bluuebunny/crossref_metadata_2025_split huggingface dataset:
MpoxRadar: a worldwide Mpox genomic surveillance dashboard
Authors: Nasri Ferdous , Kongkitimanon Kunaphas , Wittig Alice , Cortés Jorge Sánchez , Brinkmann Annika , Nitsche Andreas , Schmachtenberg Anna-Juliane , Renard Bernhard Y. , Fuchs Stephan 
Published: February 2023

ABSTRACTMonkeypox (Mpox) is mutating at an exceptional rate for a DNA virus and its global spread is concerning, making genomic surveillance a necessity. With MpoxRadar, we provide an interactive dashboard to track virus variants on mutation level worldwide. MpoxRadar allows users to select among different genomes as reference for comparison. The occurrence of mutation profiles based on the selected reference is indicated on an interactive world map that shows the respective geographic sampling site in customizable time ranges to easily follow the frequency or trend of defined mutations. Furthermore, the user can filter for specific mutations, genes, countries, genome types, and sequencing protocols and download the filtered data directly from MpoxRadar. On the server, we automatically download all Mpox genomes and metadata from the National Center for Biotechnology Information (NCBI) on a daily basis, align them with the different reference genomes, generate mutation profiles, which are stored and linked to the available metainformation in a database. This makes MpoxRadar a practical tool for the genomic survaillance of Mpox, supporting users with limited computational resources. MpoxRadar is open-source and freely accessible athttps://MpoxRadar.net.GRAPHICAL ABSTRACT
Mouthparts of the bumblebee (Bombus terrestris)exhibit poor acuity for the detection of pesticides in nectar
Authors: Parkinson Rachel H. , Scott Jennifer , Dorling Anna L. , Jones Hannah , Haslam Martha , McDermott-Roberts Alex E. , Wright Geraldine A. 
Published: February 2023

AbstractBees are important pollinators of agricultural crops, but their populations are at risk when pesticides are used. One of the largest risks bees face is poisoning of floral nectar and pollen by insecticides. Studies of bee detection of neonicotinoids have reported contradictory evidence about whether bees can taste these pesticides in sucrose solutions and hence avoid them. Here, we use an assay for the detection of food aversion combined with single-sensillum electrophysiology to test whether the mouthparts of the buff-tailed bumblebee (Bombus terrestris) detect the presence of pesticides in a solution that mimicked the nectar of oilseed rape (Brassica napus). Bees did not avoid consuming solutions containing concentrations of imidacloprid, thiamethoxam, clothianidin, or sulfoxaflor spanning six orders of magnitude, even when these solutions contained lethal doses. Only extremely high concentrations of the pesticides altered spiking in gustatory neurons through a slight reduction in firing rate or change in the rate of adaptation. These data provide strong evidence that bumblebees cannot detect or avoid field-relevant concentrations of pesticides using information from their mouthparts. As bees rarely contact floral nectar with other body parts, we predict that they are at high risk of unwittingly consuming pesticides in the nectar of pesticide-treated crops.
Early detection of white matter hyperintensities using SHIVA-WMH detector
Authors: Tsuchida Ami , Boutinaud Philippe , Verrecchia Violaine , Tzourio Christophe , Debette Stéphanie , Joliot Marc 
Published: February 2023

AbstractWhite matter hyperintensities (WMH) are well-established markers of cerebral small vessel disease (cSVD), and are associated with an increased risk of stroke, dementia, and mortality. Although their prevalence increases with age, small and punctate WMHs have been reported with surprisingly high frequency even in young, neurologically asymptomatic adults. However, most automated methods to segment WMH published to date are not optimized for detecting small and sparse WMH. Here we present the SHIVA-WMH tool, a deep-learning (DL)-based automatic WMH segmentation tool that has been trained with manual segmentations of WMH in a wide range of WMH severity. We show that it is able to detect WMH with high efficiency in subjects with only small punctate WMH as well as in subjects with large WMHs (i.e. with confluency) in evaluation datasets from three distinct databases: MRi-Share consisting of young university students, MICCAI 2017 WMH challenge dataset consisting of older patients from memory clinics, and UK Biobank with community-dwelling middle-aged and older adults. Across these three cohorts with a wide-ranging WMH load, our tool achieved voxel-level and individual lesion cluster-level Dice scores of 0.66 and 0.71, respectively, which were higher than for three reference tools tested: the lesion prediction algorithm implemented in the lesion segmentation toolbox (LST-LPA: Schmidt, 2017), PGS tool, a DL-based algorithm and the current winner of the MICCAI 2017 WMH challenge (Park et al, 2021), and HyperMapper tool (HPM: Mojiri Forooshani et al., 2022), another DL-based method with high reported performance in subjects with mild WMH burden. Our tool is publicly and openly available to the research community to facilitate investigations of WMH across a wide range of severity in other cohorts, and to contribute to our understanding of the emergence and progression of WMH.HighlightsWe propose a novel 3D Unet-based model, SHIVA-WMH detector, with much improved detection of small WMH across subjects with a wide range of WMH burden compared to existing methodsWe characterize microstructural properties of small white matter hyperintensities in young adults from MRi-Share study
One does not simply grow well: Performance of grassland plants in home and foreign soil and climate
Authors: Aares Karoline H. , Bockelie-Rosendahl Torunn , Priyadarshi Ribha , Pugnaire Francisco I. , Schöb Christian , Alifriqui Mohamed , Manrique Esteban , Jaakola Laura H. , Bråthen Kari Anne 
Published: February 2023

AbstractPlant-soil feedbacks (PSF) play a substantial role in determining plant performance in native and foreign habitats. Yet, PSF strength may be altered by climatic parameters, creating synergies. Here, we assess performance of alpine grassland species in their native and in foreign soils in an experiment including different climates.Using soil and seeds sampled from six alpine grassland sites spreading in a gradient from Northern Africa to Northern Europe, we compared plant performance in home soil and in five foreign soils, as well as home and foreign climates (simulated temperature and photoperiod in growth chambers).We found that despite a high variability in plant performance between sites, plants generally performed better in their home soil and home climate, than in foreign soil or in foreign climate. However, an interaction between soil and climate effect caused this better performance in home soil to occur only when in foreign climate. Similarly, performance improved in home climate only when plants were also placed in foreign soil.Synthesis: In contrast to predictions from the literature, no benefit from growing in foreign soils are indicated. At least on the short term, climate change alone is not suggested to affect native grassland plant performance. However, when introduced to a habitat with a similar climate to their native habitat, plants may perform as well as in their native range, but when introduced both to a new soil and climate, plants will do poorly. This finding sheds light on the interactive effect of climate and soil origin, as well as the possible success of plant introductions under a changing climate.
Bilayer charge asymmetry and oil residues destabilize membranes upon poration
Authors: Leomil Fernanda S. C. , Stephan Mareike , Pramanik Shreya , Riske Karin A. , Dimova Rumiana 
Published: February 2023

AbstractTransmembrane asymmetry is ubiquitous in cells, particularly with respect to lipids, where charged lipids are mainly restricted to one monolayer. We investigate the influence of anionic lipid asymmetry on the stability of giant unilamellar vesicles (GUVs), minimal plasma membrane models. To quantify asymmetry, we apply the fluorescence quenching assay, which is often difficult to reproduce and caution in handling the quencher is generally underestimated. Thus, we first optimize this assay and then apply it to GUVs prepared with the inverted emulsion transfer protocol using increasing fractions of anionic lipids restricted to one leaflet. This protocol is found to produce highly asymmetric bilayers, but with ∼20% interleaflet mixing. To probe the stability of asymmetric vs symmetric membranes, we expose the GUVs to porating electric pulses and monitor the fraction of destabilized vesicles. The pulses open macropores, and the GUVs either completely recover or exhibit leakage or bursting/collapse. Residual oil destabilizes porated membranes and destabilization is even more pronounced in asymmetrically charged membranes. This is corroborated by the measured pore edge tension decrease with increasing charge asymmetry. Using GUVs with membranes with imposed transmembrane pH asymmetry, we confirm that poration-triggered destabilization does not depend on the approach used to generate membrane asymmetry.
Evolution of the jasmonate ligands and their biosynthetic pathways
Authors: Chini Andrea , Monte Isabel , Zamarreño Angel M. , García-Mina José M. , Solano Roberto 
Published: February 2023

SummaryJasmonates are phytohormones that regulate multiple aspects of plant development and responses to stress, activating a conserved signaling pathway in land plants. The characterization of jasmonates biosynthetic and signaling pathways revealed that (+)-7-iso-JA-Ile (JA-Ile) is the ligand for the COI1/JAZ receptor in angiosperms, where jasmonates are synthesized through the OPR3-dependent or OPR3-independent pathways. More recently, studies on different model species identified dn-cis-OPDA, dn-iso-OPDA and Δ4-dn-iso-OPDA as the ligands of the COI1/JAZ receptor in the liverwortMarchantia polymorpha, and a receptor-independent role for several jasmonates in streptophytes. To understand the distribution of bioactive jasmonates in the green lineage and how their biosynthetic pathways evolved, we combined phylogenetic analyses and jasmonates metabolomics in representative species from different lineages. We found that both OPDA and dn-cis-OPDA are ubiquitous in land plants and present also in charophyte algae, underscoring their importance as ancestral signalling molecules. In contrast, JA-Ile biosynthesis emerged within lycophytes coincident with the evolutionary appearance of JAR1 function. We show that JA biosynthesis mediated by OPR1/OPR2 appeared in charophytes most likely as a degradation pathway of OPDA/dn-cis-OPDA before OPR3 emergence. Therefore, our results demonstrate that the OPR3-independent JA biosynthesis pathway is ancient and predates the evolutionary appearance of the OPR3-dependent pathway. Moreover, we identified a negative correlation between dn-iso-OPDA and JA-Ile in land plants which supports that dn-iso-OPDA is the relevant form of the hormone perceived by COI1/JAZ in bryophytes and lycophytes.
Non-asymptotic transients away from steady states determine cellular responsiveness to dynamic spatial-temporal signals
Authors: Nandan Akhilesh , Koseska Aneta 
Published: February 2023

AbstractMajority of the theory on cell polarization and the understanding of cellular sensing and responsiveness to localized chemical cues has been based on the idea that non-polarized and polarized cell states can be represented by stable asymptotic switching between them. The existing model classes that describe the dynamics of signaling networks underlying polarization are formulated within the framework of autonomous systems. However these models do not simultaneously capture both, robust maintenance of polarized state longer than the signal duration, and retained responsiveness to signals with complex spatial-temporal distribution. Based on recent experimental evidence for criticality organization of biochemical networks, we challenge the current concepts and demonstrate that non-asymptotic signaling dynamics arising at criticality uniquely ensures optimal responsiveness to changing chemoattractant fields. We provide a framework to characterize non-asymptotic dynamics of system’s state trajectories through a non-autonomous treatment of the system, further emphasizing the importance of (long) transient dynamics, as well as the necessity to change the mathematical formalism when describing biological systems that operate in changing environments.
Host space, not energy or symbiont size, constrains feather mite abundance across passerine bird species
Authors: del Mar Labrador María , Serrano David , Doña Jorge , Aguilera Eduardo , Arroyo José L. , Atiénzar Francisco , Barba Emilio , Bermejo Ana , Blanco Guillermo , Borràs Antoni , Calleja Juan A. , Cantó José L. , Cortés Verónica , De la Puente Javier , De Palacio Diana , Fernández-González Sofía , Figuerola Jordi , Frías Óscar , Fuertes-Marcos Benito , Garamszegi László Z. , Gordo Óscar , Gurpegui Míriam , Kovács István , Martínez José L. , Meléndez Leandro , Mestre Alexandre , Møller Anders P. , Monrós Juan S. , Moreno-Opo Rubén , Navarro Carlos , Pap Péter L. , Pérez-Tris Javier , Piculo Rubén , Ponce Carlos , Proctor Heather , Rodríguez Rubén , Sallent Ángel , Senar Juan Carlos , Tella José L. , Vágási Csongor I. , Vögeli Matthias , Jovani Roger 
Published: February 2023

AbstractComprehending symbiont abundance among host species is a major ecological endeavour, and the metabolic theory of ecology has been proposed to understand what constraints symbiont populations. We parameterized metabolic theory equations to predict how bird species’ body size and the body size of their feather mites relate to mite abundance according to four potential energy (microbial abundance, uropygial gland size) and space constraints (wing area, number of feather barbs). Predictions were compared with the empirical scaling of feather mite abundance from 26,604 birds of 106 passerine species, using phylogenetic modelling and quantile regression. Feather mite populations were strongly constrained by host space (number of feather barbs) and not energy. Moreover, feather mite species’ body size was unrelated to their abundance or to the body size of their host species. We discuss the implications of our results for our understanding of the bird-feather mite system and for symbiont abundance in general.
Novel microRNAs downregulated in breast cancer tumors bind to the 3’UTR of SNAIL, SLUG, ZEB1 and/or TWIST and decrease metastatic behavior in breast cancer cells
Authors: Pérez-Moreno Elisa , Ortega-Hernández Victoria , Zavala Valentina A , Gamboa Jorge , Fernández Wanda , Carvallo Pilar 
Published: February 2023

AbstractMetastasis, the leading cause of cancer-associated deaths, is promoted by transcription factors SNAIL, SLUG, ZEB1 and TWIST through the activation of epithelial-mesenchymal transition (EMT). MicroRNAs can suppress EMT, emerging as candidate molecular biomarkers and novel therapeutic targets. Herein, we evaluated microRNAs downregulated in breast cancer tissues expressing EMT transcription factors, to find new potential regulators of EMT. MiR-30a, miR-1271, miR-196a, miR-202, miR-210, miR-22, miR-331 and miR-34b were validated. Seven microRNAs downregulated luciferase activity through EMT transcription factors 3’UTR, and all microRNAs decreased cell migration, invasion and/or proliferation. In MDA-MB-231 cells, miR-196a and miR-22 decreased endogenous ZEB1 levels, and miR-30a endogenous CCR7 levels. These results suggest that microRNAs studied are novel regulators of EMT through the control of SNAIL, SLUG, ZEB1 and TWIST. They also regulate the metastatic behavior of cancer cells, and may control the development of lymph node metastasis through the regulation of CCR7.Graphical abstract
Assignment of molecular origins of NOE signal at −3.5 ppm in the brain
Authors: Zhao Yu , Sun Casey , Zu Zhongliang 
Published: February 2023

ABSTRACTPurposeNuclear Overhauser Enhancement mediated saturation transfer effect, termed NOE(−3.5 ppm), is a major source of chemical exchange saturation transfer (CEST) MRI contrasts at 3.5 ppm in the brain. Previous phantom experiments have demonstrated that both proteins and lipids, two major components in tissues, have substantial contributions to NOE(−3.5 ppm) signals. Their relative contributions in tissues are informative for the interpretation of NOE(−3.5 ppm) contrasts that could provide potential imaging biomarkers for relevant diseases, which remain incompletely understood.MethodsExperiments on homogenates and supernatants of brain tissues collected from healthy rats, that could isolate proteins from lipids, were performed to evaluate the relative contribution of lipids to NOE(−3.5 ppm) signals. On the other hand, experiments on ghost membranes with varied pH, and reconstituted phospholipids with different chemical compositions were conducted to study the dependence of NOE(−3.5 ppm) on physiological conditions. Besides, CEST imaging on rat brains bearing 9L tumors and healthy rat brains was performed to analyze the causes of the NOE(−3.5 ppm) contrast variations between tumors and normal tissues, and between gray matter and white matter.ResultsOur experiments reveal that lipids have dominant contributions to the NOE (−3.5 ppm) signals. Further analysis suggests that decreased NOE(−3.5 ppm) signals in tumors and higher NOE(−3.5 ppm) signals in white matter than in gray matter are mainly explained by changes in membrane lipids, rather than proteins.ConclusionNOE(−3.5 ppm) could be exploited as a highly sensitive MRI contrast for imaging membrane lipids in the brain.
Docking Domain Engineering in a Modular Polyketide Synthase and its Impact on Structure and Function
Authors: Buyachuihan Lynn , Zhao Yue , Schelhas Christian , Grininger Martin 
Published: February 2023

AbstractModular polyketide synthases (PKSs) are attractive targets for the directed, biosynthetic production of platform chemicals and pharmaceuticals by protein engineering. In this study, we analyze docking domains from the 6-deoxyerythronolide B synthase, SYNZIP domains, and the SpyCatcher:SpyTag complex as engineering tools to couple the polypeptides VemG and VemH to functional venemycin synthases. Our data show that the high-affinity interaction or covalent connection of modules, enabled by SYNZIP domains and the SpyCatcher:SpyTag complex, can be advantageous, e.g., in synthesis at low protein concentrations, but their rigidity and steric demand decrease synthesis rates. However, we also show that efficiency can be recovered when inserting a hinge region distant from the rigid interface. This study demonstrates that engineering approaches should take the conformational properties of modular PKSs into account and establishes a three-polypeptide split-venemycin synthase as an exquisitein vitroplatform for the analysis and engineering of modular PKSs.
Integrated control of non-motor and motor efforts during decision between actions
Authors: Leroy Élise , Koun Éric , Thura David 
Published: February 2023

ABSTRACTHumans daily life is characterized by a succession of voluntary actions. Since energy resources are limited, the ability to invest the appropriate amount of effort for selecting and executing these actions is a hallmark of adapted behavior. Recent studies indicate that decisions and actions share important principles, including the exchange of temporal resources when the context requires it. In the present study, we test the hypothesis that the management of energy resources is shared between decision and action too. Healthy human subjects performed a perceptual decision task where they had to choose between two levels of effort to invest in making the decision, and report it with a reaching movement. Crucially, motor difficulty gradually increased from trial to trial depending on participants’ decision performance. Results indicate a relatively mild impact of the increasing motor difficulty on the choice of the non-motor (decision) effort to invest in each trial and on decision performance. By contrast, motor performance strongly decreased depending on both the motor and decisional difficulties. Together, the results support the hypothesis of an integrated management of energy resources between decision and action. They also suggest that in the context of the present task, the mutualized resources are primarily allocated to the decision-making process to the detriment of movements.
Loss of RdDM-independent CHH methylation is sufficient for disruption of chromosome-specific rRNA gene silencing
Authors: McKinlay Anastasia , Enganti Ramya , Puppala Navinchandra V. , Saradadevi Gargi P. , Blevins Todd , Mohannath Gireesha 
Published: February 2023

SummaryArabidopsis thaliana has two nucleolus organizer regions (NORs), consisting of long tandem arrays of 45S rRNA genes on chromosomes 2 (NOR2) and 4 (NOR4). The rRNA gene subtypes mapping to NOR2 are mostly silenced during development, whereas those mapping to NOR4 are active. By analyzing DNA methylation-deficient Arabidopsis mutants, we found that the degree of disruption of NOR2 rRNA gene silencing correlates consistently with the loss of rDNA cytosine methylation in the CHH sequence context, rather than with methylation losses in CG or CHG contexts. Comparison of Arabidopsis and tomato NOR sequences revealed that rRNA gene promoter cytosines mostly occur in the CHH context, followed by fewer sites in the CHG context. By contrast, almost no CG dinucleotides occur in plant rRNA gene promoters. This prevalence of CHH sites in plant rDNA promoters suggests a mechanism to explain the stronger disruption of NOR2 gene silencing in CHH methylation mutants lacking CHROMOMETHYLASE 2 (CMT2) or DECREASE IN DNA METHYLATION 1 (DDM1) functions as compared to other DNA methylation-deficient mutant lines. Notably, CMT2 mediates CHH methylation independently of RNA-directed DNA methylation factors but with a requirement for the chromatin remodeler DDM1. Furthermore, we demonstrate that NOR2 genes are hypermethylated and exist in more condensed chromatin than NOR4 genes. Collectively, our data define a critical role for CHH methylation in plant rRNA gene silencing, which is mostly mediated by CG methylation in mammals.Significance StatementIn plants, DNA cytosine methylation occurs in three sequence contexts (CG, CHG, and CHH), but it was not clear how these distinct contexts contribute to chromosome-specific large-scale rRNA gene silencing. Using rRNA gene expression, methylation assays, and bioinformatic analysis of rDNA promoters and methylation patterns, this study shows that CHH methylation, rather than CG or CHG methylation, plays a critical role in plant rRNA gene silencing, which is mostly mediated by CG methylation in mammals.