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Andrew P Gleave - One of the best experts on this subject based on the ideXlab platform.
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a versatile Binary Vector system with a t dna organisational structure conducive to efficient integration of cloned dna into the plant genome
Plant Molecular Biology, 1992Co-Authors: Andrew P GleaveAbstract:A versatile gene expression cartridge and Binary Vector system was constructed for use in Agrobacterium-mediated plant transformation. The expression cartridge of the primary cloning Vector, pART7, comprises of cauliflower mosaic virus Cabb B-JI isolate 35S promoter, a multiple cloning site and the transcriptional termination region of the octopine synthase gene. The entire cartridge can be removed from pART7 as a Not I fragment and introduced directly into the Binary Vector, pART27, recombinants being selected by blue/white screening for beta-galactosidase. pART27 carries the RK2 minimal replicon for maintenance in Agrobacterium, the ColE1 origin of replication for high-copy maintenance in Escherichia coli and the Tn7 spectinomycin/streptomycin resistance gene as a bacterial selectable marker. The organisational structure of the T-DNA of pART27 has been constructed taking into account the right to left border, 5' to 3' model of T-DNA transfer. The T-DNA carries the chimaeric kanamycin resistance gene (nopaline synthase promoter-neomycin phosphotransferase-nopaline synthase terminator) distal to the right border relative to the lacZ' region. Utilisation of these Vectors in Agrobacterium-mediated transformation of tobacco demonstrated efficient T-DNA transfer to the plant genome.
Philippe Vain - One of the best experts on this subject based on the ideXlab platform.
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the pclean dual Binary Vector system for agrobacterium mediated plant transformation
Plant Physiology, 2007Co-Authors: Vera Thole, J W Snape, Barbara Worland, Philippe VainAbstract:The development of novel transformation Vectors is essential to the improvement of plant transformation technologies. Here, we report the construction and testing of a new multifunctional dual Binary Vector system, pCLEAN, for Agrobacterium-mediated plant transformation. The pCLEAN Vectors are based on the widely used pGreen/pSoup system and the pCLEAN-G/pCLEAN-S plasmids are fully compatible with the existing pGreen/pSoup Vectors. A single Agrobacterium can harbor (1) pCLEAN-G and pSoup, (2) pGreen and pCLEAN-S, or (3) pCLEAN-G and pCLEAN-S Vector combination. pCLEAN Vectors have been designed to enable the delivery of multiple transgenes from distinct T-DNAs and/or Vector backbone sequences while minimizing the insertion of superfluous DNA sequences into the plant nuclear genome as well as facilitating the production of marker-free plants. pCLEAN Vectors contain a minimal T-DNA (102 nucleotides) consisting of direct border repeats surrounding a 52-nucleotide-long multiple cloning site, an optimized left-border sequence, a double left-border sequence, restriction sites outside the borders, and two independent T-DNAs. In addition, selectable and/or reporter genes have been inserted into the Vector backbone sequence to allow either the counter-screening of backbone transfer or its exploitation for the production of marker-free plants. The efficiency of the different pCLEAN Vectors has been assessed using transient and stable transformation assays in Nicotiana benthamiana and/or Oryza sativa.
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transgene behaviour in populations of rice plants transformed using a new dual Binary Vector system pgreen psoup
Theoretical and Applied Genetics, 2003Co-Authors: Philippe Vain, A S Afolabi, Barbara Worland, J W SnapeAbstract:Transgene integration, expression level and stability have been studied, across two generations, in a population of rice plants transformed using a new dual Binary Vector system: pGreen/pSoup. pGreen is a small Ti Binary Vector unable to replicate in Agrobacterium without the presence of another Binary plasmid, pSoup, in the same strain. We engineered both pGreen and pSoup to contain each a different T-DNA. Transformation experiments were conducted using a pGreen Vector containing the bar and gusA expression units (no transgene in pSoup) or with a pSoup Vector containing an aphIV and gfp expression units (no transgene in pGreen). High plant transformation frequencies (up to 40%) were obtained using herbicide resistance (bar) or antibiotic resistance (aphIV) genes. Around 80% of the independently transformed plants expressed unselected reporter genes (gusA or gfp) present in the Vectors. Backbone sequences transfer was frequent (45% of lines) and occurred often in multicopy lines. Around 15–20% of the rice plant lines contained a single T-DNA integration without backbone. Integration of additional transgene copies did not improve expression levels in either T0 plants or T1 progenies. Nearly all multicopy lines contained transgenes integrated at several loci in the plant genome, showing that T-DNAs from either pGreen or pSoup frequently integrated at unlinked loci. Precise determination of loci number required the analysis of transgene presence in progeny. Segregation of transgene phenotype was generally misleading and tended to underestimate the real number of transgenic loci. The contribution of this new dual-Binary Vector system to the development of high-throughput rice transformation systems and to the production of marker-free transgenic rice plants is discussed.
Rodolphe Giroudeau - One of the best experts on this subject based on the ideXlab platform.
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Approximability and exact resolution of the multidimensional Binary Vector assignment problem
Journal of Combinatorial Optimization, 2018Co-Authors: Marin Bougeret, Guillerme Duvillié, Rodolphe GiroudeauAbstract:In this paper we consider the multidimensional Binary Vector assignment problem. An input of this problem is defined by m disjoint multisets $$V^1, V^2, \ldots , V^m$$ V 1 , V 2 , … , V m , each composed of n Binary Vectors of size p . An output is a set of n disjoint m -tuples of Vectors, where each m -tuple is obtained by picking one Vector from each multiset $$V^i$$ V i . To each m -tuple we associate a p dimensional Vector by applying the bit-wise AND operation on the m Vectors of the tuple. The objective is to minimize the total number of zeros in these n Vectors. We denote this problem by , and the restriction of this problem where every Vector has at most c zeros by . was only known to be -hard, even for . We show that, assuming the unique games conjecture, it is -hard to -approximate for any fixed and . This result is tight as any solution is a -approximation. We also prove without assuming UGC that is -hard even for . Finally, we show that is polynomial-time solvable for fixed (which cannot be extended to ).
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Multidimensional Binary Vector Assignment problem: standard, structural and above guarantee parameterizations
Discrete Mathematics & Theoretical Computer Science, 2017Co-Authors: Marin Bougeret, Guillerme Duvillié, Rodolphe Giroudeau, Rémi WatrigantAbstract:In this article we focus on the parameterized complexity of the Multidimensional Binary Vector Assignment problem (called \BVA). An input of this problem is defined by $m$ disjoint sets $V^1, V^2, \dots, V^m$, each composed of $n$ Binary Vectors of size $p$. An output is a set of $n$ disjoint $m$-tuples of Vectors, where each $m$-tuple is obtained by picking one Vector from each set $V^i$. To each $m$-tuple we associate a $p$ dimensional Vector by applying the bit-wise AND operation on the $m$ Vectors of the tuple. The objective is to minimize the total number of zeros in these $n$ Vectors. mBVA can be seen as a variant of multidimensional matching where hyperedges are implicitly locally encoded via labels attached to vertices, but was originally introduced in the context of integrated circuit manufacturing. We provide for this problem FPT algorithms and negative results ($ETH$-based results, $W$[2]-hardness and a kernel lower bound) according to several parameters: the standard parameter $k$ i.e. the total number of zeros), as well as two parameters above some guaranteed values.
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Approximability and exact resolution of the Multidimensional Binary Vector Assignment problem
2016Co-Authors: Marin Bougeret, Guillerme Duvillié, Rodolphe GiroudeauAbstract:In this paper we consider the multidimensional Binary Vector assignment problem. An input of this problem is dened by m disjoint sets V 1 , V 2 ,. .. , V m , each composed of n Binary Vectors of size p. An output is a set of n disjoint m-tuples of Vectors, where each m-tuple is obtained by picking one Vector from each set V i. To each m-tuple we associate a p dimensional Vector by applying the bit-wise AND operation on the m Vectors of the tuple. The objective is to minimize the total number of zeros in these n Vectors. We denote this problem by min 0, and the restriction of this problem where every Vector has at most c zeros by (min 0) #0≤c. (min 0) #0≤2 was only known to be APX-complete, even for m = 3 [5]. We show that, assuming the unique games conjecture, it is NP-hard to (n − ε)-approximate (min 0) #0≤1 for any xed n and ε. This result is tight as any solution is a n-approximation. We also prove without assuming UGC that (min 0) #0≤1 is APX-complete even for n = 2, and we provide an example of n − f (n, m)-approximation algorithm for min 0. Finally, we show that (min 0) #0≤1 is polynomial-time solvable for xed m (which cannot be extended to (min 0) #0≤2 according to [5]).
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FCT - Multidimensional Binary Vector Assignment Problem: Standard, Structural and Above Guarantee Parameterizations
Fundamentals of Computation Theory, 2015Co-Authors: Marin Bougeret, Guillerme Duvillié, Rodolphe Giroudeau, Rémi WatrigantAbstract:In this article we focus on the parameterized complexity of the Multidimensional Binary Vector Assignment problem (called bMVA). An input of this problem is defined by m disjoint sets \(V^1, V^2, \dots , V^m\), each composed of n Binary Vectors of size p. An output is a set of n disjoint m-tuples of Vectors, where each m-tuple is obtained by picking one Vector from each set \(V^i\). To each m-tuple we associate a p dimensional Vector by applying the bit-wise AND operation on the m Vectors of the tuple. The objective is to minimize the total number of zeros in these n Vectors. bMVA can be seen as a variant of multidimensional matching where hyperedges are implicitly locally encoded via labels attached to vertices, but was originally introduced in the context of integrated circuit manufacturing.
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On the Complexity of Wafer-to-Wafer Integration
2015Co-Authors: Guillerme Duvillié, Marin Bougeret, Vincent Boudet, Trivikram Dokka, Rodolphe GiroudeauAbstract:In this paper we consider the Wafer-to-Wafer Integration problem. A wafer is a p-dimensional Binary Vector. The input of this problem is described by m disjoints sets (called “lots”), where each set contains n wafers. The output of the problem is a set of n disjoint stacks, where a stack is a set of m wafers (one wafer from each lot). To each stack we associate a p-dimensional Binary Vector corresponding to the bit-wise AND operation of the wafers of the stack. The objective is to maximize the total number of “1” in the n stacks. We provide O(m1−ϵ) and O(p1−ϵ) non-approximability results even for n=2, as well as a pr-approximation algorithm for any constant r. Finally, we show that the problem is FPT when parameterized by p, and we use this FPT algorithm to improve the running time of the pr-approximation algorithm.
J W Snape - One of the best experts on this subject based on the ideXlab platform.
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the pclean dual Binary Vector system for agrobacterium mediated plant transformation
Plant Physiology, 2007Co-Authors: Vera Thole, J W Snape, Barbara Worland, Philippe VainAbstract:The development of novel transformation Vectors is essential to the improvement of plant transformation technologies. Here, we report the construction and testing of a new multifunctional dual Binary Vector system, pCLEAN, for Agrobacterium-mediated plant transformation. The pCLEAN Vectors are based on the widely used pGreen/pSoup system and the pCLEAN-G/pCLEAN-S plasmids are fully compatible with the existing pGreen/pSoup Vectors. A single Agrobacterium can harbor (1) pCLEAN-G and pSoup, (2) pGreen and pCLEAN-S, or (3) pCLEAN-G and pCLEAN-S Vector combination. pCLEAN Vectors have been designed to enable the delivery of multiple transgenes from distinct T-DNAs and/or Vector backbone sequences while minimizing the insertion of superfluous DNA sequences into the plant nuclear genome as well as facilitating the production of marker-free plants. pCLEAN Vectors contain a minimal T-DNA (102 nucleotides) consisting of direct border repeats surrounding a 52-nucleotide-long multiple cloning site, an optimized left-border sequence, a double left-border sequence, restriction sites outside the borders, and two independent T-DNAs. In addition, selectable and/or reporter genes have been inserted into the Vector backbone sequence to allow either the counter-screening of backbone transfer or its exploitation for the production of marker-free plants. The efficiency of the different pCLEAN Vectors has been assessed using transient and stable transformation assays in Nicotiana benthamiana and/or Oryza sativa.
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transgene behaviour in populations of rice plants transformed using a new dual Binary Vector system pgreen psoup
Theoretical and Applied Genetics, 2003Co-Authors: Philippe Vain, A S Afolabi, Barbara Worland, J W SnapeAbstract:Transgene integration, expression level and stability have been studied, across two generations, in a population of rice plants transformed using a new dual Binary Vector system: pGreen/pSoup. pGreen is a small Ti Binary Vector unable to replicate in Agrobacterium without the presence of another Binary plasmid, pSoup, in the same strain. We engineered both pGreen and pSoup to contain each a different T-DNA. Transformation experiments were conducted using a pGreen Vector containing the bar and gusA expression units (no transgene in pSoup) or with a pSoup Vector containing an aphIV and gfp expression units (no transgene in pGreen). High plant transformation frequencies (up to 40%) were obtained using herbicide resistance (bar) or antibiotic resistance (aphIV) genes. Around 80% of the independently transformed plants expressed unselected reporter genes (gusA or gfp) present in the Vectors. Backbone sequences transfer was frequent (45% of lines) and occurred often in multicopy lines. Around 15–20% of the rice plant lines contained a single T-DNA integration without backbone. Integration of additional transgene copies did not improve expression levels in either T0 plants or T1 progenies. Nearly all multicopy lines contained transgenes integrated at several loci in the plant genome, showing that T-DNAs from either pGreen or pSoup frequently integrated at unlinked loci. Precise determination of loci number required the analysis of transgene presence in progeny. Segregation of transgene phenotype was generally misleading and tended to underestimate the real number of transgenic loci. The contribution of this new dual-Binary Vector system to the development of high-throughput rice transformation systems and to the production of marker-free transgenic rice plants is discussed.
Marin Bougeret - One of the best experts on this subject based on the ideXlab platform.
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Approximability and exact resolution of the multidimensional Binary Vector assignment problem
Journal of Combinatorial Optimization, 2018Co-Authors: Marin Bougeret, Guillerme Duvillié, Rodolphe GiroudeauAbstract:In this paper we consider the multidimensional Binary Vector assignment problem. An input of this problem is defined by m disjoint multisets $$V^1, V^2, \ldots , V^m$$ V 1 , V 2 , … , V m , each composed of n Binary Vectors of size p . An output is a set of n disjoint m -tuples of Vectors, where each m -tuple is obtained by picking one Vector from each multiset $$V^i$$ V i . To each m -tuple we associate a p dimensional Vector by applying the bit-wise AND operation on the m Vectors of the tuple. The objective is to minimize the total number of zeros in these n Vectors. We denote this problem by , and the restriction of this problem where every Vector has at most c zeros by . was only known to be -hard, even for . We show that, assuming the unique games conjecture, it is -hard to -approximate for any fixed and . This result is tight as any solution is a -approximation. We also prove without assuming UGC that is -hard even for . Finally, we show that is polynomial-time solvable for fixed (which cannot be extended to ).
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Multidimensional Binary Vector Assignment problem: standard, structural and above guarantee parameterizations
Discrete Mathematics & Theoretical Computer Science, 2017Co-Authors: Marin Bougeret, Guillerme Duvillié, Rodolphe Giroudeau, Rémi WatrigantAbstract:In this article we focus on the parameterized complexity of the Multidimensional Binary Vector Assignment problem (called \BVA). An input of this problem is defined by $m$ disjoint sets $V^1, V^2, \dots, V^m$, each composed of $n$ Binary Vectors of size $p$. An output is a set of $n$ disjoint $m$-tuples of Vectors, where each $m$-tuple is obtained by picking one Vector from each set $V^i$. To each $m$-tuple we associate a $p$ dimensional Vector by applying the bit-wise AND operation on the $m$ Vectors of the tuple. The objective is to minimize the total number of zeros in these $n$ Vectors. mBVA can be seen as a variant of multidimensional matching where hyperedges are implicitly locally encoded via labels attached to vertices, but was originally introduced in the context of integrated circuit manufacturing. We provide for this problem FPT algorithms and negative results ($ETH$-based results, $W$[2]-hardness and a kernel lower bound) according to several parameters: the standard parameter $k$ i.e. the total number of zeros), as well as two parameters above some guaranteed values.
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Approximability and exact resolution of the Multidimensional Binary Vector Assignment problem
2016Co-Authors: Marin Bougeret, Guillerme Duvillié, Rodolphe GiroudeauAbstract:In this paper we consider the multidimensional Binary Vector assignment problem. An input of this problem is dened by m disjoint sets V 1 , V 2 ,. .. , V m , each composed of n Binary Vectors of size p. An output is a set of n disjoint m-tuples of Vectors, where each m-tuple is obtained by picking one Vector from each set V i. To each m-tuple we associate a p dimensional Vector by applying the bit-wise AND operation on the m Vectors of the tuple. The objective is to minimize the total number of zeros in these n Vectors. We denote this problem by min 0, and the restriction of this problem where every Vector has at most c zeros by (min 0) #0≤c. (min 0) #0≤2 was only known to be APX-complete, even for m = 3 [5]. We show that, assuming the unique games conjecture, it is NP-hard to (n − ε)-approximate (min 0) #0≤1 for any xed n and ε. This result is tight as any solution is a n-approximation. We also prove without assuming UGC that (min 0) #0≤1 is APX-complete even for n = 2, and we provide an example of n − f (n, m)-approximation algorithm for min 0. Finally, we show that (min 0) #0≤1 is polynomial-time solvable for xed m (which cannot be extended to (min 0) #0≤2 according to [5]).
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FCT - Multidimensional Binary Vector Assignment Problem: Standard, Structural and Above Guarantee Parameterizations
Fundamentals of Computation Theory, 2015Co-Authors: Marin Bougeret, Guillerme Duvillié, Rodolphe Giroudeau, Rémi WatrigantAbstract:In this article we focus on the parameterized complexity of the Multidimensional Binary Vector Assignment problem (called bMVA). An input of this problem is defined by m disjoint sets \(V^1, V^2, \dots , V^m\), each composed of n Binary Vectors of size p. An output is a set of n disjoint m-tuples of Vectors, where each m-tuple is obtained by picking one Vector from each set \(V^i\). To each m-tuple we associate a p dimensional Vector by applying the bit-wise AND operation on the m Vectors of the tuple. The objective is to minimize the total number of zeros in these n Vectors. bMVA can be seen as a variant of multidimensional matching where hyperedges are implicitly locally encoded via labels attached to vertices, but was originally introduced in the context of integrated circuit manufacturing.
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On the Complexity of Wafer-to-Wafer Integration
2015Co-Authors: Guillerme Duvillié, Marin Bougeret, Vincent Boudet, Trivikram Dokka, Rodolphe GiroudeauAbstract:In this paper we consider the Wafer-to-Wafer Integration problem. A wafer is a p-dimensional Binary Vector. The input of this problem is described by m disjoints sets (called “lots”), where each set contains n wafers. The output of the problem is a set of n disjoint stacks, where a stack is a set of m wafers (one wafer from each lot). To each stack we associate a p-dimensional Binary Vector corresponding to the bit-wise AND operation of the wafers of the stack. The objective is to maximize the total number of “1” in the n stacks. We provide O(m1−ϵ) and O(p1−ϵ) non-approximability results even for n=2, as well as a pr-approximation algorithm for any constant r. Finally, we show that the problem is FPT when parameterized by p, and we use this FPT algorithm to improve the running time of the pr-approximation algorithm.