bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular mechanisms of heart field specific cardiomyocyte differentiation- a computational modeling approach
Authors: Argyris Georgios , Zeegelaar Ricco , Post Janine N. 
Published: December 2024

AbstractTissue 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

AbstractAnimals 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.1Key PointsWe 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

AbstractThe 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.TeaserCharacterisation 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

AbstractThe 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

AbstractIn 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

AbstractPublication 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

ABSTRACTCrassulacean 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 SummaryRobust 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

AbstractMediterranean 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

AbstractHost-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

AbstractDefects 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

AbstractBrassinosteroid (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

AbstractColor 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

1AbstractParkinson’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

AbstractUsing 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.