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At least 973 records · Page 54Linked to original sources
PubMed2005

A high- and low-temperature inducible Arabidopsis thaliana HSP101 promoter located in a nonautonomous mutator-like element.

Transcriptional activity of a 573-bp fragment of HSP101 (At1g74310) incorporated into a Mutator-like element (MULE) transposon was investigated in Arabidopsis thaliana Columbia. Sequence identity between the HSP101-MULE arrangement and a continuous segment of the original HSP101 promoter, 5' UTR exon, and open reading frame (ORF) was high (87%) but lower in the 5' UTR intron (69%). Collectively, the HSP101 ORF, the MULE 5' terminal inverted repeat (TIR), and the 1.3 kb immediately upstream of the TIR is located on chromosome IV, and we refer to it as HSP101B. Located within the HSP101B promoter, upstream of 2 heat shock elements (HSEs), are 4 COR15a-like low-temperature response elements (LTREs). The HSP101B ORF was transcribed in the leaves and influorescences of high-temperature stress (HTS) treated Arabidopsis thaliana but not in low-temperature stress (LTS) and control plants. Transiently transformed Arabidopsis seedlings, as well as stable transformed lines of Linum usitatissimum (flax) and Brassica napus (canola) containing a HSP101B promoter:GUS construct, showed either LTS-, or LTS- and HTS-, induced beta-glucuronidase expression. Results from PCR amplifications of HpaII- and MspI-digested Arabidopsis genomic DNA suggest that endogenous expression of HSP101B may be downregulated by partial methylation of the HSP101B sequence between the TIRs of the associated MULE.

Arabidopsis↗
PubMed1989

Molecular analysis of an alcohol dehydrogenase (Adh) gene from chromosome 1 of wheat.

We have cloned and determined the nucleotide sequence of a gene encoding alcohol dehydrogenase (Adh) from Triticum aestivum cv. Millewa. Southern analysis using cv. Chinese Spring nullisomic-tetrasomic and ditelosomic lines established that the cloned gene mapped to the long arm of chromosome 1A and does not correspond to any previously identified wheat Adh locus. Southern analysis also provided evidence for triplicate copies of this Adh gene on the homoeologous group 1 chromosomes, while Northern blots indicated that the homoeologous group 1 Adh genes, like several other plant Adh genes, are transcribed under anaerobic conditions. Sequence analysis indicates that the cloned gene has a structure similar to both monocot and dicot Adh genes with an open reading frame encoding a polypeptide of 379 amino acids. Sequences important for eucaryotic gene expression such as the TATA box, polyadenylation signal, and intron splice sites were found in the expected positions. The open reading frame is interrupted by 8 introns which are in identical positions with 8 of the 9 introns in maize and pea Adh genes, suggesting that during evolution there are processes occurring that result in the loss of introns. Sequence analysis also revealed that the cloned wheat Adh gene shared extensive homology with the barley Adh3 gene not only in the coding region but also in the noncoding regions. However, this homology is discontinuous as a result of a 1.8-kbp insertion (TLM), which is present in the cloned wheat Adh gene and absent in the barley Adh3 gene. Sequence analysis of this insertion reveals features characteristic of the short terminal inverted repeat class of eucaryotic transposable elements. We have no evidence for the transposition of the TLM element. However, Southern blots reveal multiple copies of sequences related to TLM in the wheat genome and in other closely related species, suggesting that transposition may once have played an important role in the evolution of the Gramineae family.

Alcohol Dehydrogenase↗
PubMed1997

Insertion sequence IST3091 of Thiobacillus ferrooxidans.

An insertion sequence, designated as IST3091, was located adjacent to the putative origin of replication region of plasmid pTFI91 of Thiobacillus ferrooxidans TFI-91. The DNA sequence of the transposase gene of IST3091 revealed similarity with that of IS30, IS1086, IS4351, and the integrase gene of SpV1-R8A2 B (a bacteriophage of Spiroplasma citri). The sequence of IST3091 is 1063 bp long with partially matched 30-bp terminal inverted repeats. Several restriction fragments of plasmid pTFI91 of T. ferrooxidans containing the IST3091 element were cloned into the vector pHSG398. The hybrid plasmids (pBTL) were transformed into Escherichia coli NK7379 containing a miniF plasmid, which was devoid of transposable elements. The transposition function of the IST3091 element was confirmed by mobilizing hybrid plasmids via conjugation from transformed E. coli NK7379 (donor) to E. coli M8820 (recipient). The presence of the transposed element in transconjugants was detected by polymerase chain reaction amplification.

Amino Acid Sequence↗
PubMed2006

Recombinant baculovirus containing the diphtheria toxin A gene for malignant glioma therapy.

Insect baculoviruses are capable of infecting mammalian glial cells in the central nervous system. We investigated in the current study the feasibility of using the viruses as toxin gene vectors to eliminate malignant glioma cells in the brain. We first confirmed that glioma cells were permissive to baculovirus infection, with variable transduction efficiencies at 100 viral particles per cell and ranging between 35% and 70% in seven human and rat glioma cell lines. We then developed a recombinant baculovirus vector accommodating the promoter of glial fibrillary acidic protein (GFAP) to minimize possible side effects caused by overexpression of a therapeutic gene in sensitive neurons. We placed the GFAP promoter into a baculovirus expression cassette, in which the enhancer of human cytomegalovirus immediate-early gene and the inverted terminal repeats of adeno-associated virus were employed to improve the relatively low transcriptional activity of the cellular promoter. This recombinant baculovirus significantly improved transduction in glioma cells, providing the efficiency in C6 rat glioma cells up to 96%. When used to produce the A-chain of diphtheria toxin intracellularly in a rat C6 glioma xenograft model, the baculovirus effectively suppressed tumor development. The new baculovirus vector circumvents some of the inherent problems associated with mammalian viral vectors and provides an additional option for cancer gene therapy.

Animals↗
PubMed2000

Sequence analysis of porcine adenovirus type 3 E1 region, pIX and pIVa2 genes, and two novel open reading frames.

The porcine adenovirus type 3 (PAd3) genome between map units 0 and 13.7 was sequenced and compared with similar regions of other adenoviruses. This region consists of the left inverted terminal repeat sequences involved in DNA packaging, the entire early region 1 (E1) and the protein IX (pIX) transcription unit. The lower strand contains the C-terminal end of IVa2 of the E2A transcriptional unit and two novel open reading frames (ORFs). The E1 transcription unit consists of ORFs for proteins homologous to the E1A, E1B-17k and E1B-55k of both human adenovirus type 5 (HAd5) and bovine adenovirus type 3 (BAd3). The predicted PAd3 pIX demonstrated homology with the N-terminal portion of the pIXs of HAd5 and BAd3. On the lower strand, immediately after the putative IVa2 ORF, there are two unique ORFs of 208 and 203 amino acid residues that showed homology with Epstein-Barr virus nuclear antigens and other cellular transcription factors.

Adenovirus E1A Proteins↗
PubMed2003

Requirements for adeno-associated virus-derived non-viral vectors to achieve stable and site-specific integration of plasmid DNA in liver carcinoma cells.

BACKGROUND AND AIMS: Adeno-associated virus (AAV) is the only known virus capable of site-specific genomic integration in human cells. Thus, AAV-based vectors may be an attractive option to achieve prolonged transgene expression in human cells. We therefore studied the minimal elements of gene therapy vectors necessary for stable integration and tested the effectiveness of this approach in hepatoma cells. METHODS: Plasmids were constructed that contained a GFPneo fusion transgene with or without the AAV-inverted terminal repeats (ITRs). In addition, Rep protein was either encoded in CIS or supplied in TRANS by co-transfections. Stable clones were analyzed by Southern blotting for site-specific integration. RESULTS: The ITRs alone conferred neither stable nor site-specific transgene integration. Expression of Rep protein in CIS or TRANS resulted in an increased frequency of integration regardless of the presence of ITRs. It was shown that in the absence of the ITRs, other Rep-binding site (RBS) like sequences such as the ColE1 sequence present in plasmid backbones can function as RBS. Site-specific integration was achieved in up to 26% of clones derived from hepatoma cells. CONCLUSION: Both expression of Rep proteins and inclusion of a RBS are necessary for enhanced and stable integration of AAV-based non-viral vectors. A novel two-plasmid system capable of achieving stable and site-specific gene transfer in hepatoma cells is introduced.

Carcinoma, Hepatocellular↗
PubMed1992

Molecular cloning and restriction enzyme analysis of bovine adenovirus type 3.

Bovine adenovirus type 3 (BAV3) is a DNA virus that causes respiratory and gastrointestinal disorders in cattle. The viral genome consists of a linear double-stranded DNA molecule (35,000 base pairs) with inverted terminal repeats at each of its 5' molecular ends. We have subcloned 10 HindIII fragments spanning 4.9-96.0%, 5 EcoRI fragments spanning 3.4-89.5% and 2 XbaI fragments spanning 35.7-82.9% of the BAV3 (strain WBR-1) genome into the bacterial cloning vector pUC19. The subcloning of the viral genome facilitated the construction of linear restriction enzyme maps for BamHI, ClaI, EcoRI, HindIII, KpnI, NotI, NspV, PstI, PvuI, SalI, XbaI and XhoI. In this study we report on the molecular cloning and restriction endonuclease mapping of the BAV3 genome.

Adenoviridae↗
PubMed1992

Gene expression from adeno-associated virus vectors in airway epithelial cells.

Lung diseases such as cystic fibrosis (CF) might be treated by gene therapy using viral vectors delivered to the airway. One potential vector is the defective human parvovirus, adeno-associated virus (AAV). We examined the AAV p5 transcription promoter for gene expression in immortalized cell lines derived from the airway (IB3-1) or pancreas (CFPAC-1) of CF patients. AAV vectors expressing the prokaryotic genes cat (pAAVp5cat) or neo (pAAVp5neo) from the p5 promoter were evaluated after introduction into IB3-1 or CFPAC-1 cells by lipofection. In transient assays in both cell lines, the cat gene was expressed 5- to 10-fold more efficiently from the p5 promoter than from a simian virus 40 early gene promoter (pSVcat). IB3-1 cells were transformed stably to geneticin resistance by pAAVp5neo at a 5-fold higher efficiency than by an SVneo vector. The AAV inverted terminal repeat (ITR) region immediately upstream of the p5 promoter appears to have an enhancer effect and the promoter also contains a CREB site which confers a response to forskolin. In IB3-1 cells, expression of the cat gene from a p5 promoter was decreased about 5-fold by deletion of both the upstream ITR and the CREB site. The AAVp5neo vector was also packaged into AAV particles and used to infect IB3-1 cells as a transducing virus. Under these conditions, 60 to 70% of the cells could be stably transformed to geneticin resistance. Thus, AAV transducing vectors appear to be a highly efficient delivery system for stable integration and expression of genes in cultured airway epithelial cells.

Base Sequence↗
PubMed2003

Sex significantly influences transduction of murine liver by recombinant adeno-associated viral vectors through an androgen-dependent pathway.

A systematic evaluation of the influence of sex on transduction by recombinant adeno-associated viral vector (rAAV) indicated that transgene expression after liver-targeted delivery of vector particles was between 5- to 13-fold higher in male mice compared with female mice, irrespective of the proviral promoter or cDNA and mouse strain. Molecular analysis revealed that the rAAV genome was stably retained in male liver at levels that were 7-fold higher than those observed in females. Further, the sex difference in transduction was observed with AAV-2- and AAV-5-based vectors, which use distinct receptor complexes for infection. In concordance with the differences in AAV transduction, gel shift analysis with nuclear extracts derived from the liver of mice and humans revealed substantially higher binding of host nuclear protein to the rep-binding site (RBS) of AAV inverted terminal repeat (ITR) in males compared with females. Transduction efficiency and binding of nuclear protein to RBS was dramatically reduced in male mice by castration. In contrast, although oophorectomy did not significantly influence rAAV transduction, administration of 5alpha dihydrotestosterone, prior to gene transfer, increased stable hepatocyte gene transfer in females to levels observed in male mice, implying that androgens significantly influence hepatocyte gene transfer. Interestingly, sex did not have a significant effect on AAV gene transfer into nonhepatic tissue, indicating that there are distinct tissue- and sex-specific differences in the mechanisms responsible for efficient transduction with this vector. These results have significant implications for gene therapy of autosomal and acquired disorders affecting the liver.

Androgens↗
PubMed2006

P elements and MITE relatives in the whole genome sequence of Anopheles gambiae.

BACKGROUND: Miniature Inverted-repeat Terminal Elements (MITEs), which are particular class-II transposable elements (TEs), play an important role in genome evolution, because they have very high copy numbers and display recurrent bursts of transposition. The 5' and 3' subterminal regions of a given MITE family often show a high sequence similarity with the corresponding regions of an autonomous Class-II TE family. However, the sustained presence over a prolonged evolutionary time of MITEs and TE master copies able to promote their mobility has been rarely reported within the same genome, and this raises fascinating evolutionary questions. RESULTS: We report here the presence of P transposable elements with related MITE families in the Anopheles gambiae genome. Using a TE annotation pipeline we have identified and analyzed all the P sequences in the sequenced A. gambiae PEST strain genome. More than 0.49% of the genome consists of P elements and derivates. P elements can be divided into 9 different subfamilies, separated by more than 30% of nucleotide divergence. Seven of them present full length copies. Ten MITE families are associated with 6 out of the 9 Psubfamilies. Comparing their intra-element nucleotide diversities and their structures allows us to propose the putative dynamics of their emergence. In particular, one MITE family which has a hybrid structure, with ends each of which is related to a different P-subfamily, suggests a new mechanism for their emergence and their mobility. CONCLUSION: This work contributes to a greater understanding of the relationship between full-length class-II TEs and MITEs, in this case P elements and their derivatives in the genome of A. gambiae. Moreover, it provides the most comprehensive catalogue to date of P-like transposons in this genome and provides convincing yet indirect evidence that some of the subfamilies have been recently active.

Animals↗
PubMed2006

Mariner mutagenesis of Brucella melitensis reveals genes with previously uncharacterized roles in virulence and survival.

BACKGROUND: Random gene inactivation used to identify cellular functions associated with virulence and survival of Brucella spp has relied heavily upon the use of the transposon Tn5 that integrates at G/C base pairs. Transposons of the mariner family do not require species-specific host factors for efficient transposition, integrate nonspecifically at T/A base pairs, and, at a minimum, provide an alternative approach for gene discovery. In this study, plasmid vector pSC189, containing both the hyperactive transposase C9 and transposon terminal inverted repeats flanking a kanamycin resistance gene, were used to deliver Himar1 transposable element into the B. melitensis genome. Conjugation was performed efficiently and rapidly in less than one generation in order to minimize the formation of siblings while assuring the highest level of genome coverage. RESULTS: Although previously identified groups or classes of genes required for virulence and survival were represented in the screen, additional novel identifications were revealed and may be attributable to the difference in insertion sequence biases of the two transposons. Mutants identified using a fluorescence-based macrophage screen were further evaluated using gentamicin-based protection assay in macrophages, survival in the mouse splenic clearance model and growth in vitro to identify mutants with reduced growth rates. CONCLUSION: The identification of novel genes within previously described groups was expected, and nearly two-thirds of the 95 genes had not been previously reported as contributing to survival and virulence using random Tn5-based mutagenesis. The results of this work provide added insight with regard to the regulatory elements, nutritional demands and mechanisms required for efficient intracellular growth and survival of the organism.

Animals↗
PubMed2006

Genomic sequence and analysis of a vaccinia virus isolate from a patient with a smallpox vaccine-related complication.

BACKGROUND: Vaccinia virus (VACV)-DUKE was isolated from a lesion on a 54 year old female who presented to a doctor at the Duke University Medical Center. She was diagnosed with progressive vaccinia and treated with vaccinia immune globulin. The availability of the VACV-DUKE genome sequence permits a first time genomic comparison of a VACV isolate associated with a smallpox vaccine complication with the sequence of culture-derived clonal isolates of the Dryvax vaccine. RESULTS: This study showed that VACV-DUKE is most similar to VACV-ACAM2000 and CLONE3, two VACV clones isolated from the Dryvax vaccine stock confirming VACV-DUKE as an isolate from Dryvax. However, VACV-DUKE is unique because it is, to date, the only Dryvax clone isolated from a patient experiencing a vaccine-associated complication. The 199,960 bp VACV-DUKE genome encodes 225 open reading frames, including 178 intact genes and 47 gene fragments. Between VACV-DUKE and the other Dryvax isolates, the major genomic differences are in fragmentation of the ankyrin-like, and kelch-like genes, presence of a full-length Interferon-alpha/beta receptor gene, and the absence of a duplication of 12 ORFs in the inverted terminal repeat. Excluding this region, the DNA sequence of VACV-DUKE differs from the other two Dryvax isolates by less than 0.4%. DNA sequencing also indicated that there was little heterogeneity in the sample, supporting the hypothesis that virus from an individual lesion is clonal in origin despite the fact that the vaccine is a mixed population. CONCLUSION: Virus in lesions that result from progressive vaccinia following vaccination with Dryvax are likely clonal in origin. The genomic sequence of VACV-DUKE is overall very similar to that of Dryvax cell culture-derived clonal isolates. Furthermore, with the sequences of multiple clones from Dryvax we can begin to appreciate the diversity of the viral population in the smallpox vaccine.

Female↗
PubMed2006

Intrathecal long-term gene expression by self-complementary adeno-associated virus type 1 suitable for chronic pain studies in rats.

BACKGROUND: Intrathecal (IT) gene transfer is an attractive approach for targeting spinal mechanisms of nociception but the duration of gene expression achieved by reported methods is short (up to two weeks) impairing their utility in the chronic pain setting. The overall goal of this study was to develop IT gene transfer yielding true long-term transgene expression defined as > or = 3 mo following a single vector administration. We defined "IT" administration as atraumatic injection into the lumbar cerebrospinal fluid (CSF) modeling a lumbar puncture. Our studies focused on recombinant adeno-associated virus (rAAV), one of the most promising vector types for clinical use. RESULTS: Conventional single stranded rAAV2 vectors performed poorly after IT delivery in rats. Pseudotyping of rAAV with capsids of serotypes 1, 3, and 5 was tested alone or in combination with a modification of the inverted terminal repeat. The former alters vector tropism and the latter allows packaging of self-complementary rAAV (sc-rAAV) vectors. Combining both types of modification led to the identification of sc-rAAV2/l as a vector that performed superiorly in the IT space. IT delivery of 3 x 10e9 sc-rAAV2/l particles per animal led to stable expression of enhanced green fluorescent protein (EGFP) for > or = 3 mo detectable by Western blotting, quantitative PCR, and in a blinded study by confocal microscopy. Expression was strongest in the cauda equina and the lower sections of the spinal cord and only minimal in the forebrain. Microscopic examination of the SC fixed in situ with intact nerve roots and meninges revealed strong EGFP fluorescence in the nerve roots. CONCLUSION: sc-rAAVl mediates stable IT transgene expression for > or = 3 mo. Our findings support the underlying hypothesis that IT target cells for gene transfer lack the machinery for efficient conversion of the single-stranded rAAV genome into double-stranded DNA and favor uptake of serotype 1 vectors over 2. Experiments presented here will provide a rational basis for utilizing IT rAAV gene transfer in basic and translational studies on chronic pain.

Animals↗
PubMed1999

Characterization of the chalcone synthase genes expressed in flowers of the common and Japanese morning glories.

The CHS genes encoding chalcone synthase for flavonoid biosynthesis in the common and Japanese morning glories comprise a multigene family. Among these Ipomoea CHS genes, the CHS-D gene is the most abundantly expressed in the pigmented young flower buds and is primarily responsible for flower pigmentation. Majority of the remaining CHS transcripts in the flower buds are produced from the CHS-E gene. We characterized the genomic DNA segments of these CHS-D and CHS-E genes. Both genes have two exons with identical intron positions and carry several copies of two mobile element-like sequences with short terminal inverted repeats, MELS3 and MELS6 of around 200-300 bp. Small tandem repeats were also found in these CHS gene regions. The CHS-D and CHS-E genes are expressed predominantly in flower limbs and tubes, respectively. These structural and functional features and their evolutionary implications are discussed.

Acyltransferases↗
PubMed2005

Folbos, a new foldback element in rice.

A new class I foldback element, Folbos, has been discovered in O. sativa L. Its long terminal inverted repeats (IVRs) are 303 and 331 bp long and the left one encodes a short open reading frame of 76 codons. The IVRs consist of inner and outer domains, the latter built up of 6 tandem repeats of about 30 bp each. The central region is represented by 90 bp conservative stretch adjacent to a variable length (19-33 bp) A-tail, which in most cases includes the sequence 5'-TGACTT-3'. Folbos targets AT-rich regions and the insertion results in 7 bp target site duplications. Half of the copies found in annotated sequences of O. sativa japonica cv. Nipponbare are positioned in close proximity to (< 1kb) or within the transcribed regions, thus they have the potential to contribute to plant genome evolution.

Base Sequence↗
PubMed1993

Classification and relationships of rice strains with AA genome by identification of transposable elements at nine loci.

We analyzed the presence of p-SINE1 members at five loci in the rice strains belonging to seven species with AA genome in the Oryza genus by the methods including polymerase chain reaction (PCR). Four p-SINE1 members (p-SINE1-r3, r4, r5 and r7) were present at the corresponding loci in all the strains examined. One member (p-SINE1-r6) was, however, not present at the corresponding locus in most of the African strains of O. glaberrima and O. barthii, but was in the other strains. The PCR-amplified fragments containing p-SINE1-r4 in many strains were found to be larger due to insertion of either one of two transposable elements, named Tnr2 and Ret1, within or near p-SINE1-r4, respectively: Tnr2 is 157 bp in length with terminal inverted repeat sequences of about 56 bp; Ret1 is only 13 bp in length with a T stretch at its end. Tnr2 was not present in the corresponding locus in all the strains belonging to O. sativa Japonica and in some strains of O. rufipogon and O. longistaminata, while Ret1 was present only in the two strains of O. longistaminata. These results and previous ones obtained from the analysis of the other two p-SINE1 members (p-SINE1-r1 and r2) in the Wx gene indicate that the elements, such as p-SINE1-r6, Tnr2, Ret1 and p-SINE1-r2, have been inserted into the respective loci during divergence of the rice species with AA genome. The patterns for the presence and absence of the transposable elements at the respective loci enabled us to classify the rice strains with AA genome into ten groups and to infer their relationships.

Base Sequence↗
PubMed1998

Physical mapping of the linear plasmid pSLA2-L and localization of the eryAI and actI homologs.

The 200-kb linear plasmid pSLA2-L was suggested to be involved in the production of lankamycin and lankacidin in Streptomyces rochei 7434AN4. In this study, we have constructed a physical map for 23 PstI fragments of pSLA2-L, the sum of which was 206 kb. Detailed restriction maps for both ends of pSLA2-L revealed the presence of terminal inverted repeats, the size of which was found to be 2.1 kb by cloning and sequencing of the end-points. Hybridization experiments using two polyketide biosynthetic genes, eryAI and actI, located their homologous regions on PstI fragments A and I, respectively.

Anti-Bacterial Agents↗
PubMed2005

Construction and characterization of helper-dependent adenoviral vectors for sustained in vivo gene therapy.

A helper-dependent adenoviral (HDAd) vector is the most recently developed adenoviral vector. It does not contain any viral coding sequences except the inverted terminal repeat for replication origin and the packaging signal. Its safety profile and duration of transgene expression in vivo have improved substantially compared to early generation adenoviruses. Despite its usefulness for experimental gene therapy, technical difficulties in producing the HDAd vector have hampered its wide application. This chapter illustrates important considerations in vector design, unique features of this system, and an overview of vector production, which is followed by a step-by-step protocol for vector production. Vector characterization and troubleshooting are also provided at appropriate steps.

Adenoviridae↗