Phenotype of barley <i>breviaristatum-e</i> (<i>ari-e</i>).

<p>(A) Comparison of overall plant height between the wild type cv. Bowman (left) and <i>ari-e</i>.<i>1</i> mutant NIL BW042 (right); scale bar: 10 cm (B) Spikes of barley lines Bowman, BW042 (<i>ari-e</i>.<i>1</i>), Maythorpe, Golden Promise (from left to right). Mutant lines are characterized by reduced awn length. (C) Seed shape of cvs. Maythorpe (left) and Golden Promise (right). (D) Gross morphology in the vegetative phase (from left to right: Bowman, BW042 (<i>ari-e</i>.<i>1</i>), Maythorpe, Golden Promise). Mutant lines appear more upright due to narrow leaf angles; scale bar: 10 cm.</p

Structure of the <i>HvDep1</i> gene and the encoded polypeptide.

<p>(A) Graphic representation of the barley whole genome shotgun contig bowman_contig_881907 comprising the <i>HvDep1</i> coding sequence. 500-bp intervals are indicated with vertical bars. The coding sequence is shown as black boxes. The <i>HvDep1</i> coding sequence consists of five exons and four introns. The <i>ari-e</i> mutant lines cv. Golden Promise and BW043 (<i>ari-e</i>.GP) show an insertion of a single nucleotide in exon 2 after bp 1508, and lines <i>ari-e</i>.<i>39</i>, <i>ari-e</i>.<i>156</i> and <i>ari-e</i>.<i>166</i> show a nucleotide exchange in exon 3 at bp 2007 after the ATG start codon (details shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0168924#pone.0168924.t003" target="_blank">Table 3</a>). (B) Putative functional domains in the 295 amino-acid HvDEP1 protein. Using TMPRED (<a href="http://ch.embnet.org/software/TMPRED_form.html" target="_blank">ch.embnet.org/software/TMPRED_form.html</a>) and PROSITE (expasy.ch/prosite) a transmembrane domain, a putative tumor necrosis factor receptor (TNFR) ⁄ nerve growth factor receptor (NGFR) family cysteine-rich signature and von Willebrand factor type C (VWFC) cysteine-rich modules were predicted for HvDEP1. In a previous study [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0168924#pone.0168924.ref007" target="_blank">7</a>] the Arabidopsis AGG3 γ-subunit was predicted to contain similar domains.</p

List of 11 agronomic, yield and yield related characters that were measured across 12 possible trial locations for the Derkado x B83-12/21/5 population.

<p>List of 11 agronomic, yield and yield related characters that were measured across 12 possible trial locations for the Derkado x B83-12/21/5 population.</p

Grain yield measured in field trials in Denmark.

<p>Values obtained for (A) grain number per plant and (B) grain weight per plant from field grown lines (summer 2014 in Denmark). The number of individuals considered for each line is given in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0168924#pone.0168924.t004" target="_blank">Table 4</a>. T-tests were performed to test for significant differences between respective wild type and mutant lines. Statistically significant differences are indicated by asterisks within the figure (threshold: * p < 0.05, ** p < 0.01, *** p < 0.001). Average values concerning grain number per plant and grain weight per plant respectively were 49.4% and 40.3% for BW042 and 51.7% and 39.7% for BW043 in comparison to Bowman and 81.6% and 66.7% for Golden Promise in comparison to Maythorpe.</p

Description <i>of breviaristatum-e</i> (<i>ari-e</i>) mutant lines.

<p>Description <i>of breviaristatum-e</i> (<i>ari-e</i>) mutant lines.</p

Complementation of <i>ari-e</i> in Golden Promise with full length and truncated forms of <i>HvDep1</i>.

<p>(A) and (B) Phenotype of Golden Promise, carrying the <i>ari-e</i>.GP loss-of-function allele, compared to (C) and (D) Golden Promise full-length pUBI:<i>HvDep1</i> transformants and (E) and (F) Golden Promise pUBI: <i>HvDep1</i>Δ152 transformants. In the later, only the first 152 amino-acid residues of HvDEP1 are translated. Plants with the pUBI: <i>HvDep1</i>Δ152 transformation developed very few spikes and no fertile seeds.</p

RD-Connect: an integrated platform connecting databases, registries, biobanks and clinical bioinformatics for rare disease research

<p><strong>Abstract:</strong></p> <p>Despite many examples of excellent practice, rare disease (RD) research is still frequently fragmented by data type and disease. Individual efforts often have little interoperability and almost no systematic connection of detailed clinical information with genetic information, biomaterial availability or research/trial datasets. Linking data at both an individual-patient and whole-cohort level enables researchers to gain a better overview of their disease of interest, while providing access to data from other research groups in a secure fashion allows researchers in multiple institutions to compare results and gain new insights. Funded by the EU Seventh Framework Programme under the International Rare Diseases Research Consortium (IRDiRC), RD-Connect is a global infrastructure project which links databases, registries, biobanks and clinical bioinformatics data used in RD research into a central research resource. RD-Connect’s primary objectives are:</p> <p>• Harmonisation and development of common standards for RD patient registries by developing a common registry infrastructure and data elements</p> <p>• Harmonisation and development of common standards and catalogue for RD biobanks that collect and provide standardised, quality-controlled biomaterials for translational research</p> <p>• Development of clinical bioinformatics tools for analysis and integration of molecular and clinical data to discover new disease genes, pathways and therapeutic targets</p> <p>• Development of an integrated platform to host and analyse data from omics research projects</p> <p>• Development of mechanisms for incorporating patient interests and engaging with stakeholders</p> <p>• Development of best ethical practices and a proposal for a regulatory framework for linking medical and personal data related to RD.</p> <p>RD-Connect will accept data generated by IRDiRC projects such as EURenOmics, which focuses on causes, diagnostics, biomarkers and disease models for rare kidney disorders, and Neuromics, which uses next generation whole exome sequencing to increase genetic knowledge of rare neurodegenerative and neuromuscular disorders. The “siloed” nature of individual research efforts is a continued bottleneck for cutting-edge research towards diagnosis and therapy development in RD. RD-Connect aims to unite existing infrastructures and integrate the latest tools in order to create a comprehensive combined omics data, biobanking, data analysis and patient registry platform for RD used by researchers across the world.</p

Phenotype of <i>ari-e</i> mutant lines in a cv. Foma genetic background.

<p>Barley lines Foma (A), <i>ari-e</i>.<i>119</i> (B), <i>ari-e</i>.<i>156</i> (C), <i>ari-e</i>.<i>166</i> (D), <i>ari-e</i>.<i>178</i> (E), <i>ari-e</i>.<i>222</i> (F), <i>ari-e</i>.<i>228</i> (G) during the vegetative growth phase when grown in the greenhouse. All pictures show three plants in one pot sown on the same day. Only <i>ari-e</i>.<i>119</i>, <i>ari-e</i>.<i>156</i> and <i>ari-e</i>.<i>166</i> show the characteristic erect phenotype of <i>ari-e</i> mutants and mutations in <i>HvDep1</i> were only found in these lines. Scale bar: 10 cm</p

QTL profiles for 12 agronomic and yield related characters for chromosome 5H from the Derkado x B83-12/21/5 map.

<p>QTL profiles for 12 agronomic and yield related characters for chromosome 5H from the Derkado x B83-12/21/5 map. The position of the <i>Ari-e</i>/<i>Dep1</i> locus is indicated by the solid vertical arrow and the flanking SNP markers by vertical dashed arrows. BOPA1 SNPs 11_20265 and 11_20392 are placed at position 48.38 cM in the barley draft assembly [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0168924#pone.0168924.ref031" target="_blank">31</a>]. The significance threshold (3.4) for a QTL in this population is indicated by the straight dashed horizontal line. SPW: Single Plant Weight of grain; TGW: Thousand Grain Weight; Spec_WT: specific grain weight [kg/hl]; MSW: Main Stem Weight, weight of grain from the tallest tiller of plants.</p

RD-Connect: first year review

<p>In its first year of operation, RD-Connect has successfully achieved its objectives for the period and has begun to establish its position as an important part of the global rare disease research infrastructure. Owing to the need to integrate with existing initiatives, the primary focus of the year has been on ensuring that RD-Connect activities are fully aligned with the needs of the associated projects that will submit data to the system, and on developing interoperability with related tools and projects operating in the same area.<br>Achievements include:<br>• Established strong collaborations with EURenOmics and Neuromics<br>• Incorporation of new associated partners involved in related work<br>• Representation on IRDiRC Scientific Committees and working groups has helped ensure harmonisation with IRDiRC activities<br>• The foundations for the integrated platform have been put in place, ensuring interoperability with other systems and meeting the requirements of IRDiRC projects generating omics data that will be linked with RD-Connect<br>• The first set of data from NeurOmics and EURenOmics will be uploaded in early 2014 after which time data from other IRDiRC projects may be accepted<br>• Various suites of clinical bioinformatics tools to extract knowledge from high throughput experiments, clinical databases and biobanks are being developed<br>• Extensive engagement with ontology developers and the associated projects has ensured that the submitted omics data will be accompanied by standardised phenotypic descriptions using HPO<br>• An extensive mapping exercise carried out jointly with the registry and biobanking WP has resulted in a list of patient registries and biobanks that will now be surveyed to establish their research focus, utility for research and invited to participate in RD-Connect activities<br>• Progress in evaluating the various options to implement a globally unique identifier<br>• Progress towards the development of the biobank catalogue, database structure and biobanking standards<br>• Proactive engagement with the ethical issues raised by omics experiments and patient data sharing<br>• Draft charter with principles and template for sharing and access to data</p> <p> </p