bluuebunny/crossref_metadata_2025_split huggingface dataset:
What Markov state models can and cannot do: Correlation versus path-based observables in protein folding models
Authors: Suárez Ernesto , Wiewiora Rafal P. , Wehmeyer Chris , Noé Frank , Chodera John D. , Zuckerman Daniel M. 
Published: November 2020

AbstractMarkov state models (MSMs) have been widely applied to study the kinetics and pathways of protein conformational dynamics based on statistical analysis of molecular dynamics (MD) simulations. These MSMs coarse-grain both configuration space and time in ways that limit what kinds of observables they can reproduce with high fidelity over different spatial and temporal resolutions. Despite their popularity, there is still limited understanding of which biophysical observables can be computed from these MSMs in a robust and unbiased manner, and which suffer from the space-time coarse-graining intrinsic in the MSM model. Most theoretical arguments and practical validity tests for MSMs rely on long-time equilibrium kinetics, such as the slowest relaxation timescales and experimentally observable time-correlation functions. Here, we perform an extensive assessment of the ability of well-validated protein folding MSMs to accuractely reproduce path-based observable such as mean first-passage times (MFPTs) and transition path mechanisms compared to a direct trajectory analysis. We also assess a recently proposed class of history-augmented MSMs (haMSMs) that exploit additional information not accounted for in standard MSMs. We conclude with some practical guidance on the use of MSMs to study various problems in conformational dynamics of biomolecules. In brief, MSMs can accurately reproduce correlation functions slower than the lag time, but path-based observables can only be reliably reproduced if the lifetimes of states exceed the lag time, which is a much stricter requirement. Even in the presence of short-lived states, we find that haMSMs reproduce path-based observables more reliably.
Bulk flow of cerebrospinal fluid observed in periarterial spaces is not an artifact of injection
Authors: Raghunandan Aditya , Ladrón-de-Guevara Antonio , Tithof Jeffrey , Mestre Humberto , Nedergaard Maiken , Thomas John H. , Kelley Douglas H. 
Published: November 2020

AbstractCerebrospinal fluid (CSF) flowing through periarterial spaces is integral to the brain’s mechanism for clearing metabolic waste products. Experiments that track tracer particles injected into the cisterna magna of mouse brains have shown evidence of pulsatile CSF flow in pial periarterial spaces, with a bulk flow in the same direction as blood flow. However, the driving mechanism remains elusive. Several studies have suggested that the bulk flow might be an artifact, driven by the injection itself. Here, we address this hypothesis with newin vivoexperiments where tracer particles are injected into the cisterna magna using a dual-syringe system, with simultaneous injection and withdrawal of equal amounts of fluid. This method produces no net increase in CSF volume and no significant increase in intracranial pressure. Yet, particle-tracking reveals flows in the pial periarterial spaces that are completely consistent with the flows observed in earlier experiments with single-syringe injection.
The SARS-CoV-2 and other human coronavirus spike proteins are fine-tuned towards temperature and proteases of the human airways
Authors: Laporte Manon , Stevaert Annelies , Raeymaekers Valerie , Van Berwaer Ria , Martens Katleen , Pöhlmann Stefan , Naesens Lieve 
Published: November 2020

ABSTRACTThe high transmissibility of SARS-CoV-2 is related to abundant replication in the upper airways, which is not observed for the other highly pathogenic coronaviruses SARS-CoV-1 and MERS-CoV. We here reveal features of the coronavirus spike (S) protein, which optimize the virus towards different parts of the respiratory tract. First, the SARS-CoV-2 spike (SARS-2-S) reached higher levels in pseudoparticles when produced at 33°C instead of 37°C. Even stronger preference for the upper airway temperature of 33°C was evident for the S protein of HCoV-229E, a common cold coronavirus. In contrast, the S proteins of SARS-CoV-1 and MERS-CoV favored 37°C, in accordance with their preference for the lower airways. Next, SARS-2-S proved efficiently activated by TMPRSS13, besides the previously identified host cell protease TMPRSS2, which may broaden the cell tropism of SARS-CoV-2. TMPRSS13 was found to be an effective spike activator for the virulent coronaviruses but not the common cold HCoV-229E virus. Activation by these proteases requires pre-cleavage of the SARS-2-S S1/S2 cleavage loop, and both its furin motif and extended loop length proved critical to achieve virus entry into airway epithelial cells. Finally, we show that the D614G mutation in SARS-2-S increases S protein stability and expression at 37°C, and promotes virus entry via cathepsin B/L activation. These spike properties might promote virus spread, potentially explaining why the G614 variant is currently predominating worldwide. Collectively, our findings indicate how the coronavirus spike protein is fine-tuned towards the temperature and protease conditions of the airways, to enhance virus transmission and pathology.SIGNIFICANCE STATEMENTThe rapid spread of SARS-CoV-2, the cause of COVID-19, is related to abundant replication in the upper airways, which is not observed for other highly pathogenic human coronaviruses. We here reveal features of the coronavirus spike (S) protein, which optimize the virus towards different parts of the respiratory tract. Coronavirus spikes exhibit distinct temperature preference to precisely match the upper (~33°C) or lower (37°C) airways. We identified airway proteases that activate the spike for virus entry into cells, including one protease that may mediate coronavirus virulence. Also, a link was seen between spike stability and entry via endosomal proteases. This mechanism of spike fine-tuning could explain why the SARS-CoV-2 spike-D614G mutant is more transmissible and therefore globally predominant.
Subsidy Accessibility Drives Asymmetric Food Web Responses
Authors: Gutgesell Marie , McMeans Bailey C. , Guzzo Matthew M. , deGroot Valesca , Fisk Aaron T. , Johnson Timothy B. , McCann Kevin S. 
Published: November 2020

AbstractGlobal change is fundamentally altering flows of natural and anthropogenic subsidies across space and time. After a pointed call for research on subsidies in the 1990s, an industry of empirical work has documented the ubiquitous role subsidies play in ecosystem structure, stability and function. Here, we argue that physical constraints (e.g., water temperature) and species traits can govern a species’ accessibility to resource subsidies, and that these physical constraints have been largely overlooked in the subsidy literature. We examined the input of a high quality, point-source anthropogenic subsidy into a recipient freshwater lake food web (i.e., released net-pen aquaculture feed in Parry Sound, Lake Huron), to demonstrate the importance of subsidy accessibility in governing recipient whole food web responses. By using a combined bio-tracer approach, we detect a gradient in accessibility of the anthropogenic subsidy within the surrounding food web driven by the thermal tolerances of three constituent species. This thermally-driven accessibility gradient drives asymmetrical changes in food web structure, effectively rewiring the recipient lake food web and altering patterns in secondary production with yet unknown stability consequences. Since aquaculture is predicted to increase significantly in coming decades to support growing human populations, and global change is altering temperature regimes, then this form of food web alteration may be expected to occur frequently. We argue that subsidy accessibility is a key characteristic of recipient food web interactions that must be considered when trying to understand the impacts of subsidies on ecosystem stability and function under continued global change.
Essential role of non-vesicular lipid transport in microtubule-controlled cell polarisation
Authors: Hersberger-Trost M. , Dreher D. , Huisman S.M. , Kijowski A.R. , Gemünden M. , Klemm R.W. , Brunner D. 
Published: November 2020

AbstractCell polarisation is a fundamental biological process. Fission yeast is a key model system to study the molecular basis of microtubule-controlled cell polarisation. In this process, cells define prospective growth sites by generating distinct plasma membrane domains enriched inde novosynthesised sterols. Microtubules restrict the number and location of these domains by depositing factors at the cell poles. The mechanisms underlying such sterol-rich membrane domain formation and polarisation are largely unknown. We found that the oxysterol-binding proteins kes1p, osh2p and kes3p define three independent sterol delivery pathways to the plasma membrane. These mediate different phases of cell polarisation in a phosphoinositide-dependent fashion and differ in their requirement for vesicular trafficking steps. The redundant, kes1p- and osh2p-dependent pathways are vital and prime cell polarisation by mediating the formation of randomly distributed sterol-rich plasma membrane domains. Subsequent microtubule-controlled polarisation of these domains preferentially employs kes1p that directly delivers sterols to the plasma membrane independent of cdc42p. In cells lacking kes1p, polarisation becomes cdc42p-dependent, utilising mainly the kes3p-dependent pathway. Our study uncovers an essential biological function for non-vesicular lipid transport and establishes a molecular basis for different sterol-delivery pathways acting in cdc42p-independent and cdc42p-dependent cell polarisation.
Neutrophil extracellular traps induce the epithelial-mesenchymal transition: implications in post-COVID-19 fibrosis
Authors: Pandolfi Laura , Bozzini Sara , Frangipane Vanessa , Percivalle Elena , De Luigi Ada , Violatto Martina Bruna , Lopez Gianluca , Gabanti Elisa , Carsana Luca , D’Amato Maura , Morosini Monica , De Amici Mara , Nebuloni Manuela , Fossali Tommaso , Colombo Riccardo , Saracino Laura , Codullo Veronica , Gnecchi Massimiliano , Bigini Paolo , Baldanti Fausto , Lilleri Daniele , Meloni Federica 
Published: November 2020

AbstractThe release of neutrophil extracellular traps (NETs), a process termed NETosis, avoids pathogen spread but may cause tissue injury. NETs have been found in severe COVID-19 patients, but their role in disease development is still unknown. The aim of this study is to assess the capacity of NETs to drive epithelial-mesenchymal transition (EMT) of lung epithelial cells and to analyze the involvement of NETs in COVID-19.Neutrophils activated with PMA (PMA-Neu), a stimulus known to induce NETs formation, induce both EMT and cell death in the lung epithelial cell line, A549. Notably, NETs isolated from PMA-Neu induce EMT without cell damage. Bronchoalveolar lavage fluid of severe COVID-19 patients showed high concentration of NETs. Thus, we tested in anin vitroalveolar model the hypothesis that virus-induced NET may drive EMT. Co-culturing A549 at air-liquid interface with alveolar macrophages, neutrophils and SARS-CoV2, we demonstrated a significant induction of the EMT in A549 together with high concentration of NETs, IL8 and IL1β, best-known inducers of NETosis. Lung tissues of COVID-19 deceased patients showed that epithelial cells are characterized by increased mesenchymal markers. These results show for the first time that NETosis plays a major role in triggering lung fibrosis in COVID-19 patients.
StableDNMT3LOverexpression in SH-SY5Y Neurons Recreates a Facet of the Genome-Wide Down Syndrome DNA Methylation Signature
Authors: Laufer Benjamin I. , Gomez J. Antonio , Jianu Julia M. , LaSalle Janine M. 
Published: November 2020

AbstractDown syndrome (DS) is characterized by a genome-wide profile of differential DNA methylation that is skewed towards hypermethylation in most tissues, including brain. The molecular mechanisms involve the overexpression of genes related to DNA methylation on chromosome 21. Here, we stably overexpressed the chromosome 21 gene DNA methyltransferase 3L (DNMT3L) in the human SH-SY5Y neuroblastoma cell line and assayed DNA methylation at over 26 million CpGs by whole genome bisulfite sequencing at three different developmental phases (undifferentiated, differentiating, and differentiated).DNMT3Loverexpression resulted in global CpG and CpG island hypermethylation as well as thousands of differentially methylated regions (DMRs). TheDNMT3LDMRs were skewed towards hypermethylation and mapped to genes involved in neurodevelopment, cellular signaling, and gene regulation. Merging the DMRs into a consensus profile where the cell lines clustered by genotype and then phase demonstrated that different regions of common genes are affected. The hypermethylated DMRs from all pairwise comparisons were enriched for regions of bivalent chromatin marked by H3K4me3 as well as differentially methylated CpGs from previous DS studies of diverse tissues. In contrast, the hypomethylated DMRs from all pairwise comparisons displayed a tissue-specific profile enriched for regions of heterochromatin marked by H3K9me3 during embryonic development. Taken together, we propose a mechanism whereby regions of bivalent chromatin that lose H3K4me3 during development are targeted by excess DNMT3L and become hypermethylated, while excess DNMT3L also evicts DNMT3A from heterochromatin, resulting in hypomethylation. Overall, these findings demonstrate thatDNMT3Loverexpression during neurodevelopment recreates a facet of the DS DNA methylation signature.
Potentiation of Long-Acting β2-Agonist and Glucocorticoid Responses in Human Airway Epithelial Cells by Modulation of Intracellular cAMP
Authors: Kim Yechan , Hou Vincent , Huff Ryan D. , Aguiar Jennifer A. , Revill Spencer , Tiessen Nicholas , Cao Quynh , Miller Matthew S. , Inman Mark D. , Ask Kjetil , Doxey Andrew C. , Hirota Jeremy A. 
Published: November 2020

ABSTRACTIntroductionOver 300 million people in the world live with asthma, resulting in 500,000 annual global deaths with future increases expected. It is estimated that around 50-80% of asthma exacerbations are due to viral infections. Currently, a combination of long-acting beta agonists (LABA) for bronchodilation and glucocorticoids (GCS) to control lung inflammation represent the dominant strategy for the management of asthma, however it is still sub-optimal in 35-50% of moderate-severe asthmatics resulting in persistent lung inflammation, impairment of lung function, and risk of mortality. Mechanistically, LABA/GCS combination therapy results in synergistic efficacy mediated by intracellular cyclic adenosine monophosphate (cAMP).HypothesisIncreasing intracellular cAMP during LABA/GCS combination therapy via inhibiting phosphodiesterase 4 (PDE4) and/or blocking export of cAMP by ATP Binding Cassette Transporter C4 (ABCC4), will potentiate anti-inflammatory responses of mainstay LABA/GCS therapy.MethodsExpression and localization experiments were performed usingin situhybridization and immunohistochemistry in human lung tissue from healthy subjects, while confirmatory transcript and protein expression analyses were performed in primary human airway epithelial cells and cell lines. Intervention experiments were performed on the human airway epithelial cell line, HBEC-6KT, by pre-treatment with combinations of LABA/GCS with PDE4 and/or ABCC4 inhibitors followed by Poly I:C or imiquimod challenge as a model for viral stimuli. Cytokine readouts for IL-6, IL-8, CXCL10/IP-10, and CCL5/RANTES were quantified by ELISA.ResultsUsing archived human lung and human airway epithelial cells, ABCC4 gene and protein expression were confirmedin vitroandin situ. LABA/GCS attenuation of Poly I:C or imiquimod-induced IL-6 and IL-8 was potentiated with ABCC4 and PDE4 inhibition, which was greater when ABCC4 and PDE4 inhibition was combined. Modulation of cAMP levels had no impact on LABA/GCS modulation of Poly I:C-induced CXCL10/IP-10 or CCL5/RANTES.ConclusionModulation of intracellular cAMP levels by PDE4 or ABCC4 inhibition is able to potentiate LABA/GCS efficacy in human airway epithelial cells challenged with viral stimuli. The data suggests further exploration of the value of adding cAMP modulators to mainstay LABA/GCS therapy in asthma for potentiated anti-inflammatory efficacy.
Increased and ectopic expression ofTriticum polonicum VRT-A2underlies elongated glumes and grains in hexaploid wheat in a dosage-dependent manner
Authors: Adamski Nikolai M. , Simmonds James , Brinton Jemima F. , Backhaus Anna E. , Chen Yi , Smedley Mark , Hayta Sadiye , Florio Tobin , Crane Pamela , Scott Peter , Pieri Alice , Hall Olyvia , Barclay J. Elaine , Clayton Myles , Doonan John H. , Nibau Candida , Uauy Cristobal 
Published: November 2020

AbstractFlower development is a major determinant of yield in crops. In wheat, natural variation for the size of spikelet and floral organs is particularly evident inTriticum polonicum, a tetraploid subspecies of wheat with long glumes, lemmas, and grains. Using map-based cloning, we identifiedVRT2, a MADS-box transcription factor belonging to theSVPfamily, as the gene underlying theT. polonicumlong-glume (P1)locus. The causalP1mutation is a sequence re-arrangement in intron-1 that results in both increased and ectopic expression of theT. polonicum VRT-A2allele. Based on allelic variation studies, we propose that the intron-1 mutation inVRT-A2is the uniqueT. polonicumspecies defining polymorphism, which was later introduced into hexaploid wheat via natural hybridizations. Near-isogenic lines differing for theP1locus revealed a gradient effect ofP1across florets. Transgenic lines of hexaploid wheat carrying theT. polonicum VRT-A2allele show that expression levels ofVRT-A2are highly correlated with spike, glume, grain, and floral organ length. These results highlight how changes in expression profiles, through variation incis-regulation, can impact on agronomic traits in a dosage-dependent manner in polyploid crops.One-sentence summaryAn intron-1 rearrangement in the MADS-box transcription factorVRT-A2leads to its misexpression and defines the long-glume phenotype of Polish wheat (T. polonicum).
Working Memory Gates Visual Input to Primate Prefrontal Neurons
Authors: Noudoost Behrad , Clark Kelsey L. , Moore Tirin 
Published: November 2020

AbstractVisually guided behavior relies on the integration of sensory input with information held in working memory. Yet it remains unclear how this is accomplished at the level of neural circuits. We studied the direct visual cortical inputs to neurons within a visuomotor area of prefrontal cortex in behaving monkeys. We show that the synaptic efficacy of visual cortical input to prefrontal cortex is gated by information held in working memory. Surprisingly, visual input to prefrontal neurons was found to target those with both visual and motor properties, rather than preferentially targeting other visual neurons. Furthermore, activity evoked from visual cortex was larger in magnitude, more synchronous, and more rapid, when monkeys remembered locations that matched the location of visual input. These results indicate that working memory directly influences the circuitry that transforms visual input into visually guided behavior.
AGORA2: Large scale reconstruction of the microbiome highlights wide-spread drug-metabolising capacities
Authors: Heinken Almut , Acharya Geeta , Ravcheev Dmitry A. , Hertel Johannes , Nyga Malgorzata , Okpala Onyedika Emmanuel , Hogan Marcus , Magnúsdóttir Stefanía , Martinelli Filippo , Preciat German , Edirisinghe Janaka N. , Henry Christopher S. , Fleming Ronan M.T. , Thiele Ines 
Published: November 2020

AbstractThe human microbiome influences the efficacy and safety of a wide variety of commonly prescribed drugs, yet comprehensive systems-level approaches to interrogate drug-microbiome interactions are lacking. Here, we present a computational resource of human microbial genome-scale reconstructions, deemed AGORA2, which accounts for 7,206 strains, includes microbial drug degradation and biotransformation, and was extensively curated based on comparative genomics and literature searches. AGORA2 serves as a knowledge base for the human microbiome and as a metabolic modelling resource. We demonstrate the latter by mechanistically modelling microbial drug metabolism capabilities in single strains and pairwise models. Moreover, we predict the individual-specific drug conversion potential in a cohort of 616 colorectal cancer patients and controls. This analysis reveals that some drug activation capabilities are present in only a subset of individuals, moreover, drug conversion potential correlate with clinical parameters. Thus, AGORA2 paves the way towards personalised, predictive analysis of host-drug-microbiome interactions.
Insights into G-Quadruplex–Hemin Dynamics Using Atomistic Simulations: Implications for Reactivity and Folding
Authors: Stadlbauer Petr , Islam Barira , Otyepka Michal , Chen Jielin , Monchaud David , Zhou Jun , Mergny Jean-Louis , Šponer Jiří 
Published: November 2020

ABSTRACTGuanine quadruplex nucleic acids (G4s) are involved in key biological processes such as replication or transcription. Beyond their biological relevance, G4s find applications as biotechnological tools since they readily bind hemin and enhance its peroxidase activity, creating a G4-DNAzyme. The biocatalytic properties of G4-DNAzymes have been thoroughly studied and used for biosensing purposes. Despite hundreds of applications and massive experimental efforts, the atomistic details of the reaction mechanism remain unclear. To help select between the different hypotheses currently under investigation, we use extended explicit-solvent molecular dynamics (MD) simulations to scrutinize the G4/hemin interaction. We find that besides the dominant conformation in which hemin is stacked atop the external G-quartets, hemin can also transiently bind to the loops and be brought to the external G-quartets through diverse delivery mechanisms. The simulations do not support the catalytic mechanism relying on a wobbling guanine. Similarly, catalytic role of the iron-bound water molecule is not in line with our results, however, given the simulation limitations, this observation should be considered with some caution. The simulations rather suggest tentative mechanisms in which the external G-quartet itself could be responsible for the unique H2O2-promoted biocatalytic properties of the G4/hemin complexes. Once stacked atop a terminal G-quartet, hemin rotates about its vertical axis while readily sampling shifted geometries where the iron transiently contacts oxygen atoms of the adjacent G-quartet. This dynamics is not apparent from the ensemble-averaged structure. We also visualize transient interactions between the stacked hemin and the G4 loops. Finally, we investigated interactions between hemin and on-pathway folding intermediates of the parallel-stranded G4 fold. The simulations suggest that hemin drives the folding of parallel-stranded G4s from slip-stranded intermediates, acting as a G4 chaperone. Limitations of the MD technique are briefly discussed.For Table of Contents Only