bluuebunny/crossref_metadata_2025_split huggingface dataset:
New Soluble Angiopoietin Analog of C4BP-ANG1 Prevents Pathological Vascular Leakage
Authors: Liu Pan , Ryczko Michael , Xie Xinfang , Taiyab Aftab , Sheardown Heather , Quaggin Susan E. , Jin Jing 
Published: April 2020

AbstractVascular leak is a key driver of organ injury in diseases such as Acute Respiratory Distress Syndrome caused by viruses, including COVID-19. Strategies that reduce enhanced permeability and vascular inflammation are promising therapeutic targets. Activation of the Angiopoietin-1 (Angpt1)-Tie2 tyrosine kinase signaling pathway is an important regulator of vascular quiescence. Here we describe the design and construction of a new soluble ANGPT1 mimetic that is a potent activator of endothelial Tie2 in vitro and in vivo. Using a chimeric fusion strategy, we replaced the extracellular matrix (ECM) binding and oligomerization domain of ANGPT1 with a heptameric scaffold derived from the C-terminus of serum complement protein C4-binding protein α (C4BP). We refer to this new fusion protein biologic as C4BP-ANG1, which forms a stable heptamer and induces TIE2 phosphorylation in cultured cells, and in the lung followingi.v.injection of mice. Injection of C4BP-ANG1 ameliorates VEGF- and lipopolysaccharide-induced vascular leakage, in keeping with the known functions of Angpt1-Tie2 in maintaining quiescent vascular stability, and therefore is a promising candidate treatment for inflammatory endothelial dysfunction.
Using a fragment-based approach to identify novel chemical scaffolds targeting the dihydrofolate reductase (DHFR) fromMycobacterium tuberculosis
Authors: Ribeiro João Augusto , Hammer Alexander , Libreros Zúñiga Gerardo Andrés , Chavez-Pacheco Sair Maximo , Tyrakis Petros , de Oliveira Gabriel Stephani , Kirkman Timothy , Bakali Jamal El , Rocco Silvana Aparecida , Sforça Mauricio Luís , Parise-Filho Roberto , Coyne Anthony G. , Blundell Tom L , Abell Chris , Bertacine Dias Marcio Vinicius 
Published: April 2020

AbstractDihydrofolate reductase (DHFR), a key enzyme involved in folate metabolism, is a widely explored target in the treatment of cancer, immune diseases, bacteria and protozoa infections. Although several antifolates have proved successful in the treatment of infectious diseases, none have been developed to combat tuberculosis, despite the essentiality ofM. tuberculosisDHFR (MtDHFR). Herein, we describe an integrated fragment-based drug discovery approach to target MtDHFR that has identified hits with scaffolds not yet explored in any previous drug design campaign for this enzyme. The application of a SAR by catalog strategy of an in house library for one of the identified fragments has led to a series of molecules that bind MtDHFR with low micromolar affinities. Crystal structures of MtDHFR in complex with compounds of this series demonstrated a novel binding mode that differs from other DHFR antifolates, thus opening perspectives for the development of novel and relevant MtDHFR inhibitors.
Integrative Frontal-Parietal Dynamics Supporting Cognitive Control
Authors: Nee Derek Evan 
Published: April 2020

AbstractCoordinating among the demands of the external environment and internal plans requires cognitive control supported by a fronto-parietal control network (FPCN). Evidence suggests that multiple control systems span the FPCN whose operations are poorly understood. Previously (Nee and D’Esposito, 2016; 2017), we detailed frontal dynamics that support control processing, but left open their role in broader cortical function. Here, I show that the FPCN consists of an external/present-oriented to internal/future-oriented cortical gradient extending outwardly from sensory-motor cortices. Areas at the ends of this gradient act in a segregative manner, exciting areas at the same level, but suppressing areas at different levels. By contrast, areas in the middle of the gradient excite areas at all levels, promoting integration of control processing. Individual differences in integrative dynamics predict higher-level cognitive ability and amenability to neuromodulation. These data suggest that an intermediary zone within the FPCN underlies integrative processing that supports cognitive control.Impact StatementThis study shows that intermediary areas within the FPCN are critical for integrating control processing, cognitive ability, and amenability to neuromodulation.
PhyDOSE: Design of Follow-up Single-cell Sequencing Experiments of Tumors
Authors: Weber Leah , Aguse Nuraini , Chia Nicholas , El-Kebir Mohammed 
Published: April 2020

AbstractThe combination of bulk and single-cell DNA sequencing data of the same tumor enables the inference of high-fidelity phylogenies that form the input to many important downstream analyses in cancer genomics. While many studies simultaneously perform bulk and single-cell sequencing, some studies have analyzed initial bulk data to identify which mutations to target in a follow-up single-cell sequencing experiment, thereby decreasing cost. Bulk data provide an additional untapped source of valuable information, composed of candidate phylogenies and associated clonal prevalence. Here, we introduce PhyDOSE, a method that uses this information to strategically optimize the design of follow-up single cell experiments. Underpinning our method is the observation that only a small number of clones uniquely distinguish one candidate tree from all other trees. We incorporate distinguishing features into a probabilistic model that infers the number of cells to sequence so as to confidently reconstruct the phylogeny of the tumor. We validate PhyDOSE using simulations and a retrospective analysis of a leukemia patient, concluding that PhyDOSE’s computed number of cells resolves tree ambiguity even in the presence of typical single-cell sequencing errors. We also conduct a retrospective analysis on an acute myeloid leukemia cohort, demonstrating the potential to achieve similar results with a significant reduction in the number of cells sequenced. In a prospective analysis, we demonstrate that only a small number of cells suffice to disambiguate the solution space of trees in a recent lung cancer cohort. In summary, PhyDOSE proposes cost-efficient single-cell sequencing experiments that yield high-fidelity phylogenies, which will improve downstream analyses aimed at deepening our understanding of cancer biology.Author summaryCancer development in a patient can be explained using a phylogeny — a tree that describes the evolutionary history of a tumor and has therapeutic implications. A tumor phylogeny is constructed from sequencing data, commonly obtained using either bulk or single-cell DNA sequencing technology. The accuracy of tumor phylogeny inference increases when both types of data are used, but single-cell sequencing may become prohibitively costly with increasing number of cells. Here, we propose a method that uses bulk sequencing data to guide the design of a follow-up single-cell sequencing experiment. Our results suggest that PhyDOSE provides a significant decrease in the number of cells to sequence compared to the number of cells sequenced in existing studies. The ability to make informed decisions based on prior data can help reduce the cost of follow-up single cell sequencing experiments of tumors, improving accuracy of tumor phylogeny inference and ultimately getting us closer to understanding and treating cancer.
Directed manipulation of membrane proteins by fluorescent magnetic nanoparticles
Authors: Li Jia Hui , Santos-Otte Paula , Au Braedyn , Rentsch Jakob , Block Stephan , Ewers Helge 
Published: April 2020

AbstractThe plasma membrane is the interface through which cells interact with their environment. Membrane proteins are embedded in the lipid bilayer of the plasma membrane and their function in this context is often linked to their specific location and dynamics within the membrane. However, few methods are available for nanoscale manipulation of membrane protein location at the single molecule level. Here, we report the use of fluorescent magnetic nanoparticles (FMNPs) to track membrane molecules and to manipulate their movement. FMNPs allow single-particle tracking (SPT) at 10 nm spatial and 5 ms temporal resolution, and using a magnetic needle, we pull membrane components laterally through the membrane with femtonewton-range forces. In this way, we successfully dragged lipid-anchored and transmembrane proteins over the surface of living cells. Doing so, we detected submembrane barriers and in combination with super-resolution microscopy could localize these barriers to the actin cytoskeleton. We present here a versatile approach to probe membrane processes in live cells via the magnetic control of membrane protein motion.
The target landscape of N4-hydroxycytidine based on its chemical neighborhood
Authors: Mestres Jordi 
Published: April 2020

AbstractN4-hydroxycytidine (NHC) has been recently reported to have promising antiviral activity against SARS-CoV-2. To join worldwide efforts in identifying potential drug targets against this pandemic, the target landscape of NHC was defined by extracting all known targets of its chemical neighborhood, including drugs, analogues, and metabolites, and by performing target predictions from two independent platforms, following the recent Public Health Assessment via Structural Evaluation (PHASE) protocol. The analysis provides a list of over 30 protein targets that could be useful in future design activities of new COVID-19 antivirals. The relevance for existing drugs within the same chemical space, such as remdesivir, is also discussed.
The adaptive response to long-term nitrogen starvation inEscherichia colirequires the breakdown of allantoin
Authors: Switzer Amy , Burchell Lynn , McQuail Josh , Wigneshweraraj Sivaramesh 
Published: April 2020

ABSTRACTBacteria initially respond to nutrient starvation by eliciting large-scale transcriptional changes. The accompanying changes in gene expression and metabolism allow the bacterial cells to effectively adapt to the nutrient starved state. How the transcriptome subsequently changes as nutrient starvation ensues is not well understood. We used nitrogen (N) starvation as a model nutrient starvation condition to study the transcriptional changes inEscherichia coliexperiencing long-term N starvation. The results reveal that the transcriptome of N starvedE. coliundergoes changes that are required to maximise chances of viability and to effectively recover growth when N starvation conditions become alleviated. We further reveal that, over time, N starvedE. colicells rely on the degradation of allantoin for optimal growth recovery when N becomes replenished. This study provides insights into the temporally coordinated adaptive responses that occur inE. coliexperiencing sustained N starvation.IMPORTANCEBacteria in their natural environments seldom encounter conditions that support continuous growth. Hence, many bacteria spend the majority of their time in states of little or no growth due to starvation of essential nutrients. To cope with prolonged periods of nutrient starvation, bacteria have evolved several strategies, primarily manifesting themselves through changes in how the information in their genes is accessed. How these coping strategies change over time under nutrient starvation is not well understood and this knowledge is not only important to broaden our understanding of bacterial cell function, but also to potentially find ways to manage harmful bacteria. This study provides insights into how nitrogen starvedEscherichia colibacteria rely on different genes during long term nitrogen starvation.
Prioritization of SARS-CoV-2 epitopes using a pan-HLA and global population inference approach
Authors: Campbell Katie M. , Steiner Gabriela , Wells Daniel K. , Ribas Antoni , Kalbasi Anusha 
Published: April 2020

SummarySARS-CoV-2 T cell response assessment and vaccine development may benefit from an approach that considers the global landscape of the human leukocyte antigen (HLA) proteins. We predicted the binding affinity between 9-mer and 15-mer peptides from the SARS-CoV-2 peptidome for 9,360 class I and 8,445 class II HLA alleles, respectively. We identified 368,145 unique combinations of peptide-HLA complexes (pMHCs) with a predicted binding affinity less than 500nM, and observed significant overlap between class I and II predicted pMHCs. Using simulated populations derived from worldwide HLA frequency data, we identified sets of epitopes predicted in at least 90% of the population in 57 countries. We also developed a method to prioritize pMHCs for specific populations. Collectively, this public dataset and accessible user interface (Shiny app:https://rstudio-connect.parkerici.org/content/13/) can be used to explore the SARS-CoV-2 epitope landscape in the context of diverse HLA types across global populations.
DNA Encoded Glycan Libraries as a next-generation tool for the study of glycan-protein interactions
Authors: Kondengaden Shukkoor M. , Zhang Jiabin , Zhang Huajie , Parameswaran Aishwarya , Kondengadan Shameer M. , Pawar Shrikant , Puthengot Akhila , Sunderraman Rajshekhar , Song Jing , Polizzi Samuel J. , Wen Liuqing , Wang Peng George 
Published: April 2020

ABSTRACTInteractions between glycans and glycan-binding proteins (GBPs) mediate diverse cellular functions, and therefore are of diagnostic and therapeutic significance. Current leading strategies for studying glycan-GBP interactions require specialized knowledge and instrumentation. In this study, we report a strategy for studying glycan-GBP interactions that uses PCR, qPCR and next-generation sequencing (NGS) technologies that are more routinely accessible. Our headpiece conjugation-code ligation (HCCL) strategy couples glycans with unique DNA codes that specify glycan sugar moieties and glycosidic linkages when sequenced. We demonstrate the technology by synthesizing a DNA encoded glycan library of 50 biologically relevant glycans (DEGL-50) and probing interactions against 25 target proteins including lectins and antibodies. Data show glycan-GPB interactions in solution that are consistent with lower content, lower throughput ELISA assays. Data further demonstrate how monovalent and multivalent headpieces can be used to increase glycan-GPB interactions and enrich signals while using smaller sample sizes. The flexibility of our modular HCCL strategy has potential for producing large glycan libraries, facilitating high content-high throughput glycan binding studies, and increasing access to lower cost glyco-analyses.Abstract Figure
The effects of transcranial direct current stimulation on corticospinal and cortico-cortical excitability and response variability: conventional versus high-definition montages
Authors: Pellegrini Michael , Zoghi Maryam , Jaberzadeh Shapour 
Published: April 2020

AbstractResponse variability following transcranial direct current stimulation (tDCS) highlights need for exploring different tDCS electrode montages. This study compared corticospinal excitability (CSE), cortico-cortical excitability and intra-individual variability following conventional and HD anodal (a-tDCS) and cathodal (c-tDCS) tDCS. Fifteen healthy young males attended four sessions at least one-week apart: conventional a-tDCS, conventional c-tDCS, HD-a-tDCS, HD-c-tDCS. TDCS was administered (1mA, 10-minutes) over the primary motor cortex (M1), via 6×4cm active and 7×5cm return electrodes (conventional tDCS) and 4×1 ring-electrodes 3.5cm apart in ring formation around M1 (HD-tDCS). For CSE, twenty-five single-pulse transcranial magnetic stimulation (TMS) peak-to-peak motor evoked potentials (MEP) were recorded at baseline, 0-minutes and 30-minutes post-tDCS. For cortico-cortical excitability, twenty-five paired-pulse MEPs with 3-millisecond (ms) inter-pulse interval (IPI) and twenty-five at 10ms assessed short-interval intracortical inhibition (SICI) and intracortical facilitation (ICF) respectively. MEP standardised z-values standard deviations represented intra-individual variability. No significant differences were reported in CSE between conventional and HD a-tDCS, but significant differences between conventional and HD c-tDCS 0-minutes post-tDCS. Intra-individual variability was significantly reduced in conventional tDCS compared to HD-tDCS for a-tDCS (0-minutes) and c-tDCS (30-minutes). No significant changes were reported in SICI and ICF. These novel findings highlight current technical issues with HD-tDCS, suggesting future tDCS studies should utilise conventional tDCS to minimise intra-individual variability, ensuring tDCS after-effects are true changes in CSE and cortico-cortical excitability.
Diversification or collapse of self-incompatibility haplotypes as a rescue process
Authors: Harkness Alexander , Goldberg Emma E. , Brandvain Yaniv 
Published: April 2020

AbstractIn angiosperm self-incompatibility systems, pollen with an allele matching the pollen recipient at the self-incompatibility locus is rejected. Extreme allelic polymorphism is maintained by frequency-dependent selection favoring rare alleles. However, two challenges limit the spread of a new allele (a tightly linked haplotype in this case) under the widespread “collaborative non-self recognition” mechanism. First, there is no obvious selective benefit for pollen compatible with non-existent stylar incompatibilities, which themselves cannot spread if no pollen can fertilize them. However, a pistil-function mutation complementary to a previously neutral pollen mutation may spread if it restores self-incompatibility to a self-compatible intermediate. Second, we show that novel haplotypes can drive elimination of existing ones with fewer siring opportunities. We calculate relative probabilities of increase and collapse in haplotype number given the initial collection of incompatibility haplotypes and the population gene conversion rate. Expansion in haplotype number is possible when population gene conversion rate is large, but large contractions are likely otherwise. A Markov chain model derived from these expansion and collapse probabilities generates a stable haplotype number distribution in the realistic range of 10–40 under plausible parameters. However, smaller populations might lose many haplotypes beyond those lost by chance during bottlenecks.
Lessons and considerations for the creation of universal primers targeting non-conserved, horizontally mobile genes
Authors: Brown Damon C. , Turner Raymond J. 
Published: April 2020

AbstractEffective and accurate primer design is an increasingly important skill as the use of PCR-based diagnostics in clinical and environmental settings is on the rise. While universal primer sets have been successfully designed for highly conserved core genes such as 16S rRNA and characteristic genes such asdsrABanddnaJ, primer sets for mobile, accessory genes such as multidrug resistance efflux pumps (MDREP) have not been explored. Here, we describe an approach to create universal primer sets for select MDREP genes chosen from five superfamilies (SMR, MFS, MATE, ABC and RND) identified in a model community of six members(Acetobacterium woodii, Bacillus subtilis, Desulfovibrio vulgaris, Geoalkalibacter subterraneus, Pseudomonas putidaandThauera aromatica).Using sequence alignments andin silicoPCR analyses, a new approach for creating universal primers sets targeting mobile, non-conserved genes has been developed and compared to more traditional approaches used for highly conserved genes. A discussion of the potential shortfalls of the primer sets designed this way are described. The approach described here can be adapted to any unique gene set and aid in creating a wider, more robust library of primer sets to detect less conserved genes and improve the field of PCR-based screening research.ImportanceIncreasing use of molecular detection methods, specifically PCR and qPCR, requires utmost confidence in the results while minimizing false positives and negatives due to poor primer designs. Frequently, these detection methods are focused on conserved, core genes which limits their applications. These screening methods are being used in various industries for specific genetic targets or key organisms such as viral or infectious strains, or characteristic genes indicating the presence of key metabolic processes. The significance of this work is to improve primer design approaches to broaden the scope of detectable genes. The use of the techniques explored here will improve detection of non-conserved genes through unique primer design approaches. Additionally, the approaches here highlight additional, important information which can be gleaned during thein silicophase of primer design which will improve our gene annotations based on sequence homologies.
Tamoxifen repurposing to combat infections by multidrug-resistant Gram-negative bacilli
Authors: Miró-Canturri Andrea , Ayerbe-Algaba Rafael , del Toro Raquel , Pachón Jerónimo , Smani Younes 
Published: April 2020

AbstractThe development of new strategic therapies for multidrug-resistant bacteria, like the use of non-antimicrobial approaches and/or drugs repurposing to be used as monotherapies or in combination with clinically relevant antibiotics, has become an urgent need. A therapeutic alternative for infections by multidrug-resistant Gram-negative bacilli (MDR-GNB) is immune system modulation to improve the infection clearance. We showed that immunocompetent mice infected byAcinetobacter baumannii, Pseudomonas aeruginosaorEscherichia coliin peritoneal sepsis models and treated with tamoxifen at 80 mg/kg/d for three days reduced the release of MCP-1 and its signalling pathway IL-18 and phosphorylated ERK1/2. This reduction of MCP-1 induced the reduction of migration of inflammatory monocytes and neutrophils from bone marrow to blood. Indeed, the treatment with tamoxifen in murine peritoneal sepsis models reduced the bacterial load in tissues and blood; and increased the mice survival from 0% to 60-100%. Tamoxifen treatment of neutropenic mice infected by these pathogens increased mice survival up to 20-60%. Furthermore, susceptibility and time-kill assays showed that the metabolites of tamoxifen, N-desmethyltamoxifen, hydroxytamoxifen and endoxifen, the three together exhibited MIC90values of 16 mg/L and were bactericidal against clinical isolates ofA. baumanniiandE. coli. This antimicrobial activity of tamoxifen metabolites parallels’ an increased membrane permeability ofA. baumanniiandE. coliwithout affecting their outer membrane proteins profiles. Together, these data showed that tamoxifen present a therapeutic efficacy against MDRA. baumannii, P. aeruginosaandE. coliin experimental models of infections and can be repurposed as new treatment for GNB infections.ImportanceAntimicrobial resistance in Gram-negative bacilli (GNB) is a global health treat. Drug repurposing, a novel approach involving the search of new indications for FDA approved drugs is gaining interest. Among them, we found the anti-cancer drug tamoxifen, which presents very promising therapeutic efficacy. The current study showed that tamoxifen presents activity in animal models of infection with MDRAcinetobacter baumannii, Pseudomonas aeruginosaandEscherichia coliby modulating the traffic of innate immune system cells and the antibacterial activity presented by its three major metabolites producedin vivoagainst these GNB. Our results offer a new candidate to be repurposed to treat severe infections caused by these pathogens.