bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ecological and genetic trade-offs driveArabidopsis thalianarange expansion in Europe
Authors: Bastias Cristina C. , Estarague Aurélien , Vile Denis , Lee Cheng-Ruei , Exposito-Alonso Moises , Violle Cyrille , Vasseur François 
Published: December 2022

AbstractHow trade-offs between traits constrain adaptation to contrasted environments is critical to understand the distribution range of a given species. InArabidopsis thaliana, genetic analyses recently revealed that a group of genotypes successfully recolonized Europe from its center after the last glaciation, outcompeting older lineages and leaving them only at the distribution margins, where environmental conditions are more stressing. However, whether trade-offs between traits related to dispersal, competition, and stress tolerance explain the success and persistence of different lineages across the species geographic range remains an open question. Here, we compared the genetic and phenotypic differentiation between 72 ecotypes originating from three geographical groups in Europe (North, South and Center). We measured key traits related to fecundity, dispersal ability, competition tolerance, and stress tolerance, and used genomic data to infer the effect of selection on these traits. We showed that a trade-off between plant fecundity and seed mass constrains the diversification ofA. thalianain Europe. In particular, the success of the cosmopolitan genotypes that recolonized Europe can be explained by their higher dispersal ability at the expense of their competitive ability and stress tolerance. Inversely, peripheral ecotypes exhibited the opposite trait syndrome: high competition and stress tolerance but low dispersal ability. Moreover, peripheral genotypes tend to differentiate from central ones at genes involved in dispersal and competitive traits such as seed mass. Combining ecological and genomic approaches, our study demonstrated the role of key ecological trade-offs as evolutionary drivers of the distribution of plant populations along a geographic gradient.SignificanceAcross geographic gradients, differential adaptive phenotypes among populations can reduce the risk of local extinctions and favor niche dynamics. However, a phenotypic advantage often comes at a cost. For instance, the competition-colonization trade-off is proposed as an important driver of plant interspecific diversity, but its role for local adaptation at the intraspecific level is still unclear. Using the broadly-distributed speciesArabidopsis thaliana, we evaluate how ecological trade-offs have shaped the demography and evolution of central and peripheral populations in its native geographic gradient. Our study demonstrates that the competition-colonization trade-off is responsible of the spatially-structured phenotypic variation ofA. thalianaacross its geographical range. Our study highlights seed mass as a key trait for plant adaptation across environmental conditions.
DNA methylation at the suppressor of cytokine signaling 3 (SOCS3) gene influences height in childhood
Authors: Issarapu Prachand , Arumalla Manisha , Elliott Hannah R. , Nongmaithem Suraj S. , Sankareswaran Alagu , Betts Modupeh , Sajjadi Sara , Kessler Noah J. , Bayyana Swati , Mansuri Sohail R. , Derakhshan Maria , Krishnaveni G. V. , Shrestha Smeeta , Kumaran Kalyanaraman , Gravio Chiara Di , Sahariah Sirazul A. , Sanderson Eleanor , Relton Caroline L. , Ward Kate A. , Moore Sophie E. , Prentice Andrew M , Lillycrop Karen A. , Fall Caroline H. D. , Silver Matt J. , Chandak Giriraj R. ,   EMPHASIS study group
Published: December 2022

AbstractHuman height is strongly influenced by genetics but the contribution of modifiable epigenetic factors is under-explored, particularly in low and middle-income countries (LMIC). We investigated links between blood DNA methylation and child height in four LMIC cohorts (n=1927) and identified a robust association at three CpGs in the suppressor of cytokine signalling 3 (SOCS3) gene which replicated in a high-income country cohort (n=879).SOCS3methylation (SOCS3m) – height associations were independent of genetic effects. Mendelian randomization analysis confirmed a causal effect ofSOCS3mon height. In longitudinal analysis in a LMIC cohort,SOCS3mexplained a maximum 9.5% of height variance in mid-childhood while the variance explained by height polygenic risk score increased from birth to 21 years (2% to 18%). Children’sSOCS3mwas associated with prenatal maternal folate and socio-economic status.In-vitrocharacterization confirmed a regulatory effect ofSOCS3mon gene expression. Our findings suggest that epigenetic modifications may play an important role in driving child height in LMIC.
Universal closed-tube barcoding for monitoring the shark and ray trade in megadiverse conservation hotspots
Authors: Prasetyo Andhika P. , Cusa Marine , Murray Joanna M. , Agung Firdaus , Muttaqin Efin , Mariani Stefano , McDevitt Allan D. 
Published: December 2022

SummaryTrade restrictions for many endangered elasmobranch species exist to disincentivise their exploitation and curb their declines. However, the variety of products and the complexity of import/export routes make trade monitoring challenging. We investigate the use of a portable, universal, DNA-based tool which would greatly facilitatein-situmonitoring. We collected shark and ray samples across the Island of Java, Indonesia, and selected 28 species (including 22 CITES-listed species) commonly encountered in landing sites and export hubs to test a recently developed real-time PCR single-assay originally developed for screening bony fish. We employed a deep learning algorithm to recognize species based on DNA melt-curve signatures. By combining visual and machine learning assignment methods, we distinguished 25 out of 28 species, 20 of which were CITES-listed. With further refinement, this method can provide a practical tool for monitoring elasmobranch trade worldwide, without the need for a lab or the bespoke design of species-specific assays.HighlightsWe applied a portable, universal, closed-tube DNA barcoding approach originally developed for bony fishes to distinguish between shark and ray species traded in Indonesia.We built a deep machine learning model to automatically assign species from the qPCR fluorescence spectra produced by two barcodesThe model achieved 79.41% accuracy for classifying 28 elasmobranch species, despite the barcode regions being designed for teleost speciesThis tool can serve as a potent single-assayin-situdiagnostic tool to regulate trade operations and it will be significantly enhanced by further optimisation of the barcode regions to fit elasmobranch DNA sequence variation
The Class VIII myosin ATM1 is required for root apical meristem function
Authors: Olatunji Damilola , Clark Natalie M. , Kelley Dior R. 
Published: December 2022

AbstractMyosins are evolutionarily conserved motor proteins that interact with actin filaments to regulate organelle transport, cytoplasmic streaming and cell growth. Plant-specific Class XI myosin proteins direct cell division and root organogenesis. However, the roles of plantspecific Class VIII myosin proteins in plant growth and development are less understood. Here, we investigated the function of an auxin-regulated Class VIII myosin, Arabidopsis thaliana Myosin 1 (ATM1), using genetics, transcriptomics, and live cell microscopy.ATM1is expressed in the primary root, adventitious roots and throughout lateral root development. ATM1 is a plasma membrane localized protein that is enriched in actively dividing cells in the root apical meristem (RAM). Loss ofATM1function results in impaired primary root growth due to decreased RAM size and reduced cell proliferation in a sugar-dependent manner. InATM1loss-of-function roots, columella reporter gene expression is diminished, and fewer columella stem cell divisions occur. In addition,atm1-1roots displayed reduced auxin responses and auxin marker gene expression. Complementation ofatm1-1with a tagged ATM1 driven under the nativeATM1promoter restored root growth and cell cycle progression in the root meristem. Collectively, these results provide novel evidence that ATM1 functions to influence cell proliferation and columella differentiation in primary roots in response to auxin and sugar cues.
Time of day analysis over a field grown developmental time course in rice
Authors: Michael Todd P. 
Published: December 2022

ABSTRACTPlants integrate time of day (TOD) information over an entire season to ensure optimal growth, flowering time, and grain fill. However, most TOD expression studies have focused on a limited number of combinations of daylength and temperature under laboratory conditions. Here we re-analyze anOryza sativa(rice) expression study that followed TOD expression in the field over an entire growing season. We find that likeArabidopsis thaliana, almost all rice genes have a TOD specific expression over the developmental time course. As has been suggested in other grasses, thermocycles were a stronger cue for TOD expression than the photocycles over the growing season. All the core circadian clock genes display consistent TOD expression over the season with the interesting exception that the two grass paralogs ofEARLY FLOWERING 3(ELF3) display a distinct phasing based on the interaction between thermo- and photo-cycles. The dataset also revealed how specific pathways are modulated to distinct TOD over the season consistent with the changing biology. The data presented here provides a resource for researchers to study how TOD expression changes under natural conditions over a developmental time course, which will guide approaches to engineer more resilient and prolific crops.
Two common issues in synchronized multimodal recordings with EEG: Jitter and Latency
Authors: Iwama Seitaro , Takemi Mitsuaki , Eguchi Ryo , Hirose Ryotaro , Morishige Masumi , Ushiba Junichi 
Published: December 2022

AbstractMultimodal recording using electroencephalogram (EEG) and other biological signals (e.g., electromyograms, eye movement, pupil information, or limb kinematics) is ubiquitous in human neuroscience research. However, the precise time alignment of data from heterogeneous sources is limited due to variable recording parameters of commercially available research devices and experimental setups. Here, we introduced the versatility of a Lab Streaming Layer (LSL)-based application for multimodal recordings of high-density EEG and other devices such as eye trackers or hand kinematics. To introduce the benefit of recording multiple devices in a time-synchronized manner, we discuss two common issues in measuring multimodal data: jitter and latency. The LSL-based system can be used for research on precise time-alignment of datasets, such as detecting stimulus-induced transient neural responses and testing hypotheses well-formulated in time by leveraging the millisecond time resolution of the system.
Mechanism of receptor assembly via the pleiotropic adipokine Leptin
Authors: Tsirigotaki Alexandra , Dansercoer Ann , Verschueren Koen H.G. , Marković Iva , Pollmann Christoph , Hafer Maximillian , Felix Jan , Birck Catherine , Van Putte Wouter , Catteeuw Dominiek , Tavernier Jan , Bazan J. Fernando , Piehler Jacob , Savvides Savvas N. , Verstraete Kenneth 
Published: December 2022

AbstractThe adipokine Leptin activates its type I cytokine receptor (LEP-R) in the hypothalamus to regulate body weight and exerts additional pleiotropic functions in immunity, fertility, and cancer. However, the structure and mechanism of Leptin-mediated LEP-R assemblies has remained unclear. Here, we show that Leptin:LEP-R assemblies adopt an unprecedented structure within the type I cytokine receptor family featuring 3:3 stoichiometry. We validate Leptin-induced trimerization of LEP-R in the plasma membrane of living cells via multicolor single molecule microscopy. In mediating such assemblies Leptin undergoes drastic restructuring that activates its site III for binding to the Ig-domain of an adjacent LEP-R molecule in the complex. These interactions are abolished by pathological mutations linked to obesity. Collectively, our study uncovers an evolutionarily conserved Leptin:LEP-R assembly as a new mechanistic blueprint for Leptin-mediated signaling in physiology and disease, including insights into how the lowly abundant signaling-competent isoforms of LEP-R can productively participate in signaling.
The potential role of human immune cells in the systemic dissemination of enterovirus-D68
Authors: Laksono Brigitta M. , Na Ayudhya Syriam Sooksawasdi , Aguilar-Bretones Muriel , Embregts Carmen W. E. , van Nierop Gijsbert P , van Riel Debby 
Published: December 2022

AbstractEnterovirus-D68 (EV-D68) often causes mild respiratory infections, but can also cause severe respiratory infections and extra-respiratory complications, including acute flaccid myelitis (AFM). Systemic dissemination of EV-D68 is crucial for the development of extra-respiratory diseases, but it is currently unclear how EV-D68 viremia occurs. We hypothesize that immune cells contribute to the systemic dissemination of EV-D68, as this is a mechanism commonly used by other enteroviruses. Therefore, we investigated the susceptibility and permissiveness of human primary immune cells for different EV-D68 isolates. In human peripheral blood mononuclear cells (PBMC) inoculated with EV-D68, only B cells were susceptible but virus replication was limited. However, B cell-rich cultures, such as Epstein-Barr virus-transformed B-lymphoblastoid cell line (BLCL) and primary lentivirus-transduced B cells, were productively infected. In BLCL, neuraminidase treatment to remove α2,6- and α2,3-linked sialic acids resulted in a significant decrease of EV-D68 infected cells, suggesting that sialic acids are the functional receptor on B cells. Subsequently, we showed that dendritic cells (DCs), particularly immature DCs, are susceptible and permissive for EV-D68 infection and that they can spread EV-D68 to autologous BLCL. Altogether, our findings suggest that immune cells, especially B cells and DCs, play an important role in the development the systemic dissemination of EV-D68 during an infection, which is an essential step towards the development of extra-respiratory complications.Author summaryEnterovirus D68 (EV-D68) is an emerging respiratory virus that has caused outbreaks worldwide since 2014. EV-D68 infects primarily respiratory epithelial cells and the infection commonly results in mild respiratory diseases. However, EV-D68 infection is also associated with complications outside the respiratory tract, including a polio-like paralysis. Despite the severity of these extra-respiratory complications, it is unclear how EV-D68 is able to spread outside the respiratory tract and infect other organs, like the central nervous system (CNS). To understand this, we investigated if immune cells play a role in the extra-respiratory spread of EV-D68. We showed that EV-D68 can infect and replicate in specific immune cells,i.e. B cells and dendritic cells (DCs), and that the virus can be transferred from DCs to B cells. Our findings suggest that lymphoid tissues, which harbor many immune cells, can be a secondary replication site for EV-D68, from where virus is released in the circulation. Our data reveal the importance of immune cells in the systemic spread of EV-D68, which is essential for infection of extra-respiratory tissues. Intervention strategies that prevent EV-D68 infection of immune cells will therefore potentially prevent virus spread from the respiratory tract to other organs.
Prior Knowledge Biases the Perception of Body Postures
Authors: Han Qiu , Gandolfo Marco , Peelen Marius V. 
Published: December 2022

AbstractBody postures provide information about others’ actions, intentions, and emotional states. However, little is known about how postures are represented in the brain’s visual system. Considering our extensive visual and motor experience with body postures, we hypothesized that priors derived from this experience may systematically bias visual body posture representations. We examined two priors: gravity and biomechanical constraints. Gravity pushes lifted body parts downwards, while biomechanical constraints limit the range of possible postures (e.g., an arm raised far behind the head cannot go down further). Across three experiments (N = 246) we probed participants’ memory of briefly presented postures using change discrimination and adjustment tasks. Results showed that lifted arms were misremembered as lower and as more similar to biomechanically plausible postures. Inverting the body stimuli eliminated both biases, implicating holistic body processing. Together, these findings show that knowledge shapes body posture representations, reflecting modulation from a combination of category-general and category-specific priors.
Reduced GS domain serine/threonine requirements of Fibrodysplasia Ossificans Progressiva mutant type I BMP receptor ACVR1 in the zebrafish
Authors: Allen Robyn S. , Jones William D. , Hale Maya , Warder Bailey N. , Shore Eileen M. , Mullins Mary C. 
Published: December 2022

AbstractFibrodysplasia ossificans progressiva (FOP) is a rare human genetic condition characterized by altered skeletal development and extra-skeletal bone formation. All cases of FOP are caused by mutations in the type I BMP receptor geneACVR1that result in over-activation of the BMP signaling pathway. Activation of the wild-type ACVR1 kinase requires assembly of a tetrameric type I and II BMP receptor complex followed by phosphorylation of the ACVR1 GS domain by type II BMP receptors. Previous studies showed that the FOP mutant ACVR1-R206H requires type II BMP receptors and presumptive GS domain phosphorylation for over-active signaling. Structural modeling of the FOP-ACVR1 mutant kinase domain supports that FOP mutations alter the conformation of the GS domain, but it is unclear how this leads to overactive signaling. Here we show using a developing zebrafish embryo BMP signaling assay that the FOP mutant receptors ACVR1-R206H and -G328R have reduced requirements for GS domain phosphorylation sites to signal compared to wild-type ACVR1. Further, ligandindependent and ligand-dependent signaling through the FOP ACVR1 receptors have distinct GS domain phosphorylation site requirements. Moreover, ACVR1-G328 showed increased GS domain serine/threonine requirements for ligand-independent signaling compared to ACVR1-R206H, whereas it exhibited reduced serine/threonine requirements for ligand-dependent signaling. Remarkably, while ACVR1-R206H does not require the type I BMP receptor partner, Bmpr1, to signal, a ligand-dependent GS domain mutant of ACVR1-R206H could signal independently of Bmpr1 only when Bmp7 ligand was overexpressed. Of note, unlike human ACVR1-R206H, the zebrafish paralog Acvr1l-R203H does not show increased signaling activity. However, in domain-swapping studies the human kinase domain, but not the human GS domain, was sufficient to confer overactive signaling to the Acvr1l-R203H receptor. Together these results reflect the importance of GS domain activation and kinase domain functions in regulating ACVR1 signaling and identify mechanisms of reduced regulatory constraints conferred by FOP mutations.
Specialized metabolic convergence in the gut microbiomes of cycad-feeding insects tolerant to β-methylamino-L-alanine (BMAA)
Authors: Gutiérrez-García Karina , Whitaker Melissa R.L. , Bustos-Díaz Edder D. , Salzman Shayla , Ramos-Aboites Hilda E. , Reitz Zachary L. , Pierce Naomi E. , Cibrián-Jaramillo Angélica , Barona-Gómez Francisco 
Published: December 2022

AbstractIngestion of the cycad toxins β-methylamino-L-alanine (BMAA) and azoxyglycosides is harmful to diverse organisms. However, some insects are specialized to feed on toxin-rich cycads with apparent immunity. Some cycad-feeding insects possess a common set of gut bacteria, which might play a role in detoxifying cycad toxins. Here, we investigated the composition of gut microbiota from a worldwide sample of cycadivorous insects and characterized the biosynthetic potential of bacteria isolated as putative keystone taxa. Cycadivorous insects shared a core gut microbiome consisting of six bacterial taxa, mainly belonging to the Proteobacteria, which we were able to isolate. To further investigate these potential keystone taxa from diverging lineages, we performed shotgun metagenomic sequencing of co-cultured bacterial sub-communities. We postulate and characterize four putative keystone bacteria fromSerratia, Pantoea, and two differentStenotrophomonaslineages. The biosynthetic potential of these microorganisms includes a suite of biosynthetic gene clusters notably rich in siderophores and carotenoid-like aryl polyene pathways. Siderophore semi-untargeted metabolomics revealed a broad range of chemically related yet diverse iron-chelating metabolites, indicating a complex evolutionary landscape in which siderophores may have converged within the guts of cycadivorous insects. Among these, we provide evidence of the occurrence of an unprecedent desferrioxamine-like biosynthetic pathway that remains to be identified. These results provide a foundation for future investigations into how cycadivorous insects tolerate diets rich in azoxyglycosides, BMAA, and other cycad toxins, and highlight convergent evolution underlying chemical diversity.
Cortical networks relating to arousal are differentially coupled to neural activity and hemodynamics
Authors: Meyer-Baese Lisa , Morrissette Arthur , Wang Yunmiao , Le Chatelier Brune , Borden Peter , Keilholz Shella , Stanley Garrett , Jaeger Dieter 
Published: December 2022

AbstractEven in the absence of specific sensory input or a behavioral task, the brain produces structured patterns of activity. This organized activity is modulated by changes in arousal. Here, we use wide-field voltage imaging to establish how arousal relates to cortical network voltage and hemodynamic activity in spontaneously behaving head-fixed male and female mice expressing the voltage-sensitive fluorescent FRET sensor Butterfly 1.2. We find that global voltage and hemodynamic signals are both positively correlated with changes in arousal with a maximum correlation of 0.5 and 0.25 respectively at a time lag of 0 seconds. We next show that arousal influences distinct cortical regions for both voltage and hemodynamic signals. These include a broad positive correlation across most sensory-motor cortices extending posteriorly to the primary visual cortex observed in both signals. In contrast, activity in prefrontal cortex is positively correlated to changes in arousal for the voltage signal while it is a slight net negative correlation observed in the hemodynamic signal. Additionally, we show that coherence between voltage and hemodynamic signals relative to arousal is strongest for slow frequencies below 0.15 Hz and is near zero for frequencies greater than 1Hz. We finally show that coupling patterns are dependent on the behavioral state of the animal with correlations being driven by periods of increased orofacial movement. Our results indicate that while hemodynamic signals show strong relations to behavior and arousal, these relations are distinct from those observed by voltage activity.Significance StatementWe leverage wide-field voltage imaging to examine the relation between cortical changes in membrane potential dynamics and hemodynamics. These two signals are then examined with respect to changes in arousal, as measured by pupil diameter, in awake head fixed mice. Our results show similarities as well as important differences in the correlation of arousal with neuronal population activity dynamics and the hemodynamic signal. Further, the spatial activity correlation maps with arousal depended differentially on the behavioral state of the animal in a frequency dependent manner. Our results indicate that the modulation of brain networks by arousal is dynamically regulated, and only partly overlap between functional networks determined from hemodynamic or voltage activity.