Coagulation Factor Xa Has No Effects on the Expression of PAR1, PAR2, and PAR4 and No Proinflammatory Effects on HL-1 Cells

Atrial fibrillation (AF), characterised by irregular high-frequency contractions of the atria of the heart, is of increasing clinical importance. The reasons are the increasing prevalence and thromboembolic complications caused by AF. So-called atrial remodelling is characterised, among other things, by atrial dilatation and fibrotic remodelling. As a result, AF is self-sustaining and forms a procoagulant state. But hypercoagulation not only appears to be the consequence of AF. Coagulation factors can exert influence on cells via protease-activated receptors (PAR) and thereby the procoagulation state could contribute to the development and maintenance of AF. In this work, the influence of FXa on Heart Like-1 (HL-1) cells, which are murine adult atrial cardiomyocytes (immortalized), was investigated. PAR1, PAR2, and PAR4 expression was detected. After incubations with FXa (5-50 nM; 4-24 h) or PAR1- and PAR2-agonists (20 µM; 4-24 h), no changes occurred in PAR expression or in the inflammatory signalling cascade. There were no time- or concentration-dependent changes in the phosphorylation of the MAP kinases ERK1/2 or the p65 subunit of NF-κB. In addition, there was no change in the mRNA expression of the cell adhesion molecules (ICAM-1, VCAM-1, fibronectin). Thus, FXa has no direct PAR-dependent effects on HL-1 cells. Future studies should investigate the influence of FXa on human cardiomyocytes or on other cardiac cell types like fibroblasts.

Breaking the Axis-Symmetry of a Single-Wall Carbon Nanotube During Its Growth

The asymmetrical growth of a single-wall carbon nanotube (SWCNT) by introducing a change of a local atomic structure, is usually inevitable and supposed to have a profound effect on the chirality control and property tailor. However, the breaking of the symmetry during SWCNT growth remains unexplored and its origins at the atomic-scale are elusive. Here, environmental transmission electron microscopy is used to capture the process of breaking the symmetry of a growing SWCNT from a sub-2-nm platinum catalyst nanoparticle in real-time, demonstrating that topological defects formed on the side of a SWCNT can serve as a buffer for stress release and inherently break its axis-symmetrical growth. Atomic-level details reveal the importance of the tube-catalyst interface and how the atom rearrangement of the solid-state platinum catalyst around the interface influences the final tubular structure. The active sites responsible for trapping carbon dimers and providing enough driving force for carbon incorporation and asymmetric growth are shown to be low-coordination step edges, as confirmed by theoretical simulations.

The Expanding Phenotypical Spectrum of WARS2-Related Disorder: Four Novel Cases with a Common Recurrent Variant

Biallelic variants in the mitochondrial form of the tryptophanyl-tRNA synthetases (WARS2) can cause a neurodevelopmental disorder with movement disorders including early-onset tremor-parkinsonism syndrome. Here, we describe four new patients, who all presented at a young age with a tremor-parkinsonism syndrome and responded well to levodopa. All patients carry the same recurrent, hypomorphic missense variant (NM_015836.4: c.37T>G; p.Trp13Gly) either together with a previously described truncating variant (NM_015836.4: c.797Cdel; p.Pro266ArgfsTer10), a novel truncating variant (NM_015836.4: c.346C>T; p.Gln116Ter), a novel canonical splice site variant (NM_015836.4: c.349-1G>A), or a novel missense variant (NM_015836.4: c.475A>C, p.Thr159Pro). We investigated the mitochondrial function in patients and found increased levels of mitochondrially encoded cytochrome C Oxidase II as part of the mitochondrial respiratory chain as well as decreased mitochondrial integrity and branching. Finally, we conducted a literature review and here summarize the broad phenotypical spectrum of reported WARS2-related disorders. In conclusion, WARS2-related disorders are diagnostically challenging diseases due to the broad phenotypic spectrum and the disease relevance of a relatively common missense change that is often filtered out in a diagnostic setting since it occurs in ~0.5% of the general European population.

Paired guide RNA CRISPR-Cas9 screening for protein-coding genes and lncRNAs involved in transdifferentiation of human B-cells to macrophages

CRISPR-Cas9 screening libraries have arisen as a powerful tool to identify protein-coding (pc) and non-coding genes playing a role along different processes. In particular, the usage of a nuclease active Cas9 coupled to a single gRNA has proven to efficiently impair the expression of pc-genes by generating deleterious frameshifts. Here, we first demonstrate that targeting the same gene simultaneously with two guide RNAs (paired guide RNAs, pgRNAs) synergistically enhances the capacity of the CRISPR-Cas9 system to knock out pc-genes. We next design a library to target, in parallel, pc-genes and lncRNAs known to change expression during the transdifferentiation from pre-B cells to macrophages. We show that this system is able to identify known players in this process, and also predicts 26 potential novel ones, of which we select four (two pc-genes and two lncRNAs) for deeper characterization. Our results suggest that in the case of the candidate lncRNAs, their impact in transdifferentiation may be actually mediated by enhancer regions at the targeted loci, rather than by the lncRNA transcripts themselves. The CRISPR-Cas9 coupled to a pgRNAs system is, therefore, a suitable tool to simultaneously target pc-genes and lncRNAs for genomic perturbation assays.

Choice of anesthesia and data analysis method strongly increases sensitivity of 18F-FDG PET imaging during experimental epileptogenesis

Purpose

Alterations in brain glucose metabolism detected by 2-deoxy-2-[¹⁸F]-fluoro-D-glucose (¹⁸F-FDG) positron emission tomography (PET) may serve as an early predictive biomarker and treatment target for epileptogenesis. Here, we aimed to investigate changes in cerebral glucose metabolism before induction of epileptogenesis, during epileptogenesis as well as during chronic epilepsy. As anesthesia is usually unavoidable for preclinical PET imaging and influences the distribution of the radiotracer, four different protocols were compared.

Procedures

We investigated ¹⁸F-FDG uptake phase in conscious rats followed by a static scan as well as dynamic scans under continuous isoflurane, medetomidine-midazolam-fentanyl (MMF), or propofol anesthesia. Furthermore, we applied different analysis approaches: atlas-based regional analysis, statistical parametric mapping, and kinetic analysis.

Results

At baseline and compared to uptake in conscious rats, isoflurane and propofol anesthesia resulted in decreased cortical ¹⁸F-FDG uptake while MMF anesthesia led to a globally decreased tracer uptake. During epileptogenesis, MMF anesthesia was clearly best distinctive for visualization of prominently increased glucometabolism in epilepsy-related brain areas. Kinetic modeling further increased sensitivity, particularly for continuous isoflurane anesthesia. During chronic epilepsy, hypometabolism affecting more or less the whole brain was detectable with all protocols.

Conclusion

This study reveals evaluation of anesthesia protocols for preclinical ¹⁸F-FDG PET imaging as a critical step in the study design. Together with an appropriate data analysis workflow, the chosen anesthesia protocol may uncover otherwise concealed disease-associated regional glucometabolic changes.

Body ownership increases the interference between observed and executed movements

When we successfully achieve willed actions, the feeling that our moving body parts belong to the self (i.e., body ownership) is barely required. However, how and to what extent the awareness of our own body contributes to the neurocognitive processes subserving actions is still debated. Here we capitalized on immersive virtual reality in order to examine whether and how body ownership influences motor performance (and, secondly, if it modulates the feeling of voluntariness). Healthy participants saw a virtual body either from a first or a third person perspective. In both conditions, they had to draw continuously straight vertical lines while seeing the virtual arm doing the same action (i.e., drawing lines) or deviating from them (i.e., drawing ellipses). Results showed that when there was a mismatch between the intended and the seen movements (i.e., participants had to draw lines but the avatar drew ellipses), motor performance was strongly "attracted" towards the seen (rather than the performed) movement when the avatar's body part was perceived as own (i.e., first person perspective). In support of previous studies, here we provide direct behavioral evidence that the feeling of body ownership modulates the interference of seen movements to the performed movements.

Nilvadipine in mild to moderate Alzheimer disease: A randomised controlled trial

BACKGROUND

This study reports the findings of the first large-scale Phase III investigator-driven clinical trial to slow the rate of cognitive decline in Alzheimer disease with a dihydropyridine (DHP) calcium channel blocker, nilvadipine. Nilvadipine, licensed to treat hypertension, reduces amyloid production, increases regional cerebral blood flow, and has demonstrated anti-inflammatory and anti-tau activity in preclinical studies, properties that could have disease-modifying effects for Alzheimer disease. We aimed to determine if nilvadipine was effective in slowing cognitive decline in subjects with mild to moderate Alzheimer disease.

METHODS AND FINDINGS

NILVAD was an 18-month, randomised, placebo-controlled, double-blind trial that randomised participants between 15 May 2013 and 13 April 2015. The study was conducted at 23 academic centres in nine European countries. Of 577 participants screened, 511 were eligible and were randomised (258 to placebo, 253 to nilvadipine). Participants took a trial treatment capsule once a day after breakfast for 78 weeks. Participants were aged >50 years, meeting National Institute of Neurological and Communicative Disorders and Stroke/Alzheimer's disease Criteria (NINCDS-ADRDA) for diagnosis of probable Alzheimer disease, with a Standardised Mini-Mental State Examination (SMMSE) score of ≥12 and <27. Participants were randomly assigned to 8 mg sustained-release nilvadipine or matched placebo. The a priori defined primary outcome was progression on the Alzheimer's Disease Assessment Scale Cognitive Subscale-12 (ADAS-Cog 12) in the modified intention-to-treat (mITT) population (n = 498), with the Clinical Dementia Rating Scale sum of boxes (CDR-sb) as a gated co-primary outcome, eligible to be promoted to primary end point conditional on a significant effect on the ADAS-Cog 12. The analysis set had a mean age of 73 years and was 62% female. Baseline demographic and Alzheimer disease-specific characteristics were similar between treatment groups, with reported mean of 1.7 years since diagnosis and mean SMMSE of 20.4. The prespecified primary analyses failed to show any treatment benefit for nilvadipine on the co-primary outcome (p = 0.465). Decline from baseline in ADAS-Cog 12 on placebo was 0.79 (95% CI, -0.07-1.64) at 13 weeks, 6.41 (5.33-7.49) at 52 weeks, and 9.63 (8.33-10.93) at 78 weeks and on nilvadipine was 0.88 (0.02-1.74) at 13 weeks, 5.75 (4.66-6.85) at 52 weeks, and 9.41 (8.09-10.73) at 78 weeks. Exploratory analyses of the planned secondary outcomes showed no substantial effects, including on the CDR-sb or the Disability Assessment for Dementia. Nilvadipine appeared to be safe and well tolerated. Mortality was similar between groups (3 on nilvadipine, 4 on placebo); higher counts of adverse events (AEs) on nilvadipine (1,129 versus 1,030), and serious adverse events (SAEs; 146 versus 101), were observed. There were 14 withdrawals because of AEs. Major limitations of this study were that subjects had established dementia and the likelihood that non-Alzheimer subjects were included because of the lack of biomarker confirmation of the presence of brain amyloid.

CONCLUSIONS

The results do not suggest benefit of nilvadipine as a treatment in a population spanning mild to moderate Alzheimer disease.

TRIAL REGISTRATION

Clinicaltrials.gov NCT02017340, EudraCT number 2012-002764-27.

Metabolic survey of Botryococcus braunii: Impact of the physiological state on product formation

The microalga Botryococcus braunii is widely regarded as a potential renewable and sustainable source for industrial applications because of its capability to produce large amounts of metabolically expensive (exo-) polysaccharides and lipids, notably hydrocarbons. A comprehensive and systematic metabolic characterization of the Botryococcus braunii race A strain CCAP 807/2 was conducted within the present study, including the detailed analysis of growth-associated and physiological parameters. In addition, the intracellular metabolome was profiled for the first time and showed growth- and product-specific fluctuations in response to the different availability of medium resources during the cultivation course. Among the identified metabolites, a constant expression of raffinose was observed for the first time under standard conditions, which has until now only been described for higher plants. Overall, the multilayered analysis during the cultivation of strain CCAP 807/2 allowed the differentiation of four distinct physiological growth phases and revealed differences in the production profiles and content of liquid hydrocarbons and carbohydrates with up to 84% of organic dry weight (oDW). In the process, an enhanced production of carbohydrates with up to 63% of oDW (1.36±0.03 g L-1) could be observed during the late linear growth phase, whereas the highest accumulation of extracellular hydrocarbons with up to 24% of oDW (0.66±0.12 g L-1) occurred mainly during the stationary growth phase. Altogether, the knowledge obtained is potentially useful for the general understanding of the overall physiology of Botryococcus braunii and provide important insights into the growth behavior and product formation of this microalga, and is thus relevant for large scale biofuel production and industrial applications.

The impact of Earth system feedbacks on carbon budgets and climate response

A number of studies have examined the size of the allowable global cumulative carbon budget compatible with limiting twenty-first century global average temperature rise to below 2°C and below 1.5°C relative to pre-industrial levels. These estimates of cumulative emissions have a number of uncertainties including those associated with the climate sensitivity and the global carbon cycle. Although the IPCC fifth assessment report contained information on a range of Earth system feedbacks, such as carbon released by thawing of permafrost or methane production by wetlands as a result of climate change, the impact of many of these Earth system processes on the allowable carbon budgets remains to be quantified. Here, we make initial estimates to show that the combined impact from typically unrepresented Earth system processes may be important for the achievability of limiting warming to 1.5°C or 2°C above pre-industrial levels. The size of the effects range up to around a 350 GtCO₂ budget reduction for a 1.5°C warming limit and around a 500 GtCO₂ reduction for achieving a warming limit of 2°C. Median estimates for the extra Earth system forcing lead to around 100 GtCO₂ and 150 GtCO₂, respectively, for the two warming limits. Our estimates are equivalent to several years of anthropogenic carbon dioxide emissions at present rates. In addition to the likely reduction of the allowable global carbon budgets, the extra feedbacks also bring forward the date at which a given warming threshold is likely to be exceeded for a particular emission pathway.This article is part of the theme issue 'The Paris Agreement: understanding the physical and social challenges for a warming world of 1.5°C above pre-industrial levels'.

How to responsibly acknowledge research work in the era of big data and biobanks: ethical aspects of the Bioresource Research Impact Factor (BRIF)

Currently, a great deal of biomedical research in fields such as epidemiology, clinical trials and genetics is reliant on vast amounts of biological and phenotypic information collected and assembled in biobanks. While many resources are being invested to ensure that comprehensive and well-organised biobanks are able to provide increased access to, and sharing of biomedical samples and information, many barriers and challenges remain to such responsible and extensive sharing. Germane to the discussion herein is the barrier to collecting and sharing bioresources related to the lack of proper recognition of researchers and clinicians who developed the bioresource. Indeed, the efforts and resources invested to set up and sustain a bioresource can be enormous and such work should be easily traced and properly recognised. However, there is currently no such system that systematically and accurately traces and attributes recognition to those doing this work or the bioresource institution itself. As a beginning of a solution to the "recognition problem", the Bioresource Research Impact Factor/Framework (BRIF) initiative was proposed almost a decade and a half ago and is currently under further development. With the ultimate aim of increasing awareness and understanding of the BRIF, in this article, we contribute the following: (1) a review of the objectives and functions of the BRIF including the description of two tools that will help in the deployment of the BRIF, the CoBRA (Citation of BioResources in journal Articles) guideline, and the Open Journal of Bioresources (OJB); (2) the results of a small empirical study on stakeholder awareness of the BRIF and (3) a brief analysis of the ethical dimensions of the BRIF which allow it to be a positive contribution to responsible biobanking.

CO2 leakage alters biogeochemical and ecological functions of submarine sands

Subseabed CO2 storage is considered a future climate change mitigation technology. We investigated the ecological consequences of CO2 leakage for a marine benthic ecosystem. For the first time with a multidisciplinary integrated study, we tested hypotheses derived from a meta-analysis of previous experimental and in situ high-CO2 impact studies. For this, we compared ecological functions of naturally CO2-vented seafloor off the Mediterranean island Panarea (Tyrrhenian Sea, Italy) to those of nonvented sands, with a focus on biogeochemical processes and microbial and faunal community composition. High CO2 fluxes (up to 4 to 7 mol CO2 m-2 hour-1) dissolved all sedimentary carbonate, and comigration of silicate and iron led to local increases of microphytobenthos productivity (+450%) and standing stocks (+300%). Despite the higher food availability, faunal biomass (-80%) and trophic diversity were substantially lower compared to those at the reference site. Bacterial communities were also structurally and functionally affected, most notably in the composition of heterotrophs and microbial sulfate reduction rates (-90%). The observed ecological effects of CO2 leakage on submarine sands were reproduced with medium-term transplant experiments. This study assesses indicators of environmental impact by CO2 leakage and finds that community compositions and important ecological functions are permanently altered under high CO2.

Genetic aspects of feed efficiency and reduction of environmental footprint in broilers: a review

Currently, optimization of feed efficiency is one of the main challenges in improvement programs of livestock and poultry genetics. The objective of this review is to present the genetic aspects of feed efficiency related traits in meat-type chicken and possible ways to reduce the environmental impact of poultry meat production with effective breeding. Basic measures of feed efficiency are defined and the genetic background of these traits, including a review of heritabilities is described. Moreover, a number of genomic regions and candidate genes determining feed efficiency traits of broilers that were detected over the past decades are described. Classical and genomic selection strategies for feed efficiency in the context of its relationships with other performance traits are discussed as well. Finally, future strategies to improve feed digestibility are described as it is expected that they will decrease wastes and greenhouse gas emission. Further genetic improvement of feed efficiency, should be examined jointly with appropriate feeding strategies in broilers.

Robust estimation of risks from small samples

Data-driven risk analysis involves the inference of probability distributions from measured or simulated data. In the case of a highly reliable system, such as the electricity grid, the amount of relevant data is often exceedingly limited, but the impact of estimation errors may be very large. This paper presents a robust non-parametric Bayesian method to infer possible underlying distributions. The method obtains rigorous error bounds even for small samples taken from ill-behaved distributions. The approach taken has a natural interpretation in terms of the intervals between ordered observations, where allocation of probability mass across intervals is well specified, but the location of that mass within each interval is unconstrained. This formulation gives rise to a straightforward computational resampling method: Bayesian interval sampling. In a comparison with common alternative approaches, it is shown to satisfy strict error bounds even for ill-behaved distributions.This article is part of the themed issue 'Energy management: flexibility, risk and optimization'.

Influence of cerebral blood vessel movements on the position of perivascular synapses

Synaptic activity is regulated and limited by blood flow, which is controlled by blood vessel dilation and contraction. Traditionally, the study of neurovascular coupling has mainly focused on energy consumption and oxygen delivery. However, the mechanical changes that blood vessel movements induce in the surrounding tissue have not been considered. We have modeled the mechanical changes that movements of blood vessels cause in neighboring synapses. Our simulations indicate that synaptic densities increase or decrease during vascular dilation and contraction, respectively, near the blood vessel walls. This phenomenon may alter the concentration of neurotransmitters and vasoactive substances in the immediate vicinity of the vessel wall and thus may have an influence on local blood flow.

The missing link: Predicting connectomes from noisy and partially observed tract tracing data

Our understanding of the wiring map of the brain, known as the connectome, has increased greatly in the last decade, mostly due to technological advancements in neuroimaging techniques and improvements in computational tools to interpret the vast amount of available data. Despite this, with the exception of the C. elegans roundworm, no definitive connectome has been established for any species. In order to obtain this, tracer studies are particularly appealing, as these have proven highly reliable. The downside of tract tracing is that it is costly to perform, and can only be applied ex vivo. In this paper, we suggest that instead of probing all possible connections, hitherto unknown connections may be predicted from the data that is already available. Our approach uses a 'latent space model' that embeds the connectivity in an abstract physical space. Regions that are close in the latent space have a high chance of being connected, while regions far apart are most likely disconnected in the connectome. After learning the latent embedding from the connections that we did observe, the latent space allows us to predict connections that have not been probed previously. We apply the methodology to two connectivity data sets of the macaque, where we demonstrate that the latent space model is successful in predicting unobserved connectivity, outperforming two baselines and an alternative model in nearly all cases. Furthermore, we show how the latent spatial embedding may be used to integrate multimodal observations (i.e. anterograde and retrograde tracers) for the mouse neocortex. Finally, our probabilistic approach enables us to make explicit which connections are easy to predict and which prove difficult, allowing for informed follow-up studies.

Common disease signatures from gene expression analysis in Huntington's disease human blood and brain

BACKGROUND

Huntington's disease (HD) is a devastating brain disorder with no effective treatment or cure available. The scarcity of brain tissue makes it hard to study changes in the brain and impossible to perform longitudinal studies. However, peripheral pathology in HD suggests that it is possible to study the disease using peripheral tissue as a monitoring tool for disease progression and/or efficacy of novel therapies. In this study, we investigated if blood can be used to monitor disease severity and progression in brain. Since previous attempts using only gene expression proved unsuccessful, we compared blood and brain Huntington's disease signatures in a functional context.

METHODS

Microarray HD gene expression profiles from three brain regions were compared to the transcriptome of HD blood generated by next generation sequencing. The comparison was performed with a combination of weighted gene co-expression network analysis and literature based functional analysis (Concept Profile Analysis). Uniquely, our comparison of blood and brain datasets was not based on (the very limited) gene overlap but on the similarity between the gene annotations in four different semantic categories: "biological process", "cellular component", "molecular function" and "disease or syndrome".

RESULTS

We identified signatures in HD blood reflecting a broad pathophysiological spectrum, including alterations in the immune response, sphingolipid biosynthetic processes, lipid transport, cell signaling, protein modification, spliceosome, RNA splicing, vesicle transport, cell signaling and synaptic transmission. Part of this spectrum was reminiscent of the brain pathology. The HD signatures in caudate nucleus and BA4 exhibited the highest similarity with blood, irrespective of the category of semantic annotations used. BA9 exhibited an intermediate similarity, while cerebellum had the least similarity. We present two signatures that were shared between blood and brain: immune response and spinocerebellar ataxias.

CONCLUSIONS

Our results demonstrate that HD blood exhibits dysregulation that is similar to brain at a functional level, but not necessarily at the level of individual genes. We report two common signatures that can be used to monitor the pathology in brain of HD patients in a non-invasive manner. Our results are an exemplar of how signals in blood data can be used to represent brain disorders. Our methodology can be used to study disease specific signatures in diseases where heterogeneous tissues are involved in the pathology.

A Novel, Unbiased Analysis Approach for Investigating Population Dynamics: A Case Study on Calanus finmarchicus and Its Decline in the North Sea

Marine populations are controlled by a series of drivers, pertaining to both the physical environment and the biological environment (trophic predator-prey interactions). There is heated debate over drivers, especially when trying to understand the causes of major ecosystem events termed regime shifts. In this work, we have researched and developed a novel methodology based on Genetic Programming (GP) for distinguishing which drivers can influence species abundance. This methodology benefits of having no a priori assumptions either on the ecological parameters used or on the underlying mathematical relationships among them. We have validated this methodology applying it to the North Sea pelagic ecosystem. We use the target species Calanus finmarchicus, a key copepod in temperate and subarctic ecosystems, along with 86 biological, hydrographical and climatic time series, ranging from local water nutrients and fish predation, to large scale climate pressure patterns. The chosen study area is the central North Sea, from 1972 to 2011, during which period there was an ecological regime shift. The GP based analysis identified 3 likely drivers of C. finmarchicus abundance, which highlights the importance of considering both physical and trophic drivers: temperature, North Sea circulation (net flow into the North Atlantic), and predation (herring). No large scale climate patterns were selected, suggesting that when there is availability of both data types, local drivers are more important. The results produced by the GP based procedure are consistent with the literature published to date, and validate the use of GP for interpreting species dynamics. We propose that this methodology holds promises for the highly non-linear field of ecology.