Transcriptome profiling of grapevine seedless segregants during berry development reveals candidate genes associated with berry weight

Indexación: Web of Science; PubMedBackground Berry size is considered as one of the main selection criteria in table grape breeding programs. However, this is a quantitative and polygenic trait, and its genetic determination is still poorly understood. Considering its economic importance, it is relevant to determine its genetic architecture and elucidate the mechanisms involved in its expression. To approach this issue, an RNA-Seq experiment based on Illumina platform was performed (14 libraries), including seedless segregants with contrasting phenotypes for berry weight at fruit setting (FST) and 6–8 mm berries (B68) phenological stages. Results A group of 526 differentially expressed (DE) genes were identified, by comparing seedless segregants with contrasting phenotypes for berry weight: 101 genes from the FST stage and 463 from the B68 stage. Also, we integrated differential expression, principal components analysis (PCA), correlations and network co-expression analyses to characterize the transcriptome profiling observed in segregants with contrasting phenotypes for berry weight. After this, 68 DE genes were selected as candidate genes, and seven candidate genes were validated by real time-PCR, confirming their expression profiles. Conclusions We have carried out the first transcriptome analysis focused on table grape seedless segregants with contrasting phenotypes for berry weight. Our findings contributed to the understanding of the mechanisms involved in berry weight determination. Also, this comparative transcriptome profiling revealed candidate genes for berry weight which could be evaluated as selection tools in table grape breeding programs.http://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-016-0789-

Mapping competency frameworks: implications for public health curricula design

This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are madeOBJECTIVES: We discuss the implications stemming from a recent competency mapping project on public health workforce education and training programs. METHODS: In line with professional practice, we reflected on the results of a major mapping exercise which examined public health competency frameworks against the Global Charter, particularly with respect to the implications for curriculum design. RESULTS: Our reflections identified five key challenges (diversity of frameworks, interpretation challenges, levels of competence, integration in curricula and knowledge vs skills-based competences) for developing internationally consistent credentialling standards. CONCLUSIONS: While the Charter provides an international benchmark for public health curricula, we argue that applying an international competency framework is challenging. Anyone working in public health should be trained in all foundation areas of public health to support public health practice and initiatives into the future and they may then choose to specialise in sub-disciplines of public health. IMPLICATIONS FOR PUBLIC HEALTH: Both theoretical and practical content must be fully integrated across public health programs to operationalise competencies. Utilising the Charter can ensure alignment with the sector needs, and curriculum mapping should be an integral part of a continual and ongoing review process

Digital Art as ‘Monetised Graphics:’ Enforcing Intellectual Property on the Blockchain

In a global economic landscape of hyper-commodification and financialisation, efforts to assimilate digital art into the high-stakes commercial art market have so far been rather unsuccessful, presumably because digital art works cannot easily assume the status of precious object worthy of collection. This essay explores the use of blockchain technologies in attempts to create proprietary digital art markets in which uncommodifiable digital art works are financialised as artificially scarce commodities. Using the decentralisation techniques and distributed database protocols underlying current cryptocurrency technologies, such efforts, exemplified here by the platform Monegraph, tend to be presented as concerns with the interest of digital artists and with shifting ontologies of the contemporary work of art. I challenge this characterisation, and argue, in a discussion that combines aesthetic theory, legal and philosophical theories of intellectual property, rhetorical analysis, and research in the political economy of new media, that the formation of proprietary digital art markets by emerging commercial platforms such as Monegraph constitutes a worrisome amplification of long-established, on-going efforts to fence in creative expression as private property. As I argue, the combination of blockchain-based protocols with established ambitions of intellectual property policy yields hybrid conceptual-computational financial technologies (such as self-enforcing smart contracts attached to digital artefacts) that are unlikely to empower artists, but which serve to financialise digital creative practices as a whole, curtailing the critical potential of the digital as an inherently dynamic and potentially uncommodifiable mode of production and artistic expression

Serum Amyloid P Component (SAP)-Like Protein From Botryllid Ascidians Provides a Clue to Amyloid Function

The HA-1 lectin isolated from Botrylloides leachii has an amino acid composition similar to that of mammalian serum amyloid protein (SAP). SAP is a universal component of mammalian amyloid deposits. Like SAP, HA-1 has a disc ultrastructure, and antibody to HA-1 binds both (a) to amyloidlike fibers deposited between rejected Botrylloides colonies and (b) to cerebral amyloid deposits in Alzheimer's disease brains. Deposition of protochordate amyloid within rejection sites and surrounding fouling organisms implies that these fibers function as barriers to allogeneic and infectious challenge. Similarly, mammalian amyloid may also function to contain inflammatory lesions and to limit the spread of certain infections. Pathological amyloidotic conditions in humans, such as Alzheimer's disease, may result from unregulated expression of this primitive encapsulation response

The Impact of a SIG on Assessment Literacy

A major aim of professional associations is to provide opportunities for professionals to interact with others, share ideas and develop in their chosen profession. Professional associations exist to provide specialized networking and development opportunities to a specific profession, group of individuals or field of study. To promote and support specialized research and communication, smaller subgroups within an association are often chartered or developed. These subgroups are typically known as Special Interest Groups. According to Jacob et al. (2013), association members join SIGs because they want to go deeper into a specialized content area and they enjoy networking with others who ‘speak the same language.’ The TESOL Arabia Testing, Assessment and Evaluation SIG (TAE SIG) has focused their professional development activities on an important trend in the field, that of language assessment literacy (LAL). Language assessment literacy has been a critical topic in English language teaching since the late 1990s. Unfortunately, this is mainly due to the fact that so many English language teachers are not assessment literate. In other words, many English language teachers lack the knowledge and skills to write effective language tests, evaluate the effectiveness of their tests, and use their test results in meaningful ways. The purpose of this chapter is to critically examine the status of LAL in the Middle East and North Africa (MENA) region and report on activities that the TAE SIG has implemented to increase LAL

ntLink: a toolkit for de novo genome assembly scaffolding and mapping using long reads

With the increasing affordability and accessibility of genome sequencing data, de novo genome assembly is an important first step to a wide variety of downstream studies and analyses. Therefore, bioinformatics tools that enable the generation of high-quality genome assemblies in a computationally efficient manner are essential. Recent developments in long-read sequencing technologies have greatly benefited genome assembly work, including scaffolding, by providing long-range evidence that can aid in resolving the challenging repetitive regions of complex genomes. ntLink is a flexible and resource-efficient genome scaffolding tool that utilizes long-read sequencing data to improve upon draft genome assemblies built from any sequencing technologies, including the same long reads. Instead of using read alignments to identify candidate joins, ntLink utilizes minimizer-based mappings to infer how input sequences should be ordered and oriented into scaffolds. Recent improvements to ntLink have added important features such as overlap detection, gap-filling and in-code scaffolding iterations. Here, we present three basic protocols demonstrating how to use each of these new features to yield highly contiguous genome assemblies, while still maintaining ntLink's proven computational efficiency. Further, as we illustrate in the alternate protocols, the lightweight minimizer-based mappings that enable ntLink scaffolding can also be utilized for other downstream applications, such as misassembly detection. With its modularity and multiple modes of execution, ntLink has broad benefit to the genomics community, from genome scaffolding and beyond. ntLink is an open-source project and is freely available from https://github.com/bcgsc/ntLink.Comment: 23 pages, 2 figure

Identification of stable QTLs for vegetative and reproductive traits in the microvine (Vitis vinifera L.) using the 18 K Infinium chip

UMR AGAP - équipe DAAV - Diversité, adaptation et amélioration de la vigne[b]Background[/b] [br/]The increasing temperature associated with climate change impacts grapevine phenology and development with critical effects on grape yield and composition. Plant breeding has the potential to deliver new cultivars with stable yield and quality under warmer climate conditions, but this requires the identification of stable genetic determinants. This study tested the potentialities of the microvine to boost genetics in grapevine. A mapping population of 129 microvines derived from Picovine x Ugni Blanc flb, was genotyped with the Illumina® 18 K SNP (Single Nucleotide Polymorphism) chip. Forty-three vegetative and reproductive traits were phenotyped outdoors over four cropping cycles, and a subset of 22 traits over two cropping cycles in growth rooms with two contrasted temperatures, in order to map stable QTLs (Quantitative Trait Loci). [br/][b]Results[/b] [br/]Ten stable QTLs for berry development and quality or leaf area were identified on the parental maps. A new major QTL explaining up to 44 % of total variance of berry weight was identified on chromosome 7 in Ugni Blanc flb, and co-localized with QTLs for seed number (up to 76 % total variance), major berry acids at green lag phase (up to 35 %), and other yield components (up to 25 %). In addition, a minor QTL for leaf area was found on chromosome 4 of the same parent. In contrast, only minor QTLs for berry acidity and leaf area could be found as moderately stable in Picovine. None of the transporters recently identified as mutated in low acidity apples or Cucurbits were included in the several hundreds of candidate genes underlying the above berry QTLs, which could be reduced to a few dozen candidate genes when a priori pertinent biological functions and organ specific expression were considered. [br/][b]Conclusions[/b] [br/]This study combining the use of microvine and a high throughput genotyping technology was innovative for grapevine genetics. It allowed the identification of 10 stable QTLs, including the first berry acidity QTLs reported so far in a Vitis vinifera intra-specific cross. Robustness of a set of QTLs was assessed with respect to temperature variatio

Metabolic effects of elevated temperature on organic acid degradation in ripening <em>Vitis vinifera</em> fruit

First published online: September 1, 2014Berries of the cultivated grapevine Vitis vinifera are notably responsive to temperature, which can influence fruit quality and hence the future compatibility of varieties with their current growing regions. Organic acids represent a key component of fruit organoleptic quality and their content is significantly influenced by temperature. The objectives of this study were to (i) manipulate thermal regimes to realistically capture warming-driven reduction of malate content in Shiraz berries, and (ii) investigate the mechanisms behind temperature-sensitive malate loss and the potential downstream effects on berry metabolism. In the field we compared untreated controls at ambient temperature with longer and milder warming (2-4 °C differential for three weeks; Experiment 1) or shorter and more severe warming (4-6 °C differential for 11 days; Experiment 2). We complemented field trials with control (25/15 °C) and elevated (35/20 °C) day/night temperature controlled-environment trials using potted vines (Experiment 3). Elevating maximum temperatures (4-10 °C above controls) during pre-véraison stages led to higher malate content, particularly with warmer nights. Heating at véraison and ripening stages reduced malate content, consistent with effects typically seen in warm vintages. However, when minimum temperatures were also raised by 4-6 °C, malate content was not reduced, suggesting that the regulation of malate metabolism differs during the day and night. Increased NAD-dependent malic enzyme activity and decreased phosphoenolpyruvate carboxylase and pyruvate kinase activities, as well as the accumulation of various amino acids and γ-aminobutyric acid, suggest enhanced anaplerotic capacity of the TCA cycle and a need for coping with decreased cytosolic pH in heated fruit.C. Sweetman, V. O. Sadras, R. D. Hancock, K. L. Soole and C. M. For

Heparan sulfate proteoglycans: structure, protein interactions and cell signaling

Heparan sulfate proteoglycans are ubiquitously found at the cell surface and extracellular matrix in all the animal species. This review will focus on the structural characteristics of the heparan sulfate proteoglycans related to protein interactions leading to cell signaling. The heparan sulfate chains due to their vast structural diversity are able to bind and interact with a wide variety of proteins, such as growth factors, chemokines, morphogens, extracellular matrix components, enzymes, among others. There is a specificity directing the interactions of heparan sulfates and target proteins, regarding both the fine structure of the polysaccharide chain as well precise protein motifs. Heparan sulfates play a role in cellular signaling either as receptor or co-receptor for different ligands, and the activation of downstream pathways is related to phosphorylation of different cytosolic proteins either directly or involving cytoskeleton interactions leading to gene regulation. The role of the heparan sulfate proteoglycans in cellular signaling and endocytic uptake pathways is also discussed.Proteoglicanos de heparam sulfato são encontrados tanto superfície celular quanto na matriz extracelular em todas as espécies animais. Esta revisão tem enfoque nas características estruturais dos proteoglicanos de heparam sulfato e nas interações destes proteoglicanos com proteínas que levam à sinalização celular. As cadeias de heparam sulfato, devido a sua variedade estrutural, são capazes de se ligar e interagir com ampla gama de proteínas, como fatores de crescimento, quimiocinas, morfógenos, componentes da matriz extracelular, enzimas, entreoutros. Existe uma especificidade estrutural que direciona as interações dos heparam sulfatos e proteínas alvo. Esta especificidade está relacionada com a estrutura da cadeia do polissacarídeo e os motivos conservados da cadeia polipeptídica das proteínas envolvidas nesta interação. Os heparam sulfatos possuem papel na sinalização celular como receptores ou coreceptores para diferentes ligantes. Esta ligação dispara vias de sinalização celular levam à fosforilação de diversas proteínas citosólicas ou com ou sem interações diretas com o citoesqueleto, culminando na regulação gênica. O papel dos proteoglicanos de heparam sulfato na sinalização celular e vias de captação endocítica também são discutidas nesta revisão.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Universidade Federal de São Paulo (UNIFESP) Departamento de BioquímicaUniversidade Federal de São Paulo (UNIFESP) Departamento de OftalmologiaUNIFESP, Depto. de BioquímicaUNIFESP, Depto. de OftalmologiaSciEL