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Results for “binary vectorization”

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PubMed1990

A Markovian model for comparing incidences of side effects.

For clinical trials that entail observations at successive visits for the occurrence of a side effect, this paper considers a likelihood-based method to compare side effect incidence rates. The method, which employs the assumption of a Markov chain of order one for the vectors of binary responses, handles missing data due to premature withdrawals. An actual numerical example and a simulated example illustrate the technique.

Clinical Trials as Topic↗

PubMed2000

Enhancing activity of epsilon in Escherichia coli and Agrobacterium tumefaciens cells.

Epsilon (epsilon) sequence is a bacterial enhancer of translation found in the bacteriophage T7 gene 10. It is believed that its enhancing effect of epsilon is due to a base-pairing with the nucleotides 458-467 from the helical domain 17 of Escherichia coli 16S rRNA. To prove this we have taken advantage of the difference of this domain in Agrobacterium tumefaciens and E. coli. To evaluate the significance of nucleotide complementarity for the enhancing activity of epsilon, a series of nucleotide sequences matching either E. coli or A. tumefaciens domain 17 are cloned in a binary expression vector in front of the chloramphenicol acetyltransferase (CAT) gene. The CAT assay shows that: (i) the epsilon in combination with an SD consensus sequence increases the yield of CAT in both microorganisms over that obtained with the SD alone; (ii) the epsilon sequence complementary to the A. tumefaciens domain 17 leads to a 2.71-fold increase in the yield of CAT in homologous cells but not in E. coli cells; (iii) the yield of CAT correlates with the free energy of base-pairing with the helical domain 17 in both microorganisms.

Agrobacterium tumefaciens↗

PubMed2002

Bax-induction gene therapy of pancreatic cancer.

BACKGROUND: Bax is a strong pro-apoptotic gene that induces programmed cell death when expressed. Human telomerase reverse transcriptase (hTERT) is the catalytic subunit for telomerase, an enzyme found to be active in more than 85% of human cancers. Recently, a binary adenoviral system (Ad/GT-Bax + Ad/hTERT-GV16) was constructed using the hTERT promoter to induce Bax gene expression in tumor cells. METHODS: To test whether human pancreatic tumor cells would respond to this system of Bax-induced apoptosis, we compared the effects of Bax gene induction with that of LacZ gene induction using the same binary system. RESULTS: Lysates of the human pancreatic cell lines PANC-28, MIA PaCa-2, and BxPC-3 showed significantly elevated levels of human telomerase using the PCR-based TRAP assay. As early as 24 h after treatment with Bax-induction gene therapy, growth inhibition was observed. Overexpression of the Bax protein was confirmed by Western blotting. Extensive apoptosis on FACS analysis at 48 h was seen after Bax induction. In addition, cytosolic cytochrome c levels increased compared to mitochondrial levels after Bax induction. Levels of caspase-3, a key downstream enzyme involved in apoptosis, also increased significantly compared to controls after treatment. None of these effects were seen with LacZ. CONCLUSION: Our results suggest that the binary adenoviral vector system, Ad/GT-Bax + Ad/hTERT-GV16, induces high levels of Bax expression that induce apoptosis in human pancreatic cancer cells.

Apoptosis↗

PubMed1994

Small-scale field tests with transgenic potato, cv. Bintje, to test resistance to primary and secondary infections with potato virus y.

The coat protein (CP) gene of the potato virus Y (PVY) strain N605 has been cloned into a plant binary expression vector and introduced into the potato variety Bintje. The transformed lines, Bt6, that contained two copies of the CP gene showed complete resistance to the homologous strain PVY-N605 and a good resistance to the related strain PVY-O803 in the greenhouse. The good resistance of Bt6 to primary and secondary infections by PVY was confirmed in two successive field tests where the virus was transmitted by its natural aphid vector.

Animals↗

PubMed1990

Agrobacterium-mediated DNA transfer in sugar pine.

DNA transfer using Agrobacterium tumefaciens has been demonstrated in sugar pine, Pinus lambertiana Dougl. Shoots derived from cytokinin-treated cotyledons formed galls after inoculation with A. tumefaciens strains containing the plasmid pTiBo542. A selectable marker, neomycin phosphotransferase II, conferring resistance to kanamycin, was transferred into sugar pine using a binary armed vector system. Callus proliferated from the galls grew without hormones and in some cases, kanamycin-resistant callus could be cultured. Southern blots provided evidence of physical transfer of T-DNA and the nptII gene. Expression of the nptII gene under control of the nos promoter was demonstrated by neomycin phosphotransferase assays. Several aspects of DNA transfer were similar to those previously observed in angiosperms transformed by A. tumefaciens. This is the first evidence for DNA transfer by Agrobacterium in this species and the first physical evidence for transfer in any pine. These results bring us closer to genetic engineering in this commercially important genus of forest trees.

DNA↗

PubMed1990

Aminoglycoside-3''-adenyltransferase confers resistance to spectinomycin and streptomycin in Nicotiana tabacum.

The bacterial gene aadA encodes the enzyme aminoglycoside-3"-adenyltransferase that confers resistance to spectinomycin and streptomycin in Escherichia coli. Chimeric genes have been constructed for expression in plants, and were introduced into Nicotiana tabacum by Agrobacterium binary transformation vectors. Spectinomycin or streptomycin in selective concentrations prevent greening of N. tabacum calli. Transgenic clones, however, formed green calli on selective media containing spectinomycin, streptomycin, or both drugs. Resistance was inherited as a dominant Mendelian trait in the seed progeny. Resistance conferred by the chimeric aadA gene can be used as a color marker similar to the resistance conferred by the streptomycin phosphotransferase gene to streptomycin.

Base Sequence↗

PubMed1987

High meiotic stability of a foreign gene introduced into tobacco by Agrobacterium-mediated transformation.

Two lines of transgenic Nicotiana tabacum transformed to kanamycin resistance by means of a binary Agrobacterium vector containing a nos-npt gene were investigated over three generations. Southern hybridization and crossing analyses revealed that a single copy of T-DNA had integrated in each line and that the kanamycin resistance was regularly transmitted to the progeny as a monogenic dominant trait. Homozygous transgenic plants were fully fertile, morphologically normal and did not significantly differ from wild-type plants in the quantitative characters examined (plant height, flowering time). The two lines showed very low, but significantly different levels of meiotic instability: kanamycin-sensitive plants occurred among backcross progeny from homozygous transgenic plants with frequencies of 6/45,000 and 25/45,000, respectively. The sensitive plants arose independently of each other and thus resulted from meiotic rather than mitotic events. These findings demonstrate for the first time that integrated foreign genes can be transmitted to progeny with the high degree of meiotic stability required for commercial varieties of crop plants. They emphasize the importance of non-homologous integration and of avoiding co-integration of inactive gene copies for achieving meiotically stable transformants.

Genetic Vectors↗

PubMed2002

A plant-transformation-competent BIBAC library from the Arabidopsis thaliana Landsberg ecotype for functional and comparative genomics.

The genome of the model plant Arabidopsis thaliana has been sequenced to near completion. To facilitate experimental determination of the function of every gene in the species, we constructed a large-insert library from the Landsberg ecotype using a plant-transformation-competent binary BAC vector, BIBAC2. The library contains 11,520 clones with an estimated average insert size of 162 kb. Of a sample of 102 clones, 17.6% had no inserts; further, in the library as a whole, 287 clones contained chloroplast DNA, and 25 contained mitochondrial DNA. Thus it is estimated that 9,295 clones originated from the nuclear genome, representing a 11.5 x coverage. The library was further characterized by screening with probes corresponding to 180-bp repeats, 5S rDNA, 18S-25S rDNA and 23 single-copy RFLP markers. The results showed that 92 clones contained 180-bp centromeric repeats, 78 contained 5S rDNA and 95 contained 18S-25S rDNA, approximately 1%, 0.8% and 1%, respectively, of the nuclear clones in the library. Screening the library with the 23 RFLP markers showed that each one hybridized to an average of seven clones. This library is the first large-insert DNA library for the widely studied Landsberg erecta strain. It will greatly facilitate gene identification by complementation screening, and will enhance analysis of the structure, organization and evolution of the A. thaliana genome.

Arabidopsis↗

PubMed2005

A reproducible genetic transformation system for cultivated Phaseolus acutifolius (tepary bean) and its use to assess the role of arcelins in resistance to the Mexican bean weevil.

A reproducible Agrobacterium tumefaciens-mediated genetic transformation method that delivers fertile and morphologically normal transgenic plants was developed for cultivated tepary bean (Phaseolus acutifolius L. Gray). Factors contributing to higher transformation efficiencies include (1) a low initial concentration of bacteria coupled with a longer cocultivation period with callus, (2) an initial selection of callus on a medium containing low levels of the selectable agent, (3) omission of the selectable agent from the medium during callus differentiation to shoots and (4) the efficient conversion of transgenic shoots into fertile plants. All plants regenerated with this procedure (T0) were stably transformed, and the introduced foreign genes were inherited in a Mendelian fashion in most of the 33 independent transformants. Integration, stable transmission and high expression levels of the transgenes were observed in the T1 and/or T3 progenies of the transgenic lines. The binary transformation vectors contained the beta-glucuronidase reporter gene, the neomycin phosphotransferase II selectable marker gene and either an arcelin 1 or an arcelin 5 gene. Arcelins are seed proteins that are very abundant in some wild P. vulgaris L. genotypes showing resistance to the storage insect Zabrotes subfasciatus (Boheman) (Coleoptera, Bruchidae). Transgenic beans from two different cultivated P. acutifolius genotypes with high arcelin levels were infested with Z. subfasciatus, but they were only marginally less susceptible to infestation than the non-transgenic P. acutifolius. Hence, the arcelin genes tested here are not major determinants of resistance against Z. subfasciatus.

Agrobacterium tumefaciens↗

PubMed2003

Agrobacterium- tumefaciens-mediated transformation of Helminthosporium turcicum, the maize leaf-blight fungus.

Agrobacterium tumefaciens has the ability to transfer its T-DNA to plants, yeast, filamentous fungi, and human cells and integrate it into their genome. Conidia of the maize pathogen Helminthosporium turcicum were transformed to hygromycin B resistance by a Agrobacterium- tumefaciens-mediated transformation system using a binary plasmid vector containing the hygromycin B phosphotransferase ( hph) and the enhanced green fluorescent protein ( EGFP) genes controlled by the gpd promoter from Agaricus bisporus and the CaMV 35S terminator. Agrobacterium- tumefaciens-mediated transformation yielded stable transformants capable of growing on increased concentrations of hygromycin B. The presence of hph in the transformants was confirmed by PCR, and integration of the T-DNA at random sites in the genome was demonstrated by Southern blot analysis. Agrobacterium- tumefaciens-mediated transformation of Helminthosporium turcicum provides an opportunity for advancing studies of the molecular genetics of the fungus and of the molecular basis of its pathogenicity on maize.

Agrobacterium tumefaciens↗

PubMed2004

Agrobacterium-mediated transformation of the wetland monocot Typha latifolia L. (Broadleaf cattail).

An Agrobacterium-mediated model transformation system was standardized for the wetland monocot Typha latifolia L. to achieve the long-term objective of introducing candidate genes for phytoremediation. Two binary plasmid vectors, pCAMBIA1301/EHA105 and pTOK233/LBA4404, both containing the gus (beta-glucuronidase) and hptII (hygromycin phosphotransferase II) genes, were used for transformation. Fifty-day-old 5 mg/l picloram-derived calli were cocultivated and selected on medium containing 20 mg/l or 40 mg/l hygromycin. Resistant calli were regenerated on medium supplemented with 5 mg/l 6-benzylaminopurine, with or without 20 mg/l or 40 mg/l hygromycin and with or without charcoal (10 g/l). Transient GUS activity in explants ranged between 28% and 36%. Hygromycin-resistant calli, selected after 3 months, showed stable GUS expression. A total of 46 plants were regenerated and established in the greenhouse; 13 showed stable GUS expression. Cocultivation of dark culture-derived calli, directly selected on regeneration medium containing 20 mg/l hygromycin and rooted on medium with 20 mg/l hygromycin was the best protocol. The addition of charcoal did not have any effect on regeneration. PCR and Southern analyses of transgenic calli and transgenic plants confirmed the presence of the introduced genes. In conclusion, T. latifolia could be genetically transformed by Agrobacterium tumefaciens.

Blotting, Southern↗

PubMed1997

Silencing of transgenes introduced into leaves by agroinfiltration: a simple, rapid method for investigating sequence requirements for gene silencing.

Agroinfiltration--the infiltration of Agrobacterium tumefaciens into intact plant levels--provides a rapid and simple way of screening large numbers of transgene constructs for silencing in response to a resident transgene. Transgenic Nicotiana sylvestris plants homozygous for the tobacco class I chitinase A gene CHN48 under the control of the cauliflower mosaic virus 35S RNA promoter (P35S) show a high incidence of postranscriptional gene silencing. We forced suspensions of A. tumefaciens, carrying P35S-CHN48 in a binary Tiplasmid vector, into wild-type and transgenic N, sylvestris leaves with a blunt-tipped plastic syringe. The infiltrated CHN48 transgene was expressed in leaves transformed with the vector alone, but not in CHN48-transformed leaves showing the silent phenotype. In contrast, expression of a chimeric P35S-E. coli beta-glucuronidase gene (uidA) infiltrated into leaves was not affected by the presence of the CHN48 transgene stably integrated in the host genome. These results show that extra copies of CHN48 are silenced by resident, silent copies of the same gene and confirm that CHN48 silencing is not the result of promoter interactions. The results also suggest that silencing of the additional CHN48 copies does not require their integration into chromosomes.

Agrobacterium tumefaciens↗

PubMed2005

Inducible excision of selectable marker gene from transgenic plants by the cre/lox site-specific recombination system.

In a plant transformation process, it is necessary to use marker genes that allow the selection of regenerated transgenic plants. However, selectable marker genes are generally superfluous once an intact transgenic plant has been established. Furthermore, they may cause regulatory difficulties for approving transgenic crop release and commercialization. We constructed a binary expression vector with the Cre/lox system with a view to eliminating a marker gene from transgenic plants conveniently. In the vector, recombinase gene cre under the control of heat shock promoter and selectable marker gene nptII under the control of CaMV35S promoter were placed between two lox P sites in direct orientation, while the gene of interest was inserted outside of the lox P sites. By using this vector, both cre and nptII genes were eliminated from most of the regenerated plants of primary transformed tobacco through heat shock treatment, while the gene of interest was retained and stably inherited. This auto-excision strategy, mediated by the Cre/lox system and subjected to heat shock treatment to eliminate a selectable marker gene, is easy to adopt and provides a promising approach to generate marker-free transgenic plants.

Base Sequence↗

PubMed1987

Wound-inducible expression of a potato inhibitor II-chloramphenicol acetyltransferase gene fusion in transgenic tobacco plants.

A potato inhibitor II gene (IIK) was isolated from a library of potato genes in lambda bacteriophage. An 8-kilobase-pair (kbp) insert was identified using a tomato inhibitor II cDNA as a hybridization probe, and a 2.6-kbp fragment containing the gene was subcloned into the plasmid pUC13 and characterized. The nucleotide sequence of the isolated gene exhibited 87% identity with the wound-inducible tomato inhibitor II cDNA sequence. The amino acid sequence of inhibitor IIK, deduced from the potato gene, exhibited 84% identity with the tomato inhibitor II protein. A 1000-bp restriction fragment from the 5' flanking region of the gene was fused to the open reading frame of the chloramphenicol acetyltransferase (CAT) gene. This fusion was terminated in two ways: (i) with a terminator sequence from the potato inhibitor II gene and (ii) with a terminator from the 6b gene of Ti plasmid pTiA6. These chimeric genes were transferred into tobacco cells via a binary Ti vector system, and transgenic plants were regenerated. The CAT gene was expressed in leaves of transformed plants in response to wounding when fused with the inhibitor IIK promoter and terminator regions. The chimeric gene containing the 6b terminator did not express CAT in response to wounding. The wound-inducible expression of CAT activity was systemic and was induced in tissues distal to the wounded tissues. The time course of wound induction of CAT activity in transgenic tobacco leaves is similar to that found for wound-inducible inhibitor I and II mRNAs in tomato leaves. These results demonstrate that sequences necessary and sufficient for wound inducibility are present within approximately 1000 bp of the control regions of the inhibitor IIK genes and that wound-inducible components of tobacco leaf cells can regulate these sequences.

Journal Article↗

PubMed2003

Gene interaction in DNA microarray data is decomposed by information geometric measure.

MOTIVATION: Given the vast amount of gene expression data, it is essential to develop a simple and reliable method of investigating the fine structure of gene interaction. We show how an information geometric measure achieves this. RESULTS: We introduce an information geometric measure of binary random vectors and show how this measure reveals the fine structure of gene interaction. In particular, we propose an iterative procedure by using this measure (called IPIG). The procedure finds higher-order dependencies which may underlie the interaction between two genes of interest. To demonstrate the method, we investigate the interaction between the two genes of interest in the data from human acute lymphoblastic leukemia cells. The method successfully discovered biologically known findings and also selected other genes as hidden causes that constitute the interaction. AVAILABILITY: Softwares are currently not available but are possibly made available in future at http://www.mns.brain.riken.go.jp/~nakahara/DNA_pub.html where all the related information is also linked.

Algorithms↗

PubMed2004

Regulated gene expression by glucocorticoids in cultured Virginia pine (Pinus virginiana Mill.) cells.

The effects of six glucocorticoids (dexamethasone, hydrocortisone, 6-methylprednisolone, prednisolone, prednisone, and triamcinolone) on inducible gene expression, based on the chimaeric transcriptional activator GVG and carried by the binary expression vector pINDEX3-m-gfp5-ER, were evaluated in transgenic Virginia pine cell cultures. The concentration that activated GVG transcription factor activity, the level of inducible m-gfp5-ER expression, and the kinetics of inducible m-gfp5-ER expression were determined for each glucocorticoid. Transgenic cells produced green fluorescence upon blue light excitation after treatment with prednisolone, prednisone, 6-methylprednisolone, dexamethasone, triamcinolone, and hydrocortisone. Green fluorescence was observed at 6-12 h after treatment of all six glucocorticoids at concentrations of 1, 3, 5, and 10 mg l(-1). Differential expression of gfp was confirmed by northern blot analysis and by quantitative fluorescence analyses of confocal images taken by a LSM 510 Laser Scanning Microscope. Fresh and dry weight increases of transgenic cell cultures were not affected by all six glucocorticoids at concentrations of 0.1, 0.5, 1, 3, and 5 mg l(-1). It is shown that triamcinolone had the most potent effect on the GVG system. Different glucocorticoids can therefore be used to regulate the GVG transcriptional activator and to induce gene expression in transgenic plant cells, and this property could be useful in establishing an optimum system of transgene regulation.

Cells, Cultured↗

PubMed1991

The nucleotide sequence and genome structure of the geminivirus miscanthus streak virus.

A tandem dimer of miscanthus streak virus (MiSV) DNA was inserted into the T-DNA of the binary plasmid vector pBIN19 and agroinoculated into several monocotyledonous plants (monocots) using Agrobacterium tumefaciens or A. rhizogenes. Disease symptoms and geminate particles were produced in maize and Panicum milaceum plants, and MiSV-specific double-stranded and single-stranded DNAs were found in these plants. The nucleotide sequence of the infectious MiSV clone, consisting of 2672 nucleotides, was determined. Four open reading frames (ORFs) for proteins of Mr greater than 10K were identified, two (V0 and V2) in the virus (+) sense and two (C1 and C2) in the complementary (-) sense, although C2 did not have an ATG start codon. Unlike other geminiviruses infecting monocots, complementary-sense ORFs did not overlap. Potential splicing donor and acceptor sites were identified in the sequence of the border region between the C terminus of ORF C1 and the N terminus of ORF C2. Amino acid sequences predicted from three (V2, C1 and C2) of these ORFs showed significant homology with the corresponding ORFs of other geminiviruses infecting monocots. A fifth ORF (V1), which showed some homology with ORF V1 of other monocot-infecting geminiviruses despite having a coding capacity for a product of Mr 8.8K, was found just upstream of ORF V2 as observed in those geminiviruses. ORF V0 showed no significant homology with ORFs present in any other geminiviruses. A mutation of V0 indicated that the C-terminal 30% of this ORF was not necessary for infection in maize, but that sequences around the mutated LspI site might have some regulatory role.

Amino Acid Sequence↗

PubMed2005

An energy function-based design method for discrete Hopfield associative memory with attractive fixed points.

An energy function-based autoassociative memory design method to store a given set of unipolar binary memory vectors as attractive fixed points of an asynchronous discrete Hopfield network (DHN) is presented. The discrete quadratic energy function whose local minima correspond to the attractive fixed points of the network is constructed via solving a system of linear inequalities derived from the strict local minimality conditions. The weights and the thresholds are then calculated using this energy function. If the inequality system is infeasible, we conclude that no such asynchronous DHN exists, and extend the method to design a discrete piecewise quadratic energy function, which can be minimized by a generalized version of the conventional DHN, also proposed herein. In spite of its computational complexity, computer simulations indicate that the original method performs better than the conventional design methods in the sense that the memory can store, and provide the attractiveness for almost all memory sets whose cardinality is less than or equal to the dimension of its elements. The overall method, together with its extension, guarantees the storage of an arbitrary collection of memory vectors, which are mutually at least two Hamming distances away from each other, in the resulting network.

Association Learning↗