Recent and dynamic transposable elements contribute to genomic divergence under asexuality

BACKGROUND

Transposable elements (TEs) are mobile pieces of genetic information with high mutagenic potential for the host genome. Transposition is often neutral or deleterious but may also generate potentially adaptive genetic variation. This additional source of variation could be especially relevant in non-recombining species reproducing asexually. However, evidence is lacking to determine the relevance of TEs in plant asexual genome evolution and their associated effects. Here, we characterize the repetitive fraction of the genome of the common dandelion, Taraxacum officinale and compare it between five accessions from the same apomictic lineage. The main objective of this study is to evaluate the extent of within-lineage divergence attributed to TE content and activity. We examined the repetitive genomic contribution, diversity, transcription and methylation changes to characterize accession-specific TEs.

RESULTS

Using low-coverage genomic sequencing, we report a highly heterogeneous TE compartment in the triploid apomict T. officinale representing up to 38.6 % of the homoploid genome. The repetitive compartment is dominated by LTR retrotransposon families accompanied by few non-LTR retrotransposons and DNA transposons. Up to half of the repeat clusters are biased towards very high read identity, indicating recent and potentially ongoing activity of these TE families. Interestingly, the five accessions are divided into two main clades based on their TE composition. Clade 2 is more dynamic than clade 1 with higher abundance of Gypsy Chromovirus sequences and transposons. Furthermore, a few low-abundant genomic TE clusters exhibit high level of transcription in two of the accessions analysed. Using reduced representation bisulfite sequencing, we detected 18.9 % of loci differentially methylated, of which 25.4 and 40.7 % are annotated as TEs or functional genes, respectively. Additionally, we show clear evidence for accession-specific TE families that are differentially transcribed and differentially methylated within the apomictic lineage, including one Copia Ale II LTR element and a PIF-Harbinger DNA transposon.

CONCLUSION

We report here a very young and dynamic repetitive compartment that enhances divergence within one asexual lineage of T. officinale. We speculate that accession-specific TE families that are both transcriptionally and epigenetically variable are more prone to trigger changes in expression on nearby coding sequences. These findings emphasize the potential of TE-induced mutations on functional genes during asexual genome evolution.

Surviving critical illness: what is next? An expert consensus statement on physical rehabilitation after hospital discharge

BACKGROUND

The study objective was to obtain consensus on physical therapy (PT) in the rehabilitation of critical illness survivors after hospital discharge. Research questions were: what are PT goals, what are recommended measurement tools, and what constitutes an optimal PT intervention for survivors of critical illness?

METHODS

A Delphi consensus study was conducted. Panelists were included based on relevant fields of expertise, years of clinical experience, and publication record. A literature review determined five themes, forming the basis for Delphi round one, which was aimed at generating ideas. Statements were drafted and ranked on a 5-point Likert scale in two additional rounds with the objective to reach consensus. Results were expressed as median and semi-interquartile range, with the consensus threshold set at ≤0.5.

RESULTS

Ten internationally established researchers and clinicians participated in this Delphi panel, with a response rate of 80 %, 100 %, and 100 % across three rounds. Consensus was reached on 88.5 % of the statements, resulting in a framework for PT after hospital discharge. Essential handover information should include information on 15 parameters. A core set of outcomes should test exercise capacity, skeletal muscle strength, function in activities of daily living, mobility, quality of life, and pain. PT interventions should include functional exercises, circuit and endurance training, strengthening exercises for limb and respiratory muscles, education on recovery, and a nutritional component. Screening tools to identify impairments in other health domains and referral to specialists are proposed.

CONCLUSIONS

A consensus-based framework for optimal PT after hospital discharge is proposed. Future research should focus on feasibility testing of this framework, developing risk stratification tools and validating core outcome measures for ICU survivors.

Heritability of Behavioral Problems in 7-Year Olds Based on Shared and Unique Aspects of Parental Views

In studies of child psychopathology, phenotypes of interest are often obtained by parental ratings. When behavioral ratings are obtained in the context of a twin study, this allows for the decomposition of the phenotypic variance, into a genetic and a non-genetic part. If a phenotype is assessed by a single rater, heritability is based on the child’s behavior as expressed in the presence of that particular rater, whereas heritability based on assessments by multiple raters allows for the estimation of the heritability of the phenotype based on rater agreement, as well as the heritability of the rater specific view of the behavior. The aim of this twin study was to quantify the rater common and rater specific contributions to the variation in children’s behavioral problems. We estimated the heritability of maternal and paternal ratings of the Child Behavior Checklist (CBCL) 6–18 empirical emotional and behavioral problem scales in a large sample of 12,310 7-year old Dutch twin pairs. Between 30 and 59% of variation in the part of the phenotype parents agree upon was explained by genetic effects. Common environmental effects that make children in the same family similar explained less variance, ranging between 0 and 32%. For unique views of their children’s behavioral problems, heritability ranged between 0 and 20% for maternal and between 0 and 22% for paternal views. Between 7 and 24% of the variance was accounted for by common environmental factors specific to mother and father’s views. The proportion of rater shared and rater specific heritability can be translated into genetic correlations between parental views and inform the design and interpretation of results of molecular genetic studies. Genetic correlations were nearly or above 0.7 for all CBCL based psychopathology scales. Such large genetic correlations suggest two practical guidelines for genome-wide association studies (GWAS): when studies have collected data from either fathers or mothers, the shared genetic aetiology in parental ratings indicates that is possible to analyze paternal and maternal assessments in a single GWAS or meta-analysis. Secondly, if a study has collected information from both parents, a gain in statistical power may be realized in GWAS by the simultaneous analysis of the data.

High-throughput assessment of context-dependent effects of chromatin proteins

BACKGROUND

Chromatin proteins control gene activity in a concerted manner. We developed a high-throughput assay to study the effects of the local chromatin environment on the regulatory activity of a protein of interest. The assay combines a previously reported multiplexing strategy based on barcoded randomly integrated reporters with Gal4-mediated tethering. We applied the assay to Drosophila heterochromatin protein 1a (HP1a), which is mostly known as a repressive protein but has also been linked to transcriptional activation.

RESULTS

Recruitment to over 1000 genomic locations revealed that HP1a is a potent repressor able to silence even highly expressing reporter genes. However, the local chromatin context can modulate HP1a function. In pericentromeric regions, HP1a-induced repression was enhanced by twofold. In regions marked by a H3K36me3-rich chromatin signature, HP1a-dependent silencing was significantly decreased. We found no evidence for an activating function of HP1a in our experimental system. Furthermore, we did not observe stable transmission of repression over mitotic divisions after loss of targeted HP1a.

CONCLUSIONS

The multiplexed tethered reporter assay should be applicable to a large number of chromatin proteins and will be a useful tool to dissect combinatorial regulatory interactions in chromatin.

Early Warning Signals for Regime Transition in the Stable Boundary Layer: A Model Study

The evening transition is investigated in an idealized model for the nocturnal boundary layer. From earlier studies it is known that the nocturnal boundary layer may manifest itself in two distinct regimes, depending on the ambient synoptic conditions: strong-wind or overcast conditions typically lead to weakly stable, turbulent nights; clear-sky and weak-wind conditions, on the other hand, lead to very stable, weakly turbulent conditions. Previously, the dynamical behaviour near the transition between these regimes was investigated in an idealized setting, relying on Monin-Obukhov (MO) similarity to describe turbulent transport. Here, we investigate a similar set-up, using direct numerical simulation; in contrast to MO-based models, this type of simulation does not need to rely on turbulence closure assumptions. We show that previous predictions are verified, but now independent of turbulence parametrizations. Also, it appears that a regime shift to the very stable state is signaled in advance by specific changes in the dynamics of the turbulent boundary layer. Here, we show how these changes may be used to infer a quantitative estimate of the transition point from the weakly stable boundary layer to the very stable boundary layer. In addition, it is shown that the idealized, nocturnal boundary-layer system shares important similarities with generic non-linear dynamical systems that exhibit critical transitions. Therefore, the presence of other, generic early warning signals is tested as well. Indeed, indications are found that such signals are present in stably stratified turbulent flows.

Positive vs. Negative: The Impact of Question Polarity in Voting Advice Applications

Online Voting Advice Applications (VAAs) are survey-like instruments that help citizens to shape their political preferences and compare them with those of political parties. Especially in multi-party democracies, their increasing popularity indicates that VAAs play an important role in opinion formation for citizens, as well as in the public debate prior to elections. Hence, the objectivity and transparency of VAAs are crucial. In the design of VAAs, many choices have to be made. Extant research in survey methodology shows that the seemingly arbitrary choice to word questions positively (e.g., 'The city council should allow cars into the city centre') or negatively ('The city council should ban cars from the city centre') systematically affects the answers. This asymmetry in answers is in line with work on negativity bias in other areas of linguistics and psychology. Building on these findings, this study investigated whether question polarity also affects the answers to VAA statements. In a field experiment (N = 31,112) during the Dutch municipal elections we analysed the effects of polarity for 16 out of 30 VAA statements with a large variety of linguistic contrasts. Analyses show a significant effect of question wording for questions containing a wide range of implicit negations (such as 'forbid' vs. 'allow'), as well as for questions with explicit negations (e.g., 'not'). These effects of question polarity are found especially for VAA users with lower levels of political sophistication. As these citizens are an important target group for Voting Advice Applications, this stresses the need for VAA builders to be sensitive to wording choices when designing VAAs. This study is the first to show such consistent wording effects not only for political attitude questions with implicit negations in VAAs, but also for political questions containing explicit negations.

Multisite Phosphorylation of NuMA-Related LIN-5 Controls Mitotic Spindle Positioning in C. elegans

During cell division, the mitotic spindle segregates replicated chromosomes to opposite poles of the cell, while the position of the spindle determines the plane of cleavage. Spindle positioning and chromosome segregation depend on pulling forces on microtubules extending from the centrosomes to the cell cortex. Critical in pulling force generation is the cortical anchoring of cytoplasmic dynein by a conserved ternary complex of Gα, GPR-1/2, and LIN-5 proteins in C. elegans (Gα–LGN–NuMA in mammals). Previously, we showed that the polarity kinase PKC-3 phosphorylates LIN-5 to control spindle positioning in early C. elegans embryos. Here, we investigate whether additional LIN-5 phosphorylations regulate cortical pulling forces, making use of targeted alteration of in vivo phosphorylated residues by CRISPR/Cas9-mediated genetic engineering. Four distinct in vivo phosphorylated LIN-5 residues were found to have critical functions in spindle positioning. Two of these residues form part of a 30 amino acid binding site for GPR-1, which we identified by reverse two-hybrid screening. We provide evidence for a dual-kinase mechanism, involving GSK3 phosphorylation of S659 followed by phosphorylation of S662 by casein kinase 1. These LIN-5 phosphorylations promote LIN-5–GPR-1/2 interaction and contribute to cortical pulling forces. The other two critical residues, T168 and T181, form part of a cyclin-dependent kinase consensus site and are phosphorylated by CDK1-cyclin B in vitro. We applied a novel strategy to characterize early embryonic defects in lethal T168,T181 knockin substitution mutants, and provide evidence for sequential LIN-5 N-terminal phosphorylation and dephosphorylation in dynein recruitment. Our data support that phosphorylation of multiple LIN-5 domains by different kinases contributes to a mechanism for spatiotemporal control of spindle positioning and chromosome segregation.

Protein kinases control biological processes by phosphorylating specific amino acids of substrate proteins. It remains a major challenge to identify which phosphorylation events are critical in vivo and how phosphorylation affects protein function. Recent developments in CRISPR/Cas9-based genetic engineering make it possible to substitute individual amino acids, which allows investigating the role of single and multi-site phosphorylation of substrates in vivo. Here, we focus on an intensively phosphorylated cell division protein, LIN-5^NuMA. C. elegans LIN-5 participates in chromosome segregation and is essential for positioning the spindle and cell cleavage plane during asymmetric cell division. Previously, we demonstrated that the polarity kinase PKC-3 phosphorylates LIN-5 to inhibit its function. Our current analysis reveals four additional phosphorylated residues that are critical for LIN-5 function. Two of these residues contribute to the interaction of LIN-5 with its binding partner GPR-1/2, whereas the other two residues are critical in dynein motor recruitment by LIN-5. Together, our results reveal that multisite phosphorylation of LIN-5 is essential to ensure proper chromosome segregation and spindle positioning.

Commercial Plant Production and Consumption Still Follow the Latitudinal Gradient in Species Diversity despite Economic Globalization

Increasing trade between countries and gains in income have given consumers around the world access to a richer and more diverse set of commercial plant products (i.e., foods and fibers produced by farmers). According to the economic theory of comparative advantage, countries open to trade will be able to consume more–in terms of volume and diversity–if they concentrate production on commodities that they can most cost-effectively produce, while importing goods that are expensive to produce, relative to other countries. Here, we perform a global analysis of traded commercial plant products and find little evidence that increasing globalization has incentivized agricultural specialization. Instead, a country’s plant production and consumption patterns are still largely determined by local evolutionary legacies of plant diversification. Because tropical countries harbor a greater diversity of lineages across the tree of life than temperate countries, tropical countries produce and consume a greater diversity of plant products than do temperate countries. In contrast, the richer and more economically advanced temperate countries have the capacity to produce and consume more plant species than the generally poorer tropical countries, yet this collection of plant species is drawn from fewer branches on the tree of life. Why have countries not increasingly specialized in plant production despite the theoretical financial incentive to do so? Potential explanations include the persistence of domestic agricultural subsidies that distort production decisions, cultural preferences for diverse local food production, and that diverse food production protects rural households in developing countries from food price shocks. Less specialized production patterns will make crop systems more resilient to zonal climatic and social perturbations, but this may come at the expense of global crop production efficiency, an important step in making the transition to a hotter and more crowded world.

Insulin-Like Growth Factor I Does Not Drive New Bone Formation in Experimental Arthritis

Introduction

Insulin like growth factor (IGF)-I can act on a variety of cells involved in cartilage and bone repair, yet IGF-I has not been studied extensively in the context of inflammatory arthritis. The objective of this study was to investigate whether IGF-I overexpression in the osteoblast lineage could lead to increased reparative or pathological bone formation in rheumatoid arthritis and/or spondyloarthritis respectively.

Methods

Mice overexpressing IGF-I in the osteoblast lineage (Ob-IGF-I^+/-) line 324–7 were studied during collagen induced arthritis and in the DBA/1 aging model for ankylosing enthesitis. Mice were scored clinically and peripheral joints were analysed histologically for the presence of hypertrophic chondrocytes and osteocalcin positive osteoblasts.

Results

90–100% of the mice developed CIA with no differences between the Ob-IGF-I^+/- and non-transgenic littermates. Histological analysis revealed similar levels of hypertrophic chondrocytes and osteocalcin positive osteoblasts in the ankle joints. In the DBA/1 aging model for ankylosing enthesitis 60% of the mice in both groups had a clinical score 1<. Severity was similar between both groups. Histological analysis revealed the presence of hypertrophic chondrocytes and osteocalcin positive osteoblasts in the toes in equal levels.

Conclusion

Overexpression of IGF-I in the osteoblast lineage does not contribute to an increase in repair of erosions or syndesmophyte formation in mouse models for destructive and remodeling arthritis.

Establishing hierarchy: the chain of events leading to the formation of silicalite-1 nanosheets

In applying a multi-scale spectroscopic and computational approach, we demonstrate that the synthesis of stacked zeolite silicalite-1 nanosheets, in the presence of a long-tail diquaternary ammonium salt surfactant, proceeds through a pre-organised phase in the condensed state. In situ small-angle X-ray scattering, coupled to paracrystalline theory, and backed by electron microscopy, shows that this phase establishes its meso-scale order within the first five hours of hydrothermal synthesis. Quasi in situ vibrational and solid-state NMR spectroscopy reveal that this meso-shaped architecture already contains some elementary zeolitic features. The key to this coupled organisation at both micro- and meso-scale, is a structure-directing agent that is ambifunctional in shaping silica at the meso-scale whilst involved in molecular recognition at the micro-scale. The latter feature is particularly important and requires the structure-directing agent to reside within the silica matrix already at early stages of the synthesis. From here, molecular recognition directs stabilization of precursor species and their specific embedding into a lattice, as shown by force-field molecular dynamics calculations. These calculations, in line with experiment, further show how it is possible to subtly tune both the zeolite topology and aspect ratio of the condensating crystals, by modifying the headgroup of the structure-directing agent.

Orthostatic Hypotension and the Long-Term Risk of Dementia: A Population-Based Study

BACKGROUND

Orthostatic hypotension (OH) is a common cause of transient cerebral hypoperfusion in the population. Cerebral hypoperfusion is widely implicated in cognitive impairment, but whether OH contributes to cognitive decline and dementia is uncertain. We aimed to determine the association between OH and the risk of developing dementia in the general population.

METHODS AND FINDINGS

Between 4 October 1989 and 17 June 1993, we assessed OH in non-demented, stroke-free participants of the population-based Rotterdam Study. OH was defined as a ≥20 mm Hg drop in systolic blood pressure (SBP) or ≥10 mm Hg drop in diastolic blood pressure (DBP) within 3 min from postural change. We furthermore calculated within participant variability in SBP related to postural change, expressed as coefficient of variation. Follow-up for dementia was conducted until 1 January 2014. We determined the risk of dementia in relation to OH and SBP variability, using a Cox regression model, adjusted for age; sex; smoking status; alcohol intake; SBP; DBP; cholesterol:high-density lipoprotein ratio; diabetes; body mass index; use of antihypertensive, lipid-lowering, or anticholinergic medication; and apolipoprotein E genotype. Finally, we explored whether associations varied according to compensatory increase in heart rate. Among 6,204 participants (mean ± standard deviation [SD] age 68.5 ± 8.6 y, 59.7% female) with a median follow-up of 15.3 y, 1,176 developed dementia, of whom 935 (79.5%) had Alzheimer disease and 95 (8.1%) had vascular dementia. OH was associated with an increased risk of dementia (adjusted hazard ratio [aHR] 1.15, 95% CI 1.00-1.34, p = 0.05), which was similar for Alzheimer disease and vascular dementia. Similarly, greater SBP variability with postural change was associated with an increased risk of dementia (aHR per SD increase 1.08, 95% CI 1.01-1.16, p = 0.02), which was similar when excluding those who fulfilled the formal criteria for OH (aHR 1.08, 95% CI 1.00-1.17, p = 0.06). The risk of dementia was particularly increased in those with OH who lacked a compensatory increase in heart rate (within lowest quartile of heart rate response: aHR 1.39, 95% CI 1.04-1.85, p-interaction = 0.05). Limitations of this study include potential residual confounding despite rigorous adjustments, and potentially limited generalisability to populations not of European descent.

CONCLUSIONS

In this population predominantly of European descent, OH was associated with an increase in long-term risk of dementia.

Novel Genetic Variants for Cartilage Thickness and Hip Osteoarthritis

Osteoarthritis is one of the most frequent and disabling diseases of the elderly. Only few genetic variants have been identified for osteoarthritis, which is partly due to large phenotype heterogeneity. To reduce heterogeneity, we here examined cartilage thickness, one of the structural components of joint health. We conducted a genome-wide association study of minimal joint space width (mJSW), a proxy for cartilage thickness, in a discovery set of 13,013 participants from five different cohorts and replication in 8,227 individuals from seven independent cohorts. We identified five genome-wide significant (GWS, P≤5·0×10-8) SNPs annotated to four distinct loci. In addition, we found two additional loci that were significantly replicated, but results of combined meta-analysis fell just below the genome wide significance threshold. The four novel associated genetic loci were located in/near TGFA (rs2862851), PIK3R1 (rs10471753), SLBP/FGFR3 (rs2236995), and TREH/DDX6 (rs496547), while the other two (DOT1L and SUPT3H/RUNX2) were previously identified. A systematic prioritization for underlying causal genes was performed using diverse lines of evidence. Exome sequencing data (n = 2,050 individuals) indicated that there were no rare exonic variants that could explain the identified associations. In addition, TGFA, FGFR3 and PIK3R1 were differentially expressed in OA cartilage lesions versus non-lesioned cartilage in the same individuals. In conclusion, we identified four novel loci (TGFA, PIK3R1, FGFR3 and TREH) and confirmed two loci known to be associated with cartilage thickness.The identified associations were not caused by rare exonic variants. This is the first report linking TGFA to human OA, which may serve as a new target for future therapies.

Fire Usage and Ancient Hominin Detoxification Genes: Protective Ancestral Variants Dominate While Additional Derived Risk Variants Appear in Modern Humans

Studies of the defence capacity of ancient hominins against toxic substances may contribute importantly to the reconstruction of their niche, including their diets and use of fire. Fire usage implies frequent exposure to hazardous compounds from smoke and heated food, known to affect general health and fertility, probably resulting in genetic selection for improved detoxification. To investigate whether such genetic selection occurred, we investigated the alleles in Neanderthals, Denisovans and modern humans at gene polymorphisms well-known to be relevant from modern human epidemiological studies of habitual tobacco smoke exposure and mechanistic evidence. We compared these with the alleles in chimpanzees and gorillas. Neanderthal and Denisovan hominins predominantly possess gene variants conferring increased resistance to these toxic compounds. Surprisingly, we observed the same in chimpanzees and gorillas, implying that less efficient variants are derived and mainly evolved in modern humans. Less efficient variants are observable from the first early Upper Palaeolithic hunter-gatherers onwards. While not clarifying the deep history of fire use, our results highlight the long-term stability of the genes under consideration despite major changes in the hominin dietary niche. Specifically for detoxification gene variants characterised as deleterious by epidemiological studies, our results confirm the predominantly recent appearance reported for deleterious human gene variants, suggesting substantial impact of recent human population history, including pre-Holocene expansions.

Statistical Analysis of Tract-Tracing Experiments Demonstrates a Dense, Complex Cortical Network in the Mouse

Anatomical tract tracing methods are the gold standard for estimating the weight of axonal connectivity between a pair of pre-defined brain regions. Large studies, comprising hundreds of experiments, have become feasible by automated methods. However, this comes at the cost of positive-mean noise making it difficult to detect weak connections, which are of particular interest as recent high resolution tract-tracing studies of the macaque have identified many more weak connections, adding up to greater connection density of cortical networks, than previously recognized. We propose a statistical framework that estimates connectivity weights and credibility intervals from multiple tract-tracing experiments. We model the observed signal as a log-normal distribution generated by a combination of tracer fluorescence and positive-mean noise, also accounting for injections into multiple regions. Using anterograde viral tract-tracing data provided by the Allen Institute for Brain Sciences, we estimate the connection density of the mouse intra-hemispheric cortical network to be 73% (95% credibility interval (CI): 71%, 75%); higher than previous estimates (40%). Inter-hemispheric density was estimated to be 59% (95% CI: 54%, 62%). The weakest estimable connections (about 6 orders of magnitude weaker than the strongest connections) are likely to represent only one or a few axons. These extremely weak connections are topologically more random and longer distance than the strongest connections, which are topologically more clustered and shorter distance (spatially clustered). Weak links do not substantially contribute to the global topology of a weighted brain graph, but incrementally increased topological integration of a binary graph. The topology of weak anatomical connections in the mouse brain, rigorously estimable down to the biological limit of a single axon between cortical areas in these data, suggests that they might confer functional advantages for integrative information processing and/or they might represent a stochastic factor in the development of the mouse connectome.

Differential lexical predictors of reading comprehension in fourth graders

The mental lexicon plays a central role in reading comprehension (Perfetti & Stafura, 2014). It encompasses the number of lexical entries in spoken and written language (vocabulary breadth), the semantic quality of these entries (vocabulary depth), and the connection strength between lexical representations (semantic relatedness); as such, it serves as an output for the decoding process and as an input for comprehension processes. Although different aspects of the lexicon can be distinguished, research on the role of the mental lexicon in reading comprehension often does not take these individual aspects of the lexicon into account. The current study used a multicomponent approach to examine whether measures of spoken and written vocabulary breadth, vocabulary depth, and semantic relatedness were differentially predictive of individual differences in reading comprehension skills in fourth-grade students. The results indicated that, in addition to nonverbal reasoning, short-term memory, and word decoding, the four measures of lexical quality substantially added (30 %) to the proportion of explained variance of reading comprehension (adding up to a total proportion of 65 %). Moreover, each individual measure of lexical quality added significantly to the prediction of reading comprehension after all other measures were taken into account, with written lexical breadth and lexical depth showing the greatest increase in explained variance. It can thus be concluded that multiple components of lexical quality play a role in children's reading comprehension.

An siRNA screen for ATG protein depletion reveals the extent of the unconventional functions of the autophagy proteome in virus replication

Autophagy is a catabolic process regulated by the orchestrated action of the autophagy-related (ATG) proteins. Recent work indicates that some of the ATG proteins also have autophagy-independent roles. Using an unbiased siRNA screen approach, we explored the extent of these unconventional functions of ATG proteins. We determined the effects of the depletion of each ATG proteome component on the replication of six different viruses. Our screen reveals that up to 36% of the ATG proteins significantly alter the replication of at least one virus in an unconventional fashion. Detailed analysis of two candidates revealed an undocumented role for ATG13 and FIP200 in picornavirus replication that is independent of their function in autophagy as part of the ULK complex. The high numbers of unveiled ATG gene-specific and pathogen-specific functions of the ATG proteins calls for caution in the interpretation of data, which rely solely on the depletion of a single ATG protein to specifically ablate autophagy.

Rapid Sediment Accumulation Results in High Methane Effluxes from Coastal Sediments

Globally, the methane (CH4) efflux from the ocean to the atmosphere is small, despite high rates of CH4 production in continental shelf and slope environments. This low efflux results from the biological removal of CH4 through anaerobic oxidation with sulfate in marine sediments. In some settings, however, pore water CH4 is found throughout the sulfate-bearing zone, indicating an apparently inefficient oxidation barrier for CH4. Here we demonstrate that rapid sediment accumulation can explain this limited capacity for CH4 removal in coastal sediments. In a saline coastal reservoir (Lake Grevelingen, The Netherlands), we observed high diffusive CH4 effluxes from the sediment into the overlying water column (0.2-0.8 mol m-2 yr-1) during multiple years. Linear pore water CH4 profiles and the absence of an isotopic enrichment commonly associated with CH4 oxidation in a zone with high rates of sulfate reduction (50-170 nmol cm-3 d-1) both suggest that CH4 is bypassing the zone of sulfate reduction. We propose that the rapid sediment accumulation at this site (~ 13 cm yr-1) reduces the residence time of the CH4 oxidizing microorganisms in the sulfate/methane transition zone (< 5 years), thus making it difficult for these slow growing methanotrophic communities to build-up sufficient biomass to efficiently remove pore water CH4. In addition, our results indicate that the high input of organic matter (~ 91 mol C m-2 yr-1) allows for the co-occurrence of different dissimilatory respiration processes, such as (acetotrophic) methanogenesis and sulfate reduction in the surface sediments by providing abundant substrate. We conclude that anthropogenic eutrophication and rapid sediment accumulation likely increase the release of CH4 from coastal sediments.

Disposable Polydimethylsiloxane (PDMS)-Coated Fused Silica Optical Fibers for Sampling Pheromones of Moths

In the past decades, the sex pheromone composition in female moths has been analyzed by different methods, ranging from volatile collections to gland extractions, which all have some disadvantage: volatile collections can generally only be conducted on (small) groups of females to detect the minor pheromone compounds, whereas gland extractions are destructive. Direct-contact SPME overcomes some of these disadvantages, but is expensive, the SPME fiber coating can be damaged due to repeated usage, and samples need to be analyzed relatively quickly after sampling. In this study, we assessed the suitability of cheap and disposable fused silica optical fibers coated with 100 μm polydimethylsiloxane (PDMS) by sampling the pheromone of two noctuid moths, Heliothis virescens and Heliothis subflexa. By rubbing the disposable PDMS fibers over the pheromone glands of females that had called for at least 15 minutes and subsequently extracting the PDMS fibers in hexane, we collected all known pheromone compounds, and we found a strong positive correlation for most pheromone compounds between the disposable PDMS fiber rubs and the corresponding gland extracts of the same females. When comparing this method to volatile collections and the corresponding gland extracts, we generally found comparable percentages between the three techniques, with some differences that likely stem from the chemical properties of the individual pheromone compounds. Hexane extraction of cheap, disposable, PDMS coated fused silica optical fibers allows for sampling large quantities of individual females in a short time, eliminates the need for immediate sample analysis, and enables to use the same sample for multiple chemical analyses.

Qualitative Evaluation of a High-Resolution 3D Multi-Sequence Intracranial Vessel Wall Protocol at 3 Tesla MRI

Background and Purpose

Intracranial vessel wall imaging using MRI has great potential as a clinical method for assessing intracranial atherosclerosis. The purpose of the current study was to compare three 3T MRI vessel wall sequences with different contrast weightings (T₁w, PD, T₂w) and dedicated sagittal orientation perpendicular to the middle cerebral artery, to the reconstructed sagittal image from a transverse 3D T₁w volumetric isotropically reconstructed turbo spin-echo acquisition (VIRTA), and provide a clinical recommendation.

Materials and Methods

The above-mentioned sequences were acquired in 10 consecutive Chinese ischemic stroke or TIA patients (age: 68 years, sex: 4 females) with angiographic-confirmed MCA stenosis at 3T. Institutional review board approval was obtained. Two raters qualitatively scored all images on overall image quality, presence of artifacts, and visibility of plaques. Data were compared using Repeated measures ANOVA and Sidak’s adjusted post hoc tests.

Results

All sequences except the T₂w sequence were able to depict the walls of the large vessels of the Circle of Willis (p<0.05). T₁w sagittal oblique VIRTA showed significantly more artifacts (p<0.01). Peripherally located plaques were sometimes missed on the sagittal sequences, but could be appreciated on the transverse T₁w VIRTA.

Conclusion

With the 3T multi-sequence vessel wall protocol we were able to assess the intracranial plaque with two different image contrast weightings. The sequence of preference to include in a clinical protocol would be the transverse 3D T₁w VIRTA based on absence of artifacts, larger coverage including the whole Circle of Willis, and excellent lesion depiction.

Location estimation of approaching objects is modulated by the observer's inherent and momentary action capabilities

Action capability may be one of the factors that can influence our percept of the world. A distinction can be made between momentary action capability (action capability at that particular moment) and inherent action capability (representing a stable action capability). In the current study, we investigated whether there was a biasing effect of these two forms of action capability on visual perception of location. In a virtual reality room, subjects had to stop a moving ball from hitting a pillar. On some trials, the ball disappeared automatically during its motion. Subjects had to estimate the location of the ball's disappearance in these trials. We expected that if action is necessary but action capability (inherent or momentary) is limiting performance, the location of approaching objects with respect to the observer is underestimated. By judging the objects to be nearer than they really are, the need to select and execute the appropriate action increases, thereby facilitating quick action (Cole et al. in Psychol Sci 24(1):34-40, 2013. doi: 10.1177/0956797612446953 ). As a manipulation of inherent action capability in a virtual environment, two groups of participants (video game players vs. non-video game players) were entered into the study (high and low action capability). Momentary action capability was manipulated by using two difficulty levels in the experiment (Easy vs. Difficult). Results indicated that inherent and momentary action capabilities interacted together to influence online location judgments: Non-players underestimated locations when the task was Difficult. Taken together, our data suggest that both inherent and momentary action capabilities influence location judgments.

Transcallosal connectivity of the human cortical motor network

The organisational and architectural configuration of white matter pathways connecting brain regions has ramifications for all facets of the human condition, including manifestations of incipient neurodegeneration. Although diffusion tensor imaging (DTI) has been used extensively to visualise white matter connectivity, due to the widespread presence of crossing fibres, the lateral projections of the corpus callosum are not normally detected using this methodology. Detailed knowledge of the transcallosal connectivity of the human cortical motor network has, therefore, remained elusive. We employed constrained spherical deconvolution (CSD) tractography—an approach that is much less susceptible to the influence of crossing fibres, in order to derive complete in vivo characterizations of white matter pathways connecting specific motor cortical regions to their counterparts and other loci in the opposite hemisphere. The revealed patterns of connectivity closely resemble those derived from anatomical tracing in primates. It was established that dorsal premotor cortex (PMd) and supplementary motor area (SMA) have extensive interhemispheric connectivity—exhibiting both dense homologous projections, and widespread structural relations with every other region in the contralateral motor network. Through this in vivo portrayal, the importance of non-primary motor regions for interhemispheric communication is emphasised. Additionally, distinct connectivity profiles were detected for the anterior and posterior subdivisions of primary motor cortex. The present findings provide a comprehensive representation of transcallosal white matter projections in humans, and have the potential to inform the development of models and hypotheses relating structural and functional brain connectivity.

An Independent Psychometric Evaluation of the PROMS Measure of Music Perception Skills

The Profile of Music Perception Skills (PROMS) is a recently developed measure of perceptual music skills which has been shown to have promising psychometric properties. In this paper we extend the evaluation of its brief version to three kinds of validity using an individual difference approach. The brief PROMS displays good discriminant validity with working memory, given that it does not correlate with backward digit span (r = .04). Moreover, it shows promising criterion validity (association with musical training (r = .45), musicianship status (r = .48), and self-rated musical talent (r = .51)). Finally, its convergent validity, i.e. relation to an unrelated measure of music perception skills, was assessed by correlating the brief PROMS to harmonic closure judgment accuracy. Two independent samples point to good convergent validity of the brief PROMS (r = .36; r = .40). The same association is still significant in one of the samples when including self-reported music skill in a partial correlation (rpartial = .30; rpartial = .17). Overall, the results show that the brief version of the PROMS displays a very good pattern of construct validity. Especially its tuning subtest stands out as a valuable part for music skill evaluations in Western samples. We conclude by briefly discussing the choice faced by music cognition researchers between different musical aptitude measures of which the brief PROMS is a well evaluated example.

Quantification of Diaphragm Mechanics in Pompe Disease Using Dynamic 3D MRI

BACKGROUND

Diaphragm weakness is the main reason for respiratory dysfunction in patients with Pompe disease, a progressive metabolic myopathy affecting respiratory and limb-girdle muscles. Since respiratory failure is the major cause of death among adult patients, early identification of respiratory muscle involvement is necessary to initiate treatment in time and possibly prevent irreversible damage. In this paper we investigate the suitability of dynamic MR imaging in combination with state-of-the-art image analysis methods to assess respiratory muscle weakness.

METHODS

The proposed methodology relies on image registration and lung surface extraction to quantify lung kinematics during breathing. This allows for the extraction of geometry and motion features of the lung that characterize the independent contribution of the diaphragm and the thoracic muscles to the respiratory cycle.

RESULTS

Results in 16 3D+t MRI scans (10 Pompe patients and 6 controls) of a slow expiratory maneuver show that kinematic analysis from dynamic 3D images reveals important additional information about diaphragm mechanics and respiratory muscle involvement when compared to conventional pulmonary function tests. Pompe patients with severely reduced pulmonary function showed severe diaphragm weakness presented by minimal motion of the diaphragm. In patients with moderately reduced pulmonary function, cranial displacement of posterior diaphragm parts was reduced and the diaphragm dome was oriented more horizontally at full inspiration compared to healthy controls.

CONCLUSION

Dynamic 3D MRI provides data for analyzing the contribution of both diaphragm and thoracic muscles independently. The proposed image analysis method has the potential to detect less severe diaphragm weakness and could thus be used to determine the optimal start of treatment in adult patients with Pompe disease in prospect of increased treatment response.

High-resolution intracranial vessel wall MRI in an elderly asymptomatic population: comparison of 3T and 7T

Objectives

Several intracranial vessel wall sequences have been described in recent literature, with either 3-T or 7-T magnetic resonance imaging (MRI). In the current study, we compared 3-T and 7-T MRI in visualising both the intracranial arterial vessel wall and vessel wall lesions.

Methods

Twenty-one elderly asymptomatic volunteers were scanned by 3-T and 7-T MRI with an intracranial vessel wall sequence, both before and after contrast administration. Two raters scored image quality, and presence and characteristics of vessel wall lesions.

Results

Vessel wall visibility was equal or significantly better at 7 T for the studied arterial segments, even though there were more artefacts hampering assessment. The better visualisation of the vessel wall at 7 T was most prominent in the proximal anterior cerebral circulation and the posterior cerebral artery. In the studied elderly asymptomatic population, 48 vessel-wall lesions were identified at 3 T, of which 7 showed enhancement. At 7 T, 79 lesions were identified, of which 29 showed enhancement. Seventy-one percent of all 3-T lesions and 59 % of all 7-T lesions were also seen at the other field strength.

Conclusions

Despite the large variability in detected lesions at both field strengths, we believe 7-T MRI has the highest potential to identify the total burden of intracranial vessel wall lesions.

Key Points

• Intracranial vessel wall visibility was equal or significantly better at 7-T MRI

• Most vessel wall lesions in the cerebral arteries were found at 7-T MRI

• Many intracranial vessel wall lesions showed enhancement after contrast administration

• Large variability in detected intracranial vessel wall lesions at both field strengths

• Seven-tesla MRI has the highest potential to identify total burden of intracranial atherosclerosis

Electronic supplementary material

The online version of this article (doi:10.1007/s00330-016-4483-3) contains supplementary material, which is available to authorized users.

Influenza pathogenicity during pregnancy in women and animal models

Pregnant women are at the highest risk to develop severe and even fatal influenza. The high vulnerability of women against influenza A virus infections during pregnancy was repeatedly highlighted during influenza pandemics including the pandemic of this century. In 2009, mortality rates were particularly high among otherwise healthy pregnant women. However, our current understanding of the molecular mechanisms involved in severe disease development during pregnancy is still very limited. In this review, we summarize the knowledge on the clinical observations in influenza A virus-infected pregnant women. In addition, knowledge obtained from few existing experimental infections in pregnant animal models is discussed. Since clinical data do not provide in-depth information on the pathogenesis of severe influenza during pregnancy, adequate animal models are urgently required that mimic clinical findings. Studies in pregnant animal models will allow the dissection of involved molecular disease pathways that are key to improve patient management and care.

Neural substrates of successful working memory and long-term memory formation in a relational spatial memory task

Working memory (WM) tasks may involve brain activation actually implicated in long-term memory (LTM). In order to disentangle these two memory systems, we employed a combined WM/LTM task, using a spatial relational (object-location) memory paradigm and analyzed which brain areas were associated with successful performance for either task using fMRI. Critically, we corrected for the performance on the respective memory task when analyzing subsequent memory effects. The WM task consisted of a delayed-match-to-sample task assessed in an MRI scanner. Each trial consisted of an indoor or outdoor scene in which the exact configuration of four objects had to be remembered. After a short delay (7–13 s), the scene was presented from a different angle and spatial recognition for two objects was tested. After scanning, participants received an unexpected subsequent recognition memory (LTM) task, where the two previously unprobed objects were tested. Brain activity during encoding, delay phase and probe phase was analyzed based on WM and LTM performance. Results showed that successful WM performance, when corrected for LTM performance, was associated with greater activation in the inferior frontal gyrus and left fusiform gyrus during the early stage of the maintenance phase. A correct decision during the WM probe was accompanied by greater activation in a wide network, including bilateral hippocampus, right superior parietal gyrus and bilateral insula. No voxels exhibited supra-threshold activity during the encoding phase, and we did not find any differential activity for correct versus incorrect trials in the WM task when comparing LTM correct versus LTM incorrect trials.

How to Study the City on Instagram

We introduce Instagram as a data source for use by scholars in urban studies and neighboring disciplines and propose ways to operationalize key concepts in the study of cities. These data can help shed light on segregation, the formation of subcultures, strategies of distinction, and status hierarchies in the city. Drawing on two datasets of geotagged Instagram posts from Amsterdam and Copenhagen collected over a twelve-week period, we present a proof of concept for how to explore and visualize sociospatial patterns and divisions in these two cities. We take advantage of both the social and the geographic aspects of the data, using network analysis to identify distinct groups of users and metrics of unevenness and diversity to identify socio-spatial divisions. We also discuss some of the limitations of these data and methods and suggest ways in which they can complement established quantitative and qualitative approaches in urban scholarship.

Discrepancy and Disliking Do Not Induce Negative Opinion Shifts

Both classical social psychological theories and recent formal models of opinion differentiation and bi-polarization assign a prominent role to negative social influence. Negative influence is defined as shifts away from the opinion of others and hypothesized to be induced by discrepancy with or disliking of the source of influence. There is strong empirical support for the presence of positive social influence (a shift towards the opinion of others), but evidence that large opinion differences or disliking could trigger negative shifts is mixed. We examine positive and negative influence with controlled exposure to opinions of other individuals in one experiment and with opinion exchange in another study. Results confirm that similarities induce attraction, but results do not support that discrepancy or disliking entails negative influence. Instead, our findings suggest a robust positive linear relationship between opinion distance and opinion shifts.

Healthcare Programmes for Truck Drivers in Sub-Saharan Africa: A Systematic Review and Meta-Analysis

BACKGROUND

Truck drivers have unique health needs, and by virtue of their continuous travel, experience difficulty in accessing healthcare. Currently, planning for effective care is hindered by lack of knowledge about their health needs and about the impact of on-going programmes on this population's health outcomes. We reviewed healthcare programmes implemented for sub-Saharan African truck drivers, assessed the evaluation methods, and examined impact on health outcomes.

METHODS

We searched scientific and institutional databases, and online search engines to include all publications describing a healthcare programme in sub-Saharan Africa where the main clients were truck drivers. We consulted experts and organisations working with mobile populations to identify unpublished reports. Forest plots of impact and outcome indicators with unadjusted risk ratios and 95% confidence intervals were created to map the impact of these programmes. We performed a subgroup analysis by type of indicator using a random-effects model to assess between-study heterogeneity. We conducted a sensitivity analysis to examine both the summary effect estimate chosen (risk difference vs. risk ratio) and model to summarise results (fixed vs. random effects).

RESULTS

Thirty-seven publications describing 22 healthcare programmes across 30 countries were included from 5,599 unique records. All programmes had an HIV-prevention focus with only three expanding their services to cover conditions other primary healthcare services. Twelve programmes were evaluated and most evaluations assessed changes in input, output, and outcome indicators. Absence of comparison groups, preventing attribution of the effect observed to the programme and lack of biologically confirmed outcomes were the main limitations. Four programmes estimated a quantitative change in HIV prevalence or reported STI incidence, with mixed results, and one provided anecdotal evidence of changes in AIDS-related mortality and social norms. Most programmes showed positive changes in risk behaviours, knowledge, and attitudes. Our conclusions were robust in sensitivity analyses.

CONCLUSION

Diverse healthcare programmes tailored to the needs of truck drivers implemented in 30 sub-Saharan African countries have shown potential benefits. However, information gaps about availability of services and their effects impede further planning and implementation of effective healthcare programmes for truck drivers.

Motor Skills Enhance Procedural Memory Formation and Protect against Age-Related Decline

The ability to consolidate procedural memories declines with increasing age. Prior knowledge enhances learning and memory consolidation of novel but related information in various domains. Here, we present evidence that prior motor experience-in our case piano skills-increases procedural learning and has a protective effect against age-related decline for the consolidation of novel but related manual movements. In our main experiment, we tested 128 participants with a sequential finger-tapping motor task during two sessions 24 hours apart. We observed enhanced online learning speed and offline memory consolidation for piano players. Enhanced memory consolidation was driven by a strong effect in older participants, whereas younger participants did not benefit significantly from prior piano experience. In a follow up independent control experiment, this compensatory effect of piano experience was not visible after a brief offline period of 30 minutes, hence requiring an extended consolidation window potentially involving sleep. Through a further control experiment, we rejected the possibility that the decreased effect in younger participants was caused by training saturation. We discuss our results in the context of the neurobiological schema approach and suggest that prior experience has the potential to rescue memory consolidation from age-related cognitive decline.

Not All Flavor Expertise Is Equal: The Language of Wine and Coffee Experts

People in Western cultures are poor at naming smells and flavors. However, for wine and coffee experts, describing smells and flavors is part of their daily routine. So are experts better than lay people at conveying smells and flavors in language? If smells and flavors are more easily linguistically expressed by experts, or more “codable”, then experts should be better than novices at describing smells and flavors. If experts are indeed better, we can also ask how general this advantage is: do experts show higher codability only for smells and flavors they are expert in (i.e., wine experts for wine and coffee experts for coffee) or is their linguistic dexterity more general? To address these questions, wine experts, coffee experts, and novices were asked to describe the smell and flavor of wines, coffees, everyday odors, and basic tastes. The resulting descriptions were compared on a number of measures. We found expertise endows a modest advantage in smell and flavor naming. Wine experts showed more consistency in how they described wine smells and flavors than coffee experts, and novices; but coffee experts were not more consistent for coffee descriptions. Neither expert group was any more accurate at identifying everyday smells or tastes. Interestingly, both wine and coffee experts tended to use more source-based terms (e.g., vanilla) in descriptions of their own area of expertise whereas novices tended to use more evaluative terms (e.g., nice). However, the overall linguistic strategies for both groups were en par. To conclude, experts only have a limited, domain-specific advantage when communicating about smells and flavors. The ability to communicate about smells and flavors is a matter not only of perceptual training, but specific linguistic training too.

GRAbB: Selective Assembly of Genomic Regions, a New Niche for Genomic Research

GRAbB (Genomic Region Assembly by Baiting) is a new program that is dedicated to assemble specific genomic regions from NGS data. This approach is especially useful when dealing with multi copy regions, such as mitochondrial genome and the rDNA repeat region, parts of the genome that are often neglected or poorly assembled, although they contain interesting information from phylogenetic or epidemiologic perspectives, but also single copy regions can be assembled. The program is capable of targeting multiple regions within a single run. Furthermore, GRAbB can be used to extract specific loci from NGS data, based on homology, like sequences that are used for barcoding. To make the assembly specific, a known part of the region, such as the sequence of a PCR amplicon or a homologous sequence from a related species must be specified. By assembling only the region of interest, the assembly process is computationally much less demanding and may lead to assemblies of better quality. In this study the different applications and functionalities of the program are demonstrated such as: exhaustive assembly (rDNA region and mitochondrial genome), extracting homologous regions or genes (IGS, RPB1, RPB2 and TEF1a), as well as extracting multiple regions within a single run. The program is also compared with MITObim, which is meant for the exhaustive assembly of a single target based on a similar query sequence. GRAbB is shown to be more efficient than MITObim in terms of speed, memory and disk usage. The other functionalities (handling multiple targets simultaneously and extracting homologous regions) of the new program are not matched by other programs. The program is available with explanatory documentation at https://github.com/b-brankovics/grabb. GRAbB has been tested on Ubuntu (12.04 and 14.04), Fedora (23), CentOS (7.1.1503) and Mac OS X (10.7). Furthermore, GRAbB is available as a docker repository: brankovics/grabb (https://hub.docker.com/r/brankovics/grabb/).

Adaptive Spike Threshold Enables Robust and Temporally Precise Neuronal Encoding

Neural processing rests on the intracellular transformation of information as synaptic inputs are translated into action potentials. This transformation is governed by the spike threshold, which depends on the history of the membrane potential on many temporal scales. While the adaptation of the threshold after spiking activity has been addressed before both theoretically and experimentally, it has only recently been demonstrated that the subthreshold membrane state also influences the effective spike threshold. The consequences for neural computation are not well understood yet. We address this question here using neural simulations and whole cell intracellular recordings in combination with information theoretic analysis. We show that an adaptive spike threshold leads to better stimulus discrimination for tight input correlations than would be achieved otherwise, independent from whether the stimulus is encoded in the rate or pattern of action potentials. The time scales of input selectivity are jointly governed by membrane and threshold dynamics. Encoding information using adaptive thresholds further ensures robust information transmission across cortical states i.e. decoding from different states is less state dependent in the adaptive threshold case, if the decoding is performed in reference to the timing of the population response. Results from in vitro neural recordings were consistent with simulations from adaptive threshold neurons. In summary, the adaptive spike threshold reduces information loss during intracellular information transfer, improves stimulus discriminability and ensures robust decoding across membrane states in a regime of highly correlated inputs, similar to those seen in sensory nuclei during the encoding of sensory information.

A neuron is a tiny computer that transforms electrical inputs into electrical outputs. While neurons have been investigated and modeled for many decades, some aspects remain elusive. Recently, it was demonstrated that the membrane (voltage) state of a neuron determines its threshold to spiking. In the present study we asked, what are the consequences of this dependence for the computation the neuron performs. We find that this so called adaptive threshold allows neurons to be more focused on inputs which arrive close in time with other inputs. Also, it allows neurons to represent their information more robustly, such that a readout of their activity is less influenced by the state the brain is in. The present use of information theory provides a solid foundation for these results. We obtained the results primarily in detailed simulations, but performed neural recordings to verify these properties in real neurons. In summary, an adaptive spiking threshold allows neurons to specifically compute robustly with a focus on tight temporal correlations in their input.

High functional diversity stimulates diversification in experimental microbial communities

There is a growing awareness that biodiversity not only drives ecosystem services but also affects evolutionary dynamics. However, different theories predict contrasting outcomes on when do evolutionary processes occur within a context of competition. We tested whether functional diversity can explain diversification patterns. We tracked the survival and diversification of a focal bacterial species (Pseudomonas fluorescens) growing in bacterial communities of variable diversity and composition. We found that high functional diversity reduced the fitness of the focal species and, at the same time, fostered its diversification. This pattern was linked to resource competition: High diversity increased competition on a portion of the resources while leaving most underexploited. The evolved phenotypes of the focal species showed a better use of underexploited resources, albeit at a cost of lower overall growth rates. As a result, diversification alleviated the impact of competition on the fitness of the focal species. We conclude that biodiversity can stimulate evolutionary diversification, provided that sufficient alternative niches are available.

Mother and adolescent expressed emotion and adolescent internalizing and externalizing symptom development: a six-year longitudinal study

In expressed emotion (EE) theory, it is held that high EE household environments enhance adolescent psychopathological distress. However, no longitudinal study has been conducted to examine if either the mother's EE or the adolescent's perception of EE predicts adolescent internalizing and externalizing symptom dimensions (an EE effect model) or vice versa (psychopathological effect model) together in one model. To unravel the reciprocal influences of maternal and adolescent perceived EE to adolescent internalizing and externalizing symptom dimensions, we tested two (i.e., one for internalizing and one for externalizing) cross-lagged panel models. In this study, it was found that both internalizing and externalizing symptom dimensions predicted the adolescent's perception of maternal EE as well as the mother's own rated EE criticism over time. The findings of this study should give both researchers and therapists a reason to reevaluate only using the EE effects model assumption in future EE studies.

Just a Cog in the Machine? The Individual Responsibility of Researchers in Nanotechnology is a Duty to Collectivize

Responsible Research and Innovation (RRI) provides a framework for judging the ethical qualities of innovation processes, however guidance for researchers on how to implement such practices is limited. Exploring RRI in the context of nanotechnology, this paper examines how the dispersed and interdisciplinary nature of the nanotechnology field somewhat hampers the abilities of individual researchers to control the innovation process. The ad-hoc nature of the field of nanotechnology, with its fluid boundaries and elusive membership, has thus far failed to establish a strong collective agent, such as a professional organization, through which researchers could collectively steer technological development in light of social and environmental needs. In this case, individual researchers cannot innovate responsibly purely by themselves, but there is also no structural framework to ensure that responsible development of nanotechnologies takes place. We argue that, in such a case, individual researchers have a duty to collectivize. In short, researchers in situations where it is challenging for individual agents to achieve the goals of RRI are compelled to develop organizations to facilitate RRI. In this paper we establish and discuss the criteria under which individual researchers have this duty to collectivize.

Novel bioinformatic developments for exome sequencing

With the widespread adoption of next generation sequencing technologies by the genetics community and the rapid decrease in costs per base, exome sequencing has become a standard within the repertoire of genetic experiments for both research and diagnostics. Although bioinformatics now offers standard solutions for the analysis of exome sequencing data, many challenges still remain; especially the increasing scale at which exome data are now being generated has given rise to novel challenges in how to efficiently store, analyze and interpret exome data of this magnitude. In this review we discuss some of the recent developments in bioinformatics for exome sequencing and the directions that this is taking us to. With these developments, exome sequencing is paving the way for the next big challenge, the application of whole genome sequencing.

Examining the Heterogeneous Genome Content of Multipartite Viruses BMV and CCMV by Native Mass Spectrometry

Since the concept was first introduced by Brian Chait and co-workers in 1991, mass spectrometry of proteins and protein complexes under non-denaturing conditions (native MS) has strongly developed, through parallel advances in instrumentation, sample preparation, and data analysis tools. However, the success rate of native MS analysis, particularly in heterogeneous mega-Dalton (MDa) protein complexes, still strongly depends on careful instrument modification. Here, we further explore these boundaries in native mass spectrometry, analyzing two related endogenous multipartite viruses: the Brome Mosaic Virus (BMV) and the Cowpea Chlorotic Mottle Virus (CCMV). Both CCMV and BMV are approximately 4.6 megadalton (MDa) in mass, of which approximately 1 MDA originates from the genomic content of the virion. Both viruses are produced as mixtures of three particles carrying different segments of the genome, varying by approximately 0.1 MDA in mass (~2%). This mixture of particles poses a challenging analytical problem for high-resolution native MS analysis, given the large mass scales involved. We attempt to unravel the particle heterogeneity using both Q-TOF and Orbitrap mass spectrometers extensively modified for analysis of very large assemblies. We show that manipulation of the charging behavior can provide assistance in assigning the correct charge states. Despite their challenging size and heterogeneity, we obtained native mass spectra with resolved series of charge states for both BMV and CCMV, demonstrating that native MS of endogenous multipartite virions is feasible. Graphical Abstract ᅟ.

Gone with the Wind: Conceiving of Moral Responsibility in the Case of GMO Contamination

Genetically modified organisms are a technology now used with increasing frequency in agriculture. Genetically modified seeds have the special characteristic of being living artefacts that can reproduce and spread; thus it is difficult to control where they end up. In addition, genetically modified seeds may also bring about uncertainties for environmental and human health. Where they will go and what effect they will have is therefore very hard to predict: this creates a puzzle for regulators. In this paper, I use the problem of contamination to complicate my ascription of forward-looking moral responsibility to owners of genetically modified organisms. Indeed, how can owners act responsibly if they cannot know that contamination has occurred? Also, because contamination creates new and unintended ownership, it challenges the ascription of forward-looking moral responsibility based on ownership. From a broader perspective, the question this paper aims to answer is as follows: how can we ascribe forward-looking moral responsibility when the effects of the technologies in question are difficult to know or unknown? To solve this problem, I look at the epistemic conditions for moral responsibility and connect them to the normative notion of the social experiment. Indeed, examining conditions for morally responsible experimentation helps to define a range of actions and to establish the related epistemic virtues that owners should develop in order to act responsibly where genetically modified organisms are concerned.

Informed Consent in Asymmetrical Relationships: an Investigation into Relational Factors that Influence Room for Reflection

In recent years, informed consent has been suggested as a way to deal with risks posed by engineered nanomaterials. We argue that while we can learn from experiences with informed consent in treatment and research contexts, we should be aware that informed consent traditionally pertains to certain features of the relationships between doctors and patients and researchers and research participants, rather than those between producers and consumers and employers and employees, which are more prominent in the case of engineered nanomaterials. To better understand these differences, we identify three major relational factors that influence whether valid informed consent is obtainable, namely dependency, personal proximity, and existence of shared interests. We show that each type of relationship offers different opportunities for reflection and therefore poses distinct challenges for obtaining valid informed consent. Our analysis offers a systematic understanding of the possibilities for attaining informed consent in the context of nanomaterial risks and makes clear that measures or regulations to improve the obtainment of informed consent should be attuned to the specific interpersonal relations to which it is supposed to apply.

Cognitive and Ocular Factors Jointly Determine Pupil Responses under Equiluminance

Changes in pupil diameter can reflect high-level cognitive signals that depend on central neuromodulatory mechanisms. However, brain mechanisms that adjust pupil size are also exquisitely sensitive to changes in luminance and other events that would be considered a nuisance in cognitive experiments recording pupil size. We implemented a simple auditory experiment involving no changes in visual stimulation. Using finite impulse-response fitting we found pupil responses triggered by different types of events. Among these are pupil responses to auditory events and associated surprise: cognitive effects. However, these cognitive responses were overshadowed by pupil responses associated with blinks and eye movements, both inevitable nuisance factors that lead to changes in effective luminance. Of note, these latter pupil responses were not recording artifacts caused by blinks and eye movements, but endogenous pupil responses that occurred in the wake of these events. Furthermore, we identified slow (tonic) changes in pupil size that differentially influenced faster (phasic) pupil responses. Fitting all pupil responses using gamma functions, we provide accurate characterisations of cognitive and non-cognitive response shapes, and quantify each response's dependence on tonic pupil size. These results allow us to create a set of recommendations for pupil size analysis in cognitive neuroscience, which we have implemented in freely available software.

A Proteomics Approach to Identify New Putative Cardiac Intercalated Disk Proteins

AIMS

Synchronous beating of the heart is dependent on the efficient functioning of the cardiac intercalated disk (ID). The ID is composed of a complex protein network enabling electrical continuity and chemical communication between individual cardiomyocytes. Recently, several different studies have shed light on increasingly prevalent cardiac diseases involving the ID. Insufficient knowledge of its composition makes it difficult to study these disease mechanisms in more detail and therefore here we aim expand the ID proteome. Here, using a combination of general membrane enrichment, in-depth quantitative proteomics and an intracellular location driven bioinformatics approach, we aim to discover new putative ID proteins in rat ventricular tissue.

METHODS AND RESULTS

General membrane isolation, enriched amongst others also with ID proteins as based on presence of the established markers connexin-43 and n-cadherin, was performed using centrifugation. By mass spectrometry, we quantitatively evaluated the level of 3455 proteins in the enriched membrane fraction (EMF) and its counterpart, the soluble cytoplasmic fraction. These data were stringently filtered to generate a final set of 97 enriched, putative ID proteins. These included Cx43 and n-cadherin, but also many interesting novel candidates. We selected 4 candidates (Flotillin-2 (FLOT2), Nexilin (NEXN), Popeye-domain-containg-protein 2 (POPDC2) and thioredoxin-related-transmembrane-protein 2 (TMX2)) and confirmed their co-localization with n-cadherin in the ID of human and rat heart cryo-sections, and isolated dog cardiomyocytes.

CONCLUSION

The presented proteomics dataset of putative new ID proteins is a valuable resource for future research into this important molecular intersection of the heart.

ANT1-mediated fatty acid-induced uncoupling as a target for improving myocellular insulin sensitivity

AIMS/HYPOTHESIS

Dissipating energy via mitochondrial uncoupling has been suggested to contribute to enhanced insulin sensitivity. We hypothesised that skeletal muscle mitochondria of endurance-trained athletes have increased sensitivity for fatty acid (FA)-induced uncoupling, which is driven by the mitochondrial protein adenine nucleotide translocase 1 (ANT1).

METHODS

Capacity for FA-induced uncoupling was measured in endurance-trained male athletes (T) and sedentary young men (UT) in an observational study and also in isolated skeletal muscle mitochondria from Zucker diabetic fatty (ZDF) rats and C2C12 myotubes following small interfering RNA (siRNA)-mediated gene silencing of ANT1. Thus, fuelled by glutamate/succinate (fibres) or pyruvate (mitochondria and myotubes) and in the presence of oligomycin to block ATP synthesis, increasing levels of oleate (fibres) or palmitate (mitochondria and myotubes) were automatically titrated while respiration was monitored. Insulin sensitivity was measured by hyperinsulinaemic-euglycaemic clamp in humans and via insulin-stimulated glucose uptake in myotubes.

RESULTS

Skeletal muscle from the T group displayed increased sensitivity to FA-induced uncoupling (p = 0.011) compared with muscle from the UT group, and this was associated with elevated insulin sensitivity (p = 0.034). ANT1 expression was increased in T (p = 0.013). Mitochondria from ZDF rats displayed decreased sensitivity for FA-induced uncoupling (p = 0.008). This difference disappeared in the presence of the adenine nucleotide translocator inhibitor carboxyatractyloside. Partial knockdown of ANT1 in C2C12 myotubes decreased sensitivity to the FA-induced uncoupling (p = 0.008) and insulin-stimulated glucose uptake (p = 0.025) compared with controls.

CONCLUSIONS/INTERPRETATION

Increased sensitivity to FA-induced uncoupling is associated with enhanced insulin sensitivity and is affected by ANT1 activity in skeletal muscle. FA-induced mitochondrial uncoupling may help to preserve insulin sensitivity in the face of a high supply of FAs.

TRIAL REGISTRATION

www.trialregister.nl NTR2002.

Weak self-association of cytochrome c peroxidase molecules observed by paramagnetic NMR

There is growing experimental evidence that many proteins exhibit a tendency for (ultra)weak homo- or hetero- oligomerization interactions. With the development of paramagnetic relaxation enhancement NMR spectroscopy it has become possible to characterize weak complexes experimentally and even detect complexes with affinities in the 1-25 mM range. We present evidence for a weak complex between cytochrome c peroxidase (CcP) molecules. In a previous study, we attached nitroxide based spin labels at three positions on CcP with the intent of observing intramolecular PRE effects. However, several intermolecular PRE effects were also observed suggesting a weak self-association between CcP molecules. The CcP-CcP complex was characterized using paramagnetic NMR and protein docking. The interaction occurs between the surface that is also part of the stereo-specific binding site for its physiological partner, cytochrome c (Cc), and several small, positively charged patches on the "back" of CcP. The CcP-CcP complex is not a stereo-specific complex. It is a dynamic ensemble of orientations, characteristic of an encounter state. The contact areas resemble those observed for CcP molecules in crystals. The CcP-CcP complex formation competes with that of the CcP-Cc complex. However, the affinity for Cc is much larger and thus it is expected that, under physiological conditions, auto-inhibition will be limited. A weak self-association between cytochrome c peroxidase molecules was characterized using paramagnetic NMR.

The Effect of Optokinetic Stimulation on Perceptual and Postural Symptoms in Visual Vestibular Mismatch Patients

Background

Vestibular patients occasionally report aggravation or triggering of their symptoms by visual stimuli, which is called visual vestibular mismatch (VVM). These patients therefore experience discomfort, disorientation, dizziness and postural unsteadiness.

Objective

Firstly, we aimed to get a better insight in the underlying mechanism of VVM by examining perceptual and postural symptoms. Secondly, we wanted to investigate whether roll-motion is a necessary trait to evoke these symptoms or whether a complex but stationary visual pattern equally provokes them.

Methods

Nine VVM patients and healthy matched control group were examined by exposing both groups to a stationary stimulus as well as an optokinetic stimulus rotating around the naso-occipital axis for a prolonged period of time. Subjective visual vertical (SVV) measurements, posturography and relevant questionnaires were assessed.

Results

No significant differences between both groups were found for SVV measurements. Patients always swayed more and reported more symptoms than healthy controls. Prolonged exposure to roll-motion caused in patients and controls an increase in postural sway and symptoms. However, only VVM patients reported significantly more symptoms after prolonged exposure to the optokinetic stimulus compared to scores after exposure to a stationary stimulus.

Conclusions

VVM patients differ from healthy controls in postural and subjective symptoms and motion is a crucial factor in provoking these symptoms. A possible explanation could be a central visual-vestibular integration deficit, which has implications for diagnostics and clinical rehabilitation purposes. Future research should focus on the underlying central mechanism of VVM and the effectiveness of optokinetic stimulation in resolving it.

Complementary Hand Responses Occur in Both Peri- and Extrapersonal Space

Human beings have a strong tendency to imitate. Evidence from motor priming paradigms suggests that people automatically tend to imitate observed actions such as hand gestures by performing mirror-congruent movements (e.g., lifting one’s right finger upon observing a left finger movement; from a mirror perspective). Many observed actions however, do not require mirror-congruent responses but afford complementary (fitting) responses instead (e.g., handing over a cup; shaking hands). Crucially, whereas mirror-congruent responses don't require physical interaction with another person, complementary actions often do. Given that most experiments studying motor priming have used stimuli devoid of contextual information, this space or interaction-dependency of complementary responses has not yet been assessed. To address this issue, we let participants perform a task in which they had to mirror or complement a hand gesture (fist or open hand) performed by an actor depicted either within or outside of reach. In three studies, we observed faster reaction times and less response errors for complementary relative to mirrored hand movements in response to open hand gestures (i.e., ‘hand-shaking’) irrespective of the perceived interpersonal distance of the actor. This complementary effect could not be accounted for by a low-level spatial cueing effect. These results demonstrate that humans have a strong and automatic tendency to respond by performing complementary actions. In addition, our findings underline the limitations of manipulations of space in modulating effects of motor priming and the perception of affordances.

Health effects of non-occupational exposure to oil extraction

Oil extraction may cause extensive environmental impact that can affect health of populations living in surrounding areas. Large populations are potentially exposed to oil extraction related contamination through residence in areas where oil extraction is conducted, especially in low and middle income countries (LMICs). Health effects among people residentially exposed to upstream oil industry contaminants have been poorly studied. Health effects of exposure to oil related contamination have been mainly studied among cleanup workers after oil spills from tankers or offshore platforms.In this paper we aim to identify the type and extension of residential exposures related to oil extraction activities and to comment on the few health studies available. We estimated that 638 million persons in LMICs inhabit rural areas close to conventional oil reservoirs. It is relevant to specifically study people residentially exposed to upstream oil industry for the following reasons: First, persons are exposed during long periods of time to oil related contamination. Second, routes of exposure differ between workers and people living close to oil fields, who can be exposed by ingestion of contaminated waters/foods and by dermal contact with contaminated water and/or land during daily activities (e.g. bathing, agricultural activities, etc.). Third, individuals potentially more susceptible to the effect of oil related contamination and not normally occupationally exposed, such as infants, children, pregnant women, elderly or people with previous health conditions, are also exposed.There are few papers studying the potential health effects of residential exposure to oil related contamination, and most of them share important limitations. There is a need for more research through the conduct of methodologically robust studies in exposed populations worldwide. Despite the difficulties in the conduct of studies in remote areas, novel approaches, such as measurement of individual exposure using biomarkers of exposure and effect, should be used. These studies should be promoted to understand the health risks associated to residential exposure to oil related contamination, support effective control policies to avoid such contamination and to sustain public health recommendations and policies to avoid exposure in already contaminated areas.

REDD+ on the rocks? Conflict Over Forest and Politics of Justice in Vietnam

In Vietnam, villagers involved in a REDD+ (reduced emissions from deforestation and forest degradation) pilot protect areas with rocks which have barely a tree on them. The apparent paradox indicates how actual practices differ from general ideas about REDD+ due to ongoing conflict over forest, and how contestations over the meaning of justice are a core element in negotiations over REDD+. We explore these politics of justice by examining how the actors involved in the REDD+ pilot negotiate the particular subjects, dimensions, and authority of justice considered relevant, and show how politics of justice are implicit to practical decisions in project implementation. Contestations over the meaning of justice are an important element in the practices and processes constituting REDD+ at global, national and local levels, challenging uniform definitions of forest justice and how forests ought to be managed.