Antibacterial effect of hydrogen peroxide-titanium dioxide suspensions in the decontamination of rough titanium surfaces

The chemical decontamination of infected dental implants is essential for the successful treatment of peri-implantitis. The aim of this study was to assess the antibacterial effect of a hydrogen peroxide-titanium dioxide (H₂O₂–TiO₂) suspension against Staphylococcus epidermidis biofilms. Titanium (Ti) coins were inoculated with a bioluminescent S. epidermidis strain for 8 h and subsequently exposed to H₂O₂ with and without TiO₂ nanoparticles or chlorhexidine (CHX). Bacterial regrowth, bacterial load and viability after decontamination were analyzed by continuous luminescence monitoring, live/dead staining and scanning electron microscopy. Bacterial regrowth was delayed on surfaces treated with H₂O₂–TiO₂ compared to H₂O₂. H₂O₂-based treatments resulted in a lower bacterial load compared to CHX. Few viable bacteria were found on surfaces treated with H₂O₂ and H₂O₂–TiO₂, which contrasted with a uniform layer of dead bacteria for surfaces treated with CHX. H₂O₂–TiO₂ suspensions could therefore be considered an alternative approach in the decontamination of dental implants.     

Attenuation of Axonal Degeneration by Calcium Channel Inhibitors Improves Retinal Ganglion Cell Survival and Regeneration After Optic Nerve Crush

Axonal degeneration is one of the initial steps in many traumatic and neurodegenerative central nervous system (CNS) disorders and thus a promising therapeutic target. A focal axonal lesion is followed by acute axonal degeneration (AAD) of both adjacent axon parts, before proximal and distal parts follow different degenerative fates at later time points. Blocking calcium influx by calcium channel inhibitors was previously shown to attenuate AAD after optic nerve crush (ONC). However, it remains unclear whether the attenuation of AAD also promotes consecutive axonal regeneration. Here, we used a rat ONC model to study the effects of calcium channel inhibitors on axonal degeneration, retinal ganglion cell (RGC) survival, and axonal regeneration, as well as the molecular mechanisms involved. Application of calcium channel inhibitors attenuated AAD after ONC and preserved axonal integrity as visualized by live imaging of optic nerve axons. Consecutively, this resulted in improved survival of RGCs and improved axonal regeneration at 28 days after ONC. We show further that calcium channel inhibition attenuated lesion-induced calpain activation in the proximity of the crush and inhibited the activation of the c-Jun N-terminal kinase pathway. Pro-survival signaling via Akt in the retina was also increased. Our data thus show that attenuation of AAD improves consecutive neuronal survival and axonal regeneration and that calcium channel inhibitors could be valuable tools for therapeutic interventions in traumatic and degenerative CNS disorders.     

Fungi inhabiting knotwood of Pinus sylvestris infected by Porodaedalea pini

Abundance and diversity of fungi in naturally formed knots of Pinus sylvestris affected by Porodaedalea pini were investigated. Samples were taken from trees that were (i) affected, with internal heartwood decay and no conks, (ii) affected, with internal heartwood decay and conks and (iii) controls. The Illumina sequencing technology was used for amplification of DNA, sequencing and analysis. In total, 566,279 raw sequences were obtained from six samples. Sequences included 74% of culturable and 8.4% of non‐culturable fungi and 17.6% of organisms with no reference sequences in NCBI. Abundance of organisms in knotwood, measured as number of OTUs, ranged from 36,272 (29,506 for fungi) to 178,535 (177,484 for fungi) and differed significantly between two trees in a stand and between stands. The highest and lowest average number of fungal OTUs occurred in infected trees with no conks and in trees with conks, respectively. Number of taxa ranged from 171 to 415 and often differed significantly between two trees in one stand and between stands. Greatest diversity occurred in control trees. The number of fungal taxa shared by two trees in one stand was 67–152 and that shared by two stands was 51–141. The majority of fungi were Ascomycota. Those most common in pines affected by P. pini were Coniochaeta hoffmannii and C. fodinicola (19.65%–59.92%). Infundichalara microchona, Leotiomycetes spp. and Rhinocladiella atrovirens were also present. Another common species, Lecanora conizaeoides, occurred most often in control trees (0.30%–8.82%). Porodaedalea pini was detected only sporadically. Non‐culturable fungi were most frequent in the control trees. The greater average abundance and smaller average diversity of fungi in knots of trees infected by P. pini suggest that the pathogen successfully competes with some fungal species and does not inhibit the growth of survivors. Some fungi detected may contribute to production of natural biocides.     

Symposium De toekomst van de informele zorg

Due to the reform of long term care in 2015, there is growing concern about whether groups at risk receive the care they need. People in need of care have to rely more on help from their social network. The increased need for informal care requires resilience and organizational skills of families, but also of volunteers, professionals and employers. What does this mean for the provision of informal care in the next decennia? The symposium ‘The future of informal care’, organized on January 26 2017 by the National Institute for Social Research and the Institute for Societal Resilience of the Vrije Universiteit, addressed possible answers to this question. In her inaugural speech Alice de Boer discussed social inequality as possible determinant and outcome of informal care. Some conclusions:Until 2050 the absolute number of 75-plus doubled to about 3 million persons, but the number of informal caregivers will decrease. In addition to the importance of social and economic resources (the ‘have & have-nots’), the ability to arrange care (the ‘can & can-nots’) gains importance.Almost half of the older employers provides informal care just before retirement. Flexibility in working hours and work location facilitates combining work and care, but about half of the employers indicates that partial retirement and working at home are no options.Informal caregivers and professionals often provide care from comparable perspectives and identities. Addressing similarities rather than differences improves their chances for collaboration.The number of adult children providing household care to older parents increased between 2002 and 2014. This suggests an increase in family solidarity, but current reform policies may increase the gender inequality in caregiving families.Spouses and children remain primary caregivers in the future, preferably supported by many different types of caregivers. Not everybody has the capabilities to organize and direct such a large care network.Providing informal care increases the risk for overburden and absence at work or education. Informal caregivers at risk remain, also in the future, women, spouses, migrants, and younger carers.     

The integrative role of cryo electron microscopy in molecular and cellular structural biology

After gradually moving away from preparation methods prone to artefacts such as plastic embedding and negative staining for cell sections and single particles, the field of cryo electron microscopy (cryo‐EM) is now heading off at unprecedented speed towards high‐resolution analysis of biological objects of various sizes. This ‘revolution in resolution’ is happening largely thanks to new developments of new‐generation cameras used for recording the images in the cryo electron microscope which have much increased sensitivity being based on complementary metal oxide semiconductor devices. Combined with advanced image processing and 3D reconstruction, the cryo‐EM analysis of nucleoprotein complexes can provide unprecedented insights at molecular and atomic levels and address regulatory mechanisms in the cell. These advances reinforce the integrative role of cryo‐EM in synergy with other methods such as X‐ray crystallography, fluorescence imaging or focussed‐ion beam milling as exemplified here by some recent studies from our laboratory on ribosomes, viruses, chromatin and nuclear receptors. Such multi‐scale and multi‐resolution approaches allow integrating molecular and cellular levels when applied to purified or in situ macromolecular complexes, thus illustrating the trend of the field towards cellular structural biology.     

Host resistance and pathogen aggressiveness are key determinants of coinfection in the wild

Coinfection, whereby the same host is infected by more than one pathogen strain, may favor faster host exploitation rates as strains compete for the same limited resources. Hence, coinfection is expected to have major consequences for pathogen evolution, virulence, and epidemiology. Theory predicts genetic variation in host resistance and pathogen infectivity to play a key role in how coinfections are formed. The limited number of studies available has demonstrated coinfection to be a common phenomenon, but little is known about how coinfection varies in space, and what its determinants are. Our aim is to understand how variation in host resistance and pathogen infectivity and aggressiveness contribute to how coinfections are formed in the interaction between fungal pathogen Podosphaera plantaginis and Plantago lanceolata. Our phenotyping study reveals that more aggressive strains are more likely to form coinfections than less aggressive strains in the natural populations. In the natural populations most of the variation in coinfection is found at the individual plant level, and results from a common garden study confirm the prevalence of coinfection to vary significantly among host genotypes. These results show that genetic variation in both the host and pathogen populations are key determinants of coinfection in the wild.     

Subcellular reprogramming of metabolism during cold acclimation in Arabidopsis thaliana

Metabolite changes in plant leaves during exposure to low temperatures involve re‐allocation of a large number of metabolites between sub‐cellular compartments. Therefore, metabolite determination at the whole cell level may be insufficient for interpretation of the functional significance of cellular compounds. To investigate the cold‐induced metabolite dynamics at the level of individual sub‐cellular compartments, an integrative platform was developed that combines quantitative metabolite profiling by gas chromatography coupled to mass spectrometry (GC‐MS) with the non‐aqueous fractionation technique allowing separation of cytosol, vacuole and the plastidial compartment. Two mutants of Arabidopsis thaliana representing antipodes in the diversion of carbohydrate metabolism between sucrose and starch were compared to Col‐0 wildtype before and after cold acclimation to investigate interactions of cold acclimation with subcellular re‐programming of metabolism. A multivariate analysis of the data set revealed dominant effects of compartmentation on metabolite concentrations that were modulated by environmental condition and genetic determinants. While for both, the starchless mutant of plastidial phospho‐gluco mutase (pgm) and a mutant defective in sucrose‐phosphate synthase A1, metabolic constraints, especially at low temperature, could be uncovered based on subcellularly resolved metabolite profiles, only pgm had lowered freezing tolerance. Metabolic profiles of pgm point to redox imbalance as a possible reason for reduced cold acclimation capacity.     

Topologically associating domains and chromatin loops depend on cohesin and are regulated by CTCF,WAPL, and PDS5 proteins

Mammalian genomes are spatially organized into compartments, topologically associating domains (TADs), and loops to facilitate gene regulation and other chromosomal functions. How compartments, TADs, and loops are generated is unknown. It has been proposed that cohesin forms TADs and loops by extruding chromatin loops until it encounters CTCF, but direct evidence for this hypothesis is missing. Here, we show that cohesin suppresses compartments but is required for TADs and loops, that CTCF defines their boundaries, and that the cohesin unloading factor WAPL and its PDS5 binding partners control the length of loops. In the absence of WAPL and PDS5 proteins, cohesin forms extended loops, presumably by passing CTCF sites, accumulates in axial chromosomal positions (vermicelli), and condenses chromosomes. Unexpectedly, PDS5 proteins are also required for boundary function. These results show that cohesin has an essential genome‐wide function in mediating long‐range chromatin interactions and support the hypothesis that cohesin creates these by loop extrusion, until it is delayed by CTCF in a manner dependent on PDS5 proteins, or until it is released from DNA by WAPL.     

Genome-wide repeat dynamics reflect phylogenetic distance in closely related allotetraploid <Emphasis Type="Italic">Nicotiana</Emphasis> (Solanaceae)

Nicotiana sect. Repandae is a group of four allotetraploid species originating from a single allopolyploidisation event approximately 5 million years ago. Previous phylogenetic analyses support the hypothesis of N. nudicaulis as sister to the other three species. This is concordant with changes in genome size, separating those with genome downsizing (N. nudicaulis) from those with genome upsizing (N. repanda, N. nesophila, N. stocktonii). However, a recent analysis reflecting genome dynamics of different transposable element families reconstructed greater similarity between N. nudicaulis and the Revillagigedo Island taxa (N. nesophila and N. stocktonii), thereby placing N. repanda as sister to the rest of the group. This could reflect a different phylogenetic hypothesis or the unique evolutionary history of these particular elements. Here we re-examine relationships in this group and investigate genome-wide patterns in repetitive DNA, utilising high-throughput sequencing and a genome skimming approach. Repetitive DNA clusters provide support for N. nudicaulis as sister to the rest of the section, with N. repanda sister to the two Revillagigedo Island species. Clade-specific patterns in the occurrence and abundance of particular repeats confirm the original (N. nudicaulis (N. repanda (N. nesophila + N. stocktonii))) hypothesis. Furthermore, overall repeat dynamics in the island species N. nesophila and N. stocktonii confirm their similarity to N. repanda and the distinctive patterns between these three species and N. nudicaulis. Together these results suggest that broad-scale repeat dynamics do in fact reflect evolutionary history and could be predicted based on phylogenetic distance.