Sample and Library Preparation for PacBio Long-Read Sequencing in Grapevine

PacBio long-read sequencing is a third-generation technology that generates long reads up to 20 kilobases (kb), unlike short-read sequencing instruments that produce up to 600 bases. Long-read sequencing is particularly advantageous in higher organisms, such as humans and plants, where repetitive regions in the genome are more abundant. The PacBio long-read sequencing uses a single molecule, real-time approach where the SMRT cells contain several zero-mode waveguides (ZMWs). Each ZMW contains a single DNA molecule bound by a DNA polymerase. All ZMWs are flushed with deoxy nucleotides with a fluorophore specific to each nucleotide. As the sequencing proceeds, the detector detects the wavelength of the fluorescence and the nucleotides are read in real-time. This chapter describes the sample and library preparation for PacBio long-read sequencing for grapevine.

Dual domestications and origin of traits in grapevine evolution

We elucidate grapevine evolution and domestication histories with 3525 cultivated and wild accessions worldwide. In the Pleistocene, harsh climate drove the separation of wild grape ecotypes caused by continuous habitat fragmentation. Then, domestication occurred concurrently about 11,000 years ago in Western Asia and the Caucasus to yield table and wine grapevines. The Western Asia domesticates dispersed into Europe with early farmers, introgressed with ancient wild western ecotypes, and subsequently diversified along human migration trails into muscat and unique western wine grape ancestries by the late Neolithic. Analyses of domestication traits also reveal new insights into selection for berry palatability, hermaphroditism, muscat flavor, and berry skin color. These data demonstrate the role of the grapevines in the early inception of agriculture across Eurasia.

A Review of Ampelometry: Morphometric Characterization of the Grape (Vitis spp.) Leaf

Grape (Vitis spp.) is one of the most important horticultural crops, cultivated worldwide on more than 7.3 million hectares for various purposes such as winemaking, fresh fruit consumption, rootstock, and ornamental plants. Based on the inter- and intraspecific morphological variability, several descriptor lists, manuals and ampelographic studies are available for identification. Among the organs, leaves have the most traits, while the young shoot, bunch and berry are also important in the characterization of the genotypes. Vitis species and cultivars are described by leaf morphological characterization developed in many ways for the identification of genotypes, to clarify synonymies and distinct clones or evaluate the diversity of wild Vitis taxa. Morphometric-also known as ampelometric-evaluation has an extensive background in the literature. However, for some reasons, only a part of the literature is cited, despite its significant scientific value. In this paper, we summarize the efforts of metric characterization of the grapevine leaf with the introduction of the scientific objectives and reviewing the studies showing the innovations in phenotyping during the past 120 years.

Gene expression profiling identifies pathways involved in seed maturation of Jatropha curcas

Background

Jatropha curcas, a tropical shrub, is a promising biofuel crop, which produces seeds with high content of oil and protein. To better understand the maturation process of J. curcas seeds and to improve its agronomic performance, a two-step approach was performed in six different maturation stages of seeds: 1) generation of the entire transcriptome of J. curcas seeds using 454-Roche sequencing of a cDNA library, 2) comparison of transcriptional expression levels using a custom Agilent 8x60K oligonucleotide microarray.

Results

A total of 793,875 high-quality reads were assembled into 19,382 unique full-length contigs, of which 13,507 could be annotated with Gene Ontology (GO) terms. Microarray data analysis identified 9111 probes (out of 57,842 probes), which were differentially expressed between the six maturation stages. The expression results were validated for 75 selected transcripts based on expression levels, predicted function, pathway, and length.

Result from cluster analyses showed that transcripts associated with fatty acid, flavonoid, and phenylpropanoid biosynthesis were over-represented in the early stages, while those of lipid storage were over-represented in the late stages. Expression analyses of different maturation stages of J. curcas seed showed that most changes in transcript abundance occurred between the two last stages, suggesting that the timing of metabolic pathways during seed maturation in J. curcas occurs in late stages. The co-expression results showed that the hubs (CB5-D, CDR1, TT8, DFR, HVA22) with the highest number of edges, associated with fatty acid and flavonoid biosynthesis, are showing a decrease in their expression during seed maturation. Furthermore, seed development and hormone pathways are significantly well connected.

Conclusion

The obtained results revealed differentially expressed sequences (DESs) regulating important pathways related to seed maturation, which could contribute to the understanding of the complex regulatory network during seed maturation with the focus on lipid, flavonoid and phenylpropanoid biosynthesis. This study provides detailed information on transcriptional changes during J. curcas seed maturation and provides a starting point for a genomic survey of seed quality traits. The results highlighted specific genes and processes relevant to the molecular mechanisms involved in Jatropha seed maturation. These data can also be utilized regarding other Euphorbiaceae species.

The Effect of Crystallinity on the Toughness of Cast Polyamide 6 Rods with Different Diameters

The present paper concentrates on the toughness and the degree of crystallinity of the magnesium-catalyzed polyamide 6 rods cast in different diametres, which are commonly used for gear manufacturing. Its toughness cannot be regarded as a constant feature due to the casting technology. The mechanical properties of the semi-finished products are sensitive to the manufactured dimension, e.g., cast diameter, which are investigated by the Charpy impact test and tensile impact test. It is generally accepted that the impact strength and tensile-impact strength correlate with the degree of crystallinity beside many other material’s feature. Crystallinity is evaluated by Differential Scanning Calorimetry. The aim of this study is to determine the relationship between toughness and crystallinity of the magnesium-catalyzed cast PA6 rods with different diameters. For the research cast rods between 40 and 300 mm diameter were selected in seven-dimensional steps. Based on the results, it was found that the toughness depends strongly on the diameter size. Furthermore, it is proved that the crystallinity explains 62.3% of the variation of the Charpy’s impact strengths, while the tensile impact method was not suitable to detect the difference between the test samples.

Assembling patchy nanorods with spheres: limitations imposed by colloidal interactions

For gold nanorods the intrinsic shape-anisotropy offers the prospect of anisotropic assembly, provided that their region-selective surface modification can be realized. Here we developed nanorods with a patchy surface chemistry, featuring positively charged molecules in the tip region and polymer molecules at the sides by careful control of molecule concentrations during ligand exchange. When these patchy nanorods are assembled with small negatively charged spherical particles, electric double layer interaction can direct the assembly of two nanospheres at the opposite ends of the nanorods. The PEG chains promote the selectivity of the procedure. As the size of the nanospheres increases, they start to shift towards the side of the nanorod due to increased van der Waals interaction. When the relative size of the nanospheres is even larger, only a single nanosphere is assembled, but instead of the tip region, they are attached to the side of the nanorods. The apparent cross-over of the region-selectivity can be interpreted in terms of colloidal interactions, i.e. the second spherical particle is excluded due to nanosphere-nanosphere electric double layer repulsion, while the large vdW attraction results in a side positioning of the single adsorbed spherical particle. The results underline the importance of absolute values of the different interaction strengths and length scales in the programmed assembly of patchy nanoscale building blocks.

Characterization of yeast isolates originating from Hungarian dairy products using traditional and molecular identification techniques

Yeast isolates collected from various Hungarian dairy products were identified using simplified identification system (SIM) and restriction fragment analysis of PCR-amplified 18S rDNA with the neighbouring ITS1 region (ITS-PCR; ribotyping). The isolates were grouped into 26 species; Geotrichum candidum, Debaryomyces hansenii, Yarrowia lipolytica, Kluyveromyces lactis and Candida catenulata were found as the predominant species. SIM and ITS-PCR proved to be useful and convenient taxonomic tools for rapid identification at species level. Two most frequent species, G. candidum and D. hansenii, were further characterized by randomly amplified polymorphic DNA (RAPD-PCR) analysis. RAPD-PCR using M13 primer resulted in discrimination between most strains of the same species and allowed a certain degree of intraspecific typing.

Identification of yeasts isolated from poultry meat

In an assessment of the potential role of yeasts in the spoilage of poultry meat, the population and species diversity of yeasts were determined on 50 commercial raw and processed chicken and turkey product samples. Initial populations (log10 cfu/g) ranged from less than 0.1 to 2.9, and increased by the expiration date to 0.4 to 5.1, respectively. 145 of 152 isolates were identified as belonging to 12 species. Yarrowia lipolytica and Candida zeylanoides were predominant, accounting for 39% and 26% of the isolates, respectively. Six different species of basidiomycetous yeasts were determined representing 24% of the isolates. The ability of the predominant yeast species to grow at refrigeration temperatures and their proteolytic and lipolytic activies suggest that yeasts may play a more significant role than previously recognised in the spoilage of poultry products.

Molecular taxonomy of yeasts

In the last two decades the application of molecular techniques has had a major impact on the classification of yeasts. The nuclear DNA relatedness has become the basis of species delineation. Molecular fingerprinting methods such as analysis of restriction fragment length polymorphisms, random amplified polymorphic DNA, PCR-amplified sequences and fragments, pulsed field gel electrophoresis of chromosome DNA and others allow intraspecies differentiation and typing. The most far reaching method has been the sequencing of various parts of ribosomal DNA that has made for the first time possible to assess the phylogenetic relationships among yeasts at different taxonomic levels. Based on the molecular data obtained so far several changes have been introduced in the classification of yeasts, however, substantial restructuring of current taxonomic schemes with the consequence of numerous nomenclatural changes must await further studies.

Candida novakii, sp. nov. a new anamorphic yeast species of ascomycetous affinity

Two strains of an undescribed species of the genus Candida were isolated from decaying wood of Quercus sp. A description of the new species Candida novakii is given.

Some remarks on "a taxonomic key for the genus Saccharomyces" (Vaughan Martini and Martini 1993)

The practicability of Vaughan Martini and Martini's "Taxonomic Key for the Genus Saccharomyces" for the separation of S. bayanus from other Saccharomyces sensu stricto species was studied. It was concluded that the ability to grow in vitamin free medium was not a suitable character for this purpose. A new wild S. bayanus strain, isolated from exudate of Carpinus betulus was also included in this study. This appears to be the third documented strain of that species isolated outside of an artificial fermentation environment.

Simplified techniques for identifying foodborne yeasts

Four problematic areas associated with the identification of foodborne yeasts are discussed. These consist of (1) the inability of conventional identification tests to recognize some common and important foodborne yeasts characterized by genomic differences (e.g., Saccharomyces cerevisiae, S. bayanus and S. pastorianus); (2) the delay in application of non-traditional identification methods such as DNA fingerprinting, chromosome karyotyping, protein electrophoretic patterns and fatty acid profiles for routine identification purposes; (3) the lack of commercially available manual or automated identification systems dedicated to the diagnosis of foodborne yeasts; and (4) the disregard for considering ecological frequency of yeasts in computerized probabilistic identification systems.

On the false positive urease activity of Yarrowia lipolytica

The ability of Yarrowia lipolytica to produce ammonia from urea was found variable on some media. The colour change of the indicator in Christensen's urea agar was not due to the urease activity of this species but was a non-specific alkalization reaction. Rapid urea broth was reliable giving no false positive results. It was found that Y. lipolytica is a urease negative yeast species.

Evaluation of simplified and commercial systems for identification of foodborne yeasts

Commercial identification kits (API 20C, API Yeast-Ident and API-Zym) were compared with a conventional but simplified identification method (SIM) for identifying seventy-two yeast isolates from fresh sweet corn. SIM failed to provide identification of two isolates. Of the twenty species identified, only eleven were included in the API 20C profile index. Three isolates were identified at the species level and three were identified at the genus level with 100% accuracy. The enzyme kit (Yeast-Ident) gave rather unreliable results, in that identification of only four isolates with 75 to 85% of appropriate reactions was made. The API 20C kit could be used to identify non-clinical yeasts, provided they were included in its database and a few additional tests (urease reaction, nitrate assimilation and glucose fermentation) were also performed.

Simplified identification of aerobic spore-formers in the investigation of foods

Bacillus spp. are among the main spoilage organisms in food due to their versatile metabolism and heat-resistant spores. Except for B. cereus, no specific identification method is available, although information about Bacillus spp. would be useful in monitoring good manufacturing practice. A simplified identification scheme for aerobic spore-formers for routine laboratory use was elaborated by reducing the number of tests to be performed; 20 Bacillus spp. common in foods were considered. Besides cell morphology six biochemical characters were selected that proved most efficient in identification. In addition, methods were developed and modified to determine these characters by only 3 tests. By applying the simplified identification scheme, 766 strains of bacilli isolated from various foods were tested and species identity of 714 strains (93%) could be determined. Most aerobic spore-formers from foods were B. subtilis, B. pumilus and B. licheniformis. The spectrum of mesophilic bacilli isolated from natural sources was broad and comprised some 20 different species. Only one-third of the thermophilic isolates proved to be identical with, or similar to, B. stearothermophilus, while the rest were identified as five other species. The simplified method merits main application in ecological studies of foods.