Alternative Splicing Events Are a Late Feature of Pathology in a Mouse Model of Spinal Muscular Atrophy

Spinal muscular atrophy is a severe motor neuron disease caused by inactivating mutations in the SMN1 gene leading to reduced levels of full-length functional SMN protein. SMN is a critical mediator of spliceosomal protein assembly, and complete loss or drastic reduction in protein leads to loss of cell viability. However, the reason for selective motor neuron degeneration when SMN is reduced to levels which are tolerated by all other cell types is not currently understood. Widespread splicing abnormalities have recently been reported at end-stage in a mouse model of SMA, leading to the proposition that disruption of efficient splicing is the primary mechanism of motor neuron death. However, it remains unclear whether splicing abnormalities are present during early stages of the disease, which would be a requirement for a direct role in disease pathogenesis. We performed exon-array analysis of RNA from SMN deficient mouse spinal cord at 3 time points, pre-symptomatic (P1), early symptomatic (P7), and late-symptomatic (P13). Compared to littermate control mice, SMA mice showed a time-dependent increase in the number of exons showing differential expression, with minimal differences between genotypes at P1 and P7, but substantial variation in late-symptomatic (P13) mice. Gene ontology analysis revealed differences in pathways associated with neuronal development as well as cellular injury. Validation of selected targets by RT–PCR confirmed the array findings and was in keeping with a shift between physiologically occurring mRNA isoforms. We conclude that the majority of splicing changes occur late in SMA and may represent a secondary effect of cell injury, though we cannot rule out significant early changes in a small number of transcripts crucial to motor neuron survival

SMN deficiency disrupts brain development in a mouse model of severe spinal muscular atrophy

Reduced expression of the survival motor neuron (SMN) gene causes the childhood motor neuron disease spinal muscular atrophy (SMA). Low levels of ubiquitously expressed SMN protein result in the degeneration of lower motor neurons, but it remains unclear whether other regions of the nervous system are also affected. Here we show that reduced levels of SMN lead to impaired perinatal brain development in a mouse model of severe SMA. Regionally selective changes in brain morphology were apparent in areas normally associated with higher SMN levels in the healthy postnatal brain, including the hippocampus, and were associated with decreased cell density, reduced cell proliferation and impaired hippocampal neurogenesis. A comparative proteomics analysis of the hippocampus from SMA and wild-type littermate mice revealed widespread modifications in expression levels of proteins regulating cellular proliferation, migration and development when SMN levels were reduced. This study reveals novel roles for SMN protein in brain development and maintenance and provides the first insights into cellular and molecular pathways disrupted in the brain in a severe form of SMA

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

A Comparison of Methods to Analyze Aquatic Heterotrophic Flagellates of Different Taxonomic Groups

Heterotrophic flagellates contribute significantly to the matter flux in aquatic and terrestrial ecosystems. Still today their quantification and taxonomic classification bear several problems in field studies, though these methodological problems seem to be increasingly ignored in current ecological studies. Here we describe and test different methods, the live-counting technique, different fixation techniques, cultivation methods like the liquid aliquot method (LAM), and a molecular single cell survey called aliquot PCR (aPCR). All these methods have been tested either using aquatic field samples or cultures of freshwater and marine taxa. Each of the described methods has its advantages and disadvantages, which have to be considered in every single case. With the live-counting technique a detection of living cells up to morphospecies level is possible. Fixation of cells and staining methods are advantageous due to the possible long-term storage and observation of samples. Cultivation methods (LAM) offer the possibility of subsequent molecular analyses, and aPCR tools might complete the deficiency of LAM in terms of the missing detection of non-cultivable flagellates. In summary, we propose a combination of several investigation techniques reducing the gap between the different methodological problems. (C) 2017 Elsevier GmbH. All rights reserved

NeurOmics: -omics research for diagnosis and therapy in rare neuromuscular and neurodegenerative diseases – an EU funded FP7 project

<p>Neuromics is an EU-funded translational research project which has the primary aim of greatly improving understanding of neuromuscular and neurodegenerative diseases. The research will study around 1100 exomes from undiagnosed patients in its aim to discover novel disease-causing and disease-modifying genes and to identify potential new therapeutic targets. Partners have also undertaken deep-phenotyping of patients using human phenotype ontology (HPO) terms. Agreements are in place to allow the secure sharing of this standardised clinical information along with WES and other –omics data both within Neuromics and with the wider rare-disease field. This will encourage collaborative partnerships and speed progress towards therapeutic and diagnostic breakthrough and improvements in care for patients. The project focusses on 10 rare, genetic neuromuscular and neurodegenerative disease groups: frontotemporal lobe degeneration; Huntington’s disease; ataxia; hereditary spastic paraplegia; spinal muscular atrophy; hereditary motor neuropathy; congenital myasthenic syndrome; muscular dystrophy and muscular channelopathy. The project brings together the leading research groups in Europe, five highly innovative SMEs and overseas experts to work together using the most sophisticated -omics technologies employing genomics, transcriptomics, proteomics and metabolomics.</p> <p>The consortium is coordinated by Olaf Riess at Tübingen University, Brunhilde Wirth at Cologne University and Gert-Jan van Ommen at Leiden University. Neuromics is working closely with RD-Connect, the rare-disease platform, in order to develop a global infrastructure for the wide sharing of research outputs of Neuromics, and other rare disease projects.</p> <p>At the end of its first year of activity, this poster describes the aims and methods used in the Neuromics project and reports on progress made so far. It highlights how Neuromics will contribute significantly to the ambitious goals of the International Rare Diseases Research Consortium (IRDiRC): deciphering the genetic causes of all rare diseases and the development of 200 new therapies by 2020.</p