bluuebunny/crossref_metadata_2025_split huggingface dataset:
A phenotypic screening platform for chronic pain therapeutics using all-optical electrophysiology
Authors: Liu Pin W. , Zhang Hongkang , Werley Christopher A. , Pichler Monika , Ryan Steve , Lewarch Caitlin , Jacques Jane , Grooms Jennifer , Ferrante John , Li Guangde , Zhang Dawei , Bremmer Nate , Barnett Adam , Chantre Romina , Elder Amy E. , Cohen Adam E. , Williams Luis A. , Dempsey Graham T. , McManus Owen B. 
Published: December 2022

AbstractChronic pain associated with osteoarthritis (OA) remains an intractable problem with few effective treatment options. New approaches are needed to model the disease biology and to drive discovery of therapeutics. Here, we present anin vitromodel of OA pain, where dorsal root ganglion (DRG) sensory neurons were sensitized by a defined mixture of disease-relevant inflammatory mediators, here called Sensitizing PAin Reagent Composition orSPARC. OA-SPARC components showed synergistic or additive effects when applied in combination and induced pain phenotypesin vivo. To measure the effect of OA-SPARC on neural firing in a scalable format for drug discovery, we used a custom system for high throughput all-optical electrophysiology. This system enabled light-based membrane voltage recordings from hundreds of neurons in parallel with single cell resolution and a throughput of up to 500,000 neurons per day, with patch clamp-like single action potential resolution. A computational framework was developed to construct a multiparameter OA-SPARC neuronal phenotype and to quantitatively assess phenotype reversal by candidate pharmacology with different mechanisms of action. We screened ~3000 approved drugs and mechanistically focused compounds, yielding data from over 1.2 million individual neurons with detailed assessment of both functional OA-SPARC phenotype rescue and orthogonal “off-target” effects. Analysis of confirmed hits revealed diverse potential analgesic mechanisms including well-known ion channel modulators as well as less characterized mechanisms including MEK inhibitors and tyrosine kinase modulators, providing validation of the platform for pain drug discovery.
Ten years of unpredictable chronic stress in zebrafish: a systematic review and meta-analysis
Authors: Gallas-Lopes Matheus , Bastos Leonardo M. , Benvenutti Radharani , Panzenhagen Alana C. , Piato Angelo , Herrmann Ana P. 
Published: December 2022

ABSTRACTThe zebrafish (Danio rerio) is a model animal that is being increasingly used in neuroscience research. A decade ago, the first study on unpredictable chronic stress (UCS) in zebrafish was published, inspired by protocols established for rodents in the early 1980’s. Since then, several studies have been published by different groups, in some cases with conflicting results. We conducted a systematic review to identify studies evaluating the effects of UCS in zebrafish and meta-analytically synthetized the data of neurobehavioral outcomes and relevant biomarkers. Literature searches were performed in three databases (PubMed, Scopus, and Web of Science) and a two-step screening process based on inclusion/exclusion criteria. The included studies underwent extraction of qualitative and quantitative data, as well as risk of bias assessment. Outcomes of included studies (n =38) were grouped into anxiety/fear- related behaviour, locomotor function, social behaviour, or cortisol level domains. UCS increased anxiety/fear-related behaviour and cortisol levels while decreased locomotor function, but a significant summary effect was not observed for social behaviour. Despite including a significant number of studies, the high heterogeneity and the methodological and reporting problems evidenced in the risk of bias analysis make it difficult to assess the internal validity of most studies and the overall validity of the model. Our review thus evidences the need to conduct well-designed experiments to better evaluate the effects of UCS on the behaviour of zebrafish.
Structural basis for specific RNA recognition by the alternative splicing factor RBM5
Authors: Soni Komal , Ankush Jagtap Pravin Kumar , Martínez-Lumbreras Santiago , Bonnal Sophie , Geerlof Arie , Stehle Ralf , Simon Bernd , Valcárcel Juan , Sattler Michael 
Published: December 2022

AbstractThe RNA-binding motif protein RBM5 belongs to a family of multi-domain RNA binding proteins that are implicated in cancer and regulate alternative splicing of genes important for apoptosis and cell proliferation and have been implicated in cancer. RBM5 harbors structural modules for RNA recognition, such as RRM domains and a Zn finger, and protein-protein interactions such as an OCRE domain. Here, we characterize binding of the RBM5 RRM1-ZnF1-RRM2 domains tocis-regulatory RNA elements. A structure of the RRM1-ZnF1 region in complex with RNA shows how the tandem domains cooperate to sandwich target RNA and specifically recognize a GG dinucleotide in a non-canonical fashion. While the RRM1-ZnF1 domains act as a single structural module, RRM2 is connected by a flexible linker and tumbles independently. However, all three domains participate in RNA binding and adopt a closed architecture upon RNA binding. Our data highlight how cooperativity and conformational modularity of multiple RNA binding domains enable the recognition of distinct RNA motifs, thereby contributing to the regulation of alternative splicing. Remarkably, we observe surprising differences in coupling of the RNA binding domains between the closely related homologs RBM5 and RBM10.HighlightsMultiple RNA binding domains enable differential recognition of distinct RNA motifs to regulate alternative splicingThe RRM1-ZnF1 domains of RBM5 mediate specific recognition ofcisregulatory RNA motifs to modulate alternative splicingRRM1-ZnF1 sandwich the target RNA for non-canonical recognition of a GG dinucleotideRRM1-ZnF1-RRM2 bind cooperatively to contiguouscis-regulatory motifs incaspase-2andNUMBpre-mRNAs
INCREASE IN INVASIVE GROUP A STREPTOCOCCAL INFECTIONS IN CHILDREN IN THE NETHERLANDS, A SURVEY AMONG 7 HOSPITALS IN 2022
Authors: van Kempen Evelien B. , Bruijning-Verhagen Patricia C.J. , Borensztajn Dorine , Vermont Clementien L. , Quaak Marjolijn S.W. , Janson Jo-Anne , Maat Ianthe , Stol Kim , Vlaminckx Bart J.M. , Wieringa Jantien W. , van Sorge Nina M. , Boeddha Navin P. , van Veen Mirjam 
Published: December 2022

AbstractBased on a survey sent to seven Dutch hospitals, we observed an substantial increase in invasive group A streptococcal infections in children in the Netherlands, comparing the pre-COVID-19 pandemic cohort of 2018-2019 to 2021-2022. The most affected age group were children between 0-5 years. Main diagnosis was pneumonia with empyema. Necrotizing fasciitis and streptococcal toxic shock syndrome were also reported in 11% and 7% respectively. A significant number was admitted to the Paediatric Intensive Care Unit. Vigilance is needed.
Long term anti-SARS-CoV-2 antibody kinetics and correlate of protection against Omicron BA.1/BA.2 infection
Authors: Perez-Saez Javier , Zaballa María-Eugenia , Lamour Julien , Yerly Sabine , Dubos Richard , Courvoisier Delphine , Villers Jennifer , Balavoine Jean-François , Pittet Didier , Kherad Omar , Vuilleumier Nicolas , Kaiser Laurent , Guessous Idris , Stringhini Silvia , Azman Andrew S. 
Published: December 2022

AbstractBinding antibody levels against SARS-CoV-2 have shown to be correlates of protection against infection with pre-Omicron lineages. This has been challenged by the emergence of immune-evasive variants, notably the Omicron sublineages, in an evolving immune landscape with high levels of cumulative incidence and vaccination coverage. This in turn limits the use of commercially available high-throughput methods to quantify binding antibodies as a tool to monitor protection at the population-level. In this work, we leverage repeated serological measurements between April 2020 and December 2021 on 1’083 participants of a population-based cohort in Geneva, Switzerland, to evaluate anti-Spike RBD antibody levels as a correlate of protection against Omicron BA.1/BA.2 infections during the December 2021-March 2022 epidemic wave. We do so by first modeling antibody dynamics in time with kinetic models. We then use these models to predict antibody trajectories into the time period where Omicron BA.1/BA.2 were the predominant circulating sub-lineages and use survival analyses to compare the hazard of having a positive SARS-CoV-2 test by antibody level, vaccination status and infection history. We find that antibody kinetics in our sample are mainly determined by infection and vaccination history, and to a lesser extent by demographics. After controlling for age and previous infections (based on anti-nucleocapsid serology), survival analyses reveal a significant reduction in the hazard of having a documented positive SARS-CoV-2 infection during the Omicron BA.1/BA.2 wave with increasing antibody levels, reaching up to a three-fold reduction for anti-S antibody levels above 800 IU/mL (HR 0.30, 95% CI 0.22-0.41). However, we did not detect a reduction in hazard among uninfected participants. Taken together these results indicate that anti-Spike RBD antibody levels, as quantified by the immunoassay used in this study, are an indirect correlate of protection against Omicron BA.1/BA.2 for individuals with a history of previous SARS-CoV-2 infection. Despite the uncertainty in what SARS-COV-2 variant will come next, these results provide reassuring insights into the continued interpretation of SARS-CoV-2 binding antibody measurements as an independent marker of protection at both the individual and population levels.
Neural computations in prosopagnosia
Authors: Faghel-Soubeyrand Simon , Richoz Anne-Raphaelle , Waeber Delphine , Woodhams Jessica , Gosselin Frédéric , Caldara Roberto , Charest Ian 
Published: December 2022

AbstractWe aimed to identify neural computations underlying the loss of face identification ability by modelling the brain activity of brain-lesioned patient PS, a well-documented case of acquired pure prosopagnosia. We collected a large dataset of high-density electrophysiological (EEG) recordings from PS and neurotypicals while they completed a one-back task on a stream of face, object, animal and scene images. We found reduced neural decoding of face identity around the N170 window in PS, and conjointly revealed normalnon-faceidentification in this patient. We used Representational Similarity Analysis (RSA) to correlate human EEG representations with those of deep neural network (DNN) models of vision and caption-level semantics, offering a window into the neural computations at play in patient PS’s deficits. Brain representational dissimilarity matrices (RDMs) were computed for each participant at 4 ms steps using cross-validated classifiers. PS’s brain RDMs showed significant reliability across sessions, indicating meaningful measurements of brain representations with RSA even in the presence of significant lesions. Crucially, computational analyses were able to reveal PS’s representational deficits in high-level visual and semantic brain computations. Such multi-modal data-driven characterisations of prosopagnosia highlight the complex nature of processes contributing to face recognition in the human brain.HighlightsWe assess the neural computations in the prosopagnosic patient PS using EEG, RSA, and deep neural networksNeural dynamics of brain-lesioned PS are reliably captured using RSANeural decoding shows normal evidence for non-face individuation in PSNeural decoding shows abnormal neural evidence for face individuation in PSPS shows impaired high-level visual and semantic neural computations
A conservedPlasmodiumprotein that localizes to liver stage nuclei is critical for late liver stage development
Authors: Goswami Debashree , Arredondo Silvia A. , Betz William , Armstrong Janna , Oualim Kenza M. Z. , Seilie Annette M. , Murphy Sean C. , Kappe Stefan H. I. , Vaughan Ashley M. 
Published: December 2022

ABSTRACTMalaria, the disease caused byPlasmodiumparasites, causes significant mortality and morbidity. Whole parasite vaccination with pre-erythrocytic parasite stages, attenuated through sporozoite irradiation or chemo-attenuation, confers sterilizing immunity against subsequent parasite infection. This provides a rationale for the creation of whole parasite vaccines that are attenuated using gene editing. Here, we report on the creation of a novel genetically attenuated parasite (GAP) by the deletion ofPlasmodium LINUP,encoding aliver stagenuclearprotein.Epitope-tagging of LINUP in the rodent malaria parasitePlasmodium yoeliishowed LINUP expression exclusively in liver stage nuclei after the onset of exo-erythrocytic schizogony.P. yoeliiparasites with a gene deletion ofLINUP(linup—) suffered an exclusive liver stage phenotype with developmental arrested late in exo-erythrocytic schizogony. Liver stages showed incomplete segregation of nuclei and, mitochondria and apicoplast. These cellular perturbations caused a defect in exo-erythrocytic merozoite formation and a concomitant severe attenuation of liver stage-to-blood stage transition.LINUPgene deletion inPlasmodium falciparumalso caused a severe defect in late liver stage differentiation. Importantly,P. falciparum linup—liver stages showed a severe defect in parasite transitioning from liver stage to viable blood stage infection. These results suggest thatP. falciparum LINUPis a useful target for late liver stage attenuation and an additional gene deletion that can be incorporated into a late liver stage-arresting replication competent whole parasite vaccine.
Neural circuit-wide analysis of gene expression during deafening-induced destabilization of birdsong
Authors: Colquitt Bradley M. , Li Kelly , Green Foad , Veline Robert , Brainard Michael S. 
Published: December 2022

AbstractSensory feedback is required for stable execution of learned motor skills, and its loss can severely disrupt motor performance. The neural mechanisms that mediate sensorimotor stability have been extensively studied at systems and physiological levels, yet relatively little is known about how disruptions to sensory input alter the molecular properties of associated motor systems. Songbird courtship song, a model for skilled behavior, is a learned and highly structured vocalization that is destabilized following deafening. Here, we sought to determine how the loss of auditory feedback modifies gene expression and its coordination across the birdsong sensorimotor circuit. To facilitate this system-wide analysis of transcriptional responses, we developed a gene expression profiling approach that enables the construction of hundreds of spatially-defined RNA-sequencing libraries. Using this method, we found that deafening preferentially alters gene expression across birdsong neural circuitry relative to surrounding areas, particularly in premotor and striatal regions. Genes with altered expression are associated with synaptic transmission, neuronal spines, and neuromodulation and show a bias toward expression in glutamatergic neurons andPvalb/Sst-class GABAergic interneurons. We also found that connected song regions exhibit correlations in gene expression that were reduced in deafened birds relative to hearing birds, suggesting that song destabilization alters the inter-region coordination of transcriptional state. Finally, lesioning LMAN, a forebrain afferent of RA required for deafening-induced song plasticity, had the largest effect on groups of genes that were also most affected by deafening. Combined, this integrated transcriptomics analysis demonstrates that the loss of peripheral sensory input drives a distributed gene expression response throughout associated sensorimotor neural circuitry and identifies specific candidate molecular and cellular mechanisms that support stability and plasticity of learned motor skills.
A temperature-tolerant CRISPR base editor mediates highly efficient and precise gene inactivationin vivo
Authors: Doll Roman M. , Boutros Michael , Port Fillip 
Published: December 2022

SummaryCRISPR nucleases generate a broad spectrum of mutations that includes undesired editing outcomes which attenuate phenotypes and complicate experimental analysis and interpretation. Here, we develop an optimised cytosine base editing system for gene inactivation inDrosophilathrough predictable C-to-T editing and identify temperature as a crucial parameter for base editing efficiency. We find that activity of an evolved version of the most widely used APOBEC1 deaminase is attenuated within the temperature range commonly used for culturingDrosophila(18-29°C) and many other ectothermic species. In contrast, an evolved CDA1 domain functions with remarkable efficiency within the same temperature range. Furthermore, we show that formation of undesired indel mutations and C-to-G/A edits is exceptionally rare inDrosophilacompared to other species. The predictable editing outcome, very high efficiency and minimal byproduct formation of this system allows for near homogeneous biallelic gene inactivationin vivoin a ubiquitous or conditional manner. This work significantly improves our ability to create precise loss-of-function alleles inDrosophilaand provides key design parameters for developing highly efficient base editing systems in other ectothermic species.
Time-resolved proximity proteomics uncovers a membrane tension-sensitive caveolin-1 interactome at the rear of migrating cells
Authors: Girardello Rossana , Martin Eleanor , Dittmar Gunnar , Ludwig Alexander 
Published: December 2022

AbstractCaveolae play fundamental roles in mechanotransduction. Critical to caveolae function is their ability to flatten out in response to an increase in membrane tension, thereby acting as a membrane reservoir to buffer acute mechanical stress. Cycles of caveolae assembly and disassembly also regulate membrane tension at the rear of migrating cells via RhoA/ROCK-mediated actomyosin contractility. However, the molecular mechanisms that couple caveolae-mediated mechanotransduction to cortical actin dynamics are poorly understood. Here we used biotin-based proximity labelling and quantitative mass spectrometry to define a caveolae-associated interactome in migrating RPE1 cells at steady state and in response to an acute increase in membrane tension induced by hypo-osmotic shock. Our data reveal a dynamic caveolae-associated protein network composed of focal adhesion proteins and cortical actin regulators that is highly sensitive to changes in membrane tension. We show that membrane tension differentially controls the association of ROCK and the RhoGAP ARHGAP29 with caveolae and that ARHGAP29 regulates caveolin-1 Y14 phosphorylation, caveolae rear localisation and RPE1 cell migration. Caveolae in turn regulate ARHGAP29 expression, most likely through the control of YAP signalling. Taken together, our work uncovers a membrane tension-dependent functional coupling between caveolae and the rear-localised actin cytoskeleton, which provides a framework for dissecting the molecular mechanisms underlying caveolae-regulated mechanotransduction pathways.
A cell atlas of human adrenal cortex development and disease
Authors: del Valle Ignacio , Young Matthew D , Kildisiute Gerda , Ogunbiyi Olumide K , Buonocore Federica , Simcock Ian C , Khabirova Eleonora , Crespo Berta , Moreno Nadjeda , Brooks Tony , Niola Paola , Swarbrick Katherine , Suntharalingham Jenifer P , McGlacken-Byrne Sinead M , Arthurs Owen J , Behjati Sam , Achermann John C 
Published: December 2022

AbstractThe adrenal glands synthesize and release essential steroid hormones such as cortisol and aldosterone, but the mechanisms underlying human adrenal gland development are not fully understood. Here, we combined single-cell and bulk RNA-sequencing, spatial transcriptomics, immunohistochemistry and micro-focus computed tomography to investigate key aspects of adrenal development in the first 20 weeks of gestation. We demonstrate rapid adrenal growth and vascularization, with cell division in the outer definitive zone (DZ). Steroidogenic pathways favor androgen synthesis in the central fetal zone (FZ), but DZ capacity to synthesize cortisol and aldosterone develops with time. Core transcriptional regulators were identified, with a role for HOPX in the DZ. Potential ligand- receptor interactions between mesenchyme and adrenal cortex were seen (e.g.,RSPO3/LGR4). Growth-promoting imprinted genes were enriched in the developing cortex (e.g.IGF2, PEG3). These findings reveal new aspects of human adrenal development, and have clinical implications for understanding primary adrenal insufficiency and related postnatal adrenal disorders, such as adrenal tumor development, steroid disorders and neonatal stress.
Shift of the insoluble content of the proteome in aging mouse brain
Authors: Molzahn Cristen , Kuechler Erich , Zemlyankina Irina , Nieves Lorenz , Ali Tahir , Cole Grace , Wang Jing , Albu Razvan F. , Zhu Mang , Cashman Neil , Gilch Sabine , Karsan Aly , Lange Philipp F. , Gsponer Jörg , Mayor Thibault 
Published: December 2022

AbstractAging and protein aggregation diseases are inextricably linked. During aging, cellular response to unfolded proteins are believed to decline which results in diminished protein homeostasis (proteostasis). Indeed, in model organisms, such asC. elegans, proteostatic decline with age has even been linked to the onset of aggregation of proteins in wild-type animals. However, this correlation has not been extensively characterized in aging mammals. To reveal the insoluble portion of the proteome, we analyzed the detergent-insoluble fraction of mouse brain tissues after high-speed centrifugation by quantitative mass spectrometry. We identified a cohort of 171 proteins enriched in the pellet fraction of older mice including the alpha crystallin small heat shock protein. We then performed a meta-analysis to compare features among distinct groups of detergent-insoluble proteins reported in the literature. Surprisingly, our analysis revealed that features associated with proteins found in the pellet fraction differ depending on the ages of the mice. In general, insoluble proteins from young models (<15 weeks) were more likely to be RNA-binding, more disordered and more likely to be found in membraneless organelles. These traits become less prominent with age within the combined dataset, as proteins with more structure enter the pellet fraction. This analysis suggests that age-related changes to proteome organization lead a specific group of proteins to enter the pellet fraction as a result of loss of proteostasis.
FOX transcription factors are common regulators of Wnt/β-catenin signaling
Authors: Moparthi Lavanya , Koch Stefan 
Published: December 2022

ABSTRACTThe Wnt/β-catenin signaling pathway is a critical regulator of development and stem cell maintenance. Mounting evidence suggests that the context-specific outcome of Wnt signaling is determined by the collaborative action of multiple transcription factors, including members of the highly conserved forkhead box (FOX) protein family. However, the contribution of FOX transcription factors to Wnt signaling has not been investigated in a systematic manner. Here, we performed uniform gain-of-function screens of all 44 human FOX transcription factors to identify and classify new regulators of the Wnt/β-catenin pathway. By combining β-catenin reporter assays with Wnt pathway-focused qPCR arrays and proximity proteomics of selected FOX family members, we determine that most FOX proteins are involved in the regulation of Wnt pathway activity and the expression of Wnt ligands and target genes. Moreover, as a proof of principle we characterize class D and I FOX transcription factors as physiologically relevant positive and negative regulators of Wnt/β-catenin signaling, respectively. We conclude that FOX proteins are common regulators of the Wnt/β-catenin pathway that may control the outcome of Wnt signaling in a tissue-specific manner.