bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline
Authors: Rahman M. Shaminur , Islam M. Rafiul , Hoque M. Nazmul , Alam A. S. M. Rubayet Ul , Akther Masuda , Puspo J. Akter , Akter Salma , Anwar Azraf , Sultana Munawar , Hossain M. Anwar 
Published: June 2020

AbstractIn order to explore nonsynonymous mutations and deletions in the spike (S) protein of SARS-CoV-2, we comprehensively analyzed 35,750 complete S protein gene sequences from across six continents and five climate zones around the world, as documented in the GISAID database as of June 24th, 2020. Through a custom Python-based pipeline for analyzing mutations, we identified 27,801 (77.77 % of spike sequences) mutated strains compared to Wuhan-Hu-1 strain. 84.40% of these strains had only single amino-acid (aa) substitution mutations, but an outlier strain from Bosnia and Herzegovina (EPI_ISL_463893) was found to possess six aa substitutions. The D614G variant of the major G clade was found to be predominant across circulating strains in all climates. We also identified 988 unique aa substitution mutations distributed across 660 positions within the spike protein, with eleven sites showing high variability – these sites had four types of aa variations at each position. Besides, 17 in-frame deletions at four major regions (three in N-terminal domain and one just downstream of the RBD) may have possible impact on attenuation. Moreover, the mutational frequency differed significantly (p= 0.003, Kruskal–Wallis test) among the SARS-CoV-2 strains worldwide. This study presents a fast and accurate pipeline for identifying nonsynonymous mutations and deletions from large dataset for any particular protein coding sequence and presents this S protein data as representative analysis. By using separate multi-sequence alignment with MAFFT, removing ambiguous sequences and in-frame stop codons, and utilizing pairwise alignment, this method can derive nonsynonymus mutations (Reference:Position:Strain). We believe this will aid in the surveillance of any proteins encoded by SARS-CoV-2, and will prove to be crucial in tracking the ever-increasing variation of many other divergent RNA viruses in the future.
Structure of human RNA Polymerase III
Authors: Ramsay Ewan Phillip , Abascal-Palacios Guillermo , Daiß Julia L. , King Helen , Gouge Jerome , Pilsl Michael , Beuron Fabienne , Morris Edward , Gunkel Philip , Engel Christoph , Vannini Alessandro 
Published: June 2020

ABSTRACTIn eukaryotes, RNA Polymerase (Pol) III is the enzyme specialised for the transcription of the entire pool of tRNAs and several other short, essential, untranslated RNAs. Pol III is a critical determinant of cellular growth and lifespan across the eukaryotic kingdom. Upregulation of Pol III transcription is often observed in cancer cells and causative Pol III mutations have been described in patients affected by severe neurodevelopmental disorders and hypersensitivity to viral infection.Harnessing CRISPR-Cas9 genome editing in HeLa cells, we isolated endogenous human Pol III and obtained a cryo-EM reconstruction at 4.0 Å. The structure of human Pol III allowed us to map the reported genetic mutations and rationalise them. Mutations causing neurodevelopmental defects cluster in hotspots that affect the stability and/or biogenesis of Pol III, thereby resulting in loss-of-function of the enzyme. Mutations affecting viral sensing are located in the periphery of the enzyme in proximity to DNA binding regions, suggesting an impairment of Pol III cytosolic viral DNA-sensing activity.Furthermore, integrating x-ray crystallography and SAXS data, we describe the structure of the RPC5 C-terminal extension, which is absent in lower eukaryotes and not visible in our EM map. Surprisingly, experiments in living cells highlight a role for the RPC5 C-terminal extension in the correct assembly and stability of the human Pol III enzyme, thus suggesting an added layer of regulation during the biogenesis of Pol III in higher eukaryotes.
Interplay between UNG and AID governs intratumoral heterogeneity in mature B cell lymphoma
Authors: Delgado Pilar , Álvarez-Prado Ángel F , Marina-Zárate Ester , Sernandez Isora V , Mur Sonia M , de la Barrera Jorge , Sanchez-Cabo Fátima , Cañamero Marta , de Molina Antonio , Belver Laura , de Yebenes Virginia G , Ramiro Almudena R 
Published: June 2020

ABSTRACTMost B cell lymphomas originate from B cells that have germinal center (GC) experience and bear chromosome translocations and numerous point mutations. GCs B cells remodel their immunoglobulin (Ig) genes by somatic hypermutation (SHM) and class switch recombination (CSR) in their immunoglobulin (Ig) genes. Activation Induced Deaminase (AID) initiates CSR and SHM by generating U:G mismatches on Ig DNA that can then be processed by Uracyl-N-glycosylase (UNG). AID promotes collateral damage in the form of chromosome translocations and off-target SHM, however, the exact contribution of AID activity to lymphoma generation and progression is not completely understood. Here we show using a conditional knock-in strategy that AID supraactivity alone is not sufficient to generate B cell transformation. In contrast, in the absence of UNG, AID supra-expression increases SHM and promotes lymphoma. Whole exome sequencing revealed that AID heavily contributes to lymphoma SHM, promoting subclonal variability and a wider range of oncogenic variants. Thus, our data provide direct evidence that UNG is a brake to AID-induced intratumoral heterogeneity and evolution of B cell lymphoma.
REV-ERB Agonism Improves Liver Pathology in a Mouse Model of NASH
Authors: Griffett Kristine , Bedia-Diaz Gonzalo , Elgendy Bahaa , Burris Thomas P. 
Published: June 2020

AbstractNon-alcoholic fatty liver disease (NAFLD) affects a significant number of people worldwide and currently there are no pharmacological treatments. NAFLD often presents with obesity, insulin resistance, and in some cases cardiovascular diseases. There is a clear need for treatment options to alleviate this disease since it often progresses to much more the much more severe non-alcoholic steatohepatitis (NASH). The REV-ERB nuclear receptor is a transcriptional repressor that regulates physiological processes involved in the development of NAFLD including lipogenesis and inflammation. We hypothesized that pharmacologically activating REV-ERB would suppress the progression of fatty liver in a mouse model of NASH. Using REV-ERB agonist SR9009 in a mouse NASH model, we demonstrate the beneficial effects of REV-ERB activation that led to an overall improvement of hepatic health by suppressing hepatic fibrosis and inflammatory response.
Event-related network changes unfold the dynamics of cortical integration during face processing
Authors: Maffei Antonio , Sessa Paola 
Published: June 2020

AbstractFace perception arises from a collective activation of brain regions in the occipital, parietal and temporal cortices. Despite wide acknowledgement that these regions act in an intertwined network, the network behavior itself is poorly understood. Here we present a study in which time-varying connectivity estimated from EEG activity elicited by facial expressions presentation was characterized using graph-theoretical measures of node centrality and global network topology. Results revealed that face perception results from a dynamic reshaping of the network architecture, characterized by the emergence of hubs located in the occipital and temporal regions of the scalp. The importance of these nodes can be observed from early stages of visual processing and reaches a climax in the same time-window in which the face-sensitive N170 is observed. Furthermore, using Granger causality, we found that the time-evolving centrality of these nodes is associated with ERP amplitude, providing a direct link between the network state and local neural response. Additionally, investigating global network topology by means of small-worldness and modularity, we found that face processing requires a functional network with a strong small-world organization that maximizes integration, at the cost of segregated subdivisions. Interestingly, we found that this architecture is not static, but instead it is implemented by the network from stimulus onset to ~200 msec. Altogether, this study reveals the event-related changes underlying face processing at the network level, suggesting that a distributed processing mechanism operates through dynamically weighting the contribution of the cortical regions involved.Data AvailabilityData and code related to this manuscript can be accessed through the OSF at this link https://osf.io/hc3sk/?view_only=af52bc4295c044ffbbd3be019cc083f4
Population Dynamics and Neuronal Polyploidy in the Developing Neocortex
Authors: Jungas Thomas , Joseph Mathieu , Fawal Mohamad-Ali , Davy Alice 
Published: June 2020

SUMMARYThe mammalian neocortex is composed of different subtypes of neurons which are generated during embryogenesis by sequential differentiation of neural progenitors. While molecular mechanisms that control neuronal production in the developing neocortex have been extensively studied, the dynamics and absolute numbers of the different progenitor and neuronal populations are still poorly characterized. Here we describe a medium throughput approach based on flow cytometry and well known identity markers of cortical subpopulations to collect quantitative data over the course of mouse neocortex development. We collected a complete dataset in a physiological developmental context on two progenitor and two neuron populations, including relative proportions and absolute numbers. Our study reveals unexpected numbers of progenitors. In addition, we discovered that a fraction of neurons in the developing mouse neocortex are polyploid.
Bright Near-infrared Anti-Stokes Fluorescence of ICG under Low Power CW Laser Excitation and its Applications in Bioimaging
Authors: Zhou Jing , Wu Di , Ye Zikang , Xue Dingwei , He Mubin , Qian Jun 
Published: June 2020

AbstractAnti-Stokes fluorescence was observed in ICG, a molecule approved by the FDA for clinical use. The wavelengths of its fluorescence are mainly located in the near-infrared band of 800 nm~900 nm, with a high quantum yield up to 8%. In order to know its generation mechanism, based on multi-photon absorption (MPA) theory, thermally activated delayed fluorescence (TADF) theory and hot band absorption theory, its power dependence, temperature dependence of absorption spectra and fluorescence spectra, and fluorescence lifetime were measured. Its generation mechanism was finally determined to be hot band absorption process. Since ICG showed bright anti-Stokes fluorescence in near-infrared region, which offers substantially longer penetration depth in biological tissues than visible light, excellent photostability and biosafety, we applied it to in vivo imaging and compared it with upconversion nanoparticles (UCNPs). The result is that ICG exhibited much stronger fluorescence than UCNPs, providing more anatomical information of samples. This contributes to a better choice for anti-Stokes fluorescence bioimaging.
Structural basis for the HMGCR interaction with UBIAD1 mutants causing Schnyder corneal dystrophy
Authors: Zhou Fengbo , Weiss Jayne S. , Li Weikai 
Published: June 2020

AbstractSchnyder corneal dystrophy (SCD) is an autosomal dominant disease characterized by abnormal deposition of cholesterol and lipid in the cornea. The molecular mechanism underlying this process, which involves the interaction between UBAID1 and HMGCR, remains unclear. Here we investigate these events within silicoapproaches. We built the homology models of UBIAD1 and HMGCR based on the existing crystal and cryo-EM structures. The UBIAD1 and HMGCR models are docked and their binding interactions are interrogated by MD simulation. We find that the transmembrane helices of UBIAD1 bind to sterol sensing domain of HMGCR. Upon binding of the GGPP substrate, UBIAD1 shows lower structural flexibility in the TM regions binding to HMGCR. The N102S and G177R mutations disrupts GGPP binding, thereby lowering the binding affinity of HMGCR. Overall, our modeling suggests that SCD mutations in UBIAD1 or lower GGPP concentration increase the structural flexibility of UBIAD1, thereby facilitating its association with HMGCR.
HLFExpression Defines the Human Hematopoietic Stem Cell State
Authors: Lehnertz Bernhard , Chagraoui Jalila , MacRae Tara , Tomellini Elisa , Corneau Sophie , Mayotte Nadine , Boivin Isabel , Sauvageau Guy 
Published: June 2020

AbstractHematopoietic stem cells (HSCs) sustain blood cell homeostasis throughout life and are able to regenerate all blood lineages following transplantation.Despite this clear functional definition, highly enriched isolation of human HSCs can currently only be achieved through combinatorial assessment of multiple surface antigens. While a number of transgenic HSC reporter mouse strains have been described, no analogous approach to prospectively isolate human HSCs has been reported.To identify genes with the most selective expression in human HSCs, we profiled population- and single-cell transcriptomes of fresh andex vivocultured cord blood derived HSPCs as well as peripheral blood, adult bone marrow and fetal liver. Based on these analyses, we propose the master transcription factorHLF(Hepatic Leukemia Factor) as one of the most specific HSC marker genes.To directly track its expression in human hematopoietic cells, we developed a genomicHLFreporter strategy, capable of selectively labeling the most immature blood cells on the basis of a single engineered parameter.Most importantly,HLF-expressing cells comprise all of the stem cell activity in culture andin vivoduring serial transplantation.Taken together, these results experimentally establishHLFas a defining gene of the human hematopoietic stem cell state and outline a new approach to continuously mark these cells with high fidelity.Key PointsIn the human blood system,HLFexpression is specific to stem cell populations in primary anatomical sites and duringex vivoexpansion.CRISPR/rAAV6-mediated integration of a genomicHLF-reporter allows selective and stable genetic labeling of human HSCsex vivoandin vivo.
Vinculin mediated axon growth requires interaction with actin but not talin
Authors: Mandal Pranay , Belapurkar Vivek , Nair Deepak , Ramanan Narendrakumar 
Published: June 2020

AbstractAxon growth requires coordination of the actin cytoskeleton by actin-binding proteins in the extending neurites. Vinculin is a major constituent of focal adhesion but its role in neuronal migration and axon growth is poorly understood. We found that vinculin deletion in mouse neocortical neurons attenuated axon growth bothin vitroandin vivo. Using different functional mutants of vinculin, we found that expression of a constitutively active vinculin significantly enhanced axon growth while the head-neck domain had a moderate inhibitory effect. Interesting, we found that vinculin-talin interaction was dispensable for axon growth and neuronal migration. Strikingly, expression of the tail domain delayed migration, increased branching and stunted axon. Inhibition of the Arp2/3 complex or abolishing the tail domain interaction with actin completely reversed the branching phenotype caused by tail domain expression without affecting axon length. Super-resolution microscopy showed increased mobile fraction of actin in tail domain expressing neurons. Our results provide novel insights into the role of vinculin and its functional domains in regulating neuronal migration and axon growth.
RING Finger Protein 11 (RNF11) modulates dopamine release inDrosophila
Authors: Champaloux Eve Privman , Donelson Nathan , Pyakurel Poojan , Wolin Danielle , Ostendorf Leah , Denno Madelaine , Borman Ryan , Burke Chris , Short-Miller Jonah C. , Yoder Maria R. , Copeland Jeffrey M. , Sanyal Subhabrata , Venton B. Jill 
Published: June 2020

AbstractRecent work indicates a role for RING finger protein 11 (RNF11) in Parkinson disease (PD) pathology, which involves the loss of dopaminergic neurons. However, the role ofRNF11in regulating dopamine neurotransmission has not been studied. In this work, we tested the effect ofRNF11RNAi knockdown or overexpression on stimulated dopamine release in the larvalDrosophilacentral nervous system. Dopamine release was stimulated using optogenetics and monitored in real-time using fast-scan cyclic voltammetry at an electrode implanted in an isolated ventral nerve cord.RNF11knockdown doubled dopamine release, but there was no decrease in dopamine fromRNF11overexpression.RNF11knockdown did not significantly increase stimulated serotonin or octopamine release, indicating the effect is dopamine specific. Dopamine clearance was also changed, asRNF11RNAi flies had a higher VmaxandRNF11overexpressing flies had a lower Vmaxthan control flies.RNF11RNAi flies had increased mRNA levels of dopamine transporter (DAT) inRNF11, confirming changes in DAT. InRNF11RNAi flies, release was maintained better for stimulations repeated at short intervals, indicating increases in the recycled releasable pool of dopamine. Nisoxetine, a DAT inhibitor, and flupenthixol, a D2 antagonist, did not affectRNF11RNAi or overexpressing flies differently than control. Thus,RNF11knockdown causes early changes in dopamine neurotransmission, and this is the first work to demonstrate thatRNF11affects both dopamine release and uptake.RNF11expression decreases in human dopaminergic neurons during PD, and that decrease may be protective by increasing dopamine neurotransmission in the surviving dopaminergic neurons.
A Parallel Ratchet-Stroke Mechanism Leads to an Optimum Force for Molecular Motor Function
Authors: Mallimadugula U.L. , Galburt E.A. 
Published: June 2020

ABSTRACTMolecular motors convert chemical potential energy into mechanical work and perform a great number of critical biological functions. Examples include the polymerization and manipulation of nucleic acids, the generation of cellular motility and contractility, the formation and maintenance of cell shape, and the transport of materials within cells. The mechanisms underlying these molecular machines are routinely divided into two categories: Brownian ratchet and power stroke. While a ratchet uses chemical energy to bias thermally activated motion, a stroke depends on a direct coupling between chemical events and motion. However, the multi-dimensional nature of protein energy landscapes allows for the possibility of multiple reaction paths connecting two states. Here, we investigate the properties of a hypothetical molecular motor able to utilize parallel ratchet and stroke translocation mechanisms. We explore motor velocity and force-dependence as a function of the energy landscape of each path and reveal the potential for such a mechanism to result in an optimum force for motor function. We explore how the presence of this optimum depends on the rates of the individual paths and show that the distribution of stepping times characterized by the randomness parameter may be used to test for parallel path mechanisms. Lastly, we caution that experimental data consisting solely of measurements of velocity as a function of ATP concentration and force cannot be used to eliminate the possibility of such a parallel path mechanism.SIGNIFICANCEMolecular motors perform various mechanical functions in cells allowing them to move, replicate and perform various housekeeping functions required for life. Biophysical studies often aim to determine the molecular mechanism by which these motors convert chemical energy to mechanical work by fitting experimental data with kinetic models that fall into one of two classes: Brownian ratchets or power strokes. However, nothinga priorirequires that a motor function via a single mechanism. Here, we consider a theoretical construct where a motor has access to both class of mechanism in parallel. Combining stochastic simulations and analytical solutions we describe unique signatures of such a mechanism that could be observed experimentally. We also show that absence of these signatures does not formally eliminate the existence of such a parallel mechanism. These findings expand our theoretical understanding of the potential motor behaviors with which to interpret experimental results.
Spatial metabolomics identifies localized chemical changes in heart tissue during chronic cardiac Chagas disease
Authors: Dean Danya A. , Gautham  , Siqueira-Neto Jair L. , McKerrow James H. , Dorrestein Pieter C. , McCall Laura-Isobel 
Published: June 2020

AbstractChagas disease (CD) is one of thirteen neglected tropical diseases caused by the parasiteTrypanosoma cruzi. CD is a vector-borne disease transmitted by triatomines but CD can also be transmitted through blood transfusions, organ transplants and congenital transmission. While endemic to Latin America,T. cruziinfects 7-8 million people worldwide and can induce severe cardiac symptoms including apical aneurysms, thromboembolisms and arrhythmias during the chronic stage of CD. However, these cardiac clinical manifestations and CD disease pathogenesis are not fully understood. Using spatial metabolomics (chemical cartography), we sought to understand the localized impact of infection on the cardiac metabolome of mice chronically infected with two divergentT. cruzistrains. Our data showed chemical differences in localized cardiac regions upon chronicT. cruziinfection, indicating that parasite infection changes the host metabolome at select sites in chronic CD. These sites were distinct from the sites of highest parasite burden. In addition, we identified acylcarnitines and phosphocholines as discriminatory chemical families within each heart region, comparing infected and uninfected samples. Overall, our study indicated overall and positional metabolic differences common to infection with differentT. cruzistrains, and identified select infection-modulated pathways. These results provide further insight into CD pathogenesis and demonstrate the advantage of a spatial perspective to understand infectious disease tropism.Author SummaryChagas disease (CD) is a tropical disease caused by the parasiteTrypanosoma cruzi. CD originated in South America; however, there are now 7-8 million people infected worldwide due to population movements. CD is transmitted through a triatomine vector, organ transplants, blood transfusions and congenital transmission. It occurs in two stages, an acute stage (usually asymptomatic) and the chronic stage. Chronic stage CD presents with severe cardiac symptoms such as heart failure, localized aneurysms and cardiomyopathy. Unfortunately, what causes severe cardiac symptoms in some individuals in chronic CD is not fully understood. Therefore, we used liquid chromatography-tandem mass spectrometry to analyze the heart tissue of chronicallyT. cruzi-infected and uninfected mice, to understand the impact of infection on the tissue metabolome. We identified discriminatory small molecules related toT. cruziinfection. We also determined that regions with the highest parasite burden are distinct from the regions with the largest changes in overall metabolite profile; these locations of high metabolic perturbation provide a molecular mechanism to why localized cardiac symptoms occur in CD. Overall, our work gives insight to chronic cardiac CD symptom development and shapes a framework for novel treatment and biomarker development.