Near‐genomewide RNAi screening for regulators of BRAFV600E‐induced senescence identifies RASEF,a gene epigenetically silenced in melanoma

The activation of oncogenes in primary cells blocks proliferation by inducing oncogene‐induced senescence (OIS), a highly potent in vivo tumor‐suppressing program. A prime example is mutant BRAF, which drives OIS in melanocytic nevi. Progression to melanoma occurs only in the context of additional alteration(s) like the suppression of PTEN, which abrogates OIS. Here, we performed a near‐genomewide short hairpin (sh)RNA screen for novel OIS regulators and identified by next generation sequencing and functional validation seven genes. While all but one were upregulated in OIS, depletion of each of them abrogated BRAF^V600E‐induced arrest. With genome‐wide DNA methylation analysis, we found one of these genes, RASEF, to be hypermethylated in primary cutaneous melanomas but not nevi. Bypass of OIS by depletion of RASEF was associated with suppression of several senescence biomarkers including senescence‐associated (SA)‐β‐galactosidase activity, interleukins, and tumor suppressor p15^INK4B. Restoration of RASEF expression inhibited proliferation. These results illustrate the power of shRNA OIS bypass screens and identify a potential novel melanoma suppressor gene.     

Multi-Fiber Tractography Visualizations for Diffusion MRI Data

In recent years, several new diffusion MRI approaches have been proposed to explore microstructural properties of the white matter, such as Q-ball imaging and spherical deconvolution-based techniques to estimate the orientation distribution function. These methods can describe the estimated diffusion profile with a higher accuracy than the more conventional second-rank diffusion tensor imaging technique. Despite many important advances, there are still inconsistent findings between different models that investigate the “crossing fibers” issue. Due to the high information content and the complex nature of the data, it becomes virtually impossible to interpret and compare results in a consistent manner. In this work, we present novel fiber tractography visualization approaches that provide a more complete picture of the microstructural architecture of fiber pathways: multi-fiber hyperstreamlines and streamribbons. By visualizing, for instance, the estimated fiber orientation distribution along the reconstructed tract in a continuous way, information of the local fiber architecture is combined with the global anatomical information derived from tractography. Facilitating the interpretation of diffusion MRI data, this approach can be useful for comparing different diffusion reconstruction techniques and may improve our understanding of the intricate white matter network.     

Bioassays using Stigeoclonium tenue Kütz. and Scenedesmus quadricauda (Turp.) Bréb. as testorganisms; a comparative study

Three different bioassays, two culture tube test methods with respectively Stigeoclonium tenue or Scenedesmus quadricauda and one bottle test with S. quadricauda, were compared. The yields obtained in the various tests were linearily correlated (r = 0.86, P < 0.001). The same primary limiting nutrient was indicated by the bioassays in most cases. However the algal growth in the tube test using Stigeoclonium was more often P-limited. In the case of S. quadricauda both test methods (tube and bottle) were nearly equally effective. The yields of N-limited samples were significantly correlated with the inorganic-N as well as total-N concentration of the water sample. A significant correlation of the ortho-P as well as total-P concentration with the yield of the P-limited assays was only found for Stigeoclonium tenue. The critical total N/P ratio (by weight) for N or P limitation was approximately 17: 1 for Stigeoclonium tenue and 22: 1 for Scenedesmus quadricauda.     

Rain events decrease boreal peatland net CO2 uptake through reduced light availability

Boreal peatlands store large amounts of carbon, reflecting their important role in the global carbon cycle. The short‐term exchange and the long‐term storage of atmospheric carbon dioxide (CO₂) in these ecosystems are closely associated with the permanently wet surface conditions and are susceptible to drought. Especially, the single most important peat forming plant genus, Sphagnum, depends heavily on surface wetness for its primary production. Changes in rainfall patterns are expected to affect surface wetness, but how this transient rewetting affects net ecosystem exchange of CO₂ (NEE) remains unknown. This study explores how the timing and characteristics of rain events during photosynthetic active periods, that is daytime, affect peatland NEE and whether rain event associated changes in environmental conditions modify this response (e.g. water table, radiation, vapour pressure deficit, temperature). We analysed an 11‐year time series of half‐hourly eddy covariance and meteorological measurements from Degerö Stormyr, a boreal peatland in northern Sweden. Our results show that daytime rain events systematically decreased the sink strength of peatlands for atmospheric CO₂. The decrease was best explained by rain associated reduction in light, rather than by rain characteristics or drought length. An average daytime growing season rain event reduced net ecosystem CO₂ uptake by 0.23–0.54 gC m^?2. On an annual basis, this reduction of net CO₂ uptake corresponds to 24% of the annual net CO₂ uptake (NEE) of the study site, equivalent to a 4.4% reduction of gross primary production (GPP) during the growing season. We conclude that reduced light availability associated with rain events is more important in explaining the NEE response to rain events than rain characteristics and changes in water availability. This suggests that peatland CO₂ uptake is highly sensitive to changes in cloud cover formation and to altered rainfall regimes, a process hitherto largely ignored.     

Appropriate use of bioresorbable vascular scaffolds in percutaneous coronary interventions: a recommendation from experienced users: A position statement on the use of bioresorbable vascular scaffolds in the Netherlands

Percutaneous coronary interventions (PCI) have become a reliable revascularisation option to treat ischaemic coronary artery disease. Drug-eluting stents (DES) are widely used as first choice devices in many procedures due to their established good medium to long term outcomes. These permanent implants, however, do not have any residual function after vascular healing following the PCI. Beyond this initial healing period, metallic stents may induce new problems, resulting in an average rate of 2 % reinterventions per year. To eliminate this potential late limitation of permanent metallic DES, bioresorbable coronary stents or ‘vascular scaffolds’ (BVS) have been developed. In a parallel publication in this journal, an overview of the current clinical performance of these scaffolds is presented. As these scaffolds are currently CE marked and commercially available in many countries and as clinical evidence is still limited, recommendations for their general usage are needed to allow successful clinical introduction.     

Fluorescently labeled collagen binding proteins allow specific visualization of collagen in tissues and live cell culture

Visualization of the formation and orientation of collagen fibers in tissue engineering experiments is crucial for understanding the factors that determine the mechanical properties of tissues. In this study, collagen-specific fluorescent probes were developed using a new approach that takes advantage of the inherent specificity of collagen binding protein domains present in bacterial adhesion proteins (CNA35) and integrins (GST-alpha1I). Both collagen binding domains were obtained as fusion proteins from an Escherichia coli expression system and fluorescently labeled using either amine-reactive succinimide (CNA35) or cysteine-reactive maleimide (GST-alpha1I) dyes. Solid-phase binding assays showed that both protein-based probes are much more specific than dichlorotriazinyl aminofluorescein (DTAF), a fluorescent dye that is currently used to track collagen formation in tissue engineering experiments. The CNA35 probe showed a higher affinity for human collagen type I than did the GST-alpha1I probe (apparent K(d) values of 0.5 and 50 microM, respectively) and showed very little cross-reactivity with noncollagenous extracellular matrix proteins. The CNA35 probe was also superior to both GST-alpha1I and DTAF in visualizing the formation of collagen fibers around live human venous saphena cells. Immunohistological experiments on rat tissue showed colocalization of the CNA35 probe with collagen type I and type III antibodies. The fluorescent probes described here have important advantages over existing methods for visualization of collagen, in particular for monitoring the formation of collagen in live tissue cultures over prolonged time periods.     

Synthesis of 2-alkoxy-8-hydroxyadenylpeptides: towards synthetic epitope-based vaccines

The preparation of three different 2-alkoxy-8-hydroxyadenylpeptide conjugates has been accomplished by solid-phase synthesis combined with 'on-resin' Cu(I) catalyzed Huisgen cycloaddition. The immunogenicity of the compounds has been evaluated in IL-12 production and antigen presentation assays.     

Motif WFYY of human PrimPol is crucial to stabilize the incoming 3′-nucleotide during replication fork restart

PrimPol is the second primase in human cells, the first with the ability to start DNA chains with dNTPs. PrimPol contributes to DNA damage tolerance by restarting DNA synthesis beyond stalling lesions, acting as a TLS primase. Multiple alignment of eukaryotic PrimPols allowed us to identify a highly conserved motif, WxxY near the invariant motif A, which contains two active site metal ligands in all members of the archeo-eukaryotic primase (AEP) superfamily. In vivo and in vitro analysis of single variants of the WFYY motif of human PrimPol demonstrated that the invariant Trp⁸⁷ and Tyr⁹⁰ residues are essential for both primase and polymerase activities, mainly due to their crucial role in binding incoming nucleotides. Accordingly, the human variant F88L, altering the WFYY motif, displayed reduced binding of incoming nucleotides, affecting its primase/polymerase activities especially during TLS reactions on UV-damaged DNA. Conversely, the Y89D mutation initially associated with High Myopia did not affect the ability to rescue stalled replication forks in human cells. Collectively, our data suggest that the WFYY motif has a fundamental role in stabilizing the incoming 3′-nucleotide, an essential requisite for both its primase and TLS abilities during replication fork restart.