bluuebunny/crossref_metadata_2025_split huggingface dataset:
Butterfly movements recorded from a UAV depict migratory flight behaviour in the wild
Authors: de Margerie Emmanuel , Monmasson Kyra 
Published: July 2024

AbstractTracking and understanding the movements of animals in the wild is a fast-growing area of research, known asmovement ecology. However, tracking small animals such as flying insects, which cannot easily carry an electronic tag, remains challenging as existing field methods are costly either in terms of equipment or tracking effort (e.g. VHF radio-tracking, scanning harmonic radar). Here we attempted to record the movements of free-flying butterflies from an unmanned aerial vehicle (UAV), maintaining a static position in the sky and recording video vertically downwards. With an appropriate flight height and image filtering algorithm, we recorded 166 flight tracks ofPierisbutterflies (P. brassicaeandP. rapae), with a median tracking length of 40 m (median flight duration 13 s), and a high temporal resolution of 30 positions per second. Average flight direction varied significantly over the course of the flying season, from a northward azimuth in June and early July, to a southward azimuth in September, a trans-generational migratory behaviour that had previously been documented by field observations or experiments in flight cages. In addition, UAV imagery unlocks the possibility to measure high-resolution flight movement patterns (e.g. path tortuosity and transverse oscillations), which will possibly help understand perceptual and locomotor mechanisms underlying spatial behaviour. We explore the technical details associated with UAV tracking methodology, and discuss its limitations, in particular the biases associated with a 2D projection of 3D flight movements, and the difficulty to distinguish between visually similar species, such asP. brassicaeandP. rapae.
Multimodal screen reveals noise regulatory proteins
Authors: García-Blay Óscar , Hu Xinyu , Wassermann Christin L. , van Bokhoven Tom , Struijs Fréderique M.B. , Hansen Maike M.K. 
Published: July 2024

SUMMARYGene-expression noise can influence cell-fate choices across pathology and physiology. However, a crucial question persists: do regulatory proteins or pathways exist that control noise independently of mean expression levels? Our integrative approach, combining single-cell RNA sequencing with proteomics and regulator enrichment analysis, reveals 32 putative noise regulators. SON, a nuclear speckle-associated protein, alters transcriptional noise without changing mean expression levels. Furthermore, SON’s noise regulation can propagate to the protein level. Long-read and total RNA sequencing shows that SON’s noise regulation does not significantly change isoform usage or splicing efficiency. Moreover, SON depletion reduces state-switching in pluripotent mouse embryonic stem cells and impacts their fate choice during differentiation. Collectively, we discover a class of proteins that regulates noise orthogonally to mean expression levels. This work serves as a proof-of-concept that can identify other functional noise-regulators throughout development and disease progression.
A powdery mildew core effector protein targets host endosome tethering complexes HOPS and CORVET
Authors: Sabelleck Björn , Deb Sohini , Spanu Pietro D. , Thordal-Christensen Hans , Panstruga Ralph 
Published: July 2024

AbstractPowdery mildew fungi are serious pathogens of many plant species. Their genomes encode extensive repertoires of secreted effector proteins that suppress host immunity. Here, we revised and analyzed the candidate secreted effector protein (CSEP) effectome of the barley powdery mildew fungus,Blumeria hordei(Bh) and identified seven CSEPs that are broadly conserved in powdery mildew fungal species, rendering them core effectors of these phytopathogens. We show that one of these, CSEP0214, interacts with the barley VPS18 protein, a core component of the CORVET and HOPS endosomal tethering complexes, mediating fusions of early endosomes and multivesicular bodies with the central vacuole, respectively. Overexpression of CSEP0214 and knockdown of eitherVPS18, HOPS-specificVPS41or CORVET-specificVPS8caused a block of the vacuolar pathway and the accumulation of the fluorescent vacuolar marker protein (SP)-RFP-AFVY in the endoplasmic reticulum. Co-immunoprecipitation and yeast two-hybrid experiments suggest that CSEP0214 blocks the interaction of VPS18 and VPS16, which are both core components of CORVET as well as HOPS. Additionally, expression of CSEP0214 blocked the hypersensitive cell death response associated with resistance gene-mediated immunity in barley, indicating that endomembrane traffic is required for this process. It also prevented callose deposition in cell wall appositions at attack sites and encasements of fungal infection structures. Our results indicate that this powdery mildew core effector is an essential immunity suppressor.One sentence summaryTheBlumeria hordeieffector protein CSEP0214 interacts with barley VPS18, a core component of the CORVET and HOPS endosomal tethering complexes, thereby interfering with host endomembrane trafficking.
Effects of copepod chemical cues on intra- and extracellular toxins in two species ofDinophysis
Authors: Pourdanandeh Milad , Séchet Véronique , Carpentier Liliane , Réveillon Damien , Hervé Fabienne , Hubert Clarisse , Hess Philipp , Selander Erik 
Published: July 2024

AbstractCopepods may contribute to harmful algal bloom formation by selectively rejecting harmful cells. Additionally, copepods and the chemical cues they exude, copepodamides, have been shown to induce increased toxin production in paralytic and amnesic toxin producing microalgae. However, it is unknown if diarrhetic shellfish toxin (DST) producers such asDinophysisrespond to copepods or copepodamides in a similar fashion. Here we expose laboratory cultures ofDinophysis sacculusandD. acuminatato direct grazing byAcartiasp. copepods or copepodamides and measure their toxins after three days. TotalDinophysis- produced toxins (DPTs), okadaic acid, pectenotoxin-2, and C9-diol ester of okadaic acid, increased by 8 - 45% inD. sacculusbut was significantly different from controls only in the highest (10 nM) copepodamide treatment whereas toxin content was not affected inD. acuminata.Growth rate was low across all groups and explained up to 91% of the variation in toxin content. DPTs were redistributed from internal compartments to the extracellular medium in the highest copepodamide treatments (5 - 10 nM), which were two to three times higher than controls and indicates an active release or passive leakage of toxins. Untargeted analysis of endometabolomes indicated significant changes in metabolite profiles for both species in response to the highest copepodamide treatments, independent of known toxins. However, it is not clear whether these are stress responses or caused by more complex mechanisms. The relatively small grazer-induced effect inDinophysisobserved here, compared to several species ofAlexandriumandPseudo-nitzschiareported previously, suggests that DPT production inDinophysisis likely not induced by copepods, except perhaps in patches with high copepod densities. Thus, DPTs may, represent either a constitutive chemical defence forDinophysis, or serve an altogether different purpose.
BCAS2 promotes primitive hematopoiesis by sequestering β-catenin within the nucleus
Authors: Ning Guozhu , Lin Yu , Ma Haixia , Zhang Jiaqi , Yang Liping , Liu Zhengyu , Li Lei , He Xinyu , Wang Qiang 
Published: July 2024

AbstractBreast carcinoma amplified sequence 2 (BCAS2), a core component of the hPrP19 complex, plays an important role in RNA-splicing and DNA damage. However, whether BCAS2 has other functions within the nucleus remains largely unknown. Here, we show that BCAS2 is essential for primitive hematopoiesis in zebrafish and mouse embryos. The activation of Wnt/β-catenin signal, which is required for hematopoietic progenitor differentiation, is significantly decreased upon depletion ofbcas2in zebrafish embryos and mouse embryonic fibroblasts. Interestingly, haploinsufficiency ofbcas2has no obvious impact on the splicing efficiency of β-catenin pre-mRNA, while significantly attenuating β-catenin nuclear accumulation. Moreover, we find that BCAS2 directly binds to β-catenin via its coiled-coil domains, thereby sequestering β-catenin within the nucleus. Thus, our results uncover a previously unknown function of BCAS2 in promoting Wnt signaling by enhancing β-catenin nuclear retention during primitive hematopoiesis.
Ecology and environment predict spatially stratified risk of highly pathogenic avian influenza in wild birds across Europe
Authors: Hayes Sarah , Hilton Joe , Mould-Quevedo Joaquin , Donnelly Christl , Baylis Matthew , Brierley Liam 
Published: July 2024

AbstractHighly pathogenic avian influenza (HPAI) represents a threat to animal health, human health, and economic prosperity, with the ongoing outbreak in wild and domestic animals since 2021 being the largest on record. This outbreak is associated with the 2.3.4.4b clade of influenza A, and it is as yet unclear what factors have contributed to its spread at the continental scale. In this study we use Bayesian additive regression trees, a machine learning method designed for probabilistic modelling of complex nonlinear phenomena, to construct species distribution models for HPAI presence across Europe. Using these models we identify factors driving the geospatial distribution of cases and project the distribution of risk across Europe. Our models are stratified by time to capture both seasonal changes in risk patterns and shifts in HPAI epidemiology associated with the introduction of the 2.3.4.4b clade. While previous studies have aimed to predict HPAI presence from physical geography, here we explicitly consider the impact of wild bird ecology by including in our model estimates of bird species richness, abundance of specific high-risk bird taxa, and “species-trait abundance indices” describing the total abundance of species with high-risk behavioural and/or dietary traits. Our projections point to a shift in concentration of risk towards cold, low-lying regions of coastal northwest Europe associated with 2.3.4.4b, with the margins of uncertainty extending that risk further into central and eastern Europe. In coastal northwest Europe specifically, we predict a persistence of high risk throughout the year. Methodologically, we demonstrate that while the majority of variation in risk can be explained by climate and other aspects of physical geography, the addition of ecological covariates represents a valuable refinement to species distribution models of HPAI.
Intravenous BCG induces a more potent airway and lung immune response than intradermal BCG in SIV-infected macaques1
Authors: Jauro Solomon , Larson Erica C. , Gleim Janelle L. , Wahlberg Brendon M. , Rodgers Mark A. , Chehab Julia C. , Lopez-Velazques Alondra E. , Ameel Cassaundra L. , Tomko Jaime A. , Sakal Jennifer L. , DeMarco Todd , Borish H. Jake , Maiello Pauline , Potter E. Lake , Roederer Mario , Lin Philana Ling , Flynn JoAnne L. , Scanga Charles A. 
Published: July 2024

AbstractTuberculosis (TB), caused byMycobacterium tuberculosis(Mtb), is one of the leading causes of death due to an infectious agent. Coinfection with HIV exacerbates Mtb infection outcomes in people living with HIV (PLWH). Bacillus Calmette-Guérin (BCG), the only approved TB vaccine, is effective in infants, but its efficacy in adolescents and adults is limited. Here, we investigated the immune responses elicited by BCG administered via intravenous (IV) or intradermal (ID) routes in Simian Immunodeficiency Virus (SIV)-infected Mauritian cynomolgus macaques (MCM) without the confounding effects of Mtb challenge. We assessed the impact of vaccination on T cell responses in the airway, blood, and tissues (lung, thoracic lymph nodes, and spleen), as well as the expression of cytokines, cytotoxic molecules, and key transcription factors. Our results showed that IV BCG induces a robust and sustained immune response, including tissue-resident memory T (TRM) cells in lungs, polyfunctional CD4+ and CD8αβ+ T cells expressing multiple cytokines, and CD8αβ+ T cells and NK cells expressing cytotoxic effectors in airways. We also detected higher levels of mycobacteria-specific IgG and IgM in the airways of IV BCG-vaccinated MCM. Although IV BCG vaccination resulted in an influx of TRMcells in lungs of MCM with controlled SIV replication, MCM with high plasma SIV RNA (>105copies/mL) typically displayed reduced T cell responses, suggesting that uncontrolled SIV or HIV replication would have a detrimental effect on IV BCG-induced protection against Mtb.
Robust data-driven segmentation of pulsatile cerebral vessels using functional magnetic resonance imaging
Authors: Wright Adam M. , Xu Tianyin , Ingram Jacob , Koo John , Zhao Yi , Tong Yunjie , Wen Qiuting 
Published: July 2024

AbstractFunctional magnetic resonance imaging (fMRI) captures rich physiological and neuronal information that can offer insights into neurofluid dynamics, vascular health, and waste clearance function. The availability of cerebral vessel segmentation could facilitate fluid dynamics research in fMRI. However, without magnetic resonance angiography scans, cerebral vessel segmentation is challenging and time-consuming. This study leverages cardiac-induced pulsatile fMRI signal to develop a data-driven, automatic segmentation of large cerebral arteries and the superior sagittal sinus (SSS). The method was validated in a local dataset by comparing it to ground truth cerebral artery and SSS segmentations. Using the Human Connectome Project (HCP) aging dataset, the method’s reproducibility was tested on 422 participants aged 36 to 100 years, each with four repeated fMRI scans. The method demonstrated high reproducibility, with an intraclass correlation coefficient > 0.7 in both cerebral artery and SSS segmentation volumes. This study demonstrates that the large cerebral arteries and SSS can be reproducibly and automatically segmented in fMRI datasets, facilitating the investigation of fluid dynamics in these regions.
Gradations in protein dynamics captured by experimental NMR are not well represented by AlphaFold2 models and other computational metrics
Authors: Gavalda-Garcia Jose , Dixit Bhawna , Díaz Adrián , Ghysels An , Vranken Wim 
Published: July 2024

AbstractThe advent of accurate methods to predict the fold of proteins initiated by AlphaFold2 is rapidly changing our understanding of proteins and helping their design. However, these methods are mainly trained on protein structures determined with X-ray diffraction, where the protein is packed in crystals at often cryogenic temperatures. They can therefore only reliably cover well-folded parts of proteins that experience few, if any, conformational changes. Experimentally, solution nuclear magnetic resonance (NMR) is the experimental method of choice to gain insight into protein dynamics at near physiological conditions. Computationally, methods such as molecular dynamics and Normal Mode Analysis (NMA) allow the estimation of a protein’s intrinsic flexibility based on a single protein structure. This work addresses, on a large scale, the relationships for proteins between the AlphaFold2 pLDDT metric, the observed dynamics in solution from NMR metrics, interpreted MD simulations, and the computed dynamics with NMA from single AlphaFold2 models and NMR ensembles. We observe that these metrics agree well for rigid residues that adopt a single well-defined conformation, which are clearly distinct from residues that exhibit dynamic behavior and adopt multiple conformations. This direct order/disorder categorisation is reflected in the correlations observed between the parameters, but becomes very limited when considering only the likely dynamic residues. The gradations of dynamics observed by NMR in flexible protein regions are therefore not represented by these computational approaches. Our results are interactively available for each protein fromhttps://bio2byte.be/af_nmr_nma/.
Immune disease dialogue of chemokine-based cell communications as revealed by single-cell RNA sequencing meta-analysis
Authors: Rahman Mouly F. , Kurlovs Andre H. , Vodnala Munender , Meibalan Elamaran , Means Terry K. , Nouri Nima , Rinaldis Emanuele de , Savova Virginia 
Published: July 2024

ABSTRACTImmune-mediated diseases are characterized by aberrant immune responses, posing significant challenges to global health. In both inflammatory and autoimmune diseases, dysregulated immune reactions mediated by tissue-residing immune and non-immune cells precipitate chronic inflammation and tissue damage that is amplified by peripheral immune cell extravasation into the tissue. Chemokine receptors are pivotal in orchestrating immune cell migration, yet deciphering the signaling code across cell types, diseases and tissues remains an open challenge. To delineate disease-specific cell-cell communications involved in immune cell migration, we conducted a meta-analysis of publicly available single-cell RNA sequencing (scRNA-seq) data across diverse immune diseases and tissues. Our comprehensive analysis spanned multiple immune disorders affecting major organs: atopic dermatitis and psoriasis (skin), chronic obstructive pulmonary disease and idiopathic pulmonary fibrosis (lung), ulcerative colitis (colon), IgA nephropathy and lupus nephritis (kidney). By interrogating ligand-receptor (L-R) interactions, alterations in cell proportions, and differential gene expression, we unveiled intricate disease- specific and common immune cell chemoattraction and extravasation patterns. Our findings delineate disease-specific L-R networks and shed light on shared immune responses across tissues and diseases. Insights gleaned from this analysis hold promise for the development of targeted therapeutics aimed at modulating immune cell migration to mitigate inflammation and tissue damage. This nuanced understanding of immune cell dynamics at the single-cell resolution opens avenues for precision medicine in immune disease management.
Genetic and selective constraints on the optimization of gene product diversity
Authors: Jiang Daohan , Kejiou Nevraj , Qiu Yi , Palazzo Alexander F. , Pennell Matt 
Published: July 2024

AbstractRNA and protein expressed from the same gene can have diverse isoforms due to various post-transcriptional and post-translational modifications. For the vast majority of alternative isoforms, It is unknown whether they are adaptive or simply biological noise. As we cannot experimentally probe the function of each isoform, we can ask whether the distribution of isoforms across genes and across species is consistent with expectations from different evolutionary processes. However, there is currently no theoretical framework that can generate such predictions. To address this, we developed a mathematical model where isoform abundances are determined collectively bycis-acting loci,trans-acting factors, gene expression levels, and isoform decay rates to predict isoform abundance distributions across species and genes in the face of mutation, genetic drift, and selection. We found that factors beyond selection, such as effective population size and the number ofcis-acting loci, significantly influence evolutionary outcomes. Notably, suboptimal phenotypes are more likely to evolve when the population is small and/or when the number ofcis-loci is large. We also explored scenarios where modification processes have both beneficial and detrimental effects, revealing a non-monotonic relationship between effective population size and optimization, demonstrating how opposing selection pressures oncis- andtrans-acting loci can constrain the optimization of gene product diversity. As a demonstration of the power of our theory, we compared the expected distribution of A-to-I RNA editing levels in coleoids and found this to be largely consistent with non-adaptive explanations.
Spike rate inference from mouse spinal cord calcium imaging data
Authors: Rupprecht Peter , Fan Wei , Sullivan Steve J. , Helmchen Fritjof , Sdrulla Andrei D. 
Published: July 2024

AbstractCalcium imaging is a key method to record the spiking activity of identified and genetically targeted neurons. However, the observed calcium signals are only an indirect readout of the underlying electrophysiological events (single spikes or bursts of spikes) and require dedicated algorithms to recover the spike rate. These algorithms for spike inference can be optimized using ground truth data from combined electrical and optical recordings, but it is not clear how such optimized algorithms perform on cell types and brain regions for which ground truth does not exist. Here, we use a state-of-the-art algorithm based on supervised deep learning (CASCADE) and a non-supervised algorithm based on non-negative deconvolution (OASIS) to test spike rate inference in spinal cord neurons. To enable these tests, we recorded specific ground truth from glutamatergic and GABAergic somatosensory neurons in the superficial dorsal horn of spinal cord in mice of both sexes. We find that CASCADE and OASIS algorithms that were designed for cortical excitatory neurons generalize well to both spinal cord cell types. However, CASCADE models re-trained on our ground truth further improved the performance, resulting in a more accurate inference of spiking activity from spinal cord neurons. We openly provide re-trained models that can be applied to spinal cord data of variable noise levels and frame rates. Together, our ground-truth recordings and analyses provide a solid foundation for the interpretation of calcium imaging data from spinal cord dorsal horn and showcase how spike rate inference can generalize between different regions of the nervous system.Significance StatementCalcium imaging is a powerful method for measuring the activity of genetically identified neurons. However, accurate interpretation of calcium transients depends on having a detailed understanding of how neuronal activity correlates with fluorescence. Such calibration recordings have been performed for cerebral cortex but not yet for most other CNS regions and neuron types. Here, we obtained ground truth data in spinal cord by conducting simultaneous calcium and electrophysiology recordings in excitatory and inhibitory neurons. We systematically investigated the transferability of cortical algorithms to spinal neuron subpopulations and generated inference algorithms optimized to excitatory and inhibitory neurons. Our study provides a foundation for the rigorous interpretation of calcium imaging data from spinal cord.Conflict of interest statementThe authors declare no competing financial conflicts of interest.
Comparing diploid and triploid apples from a diverse collection
Authors: Greaves Elaina , Davies Thomas , Myles Sean , Migicovsky Zoë 
Published: July 2024

AbstractApples (MalusX.domesticaBorkh.) are an economically important fruit species and the focus of continuing breeding efforts around the world. While most apple varieties are diploid, ploidy levels vary across the species, and triploids may be used in breeding despite poor fertility. The impact of ploidy on agricultural traits in apple is not well understood but is an important factor to consider when breeding new apple varieties. Here, we use mean heterozygosity values to categorize 970 apple accessions as diploid or triploid and then contrast apples of varying ploidy levels across 10 agriculturally important traits with sample sizes ranging from 427 to 928 accessions. After correction for multiple testing, we determine that triploids have significantly higher phenolic content. By examining historical release dates for apple varieties, our findings suggest that contemporary breeding programs are primarily releasing diploid varieties, and triploids tend to be older varieties. Ultimately, our results suggest that phenotypic differences between diploids and triploids are subtle and often insignificant indicating that triploids may not provide substantial benefit above diploids to apple breeding programs.