bluuebunny/crossref_metadata_2025_split huggingface dataset:
The SweDen risk score- predicting death 1-year after myocardial infarction
Authors: Rylance Rebecca T. , Wagner Philippe , Olesen Kevin K. W. , Carlson Jonas , Alfredsson Joakim , Jernberg Tomas , Leosdottir Margret , Johansson Pelle , Vasko Peter , Maeng Michael , Mohammad Moman A. , Erlinge David 
Published: September 2022

AbstractObjectivesOur aim was to derive, based on the SWEDEHEART registry, and validate, using the Western Denmark Heart registry, a patient-oriented risk score, the SweDen score, which could calculate the risk of 1-year mortality following a myocardial infarction (MI).MethodsThe factors included in the SweDen score were age, sex, smoking, diabetes, heart failure, and statin use. These were chosen a priori by the SWEDEHEART steering group based on the premise that the factors were information known by the patients themselves. The score was evaluated using various statistical methods such as time-dependent receiver operating characteristics curves of the linear predictor, area under the curve metrics, Kaplan-Meier survivor curves, and the calibration slope.ResultsThe area under the curve values were 0.81 in the derivation data and 0.76 in the validation data. The Kaplan-Meier curves showed similar patient profiles across datasets. The calibration slope was 1.03 (95% CI 0.99-1.08) in the validation data using the linear predictor from the derivation data.ConclusionsThe SweDen risk score is a novel tool created for patient use. The risk score calculator will be available online and presents mortality risk on a colour scale to simplify interpretation and to avoid exact life span expectancies. It provides a validated patient-oriented risk score predicting the risk of death at 1 year after suffering a MI, which visualizes the benefit of statin use and smoking cessation in a simple way.
Identification of tubulin polymerization inhibitors with a CRISPR-edited cell line with endogenous fluorescent tagging of β-tubulin and Histone 1
Authors: Khachatryan Harutyun , Barrero Carlos A. , Gordon John , Olszowy Bartlomiej , Perez-Leal Oscar 
Published: September 2022

AbstractTubulin is an essential protein to maintain the cellular structure and for the cell division process. Inhibiting tubulin polymerization has proven to be an effective method for slowing cancer cell growth. Traditionally, identifying tubulin polymerization inhibitors involved using pure tubulin for in vitro assays or procedures using cells that require cell fixing and anti-tubulin antibody staining. This study explores using a cell line developed via CRISPR genome editing as a cell model to identify tubulin polymerization inhibitors with live cells without using exogenous staining. The cell line has endogenous tagging with fluorescent proteins of β-tubulin and a nuclear protein to facilitate image cellular segmentation by high-content imaging analysis (HCI). The cells were treated with known tubulin polymerization inhibitors, colchicine and vincristine, and the presence of phenotypic changes that indicate tubulin polymerization inhibition were confirmed via HCI. A library of 429 kinase inhibitors was screened to discover tubulin polymerization inhibitors and three compounds that inhibit tubulin polymerization were found (ON-01910, HMN-214, and KX2-391). Live cell tracking analysis confirms that depolymerization of tubulin occurs rapidly after compound treatments. These results suggest that CRISPR-edited cells with fluorescent endogenous tagging of β-tubulin can be used to screen larger compound libraries containing diverse chemical families to identify novel tubulin polymerization inhibitors.
Deficits in cerebellum-dependent learning and cerebellar morphology in male and female BTBR autism model mice
Authors: Kiffmeyer Elizabeth A. , Cosgrove Jameson A. , Siganos Jenna K. , Bien Heidi E. , Vipond Jade E. , Vogt Karisa R. , Kloth Alexander D. 
Published: September 2022

AbstractRecently, there has been increased interest in the role of the cerebellum in autism spectrum disorders (ASD). In order to better understand the pathophysiological role of the cerebellum in ASD, it is necessary to have a variety of mouse models that have face validity for cerebellar disruption in humans. Here, we add to the literature on the cerebellum transgenic and induced mouse models of autism with the characterization of the cerebellum in the BTBR T+Itpr3tf/J (BTBR) inbred mouse strain, which has behavioral phenotypes that are suggestive of ASD in patients. When we examined both male and female adult BTBR mice in comparison to C57BL/6J (C57) controls, we noted that both mice showed motor coordination deficits characteristic of cerebellar function, but only the male mice showed differences in delay eyeblink conditioning, a cerebellum-dependent learning task that is also disrupted in ASD patients. Both male and female BTBR mice showed considerable expansion of and abnormal foliation in the cerebellum vermis--including significant expansion of specific lobules in the anterior cerebellum. In addition, we found a slight but significant decrease in Purkinje cell density in both male and female BTBR mice, irrespective of lobule. Furthermore, there was a marked reduction of Purkinje cell dendritic spines density in both male and female BTBR mice. These findings suggest that, for the most part, the BTBR mouse model successfully phenocopies many of the characteristics of the subpopulation of ASD patients that have a hypertrophic cerebellum. We discuss the significance of sex differences--revealed for the first time in BTBR mice, and present in only a small number of cerebellum studies--and the importance of concordance on other metrics between male and female BTBR mice.Graphical AbstractSummary of differences between BTBR mice (left) and C57 mice (right) demonstrated by this study, separated by sex.
Central metabolism is a key player in E. coli biofilm stimulation by sub-MIC antibiotics
Authors: Yaeger Luke N. , French Shawn , Brown Eric D. , Côté Jean Philippe , Burrows Lori L. 
Published: September 2022

AbstractExposure of Escherichia coli to sub-inhibitory antibiotics stimulates biofilm formation through poorly characterized mechanisms. Using a high-throughput Congo Red binding assay to report on biofilm matrix production, we screened ∼4000 E. coli K12 deletion mutants for deficiencies in this biofilm stimulation response. Mutants lacking acnA, nuoE, or lpdA failed to respond to sub-MIC novobiocin, implicating central metabolism and aerobic respiration in biofilm stimulation. These genes are members of the ArcA/B regulon – controlled by a respiration-sensitive two-component system. Mutants of arcA and arcB had a ‘pre-activated’ phenotype, where biofilm formation was already high relative to wild type in vehicle control conditions and failed to increase further with the addition of sub-MIC antibiotics. Supporting a role for respiratory stress, the biofilm stimulation response was inhibited when nitrate was provided as an alternative electron acceptor. Deletion of genes encoding the nitrate respiratory machinery abolished its effects, and nitrate respiration increased during growth with sub-MIC antibiotics. In probing the generalizability of biofilm stimulation, we found that the stimulation response to translation inhibitors was minimally affected by nitrate supplementation. Finally, using a metabolism-sensitive dye, we showed spatial co-localization of increased respiration with sub-MIC bactericidal antibiotics. By characterizing the biofilm stimulation response to sub-MIC antibiotics at a systems level, we identified multiple avenues for design of therapeutics that impair bacterial stress management.
Novel lipid biomarkers for algal resistance to viral infection in the ocean
Authors: Schleyer Guy , Kuhlisch Constanze , Ziv Carmit , Ben-Dor Shifra , Malitsky Sergey , Schatz Daniella , Vardi Assaf 
Published: September 2022

AbstractMarine viruses play a key role in regulating phytoplankton populations, greatly affecting the biogeochemical cycling of major nutrients in the ocean. Resistance to viral infection has been reported for various phytoplankton species under laboratory conditions. Nevertheless, the occurrence of resistant cells in natural populations is underexplored due to the lack of sensitive tools to detect these rare phenotypes. Consequently, our current understanding of the ecological importance of resistance and its underlying mechanisms is limited. Here, we sought to discover lipid biomarkers for the resistance of the bloom-forming alga Emiliania huxleyi to its specific virus, E. huxleyi virus (EhV). We identified novel glycosphingolipids (GSLs) that characterize resistant E. huxleyi strains by applying an untargeted lipidomics approach. Further, we detected these lipid biomarkers in E. huxleyi isolates that were recently collected from E. huxleyi blooms and used them to detect resistant cells in the demise phase of an open ocean E. huxleyi bloom. Lastly, we show that the GSL composition of E. huxleyi cultures that recover following infection and gain resistance to the virus resembles that of resistant strains. These findings highlight the metabolic plasticity and co-evolution of the GSL biosynthetic pathway and underscore its central part in this host-virus arms race.
The SARS-CoV-2 spike N-terminal domain engages 9-O-acetylated α2-8-linked sialic acids
Authors: Tomris Ilhan , Unione Luca , Nguyen Linh , Zaree Pouya , Bouwman Kim M. , Liu Lin , Li Zeshi , Fok Jelle A. , Ríos Carrasco María , van der Woude Roosmarijn , Kimpel Anne L.M. , Linthorst Mirte W. , Verpalen Enrico C.J.M , Caniels Tom G. , Sanders Rogier W. , Heesters Balthasar A. , Pieters Roland J. , Jiménez-Barbero Jesús , Klassen John S. , Boons Geert-Jan , de Vries Robert P. 
Published: September 2022

AbstractSARS-CoV-2 viruses engage ACE2 as a functional receptor with their spike protein. The S1 domain of the spike protein contains a C-terminal receptor-binding domain (RBD) and an N-terminal domain (NTD). The NTD of other coronaviruses includes a glycan-binding cleft. However, for the SARS-CoV-2 NTD protein-glycan binding was only observed weakly for sialic acids with highly sensitive methods. Amino acid changes in the NTD of Variants of Concern (VoC) shows antigenic pressure, which can be an indication of NTD-mediated receptor binding. Trimeric NTD proteins of SARS-CoV-2, Alpha, Beta, Delta, and Omicron did not reveal a receptor binding capability. Unexpectedly, the SARS-CoV-2 Beta subvariant strain (501Y.V2-1) NTD binding to Vero E6 cells was sensitive to sialidase pretreatment. Glycan microarray analyses identified a putative 9-O-acetylated sialic acid as a ligand, which was confirmed by catch-and-release ESI-MS, STD-NMR analyses, and a graphene-based electrochemical sensor. The Beta (501Y.V2-1) variant attained an enhanced glycan binding modality in the NTD with specificity towards 9-O-acetylated structures, suggesting a dual-receptor functionality of the SARS-CoV-2 S1 domain, which was quickly selected against. These results indicate that SARS-CoV-2 can probe additional evolutionary space, allowing binding to glycan receptors on the surface of target cells.Graphical abstractSynopsisCoronaviruses utilize their N-terminal domain (NTD) for initial reversible low-affinity interaction to (sialylated) glycans. This initial low-affinity/high-avidity engagement enables viral surfing on the target membrane, potentially followed by a stronger secondary receptor interaction. Several coronaviruses, such as HKU1 and OC43, possess a hemagglutinin-esterase for viral release after sialic acid interaction, thus allowing viral dissemination. Other coronaviruses, such as MERS-CoV, do not possess a hemagglutinin-esterase, but interact reversibly to sialic acids allowing for viral surfing and dissemination. The early 501Y.V2-1 subvariant of the Beta SARS-CoV-2 Variant of Concern has attained a receptor-binding functionality towards 9-O-acetylated sialic acid using its NTD. This binding functionality was selected against rapidly, most likely due to poor dissemination. Ablation of sialic acid binding in more recent SARS-CoV-2 Variants of Concern suggests a fine balance of sialic acid interaction of SARS-CoV-2 is required for infection and/or transmission.
Molecular elucidation of drug-induced abnormal assemblies of the Hepatitis B Virus capsid protein by solid-state NMR
Authors: Lecoq Lauriane , Brigandat Louis , Huber Rebecca , Fogeron Marie-Laure , Callon Morgane , Malär Alexander , Wang Shishan , Dujardin Marie , Briday Mathilde , Wiegand Thomas , Durantel David , Burdette Dara , Berke Jan Martin , Meier Beat H. , Nassal Michael , Böckmann Anja 
Published: September 2022

AbstractHepatitis B virus (HBV) capsid assembly modulators (CAMs) represent a new class of anti-HBV antivirals. CAMs disturb proper nucleocapsid assembly, by inducing formation of either aberrant assemblies (CAM-A) or of apparently normal but genome-less empty capsids (CAM-E). Classical structural approaches have revealed the CAM binding sites on the capsid protein (Cp), but conformational information on the CAM-induced off-path aberrant assemblies is lacking. We show that solid-state NMR can provide such information, including for wild-type full-length Cp183, and we find that in these assemblies, the asymmetric unit comprises a single Cp molecule rather than the four quasi-equivalent conformers typical for the icosahedral T=4 symmetry of the normal HBV capsids. Furthermore, while in contrast to truncated Cp149, full-length Cp183 assemblies appear, on the mesoscopic level, unaffected by CAM-A, NMR reveals that on the molecular level, Cp183 assemblies are equally aberrant. Finally, we use a eukaryotic cell-free system to reveal how CAMs modulate capsid-RNA interactions and capsid phosphorylation. Our results establish a structural view on assembly modulation of the HBV capsid, and they provide a rationale for recently observed differences between in-cell versus in vitro capsid assembly modulation.
pWCP is a widely distributed and highly conserved Wolbachia plasmid in Culex mosquitoes worldwide
Authors: Ghousein Amani , Tutagata Jordan , Etienne Manuel , Chaumeau Victor , Boyer Sebastien , Pages Nonito , Roiz David , Eren A. Murat , Cambray Guillaume , Reveillaud Julie 
Published: September 2022

AbstractMosquitoes represent the most important pathogen vectors and are responsible for the spread of a wide variety of poorly treatable diseases. Wolbachia are obligate intracellular bacteria that are widely distributed among arthropods and collectively represents one of the most promising solutions for vector control. In particular, Wolbachia has been shown to limit the transmission of pathogens, and to dramatically affect the reproductive behavior of their host through its phage WO. While much research has focused on deciphering and exploring the biocontrol applications of these WO-related phenotypes, the extent and potential impact of the Wolbachia mobilome remain poorly appreciated. Notably, several Wolbachia plasmids, carrying WO-like genes and Insertion Sequences (IS), thus possibly interrelated to other genetic units of the endosymbiont, have been recently discovered. Here we investigated the diversity and biogeography of the first described plasmid of Wolbachia in Culex pipiens (pWCP) in several islands and continental countries around the world—including Cambodia, Guadeloupe, Martinique, Thailand, and Mexico—together with mosquito strains from colonies that evolved for 2 to 30 years in the laboratory. Together with earlier observation, our results show that pWCP is omnipresent and strikingly conserved among Wolbachia populations within mosquitoes from distant geographies and environmental conditions. These data suggest a critical role for the plasmid in Wolbachia ecology and evolution, and the potential of a great tool for the further genetic dissection or potential manipulation of the endosymbiont.
Capillary electrophoresis mass spectrometry identifies new isomers of inositol pyrophosphates in mammalian tissues
Authors: Qiu Danye , Gu Chunfang , Liu Guizhen , Ritter Kevin , Eisenbeis Verena B. , Bittner Tamara , Gruzdev Artiom , Seidel Lea , Bengsch Bertram , Shears Stephen B. , Jessen Henning J. 
Published: September 2022

AbstractTechnical challenges have to date prevented a complete profiling of the levels of myo-inositol phosphates (InsPs) and pyrophosphates (PP-InsPs) in mammalian tissues. Here, we have deployed capillary electrophoresis mass spectrometry to identify and record the levels of InsPs and PP-InsPs in several tissues obtained from wild type mice and a newly-created PPIP5K2 knockout strain. We observe that the mouse colon harbours unusually high levels of InsPs and PP-InsPs. Additionally, the PP-InsP profile is considerably more complex than previously reported for animal cells: using chemically synthesized internal stable isotope references, and high-resolution mass spectra, we characterize two new PP-InsP isomers as 4/6-PP-InsP5and 2-PP-InsP5. The latter has not previously been described in Nature. Analysis of feces and the commercial mouse diet suggest the latter is one potential source of noncanonical isomers in the colon. However, we also identify both molecules in the heart, indicating unknown synthesis pathways in mammals. We also demonstrate that the CE-MS method is sensitive enough to measure PP-InsPs from patient samples such as colon biopsies and peripheral blood mononuclear cells (PBMCs). Strikingly, PBMCs also contain 4/6-PP-InsP5and 2-PP-InsP5. In summary, our study substantially expands PP-InsP biology in mammals.
Cryo-EM reveals the membrane binding phenomenon of EspB, a virulence factor of the Mycobacterial Type VII secretion system
Authors: Sengupta Nayanika , P. Surekha , Dutta Somnath 
Published: September 2022

ABSTRACTMycobacterium tuberculosis utilizes sophisticated machinery called the type VII secretion system to translocate virulence factors across its complex lipid membrane. ESX-1 is one of the essential and well-studied secretion systems which transport various virulence factors, including EspB. EspB, a ~36 kDa secreted substrate, has been implicated to play vital role in protecting the bacteria from hostile environment within the host cell phagosome. It is also involved in bacterial pathogenesis and has been shown to bind phospholipids. Recently, two cryo-EM structures of EspB full-length and the secreted isoforms were resolved. Despite the availability of multiple high-resolution structures of EspB, the physiological relevance and mechanism of virulence of this secreted substrate remains poorly characterized. In this current work, we implemented cryo-EM-based structural studies, including various functional assays, TEM imaging, and biophysical approach to demonstrate the interaction of EspB with lipids and bio-membrane. Our findings also indicated that EspB may play a crucial role in binding to and rupturing host mitochondrial membrane. Through cryo-EM studies we were able to show the possible membrane-binding region of EspB. Our study sheds light on host-pathogen interactions and bacterial pathogenesis mediated by EspB.
Structure and Epitope of a Neutralizing Monoclonal Antibody that Targets the Stem Helix of β Coronaviruses
Authors: Deshpande Ashlesha , Schormann Nobert , Piepenbrink Mike S. , Sobrido Luis Martinez , Kobie James J. , Walter Mark R. 
Published: September 2022

AbstractMonoclonal antibodies (MAbs) that retain neutralizing activity against distinct coronavirus (CoV) lineages and variants of concern (VoC) must be developed to protect against future pandemics. These broadly neutralizing MAbs (BNMAbs) may be used as therapeutics and/or to assist in the rational design of vaccines that induce BNMAbs. 1249A8 is a BNMAb that targets the stem helix (SH) region of CoV spike (S) protein and neutralizes Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) original strain, delta, and omicron VoC, Severe Acute Respiratory Syndrome CoV (SARS-CoV) and Middle East Respiratory Syndrome CoV (MERS-CoV). To understand its mechanism of action, the crystal structure of 1249A8 bound to a MERS-CoV SH peptide was determined at 2.1Å resolution. BNMAb 1249A8 mimics the SARS-CoV-2 S loop residues 743-749, which interact with the C-terminal end of the SH helix in the S postfusion conformation. The crystal structure shows that BNMAb 1249A8 disrupts SH secondary structure and packing rearrangements required for CoV S to adopt its prefusion conformation that mediates membrane fusion and ultimately infection. The mechanisms regulating BNMAb 1249A8 CoV S specificity are also defined. This study provides novel insights into the neutralization mechanisms of SH-targeting CoV BNMAbs that may inform vaccine development and the design of optimal BNMAb therapeutics.
Microsecond melting and revitrification of cryo samples with a correlative light-electron microscopy approach
Authors: Bongiovanni Gabriele , Harder Oliver F. , Drabbels Marcel , Lorenz Ulrich J. 
Published: September 2022

AbstractWe have recently introduced a novel approach to time-resolved cryo-electron microscopy (cryo-EM) that affords microsecond time resolution. It involves melting a cryo sample with a laser beam to allow dynamics of the embedded particles to occur. Once the laser beam is switched off, the sample revitrifies within just a few microseconds, trapping the particles in their transient configurations, which can subsequently be imaged to obtain a snap shot of the dynamics at this point in time. While we have previously performed such experiments with a modified transmission electron microscope, we here demonstrate a simpler implementation that uses an optical microscope. We believe that this will make our technique more easily accessible and hope that it will encourage other groups to apply microsecond time-resolved cryo-EM to study the fast dynamics of a variety of proteins.
Systematic mutagenesis reveals critical effector functions in the assembly and dueling of the H1-T6SS inPseudomonas aeruginosa
Authors: Wu Li-Li , Pei Tong-Tong , Yan Shuangquan , Tang Ming-Xuan , Wu Li-Wen , Li Hao , Liang Xiaoye , Sun Shuyang , Dong Tao 
Published: September 2022

AbstractPseudomonas aeruginosais an important human pathogen that can cause severe wound and lung infections. It employs the type VI secretion system (H1-T6SS) as a molecular weapon to carry out a unique dueling response to deliver toxic effectors to neighboring sister cells or other microbes after sensing an external attack. However, the underlying mechanism for such dueling is not fully understood. Here, we examined the role of all H1-T6SS effectors and VgrG proteins in assembly and signal sensing by ectopic expression, combinatorial deletion and point mutations, and imaging analyses. Expression of effectors targeting the cell wall and membrane resulted in increased H1-T6SS assembly. Deletion of individual effector andvgrGgenes had minor- to-moderate effects on H1-T6SS assembly and dueling activities. The dueling response was detectable in theP. aeruginosamutant lacking all H1-T6SS effector activities. In addition, double deletions ofvgrG1awith eithervgrG1borvgrG1cand double deletions of effector genestse5andtse6severely reduced T6SS assembly and dueling activities, suggesting their critical role in T6SS assembly. Collectively, these data highlight the diverse roles of effectors in not only dictating antibacterial functions but also their differential contributions to the assembly of the complex H1-T6SS apparatus.