miRanalyzer: an update on the detection and analysis of microRNAs in high-throughput sequencing experiments

We present a new version of miRanalyzer, a web server and stand-alone tool for the detection of known and prediction of new microRNAs in high-throughput sequencing experiments. The new version has been notably improved regarding speed, scope and available features. Alignments are now based on the ultrafast short-read aligner Bowtie (granting also colour space support, allowing mismatches and improving speed) and 31 genomes, including 6 plant genomes, can now be analysed (previous version contained only 7). Differences between plant and animal microRNAs have been taken into account for the prediction models and differential expression of both, known and predicted microRNAs, between two conditions can be calculated. Additionally, consensus sequences of predicted mature and precursor microRNAs can be obtained from multiple samples, which increases the reliability of the predicted microRNAs. Finally, a stand-alone version of the miRanalyzer that is based on a local and easily customized database is also available; this allows the user to have more control on certain parameters as well as to use specific data such as unpublished assemblies or other libraries that are not available in the web server. miRanalyzer is available at http://bioinfo2.ugr.es/miRanalyzer/miRanalyzer.php.The Ministry of Innovation and Science of the Spanish Government (BIO2010-20219 to M.H.); the Junta de Andalucia (P07FQM3163 to M.H.); the ‘Juan de la Cierva’ fellowship (to M.H.); the Department of Industry, Tourism and Trade of the Government of the Autonomous Community of the Basque Country (Etortek Research Programs 2009/20011 to A.M.A.); from the Innovation Technology Department of the Bizkaia County (to A.M.A.). Funding for open access charge: Department of Industry, Tourism and Trade of the Government of the Autonomous Community of the Basque Country (Etortek Research Programs 2009/2011 to A.M.A.)

Transport of Proteins into Mitochondria

The mitochondrial ADP/ATP carrier is an integral transmembrane protein of the inner membrane. It is synthesized on cytoplasmic ribosomes. Kinetic data suggested that this protein is transferred into mitochondria in a posttranslational manner. The following results provide further evidence for such a mechanism and provide information on its details. 1. In homologous and heterologous translation systems the newly synthesized ADP/ATP carrier protein is present in the postribosomal supernatant. 2. Analysis by density gradient centrifugation and gel filtration shows, that the ADP/ATP carrier molecules in the postribosomal fraction are present as soluble complexes with apparent molecular weights of about 120000 and 500000 or larger. The carrier binds detergents such as Triton X-100 and deoxycholate forming mixed micelles with molecular weights of about 200000–400000. 3. Incubation of a postribosomal supernatant of a reticulocyte lysate containing newly synthesized ADP/ATP carrier with mitochondria isolated from Neurospora spheroplasts results in efficient transfer of the carrier into mitochondria. About 20–30% of the transferred carrier are resistant to proteinase in whole mitochondria. The authentic mature protein is also largely resistant to proteinase in whole mitochondria and sensitive after lysis of mitochondria with detergent. Integrity of mitochondria is a prerequisite for translocation into proteinase resistant position. 4. The transfer in vitro into a proteinase-resistant form is inhibited by the uncoupler carbonyl-cyanide m-chlorophenylhydrazone but not the proteinase-sensitive binding. These observations suggest that the posttranslational transfer of ADP/ATP carrier occurs via the cytosolic space through a soluble oligomeric precursor form. This precursor is taken up by intact mitochondria into an integral position in the membrane. These findings are considered to be of general importance for the intracellular transfer of insoluble membrane proteins. They support the view that such proteins can exist in a water-soluble form its precursors and upon integration into the membrane undergo a conformational change. Uptake into the membrane may involve the cleavage of an additional sequence in some proteins, but this appears not to be a prerequisite as demonstrated by the ADP/ATP carrier protein

Different Transport Pathways of Individual Precursor Proteins in Mitochondria

Transport of mitochondrial precursor proteins into mitochondria of Neurospora crassa was studied in a cellfree reconstituted system. Precursors were synthesized in a reticulocyte lysate programmed with Neurospora mRNA and transported into isolated mitochondria in the absence of protein synthesis. Uptake of the following precursors was investigated: apocytochrome c, ADP/ATP carrier and subunit 9 of the oligomycin-sensitive ATPase. Addition of high concentrations of unlabelled chemically prepared apocytochrome c (1–10 μM) inhibited the appearance in the mitochondrial of labelled cytochrome c synthesized in vitro because the unlabelled protein dilutes the labelled one and because the translocation system has a limited capacity [apparent V is 1–3 pmol × min−1× (mg mitochondrial protein)−1]. Concentrations of added apocytochrome c exceeding the concentrations of precursor proteins synthesized in vitro by a factor of about 104 did not inhibit the transfer of ADP/ATP carrier or ATPase subunit 9 into mitochondria. Carbonylcyanide m-chlorophenylhydrazone, an uncoupler of oxidative phosphorylation, inhibited transfer in vitro of ADP/ATP carrier and of ATPase subunit 9, but not of cytochrome c. These findings suggest that cytochrome c and the other two proteins have different import pathways into mitochondria. It can be inferred from the data presented that different 'receptors' on the mitochondrial surface mediate the specific recognition of precursor proteins by mitochondria as a first step in the transport process

The infrared supernova rate in starburst galaxies

We report the results of our ongoing search for extincted supernovae (SNe) at near-infrared wavelengths. We have monitored at 2.2 micron a sample of 46 Luminous Infrared Galaxies and detected 4 SNe. The number of detections is still small but sufficient to provide the first estimate of supernova rate at near-infrared wavelengths. We measure a SN rate ofv 7.6+/-3.8 SNu which is an order of magnitude larger than observed in quiescent galaxies. On the other hand, the observed near-infrared rate is still a factor 3-10 smaller than that estimated from the far-infrared luminosity of the galaxies. Among various possibilities, the most likely scenario is that dust extinction is so high (Av>30) to obscure most SNe even in the near-IR. The role of type Ia SNe is also discussed within this context. We derive the type Ia SN rate as a function of the stellar mass of the galaxy and find a sharp increase toward galaxies with higher activity of star formation. This suggests that a significant fraction of type Ia SNe are associated with young stellar populations. Finally, as a by-product, we give the average K-band light curve of core-collapse SNe based on all the existing data, and review the relation between SN rate and far-infrared luminosity.Comment: A&A, in press, 13 page

CG dinucleotide clustering is a species-specific property of the genome

Cytosines at cytosine-guanine (CG) dinucleotides are the near-exclusive target of DNA methyltransferases in mammalian genomes. Spontaneous deamination of methylcytosine to thymine makes methylated cytosines unusually susceptible to mutation and consequent depletion. The loci where CG dinucleotides remain relatively enriched, presumably due to their unmethylated status during the germ cell cycle, have been referred to as CpG islands. Currently, CpG islands are solely defined by base compositional criteria, allowing annotation of any sequenced genome. Using a novel bioinformatic approach, we show that CG clusters can be identified as an inherent property of genomic sequence without imposing a base compositional a priori assumption. We also show that the CG clusters co-localize in the human genome with hypomethylated loci and annotated transcription start sites to a greater extent than annotations produced by prior CpG island definitions. Moreover, this new approach allows CG clusters to be identified in a species-specific manner, revealing a degree of orthologous conservation that is not revealed by current base compositional approaches. Finally, our approach is able to identify methylating genomes (such as Takifugu rubripes) that lack CG clustering entirely, in which it is inappropriate to annotate CpG islands or CG clusters

Lifetime measurements of the low-lying excited states of ²⁰⁸Po

In this study we present the preliminary results about the lifetimes of the 2₂⁺, 4₁⁺ states of ²⁰⁸Po and the upper limit of the lifetime of the 2₁⁺ state. For measuring the lifetimes of the 2₁⁺ and 4₁⁺ states the Recoil Distance Doppler Shift (RDDS) method and for the lifetime of the 2₂⁺ state the Doppler Shift Attenuation method (DSAM) were used. The resulting absolute transition strength B(M1 ; 2₂⁺ → 2₁⁺) ≥ 0.122(20) μN² reveals the predominant isovector nature of the 2₂⁺ state of ²⁰⁸Po

MethylExtract: High-Quality methylation maps and SNV calling from whole genome bisulfite sequencing data

[v2; ref status: indexed, http://f1000r.es/301]Whole genome methylation profiling at a single cytosine resolution is now feasible due to the advent of high-throughput sequencing techniques together with bisulfite treatment of the DNA. To obtain the methylation value of each individual cytosine, the bisulfite-treated sequence reads are first aligned to a reference genome, and then the profiling of the methylation levels is done from the alignments. A huge effort has been made to quickly and correctly align the reads and many different algorithms and programs to do this have been created. However, the second step is just as crucial and non-trivial, but much less attention has been paid to the final inference of the methylation states. Important error sources do exist, such as sequencing errors, bisulfite failure, clonal reads, and single nucleotide variants. We developed MethylExtract, a user friendly tool to: i) generate high quality, whole genome methylation maps and ii) detect sequence variation within the same sample preparation. The program is implemented into a single script and takes into account all major error sources. MethylExtract detects variation (SNVs – Single Nucleotide Variants) in a similar way to VarScan, a very sensitive method extensively used in SNV and genotype calling based on non-bisulfite-treated reads. The usefulness of MethylExtract is shown by means of extensive benchmarking based on artificial bisulfite-treated reads and a comparison to a recently published method, called Bis-SNP. MethylExtract is able to detect SNVs within High-Throughput Sequencing experiments of bisulfite treated DNA at the same time as it generates high quality methylation maps. This simultaneous detection of DNA methylation and sequence variation is crucial for many downstream analyses, for example when deciphering the impact of SNVs on differential methylation. An exclusive feature of MethylExtract, in comparison with existing software, is the possibility to assess the bisulfite failure in a statistical way. The source code, tutorial and artificial bisulfite datasets are available at http://bioinfo2.ugr.es/MethylExtract/ and http://sourceforge.net/projects/methylextract/, and also permanently accessible from 10.5281/zenodo.7144.This work was supported by the Spanish Government [BIO2008-01353 to JLO and BIO2010-20219 to MH], and Basque country 'AE' grant (GB)

Analysis of Transposon Interruptions Suggests Selection for L1 Elements on the X Chromosome

It has been hypothesised that the massive accumulation of L1 transposable elements on the X chromosome is due to their function in X inactivation, and that the accumulation of Alu elements near genes is adaptive. We tested the possible selective advantage of these two transposable element (TE) families with a novel method, interruption analysis. In mammalian genomes, a large number of TEs interrupt other TEs due to the high overall abundance and age of repeats, and these interruptions can be used to test whether TEs are selectively neutral. Interruptions of TEs, which are beneficial for the host, are expected to be deleterious and underrepresented compared with neutral ones. We found that L1 elements in the regions of the X chromosome that contain the majority of the inactivated genes are significantly less frequently interrupted than on the autosomes, while L1s near genes that escape inactivation are interrupted with higher frequency, supporting the hypothesis that L1s on the X chromosome play a role in its inactivation. In addition, we show that TEs are less frequently interrupted in introns than in intergenic regions, probably due to selection against the expansion of introns, but the insertion pattern of Alus is comparable to other repeats

Methodology of evaluation of morphology of the spine and the trunk in idiopathic scoliosis and other spinal deformities - 6th SOSORT consensus paper

<p>Abstract</p> <p>Background</p> <p>Comprehensive evaluation of the morphology of the spine and of the whole body is essential in order to correctly manage patients suffering from progressive idiopathic scoliosis. Although methodology of clinical and radiological examination is well described in manuals of orthopaedics, there is deficit of data which clinical and radiological parameters are considered in everyday practise. Recently, an increasing tendency to extend scoliosis examination beyond the measure of the Cobb angle can be observed, reflecting a more patient-oriented approach. Such evaluation often involves surface parameters, aesthetics, function and quality of life.</p> <p>Aim of the study</p> <p>To investigate current recommendations of experts on methodology of evaluation of the patient with spinal deformity, essentially idiopathic scoliosis.</p> <p>Methods</p> <p>Structured Delphi procedure for collecting and processing knowledge from a group of experts with a series of questionnaires and controlled opinion feedback was performed. Experience and opinions of the professionals - physicians and physiotherapists managing scoliosis patients - were studied. According to Delphi method a Meeting Questionnaire (MQ) has been developed, resulting from a preliminary Pre-Meeting Questionnaire (PMQ) which had been previously discussed and approved on line. The MQ was circulated among the SOSORT experts during Consensus Session on "Measurements" which took place at the Annual Meeting of the Society, totally 23 panellists being engaged. Clinical, radiological and surface topography parameters were checked for agreement.</p> <p>Results</p> <p>90% agreement or more was reached in 35 items and superior than 75% agreement was reached in further 25 items. An evaluation form was proposed to be used by clinicians and researchers.</p> <p>Conclusion</p> <p>The consensus was reached on evaluation of the morphology of the patient with idiopathic scoliosis, comprising clinical, radiological and, to less extend, surface topography assessment. Considering the variety of parameters indicated by the panellists, the Cobb angle, yet the gold standard, can be seen neither as the unique nor the only decisive parameter in the management of patients with idiopathic scoliosis.</p