NGSmethDB: a database for next-generation sequencing single-cytosine-resolution DNA methylation data

Next-generation sequencing (NGS) together with bisulphite conversion allows the generation of whole genome methylation maps at single-cytosine resolution. This allows studying the absence of methylation in a particular genome region over a range of tissues, the differential tissue methylation or the changes occurring along pathological conditions. However, no database exists fully addressing such requirements. We propose here NGSmethDB (http://bioinfo2.ugr.es/NGSmethDB/gbrowse/) for the storage and retrieval of methylation data derived from NGS. Two cytosine methylation contexts (CpG and CAG/CTG) are considered. Through a browser interface coupled to a MySQL backend and several data mining tools, the user can search for methylation states in a set of tissues, retrieve methylation values for a set of tissues in a given chromosomal region, or display the methylation of promoters among different tissues. NGSmethDB is currently populated with human, mouse and Arabidopsis data, but other methylomes will be incorporated through an automatic pipeline as soon as new data become available. Dump downloads for three coverage levels (1, 5 or 10 reads) are available. NGSmethDB will be useful for experimental researchers, as well as for bioinformaticians, who might use the data as input for further research

WordCluster: detecting clusters of DNA words and genomic elements

<p>Abstract</p> <p>Background</p> <p>Many <it>k-</it>mers (or DNA words) and genomic elements are known to be spatially clustered in the genome. Well established examples are the genes, TFBSs, CpG dinucleotides, microRNA genes and ultra-conserved non-coding regions. Currently, no algorithm exists to find these clusters in a statistically comprehensible way. The detection of clustering often relies on densities and sliding-window approaches or arbitrarily chosen distance thresholds.</p> <p>Results</p> <p>We introduce here an algorithm to detect clusters of DNA words (<it>k-</it>mers), or any other genomic element, based on the distance between consecutive copies and an assigned statistical significance. We implemented the method into a web server connected to a MySQL backend, which also determines the co-localization with gene annotations. We demonstrate the usefulness of this approach by detecting the clusters of CAG/CTG (cytosine contexts that can be methylated in undifferentiated cells), showing that the degree of methylation vary drastically between inside and outside of the clusters. As another example, we used <it>WordCluster </it>to search for statistically significant clusters of olfactory receptor (OR) genes in the human genome.</p> <p>Conclusions</p> <p><it>WordCluster </it>seems to predict biological meaningful clusters of DNA words (<it>k-</it>mers) and genomic entities. The implementation of the method into a web server is available at <url>http://bioinfo2.ugr.es/wordCluster/wordCluster.php</url> including additional features like the detection of co-localization with gene regions or the annotation enrichment tool for functional analysis of overlapped genes.</p

Reassessment of miRNA variant (isomiRs) composition by small RNA sequencing

IsomiRs, sequence variants of maturemicroRNAs, are usually detected and quantified using high-throughput sequencing. Many examples of their biological relevance have been reported, but sequencing artifacts identified as artificial variants might bias biological inference and therefore need to be ideally avoided. We conducted a comprehensive evaluation of 10 different small RNA sequencing protocols, exploring both a theoretically isomiR-free pool of synthetic miRNAs and HEK293T cells. We calculated that, with the exception of two protocols, less than 5% of miRNA reads can be attributed to library preparation artifacts. Randomizedend adapter protocols showed superior accuracy, with 40% of true biological isomiRs. Nevertheless, we demonstrate concordance across protocols for selected miRNAs in non-templated uridyl additions. Notably, NTA-U calling and isomiR target prediction can be inaccurate when using protocols with poor single-nucleotide resolution. Our results highlight the relevance of protocol choice for biological isomiRs detection and annotation, which has key potential implications for biomedical applications

ALFA: First Operational Experience of the MPE/MPIA Laser Guide Star System for Adaptive Optics

The sodium laser guide star adaptive optics system ALFA has been constructed at the Calar Alto 3.5-m telescope. Following the first detection of the laser beacon on the wavefront sensor in 1997 the system is now being optimized for best performance. In this contribution we discuss the current status of the launch beam and the planned improvements and upgrades. We report on the performance level achieved when it is used with the adaptive optics system, and relate various aspects of our experience during operation of the system. We have begun to produce scientific results and mention two of these.Comment: 9 pages, 6 figures, LaTeX (spie.sty). SPIE conf proc 3353, Adaptive Optical System Technologies, March 199

Severe intimate partner violence affecting both young and elderly patients of both sexes

Background Intimate partner violence (IPV) affects 25-35 % of women and men in Western countries. Despite the high prevalence of IPV among trauma patients, very little is known about the associated injuries. Most previous studies excluded male victims and IPV is often limited to violence against women. Few reports on IPV among elderly patients exist. Methods We examined self-reports of IPV among patients at two major trauma centers of the Helsinki Central Hospital in Finland. Based on previous studies, we hypothesized that we would find the most severe injuries among young and middle-aged women. Results We identified 29 patients with a total of 105 injuries; patients typically presented with multiple injuries. Half of all patients required hospitalization or surgery. Contrary to previous studies, 17 % of our cohort were male, while 17 % of patients were 65 years or older. We found that 40 % of male victims presented with a New Injury Severity Score (NISS) over 15, indicating severe trauma. Two elderly patients presented with an NISS of 27, the highest in our study. Conclusions IPV leads to severe injury across all age groups among both male and female patients. The injury mechanism should be clearly defined for all trauma patients, keeping IPV in mind as a potential cause despite patient age or gender.Peer reviewe

A Mechanism-Based Approach to Life Prediction for a Nickel-Base Alloy subjected to Cyclic and Creep-Fatigue

A large number of damage parameters have been proposed to estimate cyclic fatigue life predominantly at ambient temperatures. However, especially in aerospace and automotive industry fatigue models with a wide temperature application range are required. Here, the regimes of high temperature creep-fatigue and nonisothermal thermo-mechanical fatigue are of particular interest. Within the present work a new mechanism-based life prediction approach is proposed for a nickel-base superalloy. The ability of the model to describe fatigue at low, intermediate, and also at high temperatures is investigated. Isothermal, as well as non-isothermal loading conditions are considered. The enhanced model formulation is based on the micro crack growth parameter Z d introduced by Heitmann et al. (1984). The model incorporates a threshold concept and corrections for mean stress and creep effects. In addition the detrimental effects caused by oxygen-induced embrittlement of the near tip region are accounted for by a parabolic oxidation approach. Test data from literature is used to compare the proposed model to several other fatigue models. Basis for all life prediction approaches under investigation is the stress-strain response of the material obtained by finite element analysis. Therefore, an inelastic constitutive model is applied. The fatigue model accuracy is evaluated on a statistical basis through an evaluation of the variance in the ratio of predicted life to actual life. This is done for the entire test database as well as for subsets, like isothermal, thermo-mechanical, and dwell tests only

Visual outcome measures in pediatric myelin oligodendrocyte glycoprotein antibody-associated disease (MOGAD)

BACKGROUND: Myelin oligodendrocyte glycoprotein antibody-associated disease (MOGAD) comprises various age-dependent clinical phenotypes and may be monophasic, multiphasic, or chronic. Optic neuritis (ON) is a common manifestation and frequently appears in combination with other MOGAD phenotypes, particularly in young children. Despite permanent structural damage to the retinal nerve fiber layer (RNFL), children often experience complete visual recovery. AIMS: To analyze the progression and impact of MOGAD on the visual system of pediatric patients independently of the history of ON. METHODS: This retrospective study included children who met specific criteria: myelin oligodendrocyte glycoprotein (MOG) immunoglobulin G (IgG) seropositivity, acute presentation of MOGAD, and written general consent. Main outcome measures were global peripapillary retinal nerve fiber layer (pRNFL) thickness, and near and distance visual acuity, analyzed using descriptive statistics. RESULTS: We identified 10 patients with median age of 7.7 years at first event: 7 patients manifested with acute disseminated encephalomyelitis (ADEM) (with ON 5/7, ADEM only 1/7, with transverse myelitis (TM) 1/7), 2 with isolated ON, and 1 patient with neuromyelitis optica spectrum disorder (NMOSD)-like phenotype with ON. Among ON patients, 5/8 were affected bilaterally, with 3 initially diagnosed with unilateral ON but experiencing subsequent involvement of the fellow eye. None of the patients without previous ON showed a deterioration of visual acuity and, if evaluated, a reduction of the pRNFL. CONCLUSION: Most pediatric MOGAD-ON patients in our cohort presented with acute vison loss and optic disc edema. All patients achieved complete visual recovery, independent of number of relapses or initial visual loss. The pRNFL thickness decreased for several months and stabilized at reduced levels after 12 months in the absence of further relapses. MOGAD may not have subclinical/'silent' effects on the visual system, as visual acuity and pRNFL were not affected in patients without ON

Decoding Gene Expression Signatures Underlying Vegetative to Inflorescence Meristem Transition in the Common Bean

The tropical common bean (Phaseolus vulgaris L.) is an obligatory short-day plant that requires relaxation of the photoperiod to induce flowering. Similar to other crops, photoperiod-induced floral initiation depends on the differentiation and maintenance of meristems. In this study, the global changes in transcript expression profiles were analyzed in two meristematic tissues corresponding to the vegetative and inflorescence meristems of two genotypes with different sensitivities to photoperiods. A total of 3396 differentially expressed genes (DEGs) were identified, and 1271 and 1533 were found to be up-regulated and down-regulated, respectively, whereas 592 genes showed discordant expression patterns between both genotypes. Arabidopsis homologues of DEGs were identified, and most of them were not previously involved in Arabidopsis floral transition, suggesting an evolutionary divergence of the transcriptional regulatory networks of the flowering process of both species. However, some genes belonging to the photoperiod and flower development pathways with evolutionarily conserved transcriptional profiles have been found. In addition, the flower meristem identity genes APETALA1 and LEAFY, as well as CONSTANS-LIKE 5, were identified as markers to distinguish between the vegetative and reproductive stages. Our data also indicated that the down-regulation of the photoperiodic genes seems to be directly associated with promoting floral transition under inductive short-day lengths. These findings provide valuable insight into the molecular factors that underlie meristematic development and contribute to understanding the photoperiod adaptation in the common bean.MCIN/AEI PDI2020-114115RB-100MAPAERDF A way of making Europe European Commission European Union NextGenera-tionEU/PRT