bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of amotosalen treatment on human platelet lysate bioactivity
Authors: Christensen Christian , Jonsdottir-Buch Sandra Mjoll , Sigurjonsson Olafur Eysteinn 
Published: July 2019

AbstractBackgroundClinical application of mesenchymal stromal cells (MSCs) usually requires an in vitro expansion step to reach clinically relevant numbers. In vitro cell expansion necessitates supplementation of basal mammalian cell culture medium with growth factors. To avoid using supplements containing animal substances, human platelet lysates (hPL) produced from expired and pathogen inactivated platelet concentrates can be used in place of fetal bovine serum. Due to lack of experience and global diversity in bacterial detection strategies, most transfusion units are currently not pathogen inactivated. As blood banks are the sole source of platelet concentrates for hPL production, it is important to ensure product safety and standardized production methods. To achieve these aims, we assessed the quality of hPL produced from expired platelet concentrates with pathogen inactivation applied after platelet lysis, as well as its ability to support MSC proliferation and tri-lineage differentiation.Methodology/principal findingsBone marrow-derived MSCs (BM-MSCs) were expanded and differentiated using hPL derived from pathogen inactivated platelet lysates (hPL-PIPL), with pathogen inactivation applied after lysis of expired platelets. Results were compared to those using hPL produced from conventional expired pathogen inactivated human platelet concentrates (hPL-PIPC), with pathogen inactivation applied after soon after blood donation. hPL-PIPL treatment had lower concentrations of soluble growth factors and cytokines than hPL-PIPC treatment. When used as supplementation in cell culture, BM-MSCs proliferated at a reduced rate, but more consistently, in hPL-PIPL than in hPL-PIPC. The ability to support tri-lineage differentiation was comparable between lysates.Conclusion/significanceThese results suggest that functional hPL can be produced from expired and untreated platelet lysates by applying pathogen inactivation after platelet lysis. When carried out post-expiration, pathogen inactivation can provide a valuable tool to further standardize global hPL production methods, increase the pool of starting material, and meet the future demand for animal-free supplements in human cell culturing.
A Unique Mouse Model of Early Life Exercise Enables Hippocampal Memory and Synaptic Plasticity
Authors: Ivy Autumn S. , Yu Tim , Kramár Enikö , Parievsky Sonia , Sohn Fred , Vu Thao 
Published: July 2019

AbstractAerobic exercise is a powerful modulator of learning and memory. Molecular mechanisms underlying the cognitive benefits of exercise are well documented in adult rodents. Animal models of exercise targeting specific postnatal periods of hippocampal development and plasticity are lacking. Here we characterize a model of early-life exercise (ELE) in male and female mice designed with the goal of identifying critical periods by which exercise may have a lasting impact on hippocampal memory and synaptic plasticity. Mice freely accessed a running wheel during three postnatal periods: the 4th postnatal week (juvenile ELE, P21-27), 6th postnatal week (adolescent ELE, P35-41), or 4th-6th postnatal weeks (juvenile-adolescent ELE, P21-41). All exercise groups significantly increased their running distances over time. When exposed to a weak learning stimulus, mice that had exercised during the juvenile period were able to form lasting long-term memory for a hippocampus-dependent spatial memory task. Electrophysiological experiments revealed enhanced long-term potentiation in hippocampal CA1 the juvenile-adolescent ELE group only. Furthermore, basal synaptic transmission was significantly increased in all mice that exercised during the juvenile period. Our results suggest early-life exercise can enable hippocampal memory, synaptic plasticity, and basal synaptic physiology when occurring during postnatal periods of hippocampal maturation.
Fossil amber reveals springtails’ longstanding dispersal by social insects
Authors: Ninon Robin , Cyrille D’haese , Phillip Barden 
Published: July 2019

AbstractDispersal is essential for terrestrial organisms living in disjunct habitats and constitutes a significant challenge for the evolution of wingless taxa. Springtails (Collembola), the sister-group of all insects (with dipluran), are reported since the Lower Devonian and thought to have originally been subterranean. The order Symphypleona is reported since the early Cretaceous with genera distributed on every continent, implying an ability to disperse over oceans although never reported in marine water contrary to other springtail orders. Despite being highly widespread, modern springtails are generally rarely reported in any kind of biotic association. Interestingly, the fossil record has provided occasional occurrences of Symphypleona attached by the antennae onto the bodies of larger arthropods. Here, we document the case of a ~16 Ma old fossil association: a winged termite and ant displaying not some, but 25 springtails attached or closely connected to the body. The collembola exhibit rare features for fossils, reflecting their courtship and phoretic behaviors. By observing the modes of attachment of springtails on different arthropods, the sex representation and ratios in springtail antennal anatomies in new and previously reported cases, we infer a likely mechanism for dispersal in Symphypleona. By revealing hidden evidence of modern springtail associations with other invertebrates such as ants and termites, new compelling assemblages of fossil springtails and the drastic increase of eusocial insects’ abundance over Cenozoic (ants/termites comprising more than the third of insects in Miocene amber), we stress that attachment with winged casts of ants and termites may have been a mechanism for the worldwide dispersal of this significant springtail lineage. Moreover, by comparing the general constraints applying to the other wingless soil-dwelling arthropods known to disperse through phoresy, we suggest biases in the collection and observation of phoretic Symphypleona related to their reflexive detachment and infer that this behavior continues today. The specific case of tree resin entrapment represents the (so far) only condition uncovering the actual dispersal mechanism of springtails - one of the oldest terrestrial arthropod lineages living today. Associations with soil-dwelling social insects over time would have been at the origin of this behavioural specialization.
RNA processing machineries in Archaea: the 5’-3’ exoribonuclease aRNase J of the β-CASP family is engaged specifically with the helicase ASH-Ski2 and the 3’-5’ exoribonucleolytic RNA exosome machinery
Authors: Phung Duy Khanh , Etienne Clarisse , Batista Manon , Langendijk-Genevaux Petra , Moalic Yann , Laurent Sébastien , Morales Violette , Jebbar Mohamed , Fichant Gwennaele , Bouvier Marie , Flament Didier , Clouet-d’Orval Béatrice 
Published: July 2019

ABSTRACTA network of RNA helicases, endoribonucleases, and exoribonucleases regulates the quantity and quality of cellular RNAs. To date, mechanistic studies focused on bacterial and eukaryal systems due to the challenge of identifying the main drivers of RNA decay and processing in Archaea. Here, our data support that aRNase J, a 5’-3’ exoribonuclease of the β-CASP family conserved in Euryarchaea, engages specifically with a Ski2-like helicase and the RNA exosome to potentially exert control over RNA surveillance, and that this occurs in the vicinity of the ribosome. Proteomic landscapes and direct protein-protein interaction analyses demonstrated that aRNase J interplay with ASH-Ski2 and the Csl4 cap exosome subunit. These in vitro data are strengthened by our phylogenomic studies showing a taxonomic co-distribution of aRNase J and ASH-Ski2 among the archaeal phylogeny. Finally, our T. barophilus whole-cell extract fractionation experiments provide evidences that an aRNase J/ASH-Ski2 complex might exist in vivo and hint at an association of aRNase J with the ribosome or polysomes that is stressed in absence of ASH-Ski2. While aRNase J homologues are found among bacteria, the RNA exosome and the Ski2-like RNA helicase have eukaryotic homologues, underlining the mosaic aspect of archaeal RNA machines. Altogether, these results suggest, for the first time, a fundamental role of β-CASP RNase/helicase complex in archaeal RNA metabolism. Finally, our results position aRNase J at the junction of RNA surveillance and translation processes, thus opening new perspectives and evolutionary scenario on RNA processing players in Archaea.
Hummingbird iridescence: an unsuspected structural diversity influences colouration at multiple scales
Authors: Gruson Hugo , Elias Marianne , Andraud Christine , Djediat Chakib , Berthier Serge , Doutrelant Claire , Gomez Doris 
Published: July 2019

AbstractIridescent colours are colours that change depending on the angle of illumination or observation. They are produced when light is reflected by multilayer structures or diffracted by gratings. While this phenomenon is well understood for simple optical systems, it remains unclear how complex biological structures interact with light to produce iridescence. There are very few comparative studies at interspecific level (often focusing on a single colour patch for each species), resulting in an underestimation of structure diversity. Using an interdisciplinary approach combining physics and biology, we here quantify the colour and structure of 36 hummingbirds species evenly distributed across the phylogeny. We explore at least 2 patches per species, which are assumed to be under different selective regimes. For each patch, we measure structural features (number of layers, layer width, irregularity, spacing, etc.) of the feathers at different scales using both optical and electronic microscopy and we measure colour using a novel approach we developed to encompass the full complexity of iridescence, including its angular dependency. We discover an unsuspected diversity of structures producing iridescence in hummingbirds. We also study the effect of several structural features on the colour of the resulting signal, using both an empirical and modelling approach. Our findings demonstrate the need to take into account multiple patches per species and suggest possible evolutionary pressures causing the evolutionary transitions from one melanosome type to another.
Assembly of hundreds of novel bacterial genomes from the chicken caecum
Authors: Glendinning Laura , Stewart Robert D. , Pallen Mark J. , Watson Kellie A. , Watson Mick 
Published: July 2019

AbstractChickens are a highly important source of protein for a large proportion of the human population. The caecal microbiota plays a crucial role in chicken nutrition through the production of short chain fatty acids, nitrogen recycling and amino acid production. In this study we sequenced DNA from caecal contents samples taken from 24 chickens belonging to either a fast or slower growing breed consuming either a vegetable-only diet or a diet containing fish meal. We utilised 1.6T of Illumina data to construct 469 draft metagenome-assembled bacterial genomes, including 460 novel strains, 283 novel species and 42 novel genera. We compared our genomes to data from eight EU countries and show that these genomes are abundant within European chicken flocks. We also compared the abundance of our genomes, and the carbohydrate active enzymes they produce, between our chicken groups and demonstrate that there are both breed- and diet-specific microbiomes, as well as an overlapping core microbiome. This data will form the basis for future studies examining the composition and function of the chicken caecal microbiota.
Changes in interictal pretreatment and posttreatment EEG in childhood absence epilepsy
Authors: Glaba Pawel , Latka Miroslaw , Krause Małgorzata , Kuryło Marta , Jernajczyk Wojciech , Walas Wojciech , West Bruce J. 
Published: July 2019

AbstractSpike and wave discharges (SWDs) are the characteristic manifestation of childhood absence epilepsy (CAE). It has long been believed that they unpredictably emerge from otherwise almost normal interictal EEG. Herein, we demonstrate that pretreatment closed-eyes theta and beta EEG wavelet powers of CAE patients (20 girls and 10 boys, mean age 7.4 ± 1.9 years) are much higher than those of age-matched controls at multiple sites of 10-20 system. For example, at C4 site, we observed a 91% and 62% increase in power of theta and beta rhythms, respectively. We were able to compare the baseline and posttreatment wavelet power in 16 patients. The pharmacotherapy brought about a statistically significant decrease in delta and theta wavelet power in all the channels, e.g. for C4 the reduction was equal to 45% (delta) and 65% (theta). We also observed a less pronounced attenuation of posttreatment beta rhythm in several channels. We hypothesize that the increased theta and beta powers result from cortical hyperexcitability and propensity for epileptic spikes generation, respectively. We argue that the distinct features of CAE wavelet power spectrum may be used to define an EEG biomarker which could be used for diagnosis and monitoring of patients.
A unified framework for geneset network analysis
Authors: Fanfani Viola , Stracquadanio Giovanni 
Published: July 2019

AbstractGene and protein interaction experiments provide unique opportunities to study their wiring in a cell. Integrating this information with high-throughput functional genomics data can help identifying networks associated with complex diseases and phenotypes.Here we propose a unified statistical framework to test network properties of single and multiple genesets. We focused on testing whether a geneset exhibits network properties and if two genesets are strongly interacting with each other.We then assessed power and false discovery rate of the proposed tests, showing that tests based on a probabilistic model of gene and protein interaction are the most robust.We implemented our tests in an open-source framework, called Python Geneset Network Analysis (PyGNA), which provides an integrated environment for network studies. While most available tools are designed as web applications, we designed PyGNA to be easily integrated into existing high-performance data analysis pipelines.Our software is available on GitHub (http://github.com/stracquadaniolab/pygna) and can be easily installed from PyPi or anaconda.
Resolving the connectome – Spectrally-specific functional connectivity networks and their distinct contributions to behaviour
Authors: Becker Robert , Hervais-Adelman Alexis 
Published: July 2019

AbstractThe resting brain exhibits spontaneous patterns of activity that reflect features of the underlying neural substrate. Examination of inter-areal coupling of resting state oscillatory activity has revealed that the brain’s resting activity is composed of functional networks, whose topographies differ depending upon oscillatory frequency, suggesting a role for carrier frequency as a means of creating multiplexed, or functionally segregated, communication channels between brain areas. Using canonical correlation analysis, we examined spectrally resolved resting-state connectivity patterns derived from MEG recordings to determine the relationship between connectivity intrinsic to different frequency channels and a battery of over a hundred behavioural and demographic indicators, in a group of 89 young healthy participants. We demonstrate that each of the classical frequency bands in the range 1-40Hz (delta, theta, alpha, beta and gamma) delineates a subnetwork that is behaviourally relevant, spatially distinct, and whose expression is either negatively or positively predictive of individual traits, with the strongest link in the alpha band being negative and networks oscillating at different frequencies, such as theta, beta and gamma carrying positive function.
Hierarchical and dynamic regulation of defense-responsive specialized metabolism by WRKY and MYB transcription factors
Authors: Barco Brenden , Clay Nicole K. 
Published: July 2019

AbstractThe plant kingdom produces hundreds of thousands of specialized bioactive metabolites, some with pharmaceutical and biotechnological importance. Their biosynthesis and function have been studied for decades, but comparatively less is known about how transcription factors with overlapping functions and contrasting regulatory activities coordinately control the dynamics and output of plant specialized metabolism. Here, we performed temporal studies on pathogen-infected intact host plants with perturbed transcription factors. We identified WRKY33 as the condition-dependent master regulator and MYB51 as the dual functional regulator in a hierarchical gene network likely responsible for the gene expression dynamics and metabolic fluxes in the camalexin and 4-hydroxy-indole-3-carbonylnitrile (4OH-ICN) pathways. This network may have also facilitated the regulatory capture of the newly evolved 4OH-ICN pathway in Arabidopsis thaliana by the more-conserved transcription factor MYB51. It has long been held that the plasticity of plant specialized metabolism and the canalization of development (Waddington, 1942) should be differently regulated; our findings imply a common hierarchical regulatory architecture orchestrated by transcription factors for specialized metabolism and development, making it an attractive target for metabolic engineering.
The heterogeneous functional architecture of the posteromedial cortex is associated with selective functional connectivity differences in Alzheimer’s disease
Authors: Khan Wasim , Amad Ali , Giampietro Vincent , Werden Emilio , De Simoni Sara , O’Muircheartaigh Jonathan , Westman Eric , O’Daly Owen , Williams Steve C.R. , Brodtmann Amy 
Published: July 2019

AbstractThe posteromedial cortex (PMC) is a key region involved in the development and progression of Alzheimer’s disease (AD). Previous studies have demonstrated a heterogenous functional architecture of the region, with different subdivisions reflecting distinct connectivity profiles. However, little is understood about PMC functional connectivity and its differential vulnerability to AD pathogenesis. Using a data-driven approach, we applied a constrained independent component analysis (ICA) on healthy adults from the Human Connectome Project (HCP) to characterise the distinct functional subdivisions and unique functional-anatomic connectivity patterns of the PMC. These connectivity profiles were subsequently quantified in the Alzheimer’s Disease Neuroimaging Initiative (ADNI) study, to examine functional connectivity differences in (1) AD patients and cognitively normal (CN) participants and (2) the entire AD pathological spectrum, ranging from CN participants and participants with subjective memory complaints (SMC), through to those with mild cognitive impairment (MCI), and finally, patients diagnosed with AD. Our findings revealed decreased functional connectivity in the anterior precuneus, dorsal posterior cingulate cortex, and the central precuneus in AD patients compared to CN participants. Functional abnormalities in these subdivisions were also related to high amyloid burden and lower hippocampal volumes. Across the entire AD spectrum, functional connectivity of the central precuneus was associated with disease progression and specific deficits in memory and executive function. These findings provide new evidence showing that specific vulnerabilities in PMC functional connectivity are associated with large-scale network disruptions in AD and that these patterns may be useful for elucidating potential biomarkers for measuring disease progression in future work.
Nitric Oxide Mediates Neuro-Glial Interaction that Shapes Drosophila Circadian Behavior
Authors: Kozlov Anatoly , Nagoshi Emi 
Published: July 2019

AbstractDrosophila circadian behavior relies on the network of heterogeneous groups of clock neurons. Short -and long-range signaling within the pacemaker circuit coordinates molecular and neural rhythms of clock neurons to generate coherent behavioral output. The neurochemistry of circadian behavior is complex and remains incompletely understood. Here we demonstrate that the gaseous messenger nitric oxide (NO) is a signaling molecule linking circadian pacemaker to rhythmic locomotor activity. We show that two independent mutants lacking nitric oxide synthase (NOS) have severely disturbed locomotor behavior both in light-dark cycles and constant darkness, although molecular clocks in the main pacemaker neurons are unaffected. Behavioral phenotypes are due in part to the malformation of neurites of the main pacemaker neurons, s-LNvs. Using cell-type selective and stage-specific gain -and loss-of-function of NOS, we demonstrate that NO secreted from diverse cellular clusters non-cell-autonomously affect molecular and behavioral rhythms. We further identify glia as a major source of NO that regulates circadian locomotor output. These results reveal for the first time the critical role of NO signaling in the Drosophila circadian system and highlight the importance of neuro-glial interaction in the neural circuit output.Author summaryCircadian rhythms are daily cycles of physiological and behavioral processes found in most plants and animals on our planet from cyanobacteria to humans. Circadian rhythms allow organisms to anticipate routine daily and annual changes of environmental conditions and efficiently adapt to them. Fruit fly Drosophila melanogaster is an excellent model to study this phenomenon, as its versatile toolkit enables the study of genetic, molecular and neuronal mechanisms of rhythm generation. Here we report for the first time that gasotransmitter nitric oxide (NO) has a broad, multi-faceted impact on Drosophila circadian rhythms, which takes place both during the development and the adulthood. We also show that one of the important contributors of NO to circadian rhythms are glial cells. The second finding highlights that circadian rhythms of higher organisms are not simply controlled by the small number of pacemaker neurons but are generated by the system that consists of many different players, including glia.