bluuebunny/crossref_metadata_2025_split huggingface dataset:
In vivo recellularization of xenogeneic vascular grafts decellularized with high hydrostatic pressure method in a porcine carotid arterial interpose model
Authors: Kurokawa Shunji , Hashimoto Yoshihide , Funamoto Seiichi , Yamashita Akitatsu , Yamazaki Kazuhiro , Ikeda Tadashi , Minatoya Kenji , Kishida Akio , Masumoto Hidetoshi 
Published: May 2020

ABSTRACTAutologous vascular grafts are widely used in revascularization surgeries for small caliber targets. However, the availability of autologous conduits might be limited due to prior surgeries or the quality of vessels. Xenogeneic decellularized vascular grafts from animals potentially substitute for autologous vascular grafts. Decellularization with high hydrostatic pressure (HHP) is reported to highly preserve extracellular matrix (ECM) which would be feasible for recellularization and vascular remodeling after implantation. In the present study, we conducted xenogeneic implantation of HHP-decellularized bovine vascular grafts from dorsalis pedis arteries to porcine carotid arteries then evaluated graft patency, ECM preservation and recellularization. Surgical procedure not to damage luminal surface of the grafts from drying significantly increased the graft patency at 4 weeks after implantation (P = 0.0079). After the technical improvement, all grafts (N = 5) were patent with mild stenosis due to intimal hyperplasia at 4 weeks after implantation. Neither aneurysmal change nor massive thrombosis was observed even without administration of anticoagulants nor anti-platelet agents. Elastica van Gieson and Sirius-red stainings revealed fair preservation of ECM proteins including elastin and collagen after implantation. Luminal surface of grafts was thoroughly covered with von Willebrand factor-positive endothelium. Scanning electron microscopy on luminal surface of implanted grafts exhibited cobblestone-like endothelial cell layer which is similar to native vascular endothelium. Recellularization of tunica media with alpha-smooth muscle actin-positive smooth muscle cells was partly observed. Thus, we confirmed that HHP-decellularized grafts are feasible for xenogeneic implantation accompanied by recellularization by recipient cells.
SiCTeC: an inexpensive, easily assembled Peltier device for rapid temperature shifting during single-cell imaging
Authors: Knapp Benjamin D. , Zhu Lillian , Huang Kerwyn Casey 
Published: May 2020

AbstractSingle-cell imaging, combined with recent advances in image analysis and microfluidic technologies, have enabled fundamental discoveries of cellular responses to chemical perturbations that are often obscured by traditional liquid-culture experiments. Temperature is an environmental variable well known to impact growth and to elicit specific stress responses at extreme values; it is often used as a genetic tool to interrogate essential genes. However, the dynamic effects of temperature shifts have remained mostly unstudied at the single-cell level, due largely to engineering challenges related to sample stability, heatsink considerations, and temperature measurement and feedback. Additionally, the few commercially available temperature-control platforms are costly. Here, we report an inexpensive (<$110) and modularSingle-CellTemperatureController (SiCTeC) device for microbial imaging, based on straightforward modifications of the typical slide-sample-coverslip approach to microbial imaging, that controls temperature using a ring-shaped Peltier module and microcontroller feedback. Through stable and precise (±0.15 °C) temperature control, SiCTeC achieves reproducible and fast (1-2 min) temperature transitions with programmable waveforms between room temperature and 45 °C with an air objective. At the device’s maximum temperature of 89 °C, SiCTeC revealed thatEscherichia colicells progressively shrink and lose cellular contents. During oscillations between 30 °C and 37 °C, cells rapidly adapted their response to temperature upshifts. Furthermore, SiCTeC enabled the discovery of rapid morphological changes and enhanced sensitivity to substrate stiffness during upshifts to nonpermissive temperatures in temperature-sensitive mutants of cell-wall synthesis enzymes. Overall, the simplicity and affordability of SiCTeC empowers future studies of the temperature dependence of single-cell physiology.
An extracellular protein regulates patched-related/DAF-6-mediated sensory compartment formation inC. elegans
Authors: Hong Hui , Chen Huicheng , Zhang Yuxia , Wu Zhimao , Zhang Yingying , Zhang Yingyi , Hu Zeng , Zhang Jian , Lin Kun , Hu Jinghua , Wei Qing 
Published: May 2020

AbstractCoordination of neurite extension with surrounding glia development is critical for neuronal function, but the underlying molecular mechanisms remain poorly understood. Through a genome-wide mutagenesis screen inC. elegans, we identifieddyf-4anddaf-6as two mutants sharing similar defects in dendrite extension. DAF-6 encodes a glia-specific patched-related membrane protein that plays vital roles in glial morphogenesis. We cloneddyf-4and found that DYF-4 encodes a glia-secreted extracellular protein. Intriguingly, DYF-4 colocalizes with DAF-6 along the glial channel. Further investigations revealed that DYF-4 directly interacts with DAF-6 and regulates its proper membrane localization. Notably, reported glial suppressors ofdaf-6could also restore dendrite elongation and ciliogenesis in bothdyf-4anddaf-6mutants. Collectively, our data suggest that secreted DYF-4 likely acts as a novel ligand/regulator for the patched-related receptor DAF-6 which promotes the proper formation of the glial channel and indirectly affects neurite extension and ciliogenesis.
Impact of emerging mutations on the dynamic properties the SARS-CoV-2 main protease: anin silicoinvestigation
Authors: Amamuddy Olivier Sheik , Verkhivker Gennady M. , Bishop Özlem Tastan 
Published: May 2020

AbstractThe new coronavirus (SARS-CoV-2) is a global threat to world health and its economy. Its main protease (Mpro), which functions as a dimer, cleaves viral precursor proteins in the process of viral maturation. It is a good candidate for drug development owing to its conservation and the absence of a human homolog. An improved understanding of the protein behaviour can accelerate the discovery of effective therapies in order to reduce mortality. 100 ns all-atom molecular dynamics simulations of 50 homology modelled mutant Mprodimers were performed at pH 7 from filtered sequences obtained from the GISAID database. Protease dynamics were analysed using RMSD, RMSF, Rg, the averagedbetweenness centralityand geometry calculations. Domains from each Mproprotomer were found to generally have independent motions, while the dimer-stabilising N-finger region was found to be flexible in most mutants. A mirrored interprotomer pocket was found to be correlated to the catalytic site using compaction dynamics, and can be a potential allosteric target. The high number of titratable amino acids of Mpromay indicate an important role of pH on enzyme dynamics, as previously reported for SARS-CoV. Independent coarse-grained Monte Carlo simulations suggest a link between rigidity/mutability and enzymatic function.
AMPK regulates cell shape of cardiomyocytes by modulating turnover of microtubules through CLIP-170
Authors: Yashirogi Shohei , Katayama Toru , Nagao Takemasa , Nishida Yuya , Kioka Hidetaka , Matsui Tsubasa S , Saito Shigeyoshi , Masumura Yuki , Tsukamoto Osamu , Kato Hisakazu , Yazawa Issei , Ueda Hiromichi , Yamaguchi Osamu , Yashiro Kenta , Yamazaki Satoru , Takashima Seiji , Shintani Yasunori 
Published: May 2020

SummaryAMP-activated protein kinase (AMPK) is a multifunctional kinase that regulates microtubule (MT) dynamic instability through CLIP-170 phosphorylation; however, its physiological relevance in vivo remains to be elucidated. In this study, we identified an active form of AMPK localized at the intercalated discs in the heart, a specific cell-cell junction present between cardiomyocytes. A contractile inhibitor, MYK-461, prevented the localization of AMPK at the intercalated discs, and the effect was reversed by the removal of MYK-461, suggesting that the localization of AMPK is regulated by mechanical stress. Time-lapse imaging analysis revealed that the inhibition of CLIP-170 Ser-311 phosphorylation by AMPK leads to the accumulation of MTs at the intercalated discs. Interestingly, MYK-461 increased the individual cell area of cardiomyocytes in CLIP-170 phosphorylation-dependent manner. Moreover, heart-specific CLIP-170 S311A transgenic mice demonstrated elongation of cardiomyocytes along with accumulated MTs, leading to progressive decline in cardiac contraction. In conclusion, these findings suggest that AMPK regulates the cell shape and aspect ratio of cardiomyocytes by modulating the turnover of MTs through homeostatic phosphorylation of CLIP-170 at the intercalated discs.
The Arp1/11 Minifilament of Dynactin Primes the Endosomal Arp2/3 Complex
Authors: Fokin Artem I. , David Violaine , Oguievetskaia Ksenia , Derivery Emmanuel , Stone Caroline E. , Cao Luyan , Rocques Nathalie , Molinie Nicolas , Henriot Véronique , Aumont-Nicaise Magali , Hinckelmann Maria-Victoria , Saudou Frédéric , Le Clainche Christophe , Carter Andrew P. , Romet-Lemonne Guillaume , Gautreau Alexis M. 
Published: May 2020

AbstractDendritic actin networks develop from a first actin filament through branching by the Arp2/3 complex. At the surface of endosomes, the WASH complex activates the Arp2/3 complex and interacts with the Capping Protein for unclear reasons. Here we show that that the WASH complex interacts with Dynactin and uncaps it through its FAM21 subunit. In vitro, the uncapped Arp1/11 minifilament elongates an actin filament, which then primes the WASH-induced Arp2/3 branching reaction. In Dynactin-depleted cells or in cells where the WASH complex is reconstituted with a FAM21 mutant that cannot uncap Dynactin, formation of branched actin at the endosomal surface is impaired. Our results reveal the importance of the WASH complex in coordinating two complexes containing actin-related proteins.One Sentence SummaryDendritic actin networks grow in an autocatalytic manner starting from the uncapped minifilament of Dynactin.
Evolutionary design of optimal surface topographies for biomaterials
Authors: Vasilevich Aliaksei , Carlier Aurélie , Winkler David A. , Singh Shantanu , de Boer Jan 
Published: May 2020

AbstractNatural evolution tackles optimization by producing many genetic variants and exposing these variants to selective pressure, resulting in the survival of the fittest. We use high throughput screening of large libraries of materials with differing surface topographies to probe the interactions of implantable device coatings with cells and tissues. However, the vast size of possible parameter design space precludes a brute force approach to screening all topographical possibilities. Here, we took inspiration from Nature to optimize materials surface topographies using evolutionary algorithms. We show that successive cycles of material design, production, fitness assessment, selection, and mutation results in optimization of biomaterials designs. Starting from a small selection of topographically designed surfaces that upregulate expression of an osteogenic marker, we used genetic crossover and random mutagenesis to generate new generations of topographies.
The representation of women as authors of submissions to ecology journals during the COVID-19 pandemic
Authors: Fox Charles W. 
Published: May 2020

AbstractObservations made from papers submitted to preprint servers, and the speculation of editors on social media platforms, suggest that women are submitting fewer papers to scholarly journals than are men during the COVID-19 pandemic. Here I examine whether submissions by men and women to six ecology journals (all published by the British Ecological Society) have changed since the start of COVID disruptions. At these six ecology journals there is no evidence of a decline in the proportion of submissions that are authored by women (as either first or submitting author) since the start of the COVID-19 disruptions; the proportion of papers authored by women in the post-COVID period of 2020 has increased relative to the same period in 2019, and is higher than in the period pre-COVID in 2020. There is also no evidence of a change in the geographic pattern of submissions from across the globe.
Dose-dependent response to infection with SARS-CoV-2 in the ferret model: evidence of protection to re-challenge
Authors: Ryan Kathryn A. , Bewley Kevin R. , Fotheringham Susan A. , Brown Phillip , Hall Yper , Marriott Anthony C. , Tree Julia A. , Allen Lauren , Aram Marilyn J. , Brunt Emily , Buttigieg Karen R. , Cavell Breeze E. , Carter Daniel P. , Cobb Rebecca , Coombes Naomi S. , Godwin Kerry J. , Gooch Karen E. , Gouriet Jade , Halkerston Rachel , Harris Debbie J. , Humphries Holly E. , Hunter Laura , Ho Catherine M. K. , Kennard Chelsea L. , Leung Stephanie , Ngabo Didier , Osman Karen L. , Paterson Jemma , Penn Elizabeth J. , Pullan Steven T. , Rayner Emma , Slack Gillian S. , Steeds Kimberley , Taylor Irene , Tipton Tom , Thomas Stephen , Wand Nadina I. , Watson Robert J. , Wiblin Nathan R. , Charlton Sue , Hallis Bassam , Hiscox Julian A. , Funnell Simon , Dennis Mike J. , Whittaker Catherine J. , Catton Michael G. , Druce Julian , Salguero Francisco J. , Carroll Miles W. 
Published: May 2020

AbstractIn December 2019 an outbreak of coronavirus disease (COVID-19) emerged in Wuhan, China. The causative agent was subsequently identified and named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which rapidly spread worldwide causing a pandemic. Currently there are no licensed vaccines or therapeutics available against SARS-CoV-2 but numerous candidate vaccines are in development and repurposed drugs are being tested in the clinic. There is a vital need for authentic COVID-19 animal models to further our understanding of pathogenesis and viral spread in addition to pre-clinical evaluation of candidate interventions.Here we report a dose titration study of SARS-CoV-2 to determine the most suitable infectious dose to use in the ferret model. We show that a high (5×106pfu) and medium (5×104pfu) dose of SARS-CoV-2 induces consistent upper respiratory tract (URT) viral RNA shedding in both groups of six challenged animals, whilst a low dose (5×102pfu) resulted in only one of six displaying signs of URT viral RNA replication. The URT shedding lasted up to 21 days in the high dose animals with intermittent positive signal from day 14. Sequential culls revealed distinct pathological signs of mild multifocal bronchopneumonia in approximately 5-15% of the lung, observed on day 3 in high and medium dosed animals, with presence of mild broncho-interstitial pneumonia on day 7 onwards. No obvious elevated temperature or signs of coughing or dyspnoea were observed although animals did present with a consistent post-viral fatigue lasting from day 9-14 in the medium and high dose groups. After virus shedding ceased, re-challenged ferrets were shown to be fully protected from acute lung pathology. The endpoints of URT viral RNA replication in addition to distinct lung pathology and post viral fatigue were observed most consistently in the high dose group. This ferret model of SARS-CoV-2 infection presents a mild clinical disease (as displayed by 80% of patients infected with SARS-CoV-2). In addition, intermittent viral shedding on days 14-21 parallel observations reported in a minority of clinical cases.
Temporal evolution and adaptation of SARS-COV-2 codon usage
Authors: Posani Elisa , Dilucca Maddalena , Forcelloni Sergio , Pavlopoulou Athanasia , Georgakilas Alexandros G. , Giansanti Andrea 
Published: May 2020

AbstractThe outbreak of severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) has caused an unprecedented pandemic. Since the first sequenced whole-genome of SARS-CoV-2 on January 2020, the identification of its genetic variants has become crucial in tracking and evaluating their spread across the globe.In this study, we compared 134,905 SARS-CoV-2 genomes isolated from all affected countries since the outbreak of this novel coronavirus with the first sequenced genome in Wuhan, China to quantify the evolutionary divergence of SARS-CoV-2. Thus, we compared the codon usage patterns of SARS-CoV-2 genes encoding the membrane protein (M), envelope (E), spike surface glycoprotein (S), nucleoprotein (N), RNA-dependent RNA polymerase (RdRp). The polyproteins ORF1a and ORF1b were examined separately.We found that SARS-CoV-2 tends to diverge over time by accumulating mutations on its genome and, specifically, on the sequences encoding proteins N and S. Interestingly, different patterns of codon usage were observed among these genes. GenesSandNtend to use a narrower set of synonymous codons that are better optimized to the human host. Conversely, genesEandMconsistently use the broader set of synonymous codons, which does not vary in respect to the reference genome. CAI and SiD time evolutions show a tendency to decrease that emerge for most genes. Forsdyke plots are used to study the nature of mutations and they show a rapid evolutionary divergence of each gene, due to the low values of x-intercepets.
Phosphate and phosphite differentially impact the proteome and phosphoproteome of Arabidopsis suspension cell cultures
Authors: Mehta Devang , Ghahremani Mina , Pérez-Fernández Maria , Tan Maryalle , Schläpfer Pascal , Plaxton William C. , Uhrig R. Glen 
Published: May 2020

SUMMARYPhosphorus absorbed in the form of phosphate (H2PO4−) is an essential but limiting macronutrient for plant growth and agricultural productivity. A comprehensive understanding of how plants respond to phosphate starvation is essential to develop more phosphate-efficient crops. Here we employed label-free proteomics and phosphoproteomics to quantify protein-level responses to 48 h of phosphate versus phosphite (H2PO3−) resupply to phosphate-deprivedArabidopsis thalianasuspension cells. Phosphite is similarly sensed, taken up, and transported by plant cells as phosphate, but cannot be metabolized or used as a nutrient. Phosphite is thus a useful tool to delineate between non-specific processes related to phosphate sensing and transport, and specific responses to phosphorus nutrition. We found that responses to phosphate versus phosphite resupply occurred mainly at the level of protein phosphorylation, complemented by limited changes in protein abundance, primarily in protein translation, phosphate transport and scavenging, and central metabolism proteins. Altered phosphorylation of proteins involved in core processes such as translation, RNA splicing, and kinase signalling were especially important. We also found differential phosphorylation in response to phosphate and phosphite in 69 proteins, including splicing factors, translation factors, the PHT1;4 phosphate transporter and the HAT1 histone acetyltransferase—potential phospho-switches signalling changes in phosphorus nutrition. Our study illuminates several new aspects of the phosphate-starvation response and identifies important targets for further investigation and potential crop improvement.
Development Optimization and Validation of RT-LAMP based COVID-19 Facility in Pakistan
Authors: Haq Farhan , Sharif Salmaan , Khurshid Adnan , Shabbir Imran , Salman Muhammad , Badar Nazish , Ikram Aamir , Ahad Abdul , Malik Muhammad Faraz Arshad 
Published: May 2020

AbstractThe pandemic SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2) has created a widespread panic across the globe especially in the developing countries like Pakistan. The lack of resources and technical staff are causing havoc challenges in the detection and prevention of this global outbreak. Therefore, a less expensive and massive screening of suspected individuals for COVID-19 is required. In this study, a user-friendly technique of reverse transcription-loop mediated isothermal amplification (RT-LAMP) was designed and validated to suggest a potential RT-qPCR alternate for rapid testing of COVID-19 suspected individuals. A total of 12 COVID-19 negative and 72 COVID-19 suspected individuals were analyzed. Both RT-qPCR and RT-LAMP assays were performed for all the individuals using open reading frame (ORF 1ab), nucleoprotein (N) and Spike (S) genes. All 12 specimens which were negative using RT-qPCR were also found negative using RT-LAMP assay. Overall 62 out of 72 positive samples (detected using RT-qPCR) were found COVID-19 positive using RT-LAMP assay. Interestingly all samples (45) having Ct values less than 30 showed 100% sensitivity. However, samples with weaker Ct values (i.e., => 35) showed 54% concordance, suggesting potential false negatives or false positives in RT-LAMP or RT-qPCR results, respectively.Overall comparative assessment showed that RT-LAMP assay showed strong sensitivity and specificity and can be used as an alternative strategy for rapid COVID-19 testing. Hence, based on fast processing time, minimal risk of specimens transfer and utilizing available resources, LAMP based detection of COVID-19 is strongly advocated especially for developing countries.
DiNeR: aDifferential Graphical Model for analysis of co-regulationNetworkRewiring
Authors: Zhang Jing , Liu Jason , Lee Donghoon , Lou Shaoke , Chen Zhanlin , Gürsoy Gamze , Gerstein Mark 
Published: May 2020

AbstractBackgroundDuring transcription, numerous transcription factors (TFs) bind to targets in a highly coordinated manner to control the gene expression. Alterations in groups of TF-binding profiles (i.e. “co-binding changes”) can affect the co-regulating associations between TFs (i.e. “rewiring the co-regulator network”). This, in turn, can potentially drive downstream expression changes, phenotypic variation, and even disease. However, quantification of co-regulatory network rewiring has not been comprehensively studied.MethodsTo address this, we propose DiNeR, a computational method to directly construct a differential TF co-regulation network from paired disease-to-normal ChIP-seq data. Specifically, DiNeR uses a graphical model to capture the gained and lost edges in the co-regulation network. Then, it adopts a stability-based, sparsity-tuning criterion -- by sub-sampling the complete binding profiles to remove spurious edges -- to report only significant co-regulation alterations. Finally, DiNeR highlights hubs in the resultant differential network as key TFs associated with disease.ResultsWe assembled genome-wide binding profiles of 104 TFs in the K562 and GM12878 cell lines, which loosely model the transition between normal and cancerous states in chronic myeloid leukemia (CML). In total, we identified 351 significantly altered TF co-regulation pairs. In particular, we found that the co-binding of the tumor suppressor BRCA1 and RNA polymerase II, a well-known transcriptional pair in healthy cells, was disrupted in tumors. Thus, DiNeR successfully extracted hub regulators and discovered well-known risk genes.ConclusionsOur method DiNeR makes it possible to quantify changes in co-regulatory networks and identify alterations to TF co-binding patterns, highlighting key disease regulators. Our method DiNeR makes it possible to quantify changes in co-regulatory networks and identify alterations to TF co-binding patterns, highlighting key disease regulators.