bluuebunny/crossref_metadata_2025 huggingface dataset:
Juno Observations of Heavy Ion Energization During Transient Dipolarizations in Jupiter Magnetotail
Authors: Artemyev A. V. , Clark G. , Mauk B. , Vogt M. F. , Zhang X.‐J.
Published: May 2020

Transient magnetic reconnection and associated fast plasma flows led by dipolarization fronts play a crucial role in energetic particle acceleration in planetary magnetospheres. Despite large statistical observations on this phenomenon in the Earth's magnetotail, many important characteristics (e.g., mass or charge dependence of acceleration efficiency and acceleration scaling with the spatial scale of the system) of transient reconnection cannot be fully investigated with the limited parameter range of the Earth's magnetotail. The much larger Jovian magnetodisk, filled by a mixture of various heavy ions and protons, provides a unique opportunity for such investigations. In this study, we use recent Juno observations in Jupiter's magnetosphere to examine the properties of reconnection associated dipolarization fronts and charged particle acceleration. High‐energy fluxes of sulfur, oxygen, and hydrogen ions show clear mass‐dependent acceleration with energy ∼m1/3. We compare Juno observations with similar observations in the Earth's magnetotail and discuss possible mechanism for the observed ion acceleration.
Response of the Bay of Bengal to 3‐7‐Day Synoptic Oscillations During the Southwest Monsoon of 2019
Authors: Subrahmanyam Bulusu , Roman‐Stork Heather L. , Murty V. S. N.
Published: May 2020

The satellite‐derived precipitation over central India (73–78°E, 20–25°N) during the 2019 southwest monsoon season reveals that high‐amplitude 3‐7‐day synoptic oscillations dominated the other intraseasonal oscillations and contributed to the excess seasonal monsoon rainfall. In this paper, we address the contribution of 3‐7‐day synoptic oscillations in atmospheric and oceanic parameters during the 2019 southwest monsoon season over the Bay of Bengal (BoB). Our study reveals that both satellite observations and the Nucleus for European Modeling of the Ocean (NEMO) model simulations show high‐amplitude 3‐7‐day synoptic scale events during the 2019 monsoon. The upper 300 m of the water column responds to the basin‐scale 3‐7‐day synoptic oscillations as revealed in the vertical structures of NEMO model simulated temperature, salinity, and currents in the BoB. The synoptic scale wind stress drives strong currents in the shallow mixed layer due to salinity stratification in the northern BoB. The northward propagation of the synoptic scale oscillations is evident across the BoB but is capped to the base of the mixed layer, above which the propagation is affected by wind stress and the spread of freshwater flux. The 3‐7‐day synoptic scale oscillations in NEMO sea surface height appear to be related to synoptic scale wind‐driven convergence and divergence of waters through mesoscale eddy circulations that in turn contribute to thermocline variability, rather than the temperature and salinity in the mixed layer.
Mechanoradicals in tensed tendon collagen as a source of oxidative stress
Authors: Zapp Christopher , Obarska-Kosinska Agnieszka , Rennekamp Benedikt , Kurth Markus , Hudson David M. , Mercadante Davide , Barayeu Uladzimir , Dick Tobias P. , Denysenkov Vasyl , Prisner Thomas , Bennati Marina , Daday Csaba , Kappl Reinhard , Gräter Frauke
Published: May 2020

As established nearly a century ago, mechanoradicals originate from homolytic bond scission in polymers. The existence, nature and biological relevance of mechanoradicals in proteins, instead, are unknown. We here show that mechanical stress on collagen produces radicals and subsequently reactive oxygen species, essential biological signaling molecules. Electron-paramagnetic resonance (EPR) spectroscopy of stretched rat tail tendon, atomistic molecular dynamics simulations and quantum-chemical calculations show that the radicals form by bond scission in the direct vicinity of crosslinks in collagen. Radicals migrate to adjacent clusters of aromatic residues and stabilize on oxidized tyrosyl radicals, giving rise to a distinct EPR spectrum consistent with a stable dihydroxyphenylalanine (DOPA) radical. The protein mechanoradicals, as a yet undiscovered source of oxidative stress, finally convert into hydrogen peroxide. Our study suggests collagen I to have evolved as a radical sponge against mechano-oxidative damage and proposes a mechanism for exercise-induced oxidative stress and redox-mediated pathophysiological processes.
Effect of sequence depth and length in long-read assembly of the maize inbred NC358
Authors: Ou Shujun , Liu Jianing , Chougule Kapeel M. , Fungtammasan Arkarachai , Seetharam Arun S. , Stein Joshua C. , Llaca Victor , Manchanda Nancy , Gilbert Amanda M. , Wei Sharon , Chin Chen-Shan , Hufnagel David E. , Pedersen Sarah , Snodgrass Samantha J. , Fengler Kevin , Woodhouse Margaret , Walenz Brian P. , Koren Sergey , Phillippy Adam M. , Hannigan Brett T. , Dawe R. Kelly , Hirsch Candice N. , Hufford Matthew B. , Ware Doreen
Published: May 2020

Improvements in long-read data and scaffolding technologies have enabled rapid generation of reference-quality assemblies for complex genomes. Still, an assessment of critical sequence depth and read length is important for allocating limited resources. To this end, we have generated eight assemblies for the complex genome of the maize inbred line NC358 using PacBio datasets ranging from 20 to 75 × genomic depth and with N50 subread lengths of 11–21 kb. Assemblies with ≤30 × depth and N50 subread length of 11 kb are highly fragmented, with even low-copy genic regions showing degradation at 20 × depth. Distinct sequence-quality thresholds are observed for complete assembly of genes, transposable elements, and highly repetitive genomic features such as telomeres, heterochromatic knobs, and centromeres. In addition, we show high-quality optical maps can dramatically improve contiguity in even our most fragmented base assembly. This study provides a useful resource allocation reference to the community as long-read technologies continue to mature.
Btk SH2-kinase interface is critical for allosteric kinase activation and its targeting inhibits B-cell neoplasms
Authors: Duarte Daniel P. , Lamontanara Allan J. , La Sala Giuseppina , Jeong Sukyo , Sohn Yoo-Kyoung , Panjkovich Alejandro , Georgeon Sandrine , Kükenshöner Tim , Marcaida Maria J. , Pojer Florence , De Vivo Marco , Svergun Dmitri , Kim Hak-Sung , Dal Peraro Matteo , Hantschel Oliver
Published: May 2020

Bruton’s tyrosine kinase (Btk) is critical for B-cell maturation and activation. Btk loss-of-function mutations cause human X-linked agammaglobulinemia (XLA). In contrast, Btk signaling sustains growth of several B-cell neoplasms which may be treated with tyrosine kinase inhibitors (TKIs). Here, we uncovered the structural mechanism by which certain XLA mutations in the SH2 domain strongly perturb Btk activation. Using a combination of molecular dynamics (MD) simulations and small-angle X-ray scattering (SAXS), we discovered an allosteric interface between the SH2 and kinase domain required for Btk activation and to which multiple XLA mutations map. As allosteric interactions provide unique targeting opportunities, we developed an engineered repebody protein binding to the SH2 domain and able to disrupt the SH2-kinase interaction. The repebody prevents activation of wild-type and TKI-resistant Btk, inhibiting Btk-dependent signaling and proliferation of malignant B-cells. Therefore, the SH2-kinase interface is critical for Btk activation and a targetable site for allosteric inhibition.
The landscape of chromothripsis across adult cancer types
Authors: Voronina Natalia , Wong John K. L. , Hübschmann Daniel , Hlevnjak Mario , Uhrig Sebastian , Heilig Christoph E. , Horak Peter , Kreutzfeldt Simon , Mock Andreas , Stenzinger Albrecht , Hutter Barbara , Fröhlich Martina , Brors Benedikt , Jahn Arne , Klink Barbara , Gieldon Laura , Sieverling Lina , Feuerbach Lars , Chudasama Priya , Beck Katja , Kroiss Matthias , Heining Christoph , Möhrmann Lino , Fischer Andrea , Schröck Evelin , Glimm Hanno , Zapatka Marc , Lichter Peter , Fröhling Stefan , Ernst Aurélie
Published: May 2020

Chromothripsis is a recently identified mutational phenomenon, by which a presumably single catastrophic event generates extensive genomic rearrangements of one or a few chromosome(s). Considered as an early event in tumour development, this form of genome instability plays a prominent role in tumour onset. Chromothripsis prevalence might have been underestimated when using low-resolution methods, and pan-cancer studies based on sequencing are rare. Here we analyse chromothripsis in 28 tumour types covering all major adult cancers (634 tumours, 316 whole-genome and 318 whole-exome sequences). We show that chromothripsis affects a substantial proportion of human cancers, with a prevalence of 49% across all cases. Chromothripsis generates entity-specific genomic alterations driving tumour development, including clinically relevant druggable fusions. Chromothripsis is linked with specific telomere patterns and univocal mutational signatures in distinct tumour entities. Longitudinal analysis of chromothriptic patterns in 24 matched tumour pairs reveals insights in the clonal evolution of tumours with chromothripsis.
Par complex cluster formation mediated by phase separation
Authors: Liu Ziheng , Yang Ying , Gu Aihong , Xu Jiawen , Mao Ying , Lu Haojie , Hu Weiguo , Lei Qun-Ying , Li Zhouhua , Zhang Mingjie , Cai Yu , Wen Wenyu
Published: May 2020

The evolutionarily conserved Par3/Par6/aPKC complex regulates the polarity establishment of diverse cell types and distinct polarity-driven functions. However, how the Par complex is concentrated beneath the membrane to initiate cell polarization remains unclear. Here we show that the Par complex exhibits cell cycle-dependent condensation in Drosophila neuroblasts, driven by liquid–liquid phase separation. The open conformation of Par3 undergoes autonomous phase separation likely due to its NTD-mediated oligomerization. Par6, via C-terminal tail binding to Par3 PDZ3, can be enriched to Par3 condensates and in return dramatically promote Par3 phase separation. aPKC can also be concentrated to the Par3N/Par6 condensates as a client. Interestingly, activated aPKC can disperse the Par3/Par6 condensates via phosphorylation of Par3. Perturbations of Par3/Par6 phase separation impair the establishment of apical–basal polarity during neuroblast asymmetric divisions and lead to defective lineage development. We propose that phase separation may be a common mechanism for localized cortical condensation of cell polarity complexes.
Minimal lactazole scaffold for in vitro thiopeptide bioengineering
Authors: Vinogradov Alexander A. , Shimomura Morito , Goto Yuki , Ozaki Taro , Asamizu Shumpei , Sugai Yoshinori , Suga Hiroaki , Onaka Hiroyasu
Published: May 2020

Lactazole A is a cryptic thiopeptide from Streptomyces lactacystinaeus, encoded by a compact 9.8 kb biosynthetic gene cluster. Here, we establish a platform for in vitro biosynthesis of lactazole A, referred to as the FIT-Laz system, via a combination of the flexible in vitro translation (FIT) system with recombinantly produced lactazole biosynthetic enzymes. Systematic dissection of lactazole biosynthesis reveals remarkable substrate tolerance of the biosynthetic enzymes and leads to the development of the minimal lactazole scaffold, a construct requiring only 6 post-translational modifications for macrocyclization. Efficient assembly of such minimal thiopeptides with FIT-Laz opens access to diverse lactazole analogs with 10 consecutive mutations, 14- to 62-membered macrocycles, and 18 amino acid-long tail regions, as well as to hybrid thiopeptides containing non-proteinogenic amino acids. This work suggests that the minimal lactazole scaffold is amenable to extensive bioengineering and opens possibilities to explore untapped chemical space of thiopeptides.
Flexibility of intrinsically disordered degrons in AUX/IAA proteins reinforces auxin co-receptor assemblies
Authors: Niemeyer Michael , Moreno Castillo Elena , Ihling Christian H. , Iacobucci Claudio , Wilde Verona , Hellmuth Antje , Hoehenwarter Wolfgang , Samodelov Sophia L. , Zurbriggen Matias D. , Kastritis Panagiotis L. , Sinz Andrea , Calderón Villalobos Luz Irina A.
Published: May 2020

Cullin RING-type E3 ubiquitin ligases SCFTIR1/AFB1-5and their AUX/IAA targets perceive the phytohormone auxin. The F-box protein TIR1 binds a surface-exposed degron in AUX/IAAs promoting their ubiquitylation and rapid auxin-regulated proteasomal degradation. Here, by adopting biochemical, structural proteomics and in vivo approaches we unveil how flexibility in AUX/IAAs and regions in TIR1 affect their conformational ensemble allowing surface accessibility of degrons. We resolve TIR1·auxin·IAA7 and TIR1·auxin·IAA12 complex topology, and show that flexible intrinsically disordered regions (IDRs) in the degron’s vicinity, cooperatively position AUX/IAAs on TIR1. We identify essential residues at the TIR1 N- and C-termini, which provide non-native interaction interfaces with IDRs and the folded PB1 domain of AUX/IAAs. We thereby establish a role for IDRs in modulating auxin receptor assemblies. By securing AUX/IAAs on two opposite surfaces of TIR1, IDR diversity supports locally tailored positioning for targeted ubiquitylation, and might provide conformational flexibility for a multiplicity of functional states.
Structural basis of transmembrane coupling of the HIV-1 envelope glycoprotein
Authors: Piai Alessandro , Fu Qingshan , Cai Yongfei , Ghantous Fadi , Xiao Tianshu , Shaik Md Munan , Peng Hanqin , Rits-Volloch Sophia , Chen Wen , Seaman Michael S. , Chen Bing , Chou James J.
Published: May 2020

The prefusion conformation of HIV-1 envelope protein (Env) is recognized by most broadly neutralizing antibodies (bnAbs). Studies showed that alterations of its membrane-related components, including the transmembrane domain (TMD) and cytoplasmic tail (CT), can reshape the antigenic structure of the Env ectodomain. Using nuclear magnetic resonance (NMR) spectroscopy, we determine the structure of an Env segment encompassing the TMD and a large portion of the CT in bicelles. The structure reveals that the CT folds into amphipathic helices that wrap around the C-terminal end of the TMD, thereby forming a support baseplate for the rest of Env. NMR dynamics measurements provide evidences of dynamic coupling across the TMD between the ectodomain and CT. Pseudovirus-based neutralization assays suggest that CT-TMD interaction preferentially affects antigenic structure near the apex of the Env trimer. These results explain why the CT can modulate the Env antigenic properties and may facilitate HIV-1 Env-based vaccine design.
Variation among 532 genomes unveils the origin and evolutionary history of a global insect herbivore
Authors: You Minsheng , Ke Fushi , You Shijun , Wu Zhangyan , Liu Qingfeng , He Weiyi , Baxter Simon W. , Yuchi Zhiguang , Vasseur Liette , Gurr Geoff M. , Ward Christopher M. , Cerda Hugo , Yang Guang , Peng Lu , Jin Yuanchun , Xie Miao , Cai Lijun , Douglas Carl J. , Isman Murray B. , Goettel Mark S. , Song Qisheng , Fan Qinghai , Wang-Pruski Gefu , Lees David C. , Yue Zhen , Bai Jianlin , Liu Tiansheng , Lin Lianyun , Zheng Yunkai , Zeng Zhaohua , Lin Sheng , Wang Yue , Zhao Qian , Xia Xiaofeng , Chen Wenbin , Chen Lilin , Zou Mingmin , Liao Jinying , Gao Qiang , Fang Xiaodong , Yin Ye , Yang Huanming , Wang Jian , Han Liwei , Lin Yingjun , Lu Yanping , Zhuang Mousheng
Published: May 2020

The diamondback moth, Plutella xylostella is a cosmopolitan pest that has evolved resistance to all classes of insecticide, and costs the world economy an estimated US $4-5 billion annually. We analyse patterns of variation among 532 P. xylostella genomes, representing a worldwide sample of 114 populations. We find evidence that suggests South America is the geographical area of origin of this species, challenging earlier hypotheses of an Old-World origin. Our analysis indicates that Plutella xylostella has experienced three major expansions across the world, mainly facilitated by European colonization and global trade. We identify genomic signatures of selection in genes related to metabolic and signaling pathways that could be evidence of environmental adaptation. This evolutionary history of P. xylostella provides insights into transoceanic movements that have enabled it to become a worldwide pest.
Spider venom-derived peptide induces hyperalgesia in Nav1.7 knockout mice by activating Nav1.9 channels
Authors: Zhou Xi , Ma Tingbin , Yang Luyao , Peng Shuijiao , Li Lulu , Wang Zhouquan , Xiao Zhen , Zhang Qingfeng , Wang Li , Huang Yazhou , Chen Minzhi , Liang Songping , Zhang Xianwei , Liu Jing Yu , Liu Zhonghua
Published: May 2020

The sodium channels Nav1.7, Nav1.8 and Nav1.9 are critical for pain perception in peripheral nociceptors. Loss of function of Nav1.7 leads to congenital insensitivity to pain in humans. Here we show that the spider peptide toxin called HpTx1, first identified as an inhibitor of Kv4.2, restores nociception in Nav1.7 knockout (Nav1.7-KO) mice by enhancing the excitability of dorsal root ganglion neurons. HpTx1 inhibits Nav1.7 and activates Nav1.9 but does not affect Nav1.8. This toxin produces pain in wild-type (WT) and Nav1.7-KO mice, and attenuates nociception in Nav1.9-KO mice, but has no effect in Nav1.8-KO mice. These data indicate that HpTx1-induced hypersensitivity is mediated by Nav1.9 activation and offers pharmacological insight into the relationship of the three Nav channels in pain signalling.
Large mass-independent sulphur isotope anomalies link stratospheric volcanism to the Late Ordovician mass extinction
Authors: Hu Dongping , Li Menghan , Zhang Xiaolin , Turchyn Alexandra V. , Gong Yizhe , Shen Yanan
Published: May 2020

Volcanic eruptions are thought to be a key driver of rapid climate perturbations over geological time, such as global cooling, global warming, and changes in ocean chemistry. However, identification of stratospheric volcanic eruptions in the geological record and their causal link to the mass extinction events during the past 540 million years remains challenging. Here we report unexpected, large mass-independent sulphur isotopic compositions of pyrite with Δ33S of up to 0.91‰ in Late Ordovician sedimentary rocks from South China. The magnitude of the Δ33S is similar to that discovered in ice core sulphate originating from stratospheric volcanism. The coincidence between the large Δ33S and the first pulse of the Late Ordovician mass extinction about 445 million years ago suggests that stratospheric volcanic eruptions may have contributed to synergetic environmental deteriorations such as prolonged climatic perturbations and oceanic anoxia, related to the mass extinction.
Machine-learning-revealed statistics of the particle-carbon/binder detachment in lithium-ion battery cathodes
Authors: Jiang Zhisen , Li Jizhou , Yang Yang , Mu Linqin , Wei Chenxi , Yu Xiqian , Pianetta Piero , Zhao Kejie , Cloetens Peter , Lin Feng , Liu Yijin
Published: May 2020

The microstructure of a composite electrode determines how individual battery particles are charged and discharged in a lithium-ion battery. It is a frontier challenge to experimentally visualize and, subsequently, to understand the electrochemical consequences of battery particles’ evolving (de)attachment with the conductive matrix. Herein, we tackle this issue with a unique combination of multiscale experimental approaches, machine-learning-assisted statistical analysis, and experiment-informed mathematical modeling. Our results suggest that the degree of particle detachment is positively correlated with the charging rate and that smaller particles exhibit a higher degree of uncertainty in their detachment from the carbon/binder matrix. We further explore the feasibility and limitation of utilizing the reconstructed electron density as a proxy for the state-of-charge. Our findings highlight the importance of precisely quantifying the evolving nature of the battery electrode’s microstructure with statistical confidence, which is a key to maximize the utility of active particles towards higher battery capacity.
Interface enhanced functionalities in oxide superlattices under mechanical and electric boundary conditions
Authors: Wang Hongwei , Tang Fujie , Dhuvad Pratikkumar H. , Wu Xifan
Published: May 2020

In recent years, the inverse design of artificial materials, in the format of thin-films and superlattices, has been an active sub-field in material science. From a joint effort from both experiment and theory, scientists are searching for new engineering methods or design rules so that the materials can be custom designed with desired functionalities in theory before the materials are actually synthesized by epitaxial growth technique in laboratory. In this article, we provide a short summary of the recently proposed epitaxial strain and interface design approaches for the functional artificial oxide heterostructures. The underlying physical mechanism enabling the enhanced functional properties, such as ferroelectricity and multiferroics, are briefly reviewed. In particular, focused discussions are made on the proper treatments of both mechanical and electric boundary conditions when the oxide thin-films and superlattices are theoretically modeled by first-principles computer simulations.
Transcript profiling provides insights into molecular processes during shoot elongation in temperature-sensitive peach (Prunus persica)
Authors: Lian Xiaodong , Tan Bin , Yan Liu , Jiang Chao , Cheng Jun , Zheng Xianbo , Wang Wei , Chen Tanxing , Ye Xia , Li Jidong , Feng Jiancan
Published: May 2020

Plant growth caused by ambient temperature is thought to be regulated by a complex transcriptional network. A temperature-sensitive peach (Prunus persica) was used to explore the mechanisms behind shoot internode elongation at elevated temperatures. There was a significantly positive correlation between the length of the terminal internode (TIL) and the maximum temperature three days prior to the measuring day. Four critical growth stages (initial period and initial elongation period at lower temperature, rapid growth period and stable growth period at higher temperature) were selected for comparative RNA-seq analysis. About 6.64G clean bases were obtained for each library, and 88.27% of the data were mapped to the reference genome. Differentially expressed gene (DEG) analysis among the three pairwise comparisons resulted in the detection of several genes related to the shoot elongation in temperature-sensitive peach. HSFAs were up-regulated in response to the elevated temperature, while the up-regulated expression of HSPs might influence hormone signaling pathways. Most of DEGs involved in auxin, abscisic acid and jasmonic acid were up-regulated, while some involved in cytokinin and brassinosteroid were down-regulated. Genes related to ethylene, salicylic acid and circadian rhythm were also differentially expressed. Genes related to aquaporins, expansins, pectinesterases and endoglucanase were up-regulated, which would promote cell elongation. These results lay a foundation for further dissection of the regulatory mechanisms underlying shoot elongation at elevated temperatures.
The relation of Bleomycin Delivery Efficiency to Microbubble Sonodestruction and Cavitation Spectral Characteristics
Authors: Maciulevičius Martynas , Tamošiūnas Mindaugas , Venslauskas Mindaugas S. , Šatkauskas Saulius
Published: May 2020

The concurrent assessment of principal sonoporation factors has been accomplished in a single systemic study. Microbubble sonodestruction dynamics and cavitation spectral characteristics, ultrasound scattering and attenuation, were examined in relation to the intracellular delivery of anticancer drug, bleomycin. Experiments were conducted on Chinese hamster ovary cells coadministered with Sonovue microbubbles. Detailed analysis of the scattering and attenuation temporal functions culminated in quantification of metrics, inertial cavitation dose and attenuation rate, suitable for cavitation control. The exponents, representing microbubble sonodestruction kinetics were exploited to derive dosimetric, microbubble sonodestruction rate. High intracorrelation between empirically-attained metrics defines the relations which indicate deep physical interdependencies within inherent phenomena. Subsequently each quantified metric was validated to be well-applicable to prognosticate the efficacy of bleomycin delivery and cell viability, as indicated by strong overall correlation (R2 > 0.85). Presented results draw valuable insights in sonoporation dosimetry and contribute towards the development of universal sonoporation dosimetry model. Both bleomycin delivery and cell viability reach their respective plateau levels by the time, required to attain total microbubble sonodestruction, which accord with scattering and attenuation decrease to background levels. This suggests a well-defined criterion, feasible through signal-registration, universally employable to set optimal duration of exposure for efficient sonoporation outcome.
Disorder by design: A data-driven approach to amorphous semiconductors without total-energy functionals
Authors: Limbu Dil K. , Elliott Stephen R. , Atta-Fynn Raymond , Biswas Parthapratim
Published: May 2020

X-ray diffraction, Amorphous silicon, Multi-objective optimization, Monte Carlo methods. This paper addresses a difficult inverse problem that involves the reconstruction of a three-dimensional model of tetrahedral amorphous semiconductors via inversion of diffraction data. By posing the material-structure determination as a multiobjective optimization program, it has been shown that the problem can be solved accurately using a few structural constraints, but no total-energy functionals/forces, which describe the local chemistry of amorphous networks. The approach yields highly realistic models of amorphous silicon, with no or only a few coordination defects (≤1%), a narrow bond-angle distribution of width 9–11.5°, and an electronic gap of 0.8–1.4 eV. These data-driven information-based models have been found to produce electronic and vibrational properties of a-Si that match accurately with experimental data and rival that of the Wooten-Winer-Weaire models. The study confirms the effectiveness of a multiobjective optimization approach to the structural determination of complex materials, and resolves a long-standing dispute concerning the uniqueness of a model of tetrahedral amorphous semiconductors obtained via inversion of diffraction data.
Biochemical characteristics of the chondrocyte-enriched SNORC protein and its transcriptional regulation by SOX9
Authors: Jaiswal Prashant Kumar , Aljebali Latifa , Gaumond Marie-Hélène , Oh Chun-do , Yasuda Hideyo , Moffatt Pierre
Published: May 2020

Snorc (Small NOvel Rich in Cartilage) has been identified as a chondrocyte-specific gene in the mouse. Yet little is known about the SNORC protein biochemical properties, and mechanistically how the gene is regulated transcriptionally in a tissue-specific manner. The goals of the present study were to shed light on those important aspects. The chondrocyte nature of Snorc expression was confirmed in mouse and rat tissues, in differentiated (day 7) ATDC5, and in RCS cells where it was constitutive. Topological mapping and biochemical analysis brought experimental evidences that SNORC is a type I protein carrying a chondroitin sulfate (CS) attached to serine 44. The anomalous migration of SNORC on SDS-PAGE was due to its primary polypeptide features, suggesting no additional post-translational modifications apart from the CS glycosaminoglycan. A highly conserved SOX9-binding enhancer located in intron 1 was necessary to drive transcription of Snorc in the mouse, rat, and human. The enhancer was active independently of orientation and whether located in a heterologous promoter or intron. Crispr-mediated inactivation of the enhancer in RCS cells caused reduction of Snorc. Transgenic mice carrying the intronic multimerized enhancer drove high expression of a βGeo reporter in chondrocytes, but not in the hypertrophic zone. Altogether these data confirmed the chondrocyte-specific nature of Snorc and revealed dependency on the intronic enhancer binding of SOX9 for transcription.
Incidental learning of group trust: Predictive gaze cue matters
Authors: Sun Zhongqiang , He Zhihui , Zhang Guochao , Li Xinyu , Yu Wenjun
Published: May 2020

Human gaze is a subtle cue to deliver information and helps impression formation in social interactions. People automatically follow the gaze direction of others and shift their attention accordingly, as well as determine the trustworthiness of others based on the predictable validity of their gaze behavior, yet it remains unclear how this works at the collective level. Therefore, the current study is the first to explore the incidental learning of trust from a group’s gaze behavior. To simulate different patterns of perceiving collective information in real life, two ways of presenting group member gazes were used in the object categorization task, the simultaneous way in Experiment 1 and the sequential way in Experiment 3, and a sampling strategy was ruled out in Experiment 2. Converging findings in experiments demonstrated a typical gaze-cueing effect, and more importantly, the Predictive-valid group obtained more trust compared to the Predictive-invalid group. To enrich and expand the applicability of the incidental trust learning effect from gazes, the current study provides supportive evidence at the collective level, confirming that humans have an efficient capability to process gaze information of groups.
The pivot point arginines identified in the β-pinwheel structure of C-terminal domain from Salmonella Typhi DNA Gyrase A subunit
Authors: Sachdeva Ekta , Kaur Gurpreet , Tiwari Pragya , Gupta Deepali , Singh Tej P. , Ethayathulla Abdul S. , Kaur Punit
Published: May 2020

The essentiality of DNA Gyrase in basic cellular processes in bacterial pathogens makes it an ideal drug target. Though the Gyrase has a conserved mechanism of action, the complete DNA wrapping and binding process is still unknown. In this study, we have identified six arginine residues R556, R612, R667, R716, R766, and R817 in the DNA GyraseA – C-terminal domain from Salmonella enterica serovar Typhi (StGyrA-CTD) to be essential for DNA wrapping and sliding by a sequence and structure analysis. Through site-directed mutagenesis and EMSA studies, we observed that the substitution of R667 (blade 3) and R716 (blade 4) in StGyrA-CTD led to loss of DNA binding. Whereas, upon mutation of residue R612 (blade2), R766 (blade5) and R817 (blade6) along with supporting residue R712 (blade 4) a decrease in binding affinity was seen. Our results indicate that R667 and R716 act as a pivot point in DNA wrapping and sliding during gyrase catalytic activity. In this study, we propose that the DNA wrapping mechanism commences with DNA binding at blade3 and blade4 followed by other blades to facilitate the DNA sliding during supercoiling activity. This study provides a better understanding of the DNA binding and wrapping mechanism of GyrA-CTD in DNA Gyrase.
Body-size Scaling is Related to Gut Microbial Diversity, Metabolism and Dietary Niche of Arboreal Folivorous Flying Squirrels
Authors: Liu Po-Yu , Cheng An-Chi , Huang Shiao-Wei , Lu Hsiao-Pei , Oshida Tatsuo , Liu Wenhua , Yu Hon-Tsen
Published: May 2020

Thermal homeostasis of mammals is constrained by body-size scaling. Consequently, small mammals require considerable energy to maintain a high mass-specific metabolic rate (MSMR) and sustain target body temperature. In association with gut microbiota, mammalian hosts acquire absorbable molecules and fulfill their metabolic requirements. Our objective was to characterize gut microbes in wild mammals and relate those findings to host body-size scaling. Two large (Petaurista philippensis grandis and P. alborufus lena), one medium (Trogopterus xanthipes) and one small (Pteromys volans orii) species of flying squirrels (FS) were studied. Using 16S rRNA genes, 1,104 OTUs were detected from four FS, with 1.99% of OTUs shared among all FS. Although all FS gut microbiota were dominated by Firmicutes, they were constituted by different bacterial families. Moreover, Bacteroidetes accounted for up to 19% of gut microbiota in small FS, but was absent in large FS. Finally, based on metagenome predictions, carbohydrate and amino acid metabolism genes were enriched in small body-size FS. In conclusion, gut microbiota compositions and predictive metabolic functions were characteristic of body-size in FS, consistent with their adaptations to folivorous dietary niches.
Local biases drive, but do not determine, the perception of illusory trajectories
Authors: Gheorghes Tamara N. , Richardson Paul , Reidy John
Published: May 2020

When a dot moves horizontally across a set of tilted lines of alternating orientations, the dot appears to be moving up and down along its trajectory. This perceptual phenomenon, known as the slalom illusion, reveals a mismatch between the veridical motion signals and the subjective percept of the motion trajectory, which has not been comprehensively explained. In the present study, we investigated the empirical boundaries of the slalom illusion using psychophysical methods. The phenomenon was found to occur both under conditions of smooth pursuit eye movements and constant fixation, and to be consistently amplified by intermittently occluding the dot trajectory. When the motion direction of the dot was not constant, however, the stimulus display did not elicit the expected illusory percept. These findings confirm that a local bias towards perpendicularity at the intersection points between the dot trajectory and the tilted lines cause the illusion, but also highlight that higher-level cortical processes are involved in interpreting and amplifying the biased local motion signals into a global illusion of trajectory perception.
Repeated evolution of durophagy during ichthyosaur radiation after mass extinction indicated by hidden dentition
Authors: Huang Jian-dong , Motani Ryosuke , Jiang Da-yong , Ren Xin-xin , Tintori Andrea , Rieppel Olivier , Zhou Min , Hu Yuan-chao , Zhang Rong
Published: May 2020

Marine tetrapods quickly diversified and were established as marine top predators after the end-Permian Mass extinction (EPME). Ichthyosaurs were the forerunner of this rapid radiation but the main drivers of the diversification are poorly understood. Cartorhynchus lenticarpus is a basal ichthyosauriform with the least degree of aquatic adaptation, holding a key to identifying such a driver. The unique specimen appeared edentulous based on what was exposed but a CT scanning revealed that the species indeed had rounded teeth that are nearly perpendicular to the jaw rami, and thus completely concealed in lateral view. There are three dental rows per jaw ramus, and the root lacks infoldings of the dentine typical of ichthyopterygians. The well-developed and worn molariform dentition with three tooth rows supports the previous inference that the specimen is not of a juvenile. The premaxilla and the corresponding part of the dentary are edentulous. Molariform dentition evolved three to five times independently within Ichthyosauriformes in the Early and Middle Triassic. Convergent exploitation of hard-shelled invertebrates by different subclades of ichthyosauriforms likely fueled the rapid taxonomic diversification of the group after EPME.
Proteomic analysis upon peach fruit infection with Monilinia fructicola and M. laxa identify responses contributing to brown rot resistance
Authors: Papavasileiou Antonios , Tanou Georgia , Samaras Anastasios , Samiotaki Martina , Molassiotis Athanassios , Karaoglanidis George
Published: May 2020

Brown rot, caused by Monilinia spp., is a major peach disease worldwide. In this study, the response of peach cultivars Royal Glory (RG) and Rich Lady (RL) to infection by Monilinia fructicola or Monilinia laxa, was characterized. Phenotypic data, after artificial inoculations, revealed that ‘RL’ was relatively susceptible whereas ‘RG’ was moderately resistant to Monilinia spp. Comparative proteomic analysis identified mesocarp proteins of the 2 cultivars whose accumulation were altered by the 2 Monilinia species. Functional analysis indicated that pathogen-affected proteins in ‘RG’ were mainly involved in energy and metabolism, while, differentially accumulated proteins by the pathogen presence in ‘RL’ were involved in disease/defense and metabolism. A higher number of proteins was differentiated in ‘RG’ fruit compared to ‘RL’. Upon Monilinia spp. infection, various proteins were-down accumulated in ‘RL’ fruit. Protein identification by mass spectrometric analysis revealed that several defense-related proteins including thaumatin, formate dehydrogenase, S-formylglutathione hydrolase, CBS domain-containing protein, HSP70, and glutathione S-transferase were up-accumulated in ‘RG’ fruit following inoculation. The expression profile of selected defense-related genes, such as major latex allergen, 1-aminocyclopropane-1-carboxylate deaminase and UDP-glycoltransferase was assessed by RT-PCR. This is the first study deciphering differential regulations of peach fruit proteome upon Monilinia infection elucidating resistance responses.
Strain-induced structure and oxygen transport interactions in epitaxial La0.6Sr0.4CoO3−δ thin films
Authors: Ivanov Yurii P. , Kubicek Markus , Siebenhofer Matthäus , Viernstein Alexander , Hutter Herbert , Fleig Jürgen , Chuvilin Andrey , Zhang Zaoli
Published: May 2020

The possibility to control oxygen transport in one of the most promising solid oxide fuel cell cathode materials, La0.6Sr0.4CoO3−δ, by controlling lattice strain raises questions regarding the contribution of atomic scale effects. Here, high-resolution transmission electron microscopy revealed the different atomic structures in La0.6Sr0.4CoO3−δ thin films grown under tensile and compressive strain conditions. The atomic structure of the tensile-strained film indicated significant local concentration of the oxygen vacancies, with the average value of the oxygen non-stoichiometry being much larger than for the compressive-strained film. In addition to the vacancy concentration differences that are measured by isotope exchange depth profiling, significant vacancy ordering was found in tensile-strained films. This understanding might be useful for tuning the atomic structure of La0.6Sr0.4CoO3−δ thin films to optimize cathode performance.
Influence of hair treatments on detection of antiretrovirals by mass spectrometry imaging
Authors: Gilliland William M. , White Nicole R. , Yam Bryan H. , Mwangi Joseph N. , Prince Heather M. A. , Weideman Ann Marie , Kashuba Angela D. M. , Rosen Elias P.
Published: May 2020

IR-MALDESI mass spectrometry imaging is used to assess the effect of hair treatments on multiple antiretrovirals in single hair strands.
An efficient assay for identification and quantitative evaluation of potential polysialyltransferase inhibitors
Authors: Guo Xiaoxiao , Malcolm Jodie R. , Ali Marrwa M. , Ribeiro Morais Goreti , Shnyder Steven D. , Loadman Paul M. , Patterson Laurence H. , Falconer Robert A.
Published: May 2020

An efficient assay for quantitative identification and evaluation of polysialyltransferase inhibitors was developed, with significant application for cancer drug discovery.
Dispersive micro-solid phase extraction based on a graphene/polydopamine composite for the detection of pyrethroids in water samples
Authors: Xu Qinqin , Qiao Kexin , Yan Chen , Liu Zikai , Lu Runhua , Zhou Wenfeng
Published: May 2020

A simple, rapid, precise and environmentally friendly microextraction named dispersive micro-solid phase extraction based on a graphene/polydopamine composite as a sorbent was investigated for the analysis of four pyrethroids in water samples.
Flower-like Ag coated with molecularly imprinted polymers as a surface-enhanced Raman scattering substrate for the sensitive and selective detection of glibenclamide
Authors: Ren Xiaohui , Li Xin
Published: May 2020

The preparation and detection process of flower-like Ag@molecularly imprinted polymers (MIPs) as a surface-enhanced Raman scattering (SERS) sensor (A), and the molecular electrostatic potential (MEP) of template molecule and functional monomer (B).
Helicity of a polyacetylene directed by molecular recognition of biscalixarene and fullerene
Authors: Hirao Takehiro , Iwabe Yoshiki , Hisano Naoyuki , Haino Takeharu
Published: May 2020

The dynamic helix interconversion of the C60-appended polyacetylene was directed by the molecular recognition of a chiral biscalix[5]arene.
Solvent-free ageing reactions of rare earth element oxides: from geomimetic synthesis of new metal–organic materials towards a simple, environmentally friendly separation of scandium
Authors: Huskić Igor , Arhangelskis Mihails , Friščić Tomislav
Published: May 2020

Solvent-free accelerated ageing converts metal oxides into metal oxalate frameworks, enabling simple separation of scandium from other rare earth elements.
Flexible polyurethanes, renewable fuels, and flavorings from a microalgae oil waste stream
Authors: Phung Hai Thien An , Neelakantan Nitin , Tessman Marissa , Sherman Suryendra D. , Griffin Graham , Pomeroy Robert , Mayfield Stephen P. , Burkart Michael D.
Published: May 2020

To achieve sustainably-sourced polymers from algae, azelaic acid was prepared from an algae oil waste stream and converted into a flexible polyurethane foam. The heptanoic acid co-product was converted into both a flavoring and a renewable solvent.
Construction and application of a nonenzymatic ascorbic acid sensor based on a NiO1.0/polyaniline3.0 hybrid
Authors: Zhu Shichao , Xie Aijuan , Wei Bingyan , Tao Xiang , Zhang Jianghui , Peng Wenhao , Liu Chenyang , Gu Linyang , Xu Chengfei , Luo Shiping
Published: May 2020

The schematic diagram for the fabrication process of NiO/PANI.
Whole-genome sequence analysis and homology modelling of the main protease and non-structural protein 3 of SARS-CoV-2 reveal an aza-peptide and a lead inhibitor with possible antiviral properties
Authors: Shanker Arun K. , Bhanu Divya , Alluri Anjani , Gupta Samriddhi
Published: May 2020

SARS-CoV-2 3CLpro shows homology in binding to an aza-peptide epoxide (APE) known for the irreversible inhibition of main peptidase in SARS-CoV.
POM-based dyes featuring rigidified bithiophene π linkers: potential high-efficiency dyes for dye-sensitized solar cells
Authors: Gao Yu , Guan Wei , Yan Li-Kai , Xu Yan-Hong
Published: May 2020

A series of POM-based dyes with a triphenylamine electron donor group, cyanoacrylic acid electron acceptor group and different π linkers of thiophene derivatives were systematically investigated to analyze the influence of a rigidified bithiophene with fastening atoms (C and N) on the performance of dye-sensitized solar cells (DSSCs) based on density functional theory (DFT) and time-dependent DFT (TD-DFT) calculations.
The influence of surface roughness on the adhesive interactions and phase behavior of suspensions of calcite nanoparticles
Authors: Olarte-Plata Juan D. , Brekke-Svaland Gøran , Bresme Fernando
Published: May 2020

Nanoparticle roughness influences the adhesive interactions between calcite nanoparticles inhibiting the formation of gel phases.
Direct carbonization of organic solvents toward graphene quantum dots
Authors: Liu Hongji , Lv Xiaotong , Li Changwei , Qian Yong , Wang Xingyu , Hu Lin , Wang Yucai , Lin Wenchu , Wang Hui
Published: May 2020

We report the direct carbonization of organic solvents to graphene quantum dots without the addition of catalysts or molecular precursors.
Promoting the sulfur conversion kinetics via a solid auxiliary redox couple embedded in the cathode of Li–S batteries
Authors: Bizuneh Girum Girma , Fan Jingmin , Xu Pan , Yuan Ruming , Cao Lin , Zheng Mingsen , Dong Quan-Feng
Published: May 2020

Cobalt phthalocyanine-solid auxiliary redox mediator-embedded graphene, expediting the conversion of polysulfides and activation of Li2S in Li–S batteries.
Wall entrapment of peritrichous bacteria: a mesoscale hydrodynamics simulation study
Authors: Mousavi S. Mahdiyeh , Gompper Gerhard , Winkler Roland G.
Published: May 2020

Microswimmers such asE. Colibacteria accumulate at walls. Mesoscale hydrodynamic simulations show an intriguing dynamics due to the interplay of hydrodynamic and steric interactions, and a pronounced wobbling motion.
Spatial information in phased‐array radar
Authors: Xu Dazhuan , Shi Chao , Zhou Ying , Tu Weilin
Published: May 2020

In this study, the application of information theory to describe radar measurement problems is investigated. In Shannon's information theory, mutual information is used to quantify the reduction in the a priori uncertainty of the transmitted message. Similarly, the authors define the spatial information in the phased‐array radar as the mutual information between range, direction of arrival (DOA), scattering properties, and the received signal. Such information content is composed of two parts. The first part is range‐DOA information. The theoretical expression and its asymptotic upper bound are presented in a single target scenario. It is concluded that the range information is independent of DOA information at high signal‐to‐noise ratio. The relationship between the upper bound and the Cramér‐Rao bound is discussed. The second part is scattering information. The corresponding expression is formulated theoretically. Based on spatial information, the authors put forth a definition of entropy error (EE) to evaluate the estimation performance in the phased‐array radar. Numerical simulation of the information content confirms their theoretical observations. The regularity of information change reflects the information acquisition efficiency of a radar system, providing guidance for system designers. Numerical results of EE are also presented to demonstrate its effectiveness as an evaluation index.
Frequency regulation support from aggregation of air conditioners based on the trigger value local update strategy
Authors: Ji Yongli , Xu Qingshan
Published: May 2020

As the penetration of renewable energy sources increases, demand side resources like air conditioners (ACs), whose electricity consumptions account for a large share, present remarkable potentials as frequency reserves to maintain the electricity supply‐demand balance. This study proposes a hybrid control framework based on a central controller and local controllers, under which air conditioning loads managed by the load aggregator are constructed as a virtual generator for frequency regulation. A well‐founded setting and updating method of frequency deviation trigger values in consideration of lock on and off constraints is designed. In the level of the central controller, on the basis of priority lists, the actual droop curve composed of ACs is constructed and the initial frequency deviation trigger values are determined. In the level of the local controllers, on/off states of ACs are switched autonomously according to their trigger values. In order to prevent response power deviations caused by lock on and off constraints, a trigger value local update strategy is developed to adjust the frequency deviation trigger values in the local controllers, which would not increase communication burden between the central controller and local controllers. Simulation studies suggest the effectiveness of the proposed method.