Using parametric set constraints for locating errors in CLP programs

This paper introduces a framework of parametric descriptive directional types for constraint logic programming (CLP). It proposes a method for locating type errors in CLP programs and presents a prototype debugging tool. The main technique used is checking correctness of programs w.r.t. type specifications. The approach is based on a generalization of known methods for proving correctness of logic programs to the case of parametric specifications. Set-constraint techniques are used for formulating and checking verification conditions for (parametric) polymorphic type specifications. The specifications are expressed in a parametric extension of the formalism of term grammars. The soundness of the method is proved and the prototype debugging tool supporting the proposed approach is illustrated on examples. The paper is a substantial extension of the previous work by the same authors concerning monomorphic directional types.Comment: 64 pages, To appear in Theory and Practice of Logic Programmin

CP debugging needs and tools

Conventional programming techniques are not well suited for solving many highly combinatorial industrial problems, like scheduling, decision making, resource allocation or planning. Constraint Programming (CP), an emerging software technology, offers an original approach allowing for efficient and flexible solving of complex problems, through combined implementation of various constraint solvers and expert heuristics. Its applications are increasingly elded in various industries

CP debugging tools: Clarification of functionalities and selection of the tools

Abstract is not available

Induction of androgenesis and production of haploid embryos in anther cultures of borage (Borago officinalis L.)

[EN] Borage (Borago officinalis L.) is an important medicinal plant with different culinary, pharmaceutical and industrial properties. Unfortunately, there are no published reports on the establishment of protocols to produce DHs in this species up to now. In this work, we show for the first time the induction of borage microspores to become embryogenic calli, from which haploid embryos are produced. In addition, we evaluated the effect of using different flower bud sizes, carbon sources, concentrations of 2,4-D and BAP, cold (4 A degrees C) pretreatments and heat shock treatments. Production of total calli, embryogenic calli and callus-derived embryos was differently affected by the different parameters studied. Our results showed that the use of 5-7 mm-long flower buds, a cold (4 A degrees C) pretreatment during 4 days, a 32 A degrees C heat shock for 3 days, and the addition of 3 % maltose and 2 mgl(-1) 2,4-D and 1 mgl(-1) BAP to the culture medium, was beneficial for embryo production. Overall, this work demonstrates that DH technology is possible in borage, and opens the door for future improvements needed to finally obtain borage DH plants.Eshaghi, ZC.; Abdollahi, MR.; Moosavi, SS.; Deljou, A.; Seguí-Simarro, JM. (2015). Induction of androgenesis and production of haploid embryos in anther cultures of borage (Borago officinalis L.). Plant Cell, Tissue and Organ Culture. 122:321-329. doi:10.1007/s11240-015-0768-5S321329122Abdollahi MR, Moieni A, Javaran MJ (2004) Interactive effects of shock and culture density on embryo induction in isolated microspore culture of Brassica napus L. cv. Global Iranian J Biotech 2:97–100Bohanec B, Neskovic M, Vujicic R (1993) Anther culture and androgenetic plant regeneration in buckwheat (Fagopyrum esculentum Moench). Plant Cell Tissue Organ Cult 35:259–266Calleberg E, Johansson L (1996) Effect of gelling agents on anther cultures. In: Jain SM, Sopory SK, Veilleux RE (eds) In vitro haploid production in higher plants, vol 23. Springer, Netherlands, pp 189–203Custers JBM, Cordewener JHG, Nöllen Y, Dons JJ, van Lookeren-Campagne MM (1994) Temperature controls both gametophytic and sporophytic development in microspore cultures of Brassica napus. Plant Cell Rep 13:267–271Ferrie AMR (2013) Advances in microspore culture technology: a biotechnological tool for the improvement of medicinal plants. In: Chandra S et al (eds) Biotechnology for medicinal plants. Springer, Berlin, pp 191–206Ferrie AMR, Caswell KL (2011) Isolated microspore culture techniques and recent progress for haploid and doubled haploid plant production. Plant Cell Tissue Organ Cult 104:301–309Ferrie AMR, Bethune T, Mykytyshyn M (2011) Microspore embryogenesis in the Apiaceae. Plant Cell Tissue Organ Cult 104:399–406Forster BP, Heberle-Bors E, Kasha KJ, Touraev A (2007) The resurgence of haploids in higher plants. Trends Plant Sci 12:368–375Gamborg OL, Miller RA, Ojiwa K (1968) Nutrient requirements of suspension culture of soybean root callus. Exp Cell Res 50:151–158Guil-Guerrero JL, García-Maroto F, Vilches-Ferrón MA, López-Alonso D (2003) Gamma-linolenic acid from fourteen Boraginaceae species. Ind Crop Prod 18:85–89Horrobin DF (1983) The regulation of prostaglandin biosynthesis by the manipulation of essential fatty acid metabolism. Rev Pure Appl Pharmacol Sci 4:339–383Irikova T, Grozeva S, Rodeva V (2011) Anther culture in pepper (Capsicum annuum L.) in vitro. Acta Physiol Plant 33:1559–1570Lauxen MS, Kaltchuk-Santos E, Hu CY, Callegari-Jacques SM, Bodanese-Zanettini MH (2003) Association between floral bud size and developmental stage in soybean microspores. Braz Arch Biol Technol 46:515–520Leach CR, Mayo O, Bürger R (1990) Quantitatively determined self-incompatibility. Outcrossing in Borago officinalis. Theoret Appl Genetics 79:427–430Lichter R (1982) Induction of haploid plants from isolated pollen of Brassica napus. Z Pflanzenphysiol 105:427–434Maluszynski M, Kasha KJ, Szarejko I (2003) Published doubled haploid protocols in plant species. In: Maluszynski M, Kasha KJ, Forster BP, Szarejko I (eds) Doubled haploid production in crop plants. A manual. Kluwer, Dordrecht, pp 309–335Maraschin SF, de Priester W, Spaink HP, Wang M (2005) Androgenic switch: an example of plant embryogenesis from the male gametophyte perspective. J Exp Bot 56:1711–1726McDonald BE, Fitzpatrick K (1998) Designer Vegetable Oils. In: Mazza G (ed) Functional foods, biochemical and processing aspects. Technomic Publ Co. Inc, Lancaster, pp 265–291Ozkum D, Tipirdamaz R (2002) The effects of cold treatment and charcoal on the in vitro androgenesis of pepper (Capsicum annuum L.). Turk J Bot 26:131–139Parra-Vega V, González-García B, Seguí-Simarro JM (2013a) Morphological markers to correlate bud and anther development with microsporogenesis and microgametogenesis in pepper (Capsicum annuum L.). Acta Physiol Plant 35:627–633Parra-Vega V, Renau-Morata B, Sifres A, Seguí-Simarro JM (2013b) Stress treatments and in vitro culture conditions influence microspore embryogenesis and growth of callus from anther walls of sweet pepper (Capsicum annuum L.). Plant Cell Tissue Organ Cult 112:353–360Raquin C (1983) Utilization of different sugars as carbon sources for in vitro cultures of Petuina. Z Pflanzenphysol 111:453–457Salas P, Rivas-Sendra A, Prohens J, Seguí-Simarro JM (2012) Influence of the stage for anther excision and heterostyly in embryogenesis induction from eggplant anther cultures. Euphytica 184:235–250Seguí-Simarro JM (2010) Androgenesis revisited. Bot Rev 76:377–404Seguí-Simarro JM, Nuez F (2006) Androgenesis induction from tomato anther cultures: callus characterization. Acta Hort 725:855–861Seguí-Simarro JM, Corral-Martínez P, Parra-Vega V, González-García B (2011) Androgenesis in recalcitrant solanaceous crops. Plant Cell Rep 30:765–778Shariatpanahi ME, Bal U, Heberle-Bors E, Touraev A (2006) Stresses applied for the reprogramming of plant microspores towards in vitro embryogenesis. Physiol Plant 127:519–534Simon JE, Chadwick AF, Craker LE (1984) Herbs: an indexed bibliography. 1971–1980. The scientific literature on selected herbs, and aromatic and medicinal plants of the temperate zone. Archon Books, Hamden, CTSkrzypek E, Czyczyło-Mysza I, Marcińska I, Wędzony M (2008) Prospects of androgenetic induction in Lupinus spp. Plant Cell Tissue Organ Cult 94(2):131–137Snape JW (1989) Doubled haploid breeding: theoretical basis and practical applications. In: Mujeeb-Kazi A, Sitch LA (eds) Review of advances in plant biotechnology, 1985–1988: 2nd international symposium genetic manipulation in crops. Mexico and Manila, CIMMYT and IRRI, pp 19–30Tipirdamaz R, Ellialtioğlu Ş (1998) The effects of cold treatments and activated charcoal on ABA contents of anthers and in vitro androgenesis in eggplant (Solanum melongena L.). In: Tsekos I, Moustakas M (eds) Progress in botanical research, Proceedings of the 1st Balkan botanical congress. Kluwer Academic Publishers, The NetherlandsVagera J, Havranek P (1985) In vitro induction of androgenesis in Capsicum annuum L. and its genetic aspests. 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TILLING - a shortcut in functional genomics

Recent advances in large-scale genome sequencing projects have opened up new possibilities for the application of conventional mutation techniques in not only forward but also reverse genetics strategies. TILLING (Targeting Induced Local Lesions IN Genomes) was developed a decade ago as an alternative to insertional mutagenesis. It takes advantage of classical mutagenesis, sequence availability and high-throughput screening for nucleotide polymorphisms in a targeted sequence. The main advantage of TILLING as a reverse genetics strategy is that it can be applied to any species, regardless of its genome size and ploidy level. The TILLING protocol provides a high frequency of point mutations distributed randomly in the genome. The great mutagenic potential of chemical agents to generate a high rate of nucleotide substitutions has been proven by the high density of mutations reported for TILLING populations in various plant species. For most of them, the analysis of several genes revealed 1 mutation/200–500 kb screened and much higher densities were observed for polyploid species, such as wheat. High-throughput TILLING permits the rapid and low-cost discovery of new alleles that are induced in plants. Several research centres have established a TILLING public service for various plant species. The recent trends in TILLING procedures rely on the diversification of bioinformatic tools, new methods of mutation detection, including mismatch-specific and sensitive endonucleases, but also various alternatives for LI-COR screening and single nucleotide polymorphism (SNP) discovery using next-generation sequencing technologies. The TILLING strategy has found numerous applications in functional genomics. Additionally, wide applications of this throughput method in basic and applied research have already been implemented through modifications of the original TILLING strategy, such as Ecotilling or Deletion TILLING

An automated, cost-effective and scalable, flood-and-drain based root phenotyping system for cereals

Background: Genetic studies on the molecular mechanisms of the regulation of root growth require the characterisation of a specific root phenotype to be linked with a certain genotype. Such studies using classical labour-intensive methods are severely hindered due to the technical limitations that are associated with the impeded observation of the root system of a plant during its growth. The aim of the research presented here was to develop a reliable, cost-effective method for the analysis of a plant root phenotype that would enable the precise characterisation of the root system architecture of cereals. Results: The presented method describes a complete system for automatic supplementation and continuous sensing of culture solution supplied to plants that are grown in transparent tubes containing a solid substrate. The presented system comprises the comprehensive pipeline consisting of a modular-based and remotely-controlled plant growth system and customized imaging setup for root and shoot phenotyping. The system enables an easy extension of the experimental capacity in order to form a combined platform that is comprised of parallel modules, each holding up to 48 plants. The conducted experiments focused on the selection of the most suitable conditions for phenotyping studies in barley: an optimal size of the glass beads, diameters of the acrylic tubes, composition of a medium, and a rate of the medium flow. Conclusions: The developed system enables an efficient, accurate and highly repeatable analysis of the morphological features of the root system of cereals. Because a simple and fully-automated control system is used, the experimental conditions can easily be normalised for different species of cereals. The scalability of the module-based system allows its capacity to be adjusted in order to meet the requirements of a particular experiment