bluuebunny/crossref_metadata_2025_split huggingface dataset:
An expedited approach towards the rationale design of non-covalent SARS-CoV-2 main protease inhibitors with in vitro antiviral activity
Authors: Kitamura Naoya , Sacco Michael Dominic , Ma Chunlong , Hu Yanmei , Townsend Julia Alma , Meng Xiangzhi , Zhang Fushun , Zhang Xiujun , Kukuljac Adis , Marty Michael Thomas , Schultz David , Cherry Sara , Xiang Yan , Chen Yu , Wang Jun 
Published: December 2020

AbstractThe main protease (Mpro) of SARS-CoV-2 is a validated antiviral drug target. Several Mproinhibitors have been reported with potent enzymatic inhibition and cellular antiviral activity, including GC376, boceprevir, calpain inhibitors II and XII, each containing a reactive warhead that covalently modifies the catalytic Cys145. In this study, we report an expedited drug discovery approach by coupling structure-based design and Ugi four-component (Ugi-4CR) reaction methodology to the design of non-covalent Mproinhibitors. The most potent compound23Rhad cellular antiviral activity similar to covalent inhibitors such as GC376. Our designs were guided by overlaying the structure of SARS-CoV Mpro+ ML188 (R), a non-covalent inhibitor derived from Ug-4CR, with the X-ray crystal structures of SARS-CoV-2 Mpro+ calpain inhibitor XII/GC376/UAWJ247. Binding site analysis suggests a strategy of extending the P2 and P3 substitutions in ML188 (R) to achieve optimal shape complementary with SARS-CoV-2 Mpro. Lead optimization led to the discovery of23R, which inhibits SARS-CoV-2 Mproand SARS-CoV-2 viral replication with an IC50of 0.31 μM and EC50of 1.27 μM, respectively. The binding and specificity of23Rto SARS-CoV-2 Mprowere confirmed in a thermal shift assay and native mass spectrometry assay. The co-crystal structure of SARS-CoV-2 Mprowith23Rrevealed the P2 biphenyl fits snuggly into the S2 pocket and the benzyl group in the α-methylbenzyl faces towards the core of the enzyme, occupying a previously unexplored binding site located in between the S2 and S4 pockets. Overall, this study revealed the most potent non-covalent SARS-CoV-2 Mproinhibitors reported to date and a novel binding pocket that can be explored for Mproinhibitor design.
Vertical inheritance governs biosynthetic gene cluster evolution and chemical
diversification
Authors: Chase Alexander B. , Sweeney Douglas , Muskat Mitchell N. , Guillén-Matus Dulce , Jensen Paul R. 
Published: December 2020

ABSTRACT
While specialized metabolites are thought to mediate ecological
interactions, the evolutionary processes driving their diversification,
particularly among closely related lineages, remain poorly understood. Here, we
examine the evolutionary dynamics governing the distribution of natural product
biosynthetic gene clusters (BGCs) using 118 strains within the marine
actinomycete genus Salinispora. While previous
evidence indicated that horizontal gene transfer (HGT) largely contributed to
BGC diversity, we find that a majority of BGCs in
Salinispora genomes are conserved through
processes of vertical descent. In particular, vertical inheritance maintained
BGCs over evolutionary timescales (millions of years) allowing for BGC
diversification among Salinispora species. By
coupling the genomic analyses with high-resolution tandem mass spectrometry
(LC-MS/MS), we identified that BGC evolution in
Salinispora proceeds largely through gene
gain/loss events and constrained recombination that contributes to interspecies
diversity at the gene, pathway, and metabolite levels. Consequently, the
evolutionary processes driving BGC diversification had direct consequences for
compound production and contributed to chemical diversification, as exemplified
in our case study of the medically relevant proteosome inhibitors, the
salinosporamides. Together, our results support the concept that specialized
metabolites, and their cognate BGCs, represent functional traits associated with
niche differentiation among Salinispora
species.

GRAPHICAL ABSTRACT

SIGNIFICANCE
Natural products are traditionally exploited for their
pharmaceutical potential; yet what is often overlooked is that the
evolution of the biosynthetic gene clusters (BGCs) encoding these
small molecules likely affects the diversification of the produced
compounds and implicitly has an impact on the compounds’ activities
and ecological functions. And while the prevailing dogma in natural
product research attributes frequent and widespread horizontal gene
transfer (HGT) as an integral driver of BGC evolution, we find that
the majority of BGC diversity derives from processes of vertical
descent, with HGT events being rare. This understanding can
facilitate informed biosynthetic predictions to identify novel
natural products, in addition to uncovering how these specialized
metabolites contribute to the environmental distribution of
microbes.
Adaptive integration of self-motion and goals in posterior parietal cortex
Authors: Alexander Andrew S. , Tung Janet C. , Chapman G. William , Shelley Laura E. , Hasselmo Michael E. , Nitz Douglas A. 
Published: December 2020

AbstractAnimals engage in a variety of navigational behaviors that require different regimes of behavioral control. In the wild, rats readily switch between foraging and more complex behaviors such as chase, wherein they pursue other rats or small prey. These tasks require vastly different tracking of multiple behaviorally-significant variables including self-motion state. It is unknown whether changes in navigational context flexibly modulate the encoding of these variables. To explore this possibility, we compared self-motion processing in the multisensory posterior parietal cortex while rats performed alternating blocks of free foraging and visual target pursuit. Animals performed the pursuit task and demonstrated predictive processing by anticipating target trajectories and intercepting them. Relative to free exploration, pursuit sessions yielded greater proportions of parietal cortex neurons with reliable sensitivity to self-motion. Multiplicative gain modulation was observed during pursuit which increased the dynamic range of tuning and led to enhanced decoding accuracy of self-motion state. We found that self-motion sensitivity in parietal cortex was history-dependent regardless of behavioral context but that the temporal window of self-motion tracking was extended during target pursuit. Finally, many self-motion sensitive neurons conjunctively tracked the position of the visual target relative to the animal in egocentric coordinates, thus providing a potential coding mechanism for the observed gain changes to self-motion signals. We conclude that posterior parietal cortex dynamically integrates behaviorally-relevant information in response to ongoing task demands.
Polyamine biosynthesis and eIF5A hypusination are modulated by the DNA tumor virus KSHV and promote KSHV viral infection
Authors: Fiches Guillaume N. , Biswas Ayan , Zhou Dawei , Kong Weili , Jean Maxime , Santoso Netty G. , Zhu Jian 
Published: December 2020

AbstractPolyamines are critical metabolites involved in various cellular processes and often dysregulated in cancers. Kaposi’s sarcoma associated Herpesvirus (KSHV) is a defined oncogenic virus belonging to the sub-family of human gamma-herpesviruses. KSHV infection leads to the profound alteration of host metabolic landscape to favor the development of KSHV-associated malignancies. In our studies, we identified that polyamine biosynthesis and eIF5A hypusination are dynamically regulated by KSHV infection likely through the modulation of key enzymes of these pathways, such as ODC1, and that in return these metabolic pathways are required for both KSHV lytic switch from latency andde novoinfection. The further analysis unraveled that translation of critical KSHV latent and lytic proteins (LANA, RTA) depends on eIF5A hypusination. We also demonstrated that KSHV infection can be efficiently and specifically suppressed by using inhibitors targeting either polyamine biosynthesis or eIF5A hypusination. Above all, our results illustrated that the dynamic and profound interaction of a DNA tumor virus (KSHV) with host polyamine biosynthesis and eIF5A hypusination metabolic pathways promote viral propagation and oncogenesis, which serve as new therapeutic targets to treat KSHV-associated malignancies.
Genomic analysis provides novel insights into diversification and taxonomy ofAllorhizobium vitis(i.e.Agrobacterium vitis)
Authors: Kuzmanović Nemanja , Biondi Enrico , Overmann Jörg , Puławska Joanna , Verbarg Susanne , Smalla Kornelia , Lassalle Florent 
Published: December 2020

AbstractBackgroundAllorhizobium vitis(formerly namedAgrobacterium vitisorAgrobacteriumbiovar 3) is the primary causative agent of crown gall disease of grapevine worldwide. We obtained and analyzed whole-genome sequences of diverseAll. vitisstrains to get insights into their diversification and taxonomy.ResultsPairwise genome comparisons and phylogenomic analysis of variousAll. vitisstrains clearly indicated thatAll. vitisis not a single species, but represents a species complex composed of several genomic species. Thus, we emended the description ofAll. vitis, which now refers to a restricted group of strains within theAll. vitisspecies complex (i.e.All. vitis sensu stricto) and proposed a description of a novel species,All. ampelinumsp. nov. The type strain ofAll. vitis sensu strictoremains the current type strain ofAll. vitis, K309T. The type strain ofAll. ampelinumsp. nov. is S4T. We also identified sets of gene clusters specific to theAll. vitisspecies complex,All. vitis sensu strictoandAll. ampelinum, respectively, for which we predicted the biological function and infer the role in ecological diversification of these clades, including some we could experimentally validate.All. vitisspecies complex-specific genes confer tolerance to different stresses, including exposure to aromatic compounds. Similarly,All. vitis sensu stricto-specific genes confer the ability to degrade 4-hydroxyphenylacetate and a putative compound related to gentisic acid.All. ampelinum-specific genes have putative functions related to polyamine metabolism and nickel assimilation. Congruently with the genome-based classification,All. vitis sensu strictoandAll. ampelinumwere clearly delineated by MALDI-TOF MS analysis. Moreover, our genome-based analysis indicated thatAllorhizobiumis clearly separated from other genera of the familyRhizobiaceae.ConclusionsComparative genomics and phylogenomic analysis provided novel insights into the diversification and taxonomy ofAllorhizobium vitisspecies complex, supporting our redefinition ofAll. vitis sensu strictoand description ofAll. ampelinum. Our pan-genome analyses suggest that these species have differentiated ecologies, each relying on specialized nutrient consumption or toxic compound degradation to adapt to their respective niche.
Structural insights into glycine reuptake inhibition
Authors: Shahsavar Azadeh , Stohler Peter , Bourenkov Gleb , Zimmermann Iwan , Siegrist Martin , Guba Wolfgang , Pinard Emmanuel , Seeger Markus A. , Schneider Thomas R. , Dawson Roger J.P. , Nissen Poul 
Published: December 2020

AbstractThe human glycine transporter 1 (GlyT1) regulates glycine mediated neuronal excitation and inhibition through sodium- and chloride-dependent reuptake of the neurotransmitter1-3. Inhibition of glycine reuptake via GlyT1 prolongs neurotransmitter signaling and has long served as a key therapeutic development strategy for treatment of a broad range of central nervous system disorders including schizophrenia and cognitive impairments4. Using an inhibition state-selective sybody and serial synchrotron crystallography, we determined the structure of GlyT1 in complex with a benzoylpiperazine chemotype inhibitor at 3.4 Å resolution. The inhibitor locks GlyT1 in an inward-open conformation and binds at the intracellular gate of the release pathway, overlapping with the glycine release site. The inhibitor likely reaches GlyT1 from the cytoplasmic leaflet of the plasma membrane. The study defines the mechanism of non-competitive inhibition and enables the rational design of new, clinically efficacious GlyT1 inhibitors.
Early empirical assessment of the N501Y mutant strains of SARS-CoV-2 in the United Kingdom, October to November 2020
Authors: Leung Kathy , Shum Marcus HH , Leung Gabriel M , Lam Tommy TY , Wu Joseph T 
Published: December 2020

AbstractTwo new SARS-CoV-2 lineages with the N501Y mutation in the receptor binding domain of the spike protein have rapidly become prevalent in the UK. We estimated that the earlier 501Y lineage without amino acid deletion Δ69/Δ70 circulating mainly between early September to mid-November was 10% (6-13%) more transmissible than the 501N lineage, and the currently dominant 501Y lineage with amino acid deletion Δ69/Δ70 circulating since late September was 75% (70-80%) more transmissible than the 501N lineage.
Effect of Complete Respiratory Muscle Training (cRMT) on Dysphonia following Single CVA: A retrospective pilot study
Authors: Arnold Robert J. , Gaskill Christopher S , Bausek Nina 
Published: December 2020

AbstractBackgroundAlthough dysphonia is less prevalent than dysphagia following cerebrovascular accidents, dysphonia does contribute to the burden of disease resulting from stroke. Strengthening muscles of the larynx and respiratory tract through respiratory muscle training (RMT) has proven effective in improving voice after neurological insult. However, approaches to strengthen only the expiratory muscle groups (EMST) dominate the clinical study literature, with variable outcomes. By focusing on exhalation, the contribution of inspiratory muscles to phonation may have been overlooked. This study investigated the effect of combined respiratory muscle training (cRMT) to improve voice function in stroke patients.MethodsRecorded data of twenty patients with dysphonia following stroke were allocated to an intervention (IG) or a control group (CG) based upon whether they chose cRMT or not while awaiting pro bono voice therapy services. The intervention group (N=10) was treated daily with three 5-minute sessions of complete resistive respiratory muscle training for 28 days, while the control group (N=10) received no cRMT or other exercise intervention. Perceptual and acoustic measurements as well as a pulmonary function test were assessed pre-and post-intervention.ResultsThe intervention group demonstrated significant improvements after 28 days of combined respiratory muscle training (cRMT) in peak flow (127%), patient self-perception of voice improvement (84.41%), as well as in five of the six categories of the Consensus Auditory-Perceptual Evaluation of Voice (CAPE-V) overall severity (63.22%), breathiness (61.06%), strain (63.43%), pitch range (48.11%) and loudness (57.51%), compared to the control group who did not receive treatment. Furthermore, cRMT also led to significant improvements in maximum phonation time (212.5%) and acoustic parameters of vocal intensity and semitone range.ConclusionThis pilot study shows promise of the feasibility and effectiveness of cRMT to lessen the signs and symptoms of dysphonia while simultaneously improving breath support.
Stepwise transmigration cascade of T and B cells through the perivascular channel in lymph node high endothelial venules
Authors: Choe Kibaek , Moon Jieun , Lee Soo Yun , Song Eunjoo , Back Ju Hee , Song Joo-Hye , Hyun Young-Min , Uchimura Kenji , Kim Pilhan 
Published: December 2020

AbstractHigh endothelial venules (HEVs) effectively recruit circulating lymphocytes from the blood to lymph nodes. HEVs have endothelial cells (ECs) and perivascular sheaths consisting of fibroblastic reticular cells (FRCs). Many studies have characterized the multiple steps of lymphocyte migration interacting with ECs at the luminal side of HEVs. However, post-luminal migration steps are not well elucidated. Herein, we performed intravital imaging to investigate post-luminal T and B cell migration, consisting of trans-EC migration, crawling in the perivascular channel (a narrow space between ECs and FRCs) and trans-FRC migration. The post-luminal migration of T cells occurred in a PNAd-dependent manner. Remarkably, we found hot spots for the trans-EC and trans-FRC migration of T and B cells. Interestingly, T and B cells preferentially shared trans-FRC migration hot spots but not trans-EC migration hot spots. Furthermore, the trans-FRC T cell migration was confined to fewer sites than trans-EC T cell migration, and trans-FRC migration of T and B cells preferentially occurred at FRCs covered by CD11c+ dendritic cells in HEVs. These results suggest that HEV ECs and FRCs with perivascular DCs delicately regulate T and B cell entry into lymph nodes.
In vitro characterization of engineered red blood cells as potent viral traps against HIV-1 and SARS-CoV-2
Authors: Hoffmann Magnus A. G. , Kieffer Collin , Bjorkman Pamela J. 
Published: December 2020

AbstractEngineered red blood cells (RBCs) expressing viral receptors could be used therapeutically as viral traps as RBCs lack nuclei and other organelles required for viral replication. Here we show that the combination of a powerful erythroid-specific expression system and transgene codon optimization yields high expression levels of the HIV-1 receptors CD4 and CCR5, as well as a CD4-glycophorin A (CD4-GpA) fusion protein on enucleated RBCs. Engineered RBCs expressing CD4 and CCR5 were efficiently infected by HIV-1, but CD4 or CD4-GpA expression in the absence of CCR5 was sufficient to potently neutralize HIV-1 in vitro. To facilitate continuous large-scale production of engineered RBCs, we generated erythroblast cell lines stably expressing CD4-GpA or ACE2-GpA fusion proteins, which produced potent RBC viral traps against HIV-1 and SARS-CoV-2. Our results suggest that this approach warrants further investigation as a potential treatment against viral infections.
Modelling the contribution of iodised salt in industrially processed foods to iodine intake in Macedonia
Authors: Milevska-Kostova Neda , Karanfilski Borislav , Knowles Jacky , Codling Karen , Lazarus John H 
Published: December 2020

AbstractEvidence from the 1950s showed that Macedonia was iodine deficient. After the introduction of mandatory universal salt iodisation, the country saw a steady increase in iodine intake and decline in goitre prevalence, earning iodine-deficiency free status in 2003. Iodine status assessments in 2007 and 2016 showed adequate iodine intake among school age children (median urinary iodine concentration of 241 µg/L and 236 µg/L respectively). Macedonia participated in the 2019 piloting of the Iodine Global Network Programme Guidance on the use of iodised salt in industrially processed foods to better understand salt and iodised salt intake from food sources other than household salt.Aggregated data from the 2017 Household Consumption and Expenditure Survey (HCES) was used to determine household salt consumption, to identify widely-consumed, salt-containing industrially processed foods and estimate typical daily intake of these foods. The salt content of these foods was estimated using national standards and the Danish food composition database. The percentage of this salt that was iodised was assessed using customs data for salt imports.Although the study has its limitations, including a relatively small selection of foods, the results indicate potential iodine intake from iodised household salt and iodised salt in the selected foods of above 300% of the Estimated Average Requirement and over 220% of the Recommended Nutrient Intake for adults. This was approximately 50% of the tolerable safe Upper Level for iodine intake. The study confirmed high daily salt intake (11.2 grams from household salt only). Successful salt reduction would be expected to reduce iodine intake, however, modelling with 10% and 30% reduction implied this is unlikely to put any population group at risk of deficiency. It is recommended that design and implementation of salt iodisation and salt reduction policies are harmonized, alongside continued regular iodine status monitoring for different population groups.
CellVGAE: An unsupervised scRNA-seq analysis workflow with graph attention networks
Authors: Buterez David , Bica Ioana , Tariq Ifrah , Andrés-Terré Helena , Liò Pietro 
Published: December 2020

AbstractCurrently, single-cell RNA sequencing (scRNA-seq) allows high-resolution views of individual cells, for libraries of up to (tens of) thousands of samples. In this study, we introduce the use of graph neural networks (GNN) in the unsupervised study of scRNA-seq data, namely for dimensionality reduction and clustering. Motivated by the success of non-neural graph-based techniques in bioinformatics, as well as the now common feedforward neural networks being applied to scRNA-seq measurements, we develop an architecture based on a variational graph autoencoder with graph attention layers that works directly on the connectivity of cells. With the help of three case studies, we show that our model, named CellVGAE, can be effectively used for exploratory analysis, even on challenging datasets, by extracting meaningful features from the data and providing the means to visualise and interpret different aspects of the model. Furthermore, we evaluate the dimensionality reduction and clustering performance on 9 well-annotated datasets, where we compare with leading neural and non-neural techniques. CellVGAE outperforms competing methods in all 9 scenarios. Finally, we show that CellVGAE is more interpretable than existing architectures by analysing the graph attention coefficients. The software and code to generate all the figures are available at https://github.com/davidbuterez/CellVGAE.
DNA sequence-dependent formation of heterochromatin nanodomains
Authors: Thorn Graeme J. , Clarkson Christopher T. , Rademacher Anne , Mamayusupova Hulkar , Schotta Gunnar , Rippe Karsten , Teif Vladimir B. 
Published: December 2020

AbstractThe mammalian epigenome contains thousands of heterochromatin nanodomains (HNDs) marked by di- and trimethylation of histone H3 at lysine 9, which have a typical size of 3-10 nucleosomes. However, the (epi)genetic determinants of their location and boundaries are only partly understood. Here, we compare four HND types in mouse embryonic stem cells, that are defined by histone methylases SUV39H1/2 or GLP, transcription factor ADNP or chromatin remodeller ATRX. Based on a novel chromatin hierarchical lattice framework termed ChromHL, we are able to predict HND maps with singe-nucleotide resolution. We find that HND nucleation can be rationalized by DNA sequence specific protein binding to PAX3/9, ADNP and LINE1 repeats. Depending on type of microdomains, boundaries are determined either by CTCF binding sites or by nucleosome-nucleosome and nucleosome-HP1 interactions. Our new framework allows predicting how patterns of H3K9me2/3 and other chromatin nanodomains are established and changed in processes such as cell differentiation.