bluuebunny/crossref_metadata_2025_split huggingface dataset:
Selection-driven trait loss in independently evolved cavefish populations
Authors: Moran Rachel L. , Richards Emilie J. , Ornelas-García Claudia Patricia , Gross Joshua B. , Donny Alexandra , Wiese Jonathan , Keene Alex C. , Kowalko Johanna E. , Rohner Nicolas , McGaugh Suzanne E. 
Published: May 2023

AbstractLaboratory studies have demonstrated that a single phenotype can be produced by many different genotypes; however, in natural systems, it is frequently found that phenotypic convergence is due to parallel genetic changes. This suggests a substantial role for constraint and determinism in evolution and indicates that certain mutations are more likely to contribute to phenotypic evolution. Here we use whole genome resequencing in the Mexican tetra, Astyanax mexicanus, to investigate how selection has shaped the repeated evolution of both trait loss and enhancement across independent cavefish lineages. We show that selection on standing genetic variation and de novo mutations both contribute substantially to repeated adaptation. Our findings provide empirical support for the hypothesis that genes with larger mutational targets are more likely to be the substrate of repeated evolution and indicate that features of the cave environment may impact the rate at which mutations occur.
Mid-infrared analogue polaritonic reversed Cherenkov radiation in natural anisotropic crystals
Authors: Guo Xiangdong , Wu Chenchen , Zhang Shu , Hu Debo , Zhang Shunping , Jiang Qiao , Dai Xiaokang , Duan Yu , Yang Xiaoxia , Sun Zhipei , Zhang Shuang , Xu Hongxing , Dai Qing 
Published: May 2023

AbstractCherenkov radiation (CR) excited by fast charges can serve as on-chip light sources with a nanoscale footprint and broad frequency range. The reversed CR, which usually occurs in media with the negative refractive index or negative group-velocity dispersion, is highly desired because it can effectively separate the radiated light from fast charges thanks to the obtuse radiation angle. However, reversed CR at the mid-infrared remains challenging due to the significant loss of conventional artificial structures. Here we observe mid-infrared analogue polaritonic reversed CR in a natural van der Waals (vdW) material (i.e., α-MoO3), whose hyperbolic phonon polaritons exhibit negative group velocity. Further, the real-space image results of analogue polaritonic reversed CR indicate that the radiation distributions and angles are closely related to the in-plane isofrequency contours of α-MoO3, which can be further tuned in the heterostructures based on α-MoO3. This work demonstrates that natural vdW heterostructures can be used as a promising platform of reversed CR to design on-chip mid-infrared nano-light sources.
Bacterial capsular polysaccharides with antibiofilm activity share common biophysical and electrokinetic properties
Authors: Bernal-Bayard Joaquín , Thiebaud Jérôme , Brossaud Marina , Beaussart Audrey , Caillet Céline , Waldvogel Yves , Travier Laetitia , Létoffé Sylvie , Fontaine Thierry , Rokbi Bachra , Talaga Philippe , Beloin Christophe , Mistretta Noëlle , Duval Jérôme F. L. , Ghigo Jean-Marc 
Published: May 2023

AbstractBacterial biofilms are surface-attached communities that are difficult to eradicate due to a high tolerance to antimicrobial agents. The use of non-biocidal surface-active compounds to prevent the initial adhesion and aggregation of bacterial pathogens is a promising alternative to antibiotic treatments and several antibiofilm compounds have been identified, including some capsular polysaccharides released by various bacteria. However, the lack of chemical and mechanistic understanding of the activity of these polymers limits their use to control biofilm formation. Here, we screen a collection of 31 purified capsular polysaccharides and first identify seven new compounds with non-biocidal activity against Escherichia coli and/or Staphylococcus aureus biofilms. We measure and theoretically interpret the electrophoretic mobility of a subset of 21 capsular polysaccharides under applied electric field conditions, and we show that active and inactive polysaccharide polymers display distinct electrokinetic properties and that all active macromolecules share high intrinsic viscosity features. Despite the lack of specific molecular motif associated with antibiofilm properties, the use of criteria including high density of electrostatic charges and permeability to fluid flow enables us to identify two additional capsular polysaccharides with broad-spectrum antibiofilm activity. Our study therefore provides insights into key biophysical properties discriminating active from inactive polysaccharides. The characterization of a distinct electrokinetic signature associated with antibiofilm activity opens new perspectives to identify or engineer non-biocidal surface-active macromolecules to control biofilm formation in medical and industrial settings.
Parabolic avalanche scaling in the synchronization of cortical cell assemblies
Authors: Capek Elliott , Ribeiro Tiago L. , Kells Patrick , Srinivasan Keshav , Miller Stephanie R. , Geist Elias , Victor Mitchell , Vakili Ali , Pajevic Sinisa , Chialvo Dante R. , Plenz Dietmar 
Published: May 2023

AbstractNeurons in the cerebral cortex fire coincident action potentials during ongoing activity and in response to sensory inputs. These synchronized cell assemblies are fundamental to cortex function, yet basic dynamical aspects of their size and duration are largely unknown. Using 2-photon imaging of neurons in the superficial cortex of awake mice, we show that synchronized cell assemblies organize as scale-invariant avalanches that quadratically grow with duration. The quadratic avalanche scaling was only found for correlated neurons, required temporal coarse-graining to compensate for spatial subsampling of the imaged cortex, and suggested cortical dynamics to be critical as demonstrated in simulations of balanced E/I-networks. The corresponding time course of an inverted parabola with exponent of χ = 2 described cortical avalanches of coincident firing for up to 5 s duration over an area of 1 mm2. These parabolic avalanches maximized temporal complexity in the ongoing activity of prefrontal and somatosensory cortex and in visual responses of primary visual cortex. Our results identify a scale-invariant temporal order in the synchronization of highly diverse cortical cell assemblies in the form of parabolic avalanches.
Multidimensional cerebellar computations for flexible kinematic control of movements
Authors: Markanday Akshay , Hong Sungho , Inoue Junya , De Schutter Erik , Thier Peter 
Published: May 2023

AbstractBoth the environment and our body keep changing dynamically. Hence, ensuring movement precision requires adaptation to multiple demands occurring simultaneously. Here we show that the cerebellum performs the necessary multi-dimensional computations for the flexible control of different movement parameters depending on the prevailing context. This conclusion is based on the identification of a manifold-like activity in both mossy fibers (MFs, network input) and Purkinje cells (PCs, output), recorded from monkeys performing a saccade task. Unlike MFs, the PC manifolds developed selective representations of individual movement parameters. Error feedback-driven climbing fiber input modulated the PC manifolds to predict specific, error type-dependent changes in subsequent actions. Furthermore, a feed-forward network model that simulated MF-to-PC transformations revealed that amplification and restructuring of the lesser variability in the MF activity is a pivotal circuit mechanism. Therefore, the flexible control of movements by the cerebellum crucially depends on its capacity for multi-dimensional computations.
Unveiling an indole alkaloid diketopiperazine biosynthetic pathway that features a unique stereoisomerase and multifunctional methyltransferase
Authors: Deletti Garrett , Green Sajan D. , Weber Caleb , Patterson Kristen N. , Joshi Swapnil S. , Khopade Tushar M. , Coban Mathew , Veek-Wilson James , Caulfield Thomas R. , Viswanathan Rajesh , Lane Amy L. 
Published: May 2023

AbstractThe 2,5-diketopiperazines are a prominent class of bioactive molecules. The nocardioazines are actinomycete natural products that feature a pyrroloindoline diketopiperazine scaffold composed of two D-tryptophan residues functionalized by N- and C-methylation, prenylation, and diannulation. Here we identify and characterize the nocardioazine B biosynthetic pathway from marine Nocardiopsis sp. CMB-M0232 by using heterologous biotransformations, in vitro biochemical assays, and macromolecular modeling. Assembly of the cyclo-L-Trp-L-Trp diketopiperazine precursor is catalyzed by a cyclodipeptide synthase. A separate genomic locus encodes tailoring of this precursor and includes an aspartate/glutamate racemase homolog as an unusual D/L isomerase acting upon diketopiperazine substrates, a phytoene synthase-like prenyltransferase as the catalyst of indole alkaloid diketopiperazine prenylation, and a rare dual function methyltransferase as the catalyst of both N- and C-methylation as the final steps of nocardioazine B biosynthesis. The biosynthetic paradigms revealed herein showcase Nature’s molecular ingenuity and lay the foundation for diketopiperazine diversification via biocatalytic approaches.
Rhodium nanoparticles supported on silanol-rich zeolites beyond the homogeneous Wilkinson’s catalyst for hydroformylation of olefins
Authors: Liu Yifeng , Liu Zhiqiang , Hui Yu , Wang Liang , Zhang Jian , Yi Xianfeng , Chen Wei , Wang Chengtao , Wang Hai , Qin Yucai , Song Lijuan , Zheng Anmin , Xiao Feng-Shou 
Published: May 2023

AbstractHydroformylation is one of the largest industrially homogeneous processes that strongly relies on catalysts with phosphine ligands such as the Wilkinson’s catalyst (triphenylphosphine coordinated Rh). Heterogeneous catalysts for olefin hydroformylation are highly desired but suffer from poor activity compared with homogeneous catalysts. Herein, we demonstrate that rhodium nanoparticles supported on siliceous MFI zeolite with abundant silanol nests are very active for hydroformylation, giving a turnover frequency as high as ~50,000 h−1 that even outperforms the classical Wilkinson’s catalyst. Mechanism study reveals that the siliceous zeolite with silanol nests could efficiently enrich olefin molecules to adjacent rhodium nanoparticles, enhancing the hydroformylation reaction.
Pulcherriminic acid modulates iron availability and protects against oxidative stress during microbial interactions
Authors: Charron-Lamoureux Vincent , Haroune Lounès , Pomerleau Maude , Hall Léo , Orban Frédéric , Leroux Julie , Rizzi Adrien , Bourassa Jean-Sébastien , Fontaine Nicolas , d’Astous Élodie V. , Dauphin-Ducharme Philippe , Legault Claude Y. , Bellenger Jean-Philippe , Beauregard Pascale B. 
Published: May 2023

AbstractSiderophores are soluble or membrane-embedded molecules that bind the oxidized form of iron, Fe(III), and play roles in iron acquisition by microorganisms. Fe(III)-bound siderophores bind to specific receptors that allow microbes to acquire iron. However, certain soil microbes release a compound (pulcherriminic acid, PA) that, upon binding to Fe(III), forms a precipitate (pulcherrimin) that apparently functions by reducing iron availability rather than contributing to iron acquisition. Here, we use Bacillus subtilis (PA producer) and Pseudomonas protegens as a competition model to show that PA is involved in a peculiar iron-managing system. The presence of the competitor induces PA production, leading to precipitation of Fe(III) as pulcherrimin, which prevents oxidative stress in B. subtilis by restricting the Fenton reaction and deleterious ROS formation. In addition, B. subtilis uses its known siderophore bacillibactin to retrieve Fe(III) from pulcherrimin. Our findings indicate that PA plays multiple roles by modulating iron availability and conferring protection against oxidative stress during inter-species competition.
Epitaxial growth of highly symmetrical branched noble metal-semiconductor heterostructures with efficient plasmon-induced hot-electron transfer
Authors: Zhai Li , Gebre Sara T. , Chen Bo , Xu Dan , Chen Junze , Li Zijian , Liu Yawei , Yang Hua , Ling Chongyi , Ge Yiyao , Zhai Wei , Chen Changsheng , Ma Lu , Zhang Qinghua , Li Xuefei , Yan Yujie , Huang Xinyu , Li Lujiang , Guan Zhiqiang , Tao Chen-Lei , Huang Zhiqi , Wang Hongyi , Liang Jinze , Zhu Ye , Lee Chun-Sing , Wang Peng , Zhang Chunfeng , Gu Lin , Du Yonghua , Lian Tianquan , Zhang Hua , Wu Xue-Jun 
Published: May 2023

AbstractEpitaxial growth is one of the most commonly used strategies to precisely tailor heterostructures with well-defined compositions, morphologies, crystal phases, and interfaces for various applications. However, as epitaxial growth requires a small interfacial lattice mismatch between the components, it remains a challenge for the epitaxial synthesis of heterostructures constructed by materials with large lattice mismatch and/or different chemical bonding, especially the noble metal-semiconductor heterostructures. Here, we develop a noble metal-seeded epitaxial growth strategy to prepare highly symmetrical noble metal-semiconductor branched heterostructures with desired spatial configurations, i.e., twenty CdS (or CdSe) nanorods epitaxially grown on twenty exposed (111) facets of Ag icosahedral nanocrystal, albeit a large lattice mismatch (more than 40%). Importantly, a high quantum yield (QY) of plasmon-induced hot-electron transferred from Ag to CdS was observed in epitaxial Ag-CdS icosapods (18.1%). This work demonstrates that epitaxial growth can be achieved in heterostructures composed of materials with large lattice mismatches. The constructed epitaxial noble metal-semiconductor interfaces could be an ideal platform for investigating the role of interfaces in various physicochemical processes.
Mechanism of assembly, activation and lysine selection by the SIN3B histone deacetylase complex
Authors: Wan Mandy S. M. , Muhammad Reyhan , Koliopoulos Marios G. , Roumeliotis Theodoros I. , Choudhary Jyoti S. , Alfieri Claudio 
Published: May 2023

AbstractLysine acetylation in histone tails is a key post-translational modification that controls transcription activation. Histone deacetylase complexes remove histone acetylation, thereby repressing transcription and regulating the transcriptional output of each gene. Although these complexes are drug targets and crucial regulators of organismal physiology, their structure and mechanisms of action are largely unclear. Here, we present the structure of a complete human SIN3B histone deacetylase holo-complex with and without a substrate mimic. Remarkably, SIN3B encircles the deacetylase and contacts its allosteric basic patch thereby stimulating catalysis. A SIN3B loop inserts into the catalytic tunnel, rearranges to accommodate the acetyl-lysine moiety, and stabilises the substrate for specific deacetylation, which is guided by a substrate receptor subunit. Our findings provide a model of specificity for a main transcriptional regulator conserved from yeast to human and a resource of protein-protein interactions for future drug designs.
Structural basis for catalysis of human choline/ethanolamine phosphotransferase 1
Authors: Wang Zhenhua , Yang Meng , Yang Yufan , He Yonglin , Qian Hongwu 
Published: May 2023

AbstractPhosphatidylcholine (PC) and phosphatidylethanolamine (PE) are two primary components of the eukaryotic membrane and play essential roles in the maintenance of membrane integrity, lipid droplet biogenesis, autophagosome formation, and lipoprotein formation and secretion. Choline/ethanolamine phosphotransferase 1 (CEPT1) catalyzes the last step of the biosynthesis of PC and PE in the Kennedy pathway by transferring the substituted phosphate group from CDP-choline/ethanolamine to diacylglycerol. Here, we present the cryo-EM structures of human CEPT1 and its complex with CDP-choline at resolutions of 3.7 Å and 3.8 Å, respectively. CEPT1 is a dimer with 10 transmembrane segments (TMs) in each protomer. TMs 1-6 constitute a conserved catalytic domain with an interior hydrophobic chamber accommodating a PC-like density. Structural observations and biochemical characterizations suggest that the hydrophobic chamber coordinates the acyl tails during the catalytic process. The PC-like density disappears in the structure of the complex with CDP-choline, suggesting a potential substrate-triggered product release mechanism.
A species-level trait dataset of bats in Europe and beyond
Authors: Froidevaux Jérémy S. P. , Toshkova Nia , Barbaro Luc , Benítez-López Ana , Kerbiriou Christian , Le Viol Isabelle , Pacifici Michela , Santini Luca , Stawski Clare , Russo Danilo , Dekker Jasja , Alberdi Antton , Amorim Francisco , Ancillotto Leonardo , Barré Kévin , Bas Yves , Cantú-Salazar Lisette , Dechmann Dina K. N. , Devaux Tiphaine , Eldegard Katrine , Fereidouni Sasan , Furmankiewicz Joanna , Hamidovic Daniela , Hill Davina L. , Ibáñez Carlos , Julien Jean-François , Juste Javier , Kaňuch Peter , Korine Carmi , Laforge Alexis , Legras Gaëlle , Leroux Camille , Lesiński Grzegorz , Mariton Léa , Marmet Julie , Mata Vanessa A. , Mifsud Clare M. , Nistreanu Victoria , Novella-Fernandez Roberto , Rebelo Hugo , Roche Niamh , Roemer Charlotte , Ruczyński Ireneusz , Sørås Rune , Uhrin Marcel , Vella Adriana , Voigt Christian C. , Razgour Orly 
Published: May 2023

AbstractKnowledge of species’ functional traits is essential for understanding biodiversity patterns, predicting the impacts of global environmental changes, and assessing the efficiency of conservation measures. Bats are major components of mammalian diversity and occupy a variety of ecological niches and geographic distributions. However, an extensive compilation of their functional traits and ecological attributes is still missing. Here we present EuroBaTrait 1.0, the most comprehensive and up-to-date trait dataset covering 47 European bat species. The dataset includes data on 118 traits including genetic composition, physiology, morphology, acoustic signature, climatic associations, foraging habitat, roost type, diet, spatial behaviour, life history, pathogens, phenology, and distribution. We compiled the bat trait data obtained from three main sources: (i) a systematic literature and dataset search, (ii) unpublished data from European bat experts, and (iii) observations from large-scale monitoring programs. EuroBaTrait is designed to provide an important data source for comparative and trait-based analyses at the species or community level. The dataset also exposes knowledge gaps in species, geographic and trait coverage, highlighting priorities for future data collection.
Effects of waterlogging at different growth stages on the photosynthetic characteristics and grain yield of sorghum (Sorghum bicolor L.)
Authors: Zhang Ruidong , Yue Zhongxiao , Chen Xiaofei , Huang Ruidong , Zhou Yufei , Cao Xiong 
Published: May 2023

AbstractVarious plants, including sorghum (Sorghum bicolor L.), are exposed to waterlogging; however, little is known about the effects of waterlogging at different growth stages on sorghum. A pot experiment was conducted using two sorghum hybrids, Jinuoliang 01 (JN01) and Jinza 31 (JZ31), to investigate the effects of waterlogging at different growth stages on the photosynthesis enzyme activity, chlorophyll content, malondialdehyde (MDA) content, photosynthetic parameters, dry matter accumulation, and grain yield. The experiment was conducted using waterlogging treatments implemented at the five-leaf stage (T1), flowering stage (T2), and filling stage (T3), using standard management (no waterlogging) as a control (CK). The adverse effects of waterlogging on sorghum growth varied with the waterlogging timing, with the maximum impact at T1, followed by T2 and T3. JZ31 was more sensitive to waterlogging compared to JN01. Waterlogged conditions inhibited the photosynthetic enzyme activity and reduced the chlorophyll content and photosynthesis, ultimately lowering the biomass yield and grain yield. The maximum yield loss was observed with the T1 waterlogging treatment; the grain yield of JN01 and JZ31 decreased by 52.01–54.58% and 69.52–71.97%, respectively, compared with CK. Furthermore, the decline in grain yield in T1 was associated with reducing grain number per panicle. These findings indicate that sorghum is sensitive to waterlogging at the five-leaf stage and JZ31 is more sensitive to waterlogging than JN01, which may provide a basis for selecting genotypes and management measures to cope with waterlogging in sorghum.
Numerical solution of an electrically conducting spinning flow of hybrid nanofluid comprised of silver and gold nanoparticles across two parallel surfaces
Authors: Alqahtani Aisha M. , Bilal Muhammad , Ali Aatif , Alsenani Theyab R. , Eldin Sayed M. 
Published: May 2023

AbstractThe analysis of the energy transport mechanism received much attention from scientists and researchers. Conventional fluids like vegetable oils, water, ethylene glycol, and transformer oil play a vital role in numerous industrial activities. In certain industrial operations, the low heat conductivity of base fluids causes significant difficulties. This inevitably led to the advancement of critical aspects of nanotechnology. The tremendous significance of nanoscience is in improving the thermal transfer process in different heating transmitting equipment. Therefore, the MHD spinning flow of hybrid nanofluid (HNF) across two permeable surfaces is reviewed. The HNF is made of silver (Ag) and gold (Au) nanoparticles (NPs) in the ethylene glycol (EG). The modeled equations are non-dimensionalized and degraded to a set of ODEs through similarity substitution. The numerical procedure parametric continuation method (PCM) is used to estimate the 1st order set of differential equations. The significances of velocity and energy curves are derived versus several physical parameters. The results are revealed through Tables and Figures. It has been determined that the radial velocity curve declines with the varying values of the stretching parameter, Reynold number, and rotation factor while improving with the influence of the suction factor. Furthermore, the energy profile enhances with the rising number of Au and Ag-NPs in the base fluid.