Search

Graphical abstract, Intron retention (IR) occurs when an intron is transcribed into pre-mRNA and remains in the final mRNA. An increasing body of literature has demonstrated a major role for IR in numerous biological functions and in disease. Here we give an overview of the different computational approaches for detecting IR events from sequencing data. We show that these are based on different biological and computational assumptions that may lead to dramatically different results. We describe the various approaches for mitigating errors in detecting intron retention and for discovering IR signatures between different conditions.

microRNAs are short RNAs that reduce gene expression by binding to their targets. The accurate prediction of microRNA targets is essential to understanding the function of microRNAs. Computational predictions indicate that all human genes may be regulated by microRNAs, with each microRNA possibly targeting thousands of genes. Here we discuss computational methods for identifying mammalian microRNA targets and refining them for further experimental validation. We describe microRNA target prediction resources and procedures and how they integrate with various types of experimental techniques that aim to validate them or further explore their function. We also provide a list of target prediction databases and explain how these are curated.

Over 6000 adult managers attending an assessment centre completed a battery of tests including a ‘bright side’ personality trait measure (NEO-PI-R); a ‘dark side’/disorders measure (HDS), an ability test (GMA) and also specified, in detail, how long it had been before they were promoted to a managerial role, and also, where appropriate to a senior managerial role. Correlation analyses showed shorter times to promotion were associated with low Neuroticism, high Extraversion, high Conscientiousness, and high Intelligence, as well as being high on Bold and Colourful, but low on Cautious, Reserved and Leisurely “dark side” traits. Regressions showed the higher-order, dark side factors named “Moving against” people positively, and “Away from” and “Moving toward” people negatively, were associated with promotions. Implications for the selection and management of people, as well as limitations of this study are considered.

Intron retention (IR) is widely recognized as a consequence of mis-splicing that leads to failed excision of intronic sequences from pre-messenger RNAs. Our bioinformatic analyses of transcriptomic and proteomic data of normal white blood cell differentiation reveal IR as a physiological mechanism of gene expression control. IR regulates the expression of 86 functionally related genes, including those that determine the nuclear shape that is unique to granulocytes. Retention of introns in specific genes is associated with downregulation of splicing factors and higher GC content. IR, conserved between human and mouse, led to reduced mRNA and protein levels by triggering the nonsense-mediated decay (NMD) pathway. In contrast to the prevalent view that NMD is limited to mRNAs encoding aberrant proteins, our data establish that IR coupled with NMD is a conserved mechanism in normal granulopoiesis. Physiological IR may provide an energetically favorable level of dynamic gene expression control prior to sustained gene translation. © 2013 Elsevier Inc.

International audience; The Alternative Splicing and Transcript Diversity database (ASTD) gives access to a vast collection of alternative transcripts that integrate transcription initiation, polyadenylation and splicing variant data. Alternative transcripts are derived from the mapping of transcribed sequences to the complete human, mouse and rat genomes using an extension of the computational pipeline developed for the ASD (Alternative Splicing Database) and ATD (Alternative Transcript Diversity) databases, which are now superseded by ASTD. For the human genome, ASTD identifies splicing variants, transcription initiation variants and polyadenylation variants in 68%, 68% and 62% of the gene set, respectively, consistent with current estimates for transcription variation. Users can access ASTD through a variety of browsing and query tools, including expression state-based queries for the identification of tissue-specific isoforms. Participating laboratories have experimentally validated a subset of ASTD-predicted alternative splice forms and alternative polyadenylation forms that were not previously reported. The ASTD database can be accessed at http://www.ebi.ac.uk/astd.

Low altitude sandy plains (machair) are a distinctive feature of the Atlantic coasts of the Scottish Outer Hebrides. They formed as a result of shoreward movement of sediment consequent upon a rise in Holocene sea levels. During the long period over which machair has been forming, the earliest date proposed for their human occupation is the Neolithic. The natural origins of the machair are not disputed, but examination of deposits at sites in the islands of Benbecula and Grimsay encourages us to advance a possible anthropogenic role in the process of machair development, and also to suggest that human involvement may date from the Mesolithic period (pre-5000 BP [ca. 5730 cal BP]), a time for which archaeological evidence is lacking from the Outer Hebrides. The presence of charcoal might suggest that burning of the vegetation cover of the machair was an additional factor to the supposedly dominant marine and aeolian processes in sand mobility. Removal of shrub vegetation may also have left sand surfaces open to deflation. There remains a difficulty in separating natural from human causes in investigations of long-term coastal evolution.

Objective : To determine the technical feasibility of sural nerve grafting for restoration of cavernous nerve continuity after radical retropubic prostatectomy by the laparoscopic approach. Materials and methods : 15 potent men (mean age: 56±4 years) underwent laparoscopic radical prostatectomy with deliberate wide uni- or bilateral neurovascular bundle resection. After prostatectomy, but before the vesicourethral anastomosis, an autologous sural nerve graft was interposed between the divided end of the cavernous nerves using a laparoscopic approach. Results : All 15 procedures could be completed laparoscopically. Visual cooptation between the nerve graft and the cut ends of the neurovascular bundles was possible in all 15 cases. Surgical time for the entire procedure ranged between 210 to 275 min with 30 to 60 min of this time required for the nerve harvest and graft. Conclusion : This experience demonstrates that sural nerve graft replacement is technically feasible by the laparoscopic approach. The magnified optics, bloodless surgical field, and improved instrumentation create an optimal environment for sural nerve grafting to the cut ends of the neurovascular bundles. Quality of life survey data at 12 to 18 month follow-up will be needed to assess functional return.

Aim To assess the technical performance of the NanoString nCounter platform by profiling microRNA (miRNA) in CML patients. Methods RNA (lOOng) from 75 peripheral blood mononuclear cell samples was analysed on the nCounter miRNA panel ( n = 800 probes) in seven batches. Samples were hybridised 12-19h. We used nSolver, R, GraphPad Prism and Normfinder software for normalisation and analysis. Results Ninety-eight miRNAs were expressed at >100 copies (invariant normalised, linear counts). These exhibited an inter-sample fold change >10, and maximum fold change 12,315. QC values were: positive control linearity R 2 = 0.99-1, binding density = 0.27-1.03 (acceptable 0.05-2.25) and imaging — 0.88-1 (acceptable >0.75). Replicate sample raw miRNA counts exhibited a high Spearman’s rank correlation coefficient — 0.8678, p 0.0001. Raw data batch effects resolved after invariant miRNA or cyclic loess normalisation. Hybridisation time affected neither background nor reaction efficiency. Discussion Sample processing is more complex for miRNA analysis than mRNA analysis on the NanoString nCounter platform. Nevertheless, normalisation abrogated inter-run differences. The applications of mRNA based diagnostics using NanoString have recently expanded to diverse cancers, but ours is a first attempt at establishing utility for miRNAs. We conclude that NanoString performance is sufficiently robust to explore this advanced RNA counting technology for diverse applications in pathology.

The Caminada-Moreau barrier headland of South Louisiana is a low-profile beach and dune coastline that is transgressing rapidly over the surfaces of the abandoned Lafourche delta complex. With the passage of cold fronts (10–30 times per year) and hurricanes (once every 4 yrs), overwash events occur year round with varying degrees of frequency, intensity and geomorphological modification. This coastline consists of washover and dune surfaces that respond rapidly to overwash impact. The fine sand stored in washover deposits is easily reworked by aeolian processes into a variety of dune forms in the shore-zone that are vegetated rapidly. Geomorphological changes vary according to the position, ground elevation, and surface stability of the dunes. Independent factors are overwash surge elevations, beach gradient and the presence of pre-existing landforms. For ten years detailed surveys supplemented by aerial photographs and videotape surveys have recorded these changes. The analysis of these information sources provides insight into both the general evolution of this distinctive coastline and also the geomorphological interaction of dunes, beaches and washover deposits in different physiographic settings.