The ADI method for bounded real and positive real Lur'e equations

We propose an algorithm for the numerical solution of the Lur'e equations in the bounded real and positive real lemma for stable systems. The algorithm provides approximate solutions in low-rank factored form. We prove that the sequence of approximate solutions is monotonically increasing with respect to definiteness. If the shift parameters are chosen appropriately, the sequence is proven to be convergent to the minimal solution of the Lur'e equations. The algorithm is based on the ideas of the recently developed ADI iteration for algebraic Riccati equations. In particular, the matrices obtained in our iteration express the optimal cost in a certain projected optimal control problem

Molecular markers reliably predict post-harvest deterioration of fresh-cut lettuce in modified atmosphere packaging

Salad crops: Longer-lasting lettuce Genetic studies have shown that the rate of deterioration of cut lettuce leaves in pre-packaged salads is a highly heritable trait, governed by gene regions that could be used to breed longer-lasting varieties. Many genetic studies have aimed at breeding better varieties of lettuce (Lactuca sativa), but most have focused upon those grown for whole heads, rather than the cut leaves that are becoming increasingly popular with consumers. An international team led by Ivan Simko, of the USDA in Salinas, California, have developed a genetic assay to distinguish fast- from slow-deteriorating lettuce varieties based on a single DNA region identified in a previous study. Their marker-based test may be useful in developing lettuces that show both disease resistance during cultivation, and a longer shelf life once leaves are cut for sale

Application of in silico bulked segregant analysis for rapid development of markers linked to Bean common mosaic virus resistance in common bean

BACKGROUND: Common bean was one of the first crops that benefited from the development and utilization of molecular marker-assisted selection (MAS) for major disease resistance genes. Efficiency of MAS for breeding common bean is still hampered, however, due to the dominance, linkage phase, and loose linkage of previously developed markers. Here we applied in silico bulked segregant analysis (BSA) to the BeanCAP diversity panel, composed of over 500 lines and genotyped with the BARCBEAN_3 6K SNP BeadChip, to develop codominant and tightly linked markers to the I gene controlling resistance to Bean common mosaic virus (BCMV). RESULTS: We physically mapped the genomic region underlying the I gene. This locus, in the distal arm of chromosome Pv02, contains seven putative NBS-LRR-type disease resistance genes. Two contrasting bulks, containing BCMV host differentials and ten BeanCAP lines with known disease reaction to BCMV, were subjected to in silico BSA for targeting the I gene and flanking sequences. Two distinct haplotypes, containing a cluster of six single nucleotide polymorphisms (SNP), were associated with resistance or susceptibility to BCMV. One-hundred and twenty-two lines, including 115 of the BeanCAP panel, were screened for BCMV resistance in the greenhouse, and all of the resistant or susceptible plants displayed distinct SNP haplotypes as those found in the two bulks. The resistant/susceptible haplotypes were validated in 98 recombinant inbred lines segregating for BCMV resistance. The closest SNP (~25-32 kb) to the distal NBS-LRR gene model for the I gene locus was targeted for conversion to codominant KASP (Kompetitive Allele Specific PCR) and CAPS (Cleaved Amplified Polymorphic Sequence) markers. Both marker systems accurately predicted the disease reaction to BCMV conferred by the I gene in all screened lines of this study. CONCLUSIONS: We demonstrated the utility of the in silico BSA approach using genetically diverse germplasm, genotyped with a high-density SNP chip array, to discover SNP variation at a specific targeted genomic region. In common bean, many disease resistance genes are mapped and their physical genomic position can now be determined, thus the application of this approach will facilitate further development of codominant and tightly linked markers for use in MAS. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2164-15-903) contains supplementary material, which is available to authorized users

Application of in silico bulked segregant analysis for rapid development of markers linked to Bean common mosaic virus resistance in common bean

BACKGROUND: Common bean was one of the first crops that benefited from the development and utilization of molecular marker-assisted selection (MAS) for major disease resistance genes. Efficiency of MAS for breeding common bean is still hampered, however, due to the dominance, linkage phase, and loose linkage of previously developed markers. Here we applied in silico bulked segregant analysis (BSA) to the BeanCAP diversity panel, composed of over 500 lines and genotyped with the BARCBEAN_3 6K SNP BeadChip, to develop codominant and tightly linked markers to the I gene controlling resistance to Bean common mosaic virus (BCMV). RESULTS: We physically mapped the genomic region underlying the I gene. This locus, in the distal arm of chromosome Pv02, contains seven putative NBS-LRR-type disease resistance genes. Two contrasting bulks, containing BCMV host differentials and ten BeanCAP lines with known disease reaction to BCMV, were subjected to in silico BSA for targeting the I gene and flanking sequences. Two distinct haplotypes, containing a cluster of six single nucleotide polymorphisms (SNP), were associated with resistance or susceptibility to BCMV. One-hundred and twenty-two lines, including 115 of the BeanCAP panel, were screened for BCMV resistance in the greenhouse, and all of the resistant or susceptible plants displayed distinct SNP haplotypes as those found in the two bulks. The resistant/susceptible haplotypes were validated in 98 recombinant inbred lines segregating for BCMV resistance. The closest SNP (~25-32 kb) to the distal NBS-LRR gene model for the I gene locus was targeted for conversion to codominant KASP (Kompetitive Allele Specific PCR) and CAPS (Cleaved Amplified Polymorphic Sequence) markers. Both marker systems accurately predicted the disease reaction to BCMV conferred by the I gene in all screened lines of this study. CONCLUSIONS: We demonstrated the utility of the in silico BSA approach using genetically diverse germplasm, genotyped with a high-density SNP chip array, to discover SNP variation at a specific targeted genomic region. In common bean, many disease resistance genes are mapped and their physical genomic position can now be determined, thus the application of this approach will facilitate further development of codominant and tightly linked markers for use in MAS. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2164-15-903) contains supplementary material, which is available to authorized users

Cardiovascular Function and Structure are Preserved Despite Induced Ablation of BMP1-Related Proteinases

IntroductionBone morphogenetic protein 1 (BMP1) is part of an extracellular metalloproteinase family that biosynthetically processes procollagen molecules. BMP1- and tolloid-like (TLL1) proteinases mediate the cleavage of carboxyl peptides from procollagen molecules, which is a crucial step in fibrillar collagen synthesis. Ablating the genes that encode BMP1-related proteinases (Bmp1 and Tll1) post-natally results in brittle bones, periodontal defects, and thin skin in conditional knockout (BTKO) mice. Despite the importance of collagen to cardiovascular tissues and the adverse effects of Bmp1 and Tll1 ablation in other tissues, the impact of Bmp1 and Tll1 ablation on cardiovascular performance is unknown. Here, we investigated the role of Bmp1- and Tll1-ablation in cardiovascular tissues by examining ventricular and vascular structure and function in BTKO mice.MethodsVentricular and vascular structure and function were comprehensively quantified in BTKO mice (n=9) and in age- and sex-matched controls (n=9). Echocardiography, cardiac catheterization, and biaxial ex vivo arterial mechanical testing were performed to assess tissue function, and histological staining was used to measure collagen protein content.ResultsBmp1- and Tll1-ablation resulted in maintained hemodynamics and cardiovascular function, preserved biaxial arterial compliance, and comparable ventricular and vascular collagen protein content.ConclusionsMaintained ventricular and vascular structure and function despite post-natal ablation of Bmp1 and Tll1 suggests that there is an as-yet unidentified compensatory mechanism in cardiovascular tissues. In addition, these findings suggest that proteinases derived from Bmp1 and Tll1 post-natally have less of an impact on cardiovascular tissues compared to skeletal, periodontal, and dermal tissues