bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Global Teleconnection Signature of the Madden‐Julian Oscillation and Its Modulation by the Quasi‐Biennial Oscillation
Authors: Toms Benjamin A. , Barnes Elizabeth A. , Maloney Eric D. , van den Heever Susan C. 
Published: March 2020

AbstractRecent research has suggested that the tropical and extratropical character of the Madden‐Julian oscillation (MJO) depends on the state of the stratospheric quasi‐biennial oscillation (QBO). With this in mind, we use both reanalysis and a global climate model (CESM2‐WACCM) to analyze the global character of upper tropospheric‐lower stratospheric geopotential height anomalies connected with the MJO and quantify dependencies of these teleconnections on the state of the QBO. We find that the global teleconnection signature of the MJO depends upon the state of the QBO. Globally, within reanalysis the fraction of 20‐ to 90‐day 250‐hPa geopotential height variance linked to the MJO is largest during boreal winter and summer for easterly QBO phases and smallest during westerly QBO phases of boreal winter. The difference between QBO phases is mostly driven by changes in the tropical signature of the MJO, although during boreal winter the Northern Hemispheric teleconnections are particularly more prominent during easterly QBO phases. Otherwise, the QBO modulation of extratropical MJO teleconnections is mainly realized through changes in the locations of the teleconnections. A QBO‐MJO relationship is also apparent within CESM2‐WACCM but is weaker than that observed. This extratropical modulation implies that the regions that benefit from increased subseasonal predictability due to the MJO may also change as a function of the QBO. In a broader sense, these findings emphasize that knowledge of the tropical stratospheric state, particularly as it relates to the QBO, is important for understanding the connections between the MJO and the extratropics.
MdATG18a overexpression improves basal thermotolerance in transgenic apple by decreasing damage to chloroplasts
Authors: Huo Liuqing , Sun Xun , Guo Zijian , Jia Xin , Che Runmin , Sun Yiming , Zhu Yanfei , Wang Ping , Gong Xiaoqing , Ma Fengwang 
Published: March 2020

AbstractHigh temperature is an abiotic stress factor that threatens plant growth and development. Autophagy in response to heat stress involves the selective removal of heat-induced protein complexes. Previously, we showed that a crucial autophagy protein from apple, MdATG18a, has a positive effect on drought tolerance. In the present study, we treated transgenic apple (Malus domestica) plants overexpressing MdATG18a with high temperature and found that autophagy protected them from heat stress. Overexpression of MdATG18a in apple enhanced antioxidase activity and contributed to the production of increased beneficial antioxidants under heat stress. Transgenic apple plants exhibited higher photosynthetic capacity, as shown by the rate of CO2 assimilation, the maximum photochemical efficiency of photosystem II (PSII), the effective quantum yield, and the electron transport rates in photosystems I and II (PSI and PSII, respectively). We also detected elevated autophagic activity and reduced damage to chloroplasts in transgenic plants compared to WT plants. In addition, the transcriptional activities of several HSP genes were increased in transgenic apple plants. In summary, we propose that autophagy plays a critical role in basal thermotolerance in apple, primarily through a combination of enhanced antioxidant activity and reduced chloroplast damage.
A temporal gene expression map of Chrysanthemum leaves infected with Alternaria alternata reveals different stages of defense mechanisms
Authors: Liu Ye , Xin Jingjing , Liu Lina , Song Aiping , Guan Zhiyong , Fang Weimin , Chen Fadi 
Published: March 2020

AbstractChrysanthemum (Chrysanthemum morifolium) black spot disease (CBS) poses a major threat to Chrysanthemum cultivation owing to suitable climate conditions and current lack of resistant cultivars for greenhouse cultivation. In this study, we identified a number of genes that respond to Alternaria alternata infection in resistant and susceptible Chrysanthemum cultivars. Based on RNA sequencing technology and a weighted gene coexpression network analysis (WGCNA), we constructed a model to elucidate the response of Chrysanthemum leaves to A. alternata infection at different stages and compared the mapped response of the resistant cultivar ‘Jinba’ to that of the susceptible cultivar ‘Zaoyihong’. In the early stage of infection, when lesions had not yet formed, abscisic acid (ABA), salicylic acid (SA) and EDS1-mediated resistance played important roles in the Chrysanthemum defense system. With the formation of necrotic lesions, ethylene (ET) metabolism and the Ca2+ signal transduction pathway strongly responded to A. alternata infection. During the late stage, when necrotic lesions continued to expand, members of the multidrug and toxic compound extrusion (MATE) gene family were highly expressed, and their products may be involved in defense against A. alternata invasion by exporting toxins produced by the pathogen, which plays important roles in the pathogenicity of A. alternata. Furthermore, the function of hub genes was verified by qPCR and transgenic assays. The identification of hub genes at different stages, the comparison of hub genes between the two cultivars and the highly expressed genes in the resistant cultivar ‘Jinba’ provide a theoretical basis for breeding cultivars resistant to CBS.
Evolution and roles of cytokinin genes in angiosperms 2: Do ancient CKXs play housekeeping roles while non-ancient CKXs play regulatory roles?
Authors: Wang Xiaojing , Ding Jing , Lin Shanshan , Liu Decai , Gu Tingting , Wu Han , Trigiano Robert N. , McAvoy Richard , Huang Jinling , Li Yi 
Published: March 2020

AbstractCytokinin oxidase/dehydrogenase (CKX) is a key enzyme responsible for the degradation of endogenous cytokinins. However, the origins and roles of CKX genes in angiosperm evolution remain unclear. Based on comprehensive bioinformatic and transgenic plant analyses, we demonstrate that the CKXs of land plants most likely originated from an ancient chlamydial endosymbiont during primary endosymbiosis. We refer to the CKXs retaining evolutionarily ancient characteristics as “ancient CKXs” and those that have expanded and functionally diverged in angiosperms as “non-ancient CKXs”. We show that the expression of some non-ancient CKXs is rapidly inducible within 15 min upon the dehydration of Arabidopsis, while the ancient CKX (AtCKX7) is not drought responsive. Tobacco plants overexpressing a non-ancient CKX display improved oxidative and drought tolerance and root growth. Previous mutant studies have shown that non-ancient CKXs regulate organ development, particularly that of flowers. Furthermore, ancient CKXs preferentially degrade cis-zeatin (cZ)-type cytokinins, while non-ancient CKXs preferentially target N6-(Δ2-isopentenyl) adenines (iPs) and trans-zeatins (tZs). Based on the results of this work, an accompanying study (Wang et al. 10.1038/s41438-019-0211-x) and previous studies, we hypothesize that non-ancient CKXs and their preferred substrates of iP/tZ-type cytokinins regulate angiosperm organ development and environmental stress responses, while ancient CKXs and their preferred substrates of cZs play a housekeeping role, which echoes the conclusions and hypothesis described in the accompanying report (Wang, X. et al. Evolution and roles of cytokinin genes in angiosperms 1: Doancient IPTs play housekeeping while non-ancient IPTs play regulatory roles? Hortic Res7, (2020). 10.1038/s41438-019-0211-x).
Identification and distribution of a single nucleotide polymorphism responsible for the catechin content in tea plants
Authors: Jiang Chen-Kai , Ma Jian-Qiang , Liu Yu-Fei , Chen Jie-Dan , Ni De-Jiang , Chen Liang 
Published: March 2020

AbstractCatechins are the predominant products in tea plants and have essential functions for both plants and humans. Several genes encoding the enzymes regulating catechin biosynthesis have been identified, and the identification of single nucleotide polymorphisms (SNPs) resulting in nonsynonymous mutations within these genes can be used to establish a functional link to catechin content. Therefore, the transcriptomes of two parents and four filial offspring were sequenced using next-generation sequencing technology and aligned to the reference genome to enable SNP mining. Subsequently, 176 tea plant accessions were genotyped based on candidate SNPs using kompetitive allele-specific polymerase chain reaction (KASP). The catechin contents of these samples were characterized by high-performance liquid chromatography (HPLC), and analysis of variance (ANOVA) was subsequently performed to determine the relationship between genotypes and catechin content. As a result of these efforts, a SNP within the chalcone synthase (CHS) gene was shown to be functionally associated with catechin content. Furthermore, the geographical and interspecific distribution of this SNP was investigated. Collectively, these results will contribute to the early evaluation of tea plants and serve as a rapid tool for accelerating targeted efforts in tea breeding.
UGT74AF3 enzymes specifically catalyze the glucosylation of 4-hydroxy-2,5-dimethylfuran-3(2H)-one, an important volatile compound in Camellia sinensis
Authors: Chen Yongxian , Guo Xiangyang , Gao Ting , Zhang Na , Wan Xiaochun , Schwab Wilfried , Song Chuankui 
Published: March 2020

Abstract4-Hydroxy-2,5-dimethylfuran-3(2H)-one (HDMF) is an important odorant in some fruits, and is proposed to play a crucial role in the caramel-like notes of some teas. However, its biosynthesis and metabolism in tea plants are still unknown. Here, HDMF glucoside was unambiguously identified as a native metabolite in tea plants. A novel glucosyltransferase UGT74AF3a and its allelic protein UGT74AF3b specifically catalyzed the glucosylation of HDMF and the commercially important structural homologues 2 (or 5)-ethyl-4-hydroxy-5 (or 2)-methylfuran-3(2H)-one (EHMF) and 4-hydroxy-5-methylfuran-3(2H)-one (HMF) to their corresponding β-D-glucosides. Site-directed mutagenesis of UGT74AF3b to introduce a single A456V mutation resulted in improved HDMF and EHMF glucosylation activity and affected the sugar donor preference compared with that of the wild-type control enzyme. The accumulation of HDMF glucoside was consistent with the transcript levels of UGT74AF3 in different tea cultivars. In addition, transient UGT74AF3a overexpression in tobacco significantly increased the HDMF glucoside contents, and downregulation of UGT74AF3 transcripts in tea leaves significantly reduced the concentration of HDMF glucoside compared with the levels in the controls. The identification of HDMF glucoside in the tea plant and the discovery of a novel-specific UDP-glucose:HDMF glucosyltransferase in tea plants provide the foundation for improvement of tea flavor and the biotechnological production of HDMF glucoside.
QTL mapping and identification of SNP-haplotypes affecting yield components of Theobroma cacao L.
Authors: Fernandes Luciel dos Santos , Correa Fábio M. , Ingram Keith T. , de Almeida Alex-Alan Furtado , Royaert Stefan 
Published: March 2020

AbstractCacao is a crop of global relevance that faces constant demands for improved bean yield. However, little is known about the genomic regions controlling the crop yield and genes involved in cacao bean filling. Hence, to identify the quantitative trait loci (QTL) associated with cacao yield and bean filling, we performed a QTL mapping in a segregating mapping population comprising 459 trees of a cross between ‘TSH 1188’ and ‘CCN 51’. All variables showed considerable phenotypic variation and had moderate to high heritability values. We identified 24 QTLs using a genetic linkage map that contains 3526 single nucleotide polymorphism (SNP) markers. Haplotype analysis at the significant QTL region on chromosome IV pointed to the alleles from the maternal parent, ‘TSH 1188’, as the ones that affect the cacao yield components the most. The recombination events identified within these QTL regions allowed us to identify candidate genes that may take part in the different steps of pod growth and bean filling. Such candidate genes seem to play a significant role in the source-to-sink transport of sugars and amino acids, and lipid metabolism, such as fatty acid production. The SNP markers mapped in our study are now being used to select potential high-yielding cacao varieties through marker-assisted selection in our existing cacao-breeding experiments.
Genome-wide association studies for inflorescence type and remontancy in Hydrangea macrophylla
Authors: Wu Xingbo , Alexander Lisa W. 
Published: March 2020

AbstractInflorescence type and remontancy are two valuable traits in bigleaf hydrangea (Hydrangea macrophyllaL.) and both are recessively inherited. Molecular marker-assisted selection (MAS) can greatly reduce the time necessary to breed cultivars with desired traits. In this study, a genome-wide association study (GWAS) using 5803 single-nucleotide polymorphisms (SNPs) was performed using a panel of 82 bigleaf hydrangea cultivars. One SNP locus (Hy_CAPS_Inflo) associated with inflorescence type was identified with general linear model (GLM) and mixed linear model (MLM) methods that explained 65.5% and 36.1% of the phenotypic variations, respectively. Twenty-three SNPs associated with remontancy were detected in GLM whereas no SNP was detected in MLM. The SNP locus (Hy_CAPS_Inflo) was converted to a cleaved amplified polymorphic sequence (CAPS) marker that showed absolute identification accuracy (100%) of inflorescence type in a validation panel consisting of eighteenH. macrophyllacultivars. The SNP was investigated in 341 F1progenies using genotyping by sequencing (GBS) and co-segregated with inflorescence type (χ2 = 0.12;P = 0.73). The SNP was subsequently used for breeding selection using kompetitive allele specific PCR (KASP) technology. Future directions for the use of genomics and MAS in hydrangea breeding improvement are discussed. The results presented in this study provide insights for further research on understanding genetic mechanisms behind inflorescence type and remontancy inH. macrophylla. The CAPS and KASP markers developed here will be immediately useful for applying MAS to accelerate breeding improvement in hydrangea.
Enhanced heat tolerance of viral-infected aphids leads to niche expansion and reduced interspecific competition
Authors: Porras Mitzy F. , Navas Carlos A. , Marden James H. , Mescher Mark C. , De Moraes Consuelo M. , Pincebourde Sylvain , Sandoval-Mojica Andrés , Raygoza-Garay Juan A. , Holguin German A. , Rajotte Edwin G. , Carlo Tomás A. 
Published: March 2020

AbstractVector-borne pathogens are known to alter the phenotypes of their primary hosts and vectors, with implications for disease transmission as well as ecology. Here we show that a plant virus, barley yellow dwarf virus, increases the surface temperature of infected host plants (by an average of 2 °C), while also significantly enhancing the thermal tolerance of its aphid vectorRhopalosiphum padi (by 8 °C). This enhanced thermal tolerance, which was associated with differential upregulation of three heat-shock protein genes, allowed aphids to occupy higher and warmer regions of infected host plants when displaced from cooler regions by competition with a larger aphid species,R. maidis. Infection thereby led to an expansion of the fundamental niche of the vector. These findings show that virus effects on the thermal biology of hosts and vectors can influence their interactions with one another and with other, non-vector organisms.
Differential DNA methylation of vocal and facial anatomy genes in modern humans
Authors: Gokhman David , Nissim-Rafinia Malka , Agranat-Tamir Lily , Housman Genevieve , García-Pérez Raquel , Lizano Esther , Cheronet Olivia , Mallick Swapan , Nieves-Colón Maria A. , Li Heng , Alpaslan-Roodenberg Songül , Novak Mario , Gu Hongcang , Osinski Jason M. , Ferrando-Bernal Manuel , Gelabert Pere , Lipende Iddi , Mjungu Deus , Kondova Ivanela , Bontrop Ronald , Kullmer Ottmar , Weber Gerhard , Shahar Tal , Dvir-Ginzberg Mona , Faerman Marina , Quillen Ellen E. , Meissner Alexander , Lahav Yonatan , Kandel Leonid , Liebergall Meir , Prada María E. , Vidal Julio M. , Gronostajski Richard M. , Stone Anne C. , Yakir Benjamin , Lalueza-Fox Carles , Pinhasi Ron , Reich David , Marques-Bonet Tomas , Meshorer Eran , Carmel Liran 
Published: March 2020

AbstractChanges in potential regulatory elements are thought to be key drivers of phenotypic divergence. However, identifying changes to regulatory elements that underlie human-specific traits has proven very challenging. Here, we use 63 reconstructed and experimentally measured DNA methylation maps of ancient and present-day humans, as well as of six chimpanzees, to detect differentially methylated regions that likely emerged in modern humans after the split from Neanderthals and Denisovans. We show that genes associated with face and vocal tract anatomy went through particularly extensive methylation changes. Specifically, we identify widespread hypermethylation in a network of face- and voice-associated genes (SOX9, ACAN, COL2A1, NFIX and XYLT1). We propose that these repression patterns appeared after the split from Neanderthals and Denisovans, and that they might have played a key role in shaping the modern human face and vocal tract.
Escherichia coli adhesion portion FimH functions as an adjuvant for cancer immunotherapy
Authors: Zhang Wei , Xu Li , Park Hae-Bin , Hwang Juyoung , Kwak Minseok , Lee Peter C. W. , Liang Guang , Zhang Xiaoyan , Xu Jianqing , Jin Jun-O 
Published: March 2020

AbstractInduction of antigen-specific immune activation by the maturation of dendritic cells (DCs) is a strategy used for cancer immunotherapy. In this study, we find that FimH, which is an Escherichia coli adhesion portion, induces toll-like receptor 4-dependent and myeloid differentiation protein 2-independent DC maturation in mice in vivo. A combined treatment regimen with FimH and antigen promotes antigen-specific immune activation, including proliferation of T cells, production of IFN-γ and TNF-α, and infiltration of effector T cells into tumors, which consequently inhibits tumor growth in mice in vivo against melanoma and carcinoma. In addition, combined therapeutic treatment of anti-PD-L1 antibodies and FimH treatment efficiently inhibits CT26 tumor growth in BALB/c mice. Finally, FimH promotes human peripheral blood DC activation and syngeneic T-cell proliferation and activation. Taken together, these findings demonstrate that FimH can be a useful adjuvant for cancer immunotherapy.
Molecular dynamics simulation of graphene sinking during chemical vapor deposition growth on semi-molten Cu substrate
Authors: Xu Ziwei , Zhao Guanghui , Qiu Lu , Zhang Xiuyun , Qiao Guanjun , Ding Feng 
Published: March 2020

AbstractCopper foil is the most promising catalyst for the synthesis of large-area, high-quality monolayer graphene. Experimentally, it has been found that the Cu substrate is semi-molten at graphene growth temperatures. In this study, based on a self-developed C–Cu empirical potential and density functional theory (DFT) methods, we performed systematic molecular dynamics simulations to explore the stability of graphene nanostructures, i.e., carbon nanoclusters and graphene nanoribbons, on semi-molten Cu substrates. Many atomic details observed in the classical MD simulations agree well with those seen in DFT-MD simulations, confirming the high accuracy of the C–Cu potential. Depending on the size of the graphene island, two different sunken-modes are observed: (i) graphene island sinks into the first layer of the metal substrate and (ii) many metal atoms surround the graphene island. Further study reveals that the sinking graphene leads to the unidirectional alignment and seamless stitching of the graphene islands, which explains the growth of large single-crystal graphene on Cu foil. This study deepens our physical insights into the CVD growth of graphene on semi-molten Cu substrate with multiple experimental mysteries well explained and provides theoretic references for the controlled synthesis of large-area single-crystalline monolayer graphene.
Bio-inspired flexible artificial synapses for pain perception and nerve injuries
Authors: Lu Qifeng , Sun Fuqin , Liu Lin , Li Lianhui , Hao Mingming , Wang Zihao , Zhang Ting 
Published: March 2020

AbstractImitation of the perception system of living creatures is of great importance for the construction of artificial nerves and intelligent human-machine interfaces. However, a prominent challenge is to emulate the functions of the biological synapse, which is the basic building block of the neural system. Here, inspired by the pain perception mechanism of the living creatures, a flexible double-layer memristor was constructed, with 90% semiconducting single-wall carbon nanotubes (s-SWCNTs) covered by LiClO4doped polyoxyethylene oxide (PEO: LiClO4) as the channel materials. The carriers (protons and Li+) from PEO: LiClO4imitated the functions of Na+and K+in biological systems. A potentiation of the post-synaptic signal was observed with mild stimuli, while the post-synaptic signal was inhibited with severe stimuli with a pulse voltage larger than 1.4 V in this research. These behaviors resemble the sensation of pain, neuroprotection, and possible injuries to the neural system. To explore the underlying mechanism of the phenomenon, the fourier-transform infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy (XPS), Raman spectrum, and current (IV) sweep were carried out. It was inferred that the observed results are attributable to the interaction between carriers in PEO: LiClO4and functional groups and defects in the s-SWCNTs. The enhanced channel current results from the fulfillment of the traps by the carriers, and the suppression of the current is due to the intercalation of Li+in the s-SWCNTs. This flexible artificial synapse opens a new avenue for the construction of biocompatible electronic devices towards artificial intelligence systems.
Topography dependence of the metamagnetic phase transition in FeRh thin films
Authors: Warren J. L. , Barton C. W. , Bull C. , Thomson T. 
Published: March 2020

AbstractThe equiatomic alloy FeRh is of great scientific and technological interest due its highly unusual first-order antiferromagnetic (AF) to ferromagnetic (FM) phase transition. Here we report an exploration of the interplay between topography and phase evolution with a comprehensive magnetic force microscopy study of nominal 50 nm thick FeRh thin films and subtractively patterned wires of width 0.2 µm–2 µm. In continuous films where the surface morphology had not been optimised for smoothness, the topographical variation was observed to dominate the distribution of the magnetic transition temperatures and dictates the nucleation and growth of the magnetic phases. This observation was repeated for patterned elements, where the effects of surface morphology were more significant than those of spatial confinement. These results have clear implications for future studies of low-dimensional FeRh films, as surface topography must be considered when analysing and comparing the transition behaviour of FeRh thin films.