Seedling establishment characteristics of Paeonia ostii var. lishizhenii

The viability of Paeonia ostii var. lishizhenii seed used in this investigation was around 85% when tested under optimum conditions of tissue culture. Seedling establishment embodied radicle protrusion and breaking of epicotyl dormancy. The seed coat, an endosperm extract, and GA3 significantly influenced embryo emergence. The seed coat is not an appreciable barrier to water uptake but exhibited a degree of mechanical resistance. Both the coat and endosperm extract inhibited germination. Removal of the radicle end of the testa and soaking in GA3 (100–200mgl−1) promoted radicle growth at 15°C. Epicotyl dormancy was broken by soaking seeds in GA3 or maintaining excised embryos on Woody Plant Medium containing 1mgl−1 GA3. Chilling at 5°C for 30 days was required to break epicotyl dormancy of emerged embryos. The seed structures surrounding the embryos impose mechanical and chemical restraints on germination. The embryo itself appears to be lacking growth promoters as exogenous GA3 promoted epicotyl growth

Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly

Motivation: Eugene Myers in his string graph paper (Myers, 2005) suggested that in a string graph or equivalently a unitig graph, any path spells a valid assembly. As a string/unitig graph also encodes every valid assembly of reads, such a graph, provided that it can be constructed correctly, is in fact a lossless representation of reads. In principle, every analysis based on whole-genome shotgun sequencing (WGS) data, such as SNP and insertion/deletion (INDEL) calling, can also be achieved with unitigs. Results: To explore the feasibility of using de novo assembly in the context of resequencing, we developed a de novo assembler, fermi, that assembles Illumina short reads into unitigs while preserving most of information of the input reads. SNPs and INDELs can be called by mapping the unitigs against a reference genome. By applying the method on 35-fold human resequencing data, we showed that in comparison to the standard pipeline, our approach yields similar accuracy for SNP calling and better results for INDEL calling. It has higher sensitivity than other de novo assembly based methods for variant calling. Our work suggests that variant calling with de novo assembly be a beneficial complement to the standard variant calling pipeline for whole-genome resequencing. In the methodological aspects, we proposed FMD-index for forward-backward extension of DNA sequences, a fast algorithm for finding all super-maximal exact matches and one-pass construction of unitigs from an FMD-index. Availability: http://github.com/lh3/fermi Contact: [email protected]: Rev2: submitted version with minor improvements; 7 page

In vitro culture and establishment of Anthurium parvispathum

Sterilized seed of Anthurium parvispathum were germinated and used as explant source. The decontaminated germinated seedlings were excised and placed onto a multiplication medium containing 2mgl−1 BA and 0.2mgl−1 NAA. On average a 4-fold increase in the number of shoots produced was achieved on this medium. The shoots were subsequently placed on an elongation medium containing 20mgl−1 kinetin. The shoots elongated to a length of 2.3cm. Shoot multiplication also occurred. These were then placed onto different rooting media. The optimal rooting medium contained 0.25mgl−1 IBA which produced 3.6 roots per plantlet with a 94% success rate. It took 24weeks to progress from seed to rooted plantlets ready for acclimatization. Micropropagated plants were soaked in 0.2% Benlate to reduce fungal contamination and then placed into trays containing peat, bark and soil (1:1:1) for acclimatization. The trays were kept in a mist house for 4weeks with overhead misting and bottom heat of 30°C. They were then transferred to a green house where they were watered twice a week and sprayed with Kelpak (a seaweed concentrate) at a 1:500 dilution every second week. There was only a 2% loss during acclimatization and over the subsequent three months of growth

Malic Acid Distribution and Degradation in Grape Must During Skin Contact: The Influence of Recombinant Malo-Ethanolic Wine Yeast Strains

Wine acidity plays an important role in determining wine quality and ensuring physiochemical and microbiological stability. In high-acid wines, the L-malic acid concentration is usually reduced through bacterial malolactic fermentation, while acidulation in low-acidity wines is usually done during final blending of the wine before bottling.  This study showed that skin contact did not influence the relative concentration of L-malic acid in the pulp and juice fractions from Colombard, Ruby Cabernet and Cabernet Sauvignon grape musts, with 32%-44% of the L-malic acid present in the pulp fraction. Four recombinant malo-ethanolic (ME) Saccharomyces wine yeast strains containing the malic enzyme (mae2) and malate transporter (mael) genes of Schizasaccharomyces pombe, effectively degraded the L-malic acid in both the juice and pulp fractions of all three cultivars, with a complete degradation of malic acid in the juice fraction within 2 days

Oidium longipes, a new powdery mildew fungus on petunia in the USA: A potential threat to ornamental and vegetable solanaceous crops

This is the first North American report of Oidium longipes, an anamorphic powdery mildew species described recently in Europe. It was found on vegetatively propagated petunia grown in a commercial greenhouse in New Jersey, USA, where it caused a rapidly spreading disease. The pathogen might have originated offshore and may have already been distributed in the United States through horticultural trade. During field surveys in Europe, it was found on petunia in Hungary and Austria as well; this is the first report of O. longipes from these two countries. A detailed light microscopy study of American and European specimens of O. longipes, including freshly collected samples and authentic herbarium specimens, revealed that its conidiophore morphology is more variable than illustrated in the original species description or in subsequent works. Microcycle conidiation, a process not yet known to occur in powdery mildews, was repeatedly observed in O. longipes. The rDNA internal transcribed spacer (ITS) sequences were identical in colonies containing different conidiophore types as well as in a total of five specimens collected from petunia in the United States, Austria, Hungary, Germany, and Switzerland. A phylogenetic analysis of the ITS sequences revealed that the closest known relative of O. longipes is O. lycopersici, known to infect tomato only in Australia. Cross-inoculation tests showed that O. longipes from petunia heavily infected tobacco cv. Xanthi, while the tomato and eggplant cultivars tested were moderately susceptible to this pathogen. These results indicate that its spread represents a potential danger to a number of solanaceous crops. Our ad hoc field surveys conducted in 2006 and 2007 did not detect it outside New Jersey in the United States; all the other powdery mildew–infected petunias, collected in New York and Indiana, were infected by Podosphaera xanthii. In Europe, most of the powdery mildew–infected petunias examined in this study were infected by P. xanthii or Golovinomyces orontii. Our multiple inoculation tests revealed that the same petunia plants and even the same leaves can be infected concomitantly by O. longipes, O. neolycopersici, G. orontii, and P. xanthii. Thus, it is at present unclear to what extent O. longipes contributes to the powdery mildew epidemics that develop year after year on solanaceous plants in many parts of the world

Stress Distribution in Mandible Regulated by Bone and Dental Implant Parameters: Part I - Methodology

The complicated inter-relationships between mandibular bone components and dental implants have attracted the attention of many a structural mechanics researcher as well as many a dental practitioner. This paper describes the methodology and analysis techniques employed to enable accurate evaluation of a vast range of the implant and bone parameters. The complex material and geometric properties of the bone and implant are modelled using two-dimensional (2D) triangular and quadrilateral plane strain elements. Assumptions made in the analysis include: (a) 50% osseointegration between bone and implant; (b) linear relationships exist between the stress value and the Young’s moduli of the cancellous and cortical bone at any specific point. In the companion paper (Part II) various bone, implant and loading parameters are evaluated for their influence on the stress distribution within the bone, in particular in the mandible

Genetic Engineering of an Industrial Strain of Saccharomyces cerevisiae for L-Malic Acid Degradation via an Efficient Malo-Ethanolic Pathway

The optimal ratio of L-malic and L-tartaric acid in relation to other wine components is one of the most important aspects that ultimately determine wine quality during winemaking. Winemakers routinely rely on the judicious use of malolactic fermentation (MLF) after alcoholic fermentation to deacidify and stabilise their wines. However, due to theunreliability of the process and unsuitable sensory modifications in some grape cultivars, especially for fruity-floral wines, MLF is often regarded as problematic and undesirable. Alternative methods for reducing the amounts of L-malic acid in wine will contribute to improving the production of quality wines in the future, especially in coolclimate regions. Most wine yeast strains of Saccharomyces are unable to effectively degrade L-malic acid, whereas the fission yeast Schizosaccharomyces pombe efficiently degrades high concentrations of L-malic acid by means of malo-ethanolic fermentation. However, strains of S. pombe are not suitable for vinification due to the production of undesirable off-flavours. Previously, the 5. pombe malate permease (mael) and malic enzyme (mae2) genes were  successfully expressed under the 3-phosphoglycerate kinase (PGK1) regulatory elements in 5. cerevisiae, resulting in a recombinant laboratory strain of S. cerevisiae with an efficient malo-ethanolic pathway. Stable integration of the S. pombe malo-ethanolic pathway genes has now been obtained through the construction of a unique integration strategy in a commercial wine yeast strain. Co-transformation of the linear integration cassette containing the mael and mae2 genes and PGK1 regulatory elements and a multi-copy plasmid containing the phleomycin-resistance marker into a commercial Saccharomyces cerevisiae strain resulted in the successful transformation and integration of the malo-ethanolic genes. The recombinant 5. cerevisiae strain was successfully cured of phleomycin-resistance plasmid DNA in order to obtain malo-ethanolic yeast containing only yeast-derived DNA. The integrated malo-ethanolic genes were stable in 5. cerevisiae and during synthetic and grape must fermentation, L-malic acid was completely fermented to ethanol without any negative effect on fermentation kinetics and wine quality

Oidium neolycopersici: Intra-specific variability inferred from AFLP analysis and relationship with closely related powdery mildew fungi infecting various plant species

Previous works indicated a considerable variation in the pathogenicity, virulence, and host range of Oidium neolycopersici isolates causing tomato powdery mildew epidemics in many parts of the world. In this study, rDNA internal transcribed spacer (ITS) sequences, and amplified fragment length polymorphism (AFLP) patterns were analyzed in 17 O. neolycopersici samples collected in Europe, North America, and Japan, including those which overcame some of the tomato major resistance genes. The ITS sequences were identical in all 10 samples tested and were also identical to ITS sequences of eight previously studied O. neolycopersici specimens. The AFLP analysis revealed a high genetic diversity in O. neolycopersici and indicated that all 17 samples represented different genotypes. This might suggest the existence of either a yet unrevealed sexual reproduction or other genetic mechanisms that maintain a high genetic variability in O. neolycopersici. No clear correlation was found between the virulence and the AFLP patterns of the O. neolycopersici isolates studied. The relationship between O. neolycopersici and powdery mildew anamorphs infecting Aquilegia vulgaris, Chelidonium majus, Passiflora caerulea, and Sedum alboroseum was also investigated. These anamorphs are morphologically indistinguishable from and phylogenetically closely related to O. neolycopersici. The cross-inoculation tests and the analyses of ITS sequences and AFLP patterns jointly indicated that the powdery mildew anamorphs collected from the above mentioned plant species all represent distinct, but closely related species according to the phylogenetic species recognition. All these species were pathogenic only to their original host plant species, except O. neolycopersici which infected S. alboroseum, tobacco, petunia, and Arabidopsis thaliana, in addition to tomato, in cross-inoculation tests. This is the first genome-wide study that investigates the relationships among powdery mildews that are closely related based on ITS sequences and morphology. The results indicate that morphologically indistinguishable powdery mildews that differed in only one to five single nucleotide positions in their ITS region are to be considered as different taxa with distinct host ranges

eModeration: Towards a User Experience Evaluation Framework

eModeration (or online moderation) can improve the user experience of the examination process while lowering the risk of losing scripts or delaying the moderation process. Despite these benefits to optimising examination procedures, the application of online moderation is limited. There could be various reasons for the lack of adopting eModeration including the technical, organisational and human factors. The focus of this study is on the human factors involved in eModeration and the research is guided by the following question: What are the most important user experience constructs for valuating an electronic moderation (eModeration) system within the context of Higher Education Institutions in South Africa? This research uses a design science methodology, which comprises the development and testing of a user experience framework. In this paper, we will only report on the identification of the constructs for the user experience framework. The data generation methods will include interviews with deans from the different faculties and a survey with moderators and deans. The research was conducted at Midrand Graduate Institute, a Private Higher Education institution in South Africa. The contribution of the paper is to identify the most important user experience constructs for evaluating an eModeration system and also to provide some insights on the user experience of the two different user groups. The enriched understanding of eModerators’ and deans’ user experience of eModeration contributes to the understanding of the human factors that influence the adoption of innovative assessment practices.College of Engineering, Science and Technolog