bluuebunny/crossref_metadata_2025_split huggingface dataset:
GDF15 mediates inflammation-associated bone loss through a brain-bone axis
Authors: Van der Cruyssen Renée , Devan Jan , Heggli Irina , Burri Dominik , Gaublomme Djoere , Josipovic Ivan , Dumas Emilie , Vlieghe Carolien , Raimondo Maria Gabriella , Zakharov Pavel , Jacques Peggy , Mits Sophie De , Lukasik Zuzanna , Vuylsteke Marnik , Renson Thomas , Schots Lisa , Planckaert Guillaume , Stappers Flore , Decruy Tine , Coudenys Julie , Manuello Teddy , Vereecke Lars , Dmitriev Ruslan I. , Lambrecht Stijn , Hoorebeke Luc Van , Lambert Jo , Ravichandran Kodi , Ramming Andreas , Dudli Stefan , Schett Georg , Gracey Eric , Elewaut Dirk 
Published: November 2023

SUMMARYMetabolic mediators play an important role in regulating chronic inflammation in the body. Here we report an unexpected role for GDF15 (Growth Differentiation Factor 15), a central mediator of food intake, in inflammation-associated bone loss. GDF15 serum levels were found to be elevated in arthritis patients and inversely correlated with bone density. Despite being associated with inflammation, we found that GDF15 itself does not cause, nor contribute to, clinical or histopathological arthritis. Rather, under inflammatory conditions, GDF15 mediates trabecular bone loss through its receptor GFRAL, which is exclusively expressed in the hindbrain. GDF15-GFRAL binding results in β-adrenergic activation of MALPs (Marrow Adipocytic Lineage Precursors) in the bone marrow, which stimulate osteoclasts and trigger bone loss. These data suggest a metabolic mediator-controlled brain-bone axis in inflammation, through which bone loss is induced in a contextual rather than general manner. These findings may lead to more specific therapeutic interventions to protect bone.
Highlighting the hidden: A tagging strategy for monitoring the association of GABARAP with microtubules in living cells
Authors: Üffing Alina , Gold Lisa , Gensch Thomas , Weiergräber Oliver H. , Hoffmann Silke , Willbold Dieter 
Published: November 2023

AbstractGABARAP, like other ATG8 proteins, is a ubiquitin-like modifier and its C-terminal lipid conjugation enables association with cellular membranes. To prevent interference with the lipidation process, N-terminal fluorescent protein (FP) tagging strategies have become the standard for studying ATG8 localization and function in living cells, significantly contributing to our understanding of this protein family’s multifaceted roles.However, recent findings have unveiled potential limitations of bulky N-terminal tags, particularly regarding ATG8 functionality and localization in specific contexts.This study employed live cell imaging with particular emphasis on the GABARAP split-tandem construct, GABARAP(G116A)-mTagBFP2-GABARAP (G-B-G), which retains both a free N-terminus and a lipidation-competent C-terminus. Notably, our results revealed a robust association of G-B-G with the microtubule network in living cells which was not observed with N-terminal FP fusions of GABARAP, although earlyin vitrostudies demonstrated an interaction of GABARAP and tubulin. Since we observed alteration of the microtubule network organization for G-B-G, this construct emerges as a valuable tool, which can help shedding light on potential roles of GABARAP in microtubule-associated processes that are integral to autophagy-related and -unrelated cellular transport.
Gene acquisition by giant transposons primes eukaryotes for rapid evolution via horizontal gene transfer
Authors: Urquhart Andrew S , Gluck-Thaler Emile , Vogan Aaron A. 
Published: November 2023

AbstractHorizontal gene transfer (HGT) disseminates genetic information between species. The significance of HGT in eukaryotes is not well established, with evidence currently limited to isolated examples, typically absent of a mechanism. It has been proposed that mobile elements might be active agents of HGT in eukaryotes, as they are in prokaryotes. To test this hypothesis, we examined a gene cluster, which putatively contributes to formaldehyde resistance and is found within some members of theStarshipsuperfamily of giant transposons. Remarkably, we found four instances wheressfhas been independently acquired by distantly relatedStarships, and show that each acquisition event coincided with the element’s horizontal transfer (at least 9 HGT events in total). Our results demonstrate that acquisition of host-beneficial cargo byStarshipsprimes fungi for rapid and repeated adaptation via HGT, revealing and elevating the role of HGT in eukaryotic biology.
Compact deep neural network models of visual cortex
Authors: Cowley Benjamin R. , Stan Patricia L. , Pillow Jonathan W. , Smith Matthew A. 
Published: November 2023

AbstractA powerful approach to understanding the computations carried out in visual cortex is to develop models that predict neural responses to arbitrary images. Deep neural network (DNN) models have worked remarkably well at predicting neural responses [1, 2, 3], yet their underlying computations remain buried in millions of parameters. Have we simply replaced one complicated systemin vivowith anotherin silico? Here, we train a data-driven deep ensemble model that predicts macaque V4 responses ∼50% more accurately than currently-used task-driven DNN models. We then compress this deep ensemble to identifycompactmodels that have 5,000x fewer parameters yet equivalent accuracy as the deep ensemble. We verified that the stimulus preferences of the compact models matched those of the real V4 neurons by measuring V4 responses to both ‘maximizing’ and adversarial images generated using compact models. We then analyzed the inner workings of the compact models and discovered a common circuit motif: Compact models share a similar set of filters in early stages of processing but then specialize by heavily consolidating this shared representation with a precise readout. This suggests that a V4 neuron’s stimulus preference is determined entirely by its consolidation step. To demonstrate this, we investigated the compression step of a dot-detecting compact model and found a set of simple computations that may be carried out by dot-selective V4 neurons. Overall, our work demonstrates that the DNN models currently used in computational neuroscience are needlessly large; our approach provides a new way forward for obtaining explainable, high-accuracy models of visual cortical neurons.
An arginine-rich nuclear localization signal (ArgiNLS) strategy for streamlined image segmentation of single-cells
Authors: Szelenyi Eric R. , Navarrete Jovana S. , Murry Alexandria D. , Zhang Yizhe , Girven Kasey S. , Kuo Lauren , Cline Marcella M. , Bernstein Mollie X. , Burdyniuk Mariia , Bowler Bryce , Goodwin Nastacia L. , Juarez Barbara , Zweifel Larry S. , Golden Sam A. 
Published: November 2023

AbstractHigh-throughput volumetric fluorescent microscopy pipelines can spatially integrate whole-brain structure and function at the foundational level of single-cells. However, conventional fluorescent protein (FP) modifications used to discriminate single-cells possess limited efficacy or are detrimental to cellular health. Here, we introduce a synthetic and non-deleterious nuclear localization signal (NLS) tag strategy, called ‘Arginine-rich NLS’ (ArgiNLS), that optimizes genetic labeling and downstream image segmentation of single-cells by restricting FP localization near-exclusively in the nucleus through a poly-arginine mechanism. A single N-terminal ArgiNLS tag provides modular nuclear restriction consistently across spectrally separate FP variants. ArgiNLS performance in vivo displays functional conservation across major cortical cell classes, and in response to both local and systemic brain wide AAV administration. Crucially, the high signal-to-noise ratio afforded by ArgiNLS enhances ML-automated segmentation of single-cells due to rapid classifier training and enrichment of labeled cell detection within 2D brain sections or 3D volumetric whole-brain image datasets, derived from both staining-amplified and native signal. This genetic strategy provides a simple and flexible basis for precise image segmentation of genetically labeled single-cells at scale and paired with behavioral procedures.Significance StatementQuantifying labeled cells in fluorescent microscopy is a fundamental aspect of modern biology. Critically, the use of short nuclear localization sequences (NLS) is a key genetic modification for discriminating single-cells labeled with fluorescent proteins (FPs). However, mainstay NLS approaches typically localize proteins to the nucleus with limited efficacy, while alternative non-NLS tag strategies can enhance efficacy at the cost of cellular health. Thus, quantitative cell counting using FP labels remains suboptimal or not compatible with health and behavior. Here, we present a novel genetic tagging strategy – named ArgiNLS – that flexibly and safely achieves FP nuclear restriction across the brain to facilitate machine learning-based segmentation of single-cells at scale, delivering a timely update to the behavioral neuroscientist’s toolkit.
Metabolic connections between folate and peptidoglycan pathways inPseudomonas aeruginosainform rational design of a dual-action inhibitor
Authors: Yaeger Luke N. , Sychantha David , Luong Princeton , Shekarriz Shahrokh , Goncalves Océane , Dobrin Annamaria , Ranieri Michael R. , Lamers Ryan P. , Harvey Hanjeong , diCenzo George C. , Surette Michael , Côté Jean-Philippe , Magolan Jakob , Burrows Lori L. 
Published: November 2023

AbstractPeptidoglycan is an important bacterial macromolecule that confers cell shape and structural integrity, and a key antibiotic target. The synthesis and turnover of peptidoglycan are carefully coordinated with other cellular processes and pathways. Although there are established connections between peptidoglycan and DNA replication or outer membrane biosynthesis, connections between peptidoglycan and folate metabolism are comparatively unexplored. Folate is an essential cofactor for bacterial growth and required for the synthesis of many important metabolites. Here we show that inhibition of folate synthesis in the important Gram-negative pathogenPseudomonas aeruginosahas downstream effects on peptidoglycan metabolism and integrity. Folate inhibitors reduced expression of the AmpC β-lactamase through perturbation of peptidoglycan recycling, potentiating the activity of β-lactams normally cleaved by that resistance enzyme. Folate inhibitors also synergized with fosfomycin, which inhibits MurA - the first committed step in peptidoglycan synthesis - resulting in dose-dependent formation of round cells that underwent explosive lysis.The insights from this work were used to design a dual-active inhibitor that overcomes NDM-1-mediated meropenem resistance and synergizes with the folate inhibitor, trimethoprim. This work shows that folate and peptidoglycan metabolism are intimately connected and offers new opportunities to exploit this relationship in strategies to overcome antibiotic resistance in Gram-negative pathogens.
Spatiotemporal dynamics of successive activations across the human brain during simple arithmetic processing
Authors: Pinheiro-Chagas Pedro , Sava-Segal Clara , Akkol Serdar , Daitch Amy , Parvizi Josef 
Published: November 2023

ABSTRACTPrevious neuroimaging studies have offered unique insights about the spatial organization of activations and deactivations across the brain, however these were not powered to explore the exact timing of events at the subsecond scale combined with precise anatomical source information at the level of individual brains. As a result, we know little about the order of engagement across different brain regions during a given cognitive task. Using experimental arithmetic tasks as a prototype for human-unique symbolic processing, we recorded directly across 10,076 brain sites in 85 human subjects (52% female) using intracranial electroencephalography (iEEG). Our data revealed a remarkably distributed change of activity in almost half of the sampled sites. Notably, an orderly successive activation of a set of brain regions - anatomically consistent across subjects-was observed in individual brains. Furthermore, the temporal order of activations across these sites was replicable across subjects and trials. Moreover, the degree of functional connectivity between the sites decreased as a function of temporal distance between regions, suggesting that information is partially leaked or transformed along the processing chain. Furthermore, in each activated region, distinct neuronal populations with opposite activity patterns during target and control conditions were juxtaposed in an anatomically orderly manner. Our study complements the prior imaging studies by providing hitherto unknown information about the timing of events in the brain during arithmetic processing. Such findings can be a basis for developing mechanistic computational models of human-specific cognitive symbolic systems.Significance statementOur study elucidates the spatiotemporal dynamics and anatomical specificity of brain activations across >10,000 sites during arithmetic tasks, as captured by intracranial EEG. We discovered an orderly, successive activation of brain regions, consistent across individuals, and a decrease in functional connectivity as a function of temporal distance between regions. Our findings provide unprecedented insights into the sequence of cognitive processing and regional interactions, offering a novel perspective for enhancing computational models of cognitive symbolic systems.
QTL analysis of floral morphology polymorphisms betweenGilia yorkiiandG. capitata
Authors: DeTemple Joseph M , Chitwood Daniel H , Mosquera Veronica , Whipple Clinton J 
Published: November 2023

AbstractSpeciation is a complex process typically accompanied by significant genetic and morphological differences between sister populations. In plants, this can result in divergent floral morphologies causing pollinator differences and reproductive isolation between populations. Here, we explore floral trait differences between two recently diverged species,Gilia yorkiiandG. capitata. The distributions of floral traits in parental, F1, and F2 populations are compared, and groups of correlated traits are identified. We describe the genetic architecture of floral traits through a quantitative trait locus (QTL) analysis using an F2 population of 187 individuals. While all identified QTLs were of moderate (10-25%) effect, interestingly, many QTL intervals colocalized on Chromosomes 6 and 9, suggesting that sets of traits may share a common genetic basis. Our results provide a framework for future identification of genes involved in the evolution of floral morphology.
Distinct microcolony morphologies promote flow-dependent bacterial colonization
Authors: Hallinen Kelsey M. , Bodine Steven P. , Stone Howard A. , Muir Tom W. , Wingreen Ned S. , Gitai Zemer 
Published: November 2023

AbstractFluid flows can impact bacterial behaviors in unexpected ways (1–3). The high shear rate in heart valves should reduce colonization, but in endocarditis, valves are often counter-intuitively colonized byStaphylococcus aureusandEnterococcus faecalis(4, 5). Here we discover bacteria-specific mechanisms for preferential surface colonization in higher shear rate environments. This behavior enables bacteria that are outcompeted in low flow to dominate in high flow. Flow-dependent colonization byS. aureusandE. faecalisare mediated by distinct mechanisms that depend on each species’ microcolony morphologies: transport of a dispersal signaling molecule for clusteredS. aureusand mechanical forces for linear chains ofE. faecalis. These results suggest that microcolony morphologies have previously unappreciated costs and benefits in different environments, like those introduced by flow.One-Sentence SummaryBacterial surface colonization in high fluid flow depends upon the species’ clustered or chained microcolony morphologies.
Fluorogenic, sub-single-turnover monitoring of enzymatic reactions involving NAD(P)H provides a generalised platform for directed ultrahigh throughput evolution of biocatalysts in microdroplets
Authors: Penner Matthew , Klein Oskar James , Gantz Maximilian , Nintzel Friederike E. H. , Prowald Anne-Cathrin , Boss Sally , Barker Paul , Dupree Paul , Hollfelder Florian 
Published: November 2023

AbstractEnzyme engineering and discovery are crucial for a future sustainable bioeconomy. Harvesting new biocatalysts from large libraries through directed evolution or functional metagenomics requires accessible, rapid assays. Ultra-high throughput screening formats often require optical readouts, leading to the use of model substrates that may misreport target activity and necessitate bespoke synthesis. This is a particular challenge when screening glycosyl hydrolases, which leverage molecular recognition beyond the target glycosidic bond, so that complex chemical synthesis would have to be deployed to build a fluoro- or chromogenic substrate. In contrast, coupled assays represent a modular ‘plug-and-play’ system: any enzyme- substrate pairing can be investigated, provided the reaction can produce a common intermediate which links the catalytic reaction to a detection cascade readout. Here, we establish a detection cascade producing a fluorescent readout in response to NAD(P)H via glutathione reductase and a subsequent thiol-mediated uncaging reaction, with a low nanomolar detection limit in plates. Further scaling down to microfluidic droplet screening is possible: the fluorophore is leakage- free and we report a three orders of magnitude improved sensitivity compared to absorbance- based systems, so that less than one turnover per enzyme molecule expressed from a single cell is detectable. Our approach enables the use of non-fluorogenic substrates in droplet-based enrichments, with applicability in screening for glycosyl hydrolases and imine reductases (IREDs). To demonstrate the assay’s readiness for combinatorial experiments, one round of directed evolution was performed to select a glycosidase processing a natural substrate, beechwood xylan, with improved kinetic parameters from a pool of >106mutagenized sequences.
Human extracellular sulfatases use a dual mechanism for regulation of growth factor interactions with heparan sulfate proteoglycans
Authors: Timm Bryce M. , Follmar Julianna L. , Porell Ryan N. , Glass Kimberly , Thacker Bryan E. , Glass Charles A. , Godula Kamil 
Published: November 2023

AbstractMembrane-associated heparan sulfate (HS) proteoglycans (PGs) contribute to the regulation of extracellular cellular signaling cues, such as growth factors (GFs) and chemokines, essential for normal organismal functions and implicated in various pathophysiologies. PGs accomplish this by presenting high affinity binding sites for GFs and their receptors through highly sulfated regions of their HS polysaccharide chains. The composition of HS, and thus GF-binding specificity, are determined during biosynthetic assembly prior to installation at the cell surface. Two extracellular 6-O-endosulfatase enzymes (Sulf-1 and Sulf-2) can uniquely further edit mature HS and alter its interactions with GFs by removing specific sulfation motifs from their recognition sequence on HS. Despite being implicated as signaling regulators during development and in disease, the Sulfs have resisted structural characterization, and their substrate specificity and effects on GF interactions with HS are still poorly defined. Using a panel of PG-mimetics comprising compositionally-defined bioengineered recombinant HS (rHS) substrates in combination with GF binding and enzyme activity assays, we have discovered that Sulfs control GF-HS interactions through a combination of catalytic processing and competitive blocking of high affinity GF-binding sites, providing a new conceptual framework for understanding the functional impact of these enzymes in biological context. Although the contributions from each mechanism are both Sulf- and GF-dependent, the PG-mimetic platform allows for rapid analysis of these complex relationships.Significance StatementCells rely on extracellular signals such as growth factors (GFs) to mediate critical biological functions. Membrane-associated proteins bearing negatively charged heparan sulfate (HS) sugar chains engage with GFs and present them to their receptors, which regulates their activity. Two extracellular sulfatase (Sulf) enzymes can edit HS and alter GF interactions and activity, although the precise mechanisms remain unclear. By using chemically defined HS-mimetics as probes, we have discovered that Sulfs can modulate HS by means of catalytic alterations and competitive blocking of GF-binding sites. These unique dual activities distinguish Sulfs from other enzymes and provide clues to their roles in development and disease.
Assembly reactions of SARS-CoV-2 nucleocapsid protein with nucleic acid
Authors: Zhao Huaying , Syed Abdullah M. , Khalid Mir M. , Nguyen Ai , Ciling Alison , Wu Di , Yau Wai-Ming , Srinivasan Sanjana , Esposito Dominic , Doudna Jennifer A. , Piszczek Grzegorz , Ott Melanie , Schuck Peter 
Published: November 2023

AbstractThe viral genome of SARS-CoV-2 is packaged by the nucleocapsid (N-) protein into ribonucleoprotein particles (RNPs), 38±10 of which are contained in each virion. Their architecture has remained unclear due to the pleomorphism of RNPs, the high flexibility of N-protein intrinsically disordered regions, and highly multivalent interactions between viral RNA and N-protein binding sites in both N-terminal (NTD) and C-terminal domain (CTD). Here we explore critical interaction motifs of RNPs by applying a combination of biophysical techniques to mutant proteins binding different nucleic acids in anin vitroassay for RNP formation, and by examining mutant proteins in a viral assembly assay. We find that nucleic acid-bound N-protein dimers oligomerizeviaa recently described protein-protein interface presented by a transient helix in its long disordered linker region between NTD and CTD. The resulting hexameric complexes are stabilized by multi-valent protein-nucleic acid interactions that establish crosslinks between dimeric subunits. Assemblies are stabilized by the dimeric CTD of N-protein offering more than one binding site for stem-loop RNA. Our study suggests a model for RNP assembly where N- protein scaffolding at high density on viral RNA is followed by cooperative multimerization through protein-protein interactions in the disordered linker.