bluuebunny/crossref_metadata_2025_split huggingface dataset:
Common cardiac medications potently inhibit ACE2 binding to the SARS-CoV-2 Spike, and block virus penetration into human lung cells
Authors: Caohuy Hung , Eidelman Ofer , Chen Tinghua , Yang Qingfeng , Bera Alakesh , Walton Nathan , Pollard Harvey B. 
Published: June 2021

AbstractTo initiate SARS-CoV-2 infection, the Receptor Binding Domain (RBD) on the viral spike protein must first bind to the host receptor ACE2 protein on pulmonary and other ACE2-expressing cells. We hypothesized that cardiac glycoside drugs might block the binding reaction between ACE2 and the Spike (S) protein, and thus block viral penetration into target cells. To test this hypothesis we developed a biochemical assay for ACE2:Spike binding, and tested cardiac glycosides as inhibitors of binding. Here we report that ouabain, digitoxin, and digoxin are high-affinity competitive inhibitors of ACE2 binding to the Wuhan S1 and the European [E614G] S1 proteins. These drugs also inhibit ACE2 binding to the Wuhan RBD, as well as to RBD proteins containing the S. Africa [E484K], Mink [Y453F] and UK [N501Y] mutations. As hypothesized, we also found that ouabain and digitoxin blocked penetration by SARS-CoV-2 Spike-pseudotyped virus into human lung cells. These data indicate that cardiac glycosides may block viral penetration into the target cell by first inhibiting ACE2:Spike binding. Clinical concentrations of ouabain and digitoxin are relatively safe for short term use for subjects with normal hearts. It has therefore not escaped our attention that these common cardiac medications could be deployed worldwide as inexpensive repurposed drugs for anti-COVID-19 therapy.
Display of the self-sufficient CYP102A1 on the surface of E. coli-derived Outer Membrane Vesicles
Authors: Devriese Delphine , Surmont Pieter , Lynen Frederic , Devreese Bart 
Published: June 2021

AbstractThe cytochrome P450 (CYP) monooxygenase superfamily offers the unique ability to catalyze regio-and stereospecifical oxidation of a non-activated C-H bond. CYPs found applications in the synthesis of pharmaceuticals and drug metabolites as well as in bioremediation. They are typically used in whole-cell bioconversion processes, due to their low stability and the need for a redox partner and cofactor. Unfortunately, substrate uptake and/or product transport limitations are frequently encountered and side reactions occur due to other enzymes in the cellular environment. Here, we present a proof-of-principle of a novel cell-free cytochrome P-450 nanocatalyst based on surface display on bacterial outer membrane vesicles. The self-sufficient CYP 102A1 from Bacillus megaterium was engineered to be translocated on the outer membrane vesicles of Escherichia coli. The resulting vesicles can simply be isolated from the culture supernatant. Moreover, no expensive and elaborate enzyme purification is required. This approach shows great promise as an alternative strategy to recombinantly produce CYP enzymes for a variety of applications, such as in fine chemical production and in the development of biosensors.
A Method for Checking Recombinant Protein Quality to Troubleshoot for Discordant Immunoassays
Authors: Tran-Nguyen Thi K. 
Published: June 2021

AbstractDiscordant results of recombinant protein-based enzyme-linked immunosorbent assays (ELISA) and other antigen detection tests are a common and vexing problem in scientific research and clinical laboratories. The reproducibility of immunoassays based on antibody specificity can be adversely affected by cryptic changes in the composition of the analyte (e.g., the protein antigen). By use of sodium dodecyl sulfate-polyacrylamide gel electrophoresis and mass spectrometry analyses, we found varying levels of purity and the extent of post-translational modifications (PTMs), particularly of N-linked glycosylation and phosphorylation, among varied lots of recombinant glucose-regulated protein 78 (GRP78) expressed in Escherichia coli. We expect these lotto-lot variabilities of both purity and PTMs led to inconsistent results stemming from ELISA assays that measured GRP78 autoantibody levels in patient plasma specimens. We present these analyses to draw readers’ attention to a potentially common, yet seldom appreciated problem, in laboratory assays using recombinant proteins as antigens for antibody detection, and propose a workflow to detect and troubleshoot for this typical problem.
Gonadal sex patterns p21-induced cellular senescence in mouse and human glioblastoma
Authors: Broestl Lauren , Grandison Lucia , Shenoy Saraswati , Tallman Miranda M. , Rhee Gina , Yang Wei , Sponagel Jasmin , Kfoury-Beaumont Najla , Hill Cameron M. , Mao Diane D. , Kim Albert H. , Stewart Sheila A. , Venere Monica , Luo Jingqin , Rubin Joshua B. 
Published: June 2021

AbstractMales exhibit higher incidence and worse prognosis for the majority of cancers, including glioblastoma (GBM). Disparate survival may be related to sex-biased responses to treatment, including radiation. Using a mouse model of GBM, we show that female cells are more sensitive to radiation, and that senescence represents a major component of the radiation therapeutic response in both sexes. Correlation analyses revealed that the CDK inhibitor p21 and irradiation induced senescence were differentially regulated between male and female cells. Indeed, female cellular senescence was more sensitive to changes in p21 levels, a finding that was observed in both wildtype and transformed murine astrocytes and patient-derived GBM cell lines. Using a novel Four Core Genotypes model of GBM, we further show that sex differences in p21-induced senescence are patterned by gonadal sex. These data suggest that sex differences in p21 induced senescence contribute to the female survival advantage in GBM.
Bacillus velezensis stimulates resident rhizosphere Pseudomonas stutzeri for plant health through metabolic interactions
Authors: Sun Xinli , Xu Zhihui , Xie Jiyu , Thomsen Viktor H. , Tan Taimeng , Strube Mikael L. , Dragoš Anna , Shen Qirong , Zhang Ruifu , Kovács Ákos T. 
Published: June 2021

AbstractTrophic interactions play a central role in driving microbial community assembly and function. In gut or soil ecosystems, successful inoculants are always facilitated by efficient colonization, however, the metabolite exchanges between inoculants and resident bacteria are rarely studied, particularly in the rhizosphere. Here, we used bioinformatic, genetic, transcriptomic and metabonomic analyses to uncover syntrophic cooperation between inoculant (Bacillus velezensis SQR9) and plant-beneficial indigenous Pseudomonas stutzeri in the cucumber rhizosphere. We found that the synergistic interaction of these two species is highly environmental dependent, the emergence of syntrophic cooperation was only evident in a static nutrient-rich niche, such as pellicle biofilm in addition to the rhizosphere. Our results identified branched-chain amino acids (BCAAs) biosynthesis pathway involved in syntrophic cooperation when forming coculture biofilms. Assaying the metabolome further demonstrated metabolic facilitation among the bacterial strains. In addition, biofilm matrix components from Bacillus were essential for the interaction. Importantly, the two-species consortium promoted plant growth and helped plants alleviate salt stress. In summary, we propose a mechanism in which synergic interactions between a biocontrol bacterium and a partner species promote plant health.
Hypoxia Tolerance Declines with Age in the Absence of Methi-onine Sulfoxide Reductase (MSR) in Drosophila melanogaster
Authors: Suthakaran Nirthieca , Chandran Sanjana , Iacobelli Michael , Binninger David 
Published: June 2021

AbstractUnlike the mammalian brain, Drosophila melanogaster can tolerate several hours of hypoxia without any tissue injury by entering a protective coma known as spreading depression. However, when oxygen is reintroduced, there is an increased production of reactive oxygen species (ROS) that causes oxidative damage. Methionine sulfoxide reductase (MSR) acts to restore functionality to oxidized methionine residues. In the present study, we have characterized in vivo effects of MSR deficiency on hypoxia tolerance throughout the lifespan of Drosophila. Flies subjected to sudden hypoxia that lacked MSR activity exhibited a longer recovery time and a reduced ability to survive hypoxic stress as they approached senescence. However, when hypoxia was induced slowly, MSR deficient flies recovered significantly quicker throughout their entire adult lifespan. In addition, the wildtype and MSR deficient flies had nearly 100% survival rates throughout their lifespan. Neuro-protective signaling mediated by decreased apoptotic pathway activation, as well as gene reprogramming and metabolic downregulation are possible reasons for why MSR deficient flies have faster recovery time and a higher survival rate upon slow induction of spreading depression. Our data are the first to suggest important roles of MSR and longevity pathways in hypoxia tolerance exhibited by Drosophila.
Kinesin-binding protein remodels the kinesin motor to prevent microtubule-binding
Authors: Solon April L. , Tan Zhenyu , Schutt Katherine L. , Jepsen Lauren , Haynes Sarah E. , Nesvizhskii Alexey I. , Sept David , Stumpff Jason , Ohi Ryoma , Cianfrocco Michael A. 
Published: June 2021

ABSTRACTKinesins are tightly regulated in space and time to control their activation in the absence of cargo-binding. Kinesin-binding protein (KIFBP) was recently discovered to bind the catalytic motor heads of 8 of the 45 known kinesin superfamily members and inhibit binding to microtubules. In humans, mutation of KIFBP gives rise to Goldberg-Shprintzen syndrome (GOSHS), but the kinesin(s) that is misregulated to produce clinical features of the disease is not known. Understanding the structural mechanism by which KIFBP selects its kinesin binding partners will be key to unlocking this knowledge. Using a combination of cryo-electron microscopy and crosslinking mass spectrometry, we determined structures of KIFBP alone and in complex with two mitotic kinesins, revealing regions of KIFBP that participate in complex formation. KIFBP adopts an alpha-helical solenoid structure composed of TPR repeats. We find that KIFBP uses a 2-pronged mechanism to remodel kinesin motors and block microtubule-binding. First, KIFBP engages the microtubule-binding interface and sterically blocks interaction with microtubules. Second, KIFBP induces allosteric conformational changes to the kinesin motor head that displace a key structural element in the kinesin motor head (α-helix 4) required for microtubule binding. We identified two regions of KIFBP necessary for in vitro kinesin-binding as well as cellular regulation during mitosis. Taken together, this work establishes the mechanism of kinesin inhibition by KIFBP and provides the first example of motor domain remodeling as a means to abrogate kinesin activity.
What most influences severity and death of COVID-19 patients in Brazil? Is it clinical, social, or demographic factors? An observational study
Authors: Mafra Ana Carolina C. N. , Vieira Régis Rodrigues , Monteiro Camila N. , Cavalcante Denise F. B. , Miraglia João L. , Bonfim Daiana , Palacio Danielle C. , Martins Alessandra C. F. , de Almeida Letícia Yamawaka , Neto João Peres 
Published: June 2021

AbstractObjectiveThis study aimed to assess the space distribution and factors associated with the risk of severe acute respiratory syndrome (SARS) and death in COVID-19 patients, based on routine register data; and to develop and validate a predictive model of the risk of death from COVID-19.MethodsA cross-sectional, epidemiological study of positive SARS-CoV-2 cases, reported in the south region of the city of São Paulo, SP, Brazil, from March 2020 to February 2021. Data were obtained from the official reporting databases of the Brazilian Ministry of Health for influenza-like illness (ILI) (esus-VE, in Portuguese) and for patients hospitalized for SARS (SIVEP-Gripe). The space distribution of cases is described by 2D kernel density. To assess potential factors associated with the outcomes of interest, generalized linear and additive logistic models were adjusted. To evaluate the discriminatory power of each variable studied as well as the final model, C-statistic was used (area under the receiver operating characteristics curve). Moreover, a predictive model for risk of death was developed and validated with accuracy measurements in the development, internal and temporal (March and April 2021) validation samples.ResultsA total of 16,061 patients with confirmed COVID-19 were enrolled. Morbidities associated with a higher risk of SARS were obesity (OR=25.32) and immunodepression (OR=12.15). Morbidities associated with a higher risk of death were renal disease (OR=11.8) and obesity (OR=8.49), and clinical and demographic data were more important than the territory per se. Based on the data, a calculator was developed to predict the risk of death from COVID-19, with 92.2% accuracy in the development sample, 92.3% in the internal validation sample, and 80.0% in the temporal validation sample.ConclusionsThe risk factors for SARS and death in COVID-19 patients seeking health care, in order of relevance, were age, comorbidities, and socioeconomic factors, considering each discriminatory power.
Transcription-coupled and epigenome-encoded mechanisms direct H3K4 methylation
Authors: Oya Satoyo , Takahashi Mayumi , Takashima Kazuya , Kakutani Tetsuji , Inagaki Soichi 
Published: June 2021

AbstractMono-, di-, and trimethylation of histone H3 lysine 4 (H3K4me1/2/3) are associated with transcription, yet it remains controversial whether H3K4me1/2/3 promote or result from transcription. Our previous characterizations of Arabidopsis H3K4 demethylases suggest roles for H3K4me1 in transcription. However, the control of H3K4me1 remains unexplored in Arabidopsis, in which no methylase for H3K4me1 has been identified. Here, we identified three Arabidopsis methylases that direct H3K4me1. Analyses of their genome-wide localization using ChIP-seq and machine learning revealed that one of the enzymes cooperates with the transcription machinery, while the other two are associated with specific histone modifications and DNA sequences. Importantly, these two types of localization patterns are also found for the other H3K4 methylases in Arabidopsis and mice. These results suggest that H3K4me1/2/3 are established and maintained via interplay with transcription as well as inputs from other chromatin features, presumably enabling elaborate gene control.
MutaFrame - an interpretative visualization framework for deleteriousness prediction of missense variants in the human exome
Authors: Ancien François , Pucci Fabrizio , Vranken Wim , Rooman Marianne 
Published: June 2021

AbstractMotivationHigh-throughput experiments are generating ever increasing amounts of various -omics data, so shedding new light on the link between human disorders, their genetic causes, and the related impact on protein behavior and structure. While numerous bioinformatics tools now exist that predict which variants in the human exome cause diseases, few tools predict the reasons why they might do so. Yet, understanding the impact of variants at the molecular level is a prerequisite for the rational development of targeted drugs or personalized therapies.ResultsWe present the updated MutaFrame webserver, which aims to meet this need. It offers two deleteriousness prediction softwares, DEOGEN2 and SNPMuSiC, and is designed for bioinformaticians and medical researchers who want to gain insights into the origins of monogenic diseases. It contains information at two levels for each human protein: its amino acid sequence and its 3-dimensional structure; we used the experimental structures whenever available, and modeled structures otherwise. MutaFrame also includes higher-level information, such as protein essentiality and protein-protein interactions. It has a user-friendly interface for the interpretation of results and a convenient visualization system for protein structures, in which the variant positions introduced by the user and other structural information are shown. In this way, MutaFrame aids our understanding of the pathogenic processes caused by single-site mutations and their molecular and contextual interpretation.AvailabilityMutaframe webserver at http://mutaframe.com
Quantifying the effect of A. thaliana root on antibiotic production in the beneficial bacterium, B. subtilis
Authors: Maan Harsh , Gilhar Omri , Porat Ziv , Kolodkin-Gal Ilana 
Published: June 2021

AbstractBeneficial and probiotic bacteria play an important role in conferring the immunity of their hosts against a wide range of bacterial, viral and fungal diseases. B. subtilis is a bacterium that protects the plant from various pathogens due to its capacity to produce an extensive repertoire of antibiotics. At the same time, the plant microbiome is a highly competitive niche, with multiple microbial species competing for space and resources, a competition that can be determined by the antagonistic potential of each microbiome member. Therefore, regulating antibiotic production in the rhizosphere is of great significance to eliminate pathogens and to establish beneficial host-associated communities.In this work, we used Bacillus subtilis as a model to investigate the role of plant colonization in antibiotic production. Flow cytometry and Image-stream cytometry analysis supported the notion that A. thaliana specifically induced the transcription of the biosynthetic clusters for the non-ribosomal peptides surfactin, bacilysin and plipastatin and the polyketide bacillaene. This induction could be beneficial for the root as all clusters were shown to antagonize plant pathogens. Consistently, the root failed to induce PenP, a β-lactamase that increases only the fitness of the bacteria. Our results can be translated to improve the performance and competitiveness of beneficial members of the plant microbiome.
Fungal gasdermin-like proteins are controlled by proteolytic cleavage
Authors: Clavé Corinne , Dyrka Witold , Granger-Farbos Alexandra , Pinson Benoît , Saupe Sven J. , Daskalov Asen 
Published: June 2021

AbstractGasdermins are a family of pore-forming proteins controlling an inflammatory cell death reaction in the mammalian immune system. The pore-forming ability of the gasdermin proteins is released by proteolytic cleavage with the removal of their inhibitory C-terminal domain. Recently, gasdermin-like proteins have been discovered in fungi and characterized as cell death-inducing toxins in the context of conspecific non-self discrimination (allorecognition). Although functional analogies have been established between mammalian and fungal gasdermins, the molecular pathways regulating gasdermin activity in fungi remain largely unknown. Here, we characterize a gasdermin-based cell death reaction, controlled by the het-Q allorecognition genes in the filamentous fungus Podospora anserina. We show that the cytotoxic activity of the HET-Q1 gasdermin is controlled by proteolysis. HET-Q1 loses a ∼5 kDa C-terminal fragment during the cell death reaction in presence of a subtilisin-like serine protease, termed HET-Q2. Mutational analyses and successful reconstitution of the cell death reaction in a heterologous host (Saccharomyces cerevisiae) suggest that HET-Q2 directly cleaves HET-Q1 to induce cell death. By analysing the genomic landscape of het-Q1 homologs in fungi, we uncovered that the vast majority of the gasdermin genes are clustered with protease-encoding genes. These HET-Q2-like proteins carry either subtilisin-like or caspase-related proteases, which in some cases correspond to the N-terminal effector domain of NOD-like receptor proteins (NLRs). This study thus reveals the proteolytic regulation of gasdermins in fungi and establishes evolutionary parallels between fungal and mammalian gasdermin-dependent cell death pathways.SignificanceThe recent discovery of gasdermin-like proteins in fungi have brought to light that this family of pore-forming proteins controls cell death in two of the major eukaryotic kingdoms, fungi and mammals. Yet, the regulation of cytotoxicity of the fungal gasdermins and their molecular pathways remain uncharacterized. Here, we describe the regulation through proteolytic cleavage of the fungal gasdermin HET-Q1 and uncover that majority of fungal gasdermins are genomically clustered with protease-encoding genes. Some of these genes encode proteins with caspase-related domains and/or are members of a family of immune receptors in mammals and plants. Overall, this work contributes towards our understanding of the evolution of gasdermin-dependent cell death, enlightening multiple evolutionary parallels between signaling pathways in mammals and fungi.
New fossils of Jurassic ophiurid brittle stars (Ophiuroidea; Ophiurida) provide evidence for early clade evolution in the deep sea
Authors: Thuy Ben , Numberger-Thuy Lea D. , Pineda-Einríquez Tania 
Published: June 2021

1.SummaryUnderstanding of the evolutionary history of the ophiuroids, or brittle stars, is hampered by a patchy knowledge of the fossil record. Especially the stem members of the living clades are poorly known, resulting in blurry concepts of the early clade evolution and imprecise estimates of divergence ages. Here, we describe new ophiuroid fossil from the Lower Jurassic of France, Luxembourg, and Austria and introduce the new taxaOphiogojira labadieigen. et sp. nov. from lower Pliensbachian shallow sublittoral deposits,Ophiogojira andreuigen. et sp. nov. from lower Toarcian shallow sublittoral deposits, andOphioduplantiera noctilucagen. et sp. nov. from late Sinemurian to lower Pliensbachian bathyal deposits. A Bayesian morphological phylogenetic analysis shows thatOphiogojiraholds a basal position within the order Ophiurida, whereasOphioduplantierahas a more crownward position within the ophiurid family Ophiuridae. The position ofOphioduplantierain the evolutionary tree suggests that family-level divergences within the Ophiurida must have occurred before the late Sinemurian, and that ancient slope environments played an important role in fostering early clade evolution.
Dual control of MAPK activities by AP2C1 and MKP1 MAPK phosphatases regulates defence responses in Arabidopsis
Authors: Ayatollahi Zahra , Kazanaviciute Vaiva , Shubchynskyy Volodymyr , Kvederaviciute Kotryna , Schwanninger Manfred , Rozhon Wilfried , Stumpe Michael , Mauch Felix , Bartels Sebastian , Ulm Roman , Balazadeh Salma , Mueller-Roeber Bernd , Meskiene Irute , Schweighofer Alois 
Published: June 2021

AbstractMitogen-activated protein kinase (MAPK) cascades transmit environmental signals and induce stress and defence responses in plants. These signalling cascades are negatively controlled by specific phosphatases of the type 2C Ser/Thr protein phosphatase (PP2C) and dual-specificity phosphatase (DSP) families that inactivate stress-induced MAPKs; however, the interplay between phosphatases of these different types has remained unknown. Our work reveals that different Arabidopsis MAPK phosphatases, the PP2C-type AP2C1 and the DSP-type MKP1, exhibit both specific and overlapping functions in plant stress responses. Each single mutant and ap2c1 mkp1 double mutant displayed enhanced wound-induced activation of MAPKs MPK3, MPK4, and MPK6, as well as induction of a set of transcription factors. Moreover, ap2c1 mkp1 double mutants show an autoimmune-like response, associated with elevated levels the stress hormones salicylic acid and ethylene, and of the phytoalexin camalexin. Interestingly, this phenotype is reduced in ap2c1 mkp1 mpk6 triple mutants, suggesting that the autoimmune-like response is due to MPK6 misregulation. We conclude that the evolutionarily distant MAPK phosphatases AP2C1 and MKP1 contribute crucially to the tight control of MPK6 activity, ensuring appropriately balanced stress signalling and suppression of autoimmune-like responses during plant growth and development.HighlightDouble MAPK phosphatase mutant plants ap2c1 mkp1 exhibit constitutive, autoimmune-like stress responses, dependent on their substrate MAPK MPK6.