Ultraviolet absorbance of Sphagnum magellanicum, S. fallax and S. fuscum extracts with seasonal and species-specific variation

Bryophytes, including Sphagnum, are common species in alpine and boreal regions especially on mires, where full sunlight exposes the plants to the damaging effects of UV radiation. Sphagnum species containing UV-protecting compounds might offer a biomass source for nature-based sunscreens to replace the synthetic ones. In this study, potential compounds and those linked in cell wall structures were obtained by using methanol and alkali extractions and the UV absorption of these extracts from three common Sphagnum moss species Sphagnum magellanicum, Sphagnum fuscum and Sphagnum fallax collected in spring and autumn from western Finland are described. Absorption spectrum screening (200–900 nm) and luminescent biosensor (Escherichia coli DPD2794) methodology were used to examine and compare the protection against UV radiation. Additionally, the antioxidant potential was evaluated using hydrogen peroxide scavenging (SCAV), oxygen radical absorbance capacity (ORAC) and ferric reducing absorbance capacity (FRAP). Total phenolic content was also determined using the Folin-Ciocalteu method. The results showed that methanol extractable compounds gave higher UV absorption with the used methods. Sphagnum fallax appeared to give the highest absorption in UV-B and UV-A wavelengths. In all assays except the SCAV test, the methanol extracts of Sphagnum samples collected in autumn indicated the highest antioxidant capacity and polyphenol content. Sphagnum fuscum implied the highest antioxidant capacity and phenolic content. There was low antioxidant and UV absorption provided by the alkali extracts of these three species

Expanded national database collection and data coverage in the FINDbase worldwide database for clinically relevant genomic variation allele frequencies

FINDbase (http://www.findbase.org) is a comprehensive data repository that records the prevalence of clinically relevant genomic variants in various populations worldwide, such as pathogenic variants leading mostly to monogenic disorders and pharmacogenomics biomarkers. The database also records the incidence of rare genetic diseases in various populations, all in well-distinct data modules. Here, we report extensive data content updates in all data modules, with direct implications to clinical pharmacogenomics. Also, we report significant new developments in FINDbase, namely (i) the release of a new version of the ETHNOS software that catalyzes development curation of national/ethnic genetic databases, (ii) the migration of all FINDbase data content into 90 distinct national/ethnic mutation databases, all built around Microsoft’s PivotViewer (http://www.getpivot.com) software (iii) new data visualization tools and (iv) the interrelation of FINDbase with DruGeVar database with direct implications in clinical pharmacogenomics. The above mentioned updates further enhance the impact of FINDbase, as a key resource for Genomic Medicine applications

Metabolic Profiling of Water-Soluble Compounds from the Extracts of Dark Septate Endophytic Fungi (DSE) Isolated from Scots Pine (Pinus sylvestris L.) Seedlings Using UPLC-Orbitrap-MS

Endophytes are microorganisms living inside plant hosts and are known to be beneficial for the host plant vitality. In this study, we isolated three endophytic fungus species from the roots of Scots pine seedlings growing on Finnish drained peatland setting. The isolated fungi belonged to dark septate endophytes (DSE). The metabolic profiles of the hot water extracts of the fungi were investigated using Ultrahigh Performance Liquid Chromatography with Diode Array Detection and Electron Spray Ionization source Mass Spectrometry with Orbitrap analyzer (UPLC-DAD-ESI-MS-Orbitrap). Out of 318 metabolites, we were able to identify 220, of which a majority was amino acids and peptides. Additionally, opine amino acids, amino acid quinones, Amadori compounds, cholines, nucleobases, nucleosides, nucleotides, siderophores, sugars, sugar alcohols and disaccharides were found, as well as other previously reported metabolites from plants or endophytes. Some differences of the metabolic profiles, regarding the amount and identity of the found metabolites, were observed even though the fungi were isolated from the same host. Many of the discovered metabolites have been described possessing biological activities and properties, which may make a favorable contribution to the host plant nutrient availability or abiotic and biotic stress tolerance

A systems approach delivers a functional microRNA catalog and expanded targets for seizure suppression in temporal lobe epilepsy

Temporal lobe epilepsy is the most common drug-resistant form of epilepsy in adults. The reorganization of neural networks and the gene expression landscape underlying pathophysiologic network behavior in brain structures such as the hippocampus has been suggested to be controlled, in part, by microRNAs. To systematically assess their significance, we sequenced Argonaute-loaded microRNAs to define functionally engaged microRNAs in the hippocampus of three different animal models in two species and at six time points between the initial precipitating insult through to the establishment of chronic epilepsy. We then selected commonly up-regulated microRNAs for a functional in vivo therapeutic screen using oligonucleotide inhibitors. Argonaute sequencing generated 1.44 billion small RNA reads of which up to 82% were microRNAs, with over 400 unique microRNAs detected per model. Approximately half of the detected microRNAs were dysregulated in each epilepsy model. We prioritized commonly up-regulated microRNAs that were fully conserved in humans and designed custom antisense oligonucleotides for these candidate targets. Antiseizure phenotypes were observed upon knockdown of miR-10a-5p, miR-21a-5p, and miR-142a-5p and electrophysiological analyses indicated broad safety of this approach. Combined inhibition of these three microRNAs reduced spontaneous seizures in epileptic mice. Proteomic data, RNA sequencing, and pathway analysis on predicted and validated targets of these microRNAs implicated derepressed TGF-\u3b2 signaling as a shared seizure-modifying mechanism. Correspondingly, inhibition of TGF-\u3b2 signaling occluded the antiseizure effects of the antagomirs. Together, these results identify shared, dysregulated, and functionally active microRNAs during the pathogenesis of epilepsy which represent therapeutic antiseizure targets

The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button

Peer reviewe

Localized practices and globalized futures: challenges for Alaska coastal community youth

An article from Maritime Studies (2015) 14:

Conservation of human alternative splice events in mouse

Human and mouse genomes share similar long-range sequence organization, and have most of their genes being homologous. As alternative splicing is a frequent and important aspect of gene regulation, it is of interest to assess the level of conservation of alternative splicing. We examined mouse transcript data sets (EST and mRNA) for the presence of transcripts that both make spliced-alignment with the draft mouse genome sequence and demonstrate conservation of human transcript-confirmed alternative and constitutive splice junctions. This revealed 15% of alternative and 67% of constitutive splice junctions as conserved; however, these numbers are patently dependent on the extent of transcript coverage. Transcript coverage of conserved splice patterns is found to correlate well between human and mouse. A model, which extrapolates from observed levels of conservation at increasing levels of transcript support, estimates overall conservation of 61% of alternative and 74% of constitutive splice junctions, albeit with broad confidence intervals. Observed numbers of conserved alternative splicing events agreed with those expected on the basis of the model. Thus, it is apparent that many, and probably most, alternative splicing events are conserved between human and mouse. This, combined with the preservation of alternative frame stop codons in conserved frame breaking events, indicates a high level of commonality in patterns of gene expression between these two species

University graduate migration in Finland

Abstract A high level of human capital is considered as an essential precondition for economic performance and regional competitiveness. However, university regions do not always manage to take advantage of the full potential of local higher education, as they are not always able to retain university students after graduation. Previous studies have presented remarkable regional differences concerning the share of graduates who remain in their university region after graduation. Hence, this paper has focused on geographical distribution and inter-regional mobility of university graduates in Finland. Long-term migration behaviour of all university graduates who completed their master’s or equivalent degree in 2000–2015 was analysed using geographic information systems (GIS). The main finding of the paper is that university graduates in Finland are rather immobile, as the most active mobility takes places when transitioning from university to their first job. After that, the geographical distribution of the graduates is rather stable, which contradicts the general assumption of high mobility of university-educated people. Further, the migration flows are directed mainly towards the four largest city regions of the country, especially to the capital city region. Cross-migration between city regions with similar population sizes and population growth rate is marginal, and it seems that the difference in the population size and growth between the graduation region and the destination region has to be large enough to exceed the threshold for migration. Retaining university graduates seems to be especially challenging for the smallest and declining university regions

ASD: the alternative splicing database

Alternative splicing is widespread in mammalian gene expression, and variant splice patterns are often specific to different stages of development, particular tissues or a disease state. There is a need to systematically collect data on alternatively spliced exons, introns and splice isoforms, and to annotate this data. The Alternative Splicing Database consortium has been addressing this need, and is committed to maintaining and developing a value-added database of alternative splice events, and of experimentally verified regulatory mechanisms that mediate splice variants. In this paper we present two of the products from this project: namely, a database of computationally delineated alternative splice events as seen in alignments of EST/cDNA sequences with genome sequences, and a database of alternatively spliced exons collected from literature. The reported splice events are from nine different organisms and are annotated for various biological features including expression states and cross-species conservation. The data is presented on ASD webpages at (http://www.ebi.ac.uk/asd).T. A. Thanaraj, Stefan Stamm, Francis Clark, Jean‐Jack Riethoven, Vincent Le Texier and Juha Muil