bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analyzing the interaction of human ACE2 and RBD of spike protein of SARS-CoV-2 in perspective of Omicron variant
Authors: Samanta Arijit , Mahafujul Alam Syed Sahajada , Ali Safdar , Hoque Mehboob 
Published: December 2021

AbstractThe newly identified Omicron (B.1.1.529) variant of Severe Acute Respiratory Syndrome Voronavirus 2 (SARS-CoV-2) has steered concerns across the world due to the possession of large number of mutations leading to high infectivity and vaccine escape potential. The Omicron variant houses 32 mutations in S protein alone. The viral infectivity is determined mainly by the ability of spike (S) protein receptor binding domain (RBD) to bind to the human Angiotensin I Converting Enzyme 2 (hACE2) receptor. In this paper, the interaction of the RBDs of SARS-CoV-2 variants with hACE2 was analyzed by using protein-protein docking and compared with the novel Omicron variant. Our findings reveal that the Omicron RBD interacts strongly with hACE2 receptor via unique amino acid residues as compared to the Wuhan and many other variants. However, the interacting residues of RBD are found to be the same in Lamda (C.37) variant. These unique binding of Omicron RBD with hACE2 suggests an increased potential of infectivity and vaccine evasion potential of the new variant. The evolutionary drive of the SARS-CoV-2 may not be exclusively driven by RBD variants but surely provides for the platform for emergence of new variants.
Human 14-3-3 proteins site-selectively bind the mutational hotspot region of SARS-CoV-2 nucleoprotein modulating its phosphoregulation
Authors: Tugaeva Kristina V. , Sysoev Andrey A. , Kapitonova Anna A. , Smith Jake L. R. , Zhu Phillip , Cooley Richard B. , Antson Alfred A. , Sluchanko Nikolai N. 
Published: December 2021

AbstractPhosphorylated within its Ser/Arg-rich region, the SARS-CoV-2 nucleoprotein (N) recruits the phosphopeptide-binding human 14-3-3 proteins that play a well-recognized role in replication of many viruses. Here we use genetic code expansion to demonstrate that phosphorylation of SARS-CoV-2 N at either of two pseudo-repeats centered at Ser197 and Thr205 is sufficient for 14-3-3 binding. According to fluorescence anisotropy, the pT205-motif, present in SARS-CoV-2 but not in SARS-CoV, is preferred over the pS197-motif by all seven human 14-3-3 isoforms, which display unforeseen pT205/pS197 binding selectivity hierarchy. Crystal structures demonstrate that pS197 and pT205 are mutually exclusive 14-3-3-binding sites, whereas SAXS and biochemical data indicate 14-3-3 binding occludes the Ser/Arg-rich region, inhibiting its dephosphorylation. This Ser/Arg-rich region of N is highly prone to mutations, as exemplified by the Omicron and Delta variants, with our data suggesting how the strength of its 14-3-3 binding can be linked with the replicative fitness of the virus.
Convergent evolution of multiple mutations improves the viral fitness of SARS-CoV-2 variants by balancing positive and negative selection
Authors: Upadhyay Vaibhav , Patrick Casey , Lucas Alexandra , Mallela Krishna M.G. 
Published: December 2021

ABSTRACTMultiple mutations have been seen to undergo convergent evolution in SARS-CoV-2 variants of concern. One such evolution occurs in Beta, Gamma, and Omicron variants at three amino acid positions K417, E484, and N501 in the receptor binding domain of the spike protein. We examined the physical mechanisms underlying the convergent evolution of three mutations K417T/E484K/N501Y by delineating the individual and collective effects of mutations on binding to angiotensin converting enzyme 2 receptor, immune escape from neutralizing antibodies, protein stability and expression. Our results show that each mutation serves a distinct function that improves virus fitness supporting its positive selection, even though individual mutations have deleterious effects that make them prone to negative selection. Compared to the wild-type, K417T escapes Class 1 antibodies, has increased stability and expression; however, it has decreased receptor binding. E484K escapes Class 2 antibodies; however, it has decreased receptor binding, stability and expression. N501Y increases receptor binding; however, has decreased stability and expression. When these mutations come together, the deleterious effects are mitigated due to the presence of compensatory effects. Triple mutant K417T/E484K/N501Y has increased receptor binding, escapes both Class 1 and Class 2 antibodies, and has similar stability and expression as that of the wild-type. These results show the implications of presence of multiple mutations on virus evolution that enhance viral fitness on different fronts by balancing both positive and negative selection and improves the chances of selection of mutations together.
Establishment of a stable SARS-CoV-2 replicon system for application in high-throughput screening
Authors: Tanaka Tomohisa , Saito Akatsuki , Suzuki Tatsuya , Miyamoto Yoichi , Takayama Kazuo , Okamoto Toru , Moriishi Kohji 
Published: December 2021

AbstractExperiments with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are limited by the need for biosafety level 3 (BSL3) conditions. A SARS-CoV-2 replicon system rather than anin vitroinfection system is suitable for antiviral screening since it can be handled under BSL2 conditions and does not produce infectious particles. However, the reported replicon systems are cumbersome because of the need for transient transfection in each assay. In this study, we constructed a bacterial artificial chromosome vector (the replicon-BAC vector) including the SARS-CoV-2 replicon and a fusion gene encodingRenillaluciferase and neomycin phosphotransferase II, examined the antiviral effects of several known compounds, and then established a cell line stably harboring the replicon-BAC vector. Several cell lines transiently transfected with the replicon-BAC vector produced subgenomic replicon RNAs (sgRNAs) and viral proteins, and exhibited luciferase activity. In the transient replicon system, treatment with remdesivir or interferon-β but not with camostat or favipiravir suppressed the production of viral agents and luciferase, indicating that luciferase activity corresponds to viral replication. VeroE6/Rep3, a stable replicon cell line based on VeroE6 cells, was successfully established and continuously produced viral proteins, sgRNAs and luciferase, and their production was suppressed by treatment with remdesivir or interferon-β. Molnupiravir, a novel coronavirus RdRp inhibitor, inhibited viral replication more potently in VeroE6/Rep3 cells than in VeroE6-based transient replicon cells. In summary, our stable replicon system will be a powerful tool for the identification of SARS-CoV-2 antivirals through high-throughput screening.
Estimating the impact of implementation and timing of the COVID-19 vaccination programme in Brazil: a counterfactual analysis
Authors: Ferreira Leonardo Souto , Darcie Marquitti Flavia Maria , da Silva Rafael Lopes Paixão , Borges Marcelo Eduardo , da Costa Gomes Marcelo Ferreira , Cruz Oswaldo Gonçalves , Kraenkel Roberto André , Coutinho Renato Mendes , Prado Paulo Inácio , Bastos Leonardo Soares 
Published: December 2021

ABSTRACTBackgroundVaccines developed between 2020 - 2021 against the SARS-CoV-2 virus were designed to diminish the severity and prevent deaths due to COVID-19. However, estimates of the effectiveness of vaccination campaigns in achieving these goals remain a methodological challenge. In this work, we developed a Bayesian statistical model to estimate the number of deaths and hospitalisations averted by vaccination of older adults (above 60 years old) in Brazil.MethodsWe fit a linear model to predict the number of deaths and hospitalisations of older adults as a function of vaccination coverage in this group and casualties in younger adults. We used this model in a counterfactual analysis, simulating alternative scenarios without vaccination or with faster vaccination roll-out. We estimated the direct effects of COVID-19 vaccination by computing the difference between hypothetical and realised scenarios.FindingsWe estimated that more than 165,000 individuals above 60 years of age were not hospitalised due to COVID-19 in the first seven months of the vaccination campaign. An additional contingent of 104,000 hospitalisations could have been averted if vaccination had started earlier. We also estimated that more than 58 thousand lives were saved by vaccinations in the period analysed for the same age group and that an additional 47 thousand lives could have been saved had the Brazilian government started the vaccination programme earlier.InterpretationOur estimates provided a lower bound for vaccination impacts in Brazil, demonstrating the importance of preventing the suffering and loss of older Brazilian adults. Once vaccines were approved, an early vaccination roll-out could have saved many more lives, especially when facing a pandemic.FundingThe Coordenação de Aperfeiçoamento de Pessoal de Nível Superior – Brazil (Finance Code 001 to FMDM and LSF), Conselho Nacional de Desenvolvimento Científico e Tecnológico – Brazil (grant number: 315854/2020-0 to MEB, 141698/2018-7 to RLPS, 313055/2020-3 to PIP, 311832/2017-2 to RAK), Fundação de Amparo à Pesquisa do Estado de São Paulo – Brazil (contract number: 2016/01343-7 to RAK), Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro – Brazil (grant number: E-26/201.277/2021 to LSB) and Inova Fiocruz/Fundação Oswaldo Cruz – Brazil (grant number: 48401485034116) to LSB, OGC and MGFC. The funding agencies had no role in the conceptualization of the study.
Mature Neurons’ sensitivity to oxidative stress is epigenetically programmed by alternative splicing and mRNA stability
Authors: Zhou Yuan , Rashad Sherif , Tominaga Teiji , Niizuma Kuniyasu 
Published: December 2021

AbstractNeuronal differentiation is a complex process that entails extensive morphological, transcriptional, metabolic, and functional changes that dictate neuronal lineage commitment. Much less understood is the role that epigenetic and epi-transcriptional reprogramming plays in the process of neuronal differentiation and maturation. To depict the whole landscape of transcriptomics and epigenetic changes during neuronal differentiation and maturation, we differentiated SH-SY5Y cells and performed RNA sequencing on differentiated and undifferentiated cells. 728 differentially expressed genes (DEGs) enriched in synaptic signaling and cell morphogenesis pathways were observed. Moreover, transcriptome-wide mRNA stability profiling revealed that genes with altered stability were exceptionally enriched for redox homeostasis pathways. Mature neurons are known to be highly sensitive to oxidative stress, which is crucial in the pathophysiology of neurodegenerative disease. Our results suggest that this heightened sensitivity is regulated at the mRNA stability level (i.e., epigenetic) rather than at the transcriptional level. Alternative splicing analysis revealed the exon skipping and alternative mRNA isoforms enriched for morphogenesis related pathway. Alternatively, alternative 5 and 3 prime splicing site, intron retention and mutually exclusive exon events exclusively clustered in the translation and translation initiation pathways, suggesting the potential effect of alternative splicing on translation following neuronal maturation. Splice motif analysis revealed enriched motifs for RBPs that regulate various splice types and can be further correlated to distinct phenotypical changes during neuronal differentiation and maturation. Here we present an extensive exploration of the transcriptional and epigenetic changes and their potential association with the process of neuronal differentiation, providing a new insight into understanding the molecular mechanism of neuronal function and behavior.
An ultrapotent RBD-targeted biparatopic nanobody neutralizes broad SARS-CoV-2 variants
Authors: Chi Xiaojing , Zhang Xinhui , Pan Shengnan , Yu Yanying , Lin Tianli , Duan Huarui , Liu Xiuying , Chen Wenfang , Yang Xuehua , Ding Qiang , Wang Jianwei , Yang Wei 
Published: December 2021

AbstractThe wide transmission and host adaptation of SARS-CoV-2 have led to the rapid accumulation of mutations, posing significant challenges to the effectiveness of vaccines and therapeutic antibodies. Although several neutralizing antibodies were authorized for emergency clinical use, convalescent patients derived natural antibodies are vulnerable to SARS-CoV-2 Spike mutation. Here, we describe the screen of a panel of SARS-CoV-2 receptor-binding domain (RBD) targeted nanobodies (Nbs) from a synthetic library and the design of a biparatopic Nb, named Nb1-Nb2, with tight affinity and super wide neutralization breadth against multiple SARS-CoV-2 variants of concern. Deep-mutational scanning experiments identify the potential binding epitopes of the Nbs on the RBD and demonstrate that biparatopic Nb1-Nb2 has a strong escape resistant feature against more than 60 tested RBD amino acid substitutions. Using pseudovirion-based and trans-complementation SARS-CoV-2 tools, we determine that the Nb1-Nb2 broadly neutralizes multiple SARS-CoV-2 variants, including Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), Lambda (C.37), Kappa (B.1.617.1) and Mu (B.1.621). Furthermore, a heavy chain antibody is constructed by fusing the human IgG1 Fc to Nb1-Nb2 (designated as Nb1-Nb2-Fc) to improve its neutralization potency, yield, stability and potential half-life extension. For the new Omicron variant (B.1.1.529) that harbors unprecedented multiple RBD mutations, Nb1-Nb2-Fc keeps a firm affinity (KD < 1.0×10−12 M) and strong neutralizing activity (IC50 = 0.0017 nM). Together, we developed a tetravalent biparatopic human heavy chain antibody with ultrapotent and broad-spectrum SARS-CoV-2 neutralization activity which highlights the potential clinical applications.
Force Recruitment of Neuromuscular Magnetic Stimulation Predicted Through High-Resolution Anatomical 3D Models
Authors: Goetz S.M. , Weyh T. , Kammermann J. , Helling F. , Li Z. 
Published: December 2021

AbstractNeuromuscular magnetic stimulation is a promising tool in neurorehabilitation due to its deeper penetration, notably lower distress, and respectable force levels compared to electrical stimulation. However, this method faces great challenges from a technological perspective. The systematic design of better equipment and the incorporation into modern training setups requires better understanding of the mechanisms and predictive quantitative models of the recruited forces. This article proposes a model for simulating the force recruitment in isometric muscle stimulation of the thigh extensors based on previous theoretical and experimental findings. The model couples a 3D field model for the physics with a parametric recruitment model, which is identified with a mixed-effects design to learn the most likely model based on available experimental data with a wide range of field conditions. This approach intentionally keeps the model as mathematically simple and statistically parsimonious as possible in order to avoid over-fitting. The coupled model is able to accurately predict key phenomena observed so far, such as a threshold shift for different distances between coil and body, the different recruiting performance of various coils with available measurement data in the literature, and the saturation behaviour with its onset amplitude. The presented recruitment model could also be readily incorporated into dynamic models for biomechanics as soon as sufficient experimental data are available for calibration.
Short OGA is targeted to the mitochondria and regulates mitochondrial reactive oxygen species level
Authors: Pagesy Patrick , Bouaboud Abdelouhab , Feng Zhihao , Hulin Philippe , Issad Tarik 
Published: December 2021

AbstractO-GlcNAcylation is a reversible post-translational modification involved the regulation of cytosolic, nuclear and mitochondrial proteins. Only two enzymes, OGT and OGA, control attachment and removal of O-GlcNAc on proteins, respectively. Whereas a variant OGT (mOGT) has been proposed as the main isoform that O-GlcNAcylates proteins in mitochondria, identification of a mitochondrial OGA has not been performed yet. Two splice variants of OGA (short and long isoforms) have been described previously. In this work, using cell fractionation experiments, we show that short-OGA is preferentially recovered in mitochondria-enriched fractions from HEK-293T cells as well as mouse embryonic fibroblasts. Moreover, fluorescent microscopy imaging confirmed that GFP-tagged short-OGA is addressed to mitochondria. In addition, using a BRET-based mitochondrial O-GlcNAcylation biosensor, we show that co-transfection of short-OGA markedly reduced O-GlcNAcylation of the biosensor, whereas long-OGA had no significant effect. Finally, using genetically encoded or chemical fluorescent mitochondrial probes, we showed that short-OGA overexpression increases mitochondrial ROS levels, whereas long-OGA had no significant effect. Together, our work reveals that the short-OGA isoform is targeted to the mitochondria where it regulates ROS homoeostasis.
Rapid and sensitive single cell RNA sequencing with SHERRY2
Authors: Di Lin , Liu Bo , Lyu Yuzhu , Zhao Shihui , Pang Yuhong , Zhang Chen , Wang Jianbin , Qi Hai , Shen Jie , Huang Yanyi 
Published: December 2021

AbstractPrevalent single cell transcriptomic profiling (scRNA-seq) mechods are mainly based on synthesis and enrichment of full-length double-stranded complementary DNA. These approaches are challenging to generate accurate quantification of transcripts when their abundance is low or their full-length amplifications are difficult. Based on our previous finding that Tn5 transposase can directly cut-and-tag DNA/RNA hetero-duplexes, we present SHERRY2, a specifically optimized protocol for scRNA-seq without second strand cDNA synthesis. SHERRY2 is free of pre-amplification and eliminates the sequence-dependent bias. In comparison with other widely-used scRNA-seq methods, SHERRY2 exhibits significantly higher sensitivity and accuracy even for single nuclei. Besides, SHERRY2 is simple and robust, and can be easily scaled up to high-throughput experiments. When testing single lymphocytes and neuron nuclei, SHERRY2 not only obtained accurate countings of transcription factors and long non-coding RNAs, but also provided bias-free results that enriched genes in specific cellular components or functions, which outperformed other protocols. With a few thousand cells sequenced by SHERRY2, we confirmed expression and dynamics of Myc in different cell types of germinal centers, which were previously only revealed by gene-specific amplification methods. SHERRY2 is able to provide high sensitivity, high accuracy, and high throughput for those applications that require high number of genes identified in each cell. It can reveal the subtle transcriptomic difference between cells and facilitate important biological discoveries.
Gdnf, a germ cell-derived factor, regulates zebrafish germ cell stemness through the creation of new spermatogonial niches (germ and Sertoli cells) and inhibition of spermatogonial differentiation in an autocrine and paracrine manners
Authors: Doretto Lucas B. , Butzge Arno J. , Nakajima Rafael T. , Martinez Emanuel R. M. , Marques Beatriz , da Silva Rodrigues Maira , Rosa Ivana F. , Ricci Juliana M. B. , Tovo-Neto Aldo , Costa Daniel F. , Malafaia Guilherme , Shao Changwei , Nóbrega Rafael H. 
Published: December 2021

AbstractGlial cell line-derived neurotrophic factor (GDNF) and its receptor (GDNF Family Receptor α1 - GFRα1) are well known to mediate spermatogonial stem cell (SSC) proliferation and survival in the mammalian testes. In nonmammalian species, Gdnf and Gfrα1 orthologs have been found but their functions remain poorly investigated in the testis. Considering this background, this study aimed to understand the roles of Gdnf-Gfrα1 signaling pathway in the zebrafish testis by combining in vivo, in silico and ex vivo approaches. Our analysis showed that zebrafish exhibited two paralogs of Gndf (gdnfa and gdnfb) and its receptor, Gfrα1 (gfrα1a and gfrα1b), in agreement with the teleost-specific third round (3R) of whole genome duplication. Expression analysis further revealed that gdnfa and gfrα1a were the most expressed copies in the zebrafish adult testes. Subsequently, we demonstrated that gdnfa is expressed in the germ cells, while Gfrα1a was detected in early spermatogonia (mainly in types Aund and Adiff) and Sertoli cells. Functional ex vivo analysis showed that Gdnf promoted the creation of new available niches by stimulating proliferation of both type Aund spermatogonia and their surrounding Sertoli cells, but without changing pou5f3 mRNA levels. Strikingly, Gdnf also inhibited late spermatogonial differentiation as shown by the decrease of type B spermatogonia and down-regulation of dazl in the co-treatment with Fsh. Altogether, our data revealed for the first time that a germ cell-derived factor is associated with maintaining germ cell stemness through the creation of new available niches, supporting development of differentiating spermatogonial cysts and inhibiting late spermatogonial differentiation in autocrine and paracrine manners.
Integrated cytometry with machine learning applied to high-content imaging of human kidney tissue for in-situ cell classification and neighborhood analysis
Authors: Winfree Seth , McNutt Andrew T. , Khochare Suraj , Borgard Tyler J. , Barwinska Daria , Sabo Angela R. , Ferkowicz Michael J. , Williams James C. , Lingeman James E. , Gulbronson Connor J , Kelly Katherine J. , Sutton Timothy A. , Dagher Pierre C. , Eadon Michael T. , Dunn Kenneth W. , El-Achkar Tarek M. 
Published: December 2021

AbstractThe human kidney is a complex organ with various cell types that are intricately organized to perform key physiological functions and maintain homeostasis. New imaging modalities such as mesoscale and highly multiplexed fluorescence microscopy are increasingly applied to human kidney tissue to create single cell resolution datasets that are both spatially large and multi-dimensional. These single cell resolution high-content imaging datasets have a great potential to uncover the complex spatial organization and cellular make-up of the human kidney. Tissue cytometry is a novel approach used for quantitative analysis of imaging data, but the scale and complexity of such datasets pose unique challenges for processing and analysis. We have developed the Volumetric Tissue Exploration and Analysis (VTEA) software, a unique tool that integrates image processing, segmentation and interactive cytometry analysis into a single framework on desktop computers. Supported by an extensible and open-source framework, VTEA’s integrated pipeline now includes enhanced analytical tools, such as machine learning, data visualization, and neighborhood analyses for hyperdimensional large-scale imaging datasets. These novel capabilities enable the analysis of mesoscale two and three-dimensional multiplexed human kidney imaging datasets (such as CODEX and 3D confocal multiplexed fluorescence imaging). We demonstrate the utility of this approach in identifying cell subtypes in the kidney based on labels, spatial association and their microenvironment or neighborhood membership. VTEA provides integrated and intuitive approach to decipher the cellular and spatial complexity of the human kidney and complement other transcriptomics and epigenetic efforts to define the landscape of kidney cell types.