bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unbiased interrogation of memory B cells from convalescent COVID-19 patients reveals a broad antiviral humoral response targeting SARS-CoV-2 antigens beyond the spike protein
Authors: DiMuzio Jillian M. , Heimbach Baron C. , Howanski Raymond J. , Dowling John P. , Patel Nirja B. , Henriquez Noeleya , Nicolescu Chris , Nath Mitchell , Polley Antonio , Bingaman Jamie L. , Smith Todd , Harman Benjamin C. , Robinson Matthew K. , Morin Michael J. , Nikitin Pavel A. 
Published: January 2021

AbstractPatients who recover from SARS-CoV-2 infections produce antibodies and antigen-specific T cells against multiple viral proteins. Here, an unbiased interrogation of the anti-viral memory B cell repertoire of convalescent patients has been performed by generating large, stable hybridoma libraries and screening thousands of monoclonal antibodies to identify specific, high-affinity immunoglobulins (Igs) directed at distinct viral components. As expected, a significant number of antibodies were directed at the Spike (S) protein, a majority of which recognized the full-length protein. These full-length Spike specific antibodies included a group of somatically hypermutated IgMs. Further, all but one of the six COVID-19 convalescent patients produced class-switched antibodies to a soluble form of the receptor-binding domain (RBD) of S protein. Functional properties of anti-Spike antibodies were confirmed in a pseudovirus neutralization assay. Importantly, more than half of all of the antibodies generated were directed at non-S viral proteins, including structural nucleocapsid (N) and membrane (M) proteins, as well as auxiliary open reading frame-encoded (ORF) proteins. The antibodies were generally characterized as having variable levels of somatic hypermutations (SHM) in all Ig classes and sub-types, and a diversity of VLand VHgene usage. These findings demonstrated that an unbiased, function-based approach towards interrogating the COVID-19 patient memory B cell response may have distinct advantages relative to genomics-based approaches when identifying highly effective anti-viral antibodies directed at SARS-CoV-2.
Low-cost, scalable, and automated fluid sampling for fluidics applications
Authors: Booeshaghi A. Sina , Kil Yeokyoung (Anne) , (Joseph) Min Kyung Hoi , Gehring Jase , Pachter Lior 
Published: January 2021

AbstractWe present colosseum, a low-cost, modular, and automated fluid sampling device for scalable fluidic applications. The colosseum fraction collector uses a single motor, can be built for less than $100 using off-the-shelf and 3D-printed components, and can be assembled in less than an hour. Build Instructions and source files are available athttps://github.com/pachterlab/colosseum.
Thermal laser ablation with tunable lesion size reveals multiple origins of seizure-like convulsions inCaenorhabditis elegans
Authors: Fouad Anthony D. , Liu Alice , Du Angelica , Bhirgoo Priya D. , Fang-Yen Christopher 
Published: January 2021

AbstractLaser microsurgery has long been an important means of assessing the functions of specific cells and tissues. Most laser ablation systems use short, highly focused laser pulses to create plasma-mediated lesions with dimensions on the order of the wavelength of light. While the small size of the lesion enables ablation with high spatial resolution, it also makes it difficult to ablate larger structures. We developed an infrared laser ablation system capable of thermally lesioning tissues with spot sizes tunable by the duration and amplitude of laser pulses. We used our laser system in the roundwormC. elegansto kill single neurons and to sever the dorsal and ventral nerve cords, structures that are difficult to lesion using a plasma-based ablation system. We used these ablations to investigate the source of convulsions in a gain-of-function mutant for the acetylcholine receptor ACR-2. Severing the ventral nerve cord caused convulsions to occur independently anterior and posterior to the lesion, suggesting that convulsions can arise independently from distinct subsets of the motor circuit.
Genome-scale metabolic modeling reveals SARS-CoV-2-induced metabolic changes and antiviral targets
Authors: Cheng Kuoyuan , Martin-Sancho Laura , Pal Lipika R. , Pu Yuan , Riva Laura , Yin Xin , Sinha Sanju , Nair Nishanth Ulhas , Chanda Sumit K. , Ruppin Eytan 
Published: January 2021

AbstractTremendous progress has been made to control the COVID-19 pandemic caused by the SARS-CoV-2 virus. However, effective therapeutic options are still rare. Drug repurposing and combination represent practical strategies to address this urgent unmet medical need. Viruses, including coronaviruses, are known to hijack host metabolism to facilitate viral proliferation, making targeting host metabolism a promising antiviral approach. Here, we describe an integrated analysis of 12 publishedin vitroand human patient gene expression datasets on SARS-CoV-2 infection using genome-scale metabolic modeling (GEM), revealing complicated host metabolism reprogramming during SARS-CoV-2 infection. We next applied the GEM-based metabolic transformation algorithm to predict anti-SARS-CoV-2 targets that counteract the virus-induced metabolic changes. We successfully validated these targets using published drug and genetic screen data and by performing an siRNA assay in Caco-2 cells. Further generating and analyzing RNA-sequencing data of remdesivir-treated Vero E6 cell samples, we predicted metabolic targets acting in combination with remdesivir, an approved anti-SARS-CoV-2 drug. Our study provides clinical data-supported candidate anti-SARS-CoV-2 targets for future evaluation, demonstrating host metabolism-targeting as a promising antiviral strategy.
N-terminally truncated helper NLRNRG1Cantagonizes immunity mediated by its full-length neighborsNRG1AandNRG1B
Authors: Wu Zhongshou , Tian Lei , Li Xin 
Published: January 2021

AbstractBoth animals and plants utilize nucleotide-binding leucine-rich repeat immune receptors (NLRs) to perceive the presence of pathogen-derived molecules and induce immune responses.NLRgenes are far more abundant and diverse in higher plants. Interestingly, truncated NLRs, which lack one or more of the canonical domains, are also commonly encoded in plant genomes. However, little is known about their functions, especially regarding the N-terminally truncated ones. Here, we show thatArabidopsis thaliana(A. thaliana) N-terminally truncated helper NLR geneNRG1C(N REQUIREMENT GENE 1) is highly induced upon pathogen infection and in autoimmune mutants. The immune response and cell death conferred by some TIR (Toll/interleukin-1 receptor)-type NLRs (TNLs) are compromised in theNRG1Coverexpression lines. Detailed genetic analysis revealed that NRG1C antagonizes the immunity mediated by its full-length neighborsNRG1AandNRG1B. Biochemical tests indicate that NRG1C possibly interferes with the EDS1-SAG101 complex, which likely signals together with NRG1A/1B. Interestingly, Brassicaceae NRG1Cs are functionally exchangeable, and theNicotiana benthamiana(N. benthamiana) N-terminally truncated helper NLR NRG2 antagonizes NRG1 in tobacco. Together, our study uncovers an unexpected negative role of N-terminally truncated helper NLRs in different plants.
Pipeline for generating stable large genomic deletions in zebrafish, from small domains to whole gene excisions
Authors: Tromp Alisha , Robinson Kate , Hall Thomas E. , Mowry Bryan , Giacomotto Jean 
Published: January 2021

ABSTRACTHere we describe a short feasibility study and methodological framework for the production of stable, CRISPR/Cas9-based, large genomic deletions in zebrafish, ranging from several base pairs (bp) to hundreds of kilobases (kb). Using a cocktail of four sgRNAs targeting a single genomic region mixed with a marker-sgRNA against the pigmentation genetyrosinase(tyr), we demonstrate that one can easily and accurately excise genomic regions such as promoters, protein domains, specific exons or whole genes. We exemplify this technique with a complex gene family, neurexins, composed of three duplicated genes with multiple promoters and intricate splicing processes leading to thousands of isoforms. We precisely deleted small regions such as their transmembrane domains (150bp deletion in average) to their entire genomic locus (300kb deletion fornrxn1Afor instance). We find that both the concentration and ratio of Cas9/sgRNAs are critical for the successful generation of these large deletions and, interestingly, that their transmission frequency does not decrease with increasing distance between sgRNA target sites. Considering the growing reports and debate about genetically compensated small indel mutants, the use of large-deletion approaches is likely to be widely adopted in studies of gene function. This strategy will also be key to the study of non-coding genomic regions.
Phage Cocktails can Prevent the Evolution of Phage-ResistantEnterococcus
Authors: Wandro Stephen , Ghatbale Pooja , Attai Hedieh , Hendrickson Clark , Samillano Cyril , Suh Joy , Pride David T. , Whiteson Katrine 
Published: January 2021

ABSTRACTAntibiotic resistantEnterococcusinfections are a major health crisis that requires the development of alternative therapies. Phage therapy could be an alternative to antibiotics and has shown promise inin vitroand in early clinical studies. Phage therapy is often deployed as a cocktail of phages, but there is little understanding of how to most effectively combine phages. Here we utilized a collection of 20Enterococcusphages to test principles of phage cocktail design and determine the phenotypic effects of evolving phage resistance inEnterococcusisolates that were susceptible or resistant to antibiotics (e.g., Vancomycin Resistant Enterococcus (VRE)). We tested the ability of each phage to clearEnterococcushost cultures and prevent the emergence of phage resistantEnterococcus. We found that some phages which were ineffective individually were effective at clearing the bacterial culture when used in cocktails. To understand the dynamics within phage cocktails, we used qPCR to track which phages increased in abundance in each cocktail, and saw dynamics ranging from one dominant phage to even phage growth. Further, we isolated several phage-resistant mutants to test for altered Vancomycin sensitivity. We found that mutants tended to have no change or slightly increased resistance to Vancomycin. By demonstrating the efficacy of phage cocktails in suppressing growth of antibiotic susceptible and VRE clinical isolates when exposed to phages, this work will help to inform cocktail design for future phage therapy applications.IMPORTANCEAntibiotic resistantEnterococcusinfections are a major health crisis that requires the development of alternative therapies. Phage therapy could be an alternative to antibiotics and has shown promise inin vitroand in early clinical studies. Phage therapy in the form of cocktails is often suggested, with similar goals as the combination therapy that has been successful in the treatment of HIV infection, but there is little understanding about how to combine phages most effectively. Here we utilized a collection of 20Enterococcusphages to test whether several phage cocktails could prevent the host from evolving resistance to therapy and to determine whether evolving resistance to phages affected host susceptibility to antibiotics. We showed that cocktails of two or three unrelated phages often prevented the growth of phage-resistant mutants, when the same phages applied individually were not able to.
Diminished miRNA activity is associated with aberrant cytoplasmic intron retention in ALS pathogenesis
Authors: Petric-Howe Marija , Crerar Hamish , Neeves Jacob , Tyzack Giulia E. , Patani Rickie , Luisier Raphaëlle 
Published: January 2021

SUMMARYIntron retention (IR) is now recognized as a dominant splicing event during motor neuron (MN) development, however the role and regulation of intron-retaining transcripts (IRTs) localized to the cytoplasm remain particularly understudied. By resolving the spatiotemporal dynamics of IR underlying distinct stages of MN lineage restriction, we identify a cytoplasmic group of IRTs that is not associated with reduced expression of their own genes but instead with an upregulation of predicted target genes of specific miRNAs, the motifs of which are enriched within the intronic sequences of this group. Next, we show that ALS-causing VCP mutations lead to a selective increase in IR of this particular class of introns. This in turn temporally coincides with an increase in the expression level of predicted target genes of these miRNAs, providing a potential mechanistic insight into ALS pathogenesis. Altogether, we propose a novel role for the cytoplasmic intronic sequences in regulating miRNA activity through miRNA sequestration, which potentially contributes to ALS pathogenesis.
Vasopressin V2 is a promiscuous G protein-coupled receptor that is biased by its peptide ligands
Authors: Heydenreich Franziska M. , Plouffe Bianca , Rizk Aurélien , Milić Dalibor , Zhou Joris , Breton Billy , Le Gouill Christian , Inoue Asuka , Bouvier Michel , Veprintsev Dmitry B. 
Published: January 2021

AbstractActivation of the G protein-coupled receptors by agonists may result in the activation of one or more G proteins, and in the recruitment of arrestins. The balance of activation of different pathways can be influenced by the ligand. Using BRET-based biosensors, we showed that the vasopressin V2 receptor activates or at least engages many different G proteins across all G protein subfamilies in response to its native agonist arginine vasopressin (AVP). This includes members of the Gi/o and G12/13 families that have not been previously reported. These signalling pathways are also activated by the synthetic peptide desmopressin and natural homologs of AVP, namely oxytocin and the non-mammalian hormone vasotocin. They demonstrated varying degrees of functional selectivity relative to AVP, as quantified using the operational model for quantifying ligand bias. Additionally, we modelled G protein activation as a Michaelis-Menten reaction. This approach provided a complementary way to quantify signalling bias, with an added benefit of clear separation of the effects of ligand affinity from the intrinsic activity of the receptor. These results showed that V2 receptor is not only promiscuous in its ability to engage several G proteins, but also that its signalling profile could be easily biased by small structural changes in the ligand.
IL-6 blockade suppresses the blood-brain barrier disorder, leading to prevention of onset of NMOSD
Authors: Takeshita Yukio , Fujikawa Susumu , Serizawa Kenichi , Fujisawa Miwako , Matsuo Kinya , Nemoto Joe , Shimizu Fumitaka , Sano Yasuteru , Tomizawa-Shinohara Haruna , Miyake Shota , Ransohoff Richard M. , Kanda Takashi 
Published: January 2021

AbstractNeuromyelitis optica spectrum disorder (NMOSD) is an autoimmune astrocytopathy caused by antibodies against the aquaporin 4(AQP4) in end-feet of astrocytes. Breakdown of the blood–brain barrier (BBB) allowing ingress of AQP4 antibodies into the central nervous system (CNS) plays a key role in NMOSD. Although IL-6 blockade therapies such as satralizumab are effective in NMOSD, the therapeutic mechanism of IL-6 blockade, especially with respect to BBB disruption, are not fully understood because of the lack of the human models that are specialized to evaluate the BBB function.We constructed new in vitro human BBB models for evaluating continued barrier function, leukocyte transmigration and intracerebral transferability of IgGs utilizing the newly established triple co-culture system. In vitro and vivo experiments revealed that NMO-IgG increased intracerebral transferability of satralizumab, and that satralizumab suppressed the NMO-IgG-induced transmigration of T cells and barrier dysfunction. These results suggest that satralizumab, which can pass through the BBB in the presence of NMO-IgG, suppresses the barrier dysfunction and the disrupting controlled cellular infiltration at the BBB, leading to prevention of onset of NMOSD.One sentence summarySatralizumab and IL-6 blockade prevent lymphocyte migration and barrier dysfunction induced by NMO-IgG in EAE and novel triple co-culture BBB models.
Structural insights into a novel family of integral membrane siderophore reductases
Authors: Josts Inokentijs , Veith Katharina , Normant Vincent , Schalk Isabelle J. , Tidow Henning 
Published: January 2021

AbstractGram-negative bacteria take up the essential ion Fe3+as ferric-siderophore complexes through their outer membrane using TonB-dependent transporters. However, the subsequent route through the inner membrane differs across many bacterial species and siderophore chemistries and is not understood in detail. Here, we report the crystal structure of the inner membrane protein FoxB (fromP. aeruginosa) that is involved in Fe-siderophore uptake. The structure revealed a novel fold with two tightly-bound heme molecules. In combination with functional studies these results establish FoxB as an inner membrane reductase involved in the release of iron from ferrioxamine during Fe-siderophore uptake.
Interneuron activity-structural plasticity association is driven by context-dependent sensory experience
Authors: Saha Soham , Meng John Hongyu , Riecke Hermann , Agoranos Georgios , Sailor Kurt A. , Lledo Pierre-Marie 
Published: January 2021

AbstractNeuronal dendritic spine dynamics provide a plasticity mechanism for altering brain circuit connectivity to integrate new information for learning and memory. Previousin vivostudies in the olfactory bulb (OB) showed that regional increases in activity caused localized spine stability, at a population level, yet how activity affects spine dynamics at an individual neuron level remains unknown. In this study, we trackedin vivothe correlation between an individual neuron’s activity and its dendritic spine dynamics of OB granule cell (GC) interneurons. Odor experience caused a consistent correlation between individual GC activity and spine stability. Dissecting the components of the OB circuit showed that increased principal cell (MC) activity was sufficient to drive this correlation, whereas cell-autonomously driven GC activity had no effect. A mathematical model was able to replicate the GC activity-spine stability correlation and showed MC output having improved odor discriminability while retaining odor memory. These results reveal that GC spine plasticity provides a sufficient network mechanism to decorrelate odors and maintain a memory trace.
Differential chemoarchitecture of Purkinje neurons contributes to intrinsic firing properties
Authors: Brandenburg Cheryl , Smith Lindsey A. , Kilander Michaela B.C. , Bridi Morgan S. , Lin Yu-Chih , Huang Shiyong , Blatt Gene J. 
Published: January 2021

SummaryPurkinje cells (PCs) are central to cerebellar information coding and appreciation for the diversity of their firing patterns and molecular profiles is growing. Heterogeneous subpopulations of PCs have been identified that display differences in intrinsic firing properties without clear mechanistic insight into what underlies the divergence in firing parameters. Although long used as a general PC marker, we report that the calcium binding protein parvalbumin labels a subpopulation of PCs with a conserved distribution pattern across the animals examined. We trained a convolutional neural network to recognize the parvalbumin-positive subtype and create maps of whole cerebellar distribution and find that PCs within these areas have differences in spontaneous firing that can be modified by altering calcium buffer content. These subtypes also show differential responses to potassium and calcium channel blockade, suggesting a mechanistic role for variability in PC intrinsic firing through differences in ion channel composition. It is proposed that ion channels drive the diversity in PC intrinsic firing phenotype and parvalbumin calcium buffering provides capacity for the highest firing rates observed. These findings open new avenues for detailed classification of PC subtypes.
The crystal structure of Cu2GeSe3 and the structure-types of the I2-IV-VI3 family of semiconducting compounds
Authors: Dugarte-Dugarte Analio , Ramírez Pineda Nahum , Nieves Luis , Henao José Antonio , Díaz de Delgado Graciela , Delgado José Miguel 
Published: January 2021

Almost 50 years after the initial report, the crystal structure of Cu2GeSe3, a I2-IV-VI3 semiconductor, has been revised using modern single-crystal X-ray diffraction data. The structure of this material can be properly described in the monoclinic space group Cc (No. 9) with unit-cell parameters a = 6.7703 (4) Å, b = 11.8624 (5) Å, c = 6.7705 (4) Å, β = 108.512 (6)°, V = 515.62 (5) Å3, Z = 4, rather than in the orthorhombic space group Imm2 (No. 44) with unit-cell parameters a = 11.860 (3), b = 3.960 (1), c = 5.485 (2) Å, V = 257.61 Å3, Z = 2, as originally proposed [Parthé & Garín (1971). Monatsh. Chem.
102, 1197–1208]. Contrary to what was observed in the orthorhombic structure, the distortions of the tetrahedra in the monoclinic structure are consistent with the distortions expected from considerations derived from the bond valence model. A brief revision of the structures reported for the I2-IV-VI3 family of semiconducting compounds (I: Cu, Ag; IV: Si, Ge, Sn; and VI: S, Se, Te) is also presented.
The income elasticity of import demand: A meta‐survey
Authors: El‐Shagi Makram , Sawyer William C. , Tochkov Kiril 
Published: January 2021

AbstractImport demand has been a major research topic in international economics for the past 80 years because of its importance for analyzing trade and evaluating trade policies. The goal of this paper is to survey the literature and conduct a meta‐analysis of empirical studies on import demand with the intention of clarifying the effect of economic development on income elasticity. In particular, we test the hypothesis that higher income levels are associated with a more elastic import demand. We apply a combination of parametric and non‐parametric methods on estimates from a sample of 152 papers published over the period 1975–2014 and find that this relationship is significant and robust. Specifically, kernel densities of income elasticity estimates for high‐income countries in North America and Europe are shown to exceed those for poorer parts of the world. The results from quantile regressions confirm this pattern and establish its robustness when controlling for the effect of model specifications.