bluuebunny/crossref_metadata_2025 huggingface dataset:
Corynebacterium kroppenstedtii breast abscesses in context, a retrospective cohort study
Authors: Stevenson Daniel R. , Das Satya , Lambourne Jonathan , Ledwidge Serena F.C. , Johnson Laura , Rosmarin Caryn
Published: December 2022

Corynebacterium kroppenstedtiibreast abscesses and granulomatous mastitis have gained increased recognition in the 20 years since their association was first described. No studies to date have described this organism in the context of all breast abscess pathogens. We retrospectively reviewed 160 community-acquired breast abscess samples from 135 patients in a 3 year period, describing the organisms isolated along with risk factors, site of infection and outcomes. We compared patient subgroups with acute and chronic abscesses, the latter defined as having a requirement for repeat aspiration more than 1 month apart. The prevalence ofC. kroppenstedtiibreast abscesses was 8 % in all patients (11/135), rising to 32 % in chronic abscesses (10/31), but only 1 % in acute abscesses (1/104;P<0.01). Only 10 % (1/10) of patients withC. kroppenstedtiichronic abscesses were smokers, whereas 75 % of patients (15/20) with non-C. kroppenstedtiichronic abscesses were smokers (P=0.01).C. kroppenstedtiishould be considered in recurrent and prolonged infections, especially in non-smokers, and diagnostic methods altered accordingly. IdentifyingC. kroppenstedtiiprovides diagnostic clarity and alters management with recommendations for longer courses of treatment using non-beta-lactam antibiotics.
Fibroblast Growth Factor 5 (FGF5) and Its Missense Mutant FGF5-H174 Underlying Trichomegaly: A Molecular Dynamics Simulation Investigation
Authors: Hoang Skyler H.
Published: December 2022

The missense mutation Y174H of FGF5 (FGF5-H174) had been associated with trichomegaly, characterized by abnormally long and pigmented eyelashes. The amino acid tyrosine (Tyr/Y) is conserved across many species, proposedly holding important characteristics for the functions of FGF5. One-microsecond molecular dynamics simulations along with protein-protein docking and residue interacting network analysis were employed to investigate the structural dynamics and binding mode of both wild-type (FGF5-WT) and its mutated counterpart (FGF5-Y174H). It was found that the mutation caused decreases in number of hydrogen bonds within the protein, sheet secondary structure, interaction of residues 174 with others, and number of salt-bridges. On the other hand, the mutation showed increases in solvent accessible surface area, number of hydrogen bonds between the protein and solvent, coil secondary structure, protein C-alpha backbone root mean square deviation, protein residue root mean square fluctuations, as well as occupied conformational space. In addition, protein-protein docking integrated with molecular dynamics simulations and molecular mechanics - Poisson-Boltzmann surface area (MM/PBSA) binding energy calculation demonstrated that the mutated variant possessed stronger binding affinity towards fibroblast growth factor receptor 1 (FGFR1). However, residue interaction network analysis demonstrated that the binding mode was drastically different from that of the FGF5-WT-FGFR1 complex. In conclusion, the missense mutation conferred more instability, stronger binding affinity towards FGFR1 but with distinctively altered binding mode or residue connectivity. These findings might help explain the decreased activation of FGFR1, underlying trichomegaly.
Range restricted old and young lineages show the southern Western Ghats to be both a museum and a cradle of diversity for woody plants
Authors: Gopal Abhishek , Bharti D. K. , Page Navendu , Dexter Kyle G. , Krishnamani Ramanathan , Kumar Ajith , Joshi Jahnavi
Published: December 2022

The Western Ghats (WG) mountain chain is a global biodiversity hotspot with high diversity and endemicity of woody plants. The latitudinal breadth of the WG offers an opportunity to determine the evolutionary drivers of latitudinal diversity patterns. We examined the spatial patterns of evolutionary diversity using complementary phylogenetic diversity and endemism measures. To examine if different regions of the WG serve as a museum or cradle of evolutionary diversity, we examined the distribution of 470 species based on distribution modelling and occurrence locations across the entire region. In accordance with the expectation, we found that the southern WG is both a museum and cradle of woody plant evolutionary diversity, as a higher proportion of both old and young evolutionary lineages are restricted to the southern WG. The diversity gradient is likely driven by high geo-climatic stability in the south and phylogenetic niche conservatism for moist and aseasonal sites. This is corroborated by persistent lineage nestedness at almost all evolutionary depths (10–135 million years), and a strong correlation of evolutionary diversity with drought seasonality, precipitation and topographic heterogeneity. Our results highlight the global value of the WG, demonstrating, in particular, the importance of protecting the southern WG – an engine of plant diversification and persistence.
FrustraPocket: A protein–ligand binding site predictor using energetic local frustration
Authors: Freiberger Maria I. , Clemente Camila M. , Valero Eneko , Pombo Jorge G. , Leonetti Cesar O. , Ravetti Soledad , Parra R. Gonzalo , Ferreiro Diego U.
Published: December 2022

Proteins are evolved polymers that minimize their free energy upon folding to their native states. Still, many folded proteins display energetic conflict between residues in various regions that can be identified as highly frustrated, and these have been shown to be related to several physiological functions. Here we show that small-ligand binding sites are typically enriched in locally frustrated interactions in the unbound state. We built a tool using a simple machine learning algorithm named FrustraPocket that combines the notion of small-molecule binding pockets and the localization of clusters of highly frustrated interactions to identify potential protein-ligand binding sites solely from the unbound forms.

Availability and implementation (github)

https://github.com/CamilaClemente/FrustraPocket/

Docker container

https://hub.docker.com/r/proteinphysiologylab/frustrapocket
Global and cell type-specific immunological hallmarks of severe dengue progression
Authors: Ghita Luca , Yao Zhiyuan , Xie Yike , Duran Veronica , Cagirici Halise Busra , Samir Jerome , Osman Ilham , Agudelo Rojas Olga Lucia , Sanz Ana Maria , Sahoo Malaya Kumar , Robinson Makeda L. , Gelvez Rosa Margarita , Bueno Nathalia , Luciani Fabio , Pinsky Benjamin A. , Montoya Jose G. , Estupiñan Cardenas Maria Isabel , Villar Centeno Luis Angel , Rojas Garrido Elsa Marina , Rosso Fernando , Quake Stephen R. , Zanini Fabio , Einav Shirit
Published: December 2022

Severe dengue (SD) is a major cause of morbidity and mortality impacting approximately 5 million of the 400 million people infected with dengue virus (DENV) annually. To define DENV target cells and immunological hallmarks of SD progression in children’s blood, we integrated virus-inclusive single cell RNA-Seq 2 (viscRNA-Seq 2) with functional assays. Beyond myeloid cells, in natural infection, B cells harbor replicating DENV capable of infecting permissive cells. Alterations in cell type abundance, gene and protein expression and secretion, and cell-cell communications point towards increased migration and inflammation in SD progressors (SDp). Concurrently, antigen presenting cells from SDp demonstrate intact uptake, yet impaired interferon responses and antigen presentation, in part DENV-modulated. Increased activation, regulation, and exhaustion of effector responses and expansion of HLA-DR-expressing, possibly compensatory, adaptive-like NK cells also characterize SDp. These findings reveal DENV target cells in the human blood and provide insight into SD pathogenesis beyond antibody-mediated enhancement.
Reimagining Gene-Environment Interaction Analysis for Human Complex Traits
Authors: Miao Jiacheng , Song Gefei , Wu Yixuan , Hu Jiaxin , Wu Yuchang , Basu Shubhashrita , Andrews James S. , Schaumberg Katherine , Fletcher Jason M. , Schmitz Lauren L. , Lu Qiongshi
Published: December 2022

In this study, we introduce PIGEON—a novel statistical framework for quantifying and estimating polygenic gene-environment interaction (GxE) using a variance component analytical approach. Based on PIGEON, we outline the main objectives in GxE studies, demonstrate the flaws in existing GxE approaches, and introduce an innovative estimation procedure which only requires summary statistics as input. We demonstrate the statistical superiority of PIGEON through extensive theoretical and empirical analyses and showcase its performance in multiple analytic settings, including a quasi-experimental GxE study of health outcomes, gene-by-sex interaction for 530 traits, and gene-by-treatment interaction in a randomized clinical trial. Our results show that PIGEON provides an innovative solution to many long-standing challenges in GxE inference and may fundamentally reshape analytical strategies in future GxE studies.
Lacustrine speciation associated with chromosomal inversion in a lineage of riverine fishes
Authors: MacGuigan Daniel J. , Krabbenhoft Trevor J. , Harrington Richard C. , Wainwright Dylan K. , Backenstose Nathan J. C. , Near Thomas J.
Published: December 2022

Geographic isolation is the primary driver of speciation in many vertebrate lineages. This trend is exemplified by North American darters, a clade of freshwater fishes where nearly all sister species pairs are allopatric and separated by millions of years of divergence. One of the only exceptions is the Lake Waccamaw endemicEtheostoma perlongumand its riverine sister speciesE. maculaticeps,which have no physical barriers to gene flow. Here we show that lacustrine speciation ofE. perlongumis characterized by morphological and ecological divergence likely facilitated by a large chromosomal inversion. WhileEtheostoma perlongumis phylogenetically nested within the geographically widespreadE. maculaticeps, there is a sharp genetic and morphological break coinciding with the lake-river boundary in the Waccamaw River system. Despite recent divergence, an active hybrid zone, and ongoing gene flow, analyses using ade novoreference genome reveal a 9 Mb chromosomal inversion with elevated divergence betweenE. perlongumandE. maculaticeps.This region exhibits striking synteny with known inversion supergenes in two distantly related fish lineages, suggesting deep evolutionary convergence of genomic architecture. Our results illustrate that rapid, ecological speciation with gene flow is possible even in lineages where geographic isolation is the dominant mechanism of speciation.
Unraveling the effects of virtual reality overground walking on dynamic balance and postural control
Authors: Horsak Brian , Simonlehner Mark , Dumphart Bernhard , Siragy Tarique
Published: December 2022

This study analyzed the effects of walking freely in Virtual Reality (VR) compared to walking in the real-world on dynamic balance and postural control. For this purpose nine male and twelve female healthy participants underwent standard 3D gait analysis while walking randomly in a real laboratory and in a room-scale overground VR environment resembling the real laboratory. The VR was delivered to participants by a head-mounted-display which was operated wirelessly and calibrated to the real-world. Dynamic balance was assessed with three outcomes: the Margin of Stability (MOS) in the anteroposterior (AP-MOS) and mediolateral (ML-MOS) directions at initial-contact, the relationship between the mediolateral Center of Mass (COM) position and acceleration at mid-stance with subsequent step width, and trunk kinematics during the entire gait cycle. We observed increased mediolateral (ML) trunk linear velocity variability, an increased coupling of the COM position and acceleration with subsequent step width, and a decrease in AP-MOS while walking in VR, but no change in ML-MOS when walking in VR. We conclude that walking in VR results in a less reliable optical flow, indicated by increased mediolateral trunk kinematic variability, which seems to be compensated by the participants by slightly reweighing sensorimotor input and thereby consciously tightening the coupling between the COM and foot placement to avoid a loss of balance. Our results are particularly valuable for future developers who want to use VR to support gait analysis and rehabilitation.
3D chromatin interactions involvingDrosophilainsulators are infrequent but preferential and arise before TADs and transcription
Authors: Messina Olivier , Raynal Flavien , Gurgo Julian , Fiche Jean-Bernard , Pancaldi Vera , Nollmann Marcelo
Published: December 2022

In mammals, insulators contribute to the regulation of loop extrusion to organize chromatin into topologically associating domains. InDrosophilathe role of insulators in 3D genome organization is, however, under current debate. Here, we addressed this question by combining bioinformatics analysis and multiplexed chromatin imaging. We describe a class ofDrosophilainsulators enriched at regions forming preferential chromatin interactions genome-wide. Notably, most of these 3D interactions do not involve TAD borders. Multiplexed imaging shows that these interactions occur infrequently, and only rarely involve multiple genomic regions coalescing together in space in single cells. Finally, we show that non-border preferential 3D interactions enriched in this class of insulators arise before TADs and transcription duringDrosophiladevelopment. Our results are inconsistent with insulators forming stable hubs in single cells, and instead suggest that they fine-tune existing 3D chromatin interactions, providing an additional regulatory layer for transcriptional regulation.
Differentiation of leukocytes in bronchoalveolar lavage fluid samples using higher harmonic generation microscopy and deep learning
Authors: van Huizen L.M.G. , Blokker M. , Rip Y. , Veta M. , Kalverda K.A. , Bonta P.I. , Duitman J.W. , Groot M.L.
Published: December 2022

In many diseases such as interstitial lung diseases (ILDs), patient diagnosis relies on diagnostic analysis of bronchoalveolar lavage fluid (BALF) and biopsies. In BALF the differentiation of neutrophils, eosinophils, lymphocytes, and macrophages can contribute to diagnose the underlying ILD entity. To analyze the BALF standard cytological techniques are labor-intensive and time-consuming. Studies have shown promising cell identification performance on blood fractions analyzed by third harmonic generation (THG) and multiphoton excited autofluorescence (MPEF) microscopy. Here, we extend this to BALF samples, and we trained a deep learning algorithm for automated analysis on the image level against reference cytology. We imaged blood fractions from three healthy individuals and one asthma patients, and six BALFs from ILD patients. We determined the leukocyte characteristics in terms of cellular and nuclear morphology, and THG and MPEF signal intensity. A deep learning model was trained on both blood fractions and BALF 2D images was used to estimate the leukocyte ratios by using only the standard cytology differential cell ratios at the image-level as reference. The deep learning network has learned to identify individual cells and was able to provide a reasonable estimate of the leukocyte percentage, coming within a 2 to 10% margin in BALF samples in the hold-out testing set. We suggest that the performance of the combined label free imaging and AI analysis can be improved further by collecting 3D data and data of additional fluid samples of various ILD diseases and healthy samples, THG/MPEF microscopy in combination with deep learning is a promising technique for instant differentiation and quantification of leukocytes. Immediate feedback on leukocyte ratios will not only speed-up the diagnostic process but can also reduce costs, the workload and reduce inter-observer variations.
Polychrome labeling reveals skeletal triradiate and elongation dynamics and abnormalities in patterning cue-perturbed embryos
Authors: Descoteaux Abigail E. , Zuch Daniel T. , Bradham Cynthia A.
Published: December 2022

The larval skeleton of the sea urchinLytechinus variegatusis an ideal model system for studying skeletal patterning; however, our understanding of the etiology of skeletal patterning in sea urchin larvae is limited due to the lack of approaches to live-image skeleton formation. Calcium-binding fluorochromes have been used to study the temporal dynamics of bone growth and healing. To date, only calcein green has been used in sea urchin larvae to fluorescently label the larval skeleton. Here, we optimize labeling protocols for four other calcium-binding fluorochromes-alizarin red, xylenol orange, tetracycline, and calcein blue- and demonstrate that these fluorochromes can be used individually or in nested pulse-chase experiments to understand the temporal dynamics of skeletogenesis and patterning. Using this pulse-chase approach we reveal that the initiation of skeletogenesis begins around 15 hours post fertilization, which is earlier than previously thought. We also explore the timing of triradiate formation in embryos treated with a range of patterning perturbagens, and demonstrate that triradiates form late and asynchronously in embryos ventralized via treatment with either nickel at early gastrula stage or with chlorate from fertilization. Finally, we measure the extent of fluorochrome incorporation in triple-labeled embryos to determine the elongation rate of numerous skeletal elements throughout early skeletal patterning and compare this to the rate of skeletal growth in axitinib-treated embryos. We find that skeletal elements elongate much more slowly in axitinib-treated embryos, and that axitinib treatment is sufficient to induce abnormal orientation of the triradiates.

Highlights

Calcium-binding fluorochromes selectively label the sea urchin larval skeleton

Pulsed, nested polychrome labeling offers temporal insight into skeletal patterning

Triradiate formation is delayed and asynchronous in ventralized embryos

VEGFR inhibition slows skeletal elongation and perturbs triradiate orientation
Investigating the folding dynamics of NS2B protein of Zika virus
Authors: Kumar Ankur , Kumar Prateek , Mishra Pushpendra Mani , Giri Rajanish
Published: December 2022

NS2B protein of the Zika virus acts as a co-factor for NS3 protease where only the cytosolic domain of NS2B is sufficient for the protease activity. At the same time, NS2B also involves in remodeling the NS3 protease structure. In isolation, we previously proved the NS2B cytosolic domain (residues 49-95) as a disordered type peptide conformation. Further, this study investigated the overall dynamics of NS2B full-length protein. Our Alphafold2 structure modeling system revealed surprising similarities between selected flavivirus NS2B proteins. This similarity reflects that the NS2B protein across flavivirus is conserved fold-wise. The MD simulation of Zika virus NS2B full-length protein shows that the cytosolic domain as a part of full-length protein is a disorder region supporting our previous experimental finding, which suggests the disordered nature of the cytosolic domain in isolation. Since the cytosolic domain of NS2B is essential for protease activity, we have also investigated the folding and dynamics of the NS2B cytosolic domain (residues 49-95) that shows the disorder to alpha helix transition in TFE. On the other hand, in the presence of SDS, macromolecular crowder like ficoll and PEG do not induce secondary structural change. This dynamics study could have implications for some unknown folds of the NS2B protein.
An ESCRT grommet cooperates with a diffusion barrier to maintain nuclear integrity
Authors: Ader Nicholas R. , Chen Linda , Surovtsev Ivan V. , Chadwick William L. , Rodriguez Elisa C. , King Megan C. , Lusk C. Patrick
Published: December 2022

The molecular mechanisms by which the endosomal sorting complexes required for transport (ESCRT) proteins contribute to the integrity of the nuclear envelope (NE) barrier are not fully defined. Here, we leveraged the single NE hole generated by mitotic extrusion of theSchizosaccharomyces pombespindle pole body (SPB) to reveal two modes of ESCRT function executed by distinct complements of ESCRT-III proteins, both depending on CHMP7/Cmp7. A grommet-like function is required to restrict the NE hole in anaphase B, while replacement of Cmp7 by a sealing module ultimately closes the NE in interphase. Without Cmp7, nucleocytoplasmic compartmentalization surprisingly remains intact despite NE discontinuities up to 550 nm, suggesting mechanisms to prevent diffusion through these holes. We implicate SPB proteins as key components of a diffusion barrier acting with Cmp7 in anaphase B. Thus, NE remodeling mechanisms cooperate with proteinaceous diffusion barriers beyond nuclear pore complexes to protect the nuclear compartment.
Human Airway Mucociliary Tissue Cultures Chronically Exposed to E-Cigarette Vapors Exhibit Altered Cell Populations and Increased Secretion of Immunomodulatory Cytokines
Authors: Manna Vincent J. , Dwyer Shannon , Pizutelli Vanessa , Caradonna Salvatore J.
Published: December 2022

Vape-pens or electronic cigarettes (e-cigarettes) are handheld battery powered devices that use a vape-liquid to produce a vapor that is inhaled by the user. The active ingredients in commercial vape-liquids are commonly nicotine, tetrahydrocannabinol or cannabidiol. A consequence of the rise in e-cigarette usage was the 2019 emergence of a vaping-induced respiratory disease denoted ‘e-cigarette or vaping use-associated lung injury’ (EVALI). One of the suspected causes of EVALI is Vitamin E Acetate (VEA), which was found to be a diluent in certain illicit tetrahydrocannabinol vape-pens, whereas nicotine is commonly diluted in equal parts propylene glycol and vegetable glycerin (PG:VG). The prevalent use of e-cigarettes by both adult and young adult populations and the emergence of a novel illness has made understanding how e-cigarette vapors affect our respiratory tissues a public health concern. We have designed and produced a simple device that can operate commercial e-cigarettes and deliver the vapor to a chamber containing a standard cell culture multi-well plate. Here we utilize our device to investigate how human airway mucociliary tissue cultures respond after chronic exposure to vapors produced from either PG:VG or VEA. We note several differences between how PG:VG and VEA vapors interact with and alter airway tissue cultures and suggest potential mechanisms for how VEA-vapors can exacerbate EVALI symptoms. Our device combined with primary human airway tissue cultures make an economical and compact model system that allows for animal-free investigations into the acute and chronic consequences of e-cigarette vapors on primary respiratory cells.
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

Chronic 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

The 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

The 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.

Highlights

Multiple RNA binding domains enable differential recognition of distinct RNA motifs to regulate alternative splicing

The RRM1-ZnF1 domains of RBM5 mediate specific recognition ofcisregulatory RNA motifs to modulate alternative splicing

RRM1-ZnF1 sandwich the target RNA for non-canonical recognition of a GG dinucleotide

RRM1-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

Based 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

Binding 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

We 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.

Highlights

We assess the neural computations in the prosopagnosic patient PS using EEG, RSA, and deep neural networks

Neural dynamics of brain-lesioned PS are reliably captured using RSA

Neural decoding shows normal evidence for non-face individuation in PS

Neural decoding shows abnormal neural evidence for face individuation in PS

PS 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

Malaria, 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

Sensory 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

CRISPR 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

Caveolae 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

The 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

Aging 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

The 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.