Alliance of Genome Resources Portal: unified model organism research platform

The Alliance of Genome Resources (Alliance) is a consortium of the major model organism databases and the Gene Ontology that is guided by the vision of facilitating exploration of related genes in human and well-studied model organisms by providing a highly integrated and comprehensive platform that enables researchers to leverage the extensive body of genetic and genomic studies in these organisms. Initiated in 2016, the Alliance is building a central portal (www.alliancegenome.org) for access to data for the primary model organisms along with gene ontology data and human data. All data types represented in the Alliance portal (e.g. genomic data and phenotype descriptions) have common data models and workflows for curation. All data are open and freely available via a variety of mechanisms. Long-term plans for the Alliance project include a focus on coverage of additional model organisms including those without dedicated curation communities, and the inclusion of new data types with a particular focus on providing data and tools for the non-model-organism researcher that support enhanced discovery about human health and disease. Here we review current progress and present immediate plans for this new bioinformatics resource

Alliance of Genome Resources Portal: unified model organism research platform

The Alliance of Genome Resources (Alliance) is a consortium of the major model organism databases and the Gene Ontology that is guided by the vision of facilitating exploration of related genes in human and well-studied model organisms by providing a highly integrated and comprehensive platform that enables researchers to leverage the extensive body of genetic and genomic studies in these organisms. Initiated in 2016, the Alliance is building a central portal (www.alliancegenome.org) for access to data for the primary model organisms along with gene ontology data and human data. All data types represented in the Alliance portal (e.g. genomic data and phenotype descriptions) have common data models and workflows for curation. All data are open and freely available via a variety of mechanisms. Long-term plans for the Alliance project include a focus on coverage of additional model organisms including those without dedicated curation communities, and the inclusion of new data types with a particular focus on providing data and tools for the non-model-organism researcher that support enhanced discovery about human health and disease. Here we review current progress and present immediate plans for this new bioinformatics resource

Isolation and characterization of Staufen- and Barentsz- containing ribonucleoprotein particles from rat brain

Zweitveröffentlichung. Die Lokalisation von spezifischen mRNAs ist ein hochkonservierter Mechanismus, um die Expression bestimmter Gene posttranskriptional zu kontrollieren. Dadurch wird die räumlich und zeitlich regulierte Translation von Proteinen in subzellulären Kompartimenten ermöglicht. Die lokale Proteinsynthese ist essentiell für viele Vorgänge in der Entwicklung, spielt aber auch in reifen polarisierenden Zellen, einschließlich Neuronen und Gliazellen eine wichtige Rolle. Man nimmt an, dass die Lokalisierung bestimmter mRNAs in die Dendriten reifer Neurone und die anschließende lokale Proteinsynthese zu Veränderungen bei der synaptischen Plastizität führen und infolgedessen an Lern- und Gedächtnisvorgängen im Gehirn beteiligt sind. Für den Transport werden die lokalisierten mRNAs zunächst im Zellkern in Ribonukleoproteinpartikeln (RNPs) verpackt, exportiert und aktiv entlang des Zytoskeletts an den Ort ihrer Bestimmung befördert. Obwohl schon einige Komponenten der Transportmaschinerie identifiziert wurden, ist der zugrundeliegende molekulare Mechanismus der mRNA Lokalisation noch weitgehend unverstanden. In der vorliegenden Arbeit wurden anhand von drei etablierten Markerproteinen der mRNA Lokalisierung, Barentsz (Btz), Staufen 1 (Stau1) und Staufen 2 (Stau2), Transport-RNPs aus löslichem Rattenhirnextrakt isoliert und deren Zusammensetzung analysiert. Dabei wurde zunächst eine Methode etabliert, die es erlaubt, intakte, neuronale RNPs anzureichern und anschließend mit selbsthergestellten mono-spezifischen Antikörpern zu isolieren. Die Proteine der entsprechenden Transport-RNPs wurden über Massenspektrometrie identifiziert und bestimmte Kandidaten in einer umfangreichen Western Blot-Analyse validiert. Neben einer Vielzahl von RNA-Bindeproteinen, die in verschiedene Gruppen eingeteilt wurden, konnte dabei ein vollständiger Motorproteinkomplex (Kinesin-2) identifiziert werden. Außerdem wurde eine mögliche Protein-Protein Wechselwirkung zwischen Btz und der Casein Kinase II sowie eine RNA-abhängige Interaktion zwischen Stau2 und dem zipcode-Bindeprotein 1 charakterisiert. Zudem gelang der Nachweis von vier dendritisch lokalisierten mRNAs in den endogenen Btz- bzw. Stau2-RNPs mittels RT-PCR. Darüberhinaus ergaben erste Isolierungen von nukleären RNPs deutliche Unterschiede im Vergleich zu den zytoplasmatischen Komplexen. Durch die in dieser Arbeit etablierte Methode gelang der spezifische Nachweis von sowohl Proteinen, als auch von RNAs der RNPs. Somit ist ein erster wichtiger Schritt in Richtung der Entschlüsselung der Transportmaschinerie erfolgt. Diese Daten bilden die Grundlage für zahlreiche zukünftige Studien, die zu einem besseren Verständnis des Mechanismus der mRNA Lokalisation beitragen werden.mRNA localisation is a highly conserved mechanism to regulate the expression of specific genes at a posttranscriptional level. It serves to control both spatial and temporal protein expression at various subcellular sites. The resulting local protein synthesis is known to be required for various processes during development, but is also important in mature polarised cells, including neurons and glia. In neurons it is believed to contribute to the activity-induced plasticity of individual synapses and thus to learning and memory. Localised mRNAs are recognised by RNA binding proteins in the nucleus and cytoplasm and are packaged into ribonucleoproteinparticles (RNPs). After nuclear export RNPs are actively transported along the cytoskeleton to their final destination within the cell. Previous studies have revealed some components of the transport machinery but the underlying mechanism of mRNA localisation is still poorly understood. To elucidate the composition of RNA particles, three protein components of the transport machinery, Barentsz (Btz), Staufen 1 (Stau1) and Staufen 2 (Stau2), were used as molecular handles to isolate RNA transport granules from rat neuronal extracts. A two step isolation procedure was established. First, endogenous neuronal RNPs were biochemically enriched via gradient fractionation. Second, the respective endogenous RNPs were immunoprecipitated using high affinity mono-specific antibodies. Protein components were analysed via mass spectrometry followed by a comprehensive Western blot analyses. In addition to a number of RNA-binding proteins, a complete motor protein complex (Kinesin-2) was identified. Furthermore a putative new protein-protein interaction between Btz and the casein kinase II, as well as a novel RNA-mediated interaction between Stau2 and the zipcode binding protein 1 were characterized. Moreover four localised mRNAs were specifically isolated from endogenous Btz- and Stau2-RNPs. Additionally, preliminary experiments have revealed clear differences between nuclear and cytoplasmic neuronal Btz-, Stau1- and Stau2-RNPs, respectively. Using this biochemical purification method both proteins and RNAs were specifically isolated and identified from endogenous neuronal RNPs. This is a first and important step to elucidate the composition of the mRNA-transport machinery. Based on this data future functional studies will reveal further insight into the mechanism of mRNA localisation

Restriction-Spectrum Imaging of Bevacizumab-Related Necrosis in a Patient with GBM

Importance: With the increasing use of antiangiogenic agents in the treatment of high-grade gliomas, we are becoming increasingly aware of distinctive imaging findings seen in a subset of patients treated with these agents. Of particular interest is the development of regions of marked and persistent restricted diffusion. We describe a case with histopathologic validation, confirming that this region of restricted diffusion represents necrosis and not viable tumor. Observations: We present a case report of a 52-year-old man with GBM treated with temozolomide, radiation, and concurrent bevacizumab following gross total resection. The patient underwent sequential MRI’s which included restriction-spectrum imaging (RSI), an advanced diffusion-weighted imaging (DWI) technique, and MR perfusion. Following surgery, the patient developed an area of restricted diffusion on RSI which became larger and more confluent over the next several months. Marked signal intensity on RSI and very low cerebral blood volume (CBV) on MR perfusion led us to favor bevacizumab-related necrosis over recurrent tumor. Subsequent histopathologic evaluation confirmed coagulative necrosis. Conclusion and Relevance: Our report increases the number of pathologically proven cases of bevacizumab-related necrosis in the literature from three to four. Furthermore, our case demonstrates this phenomenon on RSI, which has been shown to have good sensitivity to restricted diffusion

Differential retinoic acid signaling in tumors of long- and short-term glioblastoma survivors

Although the prognosis of most glioblastoma patients is poor, 3%-5% patients show long-term survival of 36 months or longer after diagnosis. To study the differences in activation of biochemical pathways, we performed mRNA and protein expression analyses of primary glioblastoma tissues from 11 long-term survivors (LTS; overall survival ≥ 36 months) and 12 short-term survivors (STS; overall survival ≤ 6 months). The mRNA expression ratio of the retinoic acid transporters fatty acid-binding protein 5 (FABP5) and cellular retinoic acid-binding protein 2 (CRABP2), which regulate the differential delivery of retinoic acid to either antioncogenic retinoic acid receptors or prooncogenic nuclear receptor peroxisome proliferator-activated receptor delta, was statistically significantly higher in the tumor tissues of STS than those of LTS (median ratio in STS tumors = 3.64, 10th-90th percentile = 1.43-4.54 vs median ratio in LTS tumors = 1.42, 10th-90th percentile = −0.98 to 2.59; P < .001). High FABP5 protein expression in STS tumors was associated with highly proliferating tumor cells and activation of 3-phosphoinositide-dependent protein kinase-1 and v-akt murine thymoma viral oncogene homolog. The data suggest that retinoic acid signaling activates different targets in glioblastomas from LTS and STS. All statistical tests were two-side

Making Linked Data SPARQL with the InterMine Biological Data Warehouse

Abstract. InterMine is a system for integrating, analysing, and republishing biological data from multiple sources. It provides access to these data via a web user interface and programmatic web services. However, the precise invocation of services and subsequent exploration of returned data require substantial expertise on the structure of the underlying database. Here, we describe an approach that uses Semantic Web technologies to make InterMine data more broadly accessible and reusable, in accordance with the FAIR principles. We describe a pipeline to extract, transform, and load a Linked Data representation of the InterMine store. We use Docker to bring together SPARQL-aware applications to search, browse, explore, and query the InterMine-based data. Our work therefore extends interoperability of the InterMine platform, and supports new query functionality across InterMine installations and the network of open Linked Data

<i>Nos2</i> deficiency increases the incidence of MB in <i>Ptch1</i>^+/− mice.

<p>(A) Kaplan-Meier analysis of MB incidence in 215 <i>Ptch1</i>^+/−<i>Nos2</i>^+/+ mice (orange line) versus 221 <i>Ptch1</i>^+/−<i>Nos2</i>^−/− mice (red line). <i>Ptch1</i>^+/−<i>Nos2</i>^−/− mice demonstrated an approximately two-fold increase in MB incidence (p = 0.0007, Logrank test). None of 315 wild-type (green line) and 412 <i>Ptch1</i>^+/+<i>Nos2</i>^−/−mice (blue line) (control littermates) developed any MB. Vertical ticks represent censored mice. (B–E) Histological features of MBs from <i>Ptch1</i>^+/−<i>Nos2</i>^+/+ and <i>Ptch1</i>^+/−<i>Nos2</i>^−/− mice. MBs in both genotypes (B–C, <i>Ptch1</i>^+/−<i>Nos2</i><b>^+/+</b>; D–E, <i>Ptch1</i>^+/−<i>Nos2</i>^−/−) were densely cellular primitive neuroectodermal tumors of the cerebellum corresponding histologically to the classic subtype of human MB. Hematoxylin eosin-stained sections showed no obvious differences between the genotypes concerning gross growth pattern, with well demarcated growth in the cerebellar cortex (B, D, scale bar = 500 µm), and cellular morphology (C, E, scale bar = 50 µm).</p