bluuebunny/crossref_metadata_2025 huggingface dataset:
Possible involvement of ghost introgressions in the striking diversity of Vomeronasal type 1 receptor genes in East African cichlids
Authors: Taki Shunsuke , Zhang Zicong , Aibara Mitsuto , Nagasawa Tatsuki , Nikaido Masato
Published: December 2024

Cichlids that have undergone adaptive radiation are genetically close but exhibit extreme ecological and morphological diversity, making them useful for understanding speciation mechanisms. Vomeronasal type 1 receptors (V1R) are highly conserved among teleost fish at the amino acid sequence level and believed to play a fundamental role in reproduction. We previously reported the surprisingly high sequence diversity of V1Rs among certain cichlid species, suggesting a possible role for V1Rs in their speciation. In this study, we investigated the process of evolutionary diversification of all 6 V1Rs (V1R1-6) by using the genome data of 528 cichlid species, encompassing nearly all lineages. In the case of V1R2, two highly divergent alleles (1.17%: variant sites/CDS length) without recombination were preserved and shared among cichlids found in all of the East African Great Lakes. In the case of V1R6, numerous highly variable alleles that could be derived from multiple recombination events between two highly divergent alleles (1.39%: variant sites/CDS length) were found among the Lake Victoria cichlids. Additionally, we identified highly divergent alleles of V1R1 within the tribe Tropheini, and of both V1R3 and V1R6 within Trematocarini and Ectodini. Because one of the two divergent alleles of these V1Rs emerged rapidly during cichlid evolution, they are likely to have been derived from introgression. However, despite extensive investigations, we could not identify the source lineages for these introgressions, implying that they may have become extinct. This study revealed the potential role of introgression in explaining the remarkable diversity of V1Rs in East African cichlids.
Molecular mechanisms of heart field specific cardiomyocyte differentiation- a computational modeling approach
Authors: Argyris Georgios , Zeegelaar Ricco , Post Janine N.
Published: December 2024

Tissue engineering protocols achieve building miniature hearts but mechanisms determining cell differentiation still need to be fully understood and optimized. In this study, we present a gene regulatory network (GRN) that describes the differentiation of committedcardiomyocytestowards ventricular or atrial cardiomyocytes. The GRN is coupled with Boolean dynamics and steady state analysis shows steady states which agree with the experimental expression of marker genes. Our Boolean model extends earlier work on a model describing the first and second heart field formation to include atrial and ventricular cardiomyocytes. Thus, our study paves the way for the generation of heart field-specific cardiomyocytes located in specific chambers of the fully developed heart. The Boolean model is validated through simulations and by its ability to reproduce known knockouts.
Fusing multisensory signals across channels and time
Authors: Anil Swathi , Ghosh Marcus , Goodman Dan F. M.
Published: December 2024

Abstract

Animals continuously combine information across sensory modalities and time, and use these combined signals to guide their behaviour. Picture a predator watching their prey sprint and screech through a field. To date, a range of multisensory algorithms have been proposed to model this process including linear and nonlinear fusion, which combine the inputs from multiple sensory channels via either a sum or nonlinear function. However, many multisensory algorithms treat successive observations independently, and so cannot leverage the temporal structure inherent to naturalistic stimuli. To investigate this, we introduce a novel multisensory task in which we provide the same number of task-relevant signals per trial but vary how this information is presented: from many short bursts to a few long sequences. We demonstrate that multisensory algorithms that treat different time steps as independent, perform sub-optimally on this task. However, simply augmenting these algorithms to integrate across sensory channels and short temporal windows allows them to perform surprisingly well, and comparably to fully recurrent neural networks. Overall, our work: highlights the benefits of fusing multisensory information across channels and time, shows that small increases in circuit/model complexity can lead to significant gains in performance, and provides a novel multisensory task for testing the relevance of this in biological systems.

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Key Points

We introduce a novel multisensory task in which we provide task relevant evidence via bursts of varying duration, amidst a noisy background.

Prior multisensory algorithms perform sub-optimally on this task, as they cannot leverage temporal structure.

However, they can perform better by integrating across sensory channels and short temporal windows.

Surprisingly, this allows for comparable performance to fully recurrent neural networks, while using less than one tenth the number of parameters.
Human class B1 GPCR modulation by plasma membrane lipids
Authors: Chao Kin W , Wong Linda , Oqua Affiong I , Kalayan Jas , Manchanda Yusman , Gebbie-Rayet James , Hedger George , Tomas Alejandra , Rouse Sarah L
Published: December 2024

The class B1 G protein-coupled receptor (GPCR) subfamily is a class of receptors known for their regulatory roles in metabolism and neuronal activity important as drug targets. Lipids play key functional roles in modulation of GPCR signalling, yet our understanding of the molecular level detail of specific lipid interactions with class B1 GPCRs remains limited. Here we present coarse-grained molecular dynamics (MD) simulations of the active and inactive states of 15 human class B1 family members and use aiida-gromacs to capture full provenance for the set-up of simulations in complex plasma membranes. Receptors exhibit state-dependent lipid interactions with the regulatory sterol cholesterol and phospholipid phosphatidylinositiol-4,5-bisphosphate [PI(4,5)P2] at defined locations on the receptor surface. Global analysis of trends across the subfamily reveals conserved patterns of lipid interaction dynamics. The glycosphingolipid GM3 exerts a modulatory influence on the dynamics of class B1 extracellular domains in both simulations andin vitrotime-resolved FRET assays.

Teaser

Characterisation of regulatory lipid interactions with all class B1 GPCRs.
Aerosol deposition affects water uptake and water loss of beech leaves
Authors: Koch Irmgard , Kahmen Ansgar , Burkhardt Jürgen
Published: December 2024

The deposition of aerosols on leaves could significantly influence plant-atmosphere-interaction through the formation of very thin aqueous films that allow the transport of liquid water through the stomata. Such films can be formed by deliquescence and dynamic expansion of hygroscopic aerosols (‘hydraulic activation of stomata’). Two processes that may be associated with stomatal liquid water transport are foliar water uptake (FWU) and the contribution of ‘leaky stomata’ to minimum epidermal conductance (gmin).

We investigated whether ambient aerosols affect FWU and gminofFagus sylvaticaseedlings. Plants were grown in ventilated greenhouses with ambient air or filtered, almost aerosol-free air. The gminwas determined using leaf drying curves. FWU was investigated gravimetrically and with deuterium- enriched water, starting from different leaf water potentials, by spraying freshly-cut or pre-dried leaves (60 minutes).

The presence of aerosols in the environment increased gminby about 47%, confirming previous measurements in other species. Aerosols also increased FWU measured by deuterium uptake. FWU was higher for freshly-cut leaves than for pre-dried leaves, despite the lower leaf water potential. No gravimetric weight gain could be detected.

Both the gminand FWU results are consistent with bidirectional stomatal transport of liquid water along aerosol-induced pathways. The FWU result could also have been generated by water vapor through ‘reverse transpiration’, although the functional contribution of the aerosols would remain unclear. At low leaf water potential, the pathway may dry out and become less functional for FWU, whereas it may still be noticeable as stomatal leakage, given the strong gradient of water potential from the leaf interior to the atmosphere.
Immunolocalization of fasciclin-like arabinogalactan proteins in the G-layers of poplar tension wood fibers
Authors: Takeuchi Myiuki , Perassolo Guedes Fernanda Trilstz , Laurans Françoise , Boizot Nathalie , Déjardin Annabelle , Pilate Gilles
Published: December 2024

In hardwood trees, tension wood (TW) is an adaptive mechanism used by trees to orient their stems and branches, withstand their own weight, and improve wind resistance. In many species, such as poplar, TW fiber cell walls exhibit a supplemental layer, named the G-layer, which is responsible for the mechanical properties of TW. However, the molecular mechanisms involved still need to be clarified.

The synthesis of a number of fasciclin-like arabinogalactan proteins (FLA) has been shown to be highly upregulated during tension wood formation in poplar and is potentially associated with the outstanding mechanical properties of tension wood. Three polyclonal antibodies directed against different poplar TW-specific FLA epitopes were produced and used to assess the presence of these FLAs in differentiating and mature tension wood fibers.

Using immunohistochemistry, FLAs were detected at early stages of G-layer differentiation, specifically at the inner side of G-fiber cell walls, whereas a weaker signal was detected in mature G-fibers. However, western blot analyses of protein extracts from differentiating and mature tension wood revealed increased levels of FLA in mature TW fibers, suggesting that these FLAs remained present in mature G layers but were not accessible to anti-FLA antibodies in TW histological sections.

Overall, specific FLAs involved in secondary cell wall construction are located at the inner side of the G-layer and are likely actors in the unique mechanical properties of TWs.
The extent and drivers of gender and race/ethnicity imbalance in infectious disease dynamics research
Authors: Taube Juliana C. , Merritt Alexes , Bansal Shweta
Published: December 2024

Publication practices accumulate to affect credibility and career advancement. Understanding authorship and citation practices is critical to addressing inequities. While citation bias has been demonstrated in several fields, it remains uncharacterized in infectious disease dynamics (IDD), a quantitative, interdisciplinary domain highly visible during the COVID-19 pandemic. We analyze IDD articles and their bibliographies from 2000-2019 using machine-learning algorithms to infer the gender and race/ethnicity of each article’s lead and senior author. We examine authorship and citation patterns by gender and racial group across geographic scales, including characterizing the author composition of each article’s bibliography relative to the field. Our analysis reveals persistent gender and race imbalances in IDD research. Man-authored and White-authored publications dominate the field, with little progress in racial diversification of US and UK publications over the last two decades. Woman-authored articles have the most representative citation practices but are undercited, especially when women are senior authors. In the US and UK, most citations feature White lead and senior authors, even when citing articles with lead or senior authors of color. These findings underscore the urgent need for more inclusive IDD research practices. We discuss possible mechanisms and solutions to create opportunities for researchers from underrepresented groups.
A promoter::luciferase reporter gene imaging toolkit inKalanchoë laxiflorareveals molecular elements responsible for the circadian regulation of Crassulacean acid metabolism (CAM)
Authors: Pritchard Jessica H. , Waller Jade L. , Gould Peter J. D. , Kadu Nirja , Boxall Susanna F. , Dever Louisa V. , Kneřová Jana , O’Maoileidigh Diarmuid , Hartwell James
Published: December 2024

Crassulacean acid metabolism (CAM) plants perform primary atmospheric CO2fixation at night, with timekeeping by the endogenous circadian clock. Understanding of circadian coordination of CAM remains limited to rhythmic post-translational regulation of phosphoenolpyruvate carboxylase (PPC) by a specific clock-controlled protein kinase, PPCK. Here, candidate promoter regions (∼3000 bp) of CAM-associated genes fromKalanchoë laxiflorawere coupled to a firefly luciferase reporter and stable transgenic lines of bothK. laxifloraand C3Arabidopsis thalianawere generated. InK. laxiflora,the CAM-associatedGLUCOSE 6-PHOSPHATE/PHOSPHATE TRANSLOCATOR2promoter (KlGPT2p) generated robust circadian rhythms of luciferase luminescence in constant conditions, with peak activity in leaf pair 3, where CAM-associated nocturnal CO2fixation initiated during leaf development.KlGPT2p::LUC+did not drive rhythms of luminescence inA. thalianaand theKlPPCK1promoter produced no LUC+ signal in either species. Furthermore, theCHLOROPHYLL A/B BINDING PROTEIN2promoter (KlCAB2p), a clock-controlled promoter that drives a gene involved in light-reactions of photosynthesis, drove robust rhythms in bothK. laxifloraandA. thaliana.KlCAB2pcircadian period changed during leaf development inK. laxiflora,revealing differing control by the core-clock during development.KlCAB2ppeak activity shifted to dawn inA. thalianarelative to a dusk phased peak in CAM leaves ofK. laxiflora, highlighting differences in the timing of outputs from the core clock between species. These findings establish a robustPROMOTER::LUC+reporter system in a CAM plant and highlight divergent timing driving clock controlled promoters between species, and period lengthening with leaf age inKalanchoë.

One-sentence Summary

Robust circadian rhythms of firefly luciferase in the Crassulacean acid metabolism (CAM) model speciesKalanchoë laxiflorawere driven by both CAM and non-CAM gene promoters.
The active subset of grassland soil microbiomes changes with soil depth, water availability and prominently features predatory bacteria and episymbionts
Authors: Penev Petar I. , Estera-Molina Katerina , Allen George M. , Sachdeva Rohan , Lei Shufei , Law Ka Ki , Hoff Jordan , Blazewicz Steven J. , Pett-Ridge Jennifer , Banfield Jillian F.
Published: December 2024

Mediterranean grasslands, vital natural and agricultural ecosystems, experience seasonal variation in water content that likely affect microbial activity. We used metagenomics-informed stable isotope probing to investigate how the activities of microorganisms in Angelo Reserve (2160 mm rainfall) and Hopland (956 mm rainfall) soil change over depth and the seasons. At both sites, we find that the relative abundances of organisms in shallow soil changes relatively little but the most abundant organisms vary greatly with soil depth. Notably the highest levels of isotope incorporation, indicative of growth, occurs in deep soils. The active part of the 0-10 cm soil community varies over time, especially in Hopland soils during the fall rewetting. We defined a large, novel clade of Actinomycetota with notable capacity for thiosulfate oxidation whose representatives are prevalent and active in deep soils (>20 cm) across both ecosystems. Active Saccharibacteria unexpectedly encode nucleotide synthesis genes that enabled isotope incorporation while growing in shallow Angelo soils over all time periods. In contrast to predicted episymbiotic lifestyles of Saccharibacteria, other highly active bacteria are predicted predators. Obligately predatory Pseudobdellovibrio are active in intermediate depth Hopland soils whereas bacteria of the order Haliangiales are active in shallow Angelo soils. Supporting predatory lifestyles of Haliangiales, we usedin silicostructure prediction to assemble a large protein complex that we identify as a contractile injection system. Overall, the results indicate the potential for active carbon turnover in deep grassland soil and strong seasonal changes in the active members of microbial communities, despite relatively minor shifts in community composition.
Phylogenetic and functional diversity amongDrosophila-associated metagenome-assembled genomes
Authors: Comeault Aaron A. , Orta Alberto H. , Fidler David , Nunn Tobias , Ellison Amy R. , Anspach Tayte A. , Matute Daniel R.
Published: December 2024

Host-associated microbial communities can mediate interactions between their hosts and biotic and abiotic environments. While much work has been done to document how microbiomes vary across species and environments, much less is known about the functional consequences of this variation. Here, we test for functional variation among drosophilid-associated bacteria by conducting Oxford Nanopore long-read sequencing and generating metagenome-assembled genomes (MAGs) from six species of drosophilid fly collected in association with ‘anthropogenic’ environments in North America, Europe, and Africa. Using phylogenetic analyses, we find that drosophilid flies harbor a diverse microbiome that includes core members closely related to the generaGilliamella,Orbus,Entomomonas,Dysgonomonas, and others. Comparisons with publicly available bacterial genomes show that many of these genera are associated with phylogenetically diverse insect gut microbiomes. Using functional annotations and predicted secondary metabolite biosynthetic gene clusters, we show that MAGs belonging to different bacterial orders and genera vary in gene content and predicted functions including metabolic capacity and how they respond to environmental stressors. Our results provide evidence that wild drosophilid flies harbor phylogenetically and functionally diverse microbial communities. These findings highlight a need to quantify the abundance and function of insect-associated bacteria from the generaGilliamella,Orbus,Entomomonas, and others on the performance of their insect hosts across diverse environments.
Wnt pathway modulation is required to correctly execute multiple independent cellular dynamic programs during cranial neural tube closure
Authors: Bogart Amber Huffine , Brooks Eric R.
Published: December 2024

Defects in cranial neural tube closure are among the most common and deleterious human structural birth defects. Correct cranial closure requires the coordination of multiple cell dynamic programs including cell proliferation and cell shape change. Mutations that impact Wnt signaling, including loss of the pathway co-receptor LRP6, lead to defects in cranial neural tube closure indicating that this pathway is an important mediator of this critical morphogenetic event, but the cellular dynamics under control of the Wnt pathway during closure remain unclear. Here, we use mice mutant for LRP6 to examine the consequences of conditional and global reduction in Wnt signaling, as well as conditional inactivation of APC to examine the consequences of pathway hyperactivation. Strikingly, we find that regulated Wnt signaling is required for two independent events during cranial neural tube closure. First, global reduction of Wnt leads to a surprising hyperplasia of the cranial neural folds driven by excessive cell proliferation at early pre-elevation stages. The increased tissue volume presents a mechanical blockade to efficient closure despite normal apical constriction and cell polarization at later stages. Conversely, conditional hyperactivation of the pathway at elevation stages prevents apical constriction and neural fold elevation but has no impact on cell polarization or proliferation. Together these data reveal that Wnt signaling levels must be modulated to restrict proliferation at early stages and allow for apical constriction later at elevation stages to promote efficient closure of the cranial neural tube.
TheArabidopsis14-3-3 proteins positively regulate brassinosteroid signaling by stabilizing BRASSINOSTEROID INSENSITIVE1 at the plasma membrane
Authors: Li Luyao , Luo Dexian , Yin Chengzhu , Yan Chunyan , Vanhoutte Isabelle , Li Yan , Tang Bingbing , Xiao Guorong , Feng Xinyuan , Cao Wenhui , Wang Yong , Russinova Eugenia , Liu Derui
Published: December 2024

Brassinosteroid (BR) hormones regulate various physiological and developmental processes in plants. BR signaling is primarily influenced by the abundance of the BR receptor BR INSENSITIVE1 (BRI1) at the plasma membrane, a process regulated by ubiquitination, endocytosis, and protein degradation. Despite extensive research, only a few negative regulators of BRI1 internalization and ubiquitination have been identified. In this study, we show that 14-3-3 proteins, which are conserved regulatory proteins in eukaryotes, directly interact with BRI1 at Threonine 872 (T872) within its juxtamembrane domain. In addition, Serine 858 (S858) in the juxtamembrane domain of BRI1 positively affects the phosphorylation status of T872, thereby contributing to the binding of 14-3-3 proteins to BRI1. Consequently, without altering the kinase activity of BRI1 or its interaction with the co-receptor BRI1-ASSOCIATED RECEPTOR KINASE1 (BAK1), but by inhibiting BRI1 ubiquitination, the binding of 14-3-3 proteins increased the abundance of BRI1 at the plasma membrane and enhanced BR signaling. Both non-epsilon and epsilon isoforms of 14-3-3 proteins contribute to the regulation of BRI1 and, consequently, to plant responsiveness to BRs. Our results reveled a previously undescribed function of 14-3-3 proteins in regulating BRI1 stability and, in turn, positively influencing BR signaling.
Temporal evolution of color representations measured with MEG reveals a ‘coarse to fine’ dynamic
Authors: Goddard Erin , Mullen Kathy T.
Published: December 2024

Color perception is based on the differential spectral responses of the L, M and S-cones, subsequent subcortical and cortical computations, and may include the influence of higher order factors such as language. Although the early subcortical stages of color vision are well characterised, the organization of cortical representations of color remain elusive, despite numerous models based on discrimination thresholds, appearance and categorization. An underexplored aspect of cortical color representations is their dynamic evolution. Here we compare the evolution of three different color representations over time using magnetoencephalography (MEG). We measured neural responses to 14 hues at each of 3 achromatic offsets (increment, isoluminant and decrement) while participants attended either to the exact color of the stimulus or its color category. We used a series of classification analyses, combined with multidimensional scaling (MDS) and Representational Similarity Analysis, to ask how cortical representations of color unfold over time from stimulus onset. We compared the performance of ‘higher order’ models based on hue and color category with a model based simply on stimulus cone contrast and found that all models had significant correlations with the data. However, the unique variance accounted for by each model revealed a dynamic change in hue responses over time, that was consistent with a ‘coarse to fine’ transition from a broad clustering into categorical groups to a finer within category representation. Notably, these dynamics were replicated across datasets from both tasks, suggesting they reflect a robust reorganization of cortical hue responses over time.
A FRET-Based FLIM Method to Probe Membrane-Induced Alpha-Synuclein Aggregation in Neurons
Authors: Ivey Paula-Marie E. , Salem Abdelrahman , Min Sehong , Qi Wenzhu , Sosa Magaly Guzman , Kinzer-Ursem Tamara L. , Rochet Jean-Christophe , Webb Kevin J.
Published: December 2024

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Parkinson’s disease (PD) involves the aggregation of the protein alpha-synuclein, a process promoted by interactions with intracellular membranes. To study this phenomenon in neurons for the first time, we developed a fluorescence lifetime imaging (FLIM) method using Förster resonance energy transfer and self-quenching reporters, analyzed with a custom-built FLIM microscope. This method offers insights into aggregate formation in PD and can be broadly applied to probe protein-membrane interactions in neurons.
Effects of combined application of organic fertilizer and inorganic fertilizer on soil and yield of Gaodan grass
Authors: Yi Zhixin , Liu Qiuxu , Chen Yuhui , Zhu Yunqun , Ji Yang , Lin Linxiang
Published: December 2024

Using Sorghum bicolor × sudanense as test material, the effects of inorganic fertilizer and different proportions of organic fertilizer application on soil properties, yield and quality of sorghum were studied under conventional nitrogen application levels, aiming to provide data support for efficient production of green cycle forage. Five treatments were set up in the experiment, namely blank treatment (CK), conventional fertilization (HF), equivalent cow manure organic fertilizer (NF2), equivalent sheep manure organic fertilizer (YF2), 150% equivalent cow manure organic fertilizer (NF5) and 150% equivalent sheep manure organic fertilizer (YF5). In general, NF5 treatment was excellent in improving soil organic matter, enzyme activity and nutrient content, and the yield of Gaodan grass was significantly increased.
Over a Century of Infectious Disease Surveillance in Canada: Introducing the Canadian Disease Incidence Dataset (CANDID)
Authors: Earn David J. D. , MacKinnon Gabrielle , Manzin Samara , Roswell Michael , Cygu Steve , Shi Chyunfung , Bolker Benjamin M. , Dushoff Jonathan , Walker Steven C.
Published: December 2024

Background

Canadian notifiable disease surveillance provides data on the incidence of communicable diseases, dating back to the late 19th century. The Public Health Agency of Canada offers summaries of these data (from 1924–2022) through an online portal. These summaries provide historical context for Canadian health researchers, but lack information on intra-annual and inter-provincial patterns. Sub-annual and sub-national data can be found in published documents, or requested from archives of government agencies, but are only available in typewritten or handwritten hard copies. We digitized and collated these data sources to create a resource for epidemiology and public health.

Methods

We manually entered data from scans of hard copies into spreadsheets resembling the originals, facilitating accurate transcription through easier cross-checking. We developed open-source pipelines to harmonize these spreadsheets into CSV files that blend data across sources.

Results

We assembled and processed 1,631,380 incidence values from 1903–2021. Focusing on sub-annual and sub-national data and removing redundancy yielded 934,009 weekly, monthly, or quarterly incidence values broken down by province/territory, containing 139 diseases. We give two examples of sub-annual and sub-national patterns: strong annual cycles of poliomyelitis that peaked simultaneously across provinces, and spatially heterogeneous resurgence of whooping cough in the 1990s.

Interpretation

Canada’s history of infectious disease surveillance has produced a detailed record of sub-annual and sub-national disease incidence patterns that remains largely unexplored. This important record is now available as the Canadian Disease Incidence Dataset (CANDID), hosted on a publicly accessible website along with the pipelines used to create it and scans of the original sources.
Differential fMRI neural synchrony associated with migraine during emotionally arousing naturalistic stimuli
Authors: Klamer Keva , Craig Joshua , Haines Christina , Sullivan KiAnna , Seres Peter , Ekstrand Chelsea
Published: December 2024

Migraine is a common neurological disorder that impacts approximately 12% of the general population and is characterized by moderate to severe headaches, nausea, mood changes, and fatigue. It impacts lower-level visual and auditory processing, causing hypersensitivities that lead to heightened audiovisual multisensory integration. However, the impact of migraine on the processing of complex, audiovisual stimuli is still unclear. Additionally, migraine may induce hypersensitivities to emotional arousal and valence, though the relative significance of these factors remains unknown. The current study seeks to identify how migraine impacts synchronous neural processing of complex, audiovisual stimuli, and how this differs based on the emotional arousal and valence of the stimulus. To do so, we collected functional magnetic resonance imaging data from 17 migraineurs and 25 healthy controls during the passive viewing of three audiovisual films of differing emotional arousal and valence. We identified that, in response to high arousal emotional stimuli, the migraine group showed greater neural synchrony in regions associated with multisensory integration, including the posterior superior temporal gyrus. In response to the negative valence film, the migraine group had heightened neural synchrony in bilateral cuneus and the right angular gyrus. These findings suggest that migraine involves hypersensitivity to audiovisual movies as a function of both emotional arousal and valence, with high arousal driving greater synchrony in multisensory integration and negative valence enhancing synchrony in peripheral visual processing. Overall, this research highlights distinct pathways through which emotional stimuli impacts neural processing in migraine.
Force transmission is a master regulator of mechanical cell competition
Authors: Schoenit Andreas , Monfared Siavash , Anger Lucas , Rosse Carine , Venkatesh Varun , Balasubramaniam Lakshmi , Marangoni Elisabetta , Chavrier Philippe , Mege Rene-Marc , Doostmohammadi Amin , Ladoux Benoit
Published: December 2024

Cell competition is a tissue surveillance mechanism for eliminating unwanted cells and as such is indispensable in development, infection and tumorigenesis. Although different biochemical mechanisms are proposed, due to the dearth of direct force measurements, how mechanical forces determine the competition outcome remains unclear. Here, using ex vivo tissues and different cell lines, we have discovered an unknown form of cell competition that is regulated by differences in force transmission capabilities, favoring cell types with stronger intercellular adhesion. Direct force measurements reveal increased mechanical activity at the interface of the two competing cell types in the form of large stress fluctuations which can lead to upward forces and cell elimination. We show how a winning cell type endowed with a stronger intercellular adhesion exhibits a higher resistance to elimination while benefiting from efficient force transmission to neighboring cells. This cell elimination mechanism could have broad implications of keeping strong force transmission ability for maintaining tissue boundaries and cell invasion pathology.
Pervasive phosphorylation by phage T7 kinase disarms bacterial defenses
Authors: Bartolec Tara , Mitosch Karin , Potel Clément , Corona Federico , Yang Alessio Ling Jie , Burtscher Mira Lea , Koumoutsi Alexandra , Becher Isabelle , Bobonis Jacob , Karcher Nicolai , Galardini Marco , Typas Athanasios , Savitski Mikhail M
Published: December 2024

Bacteria and bacteriophages are in a constant arms race to develop bacterial defense and phage counter-defense systems. Currently known phage counter-defense systems are specific to (the activity of) the targeted bacterial defense system. Here, we uncover a mechanism by which the T7 bacteriophage broadly counteracts bacterial defenses using protein phosphorylation. We show that the T7 protein kinase (T7K), which was believed to specifically redirect the function of a few host proteins, is in fact a hyper-promiscuous, dual-specificity kinase enacting a massive wave of phosphorylation on virtually all host and phage proteins during infection. The scale of phosphorylation vastly exceeds the number of previously known phosphorylation events in E. coli, has no sequence motif specificity, and results in a higher proteome-wide phosphorylation density than that of mammalian cells which encode ~ 500 kinases. Stoichiometry analysis of phosphorylation sites revealed a strong bias of T7K activity towards nucleic acid-binding substrates, which we show is mediated by its C-terminal DNA-binding domain. This specificity for highly stoichiometric phosphorylation of nucleic acid-binding proteins enables the deactivation of DNA-targeting or -containing bacterial defense systems. We provide mechanistic insight into how T7K weakens two such defense systems, Retron-Eco9 and DarTG1, through specific phosphorylation events, with single phosphomimetic mutations in key sites of the toxins abolishing defense. Finally, by screening a large collection of E. coli strains, we provide evidence of broad counter-defense capacities for T7K in nature, as strains counteracted contain diverse bacterial defense systems.
Generation of antigen-specific paired chain antibody sequences using large language models
Authors: Wasdin Perry T. , Johnson Nicole V. , Janke Alexis K. , Held Sofia , Marinov Toma M. , Jordaan Gwen , Vandenabeele Léna , Pantouli Fani , Gillespie Rebecca A. , Vukovich Matthew J. , Holt Clinton M. , Kim Jeongryeol , Hansman Grant , Logue Jennifer , Chu Helen Y. , Andrews Sarah F. , Kanekiyo Masaru , Sautto Giuseppe A. , Ross Ted M. , Sheward Daniel J. , McLellan Jason S. , Abu-Shmais Alexandra A. , Georgiev Ivelin S.
Published: December 2024

The traditional process of antibody discovery is limited by inefficiency, high costs, and low success rates. Recent approaches employing artificial intelligence (AI) have been developed to optimize existing antibodies and generate antibody sequences in a target-agnostic manner. In this work, we present MAGE (Monoclonal Antibody GEnerator), a sequence-based Protein Language Model (PLM) fine-tuned for the task of generating paired human variable heavy and light chain antibody sequences against targets of interest. We show that MAGE can generate novel and diverse antibody sequences with experimentally validated binding specificity against SARS-CoV-2, an emerging avian influenza H5N1, and respiratory syncytial virus A (RSV-A). MAGE represents a first-in-class model capable of designing human antibodies against multiple targets with no starting template.
Local activation of Cxcl12a signaling controls olfactory placode morphogenesis in zebrafish embryos
Authors: Zilliox Marie , Letort Gaëlle , Sanchez David , Rouviere Christian , Dufourcq Pascale , Gaits-Iacovoni Frédérique , Pizzoccaro Anne , Roussier-Michon Violaine , Blader Patrick , Batut Julie
Published: December 2024

Morphogenesis and cell-type differentiation are highly coordinated in sensory organs to ensure their function. Morphogenesis of the olfactory epithelium (OE) in zebrafish provides a unique model to study this process as undifferentiated cells aligned around the anterior neural plate mature into clusters of early olfactory neurons across a short time scale. While the Cxcl12a/Cxcr4b signaling pathway drives this process, what constraints on pathway activation apply during morphogenesis are unclear. We developed a mathematical model recapitulating Cxcl12a-mediated OE morphogenesis. Restoring Cxcl12a expression in mutants for the ligand rescues correct morphogenesis both in silico and in vivo. However, where expression of the ligand is restored is crucial for rescue, a point not predicted by our model and suggesting an unexpected level of pathway activation control. Analysis of a Cxcr4b activation reporter supports this idea. We concluded that mosaic and heterochronic Cxcl12a activation along the anteroposterior axis sculpts the olfactory epithelium.
Radiation damage behavior of soft matter in ultrafast cryo-electron microscopy (cryo-UEM)
Authors: Zhao Yimin , Qi Chen , Zhu Chunhui , Zhu Yun , Zhang Yongzhao , Gu Tongnian , Tian Huanfang , Wang Wentao , Huang Siyuan , Yang Huaixin , Li Jianqi , Sun Fei
Published: December 2024

Whether time-modulated pulsed-electron imaging in ultrafast electron microscopy (UEM) can mitigate the electron radiation damage that occurs to samples, is still controversial. The effectiveness of such mitigation effect and relevant potential application in cryo-EM remain to be explored. Herein, we built an ultrafast cryo-EM (cryo-UEM) device based on an ultrafast laser system. Using such equipment and the saturated aliphatic hydrocarbon compounds (C44H90), the fading curves of diffraction intensity and corresponding critical electron doses (Ne) of the samples were carefully measured under different imaging modes, temperatures, imaging dose rates and pulsed repetition rates. Our experimental results show that, the fading curves andNevalues of the C44H90crystals are uncorrelated with the imaging electron dose rates and do not show dependence on the dose-rate effect. As the temperature decreased, theNevalues of the sample increased, indicating the cryoprotective effect on radiation damage to the samples. Surprisingly, at a constant temperature, the fading curves andNevalues of the sample in multi-electrons-packet and near-single-electron-packet pulsed modes are all approximately the same as those in conventional continuous electron-beam mode, even when the results are obtained at different pulsed repetition rates. These results show that the time-modulated pulsed electron beam does not seem to mitigate the electron radiation damage that occurs on samples. Our findings offer new insights and experimental basis for the radiation damage behavior of samples under electron beams, and provide guidance and inspiration for elucidating the fundamental principles of radiation damage.
Development of a flexible 3D printed TPU-PVC microfluidic devices for organ-on-a-chip applications
Authors: Abdalkader Rodi Kado , Konishi Satoshi , Fujita Takuya
Published: December 2024

The development of cost-effective, flexible, and scalable microfluidic devices is crucial for advancing organ-on-a-chip (OoC) technology for drug discovery and disease modeling applications. In this study, we present a novel 3D-printed flexible microfluidic device (3D- FlexTPU-MFD) fabricated through a one-step fused deposition modeling (FDM) process using thermoplastic polyurethane (TPU) as the printing filament and polyvinyl chloride (PVC) as the bonding substrate. The device’s compatibility was evaluated with various cell types, including human primary myoblasts, human primary endothelial cells (HUVEC), and human iPSC- derived optic vesicle (OV) organoids. Myoblasts cultured within the device exhibited high viability, successful differentiation, and the formation of aligned myotube bundles, outperforming conventional well-plate cultures. Additionally, iPSC-derived OV organoids- maintained viability, displayed neurite outgrowth, and sustained expression of the eye marker PAX6. These results demonstrate that the 3D-FlexTPU-MFD effectively supports cell growth, differentiation, and alignment, making it a promising platform for tissue modeling and OoC applications in future.
Large-scale infra-slow dynamics of extracellular potentials linked to synchronous states revealed by graphene neural probes
Authors: Garcia-Cortadella R. , Cisneros-Fernandez J. , Schwesig G. , Shahidi A. , Umurzakova A. , Schäfer N. , Aguilar J. , Masvidal-Codina E. , Del Corro E. , Moahrlok R. , Kurnoth M. , Paetzold J. , Loeffler H. , Jeschke C. , Meents J. , Illa X. , Serra-Graells F. , Guimerà-Brunet A. , Garrido J. A. , Sirota A.
Published: December 2024

Brain states exhibit slow transitions that are coordinated by slowly varying homeostatic and neuromodulatory factors. These slow dynamics modulate neuronal excitability, giving rise to brain state-specific synchronous oscillatory patterns across brain regions. Such synchronous states could be reflected in local infra-slow variations in the extracellular potential, providing new insights into the organisation of spontaneous brain dynamics beyond the established fast time scales. However, mapping of the LFP across brain regions with high spatio-temporal resolution remains challenging, with the infra-slow component particularly elusive. To overcome these limitations, we developed neural probes based on arrays of up to 512 multiplexed graphene transistors, which enable DC-coupled, high-density, and large-scale recordings of surface and depth activity in freely behaving rats. Analysis of cortex-wide oscillation dynamics improves segmentation, provides new insights into global brain states and allows detection of the local oscillatory states. Brain state transitions related to changes in neuronal synchrony are found to correlate with topographically structured infra-slow dynamics. Furthermore, transregional infra-slow waves during non-REM sleep are globally coupled to diverse sleep spindle oscillatory modes independent of their localization while slow oscillations locally modulate spindle occurrence. This study shows that spatio-temporal patterns of infra-slow and slow LFP parallel the spatially organized oscillatory dynamics, reflecting the interplay between sub-cortical inputs and cortical excitability across brain states.
Abundant non-inclusion α-synuclein pathology in Lewy body-negative LRRK2-mutant cases
Authors: Jensen Nanna Møller , Vitic Zagorka , Antorini Mia R. , Bruun Viftrup Tobias , Parkkinen Laura , Jensen Poul Henning
Published: December 2024

Lewy body diseases are common neurodegenerative diseases, including Parkinson’s disease (PD) and dementia with Lewy bodies, which lead to both motor and non-motor symptoms. They are neuropathologically characterized by loss of neuromelanized neurons in the substantia nigra pars compacta and α-synuclein-immunopositive inclusions (Lewy bodies) in several types of neurons in the brain. A fraction of monogenic PD cases, however, represent a conundrum, as they can present with clinical Lewy body disease but do not have Lewy bodies upon neuropathological examination. For LRRK2, the presence or absence of Lewy bodies is not related to any specific mutation in the gene and different clinical presentation and neuropathology can be present even in the same family.

Here, we present the first evidence of widespread α-synuclein accumulation detected with proximity ligation assay (PLA) using the MJFR14-6-4-2 antibody in six Lewy body-negative LRRK2 cases and compare the levels with five patients with neuropathologically-verified Lewy body disease cases and six healthy controls. We show that non-inclusion, aggregated α-synuclein PLA signal is dominant in the LRRK2 cases, while Lewy-like PLA signal is predominant in late-stage Lewy body disease. Furthermore, LRRK2 cases displayed prominent PLA signal in pontocerebellar tracts and inferior olivary nuclei in the brainstem, which was not seen in idiopathic PD cases. These results suggest that Lewy-body negative LRRK2-related PD is not associated with a lack of α-synuclein aggregation in neurons but rather a deficiency in the formation of inclusions.
Experimental evolution of a pathogen confronted with innate immune memory increases variation in virulence
Authors: Korša Ana , Baur Moritz , Schulz Nora K.E. , Anaya-Rojas Jaime M. , Mellmann Alexander , Kurtz Joachim
Published: December 2024

Understanding the drivers and mechanisms of virulence evolution is still a major goal of evolutionary biologists and epidemiologists. Theory predicts that the way virulence evolves depends on the balance between the benefits and costs it provides to pathogen fitness. Additionally, host responses to infections, such as resistance or tolerance, play a critical role in shaping virulence evolution. But, while the evolution of pathogens has been traditionally studied under the selection pressure of host adaptive immunity, less is known about their evolution when confronted to simpler and less effective forms of immunity such as immune priming. In this study, we used a well-established insect model for immune priming – red flour beetles and their bacterial pathogenBacillus thuringiensis tenebrionis –to test whether this form of innate immune memory favors the evolution of higher virulence. Through controlled experimental evolution of the pathogen in primed versus non-primed hosts, we found no change in average virulence after eight selection cycles in primed host. However, we found a significant increase in the variation of virulence (i.e., host-killing ability) among independent pathogen lines evolved in primed host, and bacteria were unable to evolve resistance against host priming. Whole genome sequencing revealed increased activity in the bacterial mobilome (prophages and plasmids). Expression of the Cry toxin – a well-known virulence factor – was linked to evolved differences in copy number variation of thecry-carrying plasmid, though this did not correlate directly with virulence. These findings highlight that innate immune memory can drive variability in pathogen traits, which may favor adaptation to variable environments. This underscores the need to consider pathogen evolution in response to innate immune memory when applying these mechanisms in medicine, aquaculture, pest control, and insect mass production.
Transcriptional responses toin vitromacrocyclic lactone exposure inToxocara canislarvae using RNA-seq
Authors: Quintana Theresa A. , Brewer Matthew T. , Chelladurai Jeba R. Jesudoss
Published: December 2024

Toxocara canis, the causative agent of zoonotic toxocariasis in humans, is a parasitic roundworm of canids with a complex lifecycle. While macrocyclic lactones (MLs) are successful at treating adultT. canisinfections when used at FDA-approved doses in dogs, they fail to kill somatic third-stage larvae. In this study, we profiled the transcriptome of third-stage larvae derived from larvated eggs and treatedin vitrowith 10 µM of the MLs – ivermectin and moxidectin with Illumina sequencing. We analyzed transcriptional changes in comparison with untreated control larvae. In ivermectin-treated larvae, we identified 608 differentially expressed genes (DEGs), of which 453 were upregulated and 155 were downregulated. In moxidectin-treated larvae, we identified 1,413 DEGs, of which 902 were upregulated and 511 were downregulated. Notably, many DEGs were involved in critical biological processes and pathways including transcriptional regulation, energy metabolism, neuronal structure and function, physiological processes such as reproduction, excretory/secretory molecule production, host-parasite response mechanisms, and parasite elimination. We also assessed the expression of known ML targets and transporters, including glutamate-gated chloride channels (GluCls), and ATP-binding cassette (ABC) transporters, subfamily B, with a particular focus on P-glycoproteins (P-gps). We present gene names for previously uncharacterizedT. canisGluCl genes using phylogenetic analysis of nematode orthologs to provide uniform gene nomenclature. Our study revealed that the expression ofTca-glc-3and six ABCB genes, particularly four P-gps, were significantly altered in response to ML treatment. Compared to controls,Tca-glc-3,Tca-Pgp-11.2, andTca-Pgp-13.2were downregulated in ivermectin-treated larvae, whileTca-abcb1,Tca-abcb7,Tca-Pgp-11.2, andTca-Pgp-13.2were downregulated in moxidectin-treated larvae. Conversely,Tca-abcb9.1andTca-Pgp-11.3were upregulated in moxidectin-treated larvae. These findings suggest that MLs broadly impact transcriptional regulation inT. canislarvae.