bluuebunny/crossref_metadata_2025_split huggingface dataset:
ISG15 Monomer Promotes IFNα-mediated Antiviral Activity against Pseudorabies Virus by Facilitating phosphorylation of STAT1/STAT2
Authors: Liu Huimin , Li Chen , He Wenfeng , Chen Jing , Yang Guoqing , Chen Lu , Chang Hongtao 
Published: May 2022

ABSTRACTPseudorabies virus (PRV), which presently lacks both an antiviral drug and a viable therapeutic option, is a major viral pathogen that poses a danger to the pig industry worldwide. Interferon-stimulated gene 15 (ISG15) is strongly upregulated during viral infections and has been reported to have proviral or antiviral properties, depending on the virus and host species. Our previous studies demonstrated ISG15 was remarkably upregulated during PRV infection, and the overexpression of ISG15 inhibited PRV replication. Nevertheless, the exact mechanism through which ISG15 influences PRV replication poorly understood unclear. Here, we demonstrate that ISG15 accumulation induced by PRV infection requires viral gene expression and viral growth. Conjugation inhibition assays showed that ISG15 imposes its antiviral effects via unconjugated (free) ISG15 and affects the viral release. In addition, we found ISG15 promoted IFNα-mediated antiviral activity against PRV by facilitating the phosphorylation of STAT1 and STAT2, along with an increase of ISGF3-induced ISRE promoter activity. Furthermore, we evaluated the role of ISG15 in host defense to control PRV infection by using ISG15-/- mice model. When challenged with PRV, ISG15-/- mice exhibited increased morbidity and mortality, as well as viral load compared to WT mice. Pathological examination revealed increased lesions, mononuclear cellular infiltration and neuronal death in the brains of ISG15-/- mice, along with the upregulation of the cytokines. Our findings establish the importance of ISG15 in IFNα-induced antiviral response and in the control of PRV infection.
Attention Deficit Hyperactivity Disorder Symptoms and Brain Morphology: Examining Confounding Bias
Authors: Dall’Aglio Lorenza , Kim Hannah H. , Lamballais Sander , Labrecque Jeremy , Muetzel Ryan L. , Tiemeier Henning 
Published: May 2022

ABSTRACTBackgroundAssociations between attention-deficit/hyperactivity disorder (ADHD) and brain morphology have been reported, although with several inconsistencies. These may partly stem from confounding bias, which could distort associations and limit generalizability. We examined how associations between brain morphology and ADHD symptoms change with adjustments for potential confounders typically overlooked in the literature (aim 1), and for IQ, which is typically corrected for but plays an unclear role (aim 2).MethodsParticipants were 10-year-old children from the Adolescent Brain Cognitive Development (N=7,961) and Generation R (N=2,531) studies. Cortical area and volume were measured with MRI and ADHD symptoms with the Child Behavior Checklist. Surface-based cross-sectional analyses were run.ResultsADHD symptoms related to widespread cortical regions when solely adjusting for demographic factors. Additional adjustments for socioeconomic and maternal behavioral confounders (aim 1) generally attenuated associations, as cluster sizes halved and effect sizes substantially reduced. Cluster sizes were further reduced when including IQ (aim 2), however, we argue that adjustments could have introduced bias (e.g., by conditioning on a collider).ConclusionsCareful confounder selection and control can help identify more robust and specific regions of associations for ADHD symptoms, across two cohorts. We provided guidance to minimizing confounding bias in psychiatric neuroimaging.FundingAuthors are supported by an NWO-VICI grant (NWO-ZonMW: 016.VICI.170.200 to HT) for HT, LDA, SL, and the Sophia Foundation S18-20, and Erasmus University and Erasmus MC Fellowship for RLM.
Label-free imaging of large samples: 3D rendering and morphological analysis within histological workflows using serial block face imaging
Authors: Malloci Marine , de Villemagne Perrine , Dorval Paul , Feyeux Magalie , Blandin Stéphanie , Schmid Guillaume , Hulin Philippe , Gilloteaux Perrine Paul 
Published: May 2022

AbstractSerial block face imaging (SFBI) is a method used to generate 3-dimensional (3D) reconstruction of a sample via serial image acquisition. Several SBFI approaches have been proposed for large samples, differing in the ability to generate contrast as well as in the nature of the detected signal. We propose a new system that detects the endogenous autofluorescence signal of paraffin-embedded samples. The sample preparation is simplified compared to other approaches, and adapted to be integrated into a routine histological preparation. More specifically, it was designed to limit reagent toxicity and to be compatible with downstream histological processing. We show the usefulness of the technique with a wide range of tissues based on the intrinsic autofluorescence signal. Optimization of quality section recovery offers the possibility to develop correlative approaches and multimodal analysis between the 3D dataset with the 2-dimensional (2D) sections. In addition, contrast and resolution of block-face images allow us to successfully perform post processing analysis and morphology quantifications. Overall, our methodology offers a simple, cost effective and rapid approach to obtain quantitative data on a large sample with no specific staining.
Extending the Boundaries of Cancer Therapeutic Complexity with Literature Data Mining
Authors: Niezni Danna , Taub-Tabib Hillel , Harris Yuval , Sason-Bauer Hagit , Amrusi Yakir , Azagury Dana , Avrashami Maytal , Launer-Wachs Shaked , Borchardt Jon , Kusold M , Tiktinsky Aryeh , Hope Tom , Goldberg Yoav , Shamay Yosi 
Published: May 2022

AbstractDrug combination therapy is a main pillar of cancer therapy but the formation of an effective combinatorial standard of care (SOC) can take many years and its length of development is increasing with complexity of treatment. In this paper, we develop a path to extend the boundaries of complexity in combinatorial cancer treatments using text data mining (TDM). We first use TDM to characterize the current boundaries of cancer treatment complexity and find that the current complexity limit for clinical trials is 6 drugs per plan and for pre-clinical research is 10. We then present a TDM based assistive technology, cancer plan builder (CPB), which we make publicly available and allows experts to create literature-anchored high complexity combination treatment (HCCT) plans of significantly larger size. We develop metrics to evaluate HCCT plans and show that experts using CPB are able to create HCCT plans at much greater speed and quality, compared to experts without CPB. We hope that by releasing CPB we enable more researchers to engage with HCCT planning and demonstrate its clinical efficacy.
Probing single cell fermentation flux and intercellular exchange networks via pH-microenvironment sensing and inverse modeling
Authors: Onesto V. , Forciniti S. , Alemanno F. , Narayanankutty K. , Chandra A. , Prasad S. , Azzariti A. , Gigli G. , Barra A. , De Martino A. , De Martino D. , del Mercato L.L. 
Published: May 2022

AbstractThe homeostatic control of their environment is an essential task of living cells. It has been hypothesized that when microenvironmental pH inhomogeneities are induced by high cellular metabolic activity, diffusing protons act as signaling molecules, driving the establishment of cross-feeding networks sustained by the cell-to-cell shuttling of overflow products such as lactate. Despite their fundamental role, the extent and dynamics of such networks is largely unknown due to the lack of methods in single cell flux analysis. In this study we provide direct experimental characterization of such exchange networks. We devise a method to quantify single cell fermentation fluxes over time by integrating high-resolution pH microenvironment sensing via ratiometric nanofibers with constraint-based inverse modeling. We apply our method to cell cultures with mixed populations of cancer cells and fibroblasts. We find that the proton trafficking underlying bulk acidification is strongly heterogeneous, with maximal single cell fluxes exceeding typical values by up to 3 orders of magnitude. In addition, a crossover in time from a networked phase sustained by densely connected “hubs” (corresponding to cells with high activity) to a sparse phase dominated by isolated dipolar motifs (i.e. by pair-wise cell-to-cell exchanges) is uncovered, which parallels the time course of bulk acidification. Our method promises to shed light on issues ranging from the homeostatic function of proton exchange to the metabolic coupling of cells with different energetic demands, and paves the way for real-time non-invasive single cell metabolic flux analysis.
Nuclear receptor ligand screening in an iPSC-derived in vitro blood-brain barrier model identifies new contributors to leptin transport
Authors: Shi Yajuan , Kim Hyosung , Hamann Catherine A. , Rhea Elizabeth M. , Brunger Jonathan M. , Lippmann Ethan S. 
Published: May 2022

AbstractBackgroundThe peptide hormone leptin exerts its function in the brain to reduce food intake and increase energy expenditure to prevent obesity. However, most obese subjects reflect the resistance to leptin even with elevated serum leptin. Considering that leptin must cross the blood-brain barrier (BBB) in several regions to enter the brain parenchyma, altered leptin transport through the BBB might play an important role in leptin resistance and other biological conditions. Here, we report the use of a human induced pluripotent stem cell (iPSC)-derived BBB model to explore mechanisms that influence leptin transport.MethodsiPSCs were differentiated into brain microvascular endothelial cell (BMEC)-like cells using standard methods. BMEC-like cells were cultured in Transwell filters, treated with ligands from a nuclear receptor agonist library, and assayed for leptin transport using an enzyme-linked immune sorbent assay. RNA sequencing was further used to identify differentially regulated genes and pathways. The role of a select hit in leptin transport was tested with the competitive substrate assay and after gene knockdown using CRISPR techniques.ResultsFollowing a screen of 73 compounds, 17β-estradiol was identified as a compound that could significantly increase leptin transport. RNA sequencing revealed many differentially expressed transmembrane transporters after 17β-estradiol treatment. Of these, cationic amino acid transporter-1 (CAT-1, encoded by SLC7A1) was selected for follow-up analyses due to its high and selective expression in BMECs in vivo. Treatment of BMEC-like cells with CAT-1 substrates, as well as knockdown of CAT-1 expression via CRISPR-mediated epigenome editing, yielded significant increases in leptin transport.ConclusionsA major female sex hormone, as well as an amino acid transporter, were revealed as regulators of leptin BBB transport in the iPSC-derived BBB model. Outcomes from this work provide insights into regulation of peptide hormone transport across the BBB.
Mapping mechanical stress in curved epithelia of designed size and shape
Authors: Marín-Llauradó Ariadna , Kale Sohan , Ouzeri Adam , Sunyer Raimon , Torres-Sánchez Alejandro , Latorre Ernest , Gómez-González Manuel , Roca-Cusachs Pere , Arroyo Marino , Trepat Xavier 
Published: May 2022

AbstractThe function of organs such as lungs, kidneys and mammary glands relies on the three-dimensional geometry of their epithelium. To adopt shapes such as spheres, tubes and ellipsoids, epithelia generate mechanical stresses that are generally unknown. Here we engineered curved epithelial monolayers of controlled size and shape and mapped their state of stress. We designed pressurized epithelia with circular, rectangular and ellipsoidal footprints. We developed a computational method to map the stress tensor in these epithelia. This method establishes a direct correspondence between epithelial shape and mechanical stress without assumptions of material properties. In epithelia with spherical geometry spanning more than one order of magnitude in radius, we show that stress weakly increases with areal strain in a size-independent manner. In epithelia with rectangular and ellipsoidal cross-section we found pronounced stress anisotropies consistent with the asymmetric distribution of tractions measured at the cell-substrate contact line. In these anisotropic profiles, cell shape tended to align with the direction of maximum principal stress but this alignment was non-universal and depended on epithelial geometry. Besides interrogating the fundamental mechanics of epithelia over a broad range of sizes and shapes, our approach will enable a systematic study of how geometry and stress influence epithelial fate and function in three-dimensions.
Ability of the Ash dieback pathogen to reproduce and to induce damage on its host are controlled by different environmental parameters
Authors: Marçais Benoit , Giraudel Arnaud , Husson Claude 
Published: May 2022

SummaryAsh dieback, induced by an invasive ascomycete,Hymenoscyphus fraxineus, has emerged in the last decade as a severe disease threatening ash populations in Europe. Future prospects for Ash are improved by the existence of individuals with natural genetic resistance to the disease and by limited disease impact in many environmental conditions where ashes are frequent. Nevertheless, it was suggested that even in those conditions, ash trees are infected and enable pathogen transmission. We studied the influence of climate and local environment on the ability ofH. fraxineusto infect, be transmitted and cause damage on its host. We showed that healthy carrier, i.e. asymptomatic individuals carryingH. fraxineus, exists and may play a significant role in ash dieback epidemiology. Environment strongly influencedH. fraxineuswith different parameters being important depending on the life cycle stage. The ability ofH. fraxineusto establish on ash leaves and to reproduce on the leaf debris in the litter (rachises) mainly depended on total precipitations in July-August and was not influenced by local tree cover. By contrast, damages to the host, and in particular shoot mortality was significantly reduced by high summer temperature in July-August and by high autumn average temperature. As a consequence, in many situations ash trees are infected and enableH. fraxineustransmission while showing limited or even no damages. We also observed a decreasing trend of severity (leaf necrosis and shoot mortality likelihood) with the time of disease presence in a plot that could be significant for the future of Ash dieback.
Viruses inhibit TIR gcADPR signaling to overcome bacterial defense
Authors: Leavitt Azita , Yirmiya Erez , Amitai Gil , Lu Allen , Garb Jeremy , Morehouse Benjamin R. , Hobbs Samuel J. , Kranzusch Philip J. , Sorek Rotem 
Published: May 2022

AbstractThe Toll/interleukin-1 receptor (TIR) domain is a key component of immune receptors that identify pathogen invasion in bacteria, plants, and animals. In the bacterial antiphage system Thoeris, as well as in plants, recognition of infection stimulates TIR domains to produce an immune signaling molecule whose molecular structure remained elusive. This molecule binds and activates the Thoeris immune effector, which then executes the immune function. We identified a large family of phage-encoded proteins, denoted here Thoeris anti-defense 1 (Tad1), that inhibit Thoeris immunity. We found that Tad1 proteins are “sponges” that bind and sequester the immune signaling molecule produced by TIR-domain proteins, thus decoupling phage sensing from immune effector activation and rendering Thoeris inactive. A high-resolution crystal structure of Tad1 bound to the signaling molecule revealed that its chemical structure is 1′–2′ glycocyclic ADPR (gcADPR), a unique molecule not previously described in other biological systems. Our results define the chemical structure of a central immune signaling molecule, and reveal a new mode of action by which pathogens can suppress host immunity.
Intermittent antibiotic treatment of bacterial biofilms favors the rapid evolution of resistance
Authors: Usui Masaru , Yoshii Yutaka , Thiriet-Rupert Stanislas , Ghigo Jean-Marc , Beloin Christophe 
Published: May 2022

ABSTRACTThe rise of antibiotic resistance in bacterial pathogens is a major health concern and the determinants of this emergence are actively studied. By contrast, although biofilms are an important cause of infections due to their high tolerance to a broad range of antimicrobials, much less is known on the development of antibiotic resistance within the biofilm environment, an issue potentially aggravating the current antibiotic crisis. Here, we compared the occurrence of resistance mutations in pathogenic Escherichia coli planktonic and biofilm populations exposed to clinically relevant cycles of lethal treatments with the aminoglycoside antibiotic amikacin. This experimental evolution approach revealed that mutations in sbmA and fusA are rapidly selected in biofilm but not in planktonic populations. The apparition of these bona fide resistance —and not tolerance— mutations is favored by the biofilm preexisting tolerance and high mutation rate. Moreover, we showed that while fusA mutations displayed a high fitness cost in planktonic conditions, these mutations were maintained in biofilms, a phenomenon further possibly amplified by the selection of fimH mutations favoring biofilm formation itself. Our study therefore provides new insights into the dynamic evolution of antibiotic resistance in biofilms, which could lead to clinically practical antibiotic regimen limiting biofilm-associated infections, while mitigating the emergence of worrisome antibiotic resistance mutations.
Sensory responses in dorsolateral striatum are modulated by motor activity in a dopamine-dependent manner
Authors: de la Torre-Martinez Roberto , Ketzef Maya , Silberberg Gilad 
Published: May 2022

SummaryThe dorsolateral striatum (DLS) receives excitatory inputs from both sensory and motor cortical regions and is involved in sensory and motor functions. In cortical regions, sensory responses are altered by motor activity, however, it is not known if such sensorimotor interactions also occur in the striatum and how they are modulated by dopamine (DA). To determine the impact of motor activity on striatal sensory processing, we performed in vivo whole-cell recordings in the DLS of awake mice during the presentation of tactile stimuli. Striatal medium spiny neurons (MSNs) were activated by both whisker stimulation and spontaneous whisking, however, responses to whisker deflection during ongoing whisking were attenuated. DA depletion reduced the representation of whisking in direct-pathway MSNs, but not in those of the indirect-pathway. Furthermore, DA depletion impaired the discrimination between ipsi- and contralateral sensory stimulation in both direct- and indirect- pathway MSNs. Our results show that sensory responses in basal ganglia circuits are modulated by motor activity and that both processes are dopamine- and cell type-dependent.
State Dependent Coupling of Hippocampal Oscillations
Authors: Modi Brijesh , Guardamagna Matteo , Stella Federico , Griguoli Marilena , Cherubini Enrico , Battaglia Francesco P. 
Published: May 2022

SUMMARYOscillations occurring simultaneously in a given area represent a physiological unit of brain states. They allow for temporal segmentation of spikes and support distinct behaviors. To establish how multiple oscillatory components co-varies simultaneously and influence neuronal firing during sleep and wakefulness, we describe a multi-variate analytical framework for constructing the state space of hippocampal oscillations. Examining the co-occurrence patterns of oscillations on the state space, across species, uncovered the presence of network constraints and distinct set of cross-frequency interactions during wakefulness as compared to sleep. We demonstrated how the state space can be used as a canvas to map the neural firing and found that distinct neurons during navigation were tuned to different set of simultaneously occurring oscillations during sleep. This multivariate analytical framework provides a window to move beyond classical bivariate pipelines, for investigating oscillations and neuronal firing, thereby allowing to factor-in the complexity of oscillation-population interactions.
Protection from Omicron and other VOCs by Bivalent S-Trimer COVID-19 Vaccine
Authors: Su Danmei , Li Xinglin , Huang Xueqin , He Cui , Zeng Cheng , Wang Qiang , Qin Wenchang , Mu Zhongquan , Ambrosino Donna , Siber George , Clemens Ralf , Liang Joshua G. , Liang Peng , Jackson Nick , Xu Rong 
Published: May 2022

AbstractThe Omicron variant of SARS-COV-2 (GISAID GRA clade [B.1.1.529, BA.1 and BA.2]) is now the single dominant Variant of Concern (VOC). The high number of mutations in the Omicron Spike (S) protein promotes humoral immunological escape. Although a third homologous boost with S, derived from the ancestral strain, was able to increase neutralizing antibody titers and breadth including to Omicron, the magnitude of virus neutralization could benefit from further optimization. Moreover, combining SARS-COV-2 strains as additional valences may address the current antigenicity range occupied by VOCs.Using Trimer-Tag™ platform we have previously demonstrated phase 3 efficacy and safety of a prototypic vaccine SCB-2019 in the SPECTRA trial and have submitted applications for licensure. Here, we successfully generated a bivalent vaccine candidate including both Ancestor and Omicron variant S-proteins. Preclinical studies demonstrate this SARS-CoV-2 bivalent S-Trimer subunit vaccine elicits high titers of neutralizing antibodies against all VOCs, with markedly enhanced Omicron specific neutralizing antibody responses.