bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of lectin receptors for conserved SARS-CoV-2 glycosylation sites
Authors: Hoffmann David , Mereiter Stefan , Oh Yoo Jin , Monteil Vanessa , Zhu Rong , Canena Daniel , Hain Lisa , Laurent Elisabeth , Grünwald-Gruber Clemens , Novatchkova Maria , Ticevic Melita , Chabloz Antoine , Wirnsberger Gerald , Hagelkruys Astrid , Altmann Friedrich , Mach Lukas , Stadlmann Johannes , Oostenbrink Chris , Mirazimi Ali , Hinterdorfer Peter , Penninger Josef M. 
Published: April 2021

AbstractNew SARS-CoV-2 variants are continuously emerging with critical implications for therapies or vaccinations. All 22 N-glycan sites of SARS-CoV-2 Spike remain highly conserved among the variants B.1.1.7, 501Y.V2 and P.1, opening an avenue for robust therapeutic intervention. Here we used a comprehensive library of mammalian carbohydrate-binding proteins (lectins) to probe critical sugar residues on the full-length trimeric Spike and the receptor binding domain (RBD) of SARS-CoV-2. Two lectins, Clec4g and CD209c, were identified to strongly bind to Spike. Clec4g and CD209c binding to Spike was dissected and visualized in real time and at single molecule resolution using atomic force microscopy. 3D modelling showed that both lectins can bind to a glycan within the RBD-ACE2 interface and thus interferes with Spike binding to cell surfaces. Importantly, Clec4g and CD209c significantly reduced SARS-CoV-2 infections. These data report the first extensive map and 3D structural modelling of lectin-Spike interactions and uncovers candidate receptors involved in Spike binding and SARS-CoV-2 infections. The capacity of CLEC4G and mCD209c lectins to block SARS-CoV-2 viral entry holds promise for pan-variant therapeutic interventions.
Predicted Utility Modulates Working Memory Fidelity in the Brain
Authors: Levin Emily J. , Brissenden James A. , Fengler Alexander , Badre David 
Published: April 2021

AbstractThe predicted utility of information stored in working memory (WM) is hypothesized to influence the strategic allocation of WM resources. Prior work has shown that when information is prioritized, it is remembered with greater precision relative to other remembered items. However, these paradigms often complicate interpretation of the effects of predicted utility on item fidelity due to a concurrent memory load. Likewise, no fMRI studies have examined whether the predicted utility of an item modulates fidelity in the neural representation of items during the memory delay without a concurrent load. In the current study, we used fMRI to investigate whether predicted utility influences fidelity of WM representations in the brain. Using a generative model multivoxel analysis approach to estimate the quality of remembered representations across predicted utility conditions, we observed that items with greater predicted utility are maintained in memory with greater fidelity, even when they are the only item being maintained. Further, we found that this pattern follows a parametric relationship where more predicted utility corresponded to greater fidelity. These precision differences could not be accounted for based on a redistribution of resources among already-remembered items. Rather, we interpret these results in terms of a gating mechanism that allows for pre-allocation of resources based on predicted value alone. This evidence supports a theoretical distinction between resource allocation that occurs as a result of load and resource pre-allocation that occurs as a result of predicted utility.
Interactome analysis ofC. eleganssynapses by TurboID-based proximity labeling
Authors: Artan Murat , Barratt Stephen , Flynn Sean M. , Begum Farida , Skehel Mark , Nicolas Armel , de Bono Mario 
Published: April 2021

AbstractProximity labelling provides a powerfulin vivotool to characterize the proteome of sub-cellular structures and the interactome of specific proteins. Using the highly active biotin ligase TurboID, we optimize a proximity labelling protocol forC. elegans. We use this protocol to characterise the proteomes of the worm’s gut, muscle, skin, and nervous system. We express TurboID exclusively in the pair of AFD neurons and show we can identify known and previously unknown proteins expressed selectively in AFD. We knock TurboID into the endogenouselks-1gene, which encodes a presynaptic active zone protein. We identify many known ELKS-1 interacting proteins as well as previously uncharacterised synaptic proteins. Versatile vectors, and the inherent advantage ofC. elegansfor biochemistry, make proximity labelling a valuable addition to the nematode’s armory.TeaserWe optimize a TurboID proximity labeling protocol for C. elegans and use it to characterize tissue and synaptic proteomes
SARS-CoV-2 binding to ACE2 triggers pericyte-mediated angiotensin-evoked cerebral capillary constriction
Authors: Hirunpattarasilp Chanawee , James Gregory , Freitas Felipe , Sethi Huma , Kittler Josef T. , Huo Jiandong , Owens Raymond J. , Attwell David 
Published: April 2021

AbstractThe SARS-CoV-2 receptor, ACE2, is found on pericytes, contractile cells enwrapping capillaries that regulate brain, heart and kidney blood flow. ACE2 converts vasoconstricting angiotensin II into vasodilating angiotensin-(1-7). In brain slices from hamster, which has an ACE2 sequence similar to human ACE2, angiotensin II alone evoked only a small capillary constriction, but evoked a large pericyte-mediated capillary constriction generated by AT1 receptors in the presence of the SARS-CoV-2 receptor binding domain (RBD). The effect of the RBD was mimicked by blocking ACE2. A mutated non-binding RBD did not potentiate constriction. A similar RBD-potentiated capillary constriction occurred in human cortical slices. This constriction reflects an RBD-induced decrease in the conversion of angiotensin II to angiotensin-(1-7). The clinically-used drug losartan inhibited the RBD-potentiated constriction. Thus AT1 receptor blockers could be protective in SARS-CoV-2 infection by reducing pericyte-mediated blood flow reductions in the brain, and perhaps the heart and kidney.
A high-throughput fluorescence polarization assay to discover inhibitors of arenavirus and coronavirus exoribonucleases
Authors: Hernández Sergio , Feracci Mikael , De Jesus Carolina Trajano , El-Kazzi Priscila , Kaci Rafik , Garlatti Laura , Decroly Etienne , Canard Bruno , Ferron François , Alvarez Karine 
Published: April 2021

AbstractViral exoribonucleases are uncommon in the world of RNA viruses. To date, this activity has been identified only in theArenaviridaeand theCoronaviridaefamilies. These exoribonucleases play important but different roles in both families: for mammarenaviruses the exoribonuclease is involved in the suppression of the host immune response whereas for coronaviruses, exoribonuclease is both involved in a proofreading mechanism ensuring the genetic stability of viral genomes and participating to evasion of the host innate immunity. Because of their key roles, they constitute attractive targets for drug development. Here we present a high-throughput assay using fluorescence polarization to assess the viral exoribonuclease activity and its inhibition. We validate the assay using three different viral enzymes from SARS-CoV-2, lymphocytic choriomeningitis and Machupo viruses. The method is sensitive, robust, amenable to miniaturization (384 well plates) and allowed us to validate the proof-of-concept of the assay by screening a small focused compounds library (23 metal chelators). We also determined the IC50 of one inhibitor common to the three viruses.HighlightsArenaviridaeandCoronaviridaeviral families share an exoribonuclease activity of common evolutionary originArenaviridaeandCoronaviridaeexoribonuclease is an attractive target for drug developmentWe present a high-throughput assay in 384 well-plates for the screening of inhibitors using fluorescence polarizationWe validated the assay by screening of a focused library of 23 metal chelators against SARS-CoV-2, Lymphocytic Choriomeningitis virus and Machupo virus exoribonucleasesWe determined the IC50by fluorescence polarization of one inhibitor common to the three viruses.
Choosing between cocaine and sucrose under the influence: testing the effect of cocaine tolerance
Authors: Vandaele Y. , Ahmed S.H 
Published: April 2021

AbstractCocaine use not only depends on the reinforcing properties of the drug, but also on its intoxicating effects on alternative nondrug activities. In animal models investigating choice between cocaine and alternative sweet rewards, the latter influence can have a dramatic impact on choice outcomes. When cocaine intoxication at the moment of choice is prevented by imposing sufficiently long intervals between choice trials, animals typically prefer the sweet reward. However, when choosing under the drug influence is permitted, animals shift their preference in favor of cocaine. We previously hypothesized that this preference shift is mainly due to a direct suppression of responding for sweet reward by cocaine intoxication. Here we tested this hypothesis by making rats tolerant to this drug-induced behavioral suppression. Contrary to our expectation, tolerance did not prevent rats from shifting their preference to cocaine when choosing under the influence. Thus, other mechanisms must be invoked to explain the influence of cocaine intoxication on choice outcomes.
Native or non-native protein-protein docking models? Molecular dynamics to the rescue
Authors: Jandova Zuzana , Vargiu Attilio Vittorio , Bonvin Alexandre M. J. J. 
Published: April 2021

ABSTRACTMolecular docking excels at creating a plethora of potential models of protein-protein complexes. To correctly distinguish the favourable, native-like models from the remaining ones remains, however, a challenge. We assessed here if a protocol based on molecular dynamics (MD) simulations would allow to distinguish native from non-native models to complement scoring functions used in docking. To this end, first models for 25 protein-protein complexes were generated using HADDOCK. Next, MD simulations complemented with machine learning were used to discriminate between native and non-native complexes based on a combination of metrics reporting on the stability of the initial models. Native models showed higher stability in almost all measured properties, including the key ones used for scoring in the CAPRI competition, namely the positional root mean square deviations and fraction of native contacts from the initial docked model. A Random Forest classifier was trained, reaching 0.85 accuracy in correctly distinguishing native from non-native complexes. Reasonably modest simulation lengths in the order of 50 to 100 ns are already sufficient to reach this accuracy, which makes this approach applicable in practice.
Structural heterogeneity in biliverdin modulates spectral properties of Sandercyanin fluorescent protein
Authors: Ghosh Swagatha , Mondal Sayan , Yadav Keerti , Aggarwal Shantanu , Schaefer Wayne F. , Narayana Chandrabhas , Ramaswamy S. 
Published: April 2021

AbstractSandercyanin, a blue homo-tetrameric lipocalin protein purified from Canadian walleye (Stizostedion vitreus), is the first far-red fluorescent protein reported in vertebrates(1–3). Sandercyanin binds non-covalently to biliverdin IXα (BLA) and fluoresces at 675nm on excitation at 375nm and 635nm(1). Sandercyanin fluorescence can be harnessed for manyin vivoapplications when engineered into a stable monomeric form. Here, we report the spectral properties and crystal structures of engineered monomeric Sandercyanin-BLA complexes. Compared to wild-type protein, monomeric Sandercyanin (∼18kDa) binds BLA with similar affinities and show a broad red-shifted absorbance spectra but possess reduced quantum efficiency. Crystal structures reveal D-ring pyrrole of BLA rotated around the C14-C15 bond, which is stabilized by neighboring aromatic residues and increased water-mediated polar contacts in the BLA-binding pocket. A tetrameric Sandercyanin variant (Tyr-142-Ala) co-displaying red- and far-red absorbing states, and reduced fluorescence shows similar conformational changes in BLA binding pocket. Our results suggest that D-ring flexibility of BLA and its rearrangement reduces the fluorescence quantum-yield of monomeric Sandercyanin. Structures of monomeric Sandercyanin could be utilized as prototypes to generate bright BLA-inducible fluorescent proteins. Further, our study postulates a mechanism for modulating photo-states in BLA-bound lipocalins, known only in phytochromes till date.Significance StatementSandercyanin is a tetrameric red fluorescent protein from a blue variant of walleye (Stizostedion vitreum)that binds to biliverdin IXα (BLA). Its biophysical properties and structures have been published earlier(1). A bright and stable monomeric Sandercyanin could be utilized as a fusion protein for fluorescence-based applications. Here we report the first structures and spectral properties of fluorescent monomeric Sandercyanin-BLA complexes and describe the molecular basis of modulated spectral properties due to rotated D-ring pyrrole around C14-C15 bond and re-shuffling of BLA-binding pocket. BLA-bound monomeric Sandercyanin could be engineered into brighter variants forin-vivoapplications. Our study also reveals an unfamiliar mechanism in BLA-binding lipocalins that regulates red- and far-red absorbance states.
A β-secretase modulator decreases Tau pathology and preserves short-term memory in a mouse model of neurofibrillary degeneration
Authors: Tautou Marie , Eddarkaoui Sabiha , Descamps Florian , Larchanché Paul-Emmanuel , Dumoulin Mélanie , Lamarre Chloé , Blum David , Buée Luc , Melnyk Patricia , Sergeant Nicolas 
Published: April 2021

AbstractA structure-activity relationship has enabled us to identify two molecules, MAGS02-14 and PEL24-199, sharing a β-secretase modulatory effect but having or not a lysosomotropic activity, respectively. More importantly, MAGS02-14 and PEL24-199 only differ from each other by a single nitrogen atom. However, which of the lysosomotropic and/or β-secretase modulating activities is necessary for the pharmacological effectin vivoremains ill-defined. To address this question, the THY-Tau22 transgenic model of NFD was treated for 6 weeks in a curative paradigm and short-term memory, Tau burden, and inflammatory processes were studied. PEL24-199, possessing only the β-secretase modulatory activity, was shown to restore the short-term memory and to reduce NFD. This effect was associated with reduced phosphorylation of Tau, increased phosphatase expression, and a decrease of astrogliosis. Our results therefore suggest that the lysosomotropic activity may be dispensable for the effect on both Aβ and Tau pathologies.
Transcriptomic analysis of resistant and susceptible responses in a new model root-knot nematode infection system usingSolanum torvumandMeloidogyne arenaria
Authors: Sato Kazuki , Uehara Taketo , Holbein Julia , Sasaki-Sekimoto Yuko , Gan Pamela , Bino Takahiro , Yamaguchi Katsushi , Ichihashi Yasunori , Maki Noriko , Shigenobu Shuji , Ohta Hiroyuki , Franke Rochus B. , Siddique Shahid , Grundler Florian M. W. , Suzuki Takamasa , Kadota Yasuhiro , Shirasu Ken 
Published: April 2021

ABSTRACTRoot-knot nematodes (RKNs) are among the most devastating pests in agriculture.Solanum torvumSw. (turkey berry) has been used as a rootstock for eggplant (aubergine) cultivation because of its resistance to RKNs, includingMeloidogyne incognitaandM. arenaria. We previously found that a pathotype ofM. arenaria, A2-J, is able to infect and propagate inS. torvum. In vitroinfection assays showed thatS. torvuminduces the accumulation of brown pigments during avirulent pathotype A2-O infection, but not during virulent A2-J infection. This experimental system is advantageous because resistant and susceptible responses can be distinguished within a few days, and because a single plant genome can yield information about both resistant and susceptible responses. Comparative RNA-sequencing analysis ofS. torvuminoculated with A2-J and A2-O at early stages of infection was used to parse the specific resistance and susceptible responses. Infection with A2-J did not induce statistically significant changes in gene expression within one day post-inoculation (DPI), but afterward, A2-J specifically induced the expression of chalcone synthase, spermidine synthase, and genes related to cell wall modification and transmembrane transport. Infection with A2-O rapidly induced the expression of genes encoding class III peroxidases, sesquiterpene synthases, and fatty acid desaturases at 1 DPI, followed by genes involved in defense, hormone signaling, and the biosynthesis of lignin at 3 DPI. Both isolates induced the expression of suberin biosynthetic genes, which may be triggered by wounding during nematode infection. Histochemical analysis revealed that A2-O, but not A2-J, induced lignin accumulation at the root tip, suggesting that physical reinforcement of cell walls with lignin is an important defense response against nematodes. TheS. torvum-RKN system can provide a molecular basis for understanding plant-nematode interactions.
Endosomal cargo recycling mediated by Gpa1 and Phosphatidylinositol-3-Kinase is inhibited by glucose starvation
Authors: Laidlaw Kamilla ME. , Paine Katherine M. , Bisinski Daniel D. , Calder Grant , Hogg Karen , Ahmed Sophia , James Sally , O’Toole Peter J. , MacDonald Chris 
Published: April 2021

ABSTRACTCell surface protein trafficking is regulated in response to nutrient availability, with multiple pathways directing surface membrane proteins to the lysosome for degradation in response to suboptimal extracellular nutrients. Internalised protein and lipid cargoes recycle back to the surface efficiently in glucose replete conditions, but this trafficking is attenuated following glucose starvation. We find cells with either reduced or hyperactive phosphatidylinositol 3-kinase (PI3K) activity are defective for recycling. Furthermore, we find the yeast Gα subunit Gpa1, an endosomal PI3K effector, is required for surface recycling of cargoes. Following glucose starvation, mRNA and protein levels of a distinct Gα subunit Gpa2 are elevated following nuclear translocation of Mig1, which inhibits recycling of various cargoes. As Gpa1 and Gpa2 interact at the surface where Gpa2 concentrates during glucose starvation, we propose this disrupts PI3K activity required for recycling, potentially diverting Gpa1 to the surface and interfering with its endosomal role in recycling. In support of this model, glucose starvation and over-expression of Gpa2 alters PI3K endosomal phosphoinositide production. Glucose deprivation therefore triggers a survival mechanism to increase retention of surface cargoes in endosomes and promote their lysosomal degradation.
Constrained flexibility of parental cooperation limits evolutionary responses to harsh conditions
Authors: Moss J.B. , Moore A.J. 
Published: April 2021

AbstractParental care is predicted to evolve to mitigate harsh environments, thus adaptive plasticity of care may be an important response to climate change. In biparental species, fitness costs may be reduced with plasticity of behavior among partners. We investigated this prediction with the burying beetle,Nicrophorus orbicollis, by exposing them to contrasting benign and harsh thermal environments. We found strong fitness costs under the harsh environment, but rather than select for more care, visualized selection was stabilizing. Examining different components of care revealed positive directional selection gradients for direct care and strong stabilizing selection gradients for indirect care, resulting in constrained evolutionary responses. Further, because males and females did not coordinate their investments, the potential for adaptive plasticity was not enhanced under biparental care. Females cared at capacity with or without male partners, while males with partners reduced direct care but maintained indirect care levels. Decision rules were not altered in different environments, suggesting no shift from sexual conflict to cooperation. We suggest that the potential for parenting to ameliorate the effects of our climate crisis may depend on the sex-specific evolutionary drivers of parental care, and that this may be best reflected in components of care.
Tuning Cell-free Composition Controls the Time-delay, Dynamics, and Productivity of TX-TL Expression
Authors: Vezeau Grace E. , Salis Howard M. 
Published: April 2021

AbstractThe composition of TX-TL cell-free expression systems are adjusted by adding macromolecular crowding agents and salts. However, the effects of these cosolutes on the dynamics of individual gene expression processes have not been systematically quantified. Here, we carry out kinetic mRNA and protein level measurements on libraries of genetic constructs using the common cosolutes PEG-8000, Ficoll-400, and magnesium glutamate. By combining these measurements with biophysical modeling, we show that cosolutes have differing effects on transcription initiation, translation initiation, and translation elongation rates with trade-offs between time-delays, expression tunability, and maximum expression productivity. We also confirm that biophysical models can predict translation initiation rates in TX-TL usingE. colilysate. We discuss how cosolute composition can be tuned to maximize performance across different cell-free applications, including biosensing, diagnostics, and biomanufacturing.
A deterministic semi-infinite global optimization method to design slotless permanent magnet machines
Authors: Amrouchi Zahia , Messine Frederic , Nadal Clement , Ouanes Mohand 
Published: April 2021

Purpose
In this work, a method to design a slotless permanent magnet machine (SPMM) based on the joint use of an analytical model and deterministic global optimization algorithms is addressed. The purpose of this study is to propose to include torque ripples as an extra constraint in the optimization phase involving de facto the study of a semi-infinite optimization problem.

Design/methodology/approach
Based on the use of a well-known analytical model describing the electromagnetic behavior of an SPMM, this analytical model has been supplemented by the calculus of the dynamic torque and its ripples to carry out a more accurate optimized sizing method of such an electromechanical converter. As a consequence, the calculated torque depends on a continuous variable, namely, the rotor angular position, resulting in the definition of a semi-infinite optimization problem. The way to solve this kind of semi-infinite problem by discretizing the rotor angular position by using a deterministic global optimization solver, that is to say COUENNE, via the AMPL modeling language is addressed.

Findings
In this study, the proposed approach is validated on some numerical tests based on the minimization of the magnet volume. Efficient global optimal solutions with torque ripples about 5% (instead of 30%) can be so obtained.

Research limitations/implications
The analytical model does not use results from the solution of two-dimensional field equations. A strong assumption is put forward to approximate the distribution of the magnetic flux density in the air gap of the SPMM.

Originality/value
The problem to design an SPMM can be efficiently formulated as a semi-infinite global optimization problem. This kind of optimization problems are hard to solve because they involve an infinity of constraints (coming from a constraint on the torque ripple). The authors show in this paper that by using analytical models, a discretization method and a deterministic global optimization code COUENNE, this problem is efficiently tackled. Some numerical results show that the deterministic global solution of the design can be reached even if the step of discretization is small.