bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antibody recognition of the Pneumovirus fusion protein trimer interface
Authors: Huang Jiachen , Diaz Darren , Mousa Jarrod J. 
Published: May 2020

AbstractHuman metapneumovirus is a leading cause of viral respiratory infection in children, and can cause severe lower respiratory infection in infants, the elderly, and immunocompromised patients. However, there remain no licensed vaccines or specific treatments for hMPV infection. Although the hMPV fusion (F) protein is the sole target of neutralizing antibodies, the immunological properties of hMPV F are still poorly understood. To further define the humoral immune response to the hMPV F protein, we isolated two new human monoclonal antibodies (mAbs), MPV458 and MPV465. Both mAbs are neutralizingin vitroand target a unique antigenic site harbored within the trimeric interface of the hMPV F protein. We determined both MPV458 and MPV465 have higher affinity for monomeric hMPV F than trimeric hMPV F. MPV458 was co-crystallized with hMPV F, and the mAb primarily interacts with an alpha helix on the F2 region of the hMPV F protein. Surprisingly, the major epitope for MPV458 lies within the trimeric interface of the hMPV F protein, suggesting significant breathing of the hMPV F protein must occur for hMPV F protein recognition of the novel epitope. In addition, significant glycan interactions were observed with a somatically mutated light chain framework residue. The data presented identifies a novel epitope on the hMPV F protein for structure-based vaccine design, and provides a new mechanism for human antibody neutralization of viral glycoproteins.
Identification of a persisting bacterial contamination of cell culture asBrevibacterium
Authors: Mahesh P.P , Retnakumar R. J , Mundayoor Sathish 
Published: May 2020

AbstractCell culture is an important prerequisite for many of the basic and applied researches in life sciences and contamination is a major problem faced by the researchers in maintaining healthy cell lines. We noted a dot like contamination in our THP1 cell line, which does not make the culture medium turbid as fast as other common contaminants and remains in the culture for many days before it makes the culture unusable. The contaminant was identified as a member of the genusBrevibacteriumand we could find that the antibiotic rifampicin effectively suppresses the growth of the bacterium.
MosMedData: Chest CT Scans with COVID-19 Related Findings Dataset
Authors: Morozov S.P. , Andreychenko A.E. , Pavlov N.A. , Vladzymyrskyy A.V. , Ledikhova N.V. , Gombolevskiy V.A. , Blokhin I.A. , Gelezhe P.B. , Gonchar A.V. , Chernina V.Yu. 
Published: May 2020

AbstractThis dataset contains anonymised human lung computed tomography (CT) scans with COVID-19 related findings, as well as without such findings. A small subset of studies has been annotated with binary pixel masks depicting regions of interests (ground-glass opacifications and consolidations). CT scans were obtained between 1st of March, 2020 and 25th of April, 2020, and provided by municipal hospitals in Moscow, Russia. Permanent link:https://mosmed.ai/datasets/covid19_1110. This dataset is licensed under a Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported (CC BY-NC-ND 3.0) License.
Regulation of SETD2 stability is important for the fidelity of H3K36me3 deposition
Authors: Bhattacharya Saikat , Workman Jerry L. 
Published: May 2020

ABSTRACTThe histone H3K36me3 mark regulates transcription elongation, pre-mRNA splicing, DNA methylation, and DNA damage repair. However, knowledge of the regulation of the enzyme SETD2, which deposits this functionally important mark, is very limited. Here we show that the poorly characterized N-terminal region of SETD2 plays a determining role in regulating the stability of SETD2. This stretch of 1-1403 amino acids contributes to the robust degradation of SETD2 by the proteasome. Besides, the SETD2 protein is aggregate-prone and forms insoluble bodies in nuclei especially upon proteasome inhibition. Removal of the N-terminal segment results in the stabilization of SETD2 and leads to a marked increase in global H3K36me3 which, uncharacteristically, happens in a Pol II-independent manner. Thus, the regulation of SETD2 levels through proteasomal mediated decay is important to maintain the fidelity of H3K36me3 deposition.
A natural single-guide RNA repurposes Cas9 to autoregulate CRISPR-Cas expression
Authors: Workman Rachael E. , Pammi Teja , Nguyen Binh T. K. , Graeff Leonardo W. , Smith Erika , Sebald Suzanne M. , Stoltzfus Marie J. , Modell Joshua W. 
Published: May 2020

SUMMARYCRISPR-Cas systems provide their prokaryotic hosts with acquired immunity against viruses and other foreign genetic elements, but how these systems are regulated to prevent auto-immunity is poorly understood. In type II CRISPR-Cas systems, a transactivating CRISPR RNA (tracrRNA) scaffold functions together with a CRISPR RNA (crRNA) guide to program Cas9 for the recognition and cleavage of foreign DNA targets. Here, we show that a long-form tracrRNA performs an unexpected second function by folding into a natural single guide that directs Cas9 to transcriptionally repress its own promoter. Further, we demonstrate that Pcas9serves as a critical regulatory node; de-repression causes a dramatic induction of Cas genes, crRNAs and tracrRNAs resulting in a 3,000-fold increase in immunization rates against unrecognized viruses. Heightened immunity comes at the cost of increased auto-immune toxicity, demonstrating the critical importance of the controller. Using a bioinformatic analysis, we provide evidence that tracrRNA-mediated autoregulation is widespread in type II CRISPR-Cas systems. Collectively, we unveil a new paradigm for the intrinsic regulation of CRISPR-Cas systems by natural single guides, which may facilitate the frequent horizontal transfer of these systems into new hosts that have not yet evolved their own regulatory strategies.
Glutathione S-transferase Pi (Gstp) Proteins Regulate Neuritogenesis in the Developing Cerebral Cortex
Authors: Liu Xiaonan , Blazejewski Sara M. , Bennison Sarah A. , Toyo-oka Kazuhito 
Published: May 2020

AbstractGSTP proteins are metabolic enzymes involved in removal of oxidative stress and intracellular signaling and also have inhibitory effects on JNK activity. However, the functions of Gstp proteins in the developing brain are unknown. In mice, there are three Gstp proteins, Gstp1, 2 and 3, while there is only one GSTP in humans. By RT-PCR analysis, we found that Gstp1 was expressed beginning at E15.5 in the cortex, but Gstp2 and 3 started expressing at E18.5. Gstp 1 and 2 knockdown caused decreased neurite number in cortical neurons, implicating them in neurite initiation. Usingin uteroelectroporation to knockdown Gstp1 and 2 in layer 2/3 pyramidal neuronsin vivo, we found abnormal swelling of the apical dendrite at P3 and reduced neurite number at P15. Using time-lapse live imaging, we found that the apical dendrite orientation was skewed compared to the control, but these defects were ameliorated. Overexpression of Gstp 1 or 2 resulted in changes in neurite length, suggesting a role in neurite elongation. We explored the molecular mechanism and found that JNK inhibition rescued reduced neurite number caused by Gstp knockdown, indicating that Gstp regulates neurite formation through JNK signaling. Thus, we found novel functions of Gstp proteins in neurite initiation during cortical development. Furthermore, the overexpression experiments suggest different functions of Gstp1 and 2 in neurite elongation. Since previous studies have shown the potential implication of Gstp in Autism Spectrum Disorder, our findings will attract more clinical interests in Gstp proteins in neurodevelopmental disorders.SignificanceNeurite formation, including neurite initiation and elongation, is the first step of generating polarized neuronal morphology in developing neurons, and thus is essential for establishing a neuronal network. Therefore, it is crucial to understand the mechanisms of neurite formation. Limited studies have been performed to clarify the mechanisms of neurite formation, especially neurite initiation. In this present study, we report a novel, essential role of Gstp in neurite initiation in mouse cortical neuronsin vitroandin vivo. We also found that Gstp regulates neurite formation via JNK signaling pathways. These findings not only provide novel functions of Gstp proteins in neuritogenesis during cortical development but also help us to understand the complexity of neurite formation.
Computational Analysis of Dynamic Allostery and Control in the SARS-CoV-2 Main Protease
Authors: Dubanevics Igors , McLeish Tom C.B. 
Published: May 2020

AbstractThe COVID-19 pandemic caused by the novel coronavirus SARS-CoV-2 has generated a global pandemic and no vaccine or antiviral drugs exist at the moment of writing. An attractive coronavirus drug target is the main protease (Mpro, also known as 3CLpro) because of its vital role in the viral cycle. A significant body of work has been focused on finding inhibitors which bind and block the active site of the main protease, but little has been done to address potential non-competitive inhibition which targets regions beyond the active site, partly because the fundamental biophysics of such allosteric control is still poorly understood. In this work, we construct an Elastic Network Model (ENM) of the SARS-CoV-2 Mprohomodimer protein and analyse the dynamics and thermodynamics of the main protease’s ENM. We found a rich and heterogeneous dynamical structure in the correlated motions, including allosterically correlated motions between the homodimeric protease’s active sites. Exhaustive 1-point and 2-point mutation scans of the ENM and their effect on fluctuation free energies confirm previously experimentally identified bioactive residues, but also suggest several new candidate regions that are distant from the active site for control of the protease function. Our results suggest new dynamically-driven control regions as possible candidates for non-competitive inhibiting binding sites in the protease, which may assist the development of current fragmentbased binding screens. The results also provide new insight into the protein physics of fluctuation allostery and its underpinning dynamical structure.
Analyzing the impact of SARS CoV-2 on the human proteome
Authors: Estrada Ernesto 
Published: May 2020

AbstractThe COVID-19 respiratory disease is caused by the novel coronavirus SARS-CoV-2, which uses the enzyme ACE2 to entry human cells. This disease is characterized by important damages at multi-organ level, partially due to the abundant expression of ACE2 in practically all human tissues. However, not every organ in which ACE2 is abundant is affected by SARS CoV-2, which suggests the existence of other multi-organ routes for transmitting the perturbations produced by the virus. We consider here diffusive processes through the protein-protein interaction (PPI) network of proteins targeted by SARS CoV-2 as such alternative route. We found a subdiffusive regime that allows the propagation of virus perturbations through the PPI network at a significant rate. By following the main subdiffusive routes across the PPI network we identify proteins mainly expressed in the heart, cerebral cortex, thymus, testis, lymph node, kidney, among others of the organs reported to be affected by COVID-19.
Full-field optical coherence tomography for the diagnosis of giant cell arteritis
Authors: Maldiney Thomas , Greigert Hélène , Martin Laurent , Benoit Emilie , Creuzot-Garcher Catherine , Gabrielle Pierre-Henry , Chassot Jean-Marie , Boccara Claude , Balvay Daniel , Tavitian Bertrand , Clément Olivier , Audia Sylvain , Bonnotte Bernard , Samson Maxime 
Published: May 2020

AbstractHistopathological examination of temporal artery biopsy (TAB) remains the gold standard for the diagnosis of giant cell arteritis (GCA) but is associated with essential limitations that emphasize the need for an upgraded pathological process. This study pioneered the use of full-field optical coherence tomography (FF-OCT) for rapid and automated on-site pathological diagnosis of GCA. Sixteen TABs (12 negative and 4 positive for GCA) were selected according to major histopathological criteria of GCA following hematoxylin-eosin-saffron-staining for subsequent acquisition with FF-OCT to compare structural modifications of the artery cell wall and thickness of each tunica. Gabor filtering of FF-OCT images was then used to compute TAB orientation maps and validate a potential automated analysis of TAB sections. FF-OCT allowed both qualitative and quantitative visualization of the main structures of the temporal artery wall, from the internal elastic lamina to thevasa vasorumand red blood cells, unveiling a significant correlation with conventional histology. FF-OCT imaging of GCA TABs revealed destruction of the media with distinct remodeling of the whole arterial wall into a denser reticular fibrous neo-intima, which is distinctive of GCA pathogenesis and accessible through automated Gabor filtering. Rapid on-site FF-OCT TAB acquisition makes it possible to identify some characteristic pathological lesions of GCA within a few minutes, paving the way for potential machine intelligence-based or even non-invasive diagnosis of GCA.
IgY antibodies against Ebola virus possess post-exposure protection and excellent thermostability
Authors: Zhang Yuan , Wei Yanqiu , Li Yunlong , Wang Xuan , Liu Yang , Tian Deyu , Jia Xiaojuan , Gong Rui , Liu Wenjun , Yang Limin 
Published: May 2020

AbstractEbola virus (EBOV) is the most virulent pathogens that cause hemorrhagic fever with high mortality rates in humans and nonhuman primates. The postexposure antibody therapies to prevent EBOV infection are considered efficient. However, due to the poor thermal stability of mammalian antibody, their application in the tropics has been limited. Here, we developed a thermostable therapeutic antibody against EBOV based on chicken immunoglobulin Y (IgY). The IgY antibodies demonstrated excellent thermal stability, which retained their neutralizing activity at 25°C for one year, in contrast to conventional polyclonal or monoclonal antibodies (MAbs). We immunized laying hens with a variety of EBOV vaccine candidates and confirmed that VSV Δ G/EBOVGP encoding the EBOV glycoprotein could induce high titer neutralizing antibodies against EBOV. The therapeutic efficacy of immune IgY antibodiesin vivowas evaluated in the newborn Balb/c mice model. Lethal dose of virus challenged mice were treated 2 or 24 h post-infection with different doses of anti-EBOV IgY. The group receiving a high dose of 106NAU/kg (neutralizing antibody units/kilogram) achieved complete protection with no signs of disease, while the low-dose group was only partially protected. In contrast, all mice receiving naïve IgY died within 10 days. In conclusion, the anti-EBOV IgY exhibits excellent thermostability and protective efficacy, and it is very promising to be developed as alternative therapeutic entities.Author SummaryAlthough several Ebola virus therapeutic antibodies have been reported in recent years, however, due to the poor thermal stability of mammalian antibody, their application in tropical endemic areas has been limited. We developed a highly thermostable therapeutic antibody against EBOV based on chicken immunoglobulin Y (IgY). The IgY antibodies demonstrated excellent thermal stability, which retained their neutralizing activity at 25°C for one year. The newborn mice receiving passive transfer of IgY achieved complete protection against a lethal dose of virus challenge indicating that the anti-EBOV IgY provides a promising countermeasure to solve the current clinical application problems of Ebola antibody-based treatments in Africa.
The NHEJ Repair of DNA Double Strand Breaks inPhyscomitrella patensDepends on the Kleisin NSE4 of the SMC5/6 Complex
Authors: Vágnerová Radka , Holá Marcela , Angelis Karel J. 
Published: May 2020

AbstractStructural maintenance of chromosomes (SMC) complexes are involve in cohesion, condensation and maintenance of genome stability. Based on the sensitivity of mutants to genotoxic stress the SMC5/6 complex is thought to play imminent role in DNA stabilization during repair by encircling DNA at the site of lesion by bridging the heteroduplex of SMC5 and SMC6 by non SMC kleisin components NSE1, 3 and 4. In this study, we tested how formation of the SMC5/6 circular structure affects mutant sensitivity to genotoxic stress, kinetics of DSB repair and insertion mutagenesis. In the mossPhyscomitrella patens SMC6andNSE4are essential single copy genes and this is why we used blocking of transcription to reveal their mutated phenotype. Even slight attenuation of transcription by dCas9 binding was enough to obtain stable lines with DSB repair defect and specific bleomycin sensitivity. Whereas survival after bleomycin or MMS treatment fully depends on active SMC6, NSE4 has little or negligible effect. We conclude that whereas circularization of SMC5/6 provided by the kleisin NSE4 is indispensable for the immediate NHEJ DSB repair response, other functions associated with SMC5/6 complex are critical to survive DNA damage.
Low-density lipoprotein receptor-related protein 1 (LRP1) is a negative regulator of oligodendrocyte progenitor cell differentiation in the adult mouse brain
Authors: Auderset Loic , Pitman Kimberley A , Cullen Carlie L , Pepper Renee E , Taylor Bruce V , Foa Lisa , Young Kaylene M 
Published: May 2020

AbstractLow-density lipoprotein receptor-related protein 1 (LRP1) is a large, endocytic cell surface receptor that is highly expressed by oligodendrocyte progenitor cells (OPCs), and LRP1 expression is rapidly downregulated as OPCs differentiate into oligodendrocytes (OLs). We report that the conditional deletion ofLrp1from adult mouse OPCs (Pdgfrα-CreER :: Lrp1fl/fl) increases the number of new myelinating OLs added to brain, but that each new cell elaborates a normal quantity of myelin. OPC proliferation is also elevated followingLrp1deletionin vivo, however, this is likely to be a secondary, homeostatic response to increased OPC differentiation, as ourin vitroexperiments show that LRP1 is a direct negative regulator of OPC differentiation, not proliferation. DeletingLrp1from adult OPCs also enhances remyelination, as cuprizone-induced lesions are smaller inLrp1-deleted mice, and parenchymal OPCs produce a larger number of mature OLs. These data suggest that the selective blockade of LRP1 function on adult OPCs may enhance myelin repair in demyelinating diseases, such as multiple sclerosis.
Mechanistic insights into ventricular arrhythmogenesis of hydroxychloroquine and azithromycin for the treatment of COVID-19
Authors: Wang Gongxin , Lu Chieh-Ju , Trafford Andrew W. , Tian Xiaohui , Flores Hannali M , Maj Piotr , Zhang Kevin , Niu Yanhong , Wang Luxi , Du Yimei , Ji Xinying , Xu Yanfang , Wu Lin , Li Dan , Herring Neil , Paterson David , Huang Christopher L.-H. , Zhang Henggui , Lei Ming , Hao Guoliang 
Published: May 2020

ABSTRACTAimsWe investigate mechanisms for potential pro-arrhythmic effects of hydroxychloroquine (HCQ) alone, or combined with azithromycin (AZM), in Covid-19 management supplementing the limited available experimental cardiac safety data.MethodsWe integrated patch-clamp studies utilizing In Vitro ProArrhythmia Assay (CiPA) Schema IC50paradigms, molecular modelling, cardiac multi-electrode array and voltage (RH237) mapping, ECG studies, and Ca2+(Rhod-2 AM) mapping in isolated Langendorff-perfused guinea-pig hearts with human in-silico ion current modelling.ResultsHCQ blocked IKrand IK1with IC50s (10±0.6 and 34±5.0 μM) within clinical therapeutic ranges, INaand ICaLat higher IC50s, leaving Itoand IKsunaffected. AZM produced minor inhibition of INa, ICaL, IKs, and IKr,, sparing IK1and Ito. HCQ+AZM combined inhibited IKrand IK1with IC50s of 7.7±0.8 μM and 30.4±3.0 μM, sparing INa, ICaLand Ito. Molecular modelling confirmed potential HCQ binding to hERG. HCQ slowed heart rate and ventricular conduction. It prolonged PR, QRS and QT intervals, and caused prolonged, more heterogeneous, action potential durations and intracellular Ca2+transients. These effects were accentuated with combined HCQ+AZM treatment, which then elicited electrical alternans, re-entrant circuits and wave break. Modelling studies attributed these to integrated HCQ and AZM actions reducing IKrand IK1, thence altering cell Ca2+homeostasis.ConclusionsCombined HCQ+AZM treatment exerts pro-arrhythmic ventricular events by synergetically inhibiting IKr, IKswith resulting effects on cellular Ca2+signalling, and action potential propagation and duration. These findings provide an electrophysiological basis for recent FDA cardiac safety guidelines cautioning against combining HCQ/AZM when treating Covid-19.
Intrinsic disorder in the T cell receptor creates cooperativity and controls ZAP70 binding
Authors: Clemens Lara , Dushek Omer , Allard Jun 
Published: May 2020

ABSTRACTMany immunoreceptors have cytoplasmic domains that are intrinsically disordered (i.e., have high configurational entropy), have multiple sites of post-translational modification (e.g., tyrosine phosphorylation), and participate in nonlinear signaling pathways (e.g., exhibiting switch-like behavior). Several hypotheses to explain the origin of these nonlinearities fall under the broad hypothesis that modification at one site changes the immunoreceptor’s entropy, which in turn changes further modification dynamics. Here we use coarse-grain simulation to study three scenarios, all related to the chains that comprise the T Cell Receptor. We find that, first, if phosphorylation induces local changes in the flexibility of TCRζ-chain, this naturally leads to rate enhancements and cooperativity. Second, we find that TCR CD3ϵcan provide a switch by modulating its residence in the plasma membrane. By constraining our model to be consistent with the previous observation that both basic residues and phosphorylation control membrane residence, we find that there is only a moderate rate enhancement of 10% between first and subsequent phosphorylation events. And third, we find that volume constraints do not limit the number of ZAP70s that can bind the TCR, but that entropic penalties lead to a 200-fold decrease in binding rate by the seventh ZAP70, potentially explaining the observation that each TCR has around six ZAP70 molecules bound following receptor triggering. In all three scenarios, our results demonstrate that phenomena that change an immunoreceptor chain’s entropy (stiffening, confinement to a membrane, and multiple simultaneous binding) can lead to nonlinearities (rate enhancement, switching, and negative cooperativity) in how the receptor participates in signaling. These polymer-entropy-driven nonlinearities may augment the nonlinearities that arise from, e.g., kinetic proofreading and cluster formation. They also suggest different design strategies for engineered receptors, e.g., whether or not to put signaling modules on one chain or multiple clustered chains.STATEMENT OF SIGNIFICANCEMany of the proteins involved in signal processing are both mechanically flexible and have multiple sites of interaction, leading to a combinatorial complexity making them challenging to study. One example is the T Cell Receptor, a key player in immunological decision making. It consists of 6 flexible chains with 20 interaction sites, and exhibits nonlinear responses to signal inputs, although the mechanisms are elusive. By using polymer physics to simulate the T Cell Receptor’s chains, this work demonstrates that several of the nonlinear responses observed experimentally emerge naturally due to constraints on the chains that change their entropy. This work points to new avenues to modulate signaling proteins for therapeutics by modulating their mechanical flexibility and spatial extent.