, or are being developed, as gene therapy vectors. Viruses with small genomes containing few essential genes have the advantage of requiring only simple complementation systems to allow packaging of foreign DNA, substituted for the entire viral coding sequences. Retroviruses and the dependent parvovirus AAV (adeno-associated virus) have been used in this way, and both possess an efficient integration mechanism which should allow long-term expression of transduced genes. In some situations, however, long-term persistence may be undesirable and there is a need for small, non-integrating viral vectors. Autonomous parvoviruses, such as LuIII, have potential as such vectors for short-term expression of therapeutic genes. We previously described recombinants of LuIII that transduced reporter genes, expressed using the viral constitutive promoter, P4. We have now generated several recombinants containing regulated promoters. A virus including a liver-specific enhancer directed 10- to 20-fold preferential expression of the luciferase reporter in transduced human hepatoma (HepG2) versus HeLa cells. In additional LuIII recombinants, the luciferase reporter was linked with chimeric promoters containing binding sequences for either the yeast GAL4 protein or the bacterial tetracycline repressor. Luciferase expression was strongly activated when these viruses were used to infect cells containing a cognate trans-activator (GAL4 or tTA, a tetracycline repressor fusion with VP16 of herpes simplex), introduced by transfection. The response to tTA could be abolished, or reduced in a graded manner, by exposure of the infected cells to tetracycline. Further results suggested that an increase in basal expression, apparently mediated by the viral left terminal inverted repeat, could be minimized by interposing polyadenylation signals between this sequence and the promoter. These results confirm that appropriate transcriptional regulation can be achieved for genes transduced by an autonomous parvovirus vector. Such vectors therefore show promise for the delivery of therapeutic genes in situations requiring cell-specific, short-term expression, eg in targeting suicide genes for ablation of cancer cells.

Cell Line↗
PubMed1996

[Sequencing of right terminal fragment of canine adenovirus type 1 vaccine strain DNA].

Current studies show that adenoviruses are more advantageous as expression vectors than other viruses. Canine adenovirus type 1 (CAV-1) vaccine strain, CLL (cannaught laboratory limited), as vectors will play more important role for the prophylaxis of zoonosis than human adenoviruses. Studies on molecular biology of CAV-1 or CLL are necessary for construction of vectors of CLL. In this paper, the right terminal of CLL DNA cleaved by Hind II was sequenced. Authors found that it contained a 238 bp inverted terminal repeats (ITR). There are three copies of 40 bp short repeat sequences in the ITR. According to the DNA structural model of human adenovirus type 2, the 40 bp short repeats are the sites that are combined with nuclear factor 1 (NF-1) that is an initiation factor of DNA replication of virus, so they are essential structure of CLL DNA.

Adenoviruses, Canine↗
PubMed1997

BARE-ID, a representative of a family of BARE-like elements of the barley genome.

In our search for transposable elements in barley, Hordeum vulgare, we have isolated and cloned two BamHI-fragments of 4.7 and 4.2 kb in length containing very abundant DNA sequences. The 4.7 kb fragment is homologous to the extended region, including more than half of the 5'-LTR and some part of the coding domain of BARE-1, a member of copia-like retrotransposon family of barley. The 4.2 kb fragment, bearing homology to BARE-1 and the WIS-2 family isolated from wheat, is unique among studied retroelements of cereals because it consists of two inverted parts, each containing homology to the LTR and UTL of BARE-1. Functional motifs for reverse transcription, two TATA-boxes and two primer-binding sites, were found within the LTRs. The element contained within this fragment was generated by significant rearrangement of a BARE-like retrotransposon, which included inversion of the extended 5'-terminal region and deletion of the internal domain. Therefore this element is named BARE-ID (BARE-inverted, deleted). A family of BARE-like elements is amplified in the H. vulgare genome compared with wild barley species. The terminal inverted repeat of BARE-ID was used as a probe for examination of evolutionary diversity within genus Hordeum. Our data are basically in agreement with the modern classification system. However, they do not support the combination of H. vulgare and H. bulbosum into one group with the same type of genome. New data concerning the possible origin of the polyploid species, H. secalinum, confirm that retrotransposons are a useful tool for phylogenetic studies.

Base Sequence↗