bluuebunny/crossref_metadata_2025_split huggingface dataset:
Recombination in Sarbecovirus lineage and mutations/insertions in spike protein linked to the emergence and adaptation of SARS-CoV-2
Authors: Sharma Amresh Kumar , Kumari Priyanka , Som Anup 
Published: May 2020

AbstractThe outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Wuhan city, China in December 2019 and thereafter its spillover across the world has created a global pandemic and public health crisis. Researchers across the world are involved in finding the origin and evolution of SARS-CoV-2, its transmission route, molecular mechanism of interaction between SARS-CoV-2 and host cells, and the cause of pathogenicity etc. In this paper, we shed light on the origin, evolution and adaptation of SARS-CoV-2 into human systems. Our phylogenetic/evolutionary analysis supported that bat-CoV-RaTG13 is the closest relative of human SARS-CoV-2, outbreak of SARS-CoV-2 took place via inter-intra species mode of transmission, and host-specific adaptation occurred in SARS-CoV-2. Furthermore, genome recombination analysis found that Sarbecoviruses, the subgenus containing SARS-CoV and SARS-CoV-2, undergo frequent recombination. Multiple sequence alignment (MSA) of spike proteins revealed the insertion of four amino acid residues “PRRA” (Proline-Arginine-Arginine-Alanine) into the SARS-CoV-2 human strains. Structural modeling of spike protein of bat-CoV-RaTG13 also shows a high number of mutations at one of the receptor binding domains (RBD). Overall, this study finds that the probable origin of SARS-CoV-2 is the results of intra-species recombination events between bat coronaviruses belonging to Sarbecovirus subgenus and the insertion of amino acid residues “PRRA” and mutations in the RBD in spike protein are probably responsible for the adaptation of SARS-CoV-2 into human systems. Thus, our findings add strength to the existing knowledge on the origin and adaptation of SARS-CoV-2, and can be useful for understanding the molecular mechanisms of interaction between SARS-CoV-2 and host cells which is crucial for vaccine design and predicting future pandemics.
A therapeutic combination of two small molecule toxin inhibitors provides pancontinental preclinical efficacy against viper snakebite
Authors: Albulescu Laura-Oana , Xie Chunfang , Ainsworth Stuart , Alsolaiss Jaffer , Crittenden Edouard , Dawson Charlotte A. , Softley Rowan , Bartlett Keirah E. , Harrison Robert A. , Kool Jeroen , Casewell Nicholas R. 
Published: May 2020

AbstractSnakebite is a medical emergency causing high mortality and morbidity in rural tropical communities that typically experience delayed access to unaffordable therapeutics. Viperid snakes are responsible for the majority of envenomings, but extensive interspecific variation in venom composition dictates that different antivenom treatments are used in different parts of the world, resulting in clinical and fiscal snakebite management challenges. Here, we show that a number of repurposed Phase 2-approved small molecules are capable of broadly neutralizing distinct viper venom bioactivitiesin vitroby inhibiting different enzymatic toxin families. Furthermore, using multiplein vivomodels of envenoming, we demonstrate that a single dose of a rationally-selected dual inhibitor combination consisting of marimastat and varespladib prevents lethality caused by venom from the most medically-important vipers of Africa, South Asia and Central America. Our findings strongly support the translation of combinations of safe and affordable enzyme inhibitors as novel broad-spectrum therapeutics for snakebite.
Metabolite profiling of experimental cutaneous leishmaniasis lesions demonstrates significant perturbations in tissue phospholipids
Authors: Parab Adwaita R. , Thomas Diane , Lostracco-Johnson Sharon , de Siqueira-Neto Jair Lage , McKerrow James , Dorrestein Pieter C. , McCall Laura-Isobel 
Published: May 2020

AbstractEach year 700,000 to 1.2 million new cases of cutaneous leishmaniasis (CL) are reported and yet CL remains one of thirteen diseases classified as neglected tropical diseases (NTDs).Leishmania majoris one of several different species of that same genus that can cause CL. Current CL treatments are limited by adverse effects and rising resistance. Studying disease metabolism at the site of infection can lead to new drug targets. In this study, samples were collected from mice infected in the ear and footpad withL. majorand analyzed by untargeted liquid chromatography-tandem mass spectrometry (LC-MS/MS). Significant differences in overall metabolite profiles were noted in the ear at the site of the lesion. Interestingly, lesion-adjacent, macroscopically healthy sites also showed alterations in specific metabolites, including select phosphocholines (PCs). Host-derived PCs in the lowerm/zrange (m/z200-799) showed an increase with infection in the ear at the lesion site, while those in the higherm/zrange (m/z800-899) were decreased with infection at the lesion site. Overall, our results expanded our understanding of the mechanisms of CL pathogenesis through the host metabolism and may lead to new curative measures against infection withLeishmania.Author summaryCutaneous leishmaniasis (CL) is one of thirteen neglected tropical diseases in the world today. It is an infectious disease with a wide distribution spanning five continents, with increasing distribution expected due to climate change. CL manifests as skin lesions and ulcers that are disabling and stigmatized. With the current treatment options being limited, studying host-pathogen metabolism can uncover mechanisms of disease pathogenesis that may lead to new curative measures against infection. In this paper we used untargeted metabolomics to address molecular-level changes occurringin vivoin experimental skin lesions ofLeishmania major. Distinct global metabolic profiles were observed. Total phosphocholines (PCs) and those in the lowerm/zranges were significantly higher at the site of the skin lesion in the ear. In addition, specific PCs as well as PCs of variedm/zranges were also affected at healthy-appearing lesion-adjacent sites, indicating that infection-induced metabolic perturbations are not restricted to the lesion site. Ultimately, these results provide essential clues to the metabolic pathways affected by CL.
Passive motor learning: Oculomotor adaptation in the absence of feedback on behavioral errors
Authors: Cain Matan , Joshua Mati 
Published: May 2020

AbstractMotor adaptation is commonly thought to be a trial-and-error process in which accuracy of movement improves with repetition of behavior. We challenged this view by testing whether erroneous movements are necessary for motor adaptation. In the eye movement system, the association between motor command and errors can be disentangled, since errors in the predicted stimulus trajectory can be perceived even without movements. We modified a smooth pursuit eye movement adaptation paradigm in which monkeys learn to make an eye movement that predicts an upcoming change in target direction. We trained monkeys to fixate on a target while covertly, an additional target initially moved in one direction and then changed direction after 250 ms. Monkeys showed a learned response to infrequent probe trials in which they were instructed to follow the moving target. Further experiments confirmed that probing learning or residual eye movement during fixation did not drive learning. These results show that movement is not necessary for motor adaptation and provide an animal model for studying how passive learning is implemented. The standard model assumes that the interaction between movement and error signals in the cerebellum underlies adaptive learning. Our results indicate that either sensory inputs are sufficient for driving learning in the cerebellum or that learning is implemented partly outside the cerebellum.
Identification of hypoxia-specific biomarkers in salmonids using RNA-sequencing and validation using high-throughput qPCR
Authors: Akbarzadeh Arash , Houde Aimee Lee S. , Sutherland Ben J.G. , Günther Oliver P. , Miller Kristina M. 
Published: May 2020

AbstractIdentifying early gene expression responses to hypoxia (i.e., low dissolved oxygen) as a tool to assess the degree of exposure to this stressor is crucial for salmonids, because they are increasingly exposed to hypoxic stress due to anthropogenic habitat change, e.g., global warming, excessive nutrient loading, and persistent algal blooms. Our goal was to discover and validate gill gene expression biomarkers specific to the hypoxia response in salmonids across multi-stressor conditions. Gill tissue was collected from 24 freshwater juvenile Chinook salmon (Oncorhynchus tshawytscha), held in normoxia [dissolved oxygen (DO) > 8 mg L−1] and hypoxia (DO = 4□5 mg L−1) in 10 and 18°C temperatures for up to six days. RNA-sequencing (RNA-seq) was then used to discover 240 differentially expressed genes between hypoxic and normoxic conditions, but not affected by temperature. The most significantly differentially expressed genes had functional roles in the cell cycle and suppression of cell proliferation associated with hypoxic conditions. The most significant genes (n = 30) were selected for real-time qPCR assay development. These assays demonstrated a strong correlation (r = 0.88; p < 0.001) between the expression values from RNA-seq and the fold changes from qPCR. Further, qPCR of the 30 candidate hypoxia biomarkers was applied to an additional 322 Chinook salmon exposed to hypoxic and normoxic conditions to reveal the top biomarkers to define hypoxic stress. Multivariate analyses revealed that smolt stage, water salinity, and morbidity status were relevant factors to consider with the expression of these genes in relation to hypoxic stress. These hypoxia candidate genes will be put into application screening Chinook salmon to determine the identity of stressors impacting the fish.
Integration of intra- and inter-sexual selection signaling
Authors: Garrison Courtney R. , Royauté Raphaël , Dochtermann Ned A. 
Published: May 2020

AbstractSexual selection can drive the evolution of dramatic morphological and behavioral signals. This selection acts on both specific components of signals and overall signals that combine multiple sources of information. By studying the structure and variability of signals and their components we can improve our understanding of how sexual selection operates. Signal integration can be understood through the lens of classical signaling hypotheses or more recently defined systems approaches. Using crickets (Acheta domesticus), we evaluated competing hypotheses about signal integration and how observed patterns of signal integration fit into both systems approaches and classic signaling hypotheses. We measured three call types of 127 male crickets multiple times for a total of 930 observations. We found evidence for an underlying integrated signaling syndrome from which both intra- and intersexual signals stemmed. This syndrome was also affected by mass, suggesting honest signaling in the species. The presence of an integrated syndrome demonstrates that intra- and intersexual signals are incorporated in a redundant signal strategy inAcheta domesticus. This support for honest and redundant signaling is also consistent with a systems framework description of signals as degenerate and functionally modular—demonstrating one way in which classic hypotheses can be integrated with modern systems approaches.
Multistability in cellular differentiation enabled by a network of three mutually repressing master regulators
Authors: Duddu Atchuta Srinivas , Sahoo Sarthak , Hati Souvadra , Jhunjhunwala Siddharth , Jolly Mohit Kumar 
Published: May 2020

AbstractIdentifying the design principles of complex regulatory networks driving cellular decision-making remains essential to decode embryonic development as well as enhance cellular reprogramming. A well-studied network motif involved in cellular decision-making is a toggle switch – a set of two opposing transcription factors A and B, each of which is a master regulator of a specific cell-fate and can inhibit the activity of the other. A toggle switch can lead to two possible states – (high A, low B) and (low A, high B), and drives the ‘either-or’ choice between these two cell-fates for a common progenitor cell. However, the principles of coupled toggle switches remains unclear. Here, we investigate the dynamics of three master regulators A, B and C inhibiting each other, thus forming three coupled toggle switches to form a toggle triad. Our simulations show that this toggle triad can lead to co-existence of cells into three differentiated ‘single positive’ phenotypes – (high A, low B, low C), (low A, high B, low C), and (low A, low B, high C). Moreover, the hybrid or ‘double positive’ phenotypes – (high A, high B, low C), (low A, high B, high C) and (high A, low B, high C) – can co-exist together with ‘single positive’ phenotypes. Including self-activation loops on A, B and C can increase the frequency of ‘double positive’ states. Finally, we apply our results to understand the cellular decision-making in terms of differentiation of naïve CD4+ T cells into Th1, Th2 and Th17 states, where hybrid Th1/Th2 and hybrid Th1/Th17 cells have been reported in addition to the Th1, Th2 and Th17 ones. Our results offer novel insights into the design principles of a multistable network topology and provides a framework for synthetic biology to design tristable systems.
Denitrification kinetics indicates nitrous oxide uptake is unaffected by electron competition in Accumulibacter
Authors: Samarpita Roy , Nirakar Pradhan , Yong NG How , Stefan Wuertz 
Published: May 2020

ABSTRACTDenitrifying phosphorus removal is a cost and energy efficient treatment technology that relies on polyphosphate accumulating organisms (DPAOs) utilizing nitrate or nitrite as terminal electron acceptor. Denitrification is a multistep process and many organisms do not possess the complete pathway, leading to the accumulation of intermediates such as nitrous oxide (N2O), a potent greenhouse gas and ozone depleting substance.CandidatusAccumulibacter organisms are prevalent in denitrifying phosphorus removal processes and, according to genomic analyses, appear to vary in their denitrification abilities based on their lineage. Yet, denitrification kinetics and nitrous oxide accumulation by Accumulibacter after long-term exposure to either nitrate or nitrite as electron acceptor have never been compared. We investigated the preferential use of the nitrogen oxides involved in denitrification and nitrous oxide accumulation in two enrichments of Accumulibacter and a competitor – the glycogen accumulating organismCandidatusCompetibacter. A metabolic model was modified to predict phosphorus removal and denitrification rates when nitrate, nitrite or N2O were added as electron acceptors in different combinations. Unlike previous studies, no N2O accumulation was observed for Accumulibacter in the presence of multiple electron acceptors. Electron competition did not affect denitrification kinetics or N2O accumulation in Accumulibacter or Competibacter. Despite the presence of sufficient internal storage polymers (polyhydroxyalkanoates, or PHA) as energy source for each denitrification step, the extent of denitrification observed was dependent on the dominant organism in the enrichment. Accumulibacter showed complete denitrification and N2O utilization, whereas for Competibacter denitrification was limited to reduction of nitrate to nitrite. These findings indicate that DPAOs can contribute to lowering N2O emissions in the presence of multiple electron acceptors under partial nitritation conditions.
A single dose SARS-CoV-2 simulating particle vaccine induces potent neutralizing activities
Authors: Yin Di , Ling Sikai , Tian Xiaolong , Li Yang , Xu Zhijue , Jiang Hewei , Zhang Xue , Wang Xiaoyuan , Shi Yi , Zhang Yan , Da Lintai , Tao Sheng-ce , Wang Quanjun , Xu Jianjiang , Ying Tianlei , Hong Jiaxu , Cai Yujia 
Published: May 2020

ABSTRACTCoronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) for which a vaccine is urgently needed to control its spreading. To facilitate the representation of a native-like immunogen without being infectious, here, we reported a SARS-CoV-2 vaccine candidate (designated ShaCoVacc) by incorporating spike-encoding mRNA inside and decorating spike protein on the surface of the virus simulating particles (VSPs) derived from lentiviral particles. We characterized the mRNA copy number, glycosylation status, transduction efficiency, and innate immune property of the new vaccine platform. Importantly, we showed the ShaCoVacc induced strong spike-specific humoral immune responses and potent neutralizing activities by a single injection. Additionally, we disclosed the epitopes of spike-specific antibodies using peptide microarray and revealed epitopes susceptible to specific neutralizing antibodies. These results support further development of ShaCoVacc as a candidate vaccine for COVID-19 and VSP may serve as a new vaccine platform for emerging infectious diseases.
Two mutations P/L and Y/C in SARS-CoV-2 helicase domain exist together and influence helicase RNA binding
Authors: Begum Feroza , Banerjee Arup Kumar , Tripathi Prem Prakash , Ray Upasana 
Published: May 2020

AbstractRNA helicases play pivotal role in RNA replication by catalysing the unwinding of complex RNA duplex structures into single strands in ATP/NTP dependent manner. SARS coronavirus 2 (SARS-CoV-2) is a single stranded positive sense RNA virus belonging to the familyCoronaviridae. The viral RNA encodes non structural protein Nsp13 or the viral helicase protein that helps the viral RNA dependent RNA polymerase (RdRp) to execute RNA replication by unwinding the RNA duplexes. In this study we identified a novel mutation at position 541of the helicase where the tyrosine (Y) got substituted with cytosine (C). We found that Y541C is a destabilizing mutation increasing the molecular flexibility and leading to decreased affinity of helicase binding with RNA. Earlier we had reported a mutation P504L in the helicase protein for which had not performed RNA binding study. Here we report that P504L mutation leads to increased affinity of helicase RNA interaction. So, both these mutations have opposite effects on RNA binding. Moreover, we found a significant fraction of isolate population where both P504L and Y541C mutations were co-existing.
Experimental glaucoma retinal proteomics identifies mutually exclusive and overlapping molecular characteristics with human glaucoma
Authors: Mirzaei Mehdi , Gupta Vivek , Chitranshi Nitin , Deng Liting , Pushpitha Kanishka , Abbasi Mojdeh , Chick Joel , Rajput Rashi , Wu Yunqi , McKay Matthew. J. , Salekdeh Ghasem H , Gupta Veer , Haynes Paul A. , Graham Stuart L. 
Published: May 2020

AbstractCurrent evidence suggests that exposure to chronically induced intraocular pressure (IOP) leads to neurodegenerative changes in the inner retina. This study aimed to determine retinal proteomic alterations in a rat model of glaucoma and compared findings with human retinal proteomics changes in glaucoma reported previously. We developed an experimental glaucoma rat model by subjecting the rats to increased IOP (9.3±0.1 vs 20.8±1.6 mm Hg) by weekly microbead injections into the eye (8 weeks). The retinal tissues were harvested from control and glaucomatous eyes and protein expression changes analysed using multiplexed quantitative proteomics approach. Immunofluorescence was performed for selected protein markers for data validation. Our study identified 4304 proteins in the rat retinas. Out of these, 139 proteins were downregulated (≤0.83) while expression of 109 proteins was upregulated (≥1.2-fold change) under glaucoma conditions (p≤0.05). Computational analysis revealed reduced expression of proteins associated with glutathione metabolism, mitochondrial dysfunction/oxidative phosphorylation, cytoskeleton and actin filament organisation, along with increased expression coagulation cascade, apoptosis, oxidative stress and RNA processing markers. Further functional network analysis highlighted the differential modulation of nuclear receptor signalling, cellular survival, protein synthesis, transport and cellular assembly pathways. Alterations in crystallin family, glutathione metabolism and mitochondrial dysfunction associated proteins shared similarities between the animal model of glaucoma and the human disease condition. In contrast, the activation of the classical complement pathway and upregulation of cholesterol transport proteins, were exclusive to the human glaucoma. These findings provide insights into the neurodegenerative mechanisms that are specifically affected in the retina in response to chronically elevated IOP.
Pre-existing and de novo humoral immunity to SARS-CoV-2 in humans
Authors: Ng Kevin W. , Faulkner Nikhil , Cornish Georgina H. , Rosa Annachiara , Harvey Ruth , Hussain Saira , Ulferts Rachel , Earl Christopher , Wrobel Antoni , Benton Donald , Roustan Chloe , Bolland William , Thompson Rachael , Agua-Doce Ana , Hobson Philip , Heaney Judith , Rickman Hannah , Paraskevopoulou Stavroula , Houlihan Catherine F. , Thomson Kirsty , Sanchez Emilie , Brealey David , Shin Gee Yen , Spyer Moira J. , Joshi Dhira , O’Reilly Nicola , Walker Philip A. , Kjaer Svend , Riddell Andrew , Moore Catherine , Jebson Bethany R. , Wilkinson Meredyth G.Ll. , Marshall Lucy R. , Rosser Elizabeth C. , Radziszewska Anna , Peckham Hannah , Ciurtin Coziana , Wedderburn Lucy R. , Beale Rupert , Swanton Charles , Gandhi Sonia , Stockinger Brigitta , McCauley John , Gamblin Steve , McCoy Laura E. , Cherepanov Peter , Nastouli Eleni , Kassiotis George 
Published: May 2020

AbstractSeveral related human coronaviruses (HCoVs) are endemic in the human population, causing mild respiratory infections1. Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the etiologic agent of Coronavirus disease 2019 (COVID-19), is a recent zoonotic infection that has quickly reached pandemic proportions2,3. Zoonotic introduction of novel coronaviruses is thought to occur in the absence of pre-existing immunity in the target human population. Using diverse assays for detection of antibodies reactive with the SARS-CoV-2 spike (S) glycoprotein, we demonstrate the presence of pre-existing humoral immunity in uninfected and unexposed humans to the new coronavirus. SARS-CoV-2 S-reactive antibodies were readily detectable by a sensitive flow cytometry-based method in SARS-CoV-2-uninfected individuals and were particularly prevalent in children and adolescents. These were predominantly of the IgG class and targeted the S2 subunit. In contrast, SARS-CoV-2 infection induced higher titres of SARS-CoV-2 S-reactive IgG antibodies, targeting both the S1 and S2 subunits, as well as concomitant IgM and IgA antibodies, lasting throughout the observation period of 6 weeks since symptoms onset. SARS-CoV-2-uninfected donor sera also variably reacted with SARS-CoV-2 S and nucleoprotein (N), but not with the S1 subunit or the receptor binding domain (RBD) of S on standard enzyme immunoassays. Notably, SARS-CoV-2-uninfected donor sera exhibited specific neutralising activity against SARS-CoV-2 and SARS-CoV-2 S pseudotypes, according to levels of SARS-CoV-2 S-binding IgG and with efficiencies comparable to those of COVID-19 patient sera. Distinguishing pre-existing and de novo antibody responses to SARS-CoV-2 will be critical for our understanding of susceptibility to and the natural course of SARS-CoV-2 infection.