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Results for “binary vectorization”

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PubMed2004

Development of a novel helper-dependent adenovirus-Epstein-Barr virus hybrid system for the stable transformation of mammalian cells.

Epstein-Barr virus (EBV) episomes are stably maintained in permissive proliferating cell lines due to EBV nuclear antigen 1 (EBNA-1) protein-mediated replication and segregation. Previous studies showed the ability of EBV episomes to confer long-term transgene expression and correct genetic defects in deficient cells. To achieve quantitative delivery of EBV episomes in vitro and in vivo, we developed a binary helper-dependent adenovirus (HDA)-EBV hybrid system that consists of one HDA vector for the expression of Cre recombinase and a second HDA vector that contains all of the sequences for the EBV episome flanked by loxP sites. Upon coinfection of cells, Cre expressed from the first vector recombined loxP sites on the second vector. The resulting circular EBV episomes expressed a transgene and contained the EBV-derived family of repeats, an EBNA-1 expression cassette, and 19 kb of human DNA that functions as a replication origin in mammalian cells. This HDA-EBV hybrid system transformed 40% of cultured cells. Transgene expression in proliferating cells was observed for over 20 weeks under conditions that selected for the expression of the transgene. In the absence of selection, EBV episomes were lost at a rate of 8 to 10% per cell division. Successful delivery of EBV episomes in vivo was demonstrated in the liver of transgenic mice expressing Cre from the albumin promoter. This novel gene transfer system has the potential to confer long-term episomal transgene expression and therefore to correct genetic defects with reduced vector-related toxicity and without insertional mutagenesis.

Adenoviridae↗

PubMed1992

A new approach for three-dimensional reconstruction of arterial ultrasonography.

This report describes a computerized approach that allows the creation of realistic three-dimensional arterial images from two-dimensional contiguous slices derived from a conventional ultrasound scan. Furthermore, the study assesses the method's feasibility and accuracy by performing in vitro cadaver artery three-dimensional reconstructions. Images are digitized into a computer, with a resolution of 512 x 480 pixels, and a dynamic range of 8 bits/pixel (256 gray scale). After edge enhancement with convolution filters through the original binary data, the intraluminal and outer edges are traced and converted to a polygon vector within a defined three-dimensional space. Serial cuts, 2 mm apart, are then "stacked" into a three-dimensional model, with interpolation of polyhedra between slices. Sixteen normal and arteriosclerotic distal aortic and common iliac arteries were obtained from fresh cadavers. Three-dimensional reconstruction models were compared with gross examination of the original artery. Anatomically accurate reconstructions were obtained, all with detailed surface information. Data analyzed included diameter, area, residual lumen, and percent stenosis. Pearson's coefficients determined for the pairs of data indicated excellent correlation (greater than or equal to 0.90) between separate measurements. With use of the described technology it is feasible to perform arterial three-dimensional reconstructions on a personal computer, with detailed and accurate surface information. The three-dimensional reconstruction method used can reliably and consistently reproduce the anatomic specimens.

Arteries↗

PubMed2006

O(log2 M) self-organizing map algorithm without learning of neighborhood vectors.

In this letter, a new self-organizing map (SOM) algorithm with computational cost O(log2 M) is proposed where M2 is the size of a feature map. The first SOM algorithm with O(M2) was originally proposed by Kohonen. The proposed algorithm is composed of the subdividing method and the binary search method. The proposed algorithm does not need the neighborhood functions so that it eliminates the computational cost in learning of neighborhood vectors and the labor of adjusting the parameters of neighborhood functions. The effectiveness of the proposed algorithm was examined by an analysis of codon frequencies of Escherichia coli (E. coli) K12 genes. These drastic computational reduction and accessible application that requires no adjusting of the neighborhood function will be able to contribute to many scientific areas.

Algorithms↗

PubMed2005

Recombinant larvicidal bacteria with markedly improved efficacy against culex vectors of west nile virus.

An urgent need exists for new agents to control mosquito vectors of disease. Mosquito larvicides based on the bacteria Bacillus thuringiensis subsp. israelensis (Bti) or B. sphaericus (Bs) are effective in many habitats, but use is limited by their high cost. Moreover, mosquito resistance evolves rapidly to Bs where it is used intensively. The efficacy of these bacteria is due to a binary protein (BsB) in Bs and four proteins (Cry4A, Cry4B, Cry11A, and Cyt1A) in Bti. Here we report the use of cyt1A promoters and a 5' mRNA stabilizing sequence to synthesize high levels of Bs2362 binary toxin in Bti strains. The recombinant BtiIPS-82/BsB showed high potency against fourth instars of Culex quinquefasciatus, a vector of West Nile virus, being 21-fold as potent as BtiIPS-82, and 32-fold as potent as Bs2362. Similar improved efficacy was obtained against larvae of Cx. tarsalis. Moreover, BtiIPS-82/BsB suppressed resistance to Bs2362 in Cx. quinquefasciatus.

Animals↗

PubMedDate not supplied

The tet-off system is more effective than the tet-on system for regulating transgene expression in a single adenovirus vector.

BACKGROUND: Control of transgene expression in mammalian cells is desirable for gene therapy and the study of gene function in basic research. This study evaluates the functionality of single adenovirus (Ad) vectors containing a tetracycline-controllable expression system (tet-off or tet-on system). METHODS: An Ad-mediated binary transgene expression system was generated containing a tet-off or a tet-on system, which introduced the gene of interest with a tetracycline-regulatable promoter and the tetracycline-responsive transcriptional activator gene into the E1 and E3 deletion regions, respectively. The functionality of the Ad-mediated tet-off and tet-on systems was compared under various conditions in vitro and in vivo. RESULTS: The Ad vector containing the tet-off system provided negative control of gene expression ranging from 20- to 500-fold, depending on the cell type and condition. In contrast, the Ad vector containing the tet-on system increased gene expression by only 2- to 28-fold and required about two-log orders higher concentration of an inducer (doxycycline) to switch on the gene expression, compared with the Ad vector containing the tet-off system. CONCLUSION: Ad vectors containing the tet-off system are a better choice for regulated gene expression than Ad vectors containing the tet-on system. Single Ad vectors containing the tetracycline-controllable expression system will greatly facilitate in vitro and in vivo analyses of gene function and may be useful for gene therapy.

Adenoviridae↗

PubMed2001

A modular polycistronic expression system for overexpressing protein complexes in Escherichia coli.

To facilitate studies of multicomponent protein complexes, I have developed an Escherichia coli expression system which coexpresses up to four polypeptides from a single plasmid. The modular nature of the system enables efficient subcloning of a gene into each of the 4 cassettes in the polycistronic expression vector. Restriction sites present in the polycistronic expression vector allow both affinity tagged and untagged complexes to be overexpressed. I demonstrate successful use of the expression system for binary and ternary complexes, including the reconstitution of the VHL-elonginC-elonginB complex in E. coli and purification of the complex by affinity and ion-exchange chromatography. This polycistronic expression system should provide an important alternative to in vitro reconstitution of multicomponent complexes.

Base Sequence↗

PubMed2006

Mutagenic probability estimation of chemical compounds by a novel molecular electrophilicity vector and support vector machine.

MOTIVATION: Mutagenicity is among the toxicological end points that pose the highest concern. The accelerated pace of drug discovery has heightened the need for efficient prediction methods. Currently, most available tools fall short of the desired degree of accuracy, and can only provide a binary classification. It is of significance to develop a discriminative and informative model for the mutagenicity prediction. RESULTS: Here we developed a mutagenic probability prediction model addressing the problem, based on datasets covering a large chemical space. A novel molecular electrophilicity vector (MEV) is first devised to represent the structure profile of chemical compounds. An extended support vector machine (SVM) method is then used to derive the posterior probabilistic estimation of mutagenicity from the MEVs of the training set. The results show that our model gives a better performance than TOPKAT (http://www.accelrys.com) and other previously published methods. In addition, a confidence level related to the prediction can be provided, which may help people make more flexible decisions on chemical ordering or synthesis. AVAILABILITY: The binary program (ZGTOX_1.1) based on our model and samples of input datasets on Windows PC are available at http://dddc.ac.cn/adme upon request from the authors.

Algorithms↗

PubMed2004

A Boolean Hebb rule for binary associative memory design.

A binary associative memory design procedure that gives a Hopfield network with a symmetric binary weight matrix is introduced in this paper. The proposed method is based on introducing the memory vectors as maximal independent sets to an undirected graph, which is constructed by Boolean operations analogous to the conventional Hebb rule. The parameters of the resulting network is then determined via the adjacency matrix of this graph in order to find a maximal independent set whose characteristic vector is close to the given distorted vector. We show that the method provides attractiveness for each memory vector and avoids spurious memories whenever the set of given memory vectors satisfy certain compatibility conditions, which implicitly imply sparsity. The applicability of the design method is finally investigated by a quantitative analysis of the compatibility conditions.

Memory↗

PubMedDate not supplied

The logistic model for predicting the non-gonoactive Aedes aegypti females.

OBJECTIVE: To estimate, using logistic regression, the likelihood of occurrence of a non-gonoactive Aedes aegypti female, previously fed human blood, with relation to body size and collection method. MATERIAL AND METHODS: This study was conducted in Monterrey, Mexico, between 1994 and 1996. Ten samplings of 60 mosquitoes of Ae. aegypti females were carried out in three dengue endemic areas: six of biting females, two of emerging mosquitoes, and two of indoor resting females. Gravid females, as well as those with blood in the gut were removed. Mosquitoes were taken to the laboratory and engorged on human blood. After 48 hours, ovaries were dissected to register whether they were gonoactive or non-gonoactive. Wing-length in mm was an indicator for body size. The logistic regression model was used to assess the likelihood of non-gonoactivity, as a binary variable, in relation to wing-length and collection method. RESULTS: Of the 600 females, 164 (27%) remained non-gonoactive, with a wing-length range of 1.9-3.2 mm, almost equal to that of all females (1.8-3.3 mm). The logistic regression model showed a significant likelihood of a female remaining non-gonoactive (Y=1). The collection method did not influence the binary response, but there was an inverse relationship between non-gonoactivity and wing-length. CONCLUSIONS: Dengue vector populations from Monterrey, Mexico display a wide-range body size. Logistic regression was a useful tool to estimate the likelihood for an engorged female to remain non-gonoactive. The necessity for a second blood meal is present in any female, but small mosquitoes are more likely to bite again within a 2-day interval, in order to attain egg maturation. The English version of this paper is available too at: http://www.insp.mx/salud/index.html.

Aedes↗

PubMed2001

Training a perceptron in a discrete weight space.

Learning in a perceptron having a discrete weight space, where each weight can take 2L+1 different values, is examined analytically and numerically. The learning algorithm is based on the training of the continuous perceptron and prediction following the clipped weights. The learning is described by a new set of order parameters, composed of the overlaps between the teacher and the continuous/clipped students. Different scenarios are examined, among them on-line learning with discrete and continuous transfer functions. The generalization error of the clipped weights decays asymptotically as exp(-Kalpha(2)) in the case of on-line learning with binary activation functions and exp(-e(|lambda|alpha)) in the case of on-line learning with continuous one, where alpha is the number of examples divided by N, the size of the input vector and K is a positive constant. For finite N and L, perfect agreement between the discrete student and the teacher is obtained for alpha~Lsqrt[ln(NL)]. A crossover to the generalization error approximately 1/alpha, characterizing continuous weights with binary output, is obtained for synaptic depth L>O(sqrt[N]).

Journal Article↗

PubMed2005

Nucleotide binding and filament assembly of recombinant yeast septin complexes.

Septins are filament-forming GTPases involved in cytokinesis and cortical organization. In the yeast Saccharomyces cerevisiae, the septins encoded by CDC3, CDC10, CDC11, and CDC12 form a high-molecular-weight complex, localized at the cytoplasmic face of the plasma membrane in the mother-bud neck. While septin function at the cellular level is fairly well understood, progress on structure-function analysis of these proteins has been slow and limited by the lack of large amounts of pure complex. While monomeric septins form apparently non-native aggregates, stable recombinant complexes of two, three, or four yeast septins can be produced by co-expression from bi-cistronic vectors in E. coli. The septin polypeptides show various degrees of saturation with guanine nucleotides in different complexes. The binary core Cdc3p-Cdc12p complex contains no bound nucleotide. While ternary complexes are partially saturated and can bind extraneously added nucleotide with micromolar affinity, only the complete four-component septin complex is fully coordinated with tightly bound GDP/GTP after chromatographic purification. We show here that the nucleotide-binding sites of the septins show drastic changes on formation of higher oligomers. Although the binary core Cdc3p-Cdc12p complex does not form filaments, the ternary and quaternary complexes form bundles of paired filaments. In the case of ternary complexes, filament formation is stimulated by guanine nucleotide, but is not dependent on the presence or absence of the gamma-phosphate.

Base Sequence↗

PubMed2001

Approaches for generating recombinant adenovirus vectors.

Various methods have been developed to facilitate the generation of recombinant adenovirus vectors, and three commercially available methods have been most widely used: the homologous recombination method in E1-complement cell lines, the homologous recombination method in bacteria, and an in vitro ligation method based on simple routine plasmid construction. These methods can insert foreign genes not only into the E1 deletion region, but also into the E3 deletion region, thereby permitting the construction of a binary transgene expression system in which heterologous genes can be inserted into both the E1 and E3 regions. By modifying the latter two methods, fiber-mutant adenovirus vectors can be also constructed in order to modify vector tropism. In this paper, we review recent advances in the construction of first generation adenovirus vectors and fiber-modified adenovirus vectors.

Adenoviridae↗

PubMed1992

A T-DNA transfer stimulator sequence in the vicinity of the right border of pRi8196.

An 8 bp sequence repeated 6 times is present to the right of the mannopine type pRi8196 T-DNA right-border sequence. Experiments were designed to test whether these repeats have a role in T-DNA transfer. Several constructs in which different lengths of pRi8196 right-border region were linked to the cucumopine synthesis gene on an Agrobacterium-Escherichia coli shuttle vector were made. The recombinant plasmids were tested for their efficiency to act as a source of T-DNA in a binary system in which a wild-type Ri plasmid provided virulence and root-inducing functions. The T-DNA transfer efficiency of the constructs was assessed by computing the relative frequency of roots containing cucumopine. Depending on the Ri plasmid used as source of virulence functions, a high level of T-DNA transfer was observed only if 6 (pRi8196) or 5 (pRiA4) repeats were present. These results were confirmed by looking for single-stranded T-DNA molecules (T-strands) in bacteria induced for virulence. The repetition of the 8 bp unit was named 'T-DNA transfer stimulator sequence' (TSS).

Base Sequence↗

PubMed1994

A sensitive promoter assay based on the transcriptional activator Tat of the HIV-1 virus.

We developed a sensitive vector system for the analysis of weak promoter activities. This promoter assay is based on the transcriptional activator protein, Tat, of human immunodeficiency virus type 1 (HIV-1). High-level expression of HIV requires activation in trans by Tat of the promoter in the long terminal repeat (LTR). Here we describe the construction of a promoterless pTat vector. Foreign promoter elements can be inserted upstream from the tat gene, and expression of Tat protein is measured in trans on a co-transfected LTR-CAT reporter plasmid. We show that this binary system is more sensitive than standard pCAT reporter assays.

3T3 Cells↗

PubMed2005

Transgenic grasspea (Lathyrus sativus L.): factors influencing agrobacterium-mediated transformation and regeneration.

A reproducible procedure was developed for genetic transformation of grasspea using epicotyl segment co-cultivation with Agrobacterium. Two disarmed Agrobacterium tumefaciens strains, EHA 105 and LBA 4404, both carrying the binary plasmid p35SGUSINT with the neomycin phosphotransferase II (nptII) gene and the beta-glucuronidase (gus)-intron, were studied as vector systems. The latter was found to have a higher transforming ability. Several key factors modifying the transformation rate were optimized. The highest transformation rate was achieved using hand-pricked explants for infection with an Agrobacterium culture corresponding to OD(600) congruent with 0.6 and diluted to a cell density of 10(9) cells ml(-1) for 10 min, followed by co-cultivation for 4 days in a medium maintained at pH 5.6. Putative transformed explants capable of forming shoots were selected on regeneration medium containing kanamycin (100 mug ml(-1)). We achieved up to 36% transient expression based on the GUS histochemical assay. Southern hybridization of genomic DNA of the kanamycin-resistant GUS-expressive shoots to a gus-intron probe substantiated the integration of the transgene. Transformed shoots were rooted on half-strength MS containing 0.5 mg l(-1) indole-3-acetic acid, acclimated in vermi-compost and established in the experimental field. Germ-line transformation was evident through progeny analysis. Among T(1) seedlings of most transgenic plant lines, kanamycin-resistant and -sensitive plants segregated in a ratio close to 3:1.

Blotting, Southern↗

PubMedDate not supplied

Comparison of support vector machine and artificial neural network systems for drug/nondrug classification.

Support vector machine (SVM) and artificial neural network (ANN) systems were applied to a drug/nondrug classification problem as an example of binary decision problems in early-phase virtual compound filtering and screening. The results indicate that solutions obtained by SVM training seem to be more robust with a smaller standard error compared to ANN training. Generally, the SVM classifier yielded slightly higher prediction accuracy than ANN, irrespective of the type of descriptors used for molecule encoding, the size of the training data sets, and the algorithm employed for neural network training. The performance was compared using various different descriptor sets and descriptor combinations based on the 120 standard Ghose-Crippen fragment descriptors, a wide range of 180 different properties and physicochemical descriptors from the Molecular Operating Environment (MOE) package, and 225 topological pharmacophore (CATS) descriptors. For the complete set of 525 descriptors cross-validated classification by SVM yielded 82% correct predictions (Matthews cc = 0.63), whereas ANN reached 80% correct predictions (Matthews cc = 0.58). Although SVM outperformed the ANN classifiers with regard to overall prediction accuracy, both methods were shown to complement each other, as the sets of true positives, false positives (overprediction), true negatives, and false negatives (underprediction) produced by the two classifiers were not identical. The theory of SVM and ANN training is briefly reviewed.

Algorithms↗

PubMed2005

Distant-dipole field in liquids and diffusion: a perturbative approach.

A perturbative approach is employed to solve the Bloch-Torrey equations in the presence of distant-dipole fields in nuclear magnetic resonance. The procedure, although only carried out to first order in the perturbation parameter a=1/k2Dtaud, could, in principle, be generalized to higher orders. Here D is the diffusivity, taud the dipolar demagnetization time, and k is the wave vector of the spatial modulation of magnetization produced by the magnetic field gradient. The results are especially interesting for dilute binary mixtures consisting of molecular species with different diffusivities. In this case the calculated two-dimensional correlation spectroscopy revamped by asymmetric Z-gradient echo detection spectra are shown to be free from some inadequacies resulting from a simplistic application of standard approximations.

Journal Article↗

PubMed1999

Plastome engineering of ribulose-1,5-bisphosphate carboxylase/oxygenase in tobacco to form a sunflower large subunit and tobacco small subunit hybrid.

Targeted gene replacement in plastids was used to explore whether the rbcL gene that codes for the large subunit of ribulose-1, 5-bisphosphate carboxylase/oxygenase, the key enzyme of photosynthetic CO2 fixation, might be replaced with altered forms of the gene. Tobacco (Nicotiana tabacum) plants were transformed with plastid DNA that contained the rbcL gene from either sunflower (Helianthus annuus) or the cyanobacterium Synechococcus PCC6301, along with a selectable marker. Three stable lines of transformants were regenerated that had altered rbcL genes. Those containing the rbcL gene for cyanobacterial ribulose-1,5-bisphosphate carboxylase/oxygenase produced mRNA but no large subunit protein or enzyme activity. Those tobacco plants expressing the sunflower large subunit synthesized a catalytically active hybrid form of the enzyme composed of sunflower large subunits and tobacco small subunits. A third line expressed a chimeric sunflower/tobacco large subunit arising from homologous recombination within the rbcL gene that had properties similar to the hybrid enzyme. This study demonstrated the feasibility of using a binary system in which different forms of the rbcL gene are constructed in a bacterial host and then introduced into a vector for homologous recombination in transformed chloroplasts to produce an active, chimeric enzyme in vivo.

Amino Acid Sequence↗