Search

This paper investigates the integration of multiple geometries present within a ReLU-based neural network. A ReLU neural network determines a piecewise affine linear continuous map, M, from an input space ℝm to an output space ℝn. The piecewise behavior corresponds to a polyhedral decomposition of ℝm. Each polyhedron in the decomposition can be labeled with a binary vector (whose length equals the number of ReLU nodes in the network) and with an affine linear function (which agrees with M when restricted to points in the polyhedron). We develop a toolbox that calculates the binary vector for a polyhedra containing a given data point with respect to a given ReLU FFNN. We utilize this binary vector to derive bounding facets for the corresponding polyhedron, extraction of “active” bits within the binary vector, enumeration of neighboring binary vectors, and visualization of the polyhedral decomposition (Python code is available at https://github.com/cglrtrgy/GoL_Toolbox). Polyhedra in the polyhedral decomposition of ℝm are neighbors if they share a facet. Binary vectors for neighboring polyhedra differ in exactly 1 bit. Using the toolbox, we analyze the Hamming distance between the binary vectors for polyhedra containing points from adversarial/nonadversarial datasets revealing distinct geometric properties. A bisection method is employed to identify sample points with a Hamming distance of 1 along the shortest Euclidean distance path, facilitating the analysis of local geometric interplay between Euclidean geometry and the polyhedral decomposition along the path. Additionally, we study the distribution of Chebyshev centers and related radii across different polyhedra, shedding light on the polyhedral shape, size, clustering, and aiding in the understanding of decision boundaries.

Utility vectors with promoters that confer desired spatial and temporal expression patterns are useful tools for studying gene and cellular function and for industrial applications. To target the expression of DNA sequences of interest to cells forming plant secondary cell walls, which generate most of the vegetative biomass, upstream regulatory sequences of the Brachypodium distachyon lignin biosynthetic gene BdPMT and the cellulose synthase genes BdCESA7 and BdCESA8 were isolated and cloned into binary vectors designed for Agrobacterium-mediated transformation of monocots. Expression patterns were assessed using the β-glucuronidase gene GUSPlus and X-glucuronide staining. All three promoters showed strong expression levels in stem tissue at the base of internodes where cell wall deposition is most active, in both vascular bundle xylem vessels and tracheids, and in interfascicular tissues, with expression less pronounced in developmentally older tissues. In leaves, BdCESA7 and BdCESA8 promoter-driven expression was strongest in leaf veins, leaf margins, and trichomes; relatively weaker and patchy expression was observed in the epidermis. BdPMT promoter-driven expression was similar to the BdCESA promoters expression patterns, including strong expression in trichomes. The intensity and extent of GUS staining varied considerably between transgenic lines, suggesting that positional effects influenced promoter activity. Introducing the BdPMT and BdCESA8 Open Reading Frames into BdPMT and BdCESA8 utility promoter binary vectors, respectively, and transforming those constructs into Brachypodium pmt and cesa8 loss-of-function mutants resulted in rescue of the corresponding mutant phenotypes. This work therefore validates the functionality of these utility promoter binary vectors for use in Brachypodium and likely other grass species. The identification, in Bdcesa8-1 T-DNA mutant stems, of an 80% reduction in crystalline cellulose levels confirms that the BdCESA8 gene is a secondary-cell-wall-forming cellulose synthase.

Boolean Petri net (BPN) and Crisp Boolean Petri net (CBPN) is a well-studied graph model since 2010 which has several applications in mathematical modeling of complex or tricky networks. Modeling any network with Petri net which can generate binary numbers as marking vectors in its reachability tree is still has much uses. In CBPN with a minimum number of transition and minimum number of steps of reachability tree, minimal execution time to run the machine has not been noted till date, thus it’s necessary to sort out this problem. Possibly it may occur due to some forbidden structure which hinders any 1-safe Petri net to be a CBPN. In this paper, we present some forbidden digraphs whose presence interrupts the generation of binary n-vectors exactly once. Any 1-safe Petri net is not a CBPN if it contains any of the subnet induced to the four forbidden structures discussed in this paper.

An efficient protocol for Agrobacterium-mediated transformation of tomato cultivars Sandra and Rocky was conducted to examine the possibility of producing transgenic tomato plants cultivars harbouring the nptII gene, conferring kanamycin resistance. To achieve this aim, tomato cotyledon explants were transformed using EHA105 Agrobacterium tumefaciens strain harboring the binary vectors pBI121 which contains Gus gene, and neomycin phosphotransferase II (nptII) as selectable marker gene under the control of a CaMV35S promoter and nopaline synthase (nos) Terminator. Transformant detection was carried out in three distinct ways. First antibiotic selection, Kanamycin at a concentration of100 mgl-1 found to be efficient for this purpose. Second histochemical GUS assay revealed the presence of blue colored zones in a number of shoots and leaves for both in vitro and the greenhouse-grown transgenic plants. Third PCR analysis indicated positive result by showing the fragment for nptII gene in tested transformants, while was absent in non-transgenic control (wild type). On the other hand, the results showed that Sandra cultivar was more efficient for regeneration and subsequently transformation frequency than Rocky cultivar, which record 26.66% of transformation frequency compared with 11.57% in Rocky cultivar. [ABSTRACT FROM AUTHOR]

Approximate nearest neighbour (ANN) search is one of the most important problems in numerous computer science applications, including data mining, machine learning and computer vision. In this paper, we address the problem of ANN for high-dimensional binary vectors and we propose a simple yet powerful search method that is based on Random Binary Search Trees (RBST). Our method is validated on a dataset of 1.25M binary local feature descriptors obtained from a real-life image-based localisation system provided by Google as a part of Project Tango (now known as ARCore). The results of an extensive evaluation of our method performed on this dataset against the state-of-the-art ANN algorithms, such as Locality Sensitive Hashing, Uniform LSH and Multi-probe LSH, show the superiority of our method in terms of retrieval precision with a performance boost of over 20%. • Random Binary Search Trees (RBST) are a relatively simple yet powerful ANN method. • RBST give better or equal results to the competing hashing algorithms. • A powerful ANN method can be created by extending a simple data structure. • Techniques like the priority search are not needed to create a good ANN method. [ABSTRACT FROM AUTHOR]

The plant kingdom abounds in countless species with potential medical uses. Many of them contain valuable secondary metabolites belonging to different classes and demonstrating anticancer, anti-inflammatory, antioxidant, antimicrobial or antidiabetic properties. Many of these metabolites, e.g., paclitaxel, vinblastine, betulinic acid, chlorogenic acid or ferrulic acid, have potential applications in medicine. Additionally, these compounds have many therapeutic and health-promoting properties. The growing demand for these plant secondary metabolites forces the use of new green biotechnology tools to create new, more productive in vitro transgenic plant cultures. These procedures have yielded many promising results, and transgenic cultures have been found to be safe, efficient and cost-effective sources of valuable secondary metabolites for medicine and industry. This review focuses on the use of various in vitro plant culture systems for the production of secondary metabolites.

Transient gene expression is fast, easy and not influenced by positional effects that potentially affect on gene expression levels in stable gene transformation. Transient expression can be applicable using agroinfilteration, biolistic and viral vectors. Agrobacterium mediated transient expression have been shown as an efficient and versatile method for analyzing transgene expression, gene scilencing, host-pathogen interactions, protein-protein interaction, and cis-element/transfactor interaction. A control vector consists of an interon containing reporter gene under control of a common promoter is often required for Cis-acting elemen analysis to standardize the variation. This study was carried out to construct a control vector based on two parental binary vectors, pGPTV and pCAMBIA3301. The constructed vector, pGCGi had an interon containing GUS reporter gene under control of the full sequence of CaMV 35S promoter. The GUS staining results revealed that the GUS intron containg gene cannot produce an active B- glucronidase enzyme in agrobacterial cells. The functional gene expression analysis of the new vector was done using agroinjection and prticle delivery system in tobacco and onion eoidermal cells respectively. The histochemical GUS staining results showed pGCGi could express the reporter gene in plant cells and culd be used as control vector in transient expression experiments.

Advancing basic and applied plant research requires the continuous innovative development of the available technology toolbox. Essential components of this toolbox are methods that simplify the assembly, delivery and expression of multiple transgenes of interest. To allow simultaneous and directional multigene assembly on the same plant transformation vector, several strategies based on overlapping sequences or restriction enzymes have recently been developed. However, the assembly of homologous and repetitive DNA sequences can be inefficient and the frequent occurrence of target sequences recognized by commonly used restriction enzymes can be a limiting factor. Here, we noted that recognition sites for the restriction enzyme SfiI are rarely occurring in plant genomes. This fact was exploited to establish a multigene assembly system called COLORFUL-Circuit. To this end, we developed a set of binary vectors which provide a flexible and cost efficient cloning platform. The gene expression cassettes in our system are flanked with unique SfiI sites, which allow simultaneous multi-gene cassette assembly in a hosting binary vector. We used COLORFUL-Circuit to transiently and stably express up to four fluorescent organelle markers in addition to a selectable marker and analyzed the impact of assembly design on coexpression efficiency. Finally, we demonstrate the utility of our optimized COLORFUL-Circuit system in an exemplary case study, in which we monitored simultaneously the subcellular behavior of multiple organelles in a biotrophic plant-microbe interaction by Confocal Laser Scanning Microscopy.

Advancing basic and applied plant research requires the continuous innovative development of the available technology toolbox. Essential components of this toolbox are methods that simplify the assembly, delivery, and expression of multiple transgenes of interest. To allow simultaneous and directional multigene assembly on the same plant transformation vector, several strategies based on overlapping sequences or restriction enzymes have recently been developed. However, the assembly of homologous and repetitive DNA sequences can be inefficient and the frequent occurrence of target sequences recognized by commonly used restriction enzymes can be a limiting factor. Here, we noted that recognition sites for the restriction enzyme SfiI are rarely occurring in plant genomes. This fact was exploited to establish a multigene assembly system called "COLORFUL-Circuit." To this end, we developed a set of binary vectors which provide a flexible and cost efficient cloning platform. The gene expression cassettes in our system are flanked with unique SfiI sites, which allow simultaneous multi-gene cassette assembly in a hosting binary vector. We used COLORFUL-Circuit to transiently and stably express up to four fluorescent organelle markers in addition to a selectable marker and analyzed the impact of assembly design on coexpression efficiency. Finally, we demonstrate the utility of our optimized "COLORFUL-Circuit" system in an exemplary case study, in which we monitored simultaneously the subcellular behavior of multiple organelles in a biotrophic plant-microbe interaction by Confocal Laser Scanning Microscopy. [ABSTRACT FROM AUTHOR]

Genetic manipulation of fungi requires quick, low-cost, efficient, high-throughput and molecular tools. In this paper, we report 22 entry constructs as new molecular tools based on the Gateway technology facilitating rapid construction of binary vectors that can be used for functional analysis of genes in fungi. The entry vectors for single, double or triple gene-deletion mutants were developed using hygromycin, geneticin and nourseothricin resistance genes as selection markers. Furthermore, entry vectors containing green fluorescent (GFP) or red fluorescent (RFP) in combination with hygromycin, geneticin or nourseothricin selection markers were generated. The latter vectors provide the possibility of gene deletion and simultaneous labelling of the fungal transformants with GFP or RFP reporter genes. The applicability of a number of entry vectors was validated in Zymoseptoria tritici , an important fungal wheat pathogen. [ABSTRACT FROM AUTHOR]

Transient gene expression is fast, easy and not influenced by positional effects that potentially affect on gene expression levels in stable gene transformation. Transient expression can be applicable using agroinfilteration, biolistic and viral vectors. Agrobacterium mediated transient expression have been shown as an efficient and versatile method for analyzing transgene expression, gene scilencing, host-pathogen interactions, protein-protein interaction, and cis-element/transfactor interaction. A control vector consists of an interon containing reporter gene under control of a common promoter is often required for Cis-acting elemen analysis to standardize the variation. This study was carried out to construct a control vector based on two parental binary vectors, pGPTV and pCAMBIA3301. The constructed vector, pGCGi had an interon containing GUS reporter gene under control of the full sequence of CaMV 35S promoter. The GUS staining results revealed that the GUS intron containg gene cannot produce an active B- glucronidase enzyme in agrobacterial cells. The functional gene expression analysis of the new vector was done using agroinjection and prticle delivery system in tobacco and onion eoidermal cells respectively. The histochemical GUS staining results showed pGCGi could express the reporter gene in plant cells and culd be used as control vector in transient expression experiments. [ABSTRACT FROM AUTHOR]

Abstract: Binary descriptors allow faster similarity computation than real-valued ones while requiring much less storage. As a result, many algorithms have recently been proposed to binarize floating-point descriptors so that they can be searched for quickly. Unfortunately, even if the similarity between vectors can be computed fast, exhaustive linear search remains impractical for truly large databases and approximate nearest neighbor (ANN) search is still required. It is therefore surprising that relatively little attention has been paid to the efficiency of ANN algorithms on binary vectors and this is the focus of this paper. We first show that binary-space Voronoi diagrams have thick boundaries, meaning that there are many points that lie at the same distance from two random points. This violates the implicit assumption made by most ANN algorithms that points can be neatly assigned to clusters centered around a set of cluster centers. As a result, state-of-the-art algorithms that can operate on binary vectors exhibit much lower performance than those that work with floating point ones. The above analysis is the first contribution of the paper. The second one is two effective ways to overcome this limitation, by appropriately randomizing either a tree-based algorithm or hashing-based one. In both cases, we show that we obtain precision/recall curves that are similar to those than can be obtained using floating point number calculation, but at much reduced computational cost. [Copyright &y& Elsevier]

We consider vectors from {0, 1}n. The weight of such a vector v is the sum of the coordinates of v. The distance ratio of a set L of vectors is dr(L) := max{ρ(x, y) : x, y ∈ L}/ min{ρ(x, y) : x, y ∈ L, x ≠ y}, where ρ(x, y) is the Hamming distance between x and y. We prove that (a) for every constant λ > 1 there are no positive constants α and C such that every set K of at least λp vectors with weight p contains a subset K' with |K'| ≥ |K|α and dr(K') ≤ C; and (b) for a set K of vectors with weight p, and a constant C > 2, there exists K' ⊆ K such that dr(K') ≤ C and |K'| ≥ |K|α, where α = 1/⌊log(p/2)/ log(C/2)⌉ [ABSTRACT FROM AUTHOR]

For more than two decades Agrobacterium-mediated stable genetic transformation of plant cells is a routine laboratory method to generate transgenic plants. The natural capability of Agrobacterium tumefaciens to infect plants is thereby exploited for transferring foreign genes into plant cells. During stable transformation engineered DNA fragments are integrated into the plant genome and can be passed on to the next generations. The host specificity of Agrobacteria to plant species is limited and the genetic mechanisms underlying host specificity are complex. Besides Arabidopsis thaliana, Agrobacterium tumefaciens is also capable of successfully transforming a large variety of other plant species, such as maize or rice. Using Agrobacteria to transform Arabidopsis is straightforward, requiring only standard laboratory equipment. Transformation by floral dip is easy and can be performed by nonspecialists. Due to its small size, short generation time, high seed production and easy handling, Arabidopsis, which has emerged as model organism for plant biology research, is frequently chosen to generate transgenic plants. This review focuses on the generation of transgenic Arabidopsis plants by Agrobacteria using the floral dip method. Besides a simplified protocol for the Agrobacteriummediated transformation, we here describe common Agrobacterium strains and suitable binary TDNA vectors. Further, we focus on plant selection to finally isolate homozygous transgenic mutant lines. [ABSTRACT FROM AUTHOR]

Since past three decades new discoveries in plant genetic engineering have shown remarkable potentials for crop improvement. Agrobacterium Ti plasmid based DNA transfer is no longer the only efficient way of introducing agronomically important genes into plants. Recent studies have explored a novel plant genetic engineering tool, Rhizobia sp ., as an alternative to Agrobacterium, thereby expanding the choice of bacterial species in agricultural plant biotechnology. Rhizobia sp. serve as an open license source with no major restrictions in plant biotechnology and help broaden the spectrum for plant biotechnologists with respect to the use of gene transfer vehicles in plants. New efficient transgenic plants can be produced by transferring genes of interest using binary vector carrying Rhizobia sp. Studies focusing on the interactions of Rhizobia sp. with their hosts, for stable and transient transformation and expression of genes, could help in the development of an adequate gene transfer vehicle. Along with being biologically beneficial, it may also bring a new means for fast economic development of transgenic plants, thus giving rise to a new era in plant biotechnology, viz. ' Rhizobia mediated transformation technology.' [ABSTRACT FROM AUTHOR]

A series of high-throughput binary cloning vectors were constructed to facilitate gene function analysis in higher plants. This vector series consists of plasmids designed for plant expression, promoter analysis, gene silencing, and green fluorescent protein fusions for protein localization. These vectors provide for high-throughput and efficient cloning utilizing sites for λ phage integrase/excisionase. In addition, unique restriction sites are incorporated in a multiple cloning site and enable promoter replacement. The entire vector series are available with complete sequence information and detailed annotations and are freely distributed to the scientific community for non-commercial uses. [ABSTRACT FROM AUTHOR]

This paper presents a method of Agrobacterium-mediated transformation for two diploid breeding lines of potato, and gives a detailed analysis of reporter gene expression. In our lab, these lines were also used to obtain tetraploid somatic hybrids. We tested four newly prepared constructs based on the pGreen vector system containing the selection gene nptII or bar under the 35S or nos promoter. All these vectors carried gus under 35S. We also tested the pDM805 vector, with the bar and gus genes respectively under the Ubi1 and Act1 promoters, which are strong for monocots. The selection efficiency (about 17%) was highest in the stem and leaf explants after transformation with pGreen where nptII was under 35S. About half of the selected plants were confirmed via PCR and Southern blot analysis to be transgenic and, depending on the combination, 0 to 100% showed GUS expression. GUS expression was strongest in multi-copy transgenic plants where gus was under Act1. The same potato lines carrying multi-copy bar under Ubi1 were also highly resistant to the herbicide Basta. The suggestion of using Agrobacterium-mediated transformation of diploid lines of potato as a model crop is discussed herein. [ABSTRACT FROM AUTHOR]

Transgenic plants, expressing recombinant proteins, are suitable alternatives for the production of relevant immunogens. In the present study, the expression of Puumala virus nucleocapsid protein in tobacco and potato plants (Nicotiana tabacum and Solanum tuberosum) and its immunogenicity was investigated. After infection of leaf discs of SR1 tobacco and tuber discs of potato cv. “Desiree” with the Agrobacterium strain LBA4404 (pAL4404, pBinAR-PUU-S) containing the 1302 bp cDNA sequence of S-RNA segment of a Puumala virus, transgenic tobacco and potato plants expressed the Puumala virus nucleocapsid protein under control of the cauliflower 35S promoter. The recombinant proteins were found to be identical to the authentic Puumala virus nucleocapsid protein as analyzed by immunoblotting. Expression of the nucleocapsid protein was investigated over four plant generations (P to F4) and found to be stable (1 ng/3 μg dried leaf tissue). Transgenic tobacco plants were smaller compared to controls. The transformed potato plants were morphologically similar to control plants and produced tubers as the control potatoes. The S-antigen was expressed at a level of 1 ng protein/5 μg and 1 ng protein/4 μg dried leaf and root tissues, respectively, and remained stable in the first generation of vegetatively propagated potato plants. The immunogenicity of the Puumala virus nucleocapsid protein expressed in Nicotiana tabacum and Solanum tuberosum was investigated in New Zealand white rabbits. They were immunized with leaf extracts from transgenic tobacco and potato plants, and the serum recognized Puumala virus nucleocapsid protein. Transgenic plants expressing hantaviral proteins can thus be used for the development of cost-effective diagnostic systems and for alternative vaccination strategies. [ABSTRACT FROM AUTHOR]

Binary Ti vectors are the plasmid vectors of choice in Agrobacterium-mediated plant transformation protocols. The pGreen series of binary Ti vectors are configured for ease-of-use and to meet the demands of a wide range of transformation procedures for many plant species. This plasmid system allows any arrangement of selectable marker and reporter gene at the right and left T-DNA borders without compromising the choice of restriction sites for cloning, since the pGreen cloning sites are based on the well-known pBluescript general vector plasmids. Its size and copy number in Escherichia coli offers increased efficiencies in routine in vitro recombination procedures. pGreen can replicate in Agrobacterium only if another plasmid, pSoup, is co-resident in the same strain. pSoup provides replication functions in trans for pGreen. The removal of RepA and Mob functions has enabled the size of pGreen to be kept to a minimum. Versions of pGreen have been used to transform several plant species with the same efficiencies as other binary Ti vectors. Information on the pGreen plasmid system is supplemented by an Internet site (http://www.pgreen.ac.uk) through which comprehensive information, protocols, order forms and lists of different pGreen marker gene permutations can be found. [ABSTRACT FROM AUTHOR]

The new pPZP Agrobacterium binary vectors are versatile, relatively small, stable and are fully sequenced. The vectors utilize the pTiT37 T-DNA border regions, the pBR322 bom site for mobilization from Escherichia coli to Agrobacterium, and the ColE1 and pVS1 plasmid origins for replication in E. coli and in Agrobacterium, respectively. Bacterial marker genes in the vectors confer resistance to chloramphenicol (pPZP100 series) or spectinomycin (pPZP200 series), allowing their use in Agrobacterium strains with different drug resistance markers. Plant marker genes in the binary vectors confer resistance to kanamycin or to gentamycin, and are adjacent to the left border (LB) of the transferred region. A lacZ α-peptide, with the pUC18 multiple cloning site (MCS), lies between the plant marker gene and the right border (RB). Since the RB is transferred first, drug resistance is obtained only if the passenger gene is present in the transgenic plants. [ABSTRACT FROM AUTHOR]

Improved plant transformation vectors were constructed which utilize the pRiHRI origin of replication for highly stable maintenance in Agrobacterium tumefaciens, the ColE1 origin of replication for high copy maintenance in Escherichia coli, and a gentamycin resistance gene as a strong selectable marker for bacteria. Concise T-DNA elements were engineered with border sequences from the TL-DNA of pTiA6, the Tn5 neomycin phosphotransferase gene ( npt II) expressed from either CaMV 35S or mannopine synthase ( mas) promoters, and the lac Z′ gene segment from pUC18 as a source of unique restriction sites as well as an insertional inactivation marker for cloned DNA. The order of T-DNA components in all vectors is left border, plant marker cassette, lac Z′, and right border, respectively. The prototype vector, pCGN1547, was shown to be very stable in A. tumefaciens strain LBA4404 and to act as an efficient donor of T-DNA in tomato transformation experiments. Use of the other vectors is also described. [ABSTRACT FROM AUTHOR]

Tobacco cells are sensitive to bleomycin and phleomycin. The Tn5 and the Streptoalloteichus hindustanus (Sh) bleomycin resistance ('Ble') genes conferring resistance to these antibiotics have each been inserted into two plant expression vectors. They are flanked by the nopaline synthase (nos) or the cauliflower mosaic virus (CaMV) 35S promoters on one side, and by the nos polyadenylation signal on the other. These four chimaeric genes were introduced into the binary transformation vector pGA 492, which were thereafter mobilized into Agrobacterium tumefaciens strain LBA 4404. The resulting strains were used to transform Nicotiana tabacum cv. Xanthi nc using the leaf disc transformation procedure. In all cases, phleomycin- and bleomycin-resistant tobacco plants were regenerated from transformed cells under selective conditions; however the highest frequency of rooted plants was obtained when transformation was carried out with the 'Sh Ble' gene under the control of the 35S promoter. Phleomycin resistance was stably transmitted to sexual offspring as a dominant nuclear trait as confirmed by Southern blotting. [ABSTRACT FROM AUTHOR]

One hundred and four kanamycin-resistant Petunia 'Mitchell' plants were regenerated from leaf discs cocultivated with Agrobacterium tumefaciens strain LBA4404 containing a binary vector pCGN200. Selection for kanamycin resistance was applied during plant regeneration at the initiation of both shoots and roots. The regenerated plants were analysed for expression and inheritance of their kanamycin resistance phenotype. Approximately half of the plants showed normal Mendelian inheritance for one or two kanamycin resistance genes. In one case, the two copies were inserted at closely linked sites on homologous chromosomes, and gave <0.05% kanamycin-sensitive progeny on backcrosses. Six plants had inheritance patterns suggesting that the kanamycin gene had inserted into an essential region of DNA. Forty-five plants showed lower than expected transmission of kanamycin resistance, which was associated with low expression of the resistance phenotype in most cases. Ten plants produced segregation ratios that are not readily interpreted by Mendelian inheritance. [ABSTRACT FROM AUTHOR]

A system was established for introducing cloned genes into white clover ( Trifolium repens L.). A high regeneration white clover genotype was transformed with binary Agrobacterium vectors containing a chimaeric gene which confers kanamycin resistance. Transformed kanamycin resistant callus was obtained by culturing Agrobacterium inoculated stolon internode segments on selective medium. The kanamycin resistance phenotype was stable in cells and in regenerated shoots. Transformation was confirmed by the expression of an unselected gene, nopaline synthase in selected cells and transgenic shoots and by the detection of neomycin phosphotransferase II enzymatic activity in kanamycin resistant cells. Integration of vector DNA sequences into plant DNA was demonstrated by Southern blot hybridisation. [ABSTRACT FROM AUTHOR]

Agrobacterium tumefaciens and Agrobacterium rhizogenes are soil bacteria which transfer DNA (T-DNA) to plant cells. Two Agrobacterium strains, each with a different T-DNA, can infect plants and give rise to transformed tissue which has markers from both T-DNAs. Although marker genes from both T-DNAs are in the tissue, definitive proof that the tissue is a cellular clone and that both T-DNAs are in a single cell is necessary to demonstrate cotransformation. We have transferred two distinguishable T-DNAs, carried on binary vectors in separate Agrobacterium rhizogenes strains, into tomato cells and have recovered hairy roots which received both T-DNAs. Continued expression of marker genes from each T-DNA in hairy roots propagated from individual root tips indicated that both T-DNAs were present in a single meristem. Also, we have transferred the two different T-DNAs, carried on identical binary vector plasmids in separate Agrobacterium tumefaciens strains, into tobacco cells and recovered plants which received both T-DNAs. Transformed plants with marker genes from each T-DNA were outcrossed to wild-type tobacco plants. Distribution of the markers in the F1 generation from three cotransformed plants of independent origin showed that both T-DNAs in the plants must have been present in the same cell and that the T-DNAs were genetically unlinked. Cotransformation of plant cells with T-DNAs from two bacterial strains and subsequent segregation of the transferred genes should be useful for altering the genetic content of higher plants. [ABSTRACT FROM AUTHOR]

Cosmid binary vectors for the introduction of DNA into plant cells have been constructed. These vectors are derived from the replicon of the broad host range plasmid pRK2 and contain the T-DNA border regions between which have been placed a chimaeric gene conferring resistance to kanamycin in plant cells. Appropriate restriction endonuclease targets have also been placed between the border regions. These binary vectors, in conjunction with appropriate Agrobacterium strains, are capable of delivering DNA to plant cells in cocultivation experiments with very high efficiency. The transformation frequency is shown to be somewhat dependent on the replicon used. re]19850121 rv]19850506 ac]19850513 [ABSTRACT FROM AUTHOR]

We describe here a set of binary vectors suitable for Agrobacterium-mediated gene transfer and specially designed for studying plant promoters. These vectors are based on the use of the gus reporter gene, contain multiple unique restriction sites upstream of the gus gene, and minimal promoters for testing the effect of enhancers or activator elements. In addition, an intron-containing gus ( uidA) gene was introduced into one of these vectors in order to examine reporter gene activity in tissues where Agrobacterium contamination may be a problem or in transient expression assays. [ABSTRACT FROM AUTHOR]

A series of binary T-DNA vectors (pBECKS) has been created for use in the Agrobacterium-mediated genetic transformation of plants. The pBECKS series has corrected the undesirable features of the popular pBIN19 vector; the deleterious mutation within the coding sequence of nptII has been amended and the cloning sites are now adjacent to the right border repeat in order to reduce the possibility of producing truncated sequences of novel genes within transformants. One set of vectors incorporates various combiantions of the marker genes gusA, C1/Lc, nptII, hph, and bar, for pursuit of early and stable transformation events. A set of constructs which contain deleted T-DNA borders in various combinations and display predictably altered efficacies for gene transfer has also been created. A modular set of vectors has been designed to facilitate the insertion and transfer of novel gene sequences by providing a nptII-linked plant expression cassette or lacZ-multiple cloning site. A range of antibiotic resistance genes has been incorporated into the non-T-DNA part of the vectors in order to facilitate their selection across the range of Agrobacterium virulence strains. [ABSTRACT FROM AUTHOR]

Many algorithms, tree-searching and decoding algorithms in particular, need to generate some lists of binary vectors by increasing value of a given weight function and without omission. To this end, there are not many alternatives to the Dijkstra and the Viterbi algorithm. In this letter a technique suggested by Battail in 1986 to perform this task is reviewed. Then a new technique is deduced from it, that proves to be more efficient than all the others. As an illustration of its good performance we compare a maximum-likelihood-decoding (MLD) algorithm that can be derived from it, with current state-of-the-art complete MLD algorithms for general binary linear codes [ABSTRACT FROM PUBLISHER]

Five new binary vectors have been constructed which have the following features: (1) different plant selectable markers including neomycin phosphotransferase ( nptII), hygromycin phosphotransferase ( hpt), dihydrofolate reductase ( dhfr), phosphinothricin acetyl transferase ( bar), and bleomycin resistance ( ble); (2) selectable markers are located near the T-DNA left border and; (3) selectable marker and β-glucuronidase ( uidA) reporter genes are divergently organized for efficient expression, and can easily be removed or replaced as needed. [ABSTRACT FROM AUTHOR]

Cloning of long open reading frames (ORFs) into plant gene expression vectors and transfer of the chimeric expression cassettes into binary vectors is often hampered by the presence of restriction enzyme cleavage sites internal to the open reading frame (ORF) to be expressed. We therefore modified the commonly used expression vector pRT100 [7] and several pGPTV binary vectors [2] by replacing 6 bp restriction sites with 8 bp sequences recognized by rare-cutter restriction enzymes. [ABSTRACT FROM AUTHOR]

The plant kingdom abounds in countless species with potential medical uses. Many of them contain valuable secondary metabolites belonging to different classes and demonstrating anticancer, anti-inflammatory, antioxidant, antimicrobial or antidiabetic properties. Many of these metabolites, e.g., paclitaxel, vinblastine, betulinic acid, chlorogenic acid or ferrulic acid, have potential applications in medicine. Additionally, these compounds have many therapeutic and health-promoting properties. The growing demand for these plant secondary metabolites forces the use of new green biotechnology tools to create new, more productive in vitro transgenic plant cultures. These procedures have yielded many promising results, and transgenic cultures have been found to be safe, efficient and cost-effective sources of valuable secondary metabolites for medicine and industry. This review focuses on the use of various in vitro plant culture systems for the production of secondary metabolites. [ABSTRACT FROM AUTHOR]

The well known Hamming distance between a pair of permutations (or strings) of the same length is simply the number of pairs of different digits in these permutations. It has been an interesting topic of research to find mappings from the binary vectors to permutations of the same length such that the Hamming distance is preserved or increased. As a natural variation we introduce the Hamming gap of radius r between two permutations, which is, in a way, equivalent to the number of digits where the corresponding pair of entries differ by at least r. This is called the r -Hamming gap. We first discuss the properties of this new concept. We then show mappings from binary vectors to permutations such that the images of a pair of binary vectors (at Hamming distance d) have r -Hamming gap at least d. We also show the generalization of our findings to permutations on Z n (where n ≡ 0) instead of [ n ]. [ABSTRACT FROM AUTHOR]