bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid and Repeated Local Adaptation to Climate in an Invasive Plant
Authors: van Boheemen Lotte A. , Atwater Daniel Z. , Hodgins Kathryn A. 
Published: September 2018

SUMMARYBiological invasions provide opportunities to study evolutionary processes occurring over contemporary timescales. To explore the speed and repeatability of adaptation, we examined the divergence of life-history traits to climate, using latitude as a proxy, in the native North American and introduced European and Australian ranges of the annual plantAmbrosia artemisiifolia.We explored niche changes following introductions using climate niche dynamic models. In a common garden, we examined trait divergence by growing seeds collected across three ranges with highly distinct demographic histories. Heterozygosity-fitness associations were used to explore the effect of invasion history on potential success. We accounted for non-adaptive population differentiation using 11,598 SNPs.We revealed a centroid shift to warmer, wetter climates in the introduced ranges. We identified repeated latitudinal divergence in life-history traits, with European and Australian populations positioned at either end of the native clines.Our data indicate rapid and repeated adaptation to local climates despite the recent introductions and a bottleneck limiting genetic variation in Australia. Centroid shifts in the introduced ranges suggest adaptation to more productive environments, potentially contributing to trait divergence between the ranges.
Action-specific feature processing in the human visual cortex
Authors: Monaco Simona , Chen Ying , Menghi Nicholas , Crawford J Douglas 
Published: September 2018

AbstractSensorimotor integration involves feedforward and reentrant processing of sensory input. Grasp-related motor activity precedes and is thought to influence visual object processing. Yet, while the importance of reentrant feedback is well established in perception, the top-down modulations for action and the neural circuits involved in this process have received less attention. Do action-specific intentions influence the processing of visual information in the human cortex? Using a cue-separation fMRI paradigm, we found that action-specific instruction (manual alignment vs. grasp) influences the cortical processing of object orientation several seconds after the object had been viewed. This influence occurred as early as in the primary visual cortex and extended to ventral and dorsal visual stream areas. Importantly, this modulation was unrelated to non-specific action planning. Further, the primary visual cortex showed stronger functional connectivity with frontal-parietal areas and the inferior temporal cortex during the delay following orientation processing for align than grasping movements, strengthening the idea of reentrant feedback from dorsal visual stream areas involved in action. To our knowledge, this is the first demonstration that intended manual actions have such an early, pervasive, and differential influence on the cortical processing of vision.
ASD Diagnosis in Adults: Phenotype and Genotype Findings from a Clinically-derived Cohort
Authors: Jack F G Underwood , Kimberley M Kendall , Jennifer Berrett , Richard Anney , Marianne B.M. Van den Bree , Jeremy Hall 
Published: September 2018

AbstractBackgroundThe last decade has seen the development of services for adults presenting with symptoms of autism spectrum disorder (ASD) in the UK. Compared to children, little is known about the phenotypic and genetic characteristics of these patients.AimsThis e-cohort study aimed to examine the phenotypic and genetic characteristics of a clinically-presenting sample of adults diagnosed with ASD by specialist services.MethodsIndividuals diagnosed with ASD as adults were recruited by the National Centre for Mental Health and completed self-report questionnaires, interviews and provided DNA. 105 eligible individuals were matched to 76 healthy controls. We investigated the demographics, social history, comorbid psychiatric and physical disorders. Samples were genotyped, copy number variants (CNVs) were called and polygenic risk scores calculated.Results89.5% of individuals with ASD had at least one comorbid psychiatric diagnosis with comorbid depression (62.9%) and anxiety (55.2%) the most common. The ASD group experienced more neurological comorbidities than healthy controls, particularly migraine headache. They were less likely to have married or be in work and had more alcohol-related problems. There was a significantly higher load of autism common genetic variants in the adult ASD group compared to controls, but there was no difference in the rate of rare CNVs.ConclusionsThis study provides important information about psychiatric comorbidity in adult ASD which may be used to inform clinical practice and patient counselling. It also suggests that the polygenic load of common ASD-associated variants may be important in conferring risk within non-intellectually disabled population of adults with ASD.
The joint evolution of lifespan and self-fertilisation
Authors: Lesaffre Thomas , Billiard Sylvain 
Published: September 2018

ABSTRACTIn Angiosperms, there exists a strong association between mating system and lifespan. Most self-fertilising species are short-lived and most predominant or obligate outcrossers are long-lived. This association is generally explained by the influence of lifespan on the evolution of the mating system, considering lifespan as fixed. Yet, lifespan can itself evolve, and the mating system may as well influence the evolution of lifespan, as is suggested by joint evolutionary shifts of lifespan and mating system between sister species. In this paper, we build modifier models to study the joint evolution of self-fertilisation and lifespan, including both juvenile and adult inbreeding depression. We show that self-fertilisation is expected to promote evolution towards shorter lifespan, and that the range of conditions under which selfing can evolve rapidly shrinks as lifespan increases. We study the effects of inbreeding depression affecting various steps in the life cycle, and discuss how extrinsic mortality conditions are expected to affect evolutionary associations. In particular, we show that selfers may sometimes remain short-lived even in a very stable habitat, as a strategy to avoid the deleterious effects of inbreeding.
Interspecific plant competition mediates the metabolic and ecological signature of a plant-herbivore interaction under warming and elevated CO2
Authors: Van De Velde Helena , AbdElgawad Hamada , Asard Han , Beemster Gerrit T. S. , Selim Samy , Nijs Ivan , Bonte Dries 
Published: September 2018

AbstractBiotic interactions shape community evolution, but we lack mechanistic insights on how metabolic and ecological processes under climate change are altered by biotic interactions.We used a two-trophic model community consisting of the aphidDysaphis plantagineafeeding on the forbPlantago lanceolata, and a grass competitorLolium perennethat does not experience herbivory by the aphid. Monocultures and mixtures were exposed to the herbivory treatment and to three relevant simulated environmental changes as prevalent under current climate change (increased temperature, CO2, and increased temperature and CO2)Elevated CO2reduced the nitrogen content ofP. lanceolata, while simultaneous increases of CO2and temperature modified the plant metabolic component and the magnitude of these responses in different directions. Elevated CO2enhanced defence systems inP. lanceolata, but these effects were not altered by warming. Interspecific plant competition did, however, neutralise these responses. There were no indirect effects of climate change on aphid population growth despite changes in plant defense, nutritional quality and biomass induced by our environmental change scenarios.We thus demonstrate interactions between abiotic and biotic processes on plant metabolite profiles, but more importantly, that climate change effect on a selection of the metabolic pathways are altered by herbivory and competition. Our experiment under semi-natural conditions thus demonstrates the non-additive and often neutralizing effects of biotic interactions on plant metabolism and species performance under climate-associated environmental change.
Honey bee workers reared in a neonicotinoid contaminated in-hive environment
Authors: Odemer Richard , Odemer Franziska 
Published: September 2018

ABSTRACTWith the currently updated risk assessment of three neonicotinoid pesticides, the European Food Safety Authority has confirmed that different applications of these substances represent a risk to wild and managed bees and their use was therefore severely restricted. However, to close further gaps in knowledge, this experiment covers exposure of honey bee worker brood reared in a neonicotinoid contaminated in-hive environment with focus on the individual. In a worst case scenario, mini-hives were fed chronically with a sublethal concentration of clothianidin (15 µg/kg), which is highly toxic to bees already in small amounts. Freshly hatched workers from these colonies were subsequently marked and introduced into non-contaminated colonies, where their lifespan and behavior was monitored. Nineteen days after exposure, clothianidin treated bees had no reduced lifespan or showed any signs of behavioral impairment when compared to the control, demonstrating that social buffering is not a simple substitution of dead bees by rearing more brood. Our results suggest that the social environment plays a crucial role for the individual in terms of “superorganism resilience”. These findings are discussed in context with the current use of lower tier test systems in risk assessment and contrary results obtained from laboratory experiments.HIGHLIGHTSSublethal clothianidin treatment did not affect lifespan nor behavior of workers.Effects on individual bees reared within a mini-hive are translatable to full-sized colonies.“Superorganism resilience” is not a simple substitution of dead bees by rearing more brood.Laboratory testing in the risk assessment of plant protection products bears severe weaknesses.
Anoxygenic Photosynthesis and Dark Carbon Metabolism under micro-oxic conditions in the Purple Sulfur Bacterium “Thiodictyon syntrophicum” nov. strain Cad16T
Authors: Luedin Samuel M , Storelli Nicola , Danza Francesco , Roman Samuele , Wittwer Matthias , Pothier Joël F , Tonolla Mauro 
Published: September 2018

1.ABSTRACTThe microbial ecosystem of the meromictic Lake Cadagno (Ticino, Swiss Alps) has been studied intensively to understand metabolic functions driven by the highly abundant anoxygenic phototrophic sulfur bacteria of the families Chromatiaceae and Chlorobiaceae. It was found that the sequenced isolate “Thiodictyon syntrophicum” nov. sp. str. Cad16T, belonging to the Chromatiaceae, may fix 26% of all bulk inorganic carbon in the chemocline at day and night. With this study, we elucidated the mode of dark carbon fixation of str. Cad16Twith a combination of long-term monitoring of key physicochemical parameters with CTD,14C-incorporation experiments and quantitative proteomics ofin situdialysis bag incubations of pure cultures. Regular vertical CTD profiling during the study period in summer 2017 revealed that the chemocline sank from 12 to 14 m which was accompanied by a bloom of cyanobacteria and the subsequent oxygenation of the deeper water column. Sampling was performed both day and night in September. While CO2assimilation rates were higher during the light period, the relative change in the proteome (663 quantified proteins) was only 1% of all CDS encoded in str. Cad16T. Oxidative respiration was thereby upregulated at light, whereas stress-related mechanisms prevailed during the night. These results indicate that the low light availability due to high cell concentrations and the oxygenation of the chemocline induced a mixotrophic growth in str. Cad16T.The complete proteome data have been deposited to the ProteomeXchange with identifier PXD010641.
Identification of Kinase Inhibitors that Regulate Nuclear Receptor Nurr1 (NR4A2) Cellular Activity
Authors: Williams Kenya L. , Wells Carrow I. , Moore John T. 
Published: September 2018

AbstractThe ability to regulate the activity NR4A subfamily of nuclear receptors would be potentially useful in the treatment of multiple diseases, but to date, few regulators have been reported. This is likely due to the fact that the NR4A subfamily does not have a typical unoccupied nuclear receptor ligand binding pocket, but rather a pocket that is occupied with hydrophobic side chains of adjacent amino acids. It follows that traditional nuclear receptor assays that seek to identify ligands that bind within the ligand binding pocket would not be successful. We have thus focused on an alternate assay to identify NR4A regulators based on the fact that regulation of NR4A, at least partially, results from phosphorylation/dephosphorylation of the amino terminal region of the protein. We developed a medium throughput cellular assay using a fusion of the amino terminus of Nurr1 (NR4A2) with luciferase reporter and used the assay to screen a large and diverse protein kinase inhibitor set (PKIS). We identified multiple kinase inhibitor compounds from PKIS that significantly increased or decreased the cellular activity of Nurr1. These molecules serve as starting points to discover selective tools for regulation of Nurr1/Nurr1pathway.
The effects of demography and genetics on the neutral distribution of quantitative traits
Authors: Koch Evan M. 
Published: September 2018

1AbstractNeutral models for quantitative trait evolution are useful for identifying phenotypes under selection in natural populations. Models of quantitative traits often assume phenotypes are normally distributed. This assumption may be violated when a trait is affected by relatively few genetic variants or when the effects of those variants arise from skewed or heavy-tailed distributions. Traits such as gene expression levels and other molecular phenotypes may have these properties. To accommodate deviations from normality, models making fewer assumptions about the underlying trait genetics and patterns of genetic variation are needed. Here, we develop a general neutral model for quantitative trait variation using a coalescent approach by extending the framework developed by Schraiberand Landis(2015). This model allows interpretation of trait distributions in terms of familiar population genetic parameters because it is based on the coalescent. We show how the normal distribution resulting from the infinitesimal limit, where the number of loci grows large as the effect size per mutation becomes small, depends only on expected pairwise coalescent times. We then demonstrate how deviations from normality depend on demography through the distribution of coalescence times as well as through genetic parameters. In particular, population growth events exacerbate deviations while bottlenecks reduce them. This model also has practical applications, which we demonstrate by designing an approach to simulate from the null distribution of QST, the ratio of the trait variance between subpopulations to that in the overall population. We further show that it is likely impossible to distinguish sparsity from skewed or heavy-tailed distributions of mutational effects using only trait values sampled from a population. The model analyzed here greatly expands the parameter space for which neutral trait models can be designed.
Wdr5, Brca1 and Bard1 link the DNA damage response to the mesenchymal-to-epithelial transition during early reprogramming
Authors: Peñalosa-Ruiz Georgina , Bousgouni Vicky , Gerlach Jan Patrick , Waarlo Susan , de Ven Joris V. van , Veenstra Tim E. , Silva José C.R. , van Heeringen Simon J. , Bakal Chris , Mulder Klaas W. , Veenstra Gert Jan C. 
Published: September 2018

SUMMARYDifferentiated cells are epigenetically stable, but can be reprogrammed to pluripotency by expression of the OSKM transcription factors. Despite significant effort, relatively little is known about the cellular requirements for reprogramming and how they affect the properties of induced pluripotent stem cells (iPSC). We have performed high-content screening with siRNAs targeting 300 chromatin-associated factors. We used colony features, such as size and shape, as well as strength and homogeneity of marker gene expression to define five colony phenotypes in early reprogramming. We identified transcriptional signatures associated with these phenotypes in a secondary RNA sequencing screen. One of these phenotypes involves large colonies and an early block of reprogramming. Double knockdown epistasis experiments of the genes involved, revealed that Brca1, Bard1 and Wdr5 functionally interact and are required for both the DNA damage response and the mesenchymal-to-epithelial transition (MET), linking these processes. Moreover, the data provide a resource on the role of chromatin-associated factors in reprogramming and underline colony morphology as an important high dimensional readout for reprogramming quality.
Surface color and predictability determine contextual modulation of V1 firing and gamma oscillations
Authors: Peter Alina , Uran Cem , Klon-Lipok Johanna , Roese Rasmus , van Stijn Sylvia , Barnes William , Dowdall Jarrod R , Singer Wolf , Fries Pascal , Vinck Martin 
Published: September 2018

AbstractThe integration of direct bottom-up inputs with contextual information is a canonical motif in neocortical circuits. In area V1, neurons may reduce their firing rates when the (classical) receptive field input can be predicted by the spatial context. We previously hypothesized that gamma-synchronization (30-80Hz) provides a complementary signal to rates, encoding whether stimuli are predicted from spatial context by preferentially synchronizing neuronal populations receiving predictable inputs. Here we investigated how rates and synchrony are modulated by predictive context. Large uniform surfaces, which have high spatial predictability, strongly suppressed firing yet induced prominent gamma-synchronization, but only when they were colored. Yet, chromatic mismatches between center and surround, breaking predictability, strongly reduced gamma-synchronization while increasing firing rates. Differences between colors, including strong gamma-responses to red, arose because of stimulus adaptation to a full-screen background, with a prominent difference in adaptation between M- and L-cone signaling pathways. Thus, synchrony signals whether RF inputs are predicted from spatial context and may encode relationships across space, while firing rates increase when stimuli are unpredicted from the context.
Genomic profiling of T cell activation reveals dependency of memory T cells on CD28 costimulation
Authors: Glinos Dafni A. , Soskic Blagoje , Jostins Luke , Sansom David M. , Trynka Gosia 
Published: September 2018

SummaryT cell activation is a critical driver of immune response and if uncontrolled, it can result in failure to respond to infection or in excessive inflammation and autoimmunity. CD28 costimulatory pathway is an essential regulator of CD4 T cell responses. To deconvolute how T cell receptor (TCR) and CD28 orchestrate activation of human CD4 T cells we stimulated cells using varying intensities of TCR and CD28 signals followed by gene expression profiling. We demonstrate that T-helper differentiation and cytokine expression are controlled by CD28. Strikingly, cell cycle and cell division are sensitive to CD28 in memory cells, but under TCR control in naive cells, in contrast to the paradigm that memory cells are CD28-independent. Using a combination of chromatin accessibility and enhancer profiling, we observe that IRFs and Blimp-1 (PRDM1) motifs are enriched in naive and memory T cells in response to TCR. In contrast, memory cells initiate AP1 transcriptional regulation only when both TCR and CD28 are engaged, implicating CD28 as an amplifier of transcriptional programmes in memory cells. Lastly, we show that CD28-sensitive genes are enriched in autoimmune disease loci, pointing towards the role of memory cells and the regulation of T cell activation through CD28 in autoimmune disease development. This study provides important insights into the differential role of CD28 in naive and memory T cell responses and offers a new platform for design and interpretation of costimulatory based therapies.One-sentence summaryGenomic profiling of CD4 T cell activation reveals a sensitivity switch from TCR in naive to CD28 in memory cells.
Can machine learning automatically detect the aligned trunk in sitting directly from raw video using a depth camera?
Authors: Sanchez Maria Beatriz , Cunningham Ryan , Butler Penelope B , Loram Ian 
Published: September 2018

AbstractBackgroundThe Segmental Assessment of Trunk Control (SATCo) evaluates sitting control at seven separate trunk segments, making a judgement based on their position in space relative to a defined, aligned posture. SATCo is in regular clinical and research use and is a Recommended Instrument for Cerebral Palsy and Spinal Cord Injury-Paediatric by The National Institute of Neurological Disorders and Stroke (US). However, SATCo remains a subjective assessment.Research questionThis study tests the feasibility of providing an objective, automated identification of frames containing the aligned, reference trunk posture using deep convolutional neural network (DCNN) analysis of raw high definition and depth (HD+D) images.MethodsA SATCo was conducted on sixteen healthy male adults and recorded using a Kinect V2. For each of seven segments tested, two different trials were collected (control and no-control) to simulate a range of alignment configurations. For all images, classification of alignment obtained from a trained and validated DCNN was compared to expert clinician’s labelling.ResultsUsing leave-one-out testing, at the optimal operating threshold, the DCNN correctly classified individual images (alignment v misaligned) with average precision 92.7±16% (mean±SD).SignificanceThese results show for the first time, automation of a key component of the SATCo test, namely identification of aligned trunk posture directly from raw images (HD+D). This demonstrates the potential of machine learning to provide a fully automated, objective SATCo test to enhance assessment of trunk control in children and adults for research and treatment of various conditions including neurodisability and stroke.