bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Structural Flexibility of MAD1 Facilitates the Assembly of the Mitotic Checkpoint Complex
Authors: Chen Chu , Piano Valentina , Alex Amal , Han Simon J. Y. , In ’t Veld Pim J Huis , Roy Babhrubahan , Musacchio Andrea , Joglekar Ajit P. 
Published: July 2022

AbstractThe spindle assembly checkpoint (SAC) safeguards the genome during cell division by generating an effector molecule known as the Mitotic Checkpoint Complex (MCC). The MCC comprises two subcomplexes, and during its assembly, formation of the CDC20:MAD2 subcomplex is the rate-limiting step. Recent studies show that the rate of CDC20:MAD2 formation is significantly accelerated by the cooperative binding of CDC20 to SAC proteins MAD1 and BUB1. However, the molecular basis for this acceleration is not fully understood. Here, we demonstrate that the structural flexibility of MAD1 at a conserved hinge near the C-terminus is essential for catalytic MCC assembly. This MAD1 hinge enables the MAD1:MAD2 complex to assume a folded conformation in vivo. Importantly, truncating the hinge reduces the rate of MCC assembly in vitro and SAC signaling in vivo. Conversely, mutations that preserve hinge flexibility retain SAC signaling, indicating that the structural flexibility of the hinge, rather than a specific amino acid sequence, is important for SAC signaling. We summarize these observations in a “knitting” model that explains how the folded conformation of MAD1:MAD2 promotes CDC20:MAD2 assembly.
Model of neural induction in the ascidian embryo
Authors: Bettoni Rossana , Hudson Clare , Yasuo Hitoyoshi , de Buyl Sophie , Dupont Geneviève 
Published: July 2022

AbstractHow cell specification can be controlled in a reproducible manner is a fundamental question in development biology. In ascidians, a group of marine invertebrate chordates, geometry plays a key role in achieving this control. Here, we use mathematical modeling to demonstrate that geometry dictates the neural-epidermal cell fate choice in the 32-cell stage ascidian embryo by a two-step process involving first the modulation of ERK signaling and second, the expression of the neural marker gene,Otx. The model describes signal transduction by the ERK pathway that is stimulated by FGF and repressed by ephrin, and ERK-mediated control ofOtxgene expression, which involves both an activator and an inhibitor of transcription. Considering the measured area of cell surface contacts with FGF- or ephrin-expressing cells as inputs, the solutions of the model reproduce the experimental observations about ERK activation andOtxexpression in the different cells under normal and perturbed conditions. Sensitivity analyses and computations of Hill coefficients allow to quantify the robustness of the specification mechanism controlled by cell surface area and to identify the respective role played by each signaling input. Simulations also predict in which conditions the dual control of gene expression by an activator and an inhibitor that are both under the control of ERK can induce a robust ON/OFF control of neural fate induction.Author summaryThe development of a single cell zygote into a multicellular embryo occurs thanks to the combination of cell division and cell specification. The latter process corresponds to the progressive acquisition by the embryonic cells of their final physiological and functional characteristics, which rely on well-defined signaling-controlled genetic programs. The origin of the great robustness of cell specification remains poorly understood. Here, we address this question in the framework of the embryonic neural fate induction in ascidians, which are marine invertebrates. At the 32-cells stage, four cells identified by their precise location in the embryo adopt neural fate. On the basis of experimental observations, we develop a mathematical model that predicts that the choice between the neural or epidermal fate is controlled by the cell surface areas of the cells in contact with two antagonistic signals, FGF and ephrin. Our findings provide a computational confirmation of the major role played by the geometry of the embryo in controlling cell lineage acquisition during ascidian development.
Pro-apoptotic and anti-invasive properties underscore the tumor suppressing impact of myoglobin on subset of human breast cancer cells
Authors: Aboouf Mostafa A. , Armbruster Julia , Thiersch Markus , Guscetti Franco , Kristiansen Glen , Schraml Peter , Bicker Anne , Petry Ruben , Hankeln Thomas , Gassmann Max , Gorr Thomas A. 
Published: July 2022

AbstractExpression of myoglobin (MB), well known as the oxygen storage and transport protein of myocytes, is a novel hallmark of the luminal subtype in breast cancer patients and correlates with better prognosis. The mechanisms by which MB impacts mammary tumorigenesis are hitherto unclear. We aimed to unravel this role, by using CRISPR/Cas9 technology to generate MB-deficient clones of MCF7 and SKBR3 breast cancer cell lines and subsequently characterize them by transcriptomics plus molecular and functional analyses. As main findings, loss of MB, at normoxia, upregulated the expression of cell cyclins and increased cell survival while it prevented apoptosis in MCF7 cells. Also, MB-deficient cells were less sensitive to doxorubicin but not ionizing radiation. Under hypoxia, loss of MB enhanced partial epithelial to mesenchymal transition, thus augmenting the migratory and invasive cell behavior. Notably, in human invasive mammary ductal carcinoma tissues, MB and apoptotic marker levels were positively correlated. In addition, MB protein expression in invasive ductal carcinomas was associated with a positive prognostic value, independent of the known tumor suppressor p53. In conclusion, we provide multiple lines of evidence that endogenous MB in cancer cells by itself exerts novel tumor-suppressive roles through which it can reduce cancer malignancy.
Phospholipids Diffusion on the Surface of Model Lipid Droplets
Authors: Asfia Shima , Seemann Ralf , Fleury Jean-Baptiste 
Published: July 2022

AbstractLipid droplets (LD) are organelles localized in the membrane of the Endoplasmic Reticulum (ER) that play an important role in metabolic functions. They consist of a core of neutral lipids surrounded by a monolayer of phosphoplipids and proteins resembling an oil-in-water emulsion droplet. Many studies have focused on the biophysical properties of these LDs. However, despite numerous efforts, we are lacking information on the mobility of phospholipids on the LDs surface, although they may play a key role in the protein distribution. In this article, we developed a microfluidic setup that allows the formation of a triolein-buffer interface decorated with a phospholipid monolayer. Using this setup, we measured the motility of phospholipid molecules by performing Fluo-rescent Recovery After Photobleaching (FRAP) experiments for different lipidic compositions. The results of the FRAP measurements reveal that the motility of phospholipids is controlled by the monolayer packing decorating the interface.
LipIDens: Simulation assisted interpretation of lipid densities in cryo-EM structures of membrane proteins
Authors: Ansell T. Bertie , Song Wanling , Coupland Claire E. , Carrique Loic , Corey Robin A. , Duncan Anna L. , Cassidy C. Keith , Geurts Maxwell M. G. , Rasmussen Tim , Ward Andrew B. , Siebold Christian , Stansfeld Phillip J. , Sansom Mark S. P. 
Published: July 2022

AbstractCryo-electron microscopy (cryo-EM) enables the determination of membrane protein structures in native-like environments. Characterising how membrane proteins interact with the surrounding membrane lipid environment is assisted by resolution of lipid-like densities visible in cryo-EM maps. Nevertheless, establishing the molecular identity of putative lipid and/or detergent densities remains challenging. Here we present LipIDens, a pipeline for molecular dynamics (MD) simulation-assisted interpretation of lipid and lipid-like densities in cryo-EM structures. The pipeline integrates the implementation and analysis of multi-scale MD simulations for identification, ranking and refinement of lipid binding poses which superpose onto cryo-EM map densities. Thus, LipIDens enables direct integration of experimental and computational structural approaches to facilitate the interpretation of lipid-like cryo-EM densities and to reveal the molecular identities of protein-lipid interactions within a bilayer environment. The LipIDens code is open-source and embedded within a notebook format to assist automation and usability.
Fecal virome transfer improves proliferation of commensal gut Akkermansia muciniphila and unexpectedly enhances the fertility rate in laboratory mice
Authors: Sølbeck Rasmussen Torben , Junker Mentzel Caroline M. , Danielsen Malene Refslund , Jakobsen Rasmus Riemer , Fisker Zachariassen Line Sidsel , Castro Mejia Josue Leonardo , Hansen Lars Hestbjerg , Hansen Axel Kornerup , Nielsen Dennis Sandris 
Published: July 2022

AbstractProbiotics have been suggested as nutritional supplements to improve gastrointestinal health. However, the probiotics marketed today only colonize the densely populated gut to a limited extent. Bacteriophages comprise the majority of viruses in the human gut virome and there are strong indications that they play important roles in shaping the gut microbiome (GM). Here we investigate the use of fecal virome transplantation (FVT) as a mean to alter GM composition to lead the way for persistent colonization of two types of probiotics: Lacticaseibacillus rhamnosus GG (LGG) representing a well-established probiotic and Akkermansia muciniphila (AKM) representing a putative next-generation probiotic. Male and female C57BL/6NTac mice were cohoused in pairs at 4 weeks of age and received the following treatment by oral gavage at week 5 and 6: AKM+FVT, probiotic sham (Pro-sham)+FVT, LGG+Saline, AKM+Saline, and control (Pro-sham+Saline). The FVT originated from donor mice with high relative abundance of A. muciniphila. All animals were terminated at age 9 weeks. The FVT treatment did not increase the relative abundance of the administered LGG or AKM in the recipient mice. Instead FVT significantly (p<0.05) increased the abundance of naturally occurring A. muciniphila compared to the control. This highlights the potential of stimulating the commensal “probiotics” that already are permanent members of the gut. Being co-housed male and female, a fraction of the female mice became pregnant. Unexpectedly, the FVT treated mice were found to have a significantly (p<0.05) higher fertility rate independent of probiotic administration. These preliminary observations urge for follow-up studies investigating GM/fertility interactions.
Noradrenergic signaling in the rodent orbitofrontal cortex is required to update goal-directed actions
Authors: Cerpa Juan-Carlos , Piccin Alessandro , Dehove Margot , Lavigne Marina , Kremer Eric J. , Wolff Mathieu , Parkes Shauna L. , Coutureau Etienne 
Published: July 2022

SUMMARYIn a constantly changing environment, organisms must track the current relationship between actions and their specific consequences and use this information to guide decision-making. Such goal-directed behavior relies on circuits involving cortical and subcortical structures. Notably, a functional heterogeneity exists within the medial prefrontal, insular, and orbitofrontal cortices (OFC) in rodents. The role of the latter in goal-directed behavior has been debated, but recent data indicate that the ventral and lateral subregions of the OFC are needed to integrate changes in the relationships between actions and their outcomes. Neuromodulatory agents are also crucial components of prefrontal functions and behavioral flexibility might depend upon the noradrenergic modulation of prefrontal cortex. Therefore, we assessed whether noradrenergic innervation of the OFC plays a role in updating action-outcome relationships. We used an identity-based reversal task and found that depletion or chemogenetic silencing of noradrenergic inputs within the OFC rendered rats unable to associate new outcomes with previously acquired actions. Silencing of noradrenergic inputs in the medial prefrontal cortex or depletion of dopaminergic inputs in the OFC did not reproduce this deficit. Together, our results indicate that noradrenergic projections to the OFC are required to update goal-directed actions.GRAPHICAL ABSTRACTHIGHLIGHTSRats learn initial action-outcome associations in an instrumental taskNoradrenergic depletion in the OFC prevents the encoding and expression of these associations following reversal learningDopaminergic depletion in the OFC does not result in behavioral deficitsLC:OFC noradrenergic projections are required to update action-outcome associationsIN BRIEFCerpa et al. investigate whether noradrenergic projections from the locus coeruleus (LC) to the orbitofrontal cortex are involved in updating previously established goal-directed actions following environmental change. They find that these LC projections are required to both encode and express reversed action-outcome associations in rats.
A Novel Homeostatic Mechanism Tunes PI(4,5)P2-dependent Signaling at the Plasma Membrane
Authors: Wills Rachel C. , Doyle Colleen P. , Zewe James P. , Pacheco Jonathan , Hansen Scott D. , Hammond Gerald R. V. 
Published: July 2022

AbstractThe lipid molecule phosphatidylinositol (4,5)-bisphosphate (PI(4,5)P2) controls all aspects of plasma membrane (PM) function in animal cells, from its selective permeability to the attachment of the cytoskeleton. Although disruption of PI(4,5)P2is associated with a wide range of diseases, it remains unclear how cells sense and maintain PI(4,5)P2levels to support various cell functions. Here, we show that the PIP4K family of enzymes that synthesize PI(4,5)P2via a minor pathway, also function as sensors of tonic PI(4,5)P2levels. PIP4Ks are recruited to the PM by elevated PI(4,5)P2levels, where they inhibit the major PI(4,5)P2-synthesizing PIP5Ks. Perturbation of this simple homeostatic mechanism reveals differential sensitivity of PI(4,5)P2-dependent signaling to elevated PI(4,5)P2levels. These findings reveal that a subset of PI(4,5)P2-driven functions may drive disease associated with disrupted PI(4,5)P2homeostasis.One-Sentence SummaryThe enzyme PIP4K functions as both a sensor and negative regulator of PI(4,5)P2synthesis by the closely related PIP5K enzymes, tuning the activity of numerous membrane functions.
A novel fold for acyltransferase-3 (AT3) proteins provides a framework for transmembrane acyl-group transfer
Authors: Newman Kahlan E. , Tindall Sarah N. , Mader Sophie L. , Khalid Syma , Thomas Gavin H. , van der Woude Marjan W. 
Published: July 2022

AbstractAcylation of diverse carbohydrates occurs across all domains of life and can be catalysed by proteins with a membrane bound acyltransferase-3 (AT3) domain (PF01757). In bacteria, these proteins are essential in processes including symbiosis, resistance to viruses and antimicrobials, and biosynthesis of antibiotics, yet their structure and mechanism is largely unknown. In this study, evolutionary co-variance analysis was used to build a computational model of the structure of a bacterial O-antigen modifying acetyltransferase, OafB. The resulting structure exhibited a novel fold for the AT3 domain, which molecular dynamics simulations demonstrated is stable in the membrane. The AT3 domain contains 10 transmembrane helices arranged to form a large cytoplasmic cavity lined by residues known to be essential for function. Further molecular dynamics simulations support a model where the acyl-coA donor spans the membrane through accessing a pore created by movement of an important loop capping the inner cavity, enabling OafB to present the acetyl group close to the likely catalytic resides on the extracytoplasmic surface. Limited but important interactions with the fused SGNH domain in OafB are identified and modelling suggests this domain is mobile and can both accept acyl-groups from the AT3 and then reach beyond the membrane to reach acceptor substrates. Together this new general model of AT3 function provides a framework for the development of inhibitors that could abrogate critical functions of bacterial pathogens.
AncientClostridiumDNA and variants of tetanus neurotoxins associated with human archaeological remains
Authors: Hodgins Harold P. , Chen Pengsheng , Lobb Briallen , Wei Xin , Tremblay Benjamin JM , Mansfield Michael J. , Lee Victoria CY , Lee Pyung-Gang , Coffin Jeffrey , Duggan Ana T. , Dolphin Alexis E. , Renaud Gabriel , Dong Min , Doxey Andrew C. 
Published: July 2022

SUMMARYThe analysis of microbial genomes from human archaeological samples offers a historic snapshot of ancient pathogens and provides insights into the origins of modern infectious diseases. Here, through a large-scale metagenomic analysis of archeological samples, we discovered bacterial species related to modern-dayClostridium tetani, which produces the tetanus neurotoxin (TeNT) and causes the disease tetanus. We assembled draft genomes from 38 distinct human archeological samples spanning five continents and dating to as early as ~4000 BCE. These genomes had varying levels of completeness and a subset of them displayed hallmarks of ancient DNA damage. While 24 fall into knownC. tetaniclades, phylogenetic analysis revealed novelC. tetanilineages, as well as two novelClostridiumspecies (“Clostridiumsp. X and Y”) closely related toC. tetani. Within these genomes, we found 13 TeNT variants with unique substitution profiles, including a subgroup of TeNT variants found exclusively in ancient samples from South America. We experimentally tested a TeNT variant selected from a ~6000-year-old Chilean mummy sample and found that it induced tetanus muscle paralysis in mice with potency comparable to modern TeNT. Our work identifies neurotoxigenicC. tetaniin ancient DNA, newClostridiumspecies unique to ancient human samples, and a novel variant of TeNT that can cause disease in mammals.
Pseudomonas aeruginosa transcriptome analysis in a cystic fibrosis lung model reveals metabolic changes accompanying biofilm maturation and increased antibiotic tolerance over time
Authors: Harrington Niamh E. , Allen Freya , Garcia-Maset Ramón , Harrison Freya 
Published: July 2022

AbstractThe opportunistic pathogen Pseudomonas aeruginosa forms biofilm infections in the lungs of people with the genetic condition cystic fibrosis (CF) that can persist for decades. There are numerous P. aeruginosa lifestyle changes associated with chronic biofilm infection cued by the CF lung environment. These include a loss of virulence, metabolic changes, and increased antimicrobial tolerance. We have investigated P. aeruginosa PA14 biofilm infection over 7 d in an ex vivo pig lung (EVPL) model for CF, previously shown to facilitate formation of a clinically-relevant P. aeruginosa biofilm structure with gene expression comparable to human infection. We extracted and sequenced P. aeruginosa RNA from EVPL-associated biofilms 24 h, 48 h, and 7 d after infection, and compared gene expression between sequential time points. We also investigated tolerance to polymyxins across these three time points. Our results indicate that the EVPL model can maintain a P. aeruginosa biofilm population, which exhibits increased antibiotic tolerance, for at least 7 d. Differential expression of antimicrobial resistance-associated genes was not observed, however there was significant upregulation of sulfur metabolism and phenazine biosynthesis-related genes, as well as maintenance of a structured biofilm. These findings provide further insight into the incidence of increased P. aeruginosa antibiotic tolerance during infection of the CF lung, and the gene expression changes that arise as chronic infection establishes.
Activation-pathway transitions in human voltage-gated proton channels revealed by a non-canonical fluorescent amino acid
Authors: Suárez-Delgado Esteban , Orozco-Contreras M. E. , Rangel-Yescas Gisela E. , Islas León D. 
Published: July 2022

AbstractVoltage-dependent gating of the voltage-gated proton channels (HV1) remains poorly understood, partly because of the difficulty of obtaining direct measurements of voltage sensor movement in the form of gating currents. To circumvent this problem, we have implemented patch-clamp fluorometry in combination with the incorporation of the fluorescent non-canonical amino acid Anap to monitor channel opening and movement of the S4 segment. Simultaneous recording of currents and fluorescence signals allows for direct correlation of these parameters and investigation of their dependence on voltage and the pH gradient (ΔpH). We present data that indicate that Anap incorporated in the S4 helix is quenched by an aromatic residue located in the S2 helix, and that motion of the S4 relative to this quencher is responsible for fluorescence increases upon depolarization. The kinetics of the fluorescence signal reveals the existence of a very slow transition in the deactivation pathway, which seems to be singularly regulated by ΔpH. Our experiments also suggest that the voltage sensor can move after channel opening and that the absolute value of the pH can influence the channel opening step. These results shed light on the complexities of voltage-dependent opening of human HV1 channels.Significance statementThe activation mechanisms of voltage-gated proton channels (HV1) are not well understood. Here we have combined patch-clamp fluorometry and a fluorescent non-canonical amino acid to uncover transitions in the activation pathway of human HV1 that are modulated by voltage and the pH gradient.
How do firms use cloud computing to transform their organization? Evidence from a global survey
Authors: Bounfour Ahmed , Etienne Jean-Michel , Cheng Xiaolin , Nonnis Alberto 
Published: July 2022

PurposeThe paper aims to address the organizational transformation of firms for value creation resulting from cloud computing (CC).Design/methodology/approachWith reference to the theory of organizational fit, we modeled organizational transformation as a function of five aspects of CC practice: functionality, data management, roles and competences of information technology services, control and organizational culture. The output variable was tested against a set of input variables defined with reference to the technology–organization–environment (TOE) and technology acceptance model (TAM). Based on a sample of 487 companies in seven countries in Europe, Asia, and the United States, the authors distinguished two groups of firms: transformational and hyper transformational.FindingsThe results highlight the key factors that determine whether a firm falls into one of these two groups, and include perceived usefulness and perceived ease of use, complexity and compatibility of CC technology, and adequacy of resources. Top management support and government policy are found to only play a role for the transformational group while, surprisingly, vendor support had no impact for either group.Originality/valueThis research contributes to the literature on the role of digital transformation in value creation and on digitization of firms and organizational design, notably by considering the contribution of CC to the organizational dimension. To the best of the authors’ knowledge, this is the first study to make the link between TOE and TAM models and organizational fit theory, thereby going beyond the general approach to adoption found in information system research.