bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural mechanism of intracellular autoregulation of zinc uptake in ZIP transporters
Authors: Pang Changxu , Chai Jin , Zhu Ping , Shanklin John , Liu Qun 
Published: June 2023

AbstractZinc is an essential micronutrient that supports all living organisms through regulating numerous biological processes. However, the mechanism of uptake regulation by intracellular Zn2+ status remains unclear. Here we report a cryo-electron microscopy structure of a ZIP-family transporter from Bordetella bronchiseptica at 3.05 Å resolution in an inward-facing, inhibited conformation. The transporter forms a homodimer, each protomer containing nine transmembrane helices and three metal ions. Two metal ions form a binuclear pore structure, and the third ion is located at an egress site facing the cytoplasm. The egress site is covered by a loop, and two histidine residues on the loop interact with the egress-site ion and regulate its release. Cell-based Zn2+ uptake and cell growth viability assays reveal a negative regulation of Zn2+ uptake through sensing intracellular Zn2+ status using a built-in sensor. These structural and biochemical analyses provide mechanistic insight into the autoregulation of zinc uptake across membranes.
Intracranial electrophysiological and structural basis of BOLD functional connectivity in human brain white matter
Authors: Huang Yali , Wei Peng-Hu , Xu Longzhou , Chen Desheng , Yang Yanfeng , Song Wenkai , Yi Yangyang , Jia Xiaoli , Wu Guowei , Fan Qingchen , Cui Zaixu , Zhao Guoguang 
Published: June 2023

AbstractWhile functional MRI (fMRI) studies have mainly focused on gray matter, recent studies have consistently found that blood-oxygenation-level-dependent (BOLD) signals can be reliably detected in white matter, and functional connectivity (FC) has been organized into distributed networks in white matter. Nevertheless, it remains unclear whether this white matter FC reflects underlying electrophysiological synchronization. To address this question, we employ intracranial stereotactic-electroencephalography (SEEG) and resting-state fMRI data from a group of 16 patients with drug-resistant epilepsy. We find that BOLD FC is correlated with SEEG FC in white matter, and this result is consistent across a wide range of frequency bands for each participant. By including diffusion spectrum imaging data, we also find that white matter FC from both SEEG and fMRI are correlated with white matter structural connectivity, suggesting that anatomical fiber tracts underlie the functional synchronization in white matter. These results provide evidence for the electrophysiological and structural basis of white matter BOLD FC, which could be a potential biomarker for psychiatric and neurological disorders.
A viral pan-end RNA element and host complex define a SARS-CoV-2 regulon
Authors: Khan Debjit , Terenzi Fulvia , Liu GuanQun , Ghosh Prabar K. , Ye Fengchun , Nguyen Kien , China Arnab , Ramachandiran Iyappan , Chakraborty Shruti , Stefan Jennifer , Khan Krishnendu , Vasu Kommireddy , Dong Franklin , Willard Belinda , Karn Jonathan , Gack Michaela U. , Fox Paul L. 
Published: June 2023

AbstractSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, generates multiple protein-coding, subgenomic RNAs (sgRNAs) from a longer genomic RNA, all bearing identical termini with poorly understood roles in regulating viral gene expression. Insulin and interferon-gamma, two host-derived, stress-related agents, and virus spike protein, induce binding of glutamyl-prolyl-tRNA synthetase (EPRS1), within an unconventional, tetra-aminoacyl-tRNA synthetase complex, to the sgRNA 3′-end thereby enhancing sgRNA expression. We identify an EPRS1-binding sarbecoviral pan-end activating RNA (SPEAR) element in the 3′-end of viral RNAs driving agonist-induction. Translation of another co-terminal 3′-end feature, ORF10, is necessary for SPEAR-mediated induction, independent of Orf10 protein expression. The SPEAR element enhances viral programmed ribosomal frameshifting, thereby expanding its functionality. By co-opting noncanonical activities of a family of essential host proteins, the virus establishes a post-transcriptional regulon stimulating global viral RNA translation. A SPEAR-targeting strategy markedly reduces SARS-CoV-2 titer, suggesting a pan-sarbecoviral therapeutic modality.
Chirality selective magnon-phonon hybridization and magnon-induced chiral phonons in a layered zigzag antiferromagnet
Authors: Cui Jun , Boström Emil Viñas , Ozerov Mykhaylo , Wu Fangliang , Jiang Qianni , Chu Jiun-Haw , Li Changcun , Liu Fucai , Xu Xiaodong , Rubio Angel , Zhang Qi 
Published: June 2023

AbstractTwo-dimensional (2D) magnetic systems possess versatile magnetic order and can host tunable magnons carrying spin angular momenta. Recent advances show angular momentum can also be carried by lattice vibrations in the form of chiral phonons. However, the interplay between magnons and chiral phonons as well as the details of chiral phonon formation in a magnetic system are yet to be explored. Here, we report the observation of magnon-induced chiral phonons and chirality selective magnon-phonon hybridization in a layered zigzag antiferromagnet (AFM) FePSe3. With a combination of magneto-infrared and magneto-Raman spectroscopy, we observe chiral magnon polarons (chiMP), the new hybridized quasiparticles, at zero magnetic field. The hybridization gap reaches 0.25 meV and survives down to the quadrilayer limit. Via first principle calculations, we uncover a coherent coupling between AFM magnons and chiral phonons with parallel angular momenta, which arises from the underlying phonon and space group symmetries. This coupling lifts the chiral phonon degeneracy and gives rise to an unusual Raman circular polarization of the chiMP branches. The observation of coherent chiral spin-lattice excitations at zero magnetic field paves the way for angular momentum-based hybrid phononic and magnonic devices.
Energy conversion and storage via photoinduced polarization change in non-ferroelectric molecular [CoGa] crystals
Authors: Sadhukhan Pritam , Wu Shu-Qi , Kanegawa Shinji , Su Sheng-Qun , Zhang Xiaopeng , Nakanishi Takumi , Long Jeremy Ian , Gao Kaige , Shimada Rintaro , Okajima Hajime , Sakamoto Akira , Chiappella Joy G. , Huzan Myron S. , Kroll Thomas , Sokaras Dimosthenis , Baker Michael L. , Sato Osamu 
Published: June 2023

AbstractTo alleviate the energy and environmental crisis, in the last decades, energy harvesting by utilizing optical control has emerged as a promising solution. Here we report a polar crystal that exhibits photoenergy conversion and energy storage upon light irradiation. The polar crystal consists of dinuclear [CoGa] molecules, which are oriented in a uniform direction inside the crystal lattice. Irradiation with green light induces a directional intramolecular electron transfer from the ligand to a low-spin CoIIIcentre, and the resultant light-induced high-spin CoIIexcited state is trapped at low temperature, realizing energy storage. Additionally, electric current release is observed during relaxation from the trapped light-induced metastable state to the ground state, because the intramolecular electron transfer in the relaxation process is accompanied with macroscopic polarization switching at the single-crystal level. It demonstrates that energy storage and conversion to electrical energy is realized in the [CoGa] crystals, which is different from typical polar pyroelectric compounds that exhibit the conversion of thermal energy into electricity.
Language network lateralization is reflected throughout the macroscale functional organization of cortex
Authors: Labache Loïc , Ge Tian , Yeo B. T. Thomas , Holmes Avram J. 
Published: June 2023

AbstractHemispheric specialization is a fundamental feature of human brain organization. However, it is not yet clear to what extent the lateralization of specific cognitive processes may be evident throughout the broad functional architecture of cortex. While the majority of people exhibit left-hemispheric language dominance, a substantial minority of the population shows reverse lateralization. Using twin and family data from the Human Connectome Project, we provide evidence that atypical language dominance is associated with global shifts in cortical organization. Individuals with atypical language organization exhibit corresponding hemispheric differences in the macroscale functional gradients that situate discrete large-scale networks along a continuous spectrum, extending from unimodal through association territories. Analyses reveal that both language lateralization and gradient asymmetries are, in part, driven by genetic factors. These findings pave the way for a deeper understanding of the origins and relationships linking population-level variability in hemispheric specialization and global properties of cortical organization.
In vivo PAR-CLIP (viP-CLIP) of liver TIAL1 unveils targets regulating cholesterol synthesis and secretion
Authors: Vatandaslar Hasan , Garzia Aitor , Meyer Cindy , Godbersen Svenja , Brandt Laura T. L. , Griesbach Esther , Chao Jeffrey A. , Tuschl Thomas , Stoffel Markus 
Published: June 2023

AbstractSystem-wide cross-linking and immunoprecipitation (CLIP) approaches have unveiled regulatory mechanisms of RNA-binding proteins (RBPs) mainly in cultured cells due to limitations in the cross-linking efficiency of tissues. Here, we describe viP-CLIP (in vivo PAR-CLIP), a method capable of identifying RBP targets in mammalian tissues, thereby facilitating the functional analysis of RBP-regulatory networks in vivo. We applied viP-CLIP to mouse livers and identified Insig2 and ApoB as prominent TIAL1 target transcripts, indicating an important role of TIAL1 in cholesterol synthesis and secretion. The functional relevance of these targets was confirmed by showing that TIAL1 influences their translation in hepatocytes. Mutant Tial1 mice exhibit altered cholesterol synthesis, APOB secretion and plasma cholesterol levels. Our results demonstrate that viP-CLIP can identify physiologically relevant RBP targets by finding a factor implicated in the negative feedback regulation of cholesterol biosynthesis.
A 2.2 Å cryoEM structure of a quinol-dependent NO Reductase shows close similarity to respiratory oxidases
Authors: Flynn Alex J. , Antonyuk Svetlana V. , Eady Robert R. , Muench Stephen P. , Hasnain S. Samar 
Published: June 2023

AbstractQuinol-dependent nitric oxide reductases (qNORs) are considered members of the respiratory heme-copper oxidase superfamily, are unique to bacteria, and are commonly found in pathogenic bacteria where they play a role in combating the host immune response. qNORs are also essential enzymes in the denitrification pathway, catalysing the reduction of nitric oxide to nitrous oxide. Here, we determine a 2.2 Å cryoEM structure of qNOR from Alcaligenes xylosoxidans, an opportunistic pathogen and a denitrifying bacterium of importance in the nitrogen cycle. This high-resolution structure provides insight into electron, substrate, and proton pathways, and provides evidence that the quinol binding site not only contains the conserved His and Asp residues but also possesses a critical Arg (Arg720) observed in cytochrome bo3, a respiratory quinol oxidase.
In-situ spectroscopic probe of the intrinsic structure feature of single-atom center in electrochemical CO/CO2 reduction to methanol
Authors: Ren Xinyi , Zhao Jian , Li Xuning , Shao Junming , Pan Binbin , Salamé Aude , Boutin Etienne , Groizard Thomas , Wang Shifu , Ding Jie , Zhang Xiong , Huang Wen-Yang , Zeng Wen-Jing , Liu Chengyu , Li Yanguang , Hung Sung-Fu , Huang Yanqiang , Robert Marc , Liu Bin 
Published: June 2023

AbstractWhile exploring the process of CO/CO2 electroreduction (COxRR) is of great significance to achieve carbon recycling, deciphering reaction mechanisms so as to further design catalytic systems able to overcome sluggish kinetics remains challenging. In this work, a model single-Co-atom catalyst with well-defined coordination structure is developed and employed as a platform to unravel the underlying reaction mechanism of COxRR. The as-prepared single-Co-atom catalyst exhibits a maximum methanol Faradaic efficiency as high as 65% at 30 mA/cm2 in a membrane electrode assembly electrolyzer, while on the contrary, the reduction pathway of CO2 to methanol is strongly decreased in CO2RR. In-situ X-ray absorption and Fourier-transform infrared spectroscopies point to a different adsorption configuration of *CO intermediate in CORR as compared to that in CO2RR, with a weaker stretching vibration of the C–O bond in the former case. Theoretical calculations further evidence the low energy barrier for the formation of a H-CoPc-CO– species, which is a critical factor in promoting the electrochemical reduction of CO to methanol.
Revealing core-valence interactions in solution with femtosecond X-ray pump X-ray probe spectroscopy
Authors: Weakly Robert B. , Liekhus-Schmaltz Chelsea E. , Poulter Benjamin I. , Biasin Elisa , Alonso-Mori Roberto , Aquila Andrew , Boutet Sébastien , Fuller Franklin D. , Ho Phay J. , Kroll Thomas , Loe Caroline M. , Lutman Alberto , Zhu Diling , Bergmann Uwe , Schoenlein Robert W. , Govind Niranjan , Khalil Munira 
Published: June 2023

AbstractFemtosecond pump-probe spectroscopy using ultrafast optical and infrared pulses has become an essential tool to discover and understand complex electronic and structural dynamics in solvated molecular, biological, and material systems. Here we report the experimental realization of an ultrafast two-color X-ray pump X-ray probe transient absorption experiment performed in solution. A 10 fs X-ray pump pulse creates a localized excitation by removing a 1s electron from an Fe atom in solvated ferro- and ferricyanide complexes. Following the ensuing Auger–Meitner cascade, the second X-ray pulse probes the Fe 1s → 3p transitions in resultant novel core-excited electronic states. Careful comparison of the experimental spectra with theory, extracts +2 eV shifts in transition energies per valence hole, providing insight into correlated interactions of valence 3d with 3p and deeper-lying electrons. Such information is essential for accurate modeling and predictive synthesis of transition metal complexes relevant for applications ranging from catalysis to information storage technology. This study demonstrates the experimental realization of the scientific opportunities possible with the continued development of multicolor multi-pulse X-ray spectroscopy to study electronic correlations in complex condensed phase systems.
Local cation-tuned reversible single-molecule switch in electric double layer
Authors: Tong Ling , Yu Zhou , Gao Yi-Jing , Li Xiao-Chong , Zheng Ju-Fang , Shao Yong , Wang Ya-Hao , Zhou Xiao-Shun 
Published: June 2023

AbstractThe nature of molecule-electrode interface is critical for the integration of atomically precise molecules as functional components into circuits. Herein, we demonstrate that the electric field localized metal cations in outer Helmholtz plane can modulate interfacial Au-carboxyl contacts, realizing a reversible single-molecule switch. STM break junction and I-V measurements show the electrochemical gating of aliphatic and aromatic carboxylic acids have a conductance ON/OFF behavior in electrolyte solution containing metal cations (i.e., Na+, K+, Mg2+ and Ca2+), compared to almost no change in conductance without metal cations. In situ Raman spectra reveal strong molecular carboxyl-metal cation coordination at the negatively charged electrode surface, hindering the formation of molecular junctions for electron tunnelling. This work validates the critical role of localized cations in the electric double layer to regulate electron transport at the single-molecule level.
Unlocking the potentials of cyanobacterial photosynthesis for directly converting carbon dioxide into glucose
Authors: Zhang Shanshan , Sun Jiahui , Feng Dandan , Sun Huili , Cui Jinyu , Zeng Xuexia , Wu Yannan , Luan Guodong , Lu Xuefeng 
Published: June 2023

AbstractGlucose is the most abundant monosaccharide, serving as an essential energy source for cells in all domains of life and as an important feedstock for the biorefinery industry. The plant-biomass-sugar route dominates the current glucose supply, while the direct conversion of carbon dioxide into glucose through photosynthesis is not well studied. Here, we show that the potential ofSynechococcus elongatusPCC 7942 for photosynthetic glucose production can be unlocked by preventing native glucokinase activity. Knocking out two glucokinase genes causes intracellular accumulation of glucose and promotes the formation of a spontaneous mutation in the genome, which eventually leads to glucose secretion. Without heterologous catalysis or transportation genes, glucokinase deficiency and spontaneous genomic mutation lead to a glucose secretion of 1.5 g/L, which is further increased to 5 g/L through metabolic and cultivation engineering. These findings underline the cyanobacterial metabolism plasticities and demonstrate their applications for supporting the direct photosynthetic production of glucose.
ddRAD sequencing based genotyping of six indigenous dairy cattle breeds of India to infer existing genetic diversity and population structure
Authors: Masharing Nampher , Sodhi Monika , Chanda Divya , Singh Inderpal , Vivek Prince , Tiwari Manish , Kumari Parvesh , Mukesh Manishi 
Published: June 2023

AbstractThe present investigation aimed to identify genome wide SNPs and to carry out diversity and population structure study using ddRAD-seq based genotyping of 58 individuals of six indigenous milch cattle breeds (Bos indicus) such as Sahiwal, Gir, Rathi, Tharparkar, Red Sindhi and Kankrej of India. A high percentage of reads (94.53%) were mapped to theBos taurus(ARS-UCD1.2) reference genome assembly. Following filtration criteria, a total of 84,027 high quality SNPs were identified across the genome of 6 cattle breeds with the highest number of SNPs observed in Gir (34,743), followed by Red Sindhi (13,092), Kankrej (12,812), Sahiwal (8956), Tharparkar (7356) and Rathi (7068). Most of these SNPs were distributed in the intronic regions (53.87%) followed by intergenic regions (34.94%) while only 1.23% were located in the exonic regions. Together with analysis of nucleotide diversity (π = 0.373), Tajima’s D (D value ranging from − 0.295 to 0.214), observed heterozygosity (HOranging from 0.464 to 0.551), inbreeding coefficient (FISranging from − 0.253 to 0.0513) suggested for the presence of sufficient within breed diversity in the 6 major milch breeds of India. The phylogenetic based structuring, principal component and admixture analysis revealed genetic distinctness as well as purity of almost all of the 6 cattle breeds. Overall, our strategy has successfully identified thousands of high-quality genome wide SNPs that will further enrich theBos indicusrepresentation basic information about genetic diversity and structure of 6 major Indian milch cattle breeds which should have implications for better management and conservation of valuable indicine cattle diversity.
Strategy inference during learning via cognitive activity-based credit assignment models
Authors: James Ashwin , Reynaud-Bouret Patricia , Mezzadri Giulia , Sargolini Francesca , Bethus Ingrid , Muzy Alexandre 
Published: June 2023

AbstractWe develop a method for selecting meaningful learning strategies based solely on the behavioral data of a single individual in a learning experiment. We use simple Activity-Credit Assignment algorithms to model the different strategies and couple them with a novel hold-out statistical selection method. Application on rat behavioral data in a continuous T-maze task reveals a particular learning strategy that consists in chunking the paths used by the animal. Neuronal data collected in the dorsomedial striatum confirm this strategy.
Epidemiology of rhegmatogenous retinal detachment in commercially insured myopes in the United States
Authors: Ludwig Cassie A. , Vail Daniel , Al-Moujahed Ahmad , Callaway Natalia F. , Saroj Namrata , Moshfeghi Andrew , Moshfeghi Darius M. 
Published: June 2023

AbstractMyopia is a known risk factor for rhegmatogenous retinal detachment (RRD). Given global trends of increasing myopia, we aimed to determine the absolute risk (incidence rate) of RRD in non-myopes, myopes and high myopes in the United States over ten years. We performed a retrospective cohort study of 85,476,781 commercially insured patients enrolled in the Merative™ Marketscan® Research Database. The incidence rate of RRD in phakic patients in the United States was 39-fold higher in high myopes than non-myopes (868.83 per 100,000 person-years versus 22.44 per 100,000 person-years) and three-fold higher in myopes than non-myopes (67.51 per 100,000 person-years versus 22.44 per 100,000 person-years). The incidence rate was significantly higher in males in each category (P < 0.01). Combined, the incidence rate of RRD in phakic patients in the United States from 2007 to 2016 was 25.27 RRDs per 100,000 person-years, a rate higher than those in prior published studies in North America, South America, Europe, Asia, and Australia. The absolute risk of myopia and high myopia increased from 2007 to 2016. The risk of RRD in phakic high myopes rose with increasing age. Notably, the magnitude of increased risk of RRD in myopes varied substantially according to the minimum follow-up period in our models and should be accounted for when interpreting data analyses.
RNA binding by the glucocorticoid receptor attenuates dexamethasone-induced gene activation
Authors: Lammer Nickolaus C. , Ashraf Humza M. , Ugay Daniella A. , Spencer Sabrina L. , Allen Mary A. , Batey Robert T. , Wuttke Deborah S. 
Published: June 2023

AbstractThe glucocorticoid receptor (GR) is a ligand-activated transcription factor that regulates a suite of genes through direct binding of GR to specific DNA promoter elements. GR also interacts with RNA, but the function of this RNA-binding activity remains elusive. Current models speculate that RNA could repress the transcriptional activity of GR. To investigate the function of the GR-RNA interaction on GR’s transcriptional activity, we generated cells that stably express a mutant of GR with reduced RNA binding affinity and treated the cells with the GR agonist dexamethasone. Changes in the dexamethasone-driven transcriptome were quantified using 4-thiouridine labeling of RNAs followed by high-throughput sequencing. We find that while many genes are unaffected, GR-RNA binding is repressive for specific subsets of genes in both dexamethasone-dependent and independent contexts. Genes that are dexamethasone-dependent are activated directly by chromatin-bound GR, suggesting a competition-based repression mechanism in which increasing local concentrations of RNA may compete with DNA for binding to GR at sites of transcription. Unexpectedly, genes that are dexamethasone-independent instead display a localization to specific chromosomal regions, which points to changes in chromatin accessibility or architecture. These results show that RNA binding plays a fundamental role in regulating GR function and highlights potential functions for transcription factor-RNA interactions.