Evaluation of transgenic Prunus domestica L., clone C5 resistance to Plum pox virus

Plum pox virus (PPV) is one of the most devastating diseases of Prunus species. Since few sources of resistance to PPV have been identified, transgene-based resistance offers a complementary approach to developing PPV-resistant stone fruit cultivars. C5, a transgenic clone of Prunus domestica L., containing the PPV coat protein (CP) gene, has been described as highly resistant to PPV in greenhouse tests, displaying characteristics typical of post-transcriptional gene silencing (PTGS). Moreover, C5 trees exposed to natural aphid vectors in the field remained uninfected after 4 years while susceptible transgenic and untransformed trees developed severe symptoms within the first year. In our study, a high and permanent infection pressure of PPV was provided by bud grafting of inoculum in the field trial of clone C5 conducted in the Czech Republic, in which PPV-infected and healthy control trees were used. Moreover, trees with combined inoculations by PPV, ACLSV and PDV were also used in the trial. The presence of the viruses throughout the tree tissues, the relative titre of the viruses and symptoms on C5 trees have been monitored over the years. The resistance stability of C5 clones under permanent infection pressure is discussed.Keywords: PPV, C5, resistance, real-time PC

Reference Gene Selection for Quantitative Real-time PCR Normalization in Quercus suber

The use of reverse transcription quantitative PCR technology to assess gene expression levels requires an accurate normalization of data in order to avoid misinterpretation of experimental results and erroneous analyses. Despite being the focus of several transcriptomics projects, oaks, and particularly cork oak (Quercus suber), have not been investigated regarding the identification of reference genes suitable for the normalization of real-time quantitative PCR data. In this study, ten candidate reference genes (Act, CACs, EF-1α, GAPDH, His3, PsaH, Sand, PP2A, ß-Tub and Ubq) were evaluated to determine the most stable internal reference for quantitative PCR normalization in cork oak. The transcript abundance of these genes was analysed in several tissues of cork oak, including leaves, reproduction cork, and periderm from branches at different developmental stages (1-, 2-, and 3-year old) or collected in different dates (active growth period versus dormancy). The three statistical methods (geNorm, NormFinder, and CV method) used in the evaluation of the most suitable combination of reference genes identified Act and CACs as the most stable candidates when all the samples were analysed together, while ß-Tub and PsaH showed the lowest expression stability. However, when different tissues, developmental stages, and collection dates were analysed separately, the reference genes exhibited some variation in their expression levels. In this study, and for the first time, we have identified and validated reference genes in cork oak that can be used for quantification of target gene expression in different tissues and experimental conditions and will be useful as a starting point for gene expression studies in other oaks

Reference genes for quantitative reverse transcription-polymerase chain reaction expression studies in wild and cultivated peanut

<p>Abstract</p> <p>Background</p> <p>Wild peanut species (<it>Arachis </it>spp.) are a rich source of new alleles for peanut improvement. Plant transcriptome analysis under specific experimental conditions helps the understanding of cellular processes related, for instance, to development, stress response, and crop yield. The validation of these studies has been generally accomplished by quantitative reverse transcription-polymerase chain reaction (qRT-PCR) which requires normalization of mRNA levels among samples. This can be achieved by comparing the expression ratio between a gene of interest and a reference gene which is constitutively expressed. Nowadays there is a lack of appropriate reference genes for both wild and cultivated <it>Arachis</it>. The identification of such genes would allow a consistent analysis of qRT-PCR data and speed up candidate gene validation in peanut.</p> <p>Results</p> <p>A set of ten reference genes were analyzed in four <it>Arachis </it>species (<it>A. magna</it>; <it>A. duranensis</it>; <it>A. stenosperma </it>and <it>A. hypogaea</it>) subjected to biotic (root-knot nematode and leaf spot fungus) and abiotic (drought) stresses, in two distinct plant organs (roots and leaves). By the use of three programs (GeNorm, NormFinder and BestKeeper) and taking into account the entire dataset, five of these ten genes, <it>ACT1 </it>(actin depolymerizing factor-like protein), <it>UBI1 </it>(polyubiquitin), <it>GAPDH </it>(glyceraldehyde-3-phosphate dehydrogenase), <it>60S </it>(60S ribosomal protein L10) and <it>UBI2 </it>(ubiquitin/ribosomal protein S27a) emerged as top reference genes, with their stability varying in eight subsets. The former three genes were the most stable across all species, organs and treatments studied.</p> <p>Conclusions</p> <p>This first in-depth study of reference genes validation in wild <it>Arachis </it>species will allow the use of specific combinations of secure and stable reference genes in qRT-PCR assays. The use of these appropriate references characterized here should improve the accuracy and reliability of gene expression analysis in both wild and cultivated Arachis and contribute for the better understanding of gene expression in, for instance, stress tolerance/resistance mechanisms in plants.</p

Dictionaries and their users

It is only recently that dictionary users have become a central consideration in the design of dictionaries, and this focus has both stimulated and benefited from research into dictionary use. The present contribution reviews the major issues in dictionary design from the user perspective, taking stock of the relevant findings from user research, insofar as such research can assist lexicographers in producing improved lexical tools

Dynamický model ložiska kaolinu

This paper focuses on research within the project TE02000029 Competence Centre for Effective and Ecological Mining of Mineral Resources, granted by The Technology Agency of the Czech Republic, and, more specifically, on the research within its work package WP4 - Spatial modelling of mineral deposits. The focus of this work package is digital modelling of selected nonenergetic raw materials, which belong to the critical commodities, as defined by the European Union. For modelling these deposits, suitable mathematical procedures, based on study and reevaluation of archived data, are needed. One of the selected deposits is a kaolin deposit near the village Jimlíkov near the city Karlovy Vary. In this paper, we show a step-by-step procedure for creation, visualization and evaluation of a 3D model of the deposit. This methodology, along with our recently developed software allows a user to create a variant of this dynamic model for the same or similar types of deposits, enables rapid updating of these models when adding or changing the input data on the basis of new mining exploration or when changing modelling parameters such as using multiple variations interpolation parameters. Our methodology leads to a more advanced deposit evaluation, including adaptive estimates of the reserves based on the usability requirements we choose. In January 2017 our software was tried out in the company Sedlecký kaolin a. s. in Božičany and our dynamic model is fully applied in practice.Článek popisuje část řešení projektu TE02000029 - Centrum kompetence efektivní a ekologické těžby nerostných surovin (CEEMIR) financovaného Technologickou agenturou ČR, přesněji výsledky řešení Work Package WP4 - Prostorové modelování ložisek nerostných surovin. Hlavním cílem WP4 je digitální modelování vybraných neenergetických surovin, které se řadí mezi kritické komodity EU. Pro modelování ložisek se využívají vhodné matematické postupy na základě studia a přehodnocení dat z archivních materiálů. Jedním z vybraných ložisek je ložisko kaolínu v okolí obce Jimlíkov na Karlovarsku. V článku jsou popsány jednotlivé kroky metodického postupu tvorby, vizualizace a zhodnocení 3D modelu tohoto ložiska. Tato metodika spolu s nově vyvinutým programovým vybavením umožňuje vytvářet variantní dynamické modely ložiska tohoto a obdobných typů, umožňuje rychlé aktualizace těchto modelů při doplnění nebo změně vstupních dat na základě prováděného těžebního průzkumu (případně i parametrů modelování - například použití více variant parametrů interpolace). Uplatnění popsaného metodického postupu vede ke komplexnímu zhodnocení ložiska včetně variantních odhadů zásob podle zadaných podmínek využitelnosti. V lednu 2017 proběhlo zaškolení a instalace software u Sedleckého kaolinu a. s. v Božičanech a dynamický model je tak plně využíván v praxi

Předpodmínění algoritmu sledování cesty pro stokesovo proudění se skluzovou podmínkou

The Stokes problem with the stick-slip boundary condition is solved by the mixed finite element method combined with the TFETI method. An interior point method for the minimization subject to box and equality constraints is used. The preconditioned projected conjugate gradient method solves the inner linear systems. The preconditioners are tested experimentally. The aim of our research is to develop efficient solvers for modelling of a flow over hydrophobic walls that exhibits applications in engineering areas including biomedical modelling or transport of fluid.Stokesova úloha se skluzovou podmínkou je rešena smíšenou metodou konecných prvku kombinovanou s TFETI metodou. Výpocet rešení se provádí metodou vnitrních bodu urcenou k minimalizaci s oboustraným omezením a rovnostní vazbou. Predpodmínená projektovaná metoda sdružených gradientu se používá pro rešení vnitrních lineárních soustav. Úcinost predpodminovacu se testuje experimentálne. Cílem výzkumu je vyvinout efektivní rešice pro modelování proudení po hydrofobních stenách, což nachází uplatnení v inženýrských oblastech zahrnujících modelování v biomedicíne nebo pri prenosu tekutin