bluuebunny/crossref_metadata_2025_split huggingface dataset:
The rocaglate CR-31-B (-) inhibits SARS-CoV-2 replication at non-cytotoxic, low nanomolar concentrationsin vitroandex vivo
Authors: Müller Christin , Obermann Wiebke , Karl Nadja , Wendel Hans-Guido , Taroncher-Oldenburg Gaspar , Pleschka Stephan , Hartmann Roland K. , Grünweller Arnold , Ziebuhr John 
Published: November 2020

AbstractSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a betacoronavirus in the subgenusSarbecoviruscauses a respiratory disease with varying symptoms referred to as coronavirus disease 2019 (COVID-19) and is responsible for a pandemic that started in early 2020. With no vaccines or effective antiviral treatments available, and infection and fatality numbers continuing to increase globally, the quest for novel therapeutic solutions remains an urgent priority. Rocaglates, a class of plant-derived cyclopenta[b]benzofurans, exhibit broad-spectrum antiviral activity against positive- and negative-sense RNA viruses. This compound class inhibits eukaryotic initiation factor 4A (eIF4A)-dependent mRNA translation initiation, resulting in strongly reduced viral RNA translation. The synthetic rocaglate CR-31-B (-) has previously been shown to inhibit the replication of human coronaviruses, such as HCoV-229E and MERS-CoV, as well as Zika-, Lassa-, Crimean Congo hemorrhagic fever virus in primary cells. Here, we assessed the antiviral activity of CR-31-B (-) against SARS-CoV-2 using bothin vitroandex vivocell culture models. In African green monkey Vero E6 cells, CR-31-B (-) inhibited SARS-CoV-2 replication with an EC50of ~1.8 nM. In line with this, viral protein accumulation and replication/transcription complex formation were found to be strongly reduced by this compound. In anex vivoinfection system using human airway epithelial cells, CR-31-B (-) was found to cause a massive reduction of SARS-CoV-2 titers by about 4 logs to nearly non-detectable levels. The data reveal a potent anti-SARS-CoV-2 activity by CR-31-B (-), corroborating previous results obtained for other coronaviruses and supporting the idea that rocaglates may be used in first-line antiviral intervention strategies against novel and emerging RNA virus outbreaks.
Ipomoeassin-F inhibits thein vitrobiogenesis of the SARS-CoV-2 spike protein and its host cell membrane receptor
Authors: O’Keefe Sarah , Roboti Peristera , Duah Kwabena B. , Zong Guanghui , Schneider Hayden , Shi Wei Q. , High Stephen 
Published: November 2020

AbstractIn order to produce proteins essential for their propagation, many pathogenic human viruses, including SARS-CoV-2 the causative agent of COVID-19 respiratory disease, commandeer host biosynthetic machineries and mechanisms. Three major structural proteins, the spike, envelope and membrane proteins, are amongst several SARS-CoV-2 components synthesised at the endoplasmic reticulum (ER) of infected human cells prior to the assembly of new viral particles. Hence, the inhibition of membrane protein synthesis at the ER is an attractive strategy for reducing the pathogenicity of SARS-CoV-2 and other obligate viral pathogens. Using anin vitrosystem, we demonstrate that the small molecule inhibitor ipomoeassin F (Ipom-F) potently blocks the Sec61-mediated ER membrane translocation/insertion of three therapeutic protein targets for SARS-CoV-2 infection; the viral spike and ORF8 proteins together with angiotensin-converting enzyme 2, the host cell plasma membrane receptor. Our findings highlight the potential for using ER protein translocation inhibitors such as Ipom-F as host-targeting, broad-spectrum, antiviral agents.
High-throughput phenotyping methods for quantifying hair fiber morphology
Authors: Lasisi Tina , Zaidi Arslan A. , Webster Timothy Harding , Stephens Nicholas Bradley , Routch Kendall , Jablonski Nina Grace , Shriver Mark David 
Published: November 2020

AbstractQuantifying the continuous variation in human scalp hair morphology is of interest to anthropologists, geneticists, dermatologists and forensic scientists, but existing methods for studying hair form are time-consuming and not widely used. Here, we present a high-throughput sample preparation protocol for the imaging of both longitudinal (curvature) and cross-sectional scalp hair morphology. Additionally, we describe and validate a new Python package designed to process longitudinal and cross-sectional hair images, segment them, and provide measurements of interest. Lastly, we apply our methods to an admixed African-European sample (n=140), demonstrating the benefit of quantifying hair morphology over qualitative classification or racial categories, and providing evidence against the long-held belief that cross-sectional morphology predicts curvature.
High-throughput characterization of photocrosslinker-bearing ion channel variants to map residues critical for function and pharmacology
Authors: Braun Nina , Friis Søren , Ihling Christian , Sinz Andrea , Andersen Jacob , Pless Stephan A. 
Published: November 2020

AbstractIncorporation of non-canonical amino acids (ncAAs) can endow proteins with novel functionalities, such as crosslinking or fluorescence. In ion channels, the function of these variants can be studied with great precision using standard electrophysiology, but this approach is typically labor intensive and low throughput. Here, we establish a high-throughput protocol to conduct functional and pharmacological investigations of ncAA-containing hASIC1a (human acid-sensing ion channel 1a) variants in transiently transfected mammalian cells. We introduce three different photocrosslinking ncAAs into 103 positions and assess the function of the resulting 309 variants with automated patch-clamp (APC). We demonstrate that the approach is efficient and versatile, as it is amenable to assessing even complex pharmacological modulation by peptides. The data show that the acidic pocket is a major determinant for current decay and live-cell crosslinking provides insight into the hASIC1a-psalmotoxin-1 interaction. Further, we provide evidence that the protocol can be applied to other ion channels, such as P2X2 and GluA2 receptors. We therefore anticipate the approach to enable future APC-based studies of ncAA-containing ion channels in mammalian cells.
Fragment Binding to the Nsp3 Macrodomain of SARS-CoV-2 Identified Through Crystallographic Screening and Computational Docking
Authors: Schuller Marion , Correy Galen J. , Gahbauer Stefan , Fearon Daren , Wu Taiasean , Díaz Roberto Efraín , Young Iris D. , Martins Luan Carvalho , Smith Dominique H. , Schulze-Gahmen Ursula , Owens Tristan W. , Deshpande Ishan , Merz Gregory E. , Thwin Aye C. , Biel Justin T. , Peters Jessica K. , Moritz Michelle , Herrera Nadia , Kratochvil Huong T. ,   QCRG Structural Biology Consortium, Aimon Anthony , Bennett James M. , Neto Jose Brandao , Cohen Aina E. , Dias Alexandre , Douangamath Alice , Dunnett Louise , Fedorov Oleg , Ferla Matteo P. , Fuchs Martin , Gorrie-Stone Tyler J. , Holton James M. , Johnson Michael G. , Krojer Tobias , Meigs George , Powell Ailsa J. , Rack Johannes Gregor Matthias , Rangel Victor L , Russi Silvia , Skyner Rachael E. , Smith Clyde A. , Soares Alexei S. , Wierman Jennifer L. , Zhu Kang , Jura Natalia , Ashworth Alan , Irwin John , Thompson Michael C. , Gestwicki Jason E. , von Delft Frank , Shoichet Brian K. , Fraser James S. , Ahel Ivan 
Published: November 2020

ABSTRACTThe SARS-CoV-2 macrodomain (Mac1) within the non-structural protein 3 (Nsp3) counteracts host-mediated antiviral ADP-ribosylation signalling. This enzyme is a promising antiviral target because catalytic mutations render viruses non-pathogenic. Here, we report a massive crystallographic screening and computational docking effort, identifying new chemical matter primarily targeting the active site of the macrodomain. Crystallographic screening of diverse fragment libraries resulted in 214 unique macrodomain-binding fragments, out of 2,683 screened. An additional 60 molecules were selected from docking over 20 million fragments, of which 20 were crystallographically confirmed. X-ray data collection to ultra-high resolution and at physiological temperature enabled assessment of the conformational heterogeneity around the active site. Several crystallographic and docking fragment hits were validated for solution binding using three biophysical techniques (DSF, HTRF, ITC). Overall, the 234 fragment structures presented explore a wide range of chemotypes and provide starting points for development of potent SARS-CoV-2 macrodomain inhibitors.
Adsorption of Azo Dyes by a Novel Bio-Nanocomposite Based on Whey Protein Nanofibrils and Nano-clay: Equilibrium Isotherm and Kinetic Modeling
Authors: Aqdam ShabBoo Rahimi , Otzen Daniel E. , Mahmoodi Niyaz Mohammad , Morshedi Dina 
Published: November 2020

AbstractExcessive discharge of hazardous azo dyes into the aquatic ecosystem is a global environmental concern. Here, we develop a green approach to remediate dye pollutions in water by fabricating an easy-separable bio-nanocomposite, based on whey protein concentrate, its nanofibrils, and montmorillonite nano-clay. To characterize the nanocomposite, we used SEM, FT-IR, XRD, and BET techniques. Nanofibrils lead to a uniform dispersion of montmorillonite in the whey protein matrix and also reinforce the nanocomposite. The adsorption efficacy was monitored in a batch system, using cationic dyes (Chrysoidine-G, Bismarck brown-R), reactive dyes (reactive black-5, reactive orange-16), acid dyes (acid red-88, acid red-114), and direct dyes (direct violet-51, Congo red). This nanocomposite adsorbed different dye classes, cationic dyes quicker (> 82%, after 4 h), and reactive dyes slower. Then, the effect of initial dye concentration, pH, contact time, adsorbent dose, and temperature on Chrysoidine-G adsorption was explored. The adsorbent showed a high removal (>93%) for a wide concentration range of Chrysoidine-G, also acidic pH and higher temperature are more favorable for the process. Equilibrium adsorption parameters were reasonably fitted with a linear (Nernst) isotherm model. The results indicated the existence of an unlimited number of absorption sites,i.e.no saturation was achieved under our experimental conditions (qmax(Exp)= 731 mg/g). Kinetic data were fitted with pseudo-second-order and intra-particle diffusion models. We conclude that this nanocomposite is a green adsorbent with potential use for wastewater treatment and related purposes.HighlightsWe produced an easy-separable bio-nanocomposite using whey nanofibrils and MMT, with high adsorption capacityNanofibrils help disperse MMT particles uniformly in the WP matrixThe adsorbent’s performance was compared to the adsorbents in absence of MMT and nanofibrilsThis composite adsorbs cationic, anionic, direct and reactive azo dyes with different kineticsAdsorption isotherms and kinetics are studied in detail
A monoclonal antibody against staphylococcal enterotoxin B superantigen inhibits SARS-CoV-2 entry in vitro
Authors: Cheng Mary Hongying , Porritt Rebecca A. , Rivas Magali Noval , Krieger James M , Ozdemir Asli Beyza , Garcia Gustavo , Arumugaswami Vaithilingaraja , Fries Bettina C. , Arditi Moshe , Bahar Ivet 
Published: November 2020

AbstractWe recently discovered a superantigen-like motif, similar to Staphylococcal enterotoxin B (SEB), near the S1/S2 cleavage site of SARS-CoV-2 Spike protein, which might explain the multisystem-inflammatory syndrome (MIS-C) observed in children and cytokine storm in severe COVID-19 patients. We show here that an anti-SEB monoclonal antibody (mAb), 6D3, can bind this viral motif, and in particular its PRRA insert, to inhibit infection by blocking the access of host cell proteases, TMPRSS2 or furin, to the cleavage site. The high affinity of 6D3 for the furin-cleavage site originates from a poly-acidic segment at its heavy chain CDR2, a feature shared with SARS-CoV-2-neutralizing mAb 4A8. The affinity of 6D3 and 4A8 for this site points to their potential utility as therapeutics for treating COVID-19, MIS-C, or common cold caused by human coronaviruses (HCoVs) that possess a furin-like cleavage site.
Protease OMA1 Modulates Mitochondrial Bioenergetics and Ultrastructure through Dynamic Association with MICOS Complex
Authors: Viana Martonio Ponte , Levytskyy Roman M. , Anand Ruchika , Reichert Andreas S. , Khalimonchuk Oleh 
Published: November 2020

ABSTRACTRemodeling of mitochondrial ultrastructure is a complex dynamic process that is critical for a variety of mitochondrial functions and apoptosis. Although the key regulators of this process - mitochondrial contact site and cristae junction organizing system (MICOS) and GTPase Optic Atrophy 1 (OPA1) have been characterized, the mechanisms behind this regulation remain incompletely defined. Here, we found that in addition to its role in mitochondrial division, metallopeptidase OMA1 is required for maintenance of contacts between the inner and outer membranes through a dynamic association with MICOS. This association is independent of OPA1, appears to be mediated via the MICOS subunit MIC60, and is important for stability of MICOS machinery and the inner-outer mitochondrial membrane contacts. We find that OMA1-MICOS relay is required for stability of respiratory supercomplexes, optimal bioenergetic output in response to cellular insults, and apoptosis. Loss of OMA1 affects these activities; remarkably it can be partially compensated for by an artificial MICOS-emulating tether protein that bridges the inner and outer mitochondrial membranes. Our data show that OMA1-mediated support of mitochondrial ultrastructure is required for maintenance of mitochondrial architecture and bioenergetics under both basal and homeostasis-challenging conditions, and suggest a previously unrecognized role for this protease in mitochondrial physiology.
Snowball Earths, population bottlenecks, andProchlorococcusevolution
Authors: Zhang Hao , Sun Ying , Zeng Qinglu , Crowe Sean A. , Luo Haiwei 
Published: November 2020

AbstractProchlorococcusare the most abundant photosynthetic organisms in the modern ocean. A massive DNA loss event occurred in their early evolutionary history, leading to highly reduced genomes in nearly all lineages, as well as enhanced efficiency in both nutrient uptake and light absorption. The environmental landscape that shaped this ancient genome reduction, however, remained unknown. Through careful molecular clock analyses, we established that thisProchlorococcusgenome reduction occurred during the Neoproterozoic Snowball Earth climate catastrophe. The lethally low temperature and exceedingly dim light during the Snowball Earth event would have inhibitedProchlorococcusgrowth and proliferation and caused severe population bottlenecks. These bottlenecks are recorded as an excess of deleterious mutations that accumulated across genomic regions in the descendant lineages.Prochlorococcusadaptation to extreme environmental conditions during Snowball Earth intervals can be inferred by tracing the evolutionary paths of genes that encode key metabolic potential. This metabolic potential includes modified lipopolysaccharide structure, strengthened peptidoglycan biosynthesis, the replacement of a sophisticated circadian clock with an hourglass-like mechanism that resets daily for dim light adaption, and the adoption of ammonia diffusion as an efficient membrane transporter-independent mode of nitrogen acquisition. In this way, the Neoproterozoic Snowball Earth event altered the physiological characters ofProchlorococcus, shaping their ecologically vital role as the most abundant primary producers in the modern oceans.
Activation of ARTD2/PARP2 by DNA damage induces conformational changes relieving enzyme autoinhibition
Authors: Obaji Ezeogo , Maksimainen Mirko M. , Galera-Prat Albert , Lehtiö Lari 
Published: November 2020

AbstractHuman ARTD2/PARP2 is an ADP-ribosyltransferase which, when activated by 5’- phosphorylated DNA ends, catalyzes poly-ADP-ribosylation of itself, other proteins and DNA. A crystal structure of ARTD2 in complex with an activating 5’-phosphorylated DNA shows that the WGR domain bridges the dsDNA gap and joins the DNA ends. This DNA binding results in major conformational changes, reorganization of helical fragments, in the ARTD2 regulatory domain. Comparison of ARTD1-3 crystal structures reveal how binding to a DNA damage site leads to formation of a catalytically competent conformation capable of binding substrate NAD+and histone PARylation factor 1 changing the ARTD2 residue specificity from glutamate to serine when initiating DNA repair processes. The structure also reveals how the conformational changes in the autoinhibitory regulatory domain would promote the flexibility needed by the enzyme to reach the target macromolecule for ADP-ribosylation.
A comprehensive analysis of vomeronasal organ transcriptome reveals variable gene expression depending on age and function in rabbits
Authors: Villamayor PR , Robledo D , Fernández C , Gullón J , Quintela L , Sánchez-Quinteiro P , Martínez P 
Published: November 2020

ABSTRACTThe vomeronasal organ (VNO) is a chemosensory organ specialized in the detection of pheromones and consequently the regulation of behavioural responses mostly related to reproduction. VNO shows a broad variation on its organization, functionality and gene expression in vertebrates, and although the species analyzed to date have shown very specific features, its expression patterns have only been well-characterized in mice. Despite rabbits represent a model of chemocommunication, unfortunately no genomic studies have been performed on VNO of this species to date. The capacity of VNO to detect a great variety of different stimuli suggests a large number of genes with complex organization to support this function. Here we provide the first comprehensive gene expression analysis of the rabbit VNO through RNA-seq across different sexual maturation stages. We characterized the VNO transcriptome, updating the number of the two main vomeronasal receptor (VR) families, 129 V1R and 70 V2R. Among others, the expression of transient receptor potential channel 2 (TRPC2), a crucial cation channel generating electrical responses to sensory stimulation in vomeronasal neurons, along with the specific expression of some fomyl-peptide receptors and H2-Mv genes, both known to have specific roles in the VNO, revealed a the particular gene expression repertoire of this organ, but also its singularity in rabbits. Moreover, juvenile and adult VNO transcriptome showed consistent differences, which may indicate that these receptors are tuned to fulfill specific functions depending on maturation age. We also identified VNO-specific genes, including most VR and TRPC2, thus confirming their functional association with the VNO. Overall, these results represent the genomic baseline for future investigations which seek to understand the genetic basis of behavioural responses canalized through the VNO.HIGHLIGHTSFirst description of the rabbit vomeronasal organ (VNO) transcriptomeVNO contains a unique gene repertoire depending on the speciesHigh fluctuation of the VNO gene expression reveals changes dependent on age and specific functionsMost vomeronasal-receptors (VR) and transient receptor potential channel 2 (TRPC2) genes are VNO-specificReproduction-related genes shows a wide expression pattern
Evidence for co-evolution of masking and circadian phase inDrosophila melanogaster
Authors: Ghosh Arijit , Sharma Pragya , Dansana Shephali , Sheeba Vasu 
Published: November 2020

AbstractHeritable variation in the timing or circadian phases of rhythmic events with respect to daily time cues gives rise to chronotypes. Despite its importance, the mechanisms (clock or non-clock) regulating chronotypes remain elusive. Using artificial laboratory selection for divergent phasing of emergence of adults from pupae, our group has derived populations ofDrosophila melanogasterwhich areearlyandlatechronotypes for eclosion rhythm. Several circadian rhythm characteristics of these populations have since been described. We hypothesized that our selection protocol has inadvertently resulted in selection for masking, a non-clock phenomenon, in theearlychronotype due to the placement of our selection window (which includes the lights-ON transition). Based on theoretical predictions and previous studies on our populations, we designed experiments to discriminate between enhanced masking to light versus circadian clock mediated changes in determining enhanced emergence in the morning window in ourearlychronotypes. Using a series of phase-shift protocols, LD-DD transition, andT-cycle experiments, we find that ourearlychronotypes have evolved positive masking, and their apparent entrained phases are largely contributed by masking. Through skeletonT-cycle experiments, we find that in addition to the evolution of greater masking, ourearlychronotypes have also evolved advanced phase of entrainment. Furthermore, our study systematically outlines experimental approaches to examine relative contributions of clock versus non-clock control of an entrained behavior. Although it has previously been suggested that masking may confer an adaptive advantage to organisms, here we provide experimental evidence for the evolution of masking as a mean of phasing of an entrained rhythm that can complement clock control of an entrained behavior.
Expression of type I interferon-associated genes at point of antiretroviral therapy interruption predicts time to HIV virological rebound
Authors: Zacharapoulou Panagiota , Marchi Emanuele , Ogbe Ane , Robinson Nicola , Brown Helen , Jones Mathew , Parolini Lucia , Pace Matthew , Grayson Nicholas , Kaleebu Pontiano , Rees Helen , Fidler Sarah , Goulder Philip , Klenerman Paul , Frater John 
Published: November 2020

AbstractAlthough certain individuals with HIV infection can stop antiretroviral therapy (ART) without evidence of viral load rebound, the mechanisms under-pinning ‘post-treatment control’ remain unclear. Twelve individuals who had received 12 months of ART from primary HIV infection and then undertook a TI were sampled at the time of stopping therapy. Using RNA-Seq we explored gene expression in CD4 T cells to look for evidence of a mechanism that might underpin virological rebound and lead to discovery of an associated biomarker. Using independent analysis tools, genes associated with the type I interferon response were strongly associated with a delayed time to viral rebound following TI. These are the first data we are aware of that link transcriptomic signatures associated with innate immunity with control following TI. While these results need to be confirmed in larger trials, they could help define a strategy for new therapies and identify new biomarkers for remission.