bluuebunny/crossref_metadata_2025_split huggingface dataset:
CellSeg3D: self-supervised 3D cell segmentation for fluorescence microscopy
Authors: Achard Cyril , Kousi Timokleia , Frey Markus , Vidal Maxime , Paychère Yves , Hofmann Colin , Iqbal Asim , Hausmann Sebastien B. , Pagès Stéphane , Mathis Mackenzie Weygandt 
Published: May 2024

AbstractUnderstanding the complex three-dimensional structure of cells is crucial across many disciplines in biology and especially in neuroscience. Here, we introduce a set of models including a 3D transformer (SwinUNetR) and a novel 3D self-supervised learning method (WNet3D) designed to address the inherent complexity of generating 3D ground truth data and quantifying nuclei in 3D volumes. We developed a Python package called CellSeg3D that provides access to these models in Jupyter Notebooks and in a napari GUI plugin. Recognizing the scarcity of high-quality 3D ground truth data, we created a fully human-annotated mesoSPIM dataset to advance evaluation and benchmarking in the field. To assess model performance, we benchmarked our approach across four diverse datasets: the newly developed mesoSPIM dataset, a 3D platynereis-ISH-Nuclei confocal dataset, a separate 3D platynereis-Nuclei light-sheet dataset, and a challenging and densely packed Mouse-Skull-Nuclei confocal dataset. We demonstrate that our self-supervised model, WNet3D – trained without any ground truth labels – achieve performance on par with state-of-the-art supervised methods, paving the way for broader applications in label-scarce biological contexts.
A stochastic RNA editing process targets a limited number of sites in individualDrosophilaglutamatergic motoneurons
Authors: Crane Andrés B. , Jetti Suresh K. , Littleton J. Troy 
Published: May 2024

AbstractRNA editing is a post-transcriptional source of protein diversity and occurs across the animal kingdom. Given the complete profile of mRNA targets and their editing rate in individual cells is unclear, we analyzed single cell RNA transcriptomes fromDrosophilalarval tonic and phasic glutamatergic motoneuron subtypes to determine the most highly edited targets and identify cell-type specific editing. From ∼15,000 genes encoded in the genome, 316 high confidence A-to-I canonical RNA edit sites were identified, with 102 causing missense amino acid changes in proteins regulating membrane excitability, synaptic transmission, and cellular function. Some sites showed 100% editing in single neurons as observed with mRNAs encoding mammalian AMPA receptors. However, most sites were edited at lower levels and generated variable expression of edited and unedited mRNAs within individual neurons. Together, these data provide insights into how the RNA editing landscape alters protein function to modulate the properties of two well-characterized neuronal populations inDrosophila.
New highly selective antivirals for Chikungunya Virus identified from the screening of a drug-like compound library
Authors: Castro Eliana F. , Álvarez Diego E. 
Published: May 2024

AbstractChikungunya fever is a mosquito-borne disease caused by Chikungunya virus (CHIKV). Treatment of CHIKV infections is currently supportive and does not limit viral replication or symptoms of persistent chronic arthritis. Although there are multiple compounds reported as antivirals active against CHIKVin vitro, there are still no effective and safe antivirals. Thus, active research aims at the identification of new chemical structures with antiviral activity. Here, we report the screen of the Pandemic Response Box library of small molecules against a fully infectious CHIKV reporter virus. Our screening approach successfully identified previously reported CHIKV antiviral compounds within this library and further expanded potentially active hits, supporting the use of reporter-virus-based assays in high-throughput screening format as a reliable tool for antiviral drug discovery. Four molecules were identified as potential drug candidates against CHIKV: MMV1634402 (Brilacidin) and MMV102270 (Diphyllin), which were previously shown to present broad-spectrum antiviral activities, in addition to MMV1578574 (Eravacycline), and the antifungal MMV689401 (Fluopicolide), for which their antiviral potential is uncovered here.
Structural insights intoPseudomonas aeruginosalysine-specific uptake mechanism for extremely low pH regulation
Authors: Bicer Deniz , Matsuoka Rei , Moumbock Aurélien F. A. , Sukumar Preethi , Cheruvara Harish , Quigley Andrew , Pardon Els , Steyaert Jan , Henderson Peter J.F. , Caffrey Martin , Griese Julia J. , Nji Emmanuel 
Published: May 2024

AbstractUnder conditions of extremely low pH, in addition to transporting lysine, bacterial lysine-specific permease (LysP) interacts with the transcriptional regulator CadC to upregulatecadBAoperon expression.cadBAencodes CadA, which decarboxylates lysine to cadaverine, and CadB, which exports cadaverine to the environment to reduce acidity. This process is crucial for survival of pathogenic bacteria in their hosts. Here, we report the inward-occluded (3.2 – 5.3 Å) cryo-EM structure ofPseudomonas aeruginosaLysP bound to L-lysine and in complex with a nanobody. L-lysine is coordinated by hydrophobic stacking, cation-π interactions and hydrogen bonding mostly with polar uncharged LysP residues. LysP reconstituted into liposomes showed robust and specific transport of L-lysine with the transport being inhibited by L-4-thialysine (S-2-aminoethyl-L-cysteine). These findings inform our understanding of the specific recognition, inhibition, and transport mechanism of L-lysine by LysP, which will have important ramifications for the design of antibiotics to target bacterial LysP.
Distinct components of nucleoside-modified messenger RNA vaccines cooperate to instruct efficient germinal center responses
Authors: Bettini Emily , Chudnovskiy Aleksey , Protti Giulia , Nakadakari-Higa Sandra , Ceglia Simona , Castaño Diana , Chiu Joy , Muramatsu Hiromi , Mdluli Thandiswa , Abraham Edit , Lipinszki Zoltan , Maillard Ivan , Tam Ying K. , Reboldi Andrea , Pardi Norbert , Spreafico Roberto , Victora Gabriel D. , Locci Michela 
Published: May 2024

SUMMARYNucleoside-modified mRNA vaccines elicit protective antibodies through their ability to promote T follicular helper (Tfh) cells. The lipid nanoparticle (LNP) component of mRNA vaccines possesses inherent adjuvant activity. However, to what extent the nucleoside-modified mRNA can be sensed and contribute to Tfh cell responses remains largely undefined. Herein, we deconvoluted the signals induced by LNP and mRNA that instruct dendritic cells (DCs) to promote Tfh cell differentiation. We demonstrated that the nucleoside-modified mRNA drives the production of type I interferons that act on DCs to induce their maturation and the induction of Th1-biased Tfh responses. Conversely, LNP favors the acquisition of a Tfh cell-inducing program in DCs, a stronger Th2 polarization in Tfh cells, and allows for rapid mRNA translation by DCs within the draining lymph node. Our work unravels distinct adjuvant features of mRNA and LNP necessary for the induction of Tfh cells, with implications for vaccine design.
Highly sensitive mapping ofin vitrotype II topoisomerase DNA cleavage sites with SHAN-seq
Authors: Morgan Ian L. , McKie Shannon J. , Kim Rachel , Seol Yeonee , Xu Jing , Harami Gabor , Maxwell Anthony , Neuman Keir C. 
Published: May 2024

AbstractType II topoisomerases (topos) are a ubiquitous and essential class of enzymes that form transient enzyme-bound double-stranded breaks on DNA called cleavage complexes. The location and frequency of these cleavage complexes on DNA is important for cellular function, genomic stability, and a number of clinically important anticancer and antibacterial drugs, e.g., quinolones. We developed a simple high-accuracy end-sequencing (SHAN-seq) method to sensitively map type II topo cleavage complexes on DNAin vitro. Using SHAN-seq, we detectedEscherichia coligyrase and topoisomerase IV cleavage complexes at hundreds of sites on supercoiled pBR322 DNA, approximately one site every ten bp, with frequencies that varied by two-to-three orders of magnitude. These sites included previously identified sites and 20-50 fold more new sites. We show that the location and frequency of cleavage complexes at these sites are enzyme-specific and vary substantially in the presence of the quinolone, ciprofloxacin, but not with DNA supercoil chirality, i.e., negative vs. positive supercoiling. SHAN-seq’s exquisite sensitivity provides an unprecedented single-nucleotide resolution view of the distribution of gyrase and topoisomerase IV cleavage complexes on DNA. Moreover, the discovery that these enzymes can cleave DNA at orders of magnitude more sites than the relatively few previously known sites resolves the apparent paradox of how these enzymes resolve topological problems throughout the genome.
A chromosome region linked to neurodevelopmental disorders acts in distinct neuronal circuits in males and females to control locomotor behavior
Authors: Kim Jaekyoon , Vanrobaeys Yann , Davatolhagh M. Felicia , Kelvington Benjamin , Chatterjee Snehajyoti , Ferri Sarah L. , Angelakos Christopher , Mills Alea A. , Fuccillo Marc V. , Nickl-Jockschat Thomas , Abel Ted 
Published: May 2024

SummaryBiological sex shapes the manifestation and progression of neurodevelopmental disorders (NDDs). These disorders often demonstrate male-specific vulnerabilities; however, the identification of underlying mechanisms remains a significant challenge in the field. Hemideletion of the 16p11.2 region (16p11.2 del/+) is associated with NDDs, and mice modeling 16p11.2 del/+ exhibit sex-specific striatum-related phenotypes relevant to NDDs. Striatal circuits, crucial for locomotor control, consist of two distinct pathways: the direct and indirect pathways originating from D1 dopamine receptor (D1R) and D2 dopamine receptor (D2R) expressing spiny projection neurons (SPNs), respectively. In this study, we define the impact of 16p11.2 del/+ on striatal circuits in male and female mice. Using snRNA-seq, we identify sex- and cell type-specific transcriptomic changes in the D1- and D2-SPNs of 16p11.2 del/+ mice, indicating distinct transcriptomic signatures in D1-SPNs and D2-SPNs in males and females, with a ∼5-fold greater impact in males. Further pathway analysis reveals differential gene expression changes in 16p11.2 del/+ male mice linked to synaptic plasticity in D1- and D2-SPNs and GABA signaling pathway changes in D1-SPNs. Consistent with our snRNA-seq study revealing changes in GABA signaling pathways, we observe distinct changes in miniature inhibitory postsynaptic currents (mIPSCs) in D1- and D2-SPNs from 16p11.2 del/+ male mice. Behaviorally, we utilize conditional genetic approaches to introduce the hemideletion selectively in either D1- or D2-SPNs and find that conditional hemideletion of genes in the 16p11.2 region in D2-SPNs causes hyperactivity in male mice, but hemideletion in D1-SPNs does not. Within the striatum, hemideletion of genes in D2-SPNs in the dorsal lateral striatum leads to hyperactivity in males, demonstrating the importance of this striatal region. Interestingly, conditional 16p11.2 del/+ within the cortex drives hyperactivity in both sexes. Our work reveals that a locus linked to NDDs acts in different striatal circuits, selectively impacting behavior in a sex- and cell type-specific manner, providing new insight into male vulnerability for NDDs.Highlights-16p11.2 hemideletion (16p11.2 del/+) induces sex- and cell type-specific transcriptomic signatures in spiny projection neurons (SPNs).-Transcriptomic changes in GABA signaling in D1-SPNs align with changes in inhibitory synapse function.-16p11.2 del/+ in D2-SPNs causes hyperactivity in males but not females.-16p11.2 del/+ in D2-SPNs in the dorsal lateral striatum drives hyperactivity in males.-16p11.2 del/+ in cortex drives hyperactivity in both sexes.Graphic abstract
Aging leads to sex-dependent effects on pair bonding and increased number of oxytocin-producing neurons in monogamous prairie voles
Authors: Kelberman Michael A. , Winther Kelly E. , Medvedeva Yana M. , Donaldson Zoe R. 
Published: May 2024

AbstractPair bonds powerfully modulate health, which becomes particularly important when facing the detrimental effects of aging. To examine the impact of aging on relationship formation and response to loss, we examined behavior in 6-, 12-, and 18-month male and female prairie voles, a monogamous species that forms mating-based pair bonds. We found that older males (18-months) bonded quicker than younger voles, while similarly aged female voles increased partner directed affiliative behaviors. Supporting sex differences in bonding behaviors, we found that males were more likely to sample both partner and novel voles while females were more likely to display partner preference during the initial 20 minutes of the test. Using partner separation to study loss, we observed an erosion of partner preference only in 12-month females, but an overall decrease in partner-directed affiliation in females across all groups, but not in males. Finally, we found that the number of oxytocin, but not vasopressin, cells in the paraventricular hypothalamus increased during aging. These results establish prairie voles as a novel model to study the effects of normal and abnormal aging on pair bonding.Highlights18-month male voles demonstrate accelerated bond formation18-month female voles increase partner-directed huddling after 2 wksBonds erode faster in 12-month female voles after partner separationFemale behavior from partner preference tests is reflected in free interactionThe number of paraventricular hypothalamus oxytocin cells increase during aging
Computational analysis of the plasmodium falciparum-induced intraerythrocyte deformations: insights into malaria parasite egress mechanics and eryptosis
Authors: Msosa Chimwemwe , Motchon YD 
Published: May 2024

AbstractIn malaria infection, early eryptosis eliminates the protective niche provided by the infected erythrocyte, thus potentially interfering with the parasite’s survival rate in the human host, consequently presenting a putative target mechanism for antimalarial therapeutic interventions. The malaria parasite-induced oxidative stress is the primary trigger of eryptosis. Despite being barely investigated, erythrocyte membrane mechanical deformations induced by the malaria parasites during the intraerythrocyte development stage, represent a potential eryptosis trigger.A finite element model of the plasmodium falciparum-infected erythrocyte was developed and calibrated in Abaqus using pre-determined optical tweezer data of the trophozoite-infected erythrocyte. The developed model computationally predicts mechanistic correlations between erythrocyte membrane areal strain, eryptosis, erythrocyte membrane shear modulus and the volume fraction of malaria parasites in the infected erythrocyte.The model predicts the erythrocyte membrane areal strain of 3.1 % at the established rupture volume fraction (VF) of 83%, which falls within the pre-determined erythrocyte membrane lysis threshold of 2-4 %. When the erythrocyte membrane in-plane shear modulus is increased from 2.84 µN/m to 131 µN/m, the erythrocyte areal strain increases from 1.55 % to 3.2 % at the same rupture volume fraction (VF) of 83% implying that increasing the erythrocyte membrane stiffness during the malaria intra-erythrocytic development stage can potentially induce early lysis while decreasing the erythrocyte membrane stiffness can potentially induce late lysis.Understanding the mechanisms governing the exit of malaria parasites from infected erythrocytes during the late schizont stage is crucial for developing effective therapeutic interventions. Existing studies lack a comprehensive exploration of how malaria parasite-induced remodelling affects the areal strain of the erythrocyte membrane. Experimental challenges in studying infected erythrocytes have limited progress, making computational models a valuable tool. This research provides valuable insights into the mechanics of malaria-induced erythrocyte remodelling, offering a computational framework for studying parasite egress to inform potential therapeutic strategies.
Dispersal, maturation and recruitment in a long-lived, trans-continentally migrating bird
Authors: Mirski Paweł , Vansteelant Wouter , Byholm Patrik 
Published: May 2024

ABSTRACTNatal dispersal is a multi-step process. It commences when a juvenile departs from its natal site and concludes when it settles to breed for the first time. During this interim period, dispersing individuals of long-lived species undergo a wandering phase, which may span years. This phase remains one of the least studied aspects of species’ life history. We utilized a unique GPS-telemetry dataset on a slow-life history migratory bird of prey – the European honey buzzard, tracked for multiple years after fledgling. Our aim was to assess how phenology, ranging behaviour and philopatry change as individuals gain experience. Individuals exhibited variability in the age at which they first returned to their breeding range, yet all survivors settled at sites proximate to their natal nests. In subsequent returns, immatures increased the time spent within the breeding range and narrowed down their ranging to smaller areas situated even closer to their natal nests. Our study unveils the complexity and protraction inherent in natal dispersal, emphasizing the importance of individual experience and migratory improvement for successful recruitment in long-lived species.HIGHLIGHTSWe used a unique GPS telemetry dataset on honey buzzards to track their natal dispersal and recruitment in this long-lived avian migrant.All individuals gradually decreased their ranging areas, moved closer to natal sites, and increased the time spent on the breeding grounds to synchronize with adults and begin recruitment.Mortality during return migration was high and acted as a bottleneck.We found both processes to be complex and lengthy, with the overall duration depending on individual decisions regarding the timing of return migration.
Dimerization activates the Inversin complex inC. elegans
Authors: Beyrent Erika , Wei Derek T. , Beacham Gwendolyn M. , Park Sangwoo , Zheng Jian , Paszek Matthew J. , Hollopeter Gunther 
Published: May 2024

AbstractGenetic, colocalization, and biochemical studies suggest that the ankyrin repeat-containing proteins Inversin (INVS) and ANKS6 function with the NEK8 kinase to control tissue patterning and maintain organ physiology. It is unknown whether these three proteins assemble into a static “Inversin complex” or one that adopts multiple bioactive forms. Through characterization of hyperactive alleles inC. elegans, we discovered that the Inversin complex is activated by dimerization. Genome engineering of an RFP tag onto the nematode homologs of INVS (MLT-4) and NEK8 (NEKL-2) induced a gain-of-function, cyst-like phenotype that was suppressed by monomerization of the fluorescent tag. Stimulated dimerization of MLT-4 or NEKL-2 using optogenetics was sufficient to recapitulate the phenotype of a constitutively active Inversin complex. Further, dimerization of NEKL-2 bypassed a lethal MLT-4 mutant, demonstrating that the dimeric form is required for function. We propose that dynamic switching between at least two functionally distinct states—an active dimer and an inactive monomer—gates the output of the Inversin complex.
Force-activated zyxin assemblies coordinate actin nucleation and crosslinking to orchestrate stress fiber repair
Authors: Phua Donovan Y.Z. , Sun Xiaoyu , Alushin Gregory M. 
Published: May 2024

SUMMARYAs the cytoskeleton sustains cell and tissue forces, it incurs physical damage that must be repaired to maintain mechanical homeostasis. The LIM-domain protein zyxin detects force-induced ruptures in actin-myosin stress fibers, coordinating downstream repair factors to restore stress fiber integrity through unclear mechanisms. Here, we reconstitute stress fiber repair with purified proteins, uncovering detailed links between zyxin’s force-regulated binding interactions and cytoskeletal dynamics. In addition to binding individual tensed actin filaments (F-actin), zyxin’s LIM domains form force-dependent assemblies that bridge broken filament fragments. Zyxin assemblies engage repair factors through multi-valent interactions, coordinating nucleation of new F-actin by VASP and its crosslinking into aligned bundles by ɑ-actinin. Through these combined activities, stress fiber repair initiates within the cores of micron-scale damage sites in cells, explaining how these F-actin depleted regions are rapidly restored. Thus, zyxin’s force-dependent organization of actin repair machinery inherently operates at the network scale to maintain cytoskeletal integrity.
CellWalker2: multi-omic discovery of hierarchical cell type relationships and their associations with genomic annotations
Authors: Hu Zhirui , Przytycki Pawel F. , Pollard Katherine S. 
Published: May 2024

AbstractCellWalker2 is a graph diffusion-based method for single-cell genomics data integration. It extends the CellWalker model by incorporating hierarchical relationships between cell types, providing estimates of statistical significance, and adding data structures for analyzing multi-omics data so that gene expression and open chromatin can be jointly modeled. Our open-source software enables users to annotate cells using existing ontologies and to probabilistically match cell types between two or more contexts, including across species. CellWalker2 can also map genomic regions to cell ontologies, enabling precise annotation of elements derived from bulk data, such as enhancers, genetic variants, and sequence motifs. Through simulation studies, we show that CellWalker2 performs better than existing methods in cell type annotation and mapping. We then use data from the brain and immune system to demonstrate CellWalker2’s ability to discover cell type-specific regulatory programs and both conserved and divergent cell type relationships in complex tissues.
Diclofenac sensitizes multi-drug resistantAcinetobacter baumanniito colistin
Authors: Bisaro Fabiana , Jackson-Litteken Clay D. , McGuffey Jenna C. , Hooppaw Anna J. , Bodrog Sophie , Jebeli Leila , Ortiz-Marquez Juan C. , van Opijnen Tim , Scott Nichollas E. , Di Venanzio Gisela , Feldman Mario F. 
Published: May 2024

ABSTRACTAcinetobacter baumanniicauses life-threatening infections that are becoming difficult to treat due to increasing rates of multi-drug resistance (MDR) among clinical isolates. This has led the World Health Organization and the CDC to categorize MDRA. baumanniias a top priority for the research and development of new antibiotics. Colistin is the last-resort antibiotic to treat carbapenem-resistantA. baumannii. Not surprisingly, reintroduction of colistin has resulted in the emergence of colistin-resistant strains. Diclofenac is a nonsteroidal anti-inflammatory drug used to treat pain and inflammation associated with arthritis. In this work, we show that diclofenac sensitizes colistin-resistantA. baumanniiclinical strains to colistin,in vitroand in a murine model of pneumonia. Diclofenac also reduced the colistin MIC ofKlebsiella pneumoniaeandPseudomonas aeruginosaisolates. Transcriptomic and proteomic analyses revealed an upregulation of oxidative stress-related genes and downregulation of type IV pili induced by the combination treatment. Notably, the concentrations of colistin and diclofenac effective in the murine model were substantially lower than those determinedin vitro, implying a stronger synergistic effectin vivocompared toin vitro. ApilAmutant strain, lacking the primary component of the type IV pili, became sensitive to colistin in the absence of diclofenac. This suggest that the downregulation of type IV pili is key for the synergistic activity of these drugsin vivoand indicates that colistin and diclofenac exert an anti-virulence effect. Together, these results suggest that the diclofenac can be repurposed with colistin to treat MDRA. baumannii.