bluuebunny/crossref_metadata_2025_split huggingface dataset:
Satellite cell-derived extracellular vesicles reverse peroxide-induced mitochondrial dysfunction in myotubes
Authors: Shuler Kyle T. , Wilson Brittany E. , Muñoz Eric R. , Mitchell Andrew D. , Selsby Joshua T. , Hudson Matthew B. 
Published: March 2020

ABSTRACTSatellite cells (SCs) are muscle-specific stem cells that have a central role in muscle remodeling. Despite their therapeutic potential, SC-based therapies have been met with numerous logistical challenges, limiting their ability to effectively treat systemic muscle diseases, such as Duchenne muscular dystrophy (DMD). Delivery of SC-derived extracellular vesicles (SC-EVs) may unlock the potential offered by SCs and overcome their numerous limitations.PurposeThe purpose of this investigation was to determine the extent to which SC-EVs could restore mitochondrial function in cultured myotubes following oxidative injury.MethodsSC-EVs were isolated from cultured SCs from C57 mice and quantified using nanoparticle tracking analysis (NTA). C2C12 myotubes were cultured and divided into four treatment groups: untreated control, treated for 24 h with SC-EV, 24 h exposure to 50 μM H2O2followed by a 24 h recovery period with no treatment, or 24 h exposure to 50 μM H2O2followed by a 24 h treatment with SC-EV. Inter-group differences in mitochondrial function were assessed via one-way ANOVA with Tukey post hoc analysis (p<0.05).ResultsGiven the seeding density used, we calculated that each SC releases approximately 2.35 × 105± 3.10 × 104EVs per 24 h. Further, using fluorescent microscopy, we verified SC-EVs deliver cargo into myotubes, some of which was localized to the mitochondria. H2O2exposure resulted in a 42% decline in peak mitochondrial respiration (p=0.0243) as well as a 46% reduction in spare respiratory capacity (p=0.0185) relative to the untreated control group. Subsequent treatment with SC-EVs (3.12×108SC-EV; 24 h) following H2O2exposure restored 76% of peak mitochondrial respiration (p=0.0187) and 84% of spare respiratory capacity in the damaged myotubes (p=0.0198). SC-EVs did not affect mitochondrial function in the undamaged myotubes.ConclusionCollectively, these data demonstrate SC-EVs may represent a novel therapeutic approach for treatment of myopathies associated with mitochondrial dysfunction.
Engineering an RNA-based tissue-specific platform for genetic editing through use of a miRNA-enabled Cas12a
Authors: Møller Rasmus , Oishi Kohei , tenOever Benjamin R. 
Published: March 2020

ABSTRACTThe capacity to edit genomes using CRISPR-Cas systems holds immense potential for countless genetic-based diseases. However, one significant impediment preventing broad therapeutic utilization isin vivodelivery. While genetic editing at a single cell levelin vitrocan be achieved with high efficiency, the capacity to utilize these same biologic tools in a desired tissuein vivoremains challenging. Non-integrating RNA virus-based vectors constitute efficient platforms for transgene expression and surpass several barriers toin vivodelivery. However, the broad tissue tropism of viral vectors raises the concern for off-target effects. Moreover, prolonged expression of the Cas proteins, regardless of delivery method, can accumulate aberrant RNAs leading to unwanted immunological responses. In an effort to circumvent these shortcomings, here we describe a versatile RNA virus-based technology that can achieve cell-specific activity and self-inactivation by combining host microRNA (miRNA) biology with the CRISPR-Cas12a RNA-guided nuclease. Exploiting the RNase activity of Cas12a, we generated a vector that self-inactivates upon delivery of Cas12a and an accompanying CRISPR RNA (crRNA). Furthermore, we show that maturation of the crRNA can be made dependent on cell-specific miRNAs, which confers cell-specificity. We demonstrate that this genetic editing circuit delivers diminished yet sufficient levels of Cas12a to achieve effective genome editing whilst inducing a minimal immunological response. It can also function in a cell-specific manner thereby facilitatingin vivoediting and mitigating the risk of unwanted, off-target effects.
TURNOVER OR INTRASPECIFIC TRAIT VARIATION: EXPLAINING FUNCTIONAL VARIABILITY IN A NEOTROPICAL ANURAN METACOMMUNITY
Authors: Dalmolin Diego Anderson , Tozetti Alexandro Marques , Ramos Pereira Maria João 
Published: March 2020

ABSTRACTTrait variation across environmental gradients results from two processes: intraspecific variation (ITV) and turnover. Tadpoles are known to exhibit phenotypic plasticity in several traits in response to the environment, resulting from intra or interspecific variation. Here we evaluate patterns of intraspecific variation in functional traits of adult anurans (head shape, eye size and position, limb length and body mass) and their relationship with environmental variables in an anuran metacommunity in southern Brazil. From anurans sampled from 33 ponds, we decomposed trait variation into ITV and turnover and modelled trait-environment relationships. We predict that the contribution of ITV and turnover to trait variation and trait-environment relationships should vary according to the preferred habitat of the species and the analysed traits. Intraspecific variation accumulated the highest rate of trait variation for arboreal species, while interspecific variation was greater for aquatic-terrestrial species and for the whole set of species. The contributions of turnover and ITV to shifts in community mean trait values were similar between traits, but differed between species sets. Depth, distance between ponds, area ofPinussurrounding the ponds, and types of pond vegetation and substrate strongly influenced trait variation, but their relative contribution depended on the analysed traits and species sets. The great contribution of ITV for head shape and eye size and position suggests the existence of intraspecific adaptations to microhabitats, while turnover dominance in the variation of body mass and limb length suggests differences in dispersal and trophic segregation between species.
Clinical characterization and chest CT findings in laboratory-confirmed COVID-19: a systematic review and meta-analysis
Authors: Vaseghi Golnaz , Mansourian Marjan , Karimi Raheleh , Heshmat-Ghahdarijani Kiyan , Mahdavi Sadegh Baradaran , Pezeshki Amirhossein , Ataei Behrooz , Zandifar Alireza , Shafaat Omid , Javanmard Shaghayegh Haghjoo 
Published: March 2020

AbstractBackgroundImagery techniques have been used as essential parts of diagnostic workup for patients suspected for 2019-nCoV infection, Multiple studies have reported the features of chest computed tomography (CT) scans among a number of 2019-nCoV patients.MethodStudy Identification was carried out in databases (PubMed, Embase and Cochrane Library) to identify published studies examining the diagnosis, the 2019 novel coronavirus (2019-nCoV). Heterogeneity among reported prevalence was assessed by computing p-values of Cochrane Q-test and I2-statics. The pooled prevalence of treatment failure was carried out with a fixed effects meta-analysis model, generating the pooled 95% confidence interval. A random-effect model was used to pool the results since this model could incorporate the heterogeneity of the studies and therefore proved a more generalized result.ResultsAccording to the combined results of meta-analysis, the total 55% of corona patients were males. The mean age of the patients was 41.31 (34.14, 48.47). Two prevalent clinical symptoms between patients were fever, cough with prevalence of 85%, and 62%, respectively. Either Ground Glass Opacity GGO or consolidation was seen in 86% but 14% hadNO GGO or consolidation.The other rare CT symptoms were pericardial effusion, and pleural effusion with 4, 5, 7% prevalence, respectively. The most prevalent event was Either GGO or consolidation in 85% of patients.ConclusionThe most CT-scan abnormality is Either Ground Glass Opacity GGO or consolidation however in few patients none of them might be observed, so trusting in just CT findings will lead to miss some patients.
Virtual-SMLM, a virtual environment for real-time interactive SMLM acquisition
Authors: Griffié J. , Pham T.A. , Sieben C. , Lang R. , Cevher V. , Holden S. , Unser M. , Manley S. , Sage D. 
Published: March 2020

AbstractAlthough single molecule localisation microscopy enables for the visualisation of cells nanoscale organisation, its dissemination remains limited mainly due to the complexity of the associated imaging acquisition, impacting on outputs’ reliability and reproducibility. We propose here the first all-in-one fully virtual environment for SMLM acquisition:Virtual-SMLM, including on-the-fly interactivity and real time display. It relies on a novel realistic approach to simulate fluorophores photo-physics based on independent pseudo-continuous emission traces. It also facilitates for user-specific experimental and optical environment design. As such, it constitutes a unique tool for the training of both users and machine learning approaches to automated SMLM, as well as for experimental validation, whilst providing realistic data sets for the development of image reconstruction algorithms and data analysis software.
Processive and stochastic CHH methylation by plant DRM2 and CMT2 revealed by single-read methylome analysis
Authors: Harris Keith D. , Zemach Assaf 
Published: March 2020

AbstractCytosine methylome data is commonly generated through next-generation sequencing (NGS). Analyses of this data average methylation states of individual reads. We propose an alternate method of analysing single-read methylome data. Using this method, we identified patterns that relate to the mechanism of two plant non-CG methylating enzymes, DRM2 and CMT2: DRM2 has higher processivity than CMT2, and DRM2-methylated regions have higher variation among cells. Based on these patterns, we developed a classifier that predicts enzyme activity in different species and tissues. To facilitate further single-read analyses, we developed a genome browser optimised for visualising and analysing NGS data at single-read resolution.
Restoration of motor-evoked cortical activity is a distinguishing feature of the most effective rehabilitation therapy after stroke
Authors: Conti Emilia , Mascaro Anna Letizia Allegra , Scaglione Alessandro , de Vito Giuseppe , Calugi Francesco , Pasquini Maria , Pizzorusso Tommaso , Micera Silvestro , Pavone Francesco Saverio 
Published: March 2020

AbstractBackgroundAn ischemic stroke is followed by the remapping of motor representation and extensive changes in cortical excitability involving both hemispheres. Although stimulation of the ipsilesional motor cortex, especially when paired with motor training, facilitates plasticity and functional restoration, the mechanisms underneath the reshaping of cortical functionality are widely unknown.ObjectiveWe investigated the spatio-temporal features of motor-evoked cortical activity associated with generalized recovery after stroke, and its dependence on the type of rehabilitative treatment.MethodsWe designed a novel rehabilitative treatment that combines neuro-plasticizing intervention with motor training. Specifically, optogenetic stimulation of peri-infarct excitatory neurons expressing Channelrhodopsin-2 was associated with daily motor training on a robotic device. The effectiveness of the combined therapy was compared with spontaneous recovery and with the single treatments (i.e. individually administered optogenetic stimulation or motor training).ResultsWe found that only the combined therapy promotes generalized recovery of forelimb function and the rescue of spatio-temporal features of motor-evoked activity. Generalized recovery results from a new excitatory/inhibitory balance between hemispheres as revealed by the augmented motor response flanked by the increased expression of parvalbumin positive neurons in the peri-infarct area.ConclusionsOur findings demonstrate that though behavioral recovery is not necessarily associated with the restoration of pre-stroke motor-evoked activity, the reestablishment of pre-stroke activation transients was a distinguishing feature of the most efficient therapeutic approach, the combined therapy.
In vivoimaging of the kinetics of microglial self-renewal and maturation in the adult visual cortex
Authors: Mendes Monique S. , Atlas Jason , Brehm Zachary , Ladron-de-Guevara Antonio , McCall Matthew N. , Majewska Ania K. 
Published: March 2020

AbstractMicroglia are the resident immune cells in the brain with the capacity to autonomously self-renew. Under basal conditions, microglial self-renewal appears to be slow and stochastic, although microglia have the ability to proliferate very rapidly following depletion or in response to injury. Because microglial self-renewal has largely been studied using static tools, the mechanisms and kinetics by which microglia renew and acquire mature characteristics in the adult brain are not well understood. Using chronicin vivotwo-photon imaging in awake mice and PLX5622 (Colony stimulating factor 1 receptor (CSF1R) inhibitor) to deplete microglia, we set out to understand the dynamic self-organization and maturation of microglia following depletion in the visual cortex. We confirm that under basal conditions, cortical microglia show limited turnover and migration. Following depletion, however, microglial repopulation is remarkably rapid and is sustained by the dynamic division of the remaining microglia in a manner that is largely independent of signaling through the P2Y12 receptor. Mathematical modeling of microglial division demonstrates that the observed division rates can account for the rapid repopulation observedin vivo. Additionally, newly-born microglia resemble mature microglia, in terms of their morphology, dynamics and ability to respond to injury, within days of repopulation. Our work suggests that microglia rapidly self-renew locally, without the involvement of a special progenitor cell, and that newly born microglia do not recapitulate a slow developmental maturation but instead quickly take on mature roles in the nervous system.Graphical Abstract(a) Microglial dynamics during control condition. Cartoon depiction of the heterogenous microglia in the visual cortex equally spaced. (b) During the early stages of repopulation, microglia are irregularly spaced and sparse. (c) During the later stages of repopulation, the number of microglia and the spatial distribution return to baseline. (d-f) We then created and ran a mathematical model that sampled the number of microglia, (d) the persistent doublets, (e) the rapid divisions of microglia and (f) the secondary divisions of microglia during the peak of repopulation day 2-day 3. The mathematical model suggested that residual microglia can account for the rapid repopulation we observedin vivo.
Human DND1-RRM2 forms a non-canonical domain swapped dimer
Authors: Kumari Pooja , Bhavesh Neel Sarovar 
Published: March 2020

SummaryHuman DND1 (Dead end protein homolog1) is an RNA binding protein. DND1 plays pivotal role in animal development and has been implicated in cancer. DND1 consists of two RNA recognition motifs (RRMs) in tandem and a double stranded RNA binding domain at the C terminal separated by 40 residues flexible linker. The conserved RNP site in the RRM1 domain helps in specific RNA recognition while the RNP sites in RRM2 are not well conserved. DND1 has been reported to be involved in inhibition of microRNA access to target mRNA and it also associate with CCR4-NOT complex that targets mRNA. In order to understand this intriguing contrasting molecular function, we have determined the 2.3 Å resolution crystal structure of the human DND1 RRM2 domain. The structure revealed an interesting non-canonical RRM fold that is maintained by the formation of a domain swapped dimer between β1and β4strands across two chains. The domain swapping is attributed by a hinge loop between α2and β4that helps in mediating a domain swap forming anti-parallel β sheets. We have delineated the structural basis of stable dimer formation using the residue level dynamics of protein explored by NMR spectroscopy and MD simulations. Our structural and dynamics studies demonstrate the molecular basis for the dimerization of the RRM2 domain and shed light on the possibility for this motif for interaction with other proteins which helps in transcription regulation.Graphical AbstractHighlightsFirst report of a domain swapped dimer formation by an RRM identified through crystal structure determination of the human DND1 RRM2 domain.RRM2 exhibit domain swapped dimerization attributed by hinge loop and disulfide bond formation.Dimer formation is under redox regulation.Major determinants of swapping were identified.DND1 RRM2 is not involved in RNA recognition.
ppGpp influences protein protection, growth and photosynthesis inPhaeodactylum tricornutum
Authors: Avilan Luisana , Lebrun Regine , Puppo Carine , Citerne Sylvie , Cuiné Stephane , Li-Beisson Yonghua , Menand Benoit , Field Ben , Gontero Brigitte 
Published: March 2020

SummaryChloroplasts retain elements of a bacterial stress response pathway that is mediated by the signalling nucleotides guanosine penta- and tetraphosphate, or (p)ppGpp. In the model flowering plant Arabidopsis, ppGpp acts as a potent regulator of plastid gene expression and influences photosynthesis, plant growth and development. However, little is known about ppGpp metabolism or its evolution in other photosynthetic eukaryotes.Here, we studied the function of ppGpp in the diatomP. tricornutumusing transgenic lines containing an inducible system for ppGpp accumulation. We used these lines to investigate the effects of ppGpp on growth, photosynthesis, lipid metabolism and protein expression.We demonstrate that ppGpp accumulation reduces photosynthetic capacity and promotes a quiescent-like state with reduced proliferation and ageing. Strikingly, using non-targeted proteomics, we discovered that ppGpp accumulation also leads to the coordinated upregulation of a protein protection response in multiple cellular compartments.Our findings highlight the importance of ppGpp as a fundamental regulator of chloroplast function across different domains of life, and lead to new questions about the molecular mechanisms and roles of (p)ppGpp signalling in photosynthetic eukaryotes.
External mechanical cues reveal core molecular pathway behind tissue bending in plants
Authors: Baral Anirban , Morris Emily , Aryal Bibek , Jonsson Kristoffer , Verger Stéphane , Xu Tongda , Bennett Malcolm , Hamant Olivier , Bhalerao Rishikesh P. 
Published: March 2020

SummaryTissue folding is a central building block of plant and animal morphogenesis. In dicotyledonous plants, hypocotyl folds to form hook after seedling germination that protects their aerial stem cell niche during emergence from soil. Auxin response factors and auxin transport are classically thought to play a key role in this process. Here we show that the microtubule-severing enzyme katanin contributes to hook formation. However, by exposing hypocotyls to external mechanical cues mimicking the natural soil environment, we reveal that auxin response factors ARF7/ARF19, auxin influx carriers, and katanin are dispensable for apical hook formation, indicating that these factors primarily play the role of catalyzers of tissue bending in the absence of external mechanical cues. Instead, our results reveal the key roles of the non-canonical TMK-mediated auxin pathway, PIN efflux carriers and cellulose microfibrils as components of the core pathway behind hook formation in presence or absence of external mechanical cues.
The antitumoral activity of TLR7 ligands is corrupted by the microenvironment of pancreatic tumors
Authors: Rouanet Marie , Lulka Hubert , Garcin Pierre , Sramek Martin , Pagan Delphine , Valle Carine , Sarot Emeline , Pancaldi Vera , Lopez Frédéric , Buscail Louis , Cordelier Pierre 
Published: March 2020

AbstractToll like receptors are key players in the innate immune system. Recent studies have suggested that they may impact the growth of pancreatic cancer, a disease with no cure. Among them, Toll like receptor-7 shows promise for therapy but may also promote tumor growth. Thus, we aimed to better understand the mechanism of action of Toll like receptor-7 ligands in pancreatic cancer, to open the door for clinical applications.In vitro, Toll like receptor-7 ligands strongly inhibit the proliferation and induce cell death by apoptosis of pancreatic cancer cells.In vivo, while Toll like receptor-7 agonists significantly delay the growth of aggressive tumors engrafted in immunodeficient mice, they instead surprisingly promote tumor growth and accelerate animal death in immunocompetent models. Molecular investigations revealed that Toll like receptor-7 agonists strongly increase the number of tumor-promoting macrophages to drive pancreatic tumorigenesis in immunocompetent mice. This is in stark contrast with Toll like receptor-7 ligands’ great potential to inhibit pancreatic cancer cell proliferationin vitroand tumor growthin vivoin immunosuppressed models. Collectively, our findings shine a light on the duality of action of Toll like receptor-7 agonists in experimental cancer models, and calls into question their use for pancreatic cancer therapy.
Implications of error-prone long-read whole-genome shotgun sequencing on characterizing reference microbiomes
Authors: Hu Yu , Fang Li , Nicholson Christopher , Wang Kai 
Published: March 2020

SummaryLong-read sequencing techniques, such as the Oxford Nanopore Technology, can generate reads that are tens of kilobases in length, and are therefore particularly relevant for microbiome studies. However, due to the higher per-base error rates than typical short-read sequencing, the application of long-read sequencing on microbiomes remains largely unexplored. Here we deeply sequenced two human microbiota mock community samples (HM-276D and HM-277D) from the Human Microbiome Project. We showed that assembly programs consistently achieved high accuracy (~99%) and completeness (~99%) for bacterial strains with adequate coverage. We also found that long-read sequencing provides accurate estimates of species-level abundance (R=0.94 for 20 bacteria with abundance ranging from 0.005% to 64%). Our results demonstrate the feasibility to characterize complete microbial genomes and populations from error-prone Nanopore sequencing data, but also highlight necessary bioinformatics improvements for future metagenomics tool development.