bluuebunny/crossref_metadata_2025_split huggingface dataset:
Brilacidin, a COVID-19 Drug Candidate, Exhibits PotentIn VitroAntiviral Activity Against SARS-CoV-2
Authors: Bakovic Allison , Risner Kenneth , Bhalla Nishank , Alem Farhang , Chang Theresa L. , Weston Warren , Harness Jane A. , Narayanan Aarthi 
Published: October 2020

AbstractSummarySevere Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the newly emergent causative agent of coronavirus disease-19 (COVID-19), has resulted in more than one million deaths worldwide since it was first detected in 2019. There is a critical global need for therapeutic intervention strategies that can be deployed to safely treat COVID-19 disease and reduce associated morbidity and mortality. Increasing evidence shows that both natural and synthetic antimicrobial peptides (AMPs), also referred to as Host Defense Proteins/Peptides (HDPs), can inhibit SARS-CoV-2, paving the way for the potential clinical use of these molecules as therapeutic options. In this manuscript, we describe the potent antiviral activity exerted by brilacidin—ade novodesigned synthetic small molecule that captures the biological properties of HDPs—on SARS-CoV-2 in a human lung cell line (Calu-3) and a monkey cell line (Vero). These data suggest that SARS-CoV-2 inhibition in these cell culture models is primarily a result of the impact of brilacidin on viral entry and its disruption of viral integrity. Brilacidin has demonstrated synergistic antiviral activity when combined with remdesivir. Collectively, our data demonstrate that brilacidin exerts potent inhibition of SARS-CoV-2 and thus supports brilacidin as a promising COVID-19 drug candidate.HighlightsBrilacidin potently inhibits SARS-CoV-2 in an ACE2 positive human lung cell line.Brilacidin achieved a high Selectivity Index of 426 (CC50=241μM/IC50=0.565μM).Brilacidin’s main mechanism appears to disrupt viral integrity and impact viral entry.Brilacidin and remdesivir exhibit excellent synergistic activity against SARS-CoV-2.Significance StatementSARS-CoV-2, the emergent novel coronavirus, has led to the current global COVID-19 pandemic, characterized by extreme contagiousness and high mortality rates. There is an urgent need for effective therapeutic strategies to safely and effectively treat SARS-CoV-2 infection. We demonstrate that brilacidin, a synthetic small molecule with peptide-like properties, is capable of exerting potentin vitroantiviral activity against SARS-CoV-2, both as a standalone treatment and in combination with remdesivir, which is currently the only FDA-approved drug for the treatment of COVID-19.
A cell-free antibody engineering platform rapidly generates SARS-CoV-2 neutralizing antibodies
Authors: Chen Xun , Gentili Matteo , Hacohen Nir , Regev Aviv 
Published: October 2020

AbstractAntibody engineering technologies face increasing demands for speed, reliability and scale. We developed CeVICA, a cell-free antibody engineering platform that integrates a novel generation method and design for camelid heavy-chain antibody VHH domain-based synthetic libraries, optimizedin vitroselection based on ribosome display and a computational pipeline for binder prediction based on CDR-directed clustering. We applied CeVICA to engineer antibodies against the Receptor Binding Domain (RBD) of the SARS-CoV-2 spike proteins and identified >800 predicted binder families. Among 14 experimentally-tested binders, 6 showed inhibition of pseudotyped virus infection. Antibody affinity maturation further increased binding affinity and potency of inhibition. Additionally, the unique capability of CeVICA for efficient and comprehensive binder prediction allowed retrospective validation of the fitness of our synthetic VHH library design and revealed direction for future refinement. CeVICA offers an integrated solution to rapid generation of divergent synthetic antibodies with tunable affinitiesin vitroand may serve as the basis for automated and highly parallel antibody generation.
The role of anxiety in the perception of pain: exploring the cumulative & temporal mechanisms of hypercapnic analgesia
Authors: Kharko Anna Yurievna , Hansford Kirralise J , Klein Frederico B , Furlong Paul L , Hall Stephen D , Roser Matthew E 
Published: October 2020

ABSTRACTBackgroundAnxiety, evoked by continuous inspiration of a 5 – 8% CO2mixture, has been found to have an analgesic eLect on self-reported pain. The precise mechanism whereby this effect obtains remains unknown.MethodsThe present study tested whether temporal summation, the psychological counterpart of wind-up, is involved in hypercapnic analgesia. 21 healthy participants received painful transcutaneous electrical stimuli of varied intensity, during continuous inhalation of 7.5% CO2mixture and medical air, presented in a single-blinded counterbalanced order. Continuous pain ratings were acquired to measure the temporal development of the pain response. Several points and events of interest that characterise the pain response profile were extracted from the continuous data.ResultsMixed-eLects modelling demonstrated a reduction of all pain measures during inspiration of the anxiogenic mixture, but not air. This was accompanied by an increase in the psychological and physiological measures of anxiety. Analyses of the characteristic measures of temporal summation suggested that the hypercapnic mixture has an analgesic property evident from the start of the pain response. The same was true for the remainder of the response, the adaptation period, where pain ratings were also inhibited. The reduced pain ratings persisted during the remainder of the response. Anxiety was found to be a mediating factor for summative pain ratings but not the temporally sensitive TS measures, suggesting an overall, cumulative effect.ConclusionsThe findings provide an explanation for the previously observed low self-reported pain during the inhalation of an anxiogenic hypercapnic mixture.
Sea anemone genomes reveal ancestral metazoan chromosomal macrosynteny
Authors: Zimmermann Bob , Montenegro Juan D. , Robb Sofia M.C. , Fropf Whitney J. , Weilguny Lukas , He Shuonan , Chen Shiyuan , Lovegrove-Walsh Jessica , Hill Eric M. , Chen Cheng-Yi , Ragkousi Katerina , Praher Daniela , Fredman David , Schultz Darrin , Moran Yehu , Simakov Oleg , Genikhovich Grigory , Gibson Matthew C. , Technau Ulrich 
Published: October 2020

AbstractDraft genome sequences of non-bilaterian species have provided important insights into the evolution of the metazoan gene repertoire. However, there is little information about the evolution of gene clusters, genome architectures and karyotypes during animal evolution. In this regard, slowly evolving anthozoan Cnidaria, the sister group of Bilateria, are particularly informative. Here we report chromosome-level genome assemblies of two related cnidarians, the sea anemonesNematostella vectensisandScolanthus callimorphus. We find a robust set of 15 chromosomes with a clear one-to-one correspondence between the two species. Both sea anemone genomes show remarkable chromosomal conservation with other cnidarians, several bilaterians and the spongeEphydatia muelleri, allowing us to reconstruct ancestral cnidarian and metazoan chromosomal blocks, consisting of at least 19 and 16 ancestral linkage groups, respectively. We show that, in contrast to Bilateria, the Hox and NK clusters of investigated cnidarians are largely disintegrated, despite the presence of staggeredhox/gbxexpression inNematostella. This loss of microsynteny conservation may be facilitated by shorter distances between cis-regulatory sequences and their cognate transcriptional start sites. In line with that, we find no clear evidence for topologically associated domains, suggesting fundamental differences in long-range gene regulation compared to vertebrates. These data suggest that large sets of ancestral metazoan genes have been retained in ancestral linkage groups of some extant lineages, yet, higher order gene regulation with associated 3D architecture may have evolved only after the cnidarian-bilaterian split.
PRAK-03202: A triple antigen VLP vaccine candidate against SARS CoV-2
Authors: Mazumder Saumyabrata , Rastogi Ruchir , Undale Avinash , Arora Kajal , Arora Nupur Mehrotra , Pratim Biswa , Kumar Dilip , Joseph Abyson , Mali Bhupesh , Arya Vidya Bhushan , Kalyanaraman Sriganesh , Mukherjee Abhishek , Gupta Aditi , Potdar Swaroop , Roy Sourav Singha , Parashar Deepak , Paliwal Jeny , Singh Sudhir Kumar , Naqvi Aelia , Srivastava Apoorva , Singh Manglesh Kumar , Kumar Devanand , Bansal Sarthi , Rautray Satabdi , Singh Indrajeet , Fengade Pankaj , Kumar Bibekanand , Saini Manish , Jain Kshipra , Gupta Reeshu , Kundu Prabuddha Kumar 
Published: October 2020

AbstractThe rapid development of safe and effective vaccines against SARS CoV-2 is the need of the hour for the coronavirus outbreak. Here, we have developed PRAK-03202, the world’s first triple antigen VLP vaccine candidate in a highly characterizedS. cerevisiae-basedD-CryptTMplatform, which induced SARS CoV-2 specific neutralizing antibodies in BALB/c mice. Immunizations using three different doses of PRAK-03202 induces antigen specific (Spike, envelope and membrane proteins) humoral response and neutralizing potential. PBMCs from convalescent patients, when exposed to PRAK-03202, showed lymphocyte proliferation and elevated IFN-γ levels suggestive of conservation of epitopes and induction of T helper 1 (Th1)–biased cellular immune responses. These data support the clinical development and testing of PRAK-03202 for use in humans.
Antigenic Sensitivity of Membrane-Proximal Targeting Chimeric Antigen Receptors can be Fine-Tuned through Hinge Truncation
Authors: McComb Scott , Nguyen Tina , Shepherd Alex , Henry Kevin A. , Bloemberg Darin , Marcil Anne , Maclean Susanne , Gilbert Rénald , Gadoury Christine , Pon Rob , Sulea Traian , Zhu Qin , Weeratna Risini D. 
Published: October 2020

AbstractBackgroundChimeric antigen receptor (CAR) technology has revolutionized the treatment of B-cell malignancies and steady progress is being made towards CAR-immunotherapies for solid tumours. Epidermal growth factor family receptors EGFR or HER2 are commonly overexpressed in cancer and represent proven targets for CAR-T therapy; given their expression in healthy tissues it is imperative that any targeting strategy consider the potential for on-target off-tumour toxicity.MethodsHerein, we utilize high-throughput CAR screening to identify novel camelid single-domain antibody CARs (sdCARs) with high EGFR-specific CAR-T response. To optimize antigenic sensitivity of this EGFR-sdCAR, we performed progressive N-terminal truncation of the human CD8 hinge domain used as a spacer in many CAR constructs. Hinge truncation resulted in decreased CAR sensitivity to EGFR and improved selectivity for EGFR-overexpressing cells over EGFR-low target cells or healthy donor derived EGFR-positive fibroblasts. To investigate the molecular mechanism of hinge truncation, we test hinge-truncated scFv-based CARs targeting membrane proximal or membrane distal domains of EGFR-family proteins, HER2 and EGFRvIII. Finally, we proceed to test hinge variant EGFR-sdCAR functionality throughin vitroandin vivoassessments in primary T cells derived from multiple donors.ResultsFor CARs targeting membrane-proximal epitopes, hinge truncation by even a single amino acid provided fine control of the antigenic sensitivity, whereas CARs targeting membrane distal domains were not sensitive to even complete hinge domain removal. Hinge-modified EGFR-sdCARs showed consistent and predictable responses in Jurkat-CAR cells and primary human CAR-T cellsin vitroandin vivo.ConclusionsOverall, these results indicate that membrane-proximal epitope targeting CARs can be modified through hinge length tuning for programmable antigenic sensitivity and improved tumour selectivity.Abstract FigureSingle amino acid truncations of CD8-hinge domain provide precise control of CAR antigen sensitivityTruncated hinge CARs show enhanced selectivity for antigen overexpressing tumour cells and decreased activity towards healthy antigen-expressing cellsEpitope location is a critical factor in determining hinge sensitivity for a CARHinge tuning can modulate CAR-T antigenic sensivityin vitroandin vivo
UCSC Cell Browser: Visualize Your Single-Cell Data
Authors: Speir Matthew L , Bhaduri Aparna , Markov Nikolay S , Moreno Pablo , Nowakowski Tomasz J , Papatheodorou Irene , Pollen Alex A , Seninge Lucas , Kent W James , Haeussler Maximilian 
Published: October 2020

AbstractSummaryAs the use of single-cell technologies has grown, so has the need for tools to explore these large, complicated datasets. The UCSC Cell Browser is a tool that allows scientists to visualize gene expression and metadata annotation distribution throughout a single-cell dataset or multiple datasets.Availability and implementationWe provide the UCSC Cell Browser as a free website where users can explore a growing collection of single-cell datasets and a freely available python package for scientists to create stable, self-contained visualizations for their own single-cell datasets. Learn more athttps://cells.ucsc.edu.Contactcells@ucsc.edu
Gene-by-environment interactions in agricultural pest management: population effects on diet-Btinteractions in a caterpillar
Authors: Deans Carrie , Sword Gregory , Behmer Spencer , Burkness Eric , Pusztai-Carey Marianne , Hutchison W.D. 
Published: October 2020

AbstractGiven that plant nutrient content is both spatially and temporally dynamic (Lenhart et al., 2015; Deans et al., 2016, 2018), insect herbivores are exposed to an incredible amount of nutritional variability. This variability can constrain insects to feeding on sub-optimal resources, but it can also provide an opportunity for insects to regulate their intake of specific nutrients to obtain an optimal balance. Nutrient regulation has implications for pest control strategies in agricultural systems, as the nutritional state of pest species may impact their susceptibility to insecticides. Deans et al. (2017) showed that diet macronutrient balance has significant effects on the susceptibility ofHelicoverpa zealarvae to Cry1Ac, an endotoxin expressed in transgenicBtcrops. This was demonstrated using a highly inbred laboratory strain ofH. zea,limiting the applicability of these results to field populations that encompass greater genetic diversity. In this study, we assessed the impact of field-relevant macronutrient variability on the efficacy of twoBtendotoxins, Cry1Ab and Cry1Ac, using three field populations collected from different geographic regions. This was done to further understand the impact of nutritional variability onBtsusceptibility and also to determine the relevance of these effects in the field. While we saw limited differences in Cry susceptibility across populations, dietary effects were highly variable. Across populations there were distinct population-level differences in the interactions between Cry concentration and diet, the type of Cry toxin impacted by diet, and the treatment diet that produced optimal survival and performance. These results show that nutrition can have strong impacts onBtsusceptibility but also that these impacts are strongly affected by genetic background inH. zea. To accurately assessBtsusceptibility in the field, including resistance monitoring, bioassay methods should incorporate the appropriate nutritional parameters and be as localized as possible.
Amino acid transporter B0AT1 influence on ADAM17 interactions with SARS-CoV-2 receptor ACE2 putatively expressed in intestine, kidney, and cardiomyocytes
Authors: Andring Jacob T. , McKenna Robert , Stevens Bruce R. 
Published: October 2020

ABSTRACTSARS-CoV-2 exhibits significant experimental and clinical gastrointestinal, renal, and cardiac muscle tropisms responsible for local tissue-specific and systemic pathophysiology capriciously occurring in about half of COVID-19 patients. The underlying COVID-19 mechanisms engaged by these extra-pulmonary organ systems are largely unknown. We approached this knowledge gap by recognizing that neutral amino acid transporter B0AT1 (alternately called NBB, B, B0in the literature) is a common denominator expressed nearly exclusively by three particular cell types: intestinal epithelia, renal proximal tubule epithelium, and cardiomyocytes. B0AT1 provides uptake of glutamine and tryptophan. The gut is the main depot expressing over 90% of the body’s entire pool of SARS-CoV-2 receptor angiotensin converting enzyme-2 (ACE2) and B0AT1. Recent cryo-EM studies established that ACE2 forms a thermodynamically favored dimer-of-heterodimers complex with B0AT1 assembled in the form of a dimer of two ACE2:B0AT1 heterodimers anchored in plasma membranes. Prior epithelial cell studies demonstrated ACE2 chaperone trafficking of B0AT1. This contrasts with monomeric expression of ACE2 in lung pneumocytes, in which B0AT1 is undetectable. The cell types in question also express a disintegrin and metalloproteinase-17 (ADAM17) known to cleave and shed the ectodomain of monomeric ACE2 from the cell surface, thereby relinquishing protection against unchecked renin-angiotensin-system (RAS) events of COVID-19. The present study employed molecular docking modeling to examine the interplaying assemblage of ACE2, ADAM17 and B0AT1. We report that in the monomer form of ACE2, neck region residues R652-N718 provide unimpeded access to ADAM17 active site pocket, but notably R708 and S709 remained >10-15 Å distant. In contrast, interference of ADAM17 docking to ACE2 in a dimer-of-heterodimers arrangement was directly correlated with the presence of a neighboring B0AT1 subunit complexed to the partnering ACE2 subunit of the 2ACE2:2B0AT1] dimer of heterodimers, representing the expression pattern putatively exclusive to intestinal, renal and cardiomyocyte cell types. The monomer and dimer-of-heterodimers docking models were not influenced by the presence of SARS-CoV-2 receptor binding domain (RBD) complexed to ACE2. The results collectively provide the underpinnings for understanding the role of B0AT1 involvement in COVID-19 and the role of ADAM17 steering ACE2 events in intestinal and renal epithelial cells and cardiomyocytes, with implications useful for consideration in pandemic public hygiene policy and drug development.
Enhancer of Zeste Homolog 2 (Ezh2) is essential for patterning of multiple musculoskeletal tissues but dispensable for tendon differentiation
Authors: Pal Deepanwita , Riester Scott M. , Hasan Bashar , Tufa Sara F. , Dudakovic Amel , Keene Douglas R. , van Wijnen Andre J. , Schweitzer Ronen 
Published: October 2020

AbstractAn efficient musculoskeletal system depends on the precise assembly and coordinated growth and function of muscles, skeleton and tendons. However, the mechanisms that drive integrated musculoskeletal development and coordinated growth and differentiation of each of these tissues are still being uncovered. Epigenetic modifiers have emerged as critical regulators of cell fate differentiation, but so far almost nothing is known about their roles in tendon biology. Previous studies have shown that epigenetic modifications driven by Enhancer of zeste homolog 2 (EZH2), a major histone methyltransferase, have significant roles in vertebrate development including skeletal patterning and bone formation. We now find that targetingEzh2through the limb mesenchyme also has significant effects on tendon and muscle patterning, likely reflecting the essential roles of early mesenchymal cues mediated byEzh2for coordinated patterning and development of all tissues of the musculoskeletal system. Conversely, loss ofEzh2in the tendon cells did not disrupt the tendon cell fate suggesting that tenocyte differentiation and tendon maturation are independent ofEzh2signaling.
Drug synergy scoring using minimal dose response matrices
Authors: Mäkelä Petri , Zhang Si Min , Rudd Sean G 
Published: October 2020

AbstractObjectiveCombinations of pharmacological agents are essential for disease control and prevention, offering many advantages over monotherapies, with one of these being drug synergy. The state-of-the-art method to profile drug synergy in preclinical research is by using dose-response matrices in disease-appropriate models, however this approach is frequently labour intensive and cost-ineffective, particularly when performed in a medium- to high-throughput fashion. Thus, in this study, we set out to optimise a parameter of this methodology, determining the minimal matrix size that can be used to robustly detect and quantify synergy between two drugs.ResultsWe used a drug matrix reduction workflow that allowed the identification of a minimal drug matrix capable of robustly detecting and quantifying drug synergy. These minimal matrices utilise substantially less reagents and data processing power than their typically used larger counterparts. Focusing on the antileukemic efficacy of the chemotherapy combination of cytarabine and inhibitors of ribonucleotide reductase, we could show that detection and quantification of drug synergy by three common synergy models was well-tolerated despite reducing matrix size from 8×8 to 4×4. Overall, the optimisation of drug synergy scoring as presented here could inform future medium- to high-throughput drug synergy screening strategies in pre-clinical research.Abstract Figure
New cinnamid and rosmarinic acid derived compounds biosynthesized inEscherichia coliasLeishmania amazonensisarginase inhibitors
Authors: dos Santos Simone Come Julio Abel Alfredo , Zhuang Yibin , Li TianZhen , Brogi Simone , Gemma Sandra , Liu Tao , da Silva Edson Roberto 
Published: October 2020

AbstractArginase is a metalloenzyme that plays a central role inLeishmaniainfection. Previously, rosmarinic and caffeic acids were described as antileishmanial and as aLeishmania amazonensisarginase inhibitor and now, we describe the inhibition of arginase inL. amazonensisby rosmarinic acid analogs (1-7) and new caffeic acids derived amides (8-10). Caffeic acid esters and amides were produced by means of the engineered synthesis inE. coliand tested againstL. amazonensisarginase. New amides (8-10) were biosynthesized inE. colicultured with 2 mM of different combinations of feeding substrates. The most potent arginase inhibitors showed Ki(s) between 2 - 5.7 μM. Compounds2-4and7inhibited L-ARG through a noncompetitive mechanism, and9showed a competitive inhibition. By applying anin silicoprotocol we determined the binding mode of compound9. The competitive inhibitor of L-ARG targets key residues within the binding site of the enzyme establishing a metal coordination bond with the metal ions as well as a series of hydrophobic and polar contacts supporting its micromolar inhibition of L-ARG. These results highlight that the dihydroxycinnamic-derived compounds can be used as the basis for the development of new drugs using a powerful tool based on the biosynthesis of arginase inhibitors.