Genome-wide DNA methylation analysis in an antimigraine-treated preclinical model of cortical spreading depolarization.

BACKGROUND: Cortical spreading depolarization, the cause of migraine aura, is a short-lasting depolarization wave that moves across the brain cortex, transiently suppressing neuronal activity. Prophylactic treatments for migraine, such as topiramate or valproate, reduce the number of cortical spreading depression events in rodents. OBJECTIVE: To investigate whether cortical spreading depolarization with and without chronic treatment with topiramate or valproate affect the DNA methylation of the cortex. METHODS: Sprague-Dawley rats were intraperitoneally injected with saline, topiramate or valproate for four weeks when cortical spreading depolarization were induced and genome-wide DNA methylation was performed in the cortex of six rats per group. RESULTS: The DNA methylation profile of the cortex was significantly modified after cortical spreading depolarization, with and without topiramate or valproate. Interestingly, topiramate reduced by almost 50% the number of differentially methylated regions, whereas valproate increased them by 17%, when comparing to the non-treated group after cortical spreading depolarization induction. The majority of the differentially methylated regions lay within intragenic regions, and the analyses of functional group over-representation retrieved several enriched functions, including functions related to protein processing in the cortical spreading depolarization without treatment group; functions related to metabolic processes in the cortical spreading depolarization with topiramate group; and functions related to synapse and ErbB, MAPK or retrograde endocannabinoid signaling in the cortical spreading depolarization with valproate group. CONCLUSIONS: Our results may provide insights into the underlying physiological mechanisms of migraine with aura and emphasize the role of epigenetics in migraine susceptibility.

Identifying and protecting macroalgae detritus sinks toward climate change mitigation.

Harnessing natural solutions to mitigate climate change requires an understanding of carbon fixation, flux, and sequestration across ocean habitats. Recent studies have suggested that exported seaweed particulate organic carbon is stored within soft-sediment systems. However, very little is known about how seaweed detritus disperses from coastlines, or where it may enter seabed carbon stores, where it could become the target of conservation efforts. Here, focusing on regionally dominant seaweed species, we surveyed environmental DNA (eDNA) from natural coastal sediments, and studied their connectivity to seaweed habitats using a particle tracking model parameterized to reproduce seaweed detritus dispersal behavior based on laboratory observations of seaweed fragment degradation and sinking. Experiments showed that seaweed detritus density changed over time, differently across species. This, in turn, modified distances traveled by released fragments until they reached the seabed for the first time, during model simulations. Dispersal pathways connected detritus from the shore to the open ocean but, importantly, also to coastal sediments, and this was reflected by field eDNA evidence. Dispersion pathways were also affected by hydrodynamic conditions, varying in space and time. Both the properties and timing of released detritus, individual to each macroalgal population, and short-term near-seabed and medium-term water-column transport pathways, are thus seemingly important in determining the connectivity between seaweed habitats and potential sedimentary sinks. Studies such as this one, supported by further field verification of sedimentary carbon sequestration rates and source partitioning, are still needed to help quantify the role of seaweed in the ocean carbon cycle. Such studies will provide vital evidence to inform on the potential need to develop blue carbon conservation mechanisms, beyond wetlands.

4D marine conservation networks: Combining 3D prioritization of present and future biodiversity with climatic refugia.

Given the accelerating rate of biodiversity loss, the need to prioritize marine areas for protection represents a major conservation challenge. The three-dimensionality of marine life and ecosystems is an inherent element of complexity for setting spatial conservation plans. Yet, the confidence of any recommendation largely depends on shifting climate, which triggers a global redistribution of biodiversity, suggesting the inclusion of time as a fourth dimension. Here, we developed a depth-specific prioritization analysis to inform the design of protected areas, further including metrics of climate-driven changes in the ocean. Climate change was captured in this analysis by considering the projected future distribution of >2000 benthic and pelagic species inhabiting the Mediterranean Sea, combined with climatic stability and heterogeneity metrics of the seascape. We identified important areas based on both biological and climatic criteria, where conservation focus should be given in priority when designing a three-dimensional, climate-smart protected area network. We detected spatially concise, conservation priority areas, distributed around the basin, that protected marine areas almost equally across all depth zones. Our approach highlights the importance of deep sea zones as priority areas to meet conservation targets for future marine biodiversity, while suggesting that spatial prioritization schemes, that focus on a static two-dimensional distribution of biodiversity data, might fail to englobe both the vertical properties of species distributions and the fine and larger-scale impacts associated with climate change.

Effect of the Lights4Violence intervention on the sexism of adolescents in European countries.

BACKGROUND: Sexism results in a number of attitudes and behaviors that contribute to gender inequalities in social structure and interpersonal relationships. The objective of this study was to evaluate the effectiveness of Lights4Violence, an intervention program based on promoting health assets to reduce sexist attitudes in young European people. METHODS: We carried out a quasi-experimental study in a non-probabilistic population of 1146 students, aged 12-17 years. The dependent variables were the difference in the wave 1 and wave 2 values in the subscales of the Ambivalent Sexism Inventory: benevolent sexism (BS) and hostile sexism (HS). The effect of the intervention was evaluated through linear regression analyses stratified by sex. The models were adjusted by baseline subscales scores, socio-demographic and psychological variables. RESULTS: In girls, we observed a decrease in BS in the intervention group compared to the control group (ß = - 0.101; p = 0.006). In the wave2,, BS decreased more in the intervention group compared to the control group in girls with mothers with a low level of education (ß = - 0.338; p = 0.001), with a high level of social support (ß = - 0.251; p < 0.001), with greater capacity for conflict resolution (ß = - 0.201; p < 0.001) and lower levels of aggressiveness (ß = - 0.232, p < 0.001). In boys, the mean levels of HS and BH decreased in wave 2 in both the control and intervention groups. The changes observed after the wave 2 were the same in the control group and in the intervention group. No significant differences were identified between both groups. CONCLUSIONS: The implementation of the Lights4Violence was associated with a significant reduction in BS in girls, which highlights the potential of interventions aimed at supporting the personal competencies and social support. It is necessary to reinforce the inclusion of educational contents that promote reflection among boys about the role of gender and the meaning of the attributes of masculinity. TRIAL REGISTRATION: Clinicaltrials.gov : NCT03411564 . Unique Protocol ID: 776905. Date registered: 26-01-2018.

Patient-Derived Multiple Myeloma 3D Models for Personalized Medicine-Are We There Yet?

Despite the wide variety of existing therapies, multiple myeloma (MM) remains a disease with dismal prognosis. Choosing the right treatment for each patient remains one of the major challenges. A new approach being explored is the use of ex vivo models for personalized medicine. Two-dimensional culture or animal models often fail to predict clinical outcomes. Three-dimensional ex vivo models using patients' bone marrow (BM) cells may better reproduce the complexity and heterogeneity of the BM microenvironment. Here, we review the strengths and limitations of currently existing patient-derived ex vivo three-dimensional MM models. We analyze their biochemical and biophysical properties, molecular and cellular characteristics, as well as their potential for drug testing and identification of disease biomarkers. Furthermore, we discuss the remaining challenges and give some insight on how to achieve a more biomimetic and accurate MM BM model. Overall, there is still a need for standardized culture methods and refined readout techniques. Including both myeloma and other cells of the BM microenvironment in a simple and reproducible three-dimensional scaffold is the key to faithfully mapping and examining the relationship between these players in MM. This will allow a patient-personalized profile, providing a powerful tool for clinical and research applications.

Bright spots as climate-smart marine spatial planning tools for conservation and blue growth.

Marine spatial planning that addresses ocean climate-driven change ('climate-smart MSP') is a global aspiration to support economic growth, food security and ecosystem sustainability. Ocean climate change ('CC') modelling may become a key decision-support tool for MSP, but traditional modelling analysis and communication challenges prevent their broad uptake. We employed MSP-specific ocean climate modelling analyses to inform a real-life MSP process; addressing how nature conservation and fisheries could be adapted to CC. We found that the currently planned distribution of these activities may become unsustainable during the policy's implementation due to CC, leading to a shortfall in its sustainability and blue growth targets. Significant, climate-driven ecosystem-level shifts in ocean components underpinning designated sites and fishing activity were estimated, reflecting different magnitudes of shifts in benthic versus pelagic, and inshore versus offshore habitats. Supporting adaptation, we then identified: CC refugia (areas where the ecosystem remains within the boundaries of its present state); CC hotspots (where climate drives the ecosystem towards a new state, inconsistent with each sectors' present use distribution); and for the first time, identified bright spots (areas where oceanographic processes drive range expansion opportunities that may support sustainable growth in the medium term). We thus create the means to: identify where sector-relevant ecosystem change is attributable to CC; incorporate resilient delivery of conservation and sustainable ecosystem management aims into MSP; and to harness opportunities for blue growth where they exist. Capturing CC bright spots alongside refugia within protected areas may present important opportunities to meet sustainability targets while helping support the fishing sector in a changing climate. By capitalizing on the natural distribution of climate resilience within ocean ecosystems, such climate-adaptive spatial management strategies could be seen as nature-based solutions to limit the impact of CC on ocean ecosystems and dependent blue economy sectors, paving the way for climate-smart MSP.

Harnessing positive species interactions as a tool against climate-driven loss of coastal biodiversity.

Habitat-forming species sustain biodiversity and ecosystem functioning in harsh environments through the amelioration of physical stress. Nonetheless, their role in shaping patterns of species distribution under future climate scenarios is generally overlooked. Focusing on coastal systems, we assess how habitat-forming species can influence the ability of stress-sensitive species to exhibit plastic responses, adapt to novel environmental conditions, or track suitable climates. Here, we argue that habitat-former populations could be managed as a nature-based solution against climate-driven loss of biodiversity. Drawing from different ecological and biological disciplines, we identify a series of actions to sustain the resilience of marine habitat-forming species to climate change, as well as their effectiveness and reliability in rescuing stress-sensitive species from increasingly adverse environmental conditions.

Non-coding recurrent mutations in chronic lymphocytic leukaemia.

Chronic lymphocytic leukaemia (CLL) is a frequent disease in which the genetic alterations determining the clinicobiological behaviour are not fully understood. Here we describe a comprehensive evaluation of the genomic landscape of 452 CLL cases and 54 patients with monoclonal B-lymphocytosis, a precursor disorder. We extend the number of CLL driver alterations, including changes in ZNF292, ZMYM3, ARID1A and PTPN11. We also identify novel recurrent mutations in non-coding regions, including the 3' region of NOTCH1, which cause aberrant splicing events, increase NOTCH1 activity and result in a more aggressive disease. In addition, mutations in an enhancer located on chromosome 9p13 result in reduced expression of the B-cell-specific transcription factor PAX5. The accumulative number of driver alterations (0 to ≥4) discriminated between patients with differences in clinical behaviour. This study provides an integrated portrait of the CLL genomic landscape, identifies new recurrent driver mutations of the disease, and suggests clinical interventions that may improve the management of this neoplasia.

Ocean acidification and hypoxia alter organic carbon fluxes in marine soft sediments.

Anthropogenic stressors can alter the structure and functioning of infaunal communities, which are key drivers of the carbon cycle in marine soft sediments. Nonetheless, the compounded effects of anthropogenic stressors on carbon fluxes in soft benthic systems remain largely unknown. Here, we investigated the cumulative effects of ocean acidification (OA) and hypoxia on the organic carbon fate in marine sediments, through a mesocosm experiment. Isotopically labelled macroalgal detritus (13 C) was used as a tracer to assess carbon incorporation in faunal tissue and in sediments under different experimental conditions. In addition, labelled macroalgae (13 C), previously exposed to elevated CO2 , were also used to assess the organic carbon uptake by fauna and sediments, when both sources and consumers were exposed to elevated CO2 . At elevated CO2 , infauna increased the uptake of carbon, likely as compensatory response to the higher energetic costs faced under adverse environmental conditions. By contrast, there was no increase in carbon uptake by fauna exposed to both stressors in combination, indicating that even a short-term hypoxic event may weaken the ability of marine invertebrates to withstand elevated CO2 conditions. In addition, both hypoxia and elevated CO2 increased organic carbon burial in the sediment, potentially affecting sediment biogeochemical processes. Since hypoxia and OA are predicted to increase in the face of climate change, our results suggest that local reduction of hypoxic events may mitigate the impacts of global climate change on marine soft-sediment systems.

Whole-epigenome analysis in multiple myeloma reveals DNA hypermethylation of B cell-specific enhancers.

While analyzing the DNA methylome of multiple myeloma (MM), a plasma cell neoplasm, by whole-genome bisulfite sequencing and high-density arrays, we observed a highly heterogeneous pattern globally characterized by regional DNA hypermethylation embedded in extensive hypomethylation. In contrast to the widely reported DNA hypermethylation of promoter-associated CpG islands (CGIs) in cancer, hypermethylated sites in MM, as opposed to normal plasma cells, were located outside CpG islands and were unexpectedly associated with intronic enhancer regions defined in normal B cells and plasma cells. Both RNA-seq and in vitro reporter assays indicated that enhancer hypermethylation is globally associated with down-regulation of its host genes. ChIP-seq and DNase-seq further revealed that DNA hypermethylation in these regions is related to enhancer decommissioning. Hypermethylated enhancer regions overlapped with binding sites of B cell-specific transcription factors (TFs) and the degree of enhancer methylation inversely correlated with expression levels of these TFs in MM. Furthermore, hypermethylated regions in MM were methylated in stem cells and gradually became demethylated during normal B-cell differentiation, suggesting that MM cells either reacquire epigenetic features of undifferentiated cells or maintain an epigenetic signature of a putative myeloma stem cell progenitor. Overall, we have identified DNA hypermethylation of developmentally regulated enhancers as a new type of epigenetic modification associated with the pathogenesis of MM.

Diverse effects of invasive ecosystem engineers on marine biodiversity and ecosystem functions: A global review and meta-analysis.

Invasive ecosystem engineers (IEE) are potentially one of the most influential types of biological invaders. They are expected to have extensive ecological impacts by altering the physical-chemical structure of ecosystems, thereby changing the rules of existence for a broad range of resident biota. To test the generality of this expectation, we used a global systematic review and meta-analysis to examine IEE effects on the abundance of individual species and communities, biodiversity (using several indices) and ecosystem functions, focusing on marine and estuarine environments. We found that IEE had a significant effect (positive and negative) in most studies testing impacts on individual species, but the overall (cumulative) effect size was small and negative. Many individual studies showed strong IEE effects on community abundance and diversity, but the direction of effects was variable, leading to statistically non-significant overall effects in most categories. In contrast, there was a strong overall effect on most ecosystem functions we examined. IEE negatively affected metabolic functions and primary production, but positively affected nutrient flux, sedimentation and decomposition. We use the results to develop a conceptual model by highlighting pathways whereby IEE impact communities and ecosystem functions, and identify several sources of research bias in the IEE-related invasion literature. Only a few of the studies simultaneously quantified IEE effects on community/diversity and ecosystem functions. Therefore, understanding how IEE may alter biodiversity-ecosystem function relationships should be a primary focus of future studies of invasion biology. Moreover, the clear effects of IEE on ecosystem functions detected in our study suggest that scientists and environmental managers ought to examine how the effects of IEE might be manifested in the services that marine ecosystems provide to humans.

Screening of Ulva rigida, Gracilaria sp., Fucus vesiculosus and Saccharina latissima as Functional Ingredients.

The intent of the present work was to evaluate the potential of four macroalgae prevalent in Europe, namely Ulva rigida, Gracilaria sp., Fucus vesiculosus and Saccharina latissima, for application in functional foods, either in the direct form or as extracts. Accordingly, nutritional composition, the content of phytochemical antioxidants, and the inhibitory ability of key enzymes with impacts on obesity and diabetes (α-glucosidase and pancreatic lipase) or on arterial pressure (angiotensin-I converting enzyme), were evaluated. Overall, protein, lipid, ash and fiber contents of the macroalgae ranged from 9⁻24% dw, 0.5⁻3.0% dw, 20⁻32% dw, and 37⁻45% dw, respectively, making them good candidates for nutritional supplementation of several foods, particularly due to their mineral and fiber contents. In addition, brown macroalgae, in particular F. vesiculosus, stood out for its superior phenolic content, which was reflected by its high antioxidant ability and inhibition towards α-glucosidase activity (0.032 mg/mL of hydroacetonic extract inhibited 50% of the enzyme activity).

Artificial light at night alters trophic interactions of intertidal invertebrates.

Despite being globally widespread in coastal regions, the impacts of light pollution on intertidal ecosystems has received little attention. Intertidal species exhibit many night-time-dependent ecological strategies, including feeding, reproduction, orientation and predator avoidance, which are likely negatively affected by shifting light regimes, as has been observed in terrestrial and aquatic taxa. Coastal lighting may shape intertidal communities through its influence on the nocturnal foraging activity of dogwhelks (Nucella lapillus), a widespread predatory mollusc that structures biodiversity in temperate rocky shores. In the laboratory, we investigated whether the basal and foraging activity of this predator was affected by exposure to night-time lighting both in the presence and absence of olfactory predator cues (Carcinus maenas, common shore crab). Assessments of dogwhelks' behavioural responses to night-time white LED lighting were performed on individuals that had been acclimated to night-time white LED lighting conditions for 16 days and individuals that had not previously been exposed to artificial light at night. Dogwhelks acclimated to night-time lighting exhibited natural refuge-seeking behaviour less often compared to control animals, but were more likely to respond to and handle prey irrespective of whether olfactory predator cues were present. These responses suggest night-time lighting likely increased the energetic demand of dogwhelks through stress, encouraging foraging whenever food was available, regardless of potential danger. Contrastingly, whelks not acclimated under night-time lighting were more likely to respond to the presence of prey under artificial light at night when olfactory predator cues were present, indicating an opportunistic shift towards the use of visual instead of olfactory cues in risk evaluation. These results demonstrate that artificial night-time lighting influences the behaviour of intertidal fauna such that the balance of interspecific interactions involved in community structuring may be affected.

Does sex really matter? Explaining intraspecies variation in ocean acidification responses.

Ocean acidification (OA) poses a major threat to marine ecosystems globally, having significant ecological and economic importance. The number and complexity of experiments examining the effects of OA has substantially increased over the past decade, in an attempt to address multi-stressor interactions and long-term responses in an increasing range of aquatic organisms. However, differences in the response of males and females to elevated pCO2 have been investigated in fewer than 4% of studies to date, often being precluded by the difficulty of determining sex non-destructively, particularly in early life stages. Here we highlight that sex can significantly impact organism responses to OA, differentially affecting physiology, reproduction, biochemistry and ultimately survival. What is more, these impacts do not always conform to ecological theory based on differential resource allocation towards reproduction, which would predict females to be more sensitive to OA owing to the higher production cost of eggs compared with sperm. Therefore, non-sex-specific studies may overlook subtle but ecologically significant differences in the responses of males and females to OA, with consequences for forecasting the fate of natural populations in a near-future ocean.

Solutions for ecosystem-level protection of ocean systems under climate change.

The Paris Conference of Parties (COP21) agreement renewed momentum for action against climate change, creating the space for solutions for conservation of the ocean addressing two of its largest threats: climate change and ocean acidification (CCOA). Recent arguments that ocean policies disregard a mature conservation research field and that protected areas cannot address climate change may be oversimplistic at this time when dynamic solutions for the management of changing oceans are needed. We propose a novel approach, based on spatial meta-analysis of climate impact models, to improve the positioning of marine protected areas to limit CCOA impacts. We do this by estimating the vulnerability of ocean ecosystems to CCOA in a spatially explicit manner and then co-mapping human activities such as the placement of renewable energy developments and the distribution of marine protected areas. We test this approach in the NE Atlantic considering also how CCOA impacts the base of the food web which supports protected species, an aspect often neglected in conservation studies. We found that, in this case, current regional conservation plans protect areas with low ecosystem-level vulnerability to CCOA, but disregard how species may redistribute to new, suitable and productive habitats. Under current plans, these areas remain open to commercial extraction and other uses. Here, and worldwide, ocean conservation strategies under CCOA must recognize the long-term importance of these habitat refuges, and studies such as this one are needed to identify them. Protecting these areas creates adaptive, climate-ready and ecosystem-level policy options for conservation, suitable for changing oceans.

Detection of chromothripsis-like patterns with a custom array platform for chronic lymphocytic leukemia.

Chronic lymphocytic leukemia (CLL) is a common disease with highly variable clinical course. Several recurrent chromosomal alterations are associated with prognosis and may guide risk-adapted therapy. We have developed a targeted genome-wide array to provide a robust tool for ascertaining abnormalities in CLL and to overcome limitations of the 4-marker fluorescence in situ hybridization (FISH). DNA from 180 CLL patients were hybridized to the qChip®Hemo array with a high density of probes covering commonly altered loci in CLL (11q22-q23, 13q14, and 17p13), nine focal regions (2p15-p16.1, 2p24.3, 2q13, 2q36.3-q37.1, 3p21.31, 8q24.21, 9p21.3, 10q24.32, and 18q21.32-q21.33) and two larger regions (6q14.1-q22.31 and 7q31.33-q33). Overall, 86% of the cases presented copy number alterations (CNA) by array. There was a high concordance of array findings with FISH (84% sensitivity, 100% specificity); all discrepancies corresponded to subclonal alterations detected only by FISH. A chromothripsis-like pattern was detected in eight cases. Three showed concomitant shattered 5p with gain of TERT along with isochromosome 17q. Presence of 11q loss was associated with shorter time to first treatment (P = 0.003), whereas 17p loss, increased genomic complexity, and chromothripsis were associated with shorter overall survival (P < 0.001, P = 0.001, and P = 0.02, respectively). In conclusion, we have validated a targeted array for the diagnosis of CLL that accurately detects, in a single experiment, all relevant CNAs, genomic complexity, chromothripsis, copy number neutral loss of heterozygosity, and CNAs not covered by the FISH panel. This test may be used as a practical tool to stratify CLL patients for routine diagnostics or clinical trials.

Scaling up experimental ocean acidification and warming research: from individuals to the ecosystem.

Understanding long-term, ecosystem-level impacts of climate change is challenging because experimental research frequently focuses on short-term, individual-level impacts in isolation. We address this shortcoming first through an interdisciplinary ensemble of novel experimental techniques to investigate the impacts of 14-month exposure to ocean acidification and warming (OAW) on the physiology, activity, predatory behaviour and susceptibility to predation of an important marine gastropod (Nucella lapillus). We simultaneously estimated the potential impacts of these global drivers on N. lapillus population dynamics and dispersal parameters. We then used these data to parameterize a dynamic bioclimatic envelope model, to investigate the consequences of OAW on the distribution of the species in the wider NE Atlantic region by 2100. The model accounts also for changes in the distribution of resources, suitable habitat and environment simulated by finely resolved biogeochemical models, under three IPCC global emissions scenarios. The experiments showed that temperature had the greatest impact on individual-level responses, while acidification had a similarly important role in the mediation of predatory behaviour and susceptibility to predators. Changes in Nucella predatory behaviour appeared to serve as a strategy to mitigate individual-level impacts of acidification, but the development of this response may be limited in the presence of predators. The model projected significant large-scale changes in the distribution of Nucella by the year 2100 that were exacerbated by rising greenhouse gas emissions. These changes were spatially heterogeneous, as the degree of impact of OAW on the combination of responses considered by the model varied depending on local-environmental conditions and resource availability. Such changes in macro-scale distributions cannot be predicted by investigating individual-level impacts in isolation, or by considering climate stressors separately. Scaling up the results of experimental climate change research requires approaches that account for long-term, multiscale responses to multiple stressors, in an ecosystem context.

Intragenic DNA methylation in transcriptional regulation, normal differentiation and cancer.

Ever since the discovery of DNA methylation at cytosine residues, the role of this so called fifth base has been extensively studied and debated. Until recently, the majority of DNA methylation studies focused on the analysis of CpG islands associated to promoter regions. However, with the upcoming possibilities to study DNA methylation in a genome-wide context, this epigenetic mark can now be studied in an unbiased manner. As a result, recent studies have shown that not only promoters but also intragenic and intergenic regions are widely modulated during physiological processes and disease. In particular, it is becoming increasingly clear that DNA methylation in the gene body is not just a passive witness of gene transcription but it seems to be actively involved in multiple gene regulation processes. In this review we discuss the potential role of intragenic DNA methylation in alternative promoter usage, regulation of short and long non-coding RNAs, alternative RNA processing, as well as enhancer activity. Furthermore, we summarize how the intragenic DNA methylome is modified both during normal cell differentiation and neoplastic transformation.