bluuebunny/crossref_metadata_2025_split huggingface dataset:
grandR: a comprehensive package for nucleotide conversion RNA-seq data analysis
Authors: Rummel Teresa , Sakellaridi Lygeri , Erhard Florian 
Published: June 2023

AbstractMetabolic labeling of RNA is a powerful technique for studying the temporal dynamics of gene expression. Nucleotide conversion approaches greatly facilitate the generation of data but introduce challenges for their analysis. Here we present grandR, a comprehensive package for quality control, differential gene expression analysis, kinetic modeling, and visualization of such data. We compare several existing methods for inference of RNA synthesis rates and half-lives using progressive labeling time courses. We demonstrate the need for recalibration of effective labeling times and introduce a Bayesian approach to study the temporal dynamics of RNA using snapshot experiments.
Genome-wide association studies identify OsWRKY53 as a key regulator of salt tolerance in rice
Authors: Yu Jun , Zhu Chengsong , Xuan Wei , An Hongzhou , Tian Yunlu , Wang Baoxiang , Chi Wenchao , Chen Gaoming , Ge Yuwei , Li Jin , Dai Zhaoyang , Liu Yan , Sun Zhiguang , Xu Dayong , Wang Chunming , Wan Jianmin 
Published: June 2023

AbstractSalinity stress progressively reduces plant growth and productivity, while plant has developed complex signaling pathways to confront salt stress. However, only a few genetic variants have been identified to mediate salt tolerance in the major crop rice, and the molecular mechanism remains poorly understood. Here, we identify ten candidate genes associated with salt-tolerance (ST) traits by performing a genome-wide association analysis in rice landraces. We characterize two ST-related genes, encoding transcriptional factor OsWRKY53 and Mitogen-activated protein Kinase Kinase OsMKK10.2, that mediate root Na+ flux and Na+ homeostasis. We further find that OsWRKY53 acts as a negative modulator regulating expression of OsMKK10.2 in promoting ion homeostasis. Furthermore, OsWRKY53 trans-represses OsHKT1;5 (high-affinity K+transporter 1;5), encoding a sodium transport protein in roots. We show that the OsWRKY53-OsMKK10.2 and OsWRKY53-OsHKT1;5 module coordinate defenses against ionic stress. The results shed light on the regulatory mechanisms underlying plant salt tolerance.
Kv7/KCNQ potassium channels in cortical hyperexcitability and juvenile seizure-related death in Ank2-mutant mice
Authors: Oh Hyoseon , Lee Suho , Oh Yusang , Kim Seongbin , Kim Young Seo , Yang Yeji , Choi Woochul , Yoo Ye-Eun , Cho Heejin , Lee Seungjoon , Yang Esther , Koh Wuhyun , Won Woojin , Kim Ryunhee , Lee C. Justin , Kim Hyun , Kang Hyojin , Kim Jin Young , Ku Taeyun , Paik Se-Bum , Kim Eunjoon 
Published: June 2023

AbstractAutism spectrum disorders (ASD) represent neurodevelopmental disorders characterized by social deficits, repetitive behaviors, and various comorbidities, including epilepsy. ANK2, which encodes a neuronal scaffolding protein, is frequently mutated in ASD, but its in vivo functions and disease-related mechanisms are largely unknown. Here, we report that mice with Ank2 knockout restricted to cortical and hippocampal excitatory neurons (Ank2-cKO mice) show ASD-related behavioral abnormalities and juvenile seizure-related death. Ank2-cKO cortical neurons show abnormally increased excitability and firing rate. These changes accompanied decreases in the total level and function of the Kv7.2/KCNQ2 and Kv7.3/KCNQ3 potassium channels and the density of these channels in the enlengthened axon initial segment. Importantly, the Kv7 agonist, retigabine, rescued neuronal excitability, juvenile seizure-related death, and hyperactivity in Ank2-cKO mice. These results suggest that Ank2 regulates neuronal excitability by regulating the length of and Kv7 density in the AIS and that Kv7 channelopathy is involved in Ank2-related brain dysfunctions.
Dynamic active-site induced by host-guest interactions boost the Fenton-like reaction for organic wastewater treatment
Authors: Zhang Dongpeng , Li Yanxiao , Wang Pengfei , Qu Jinyong , Li Yi , Zhan Sihui 
Published: June 2023

AbstractIn heterogeneous catalysis, uncovering the dynamic evolution of active sites in the working conditions is crucial to realizing increased activity and enhanced stability of catalyst in Fenton-like activation. Herein, we capture the dynamic changes in the unit cell of Co/La-SrTiO3catalyst during the exemplary peroxymonosulfate activation process using X-ray absorption spectroscopy and in situ Raman spectroscopy, revealing the substrate tuned its structural evolution, which is the reversible stretching vibration of O-Sr-O and Co/Ti-O bonds in different orientations. This process effectively promotes the generation of key SO5* intermediates, which is beneficial to the formation of1O2and SO4•−from persulfate on the Co active site. Density functional theory and X-ray absorption spectroscopy show that the optimized structural distortion enhanced the metal-oxygen bond strength by tuning theegorbitals and increased the number of transferred electrons to peroxymonosulfate by about 3-fold, achieving excellent efficiency and stability in removing organic pollutants.
Atomic motifs govern the decoration of grain boundaries by interstitial solutes
Authors: Zhou Xuyang , Ahmadian Ali , Gault Baptiste , Ophus Colin , Liebscher Christian H. , Dehm Gerhard , Raabe Dierk 
Published: June 2023

AbstractGrain boundaries, the two-dimensional defects between differently oriented crystals, tend to preferentially attract solutes for segregation. Solute segregation has a significant effect on the mechanical and transport properties of materials. At the atomic level, however, the interplay of structure and composition of grain boundaries remains elusive, especially with respect to light interstitial solutes like B and C. Here, we use Fe alloyed with B and C to exploit the strong interdependence of interface structure and chemistry via charge-density imaging and atom probe tomography methods. Direct imaging and quantifying of light interstitial solutes at grain boundaries provide insight into decoration tendencies governed by atomic motifs. We find that even a change in the inclination of the grain boundary plane with identical misorientation impacts grain boundary composition and atomic arrangement. Thus, it is the smallest structural hierarchical level, the atomic motifs, that controls the most important chemical properties of the grain boundaries. This insight not only closes a missing link between the structure and chemical composition of such defects but also enables the targeted design and passivation of the chemical state of grain boundaries to free them from their role as entry gates for corrosion, hydrogen embrittlement, or mechanical failure.
Combinatorial encoding of odors in the mosquito antennal lobe
Authors: Singh Pranjul , Goyal Shefali , Gupta Smith , Garg Sanket , Tiwari Abhinav , Rajput Varad , Bates Alexander Shakeel , Gupta Arjit Kant , Gupta Nitin 
Published: June 2023

AbstractAmong the cues that a mosquito uses to find a host for blood-feeding, the smell of the host plays an important role. Previous studies have shown that host odors contain hundreds of chemical odorants, which are detected by different receptors on the peripheral sensory organs of mosquitoes. But how individual odorants are encoded by downstream neurons in the mosquito brain is not known. We developed an in vivo preparation for patch-clamp electrophysiology to record from projection neurons and local neurons in the antennal lobe of Aedes aegypti. Combining intracellular recordings with dye-fills, morphological reconstructions, and immunohistochemistry, we identify different sub-classes of antennal lobe neurons and their putative interactions. Our recordings show that an odorant can activate multiple neurons innervating different glomeruli, and that the stimulus identity and its behavioral preference are represented in the population activity of the projection neurons. Our results provide a detailed description of the second-order olfactory neurons in the central nervous system of mosquitoes and lay a foundation for understanding the neural basis of their olfactory behaviors.
Bacteria evolve macroscopic multicellularity by the genetic assimilation of phenotypically plastic cell clustering
Authors: Chavhan Yashraj , Dey Sutirth , Lind Peter A. 
Published: June 2023

AbstractThe evolutionary transition from unicellularity to multicellularity was a key innovation in the history of life. Experimental evolution is an important tool to study the formation of undifferentiated cellular clusters, the likely first step of this transition. Although multicellularity first evolved in bacteria, previous experimental evolution research has primarily used eukaryotes. Moreover, it focuses on mutationally driven (and not environmentally induced) phenotypes. Here we show that both Gram-negative and Gram-positive bacteria exhibit phenotypically plastic (i.e., environmentally induced) cell clustering. Under high salinity, they form elongated clusters of ~ 2 cm. However, under habitual salinity, the clusters disintegrate and grow planktonically. We used experimental evolution withEscherichia colito show that such clustering can be assimilated genetically: the evolved bacteria inherently grow as macroscopic multicellular clusters, even without environmental induction. Highly parallel mutations in genes linked to cell wall assembly formed the genomic basis of assimilated multicellularity. While the wildtype also showed cell shape plasticity across high versus low salinity, it was either assimilated or reversed after evolution. Interestingly, a single mutation could genetically assimilate multicellularity by modulating plasticity at multiple levels of organization. Taken together, we show that phenotypic plasticity can prime bacteria for evolving undifferentiated macroscopic multicellularity.
Transition of antimicrobial resistome in wastewater treatment plants: impact of process configuration, geographical location and season
Authors: Honda Ryo , Matsuura Norihisa , Sorn Sovannlaksmy , Asakura Sawako , Morinaga Yuta , Van Huy Than , Sabar Muhammad Adnan , Masakke Yalkhin , Hara-Yamamura Hiroe , Watanabe Toru 
Published: June 2023

AbstractAntimicrobial resistome in wastewater treatment plants was investigated via shotgun metagenomic analysis over a variety of geographical locations, seasons, and biological treatment configurations. The results revealed that the transition of the antimicrobial resistome occurred at two locations during wastewater treatment, which resulted in a distinctive antimicrobial resistome in influent wastewater, activated sludge, and treated effluent. The antimicrobial resistome in influent wastewater was characterized by a high abundance of antibiotic resistance genes (ARGs) on clinically important drugs, whereas sludge retained a higher abundance of multidrug ARGs associated with efflux pump. Seasonality was the primary factor affecting antimicrobial resistome in influent wastewater, which partially succeeded to the subsequent resistome of activated sludge and treated effluent. Importantly, some ARGs on clinically important drugs in influent wastewater passed through the biological treatment to be discharged in the treated effluent, except in the membrane bioreactor process.
Transition patterns of metabolic dysfunction-associated fatty liver disease status in relation to arterial stiffness progression: a health check-up cohort study
Authors: Liu Lei , Wang Changfa , Deng Shuwen , Yuan Ting , Zhu Xiaoling , Deng Yuling , Qin Yuexiang , Wang Yaqin , Yang Pingting 
Published: June 2023

AbstractMetabolic dysfunction-associated fatty liver disease (MAFLD) is a new diagnostic criterion based on hepatic steatosis and metabolic dysfunction. However, a comprehensive evaluation of the association of MAFLD dynamic transitions with arterial stiffness progression has yet to be conducted. This cohort study included 8807 Chinese health check-up participants (median follow-up = 50.2 months). Participants were categorized into four groups according to MAFLD status at baseline and follow-up (none, persistent, developed and regressed). Arterial stiffness progression was assessed by the annual brachial-ankle pulse wave velocity (ba-PWV) increase and arterial stiffness incidence. Compared with the non-MAFLD group, the annual increase in ba-PWV was highest in the persistent-MAFLD group [6.75 cm/s/year, (95% CI 4.03–9.33)], followed by the developed—[6.35 cm/s/year, (95% CI 3.80–8.91)] and the regressed—[1.27 cm/s/year, (95% CI − 2.18 to 4.72)] MAFLD groups. Similarly, compared with the non-MAFLD group, the persistent-MAFLD group had a 1.31-fold increased arterial stiffness risk [OR 1.31; 95% CI 1.03–1.66]. The associations of MAFLD transition patterns with arterial stiffness incidence did not differ across any clinically specific subgroups evaluated. Furthermore, the potential effect of dynamic changes in cardiometabolic risk factors on arterial stiffness incidence among persistent-MAFLD participants was mostly driven by annual fasting glucose and triglyceride increases. In conclusion, persistent MAFLD was associated with an increased risk of arterial stiffness development. Moreover, in persistent-MAFLD subjects, elevated blood glucose and triglyceride levels might facilitate the arterial stiffness incidence.
Key epidemiological indicators and spatial autocorrelation patterns across five waves of COVID-19 in Catalonia
Authors: Belvis Francesc , Aleta Alberto , Padilla-Pozo Álvaro , Pericàs Juan-M. , Fernández-Gracia Juan , Rodríguez Jorge P. , Eguíluz Víctor M. , De Santana Charles Novaes , Julià Mireia , Benach Joan ,   the COVID-SHINE group, Benach Núria , Cash-Gibson Lucinda , Delclós Carles , Gutiérrez-Zamora Mariana , Martínez-Herrera Eliana , Palmer John , Rojas-Gualdrón Diego-F. 
Published: June 2023

AbstractThis research studies the evolution of COVID-19 crude incident rates, effective reproduction number R(t) and their relationship with incidence spatial autocorrelation patterns in the 19 months following the disease outbreak in Catalonia (Spain). A cross-sectional ecological panel design based on n = 371 health-care geographical units is used. Five general outbreaks are described, systematically preceded by generalized values of R(t) > 1 in the two previous weeks. No clear regularities concerning possible initial focus appear when comparing waves. As for autocorrelation, we identify a wave’s baseline pattern in which global Moran’s I increases rapidly in the first weeks of the outbreak to descend later. However, some waves significantly depart from the baseline. In the simulations, both baseline pattern and departures can be reproduced when measures aimed at reducing mobility and virus transmissibility are introduced. Spatial autocorrelation is inherently contingent on the outbreak phase and is also substantially modified by external interventions affecting human behavior.
Seasonal estimation of groundwater vulnerability
Authors: Cervantes-Servin Adrian I. , Arora Meenakshi , Peterson Tim J. , Pettigrove Vincent 
Published: June 2023

AbstractIndex-based methods estimate a fixed value of groundwater vulnerability (GWV); however, the effects of time variations on this estimation have not been comprehensively studied. It is imperative to estimate a time-variant vulnerability that accounts for climatic changes. In this study, we used a Pesticide DRASTICL method separating hydrogeological factors into dynamic and static groups followed by correspondence analysis. The dynamic group is composed of depth and recharge, and the static group is composed of aquifer media, soil media, topography slope, impact of vadose zone, aquifer conductivity and land use. The model results were 42.25–179.89, 33.93–159.81, 34.08–168.74, and 45.56–205.20 for spring, summer, autumn, and winter, respectively. The results showed a moderate correlation between the model predictions and observed nitrogen concentrations with R2 = 0.568 and a high correlation for phosphorus concentrations with R2 = 0.706. Our results suggest that the time-variant GWV model provides a robust yet flexible method for investigating seasonal changes in GWV. This model is an improvement to the standard index-based methods, making them sensitive to climatic changes and portraying a true vulnerability estimation. Finally, the correction of the rating scale value fixes the problem of overestimation in standard models.
Urinary titin N-fragment as a predictor of decreased skeletal muscle mass in patients with interstitial lung diseases
Authors: Hanada Masatoshi , Ishimatsu Yuji , Sakamoto Noriho , Akiyama Yoshiko , Kido Takashi , Ishimoto Hiroshi , Oikawa Masato , Nagura Hiroki , Takeuchi Rina , Sato Shuntaro , Takahata Hideaki , Mukae Hiroshi , Kozu Ryo 
Published: June 2023

AbstractThis study aimed to examine the validity of urinary N-terminal titin fragment/creatinine (urinary N-titin/Cr) reflecting muscle damage biomarker in patients with interstitial lung disease. This retrospective study enrolled patients with interstitial lung disease. We measured urinary N-titin/Cr. Furthermore, we measured the cross-sectional areas of the pectoralis muscles above the aortic arch (PMCSA) and erector spinae muscles of the 12th thoracic vertebra muscles (ESMCSA) to assess muscle mass until 1 year. We examined the correlation between urinary N-titin/Cr and the change in muscle mass. We plotted receiver operating characteristic curves to estimate the cut-off points for urinary N-titin/Cr for distinguishing the greater-than-median and smaller-than-median reduction of muscle mass after 1 year. We enrolled 68 patients with interstitial lung disease. The median urinary N-titin/Cr value was 7.0 pmol/mg/dL. We observed significant negative correlations between urinary N-titin/Cr and changes in the PMCSA after 1 year (p < 0.001) and changes in the ESMCSA after 6 months (p < 0.001) and 1 year (p < 0.001). The cut-off points for urinary N-titin/Cr were 5.2 pmol/mg/dL and 10.4 pmol/mg/dL in the PMCSA and ESMCSA, respectively. In summary, urinary N-titin/Cr may predict muscle loss in the long-term and act as a clinically useful biomarker reflecting muscle damage.
Embryonic abnormalities and genotoxicity induced by 2,4-dichlorophenoxyacetic acid during indirect somatic embryogenesis in Coffea
Authors: de Morais Oliveira João Paulo , Silva Alex Junior da , Catrinck Mariana Neves , Clarindo Wellington Ronildo 
Published: June 2023

AbstractIndirect somatic embryogenesis (ISE) is a morphogenetic pathway in which somatic cells form callus and, later, somatic embryos (SE). 2,4-dichlorophenoxyacetic acid (2,4-D) is a synthetic auxin that promotes the proliferation and dedifferentiation of somatic cells, inducing the ISE. However, 2,4-D can cause genetic, epigenetic, physiological and morphological disorders, preventing the regeneration and/or resulting abnormal somatic embryos (ASE). We aimed to evaluate the toxic 2,4-D effect during the Coffea arabica and C. canephora ISE, assessing the SE morphology, global 5-methylcytosine levels (5-mC%) and DNA damage. Leaf explants were inoculated in media with different 2,4-D concentrations. After 90 days, the friable calli were transferred to the regeneration medium, and the number of normal and abnormal SE was monthly counted. The increase of the 2,4-D concentration increased the number of responsive explants in both Coffea. At 9.06, 18.08 and 36.24 μM 2,4-D, C. arabica presented the highest values of responsive explants, differing from C. canephora. Normal and abnormal SE regeneration increased in relation to the time and 2,4-D concentration. Global 5-mC% varied at different stages of the ISE in both Coffea. Furthermore, the 2,4-D concentration positively correlated with global 5-mC%, and with the mean number of ASE. All ASE of C. arabica and C. canephora exhibited DNA damage and showed higher global 5-mC%. The allotetraploid C. arabica exhibited greater tolerance to the toxic effect of 2,4-D than the diploid C. canephora. We conclude that synthetic 2,4-D auxin promotes genotoxic and phytotoxic disorders and promotes epigenetic changes during Coffea ISE.
Metabolic engineering of Halomonas campaniensis strain XH26 to remove competing pathways to enhance ectoine production
Authors: Shu Zhiwan , Zhang Xin , Wang Rong , Xing Jiangwa , Li Yongzhen , Zhu Derui , Shen Guoping 
Published: June 2023

AbstractEctoine has gained considerable attention as a high-value chemical with significant application potential and market demand. This study aimed to increase ectoine yields by blocking the metabolic shunt pathway of l-aspartate-4-semialdehyde, the precursor substrate in ectoine synthesis. The homoserine dehydrogenase encoded by hom in H. campaniensis strain XH26 is responsible for the metabolic shunt of l-aspartate-4-semialdehyde to glycine. CRISPR/Cas9 technology was used to seamlessly knockout hom, blocking the metabolic shunt pathway to increase ectoine yields. The ectoine yield of XH26/Δhom was 351.13 mg (g CDW)−1 after 48 h of incubation in 500 mL shake flasks using optimal medium with 1.5 mol L−1 NaCl, which was significantly higher than the 239.18 mg (g CDW)−1 of the wild-type strain. Additionally, the absence of the ectoine metabolic shunt pathway affects betaine synthesis, and thus the betaine yields of XH26/Δhom was 19.98 mg (g CDW)−1, considerably lower than the 69.58 mg (g CDW)−1 of the wild-type strain. Batch fermentation parameters were optimized, and the wild-type strain and XH26/Δhom were fermented in 3 L fermenters, resulting in a high ectoine yield of 587.09 mg (g CDW)−1 for the defective strain, which was significantly greater than the ectoine yield of 385.03 mg (g CDW)−1 of the wild-type strain. This study showed that blocking the metabolic shunt of synthetic substrates effectively increases ectoine production, and a reduction in the competitively compatible solute betaine appears to promote increased ectoine synthesis.
Global translational control by the transcriptional repressor TrcR in the filamentous cyanobacterium Anabaena sp. PCC 7120
Authors: Wang Zi-Qian , Yang Yiling , Zhang Ju-Yuan , Zeng Xiaoli , Zhang Cheng-Cai 
Published: June 2023

AbstractTranscriptional and translational regulations are important mechanisms for cell adaptation to environmental conditions. In addition to house-keeping tRNAs, the genome of the filamentous cyanobacterium Anabaena sp. strain PCC 7120 (Anabaena) has a long tRNA operon (trn operon) consisting of 26 genes present on a megaplasmid. The trn operon is repressed under standard culture conditions, but is activated under translational stress in the presence of antibiotics targeting translation. Using the toxic amino acid analog β-N-methylamino-L-alanine (BMAA) as a tool, we isolated and characterized several BMAA-resistance mutants from Anabaena, and identified one gene of unknown function, all0854, named as trcR, encoding a transcription factor belonging to the ribbon-helix-helix (RHH) family. We provide evidence that TrcR represses the expression of the trn operon and is thus the missing link between the trn operon and translational stress response. TrcR represses the expression of several other genes involved in translational control, and is required for maintaining translational fidelity. TrcR, as well as its binding sites, are highly conserved in cyanobacteria, and its functions represent an important mechanism for the coupling of the transcriptional and translational regulations in cyanobacteria.