bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic diversity in vector populations influences the transmission efficiency of an important plant virus
Authors: Leybourne Daniel J , Whitehead Mark A , Will Torsten 
Published: February 2024

AbstractThe transmission efficiency of aphid-vectored plant viruses can differ between aphid populations. Intra-species diversity (genetic variation, endosymbionts) is a key determinant of aphid phenotype; however, the extent of which intra-species diversity contributes towards variation in virus transmission efficiency is unclear. Here, we use multiple populations of two key aphid species that vector barley yellow dwarf virus (BYDV) strain PAV (BYDV-PAV), the grain aphid (Sitobion avenae) and the bird cherry-oat aphid (Rhopalosiphum padi), and examine how diversity in vector populations influences virus transmission efficiency. We use Illumina sequencing to characterise genetic and endosymbiont variation in multipleS. avenaeandR. padipopulations and conduct BYDV-PAV transmission experiments to identify links between intra-species diversity in the vector and virus transmission efficiency. We observe limited variation in the transmission efficiency ofS. avenae, with transmission efficiency consistently low for this species. However, forR. padiwe observe a range of transmission efficiency and show that BYDV transmission efficiency is influenced by genetic diversity within the vector, identifying 542 SNPs that potentially contribute towards variable transmission efficiency inR. padi. Our results represent an important advancement in our understanding of the relationship between genetic diversity, vector-virus interactions, and virus transmission efficiency.
Kaempferol exerts anti-inflammatory effects by accelerating Treg development via AhR-mediated and PU.1/IRF4-dependent transactivation of theAldh1a2/RALDH2 gene in dendritic cells
Authors: Takahashi Miki , Nagata Kazuki , Watanuki Yumi , Yamaguchi Masaki , Minamikawa Natsuki , Katagiri Mayuka , Zhao Weiting , Ito Naoto , Yashiro Takuya , Nishiyama Chiharu 
Published: February 2024

AbstractRetinaldehyde dehydrogenase 2 encoded in theAldh1a2gene (RALDH2) is expressed in intestinal dendritic cells (DCs) in mesenteric lymph nodes (MLNs) and plays a crucial role in Treg development by producing retinoic acid. In the present study, we screened food ingredients and identified kaempferol, a flavonoid, as the compound that most effectively up-regulated RALDH2 expression in DCs. The development of Foxp3+cells from OT-II-derived naïve CD4+T cells was enhanced by a co-culture with OVA peptide-pulsed bone marrow-derived DCs (BMDCs) in the presence of kaempferol or by a pre-treatment of BMDCs with kaempferol. The involvement of the aryl hydrocarbon receptor (Ahr) in the effects of kaempferol onAldh1a2expression was demonstrated byin vitroexperiments using siRNA and various agonistic or antagonistic compounds of AhR. AhR suppressedAldh1a2gene expression and kaempferol inhibited the AhR activity by functioning as an antagonist of AhR. The kaempferol treatment also increased the protein levels of PU.1 and IRF4, which are essential for transcription of theAldh1a2gene in DCs, and accelerated the subsequent recruitment of PU.1 to theAldh1a2gene. The kaempferol-induced increase in PU.1 protein levels occurred in an AhR-dependent and transcription-independent manner, whereas the kaempferol treatment transactivated theIrf4gene in DCs. The frequency of DCs exhibiting RALDH2 activity in the MLNs of mice was increased by the intraperitoneally (i.p.) administration of an AhR antagonist or by the oral administration of astragalin, a 3-O-glucoside of kaempferol. We also observed an increase in Tregs in the Peyer’s patches of C57BL/6 mice i.p. administered kaempferol-treated BMDCs. We utilized an OVA-induced food allergy model of Balb/c mice to examine the effects of kaempferolin vivoand confirmed that the rapid decrease in body temperature and allergic diarrhea observed just after the OVA challenge were significantly suppressed in mice administered kaempferol.
Differential colonization and succession dynamics of marine bacteria on different plastic polymers
Authors: Davidov Keren , Itzahri Sheli , Sinberger Liat Anabel , Oren Matan 
Published: February 2024

AbstractDuring the past decades since plastic was introduced to the world, marine microorganisms have been adapted for life on marine plastic debris, forming unique plastic-attached microbial communities. To date, little is known about the colonization and succession processes that take place on plastic surfaces in marine environments and how the plastic polymer type affects the plastic-attached microbiome composition. To address this knowledge gap, we examined the colonization and succession dynamics of marine bacteria on four common plastic polymers - PE, PP, PS, and PET-compared to glass and wood in a controlled seawater system under different temperatures. Using a simple experimental design, coupled with a long-read 16S rRNA metabarcoding pipeline and a set of complementary data analyses, we characterized the temporal trends in the composition of the bacterial microbiome developed on different surfaces over 2 - 90 days. By applying weighted gene co-expression network (WGCNA) analysis, we established co-occurrence networks and identified genera with specific succession signatures, significant enrichment on specific plastic polymers and/or strong intra-genus connections. Among them, members of genusAlcanivoraxwere significantly enriched on either PE or PP plastic surfaces as early as 2 days post-inoculation.Alcanivoraxcolonization preference to polyolefins was confirmed in colonization assays with pureAlcanivoraxstrains. Our research approach presented here may contribute to understanding how plastisphere communities are being formed and help identify taxa with specific adaptations to plastic surfaces.
CD81+fibroblasts, a unique subpopulation with accelerated cellular senescence, exaggerate inflammation and activate neutrophils via C3/C3aR1 axis in periodontitis
Authors: Fu Liangliang , Yin Chenghu , Zhao Qin , Guo Shuling , Shao Wenjun , Xia Ting , Sun Quan , Chen Liangwen , Wang Min , Xia Haibin 
Published: February 2024

AbstractPeriodontitis, a prevalent inflammatory disease worldwide, poses a significant economic burden on society and the country. Despite numerous studies, the biological molecular mechanism underlying the development and progression of periodontitis remains unclear. Previous research has established a connection between cellular senescence and periodontitis. However, the role and mechanism of cell senescence in the progression of periodontitis have not been thoroughly investigated. This study aimed to explore the involvement of cellular senescence in the pathogenesis of periodontitis and determine the underlying mechanisms. Our findings demonstrated that senescent cells accumulated during the periodontitis progress and inhibiting cellular senescence in periodontitis via administration of metformin successfully alleviated inflammation and bone loss. Moreover, several scRNA-seq analysis suggested that gingival fibroblasts were the main cell population undergoing cellular senescence during periodontitis, which helps mitigate tissue damage and bone loss. Furthermore, we identified a high expression of CD81 in the senescent gingival fibroblast population. These cells were found to actively contribute to inflammation through their potent pro-inflammatory metabolic activity and secretion of SASP-related factors. Additionally, they recruited neutrophils via the C3/C3aR1 pathway, indirectly sustaining the inflammatory response. These results provide valuable insights into the cellular and molecular basis of periodontitis-induced tissue damage, highlighting the significance of fibroblast senescence. In conclusion, our study sheds light on the relationship between CD81 and cellular senescence, suggesting its potential as a therapeutic target for periodontitis.
High phenotypic and genotypic plasticity among strains of the mushroom-forming fungusSchizophyllum commune
Authors: Marian Ioana M. , Valdes Ivan D. , Hayes Richard D. , LaButti Kurt , Duffy Kecia , Chovatia Mansi , Johnson Jenifer , Ng Vivian , Lugones Luis G. , Wösten Han A. B. , Grigoriev Igor V. , Ohm Robin A. 
Published: February 2024

AbstractSchizophyllum communeis a mushroom-forming fungus notable for its distinctive fruiting bodies with split gills. It is used as a model organism to study mushroom development, lignocellulose degradation and mating type loci. It is a hypervariable species with considerable genetic and phenotypic diversity between the strains. In this study, we systematically phenotyped 16 dikaryotic strains for aspects of mushroom development and 18 monokaryotic strains for lignocellulose degradation. There was considerable heterogeneity among the strains regarding these phenotypes. The majority of the strains developed mushrooms with varying morphologies, although some strains only grew vegetatively under the tested conditions. Growth on various carbon sources showed strain-specific profiles. The genomes of seven monokaryotic strains were sequenced and analyzed together with six previously published genome sequences. Moreover, the related speciesSchizophyllum fasciatumwas sequenced. Although there was considerable genetic variation between the genome assemblies, the genes related to mushroom formation and lignocellulose degradation were well conserved. These sequenced genomes will provide a solid basis for functional genomics analyses of the strains ofS. commune.
Regulation of temporal cytokine production by co-stimulation receptors in TCR-T cells is lost in CAR-T cells
Authors: Patel Ashna , Kutuzov Mikhail A. , Dustin Michael L. , van der Merwe P. Anton , Dushek Omer 
Published: February 2024

AbstractCD8+ T cells contribute to immune responses by producing cytokines when their T cell receptors (TCRs) recognise peptide antigens on major-histocompability-complex (pMHC) class I. However, excessive cytokine production can be harmful. For example, cytokine release syndrome (CRS) is a common toxicity observed in treatments that activate T cells, including chimeric antigen receptor (CAR)-T cell therapy. While engagement of costimulatory receptors is well known to enhance cytokine production, we have limited knowledge of their ability to regulate the kinetics of cytokine production by CAR-T cells. Here we compare early (0-12 hours) and late (12-20 hours) production of IFN-γ, IL-2, and TNF-α production by T cells stimulated via TCR or CARs in the presence or absence ligands for CD2, LFA-1, CD28, CD27, and 4-1BB. For T cells expressing TCRs and 1st-generation CARs, activation by antigen alone was sufficient to stimulate early cytokine production, while co-stimulation by CD2 and 4-1BB was required to maintain late cytokine production. In contrast, T cells expressing 2nd-generation CARs, which have intrinsic costimulatory signalling motifs, produce high levels of cytokines in both early and late periods in the absence of costimulatory receptor ligands. Losing the requirement for costimulation for sustained cytokine production may contribute to the effectiveness and/or toxicity of 2nd-generation CAR-T cell therapy.Graphical abstract
Depletion of membrane cholesterol modifies structure, dynamic and activation of Nav1.7
Authors: Albani Simone , Bhagavath Eswaran Vishal Sudha , Piergentili Alessia , de Souza Paulo Cesar Telles , Lampert Angelika , Rossetti Giulia 
Published: February 2024

AbstractCholesterol is a major component of plasma membranes and unsurprisingly plays a significant role in actively regulating the functioning of several membrane proteins in humans. Notably, recent studies have shown that cholesterol depletion can also impact transmission of potentially painful signals in the context of peripheral inflammation, via hyperexcitability of the voltage-gated sodium channel (Nav) subtype 1.9, but the structural mechanisms underlying this regulation remain to be elucidated. In this study, we focus on the role of cholesterol depletion on Nav1.7, which is primarily expressed in the peripheral sensory neurons and linked to various chronic inherited pain syndromes. Coarse-grained molecular dynamics simulations shed light on the dynamic changes of the geometry of Nav1.7 upon membrane cholesterol depletion: A loss of rigidity at key structural motifs linked to activation and fast-inactivation is observed, as well as changes in the geometry of drug-binding regions in the channel. Loss of rigidity in cholesterol depleted conditions should allow the channel to transition between different gating states more easily.In-vitrowhole-cell patch clamp experiments on HEK293t cells expressing Nav1.7 validated these predictions madein silicoat the functional level. Hyperpolarizing shifts in the voltage-dependence of activation and fast-inactivation were observed along with an acceleration of the time to peak and onset kinetics of fast inactivation. These results underline the critical role of membrane composition, and of cholesterol in particular, in influencing Nav1.7 gating characteristics. Furthermore, our results hint to a key role of the membrane environment in affecting drug effects and in pathophysiological dysregulation, sharpening our approaches for analgesics design.Supplementary datahttps://doi.org/10.5281/zenodo.10829175
A genetically-encoded nanobody sensor reveals conformational diversity in β-arrestins orchestrated by distinct seven transmembrane receptors
Authors: Sarma Parishmita , Marková Vendula Nagy , Zaidi Nashrah , Dalal Annu , Mishra Sudha , Yadav Manish K. , Mahajan Gargi , Roy Nabarun , Miclea Paul , Lazar Josef , Shukla Arun K. 
Published: February 2024

AbstractAgonist-induced interaction of G protein-coupled receptors (GPCRs) with β-arrestins (βarrs) is a critical mechanism that regulates the spatio-temporal pattern of receptor localization and downstream signaling. While the underlying mechanism governing GPCR-βarr interaction is primarily conserved and involves receptor activation and phosphorylation, there are several examples of receptor-specific fine-tuning of βarr-mediated functional outcomes. Considering the key contribution of conformational plasticity of βarrs in driving receptor-specific functional responses, it is important to develop and characterize novel sensors capable of reporting distinct βarr conformations in cellular context. Here, we design an intrabody version of a βarr-recognizing nanobody (nanobody32), referred to as intrabody32 (Ib32), in NanoLuc enzyme complementation assay format, and measure its ability to recognize βarr1 and 2 in live cells upon activation of a broad set of GPCRs. We discover that Ib32 robustly recognizes activated βarr1 and 2 in the plasma membrane as well as in the endosomes, and effectively mirrors βarr recruitment profile upon stimulation of GPCRs. We also design an Ib32 sensor for single-photon polarization microscopy with a change in linear dichroism as readout and demonstrate its utility for monitoring βarr activation upon stimulation of angiotensin receptor by its natural and biased agonists. Interestingly, when used side-by-side with a previously described sensor of βarr1 conformation known as Ib30, Ib32 uncovers distinct conformational signatures imparted on βarrs by different GPCRs, which is further corroborated using an orthogonal limited proteolysis assay. Taken together, our study presents Ib32 as a novel sensor to monitor βarr activation and leverages it to uncover conformational diversity encoded in the GPCR-βarr system with direct implications for improving the current understanding of GPCR signaling and regulatory paradigms.
Graph analysis of the guilt network highlights associations with subclinical anxiety and self-blame
Authors: Zareba Michal Rafal , Bielski Krzysztof , Costumero Victor , Visser Maya 
Published: February 2024

AbstractMaladaptive forms of guilt, such as excessive self-blame, are common characteristics of anxiety disorders. The associated network includes the superior anterior temporal lobe (sATL), underlying the conceptual representations of social meaning, and fronto-subcortical areas involved in the affective dimension of guilt. Nevertheless, despite understanding the anatomy of the guilt processing circuitry, network-level changes related to subclinical anxiety and self-blaming behaviour have not been depicted. To fill this gap, we used graph theory analyses on a resting-state functional and diffusion-weighted magnetic resonance imaging dataset of 78 healthy adults. Within the guilt network, we found increased functional contributions (higher clustering coefficient, local efficiency and strength) of the left sATL for individuals with higher self-blaming and trait-anxiety, while functional isolation (lower clustering coefficient and local efficiency) of the left pars opercularis and insula was related to higher trait-anxiety. Trait-anxiety was also linked to the structural network’s global parameters (mean clustering coefficient), with the circuitry’s architecture favouring increased local information processing in individuals with increased anxiety levels. Previous research suggests that aberrant interactions between conceptual (sATL) and affective (fronto-limbic) regions underlie maladaptive guilt and the current results align and expand on this theory by detailing network changes associated with self-blame and trait-anxiety.
Quantifying vulnerability to plant invasion across global ecosystems
Authors: Pfadenhauer William G. , Bradley Bethany A. 
Published: February 2024

AbstractThe widely-referenced “tens rule” in invasion ecology suggests that 10% of established, non-native species will become invasive. However, the accuracy of this estimate has been questioned, as the original analysis focused on small groups of plant species in Great Britain and Australia. Using a novel database of 9,501 established and 2,924 invasive plants, we provide a comprehensive evaluation of plant invasion rates and the first empirical analysis of how the tens rule varies across climate zones and spatial scales. We found that invasion rates ranged from 17% at the country scale to 25% at the continental scale. Tropical communities are often considered to be resistant to invasion, however our results showed significantly higher invasion rates in the tropics and especially on tropical islands, suggesting unexpectedly high vulnerability of these species-rich ecosystems. Our analysis provides improved, environment-specific estimates of invasion rates which are often twice as high as previous expectations. We recommend that practitioners reject the tens rule for plants and adjust future management practices to reflect these updated estimates of invasion risk.Open Research StatementThe data and code that support the findings of this study are openly available on GitHub athttps://github.com/wpfadenhauer/Global-Invasion-Rates
New insights into the mechanisms of plant isotope fractionation from combined analysis of intramolecular13C and deuterium abundances inPinus nigratree-ring glucose
Authors: Wieloch Thomas , Holloway-Phillips Meisha , Yu Jun , Niittylä Totte 
Published: February 2024

SummaryUnderstanding isotope fractionation mechanisms is fundamental for analyses of plant ecophysiology and paleoclimate based on tree-ring isotope data.To gain new insights into isotope fractionation, we analysed intramolecular13C discrimination in tree-ring glucose (Δi’,i= C-1 to C-6) and metabolic deuterium fractionation at H1and H2(εmet) combinedly. This dual-isotope approach was used for isotope-signal deconvolution.We found evidence for metabolic processes affectingΔ1’ andΔ3’ which respond to air vapour pressure deficit (VPD), and processes affectingΔ1’,Δ2’, andεmetwhich respond to precipitation but notVPD. These relationships exhibit change points dividing a period of homeostasis (1961-1980) from a period of metabolic adjustment (1983-1995). Homeostasis may result from sufficient groundwater availability. Additionally, we foundΔ5’ andΔ6’ relationships with radiation and temperature which are temporally stable and consistent with previously proposed isotope fractionation mechanisms.Based on the multitude of climate covariables, intramolecular carbon isotope analysis has a remarkable potential for climate reconstruction. While isotope fractionation beyond leaves is currently considered to be constant, we propose significant parts of the carbon and hydrogen isotope variation in tree-ring glucose originate in stems (precipitation-dependent signals). As basis for follow-up studies, we propose mechanisms introducingΔ1’,Δ2’,Δ3’, andεmetvariability.
Development of radial frequency pattern perception in macaque monkeys
Authors: Rodríguez Deliz C. L. , Lee Gerick M. , Bushnell Brittany N. , Majaj Najib J. , Movshon J. Anthony , Kiorpes Lynne 
Published: February 2024

AbstractInfant primates see poorly, and most perceptual functions mature steadily beyond early infancy. Behavioral studies on human and macaque infants show that global form perception, as measured by the ability to integrate contour information into a coherent percept, improves dramatically throughout the first several years after birth. However, it is unknown when sensitivity to curvature and shape emerges in early life. We studied the development of shape sensitivity in eighteen macaques, aged 2 months to 10 years. Using radial frequency stimuli (RFS), circular targets whose radii are modulated sinusoidally, we tested monkeys’ ability to discriminate RFS from circles as a function of the depth and frequency of sinusoidal modulation. We implemented a new 4-choice oddity task and compared the resulting data with that from a traditional 2-alternative task. Behavioral performance at all radial frequencies improved with age. Performance was better for higher radial frequencies, suggesting the developing visual system prioritizes processing of fine visual details that are ecologically relevant. By utilizing two complementary methods, we were able to capture a comprehensive developmental trajectory for shape perception.
Sensory perception of fluctuating light in Arabidopsis
Authors: Belmonte Antonela , Tissot Nicolas , Rabinovich Andrés , Ploschuk Edmundo L. , Crocco Carlos D. , Ulm Roman , Casal Jorge J. 
Published: February 2024

SummaryWhen exposed to shade from neighbours, competitive plants modify their growth patterns to improve access to light. In dense plant stands, ranging from forests to humid grasslands and crops, shade is interrupted by sunflecks penetrating the canopy. Relatively infrequent, minute-scale interruptions can significantly contribute to the daily light input. However, given the short duration and the time gap between these low frequency sunflecks (LFS), whether plants can sense them was unknown. Here we show that phytochrome B (phyB), cryptochrome 1 (cry1), cry2, and UV RESISTANCE LOCUS 8 (UVR8) cooperatively perceive LFS to reduce hypocotyl growth inArabidopsis thaliana. LFS also enhanced the expression of photosynthetic and photo-protective genes and initiated pre-emptive acclimation to water restriction. Repeated LFS increased the nuclear abundance of cry1 and UVR8. This positive feedback enhanced the sensitivity to subsequent LFS and even to the shade between LFS. LFS reduced the nuclear abundance of the growth regulator PHYTOCHROME INTERACTING FACTOR 4 (PIF4), which only slowly recovered upon return to shade, further amplifying the signal. The dynamics of the photo-sensory system under fluctuating light helps adjust plants to the prevailing conditions.