bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abnormal expression of bHLH3 disrupts a flavonoid homeostasis network, causing differences in pigment composition among mulberry fruits
Authors: Li Han , Yang Zhen , Zeng Qiwei , Wang Shibo , Luo Yiwei , Huang Yan , Xin Youchao , He Ningjia 
Published: May 2020

AbstractMulberry fruits with high concentrations of anthocyanins are favored by consumers because of their good taste, bright color, and high nutritional value. However, neither the regulatory mechanism controlling flavonoid biosynthesis in mulberry nor the molecular basis of different mulberry fruit colors is fully understood. Here, we report that a flavonoid homeostasis network comprising activation and feedback regulation mechanisms determines mulberry fruit color. In vitro and in vivo assays showed that MYBA-bHLH3-TTG1 regulates the biosynthesis of anthocyanins, while TT2L1 and TT2L2 work with bHLH3 or GL3 and form a MYB-bHLH-WD40 (MBW) complex with TTG1 to regulate proanthocyanidin (PA) synthesis. Functional and expression analyses showed thatbHLH3is a key regulator of the regulatory network controlling mulberry fruit coloration and thatMYB4is activated by MBW complexes and participates in negative feedback control of the regulatory network to balance the accumulation of anthocyanins and proanthocyanidins. Our research demonstrates that the interaction between bHLH3 and MYB4 in the homeostasis regulatory network ensures that the fruits accumulate desirable flavonoids and that this network is stable in pigment-rich mulberry fruits. However, the abnormal expression ofbHLH3disrupts the balance of the network and redirects flavonoid metabolic flux in pale-colored fruits, resulting in differences in the levels and proportions of anthocyanins, flavones, and flavonols among differently colored mulberry fruits (red, yellow, and white). The results of our study reveal the molecular basis of the diversity of mulberry fruit colors.
Gene body demethylation increases expression and is associated with self-pruning during grape genome duplication
Authors: Zou Luming , Liu Wenwen , Zhang Zhan , Edwards Everard J. , Gathunga Elias Kirabi , Fan Peige , Duan Wei , Li Shaohua , Liang Zhenchang 
Published: May 2020

AbstractA colchicine-induced autotetraploid grapevine exhibiting potentially valuable agronomic traits for grape production and breeding, including self-pruning, was identified. This study investigated DNA methylation variation and its role in gene expression during self-pruning in the autotetraploid grapevine. We used RNA-Seq to estimate differentially expressed genes between diploid and autotetraploid grapevine shoot tips. The genes showing increases in the autotetraploid were mainly related to stress response pathways, whereas those showing decreases in the autotetraploid were related to biological metabolism and biosynthesis. Whole-genome bisulfite sequencing was performed to produce single-base methylomes for the diploid and autotetraploid grapevines. Comparison between the methylomes revealed that they were conserved in CG and CHG contexts. In the autotetraploid grapevine, hypodifferentially methylated regions (DMRs) and hyper-DMRs in the gene body increased or decreased gene expression, respectively. Our results indicated that a hypo-DMR in theACO1gene body increased its expression and might promote self-pruning. This study reports that hypo-DMRs in the gene body increase gene expression in plants and reveals the mechanism underlying the changes in the modifications affecting gene expression during genome duplication. Overall, our results provide valuable information for understanding the relationships between DNA methylation, gene expression, and autotetraploid breeding in grape.
Whole-genome sequencing provides insights into the genetic diversity and domestication of bitter gourd (Momordica spp.)
Authors: Cui Junjie , Yang Yan , Luo Shaobo , Wang Le , Huang Rukui , Wen Qingfang , Han Xiaoxia , Miao Nansheng , Cheng Jiaowen , Liu Ziji , Zhang Changyuan , Feng Chengcheng , Zhu Haisheng , Su Jianwen , Wan Xinjian , Hu Fang , Niu Yu , Zheng Xiaoming , Yang Yulan , Shan Dai , Dong Zhensheng , He Weiming , Dhillon Narinder P. S. , Hu Kailin 
Published: May 2020

AbstractBitter gourd (Momordica charantia) is a popular cultivated vegetable in Asian and African countries. To reveal the characteristics of the genomic structure, evolutionary trajectory, and genetic basis underlying the domestication of bitter gourd, we performed whole-genome sequencing of the cultivar Dali-11 and the wild small-fruited line TR and resequencing of 187 bitter gourd germplasms from 16 countries. The major gene clusters (Bi clusters) for the biosynthesis of cucurbitane triterpenoids, which confer a bitter taste, are highly conserved in cucumber, melon, and watermelon. Comparative analysis among cucurbit genomes revealed that the Bi cluster involved in cucurbitane triterpenoid biosynthesis is absent in bitter gourd. Phylogenetic analysis revealed that the TR group, including 21 bitter gourd germplasms, may belong to a new species or subspecies independent from M. charantia. Furthermore, we found that the remaining 166 M. charantia germplasms are geographically differentiated, and we identified 710, 412, and 290 candidate domestication genes in the South Asia, Southeast Asia, and China populations, respectively. This study provides new insights into bitter gourd genetic diversity and domestication and will facilitate the future genomics-enabled improvement of bitter gourd.
The genome sequence of star fruit (Averrhoa carambola)
Authors: Wu Shasha , Sun Wei , Xu Zhichao , Zhai Junwen , Li Xiaoping , Li Chengru , Zhang Diyang , Wu Xiaoqian , Shen Liming , Chen Junhao , Ren Hui , Dai Xiaoyu , Dai Zhongwu , Zhao Yamei , Chen Lei , Cao Mengxia , Xie Xinyu , Liu Xuedie , Peng Donghui , Dong Jianwen , Hsiao Yu-Yun , Chen Shi-lin , Tsai Wen-Chieh , Lan Siren , Liu Zhong-Jian 
Published: May 2020

AbstractOxalidaceae is one of the most important plant families in horticulture, and its key commercially relevant genus, Averrhoa, has diverse growth habits and fruit types. Here, we describe the assembly of a high-quality chromosome-scale genome sequence for Averrhoa carambola (star fruit). Ks distribution analysis showed that A. carambola underwent a whole-genome triplication event, i.e., the gamma event shared by most eudicots. Comparisons between A. carambola and other angiosperms also permitted the generation of Oxalidaceae gene annotations. We identified unique gene families and analyzed gene family expansion and contraction. This analysis revealed significant changes in MADS-box gene family content, which might be related to the cauliflory of A. carambola. In addition, we identified and analyzed a total of 204 nucleotide-binding site, leucine-rich repeat receptor (NLR) genes and 58 WRKY genes in the genome, which may be related to the defense response. Our results provide insights into the origin, evolution and diversification of star fruit.
MYB41, MYB107, and MYC2 promote ABA-mediated primary fatty alcohol accumulation via activation of AchnFAR in wound suberization in kiwifruit
Authors: Wei Xiaopeng , Mao Linchun , Wei Xiaobo , Xia Ming , Xu Changjie 
Published: May 2020

AbstractWound damage triggers the accumulation of abscisic acid (ABA), which induces the expression of a large number of genes involved in wound suberization in plants. Fatty acyl-CoA reductase (FAR) catalyzes the generation of primary fatty alcohols by the reduction of fatty acids in suberin biosynthesis. However, the regulatory effects of transcription factors (TFs) on AchnFAR in response to ABA are unexplored. In this study, kiwifruit AchnFAR displayed a biological function analogous to that of FAR in transiently overexpressed tobacco (Nicotiana benthamiana) leaves. The positive role of TFs, including AchnMYB41, AchnMYB107, and AchnMYC2, in the regulation of AchnFAR was identified. The three TFs could individually bind to the AchnFAR promoter to activate gene transcription in yeast one-hybrid and dual-luciferase assays. Transient overexpression of TFs in tobacco leaves resulted in the upregulation of aliphatic synthesis genes (including FAR) and the increase in aliphatics, including primary alcohols, α,ω-diacids, ω-hydroxyacids, and fatty acids. Moreover, exogenous ABA treatment elevated TF-mediated AchnFAR expression and the accumulation of primary alcohols. Conversely, fluridone, an inhibitor of ABA biosynthesis, suppressed the expression of AchnFAR and TF genes and reduced the formation of primary alcohols. The results indicate that AchnMYB41, AchnMYB107, and AchnMYC2 activate AchnFAR transcription to promote ABA-mediated primary alcohol formation in wound suberization in kiwifruit.
Comparative transcriptome analysis reveals synergistic and disparate defense pathways in the leaves and roots of trifoliate orange (Poncirus trifoliata) autotetraploids with enhanced salt tolerance
Authors: Wei Tonglu , Wang Yue , Liu Ji-Hong 
Published: May 2020

Abstract
Polyploid plants often exhibit enhanced stress tolerance relative to their diploid counterparts, but the physiological and molecular mechanisms of this enhanced stress tolerance remain largely unknown. In this study, we showed that autotetraploid trifoliate orange (Poncirus trifoliata (L.) Raf.) exhibited enhanced salt tolerance in comparison with diploid progenitors. Global transcriptome profiling of diploid and tetraploid plants with or without salt stress by RNA-seq revealed that the autotetraploids displayed specific enrichment of differentially expressed genes. Interestingly, the leaves and roots of tetraploids exhibited different expression patterns of a variety of upregulated genes. Genes related to plant hormone signal transduction were enriched in tetraploid leaves, whereas those associated with starch and sucrose metabolism and proline biosynthesis were enriched in roots. In addition, genes encoding different antioxidant enzymes were upregulated in the leaves (POD) and roots (APX) of tetraploids under salt stress. Consistently, the tetraploids accumulated higher levels of soluble sugars and proline but less ROS under salt stress compared to the diploids. Moreover, several genes encoding transcription factors were induced specifically or to higher levels in the tetraploids under salt stress. Collectively, this study demonstrates that the activation of various multifaceted defense systems in leaves and roots contributes to the enhanced salt tolerance of autotetraploids.
Comparative population genomics dissects the genetic basis of seven domestication traits in jujube
Authors: Guo Mingxin , Zhang Zhongren , Cheng Yanwei , Li Sunan , Shao Peiyin , Yu Qiang , Wang Junjie , Xu Gan , Zhang Xiaotian , Liu Jiajia , Hou Linlin , Liu Hanxiao , Zhao Xusheng 
Published: May 2020

AbstractJujube (Ziziphus jujuba Mill.) is an important perennial fruit tree with a range of interesting horticultural traits. It was domesticated from wild jujube (Ziziphus acidojujuba), but the genomic variation dynamics and genetic changes underlying its horticultural traits during domestication are poorly understood. Here, we report a comprehensive genome variation map based on the resequencing of 350 accessions, including wild, semi-wild and cultivated jujube plants, at a >15× depth. Using the combination of a genome-wide association study (GWAS) and selective sweep analysis, we identified several candidate genes potentially involved in regulating seven domestication traits in jujube. For fruit shape and kernel shape, we integrated the GWAS approach with transcriptome profiling data, expression analysis and the transgenic validation of a candidate gene to identify a causal gene, ZjFS3, which encodes an ethylene-responsive transcription factor. Similarly, we identified a candidate gene for bearing-shoot length and the number of leaves per bearing shoot and two candidate genes for the seed-setting rate using GWAS. In the selective sweep analysis, we also discovered several putative genes for the presence of prickles on bearing shoots and the postharvest shelf life of fleshy fruits. This study outlines the genetic basis of jujube domestication and evolution and provides a rich genomic resource for mining other horticulturally important genes in jujube.
Genome-wide analysis of NDR1/HIN1-like genes in pepper (Capsicum annuum L.) and functional characterization of CaNHL4 under biotic and abiotic stresses
Authors: Liu Changyun , Peng Haoran , Li Xinyu , Liu Chaolong , Lv Xing , Wei Xuefeng , Zou Aihong , Zhang Jian , Fan Guangjin , Ma Guanhua , Ma Lisong , Sun Xianchao 
Published: May 2020

AbstractPlant NDR1/HIN1-like (NHL) genes play an important role in triggering plant defenses in response to biotic stresses. In this study, we performed a genome-wide identification of theNHLgenes in pepper (Capsicum annuumL.) and characterized the functional roles of theseCaNHLgenes in response to abiotic stresses and infection by different pathogens. Phylogenetic analysis revealed thatCaNHLs can be classified into five distinct subgroups, with each group containing generic and specific motifs. Regulatory element analysis showed that the majority of the promoter regions of the identifiedCaNHLs contain jasmonic acid (JA)-responsive and salicylic acid (SA)-responsive elements, and transcriptomic analysis revealed thatCaNHLgenes are expressed in all the examined tissues of pepper. TheCaNHL1,CaNHL4,CaNHL6,CaNHL10,CaNHL11, andCaNHL12genes were significantly upregulated under abiotic stress as well as in response to different pathogens, such as TMV,Phytophthora capsiciandPseudomonas syringae. In addition, we found that CaNHL4 localizes to the plasma membrane.CaNHL4-silenced pepper plants display significantly increased susceptibility to TMV,Phytophthora capsiciandPseudomonas syringae, exhibiting reduced expression of JA-related and SA-related genes and reduced ROS production. However, transient overexpression ofCaNHL4in pepper increases the expression of JA-related and SA-related genes, enhances the accumulation of ROS, and inhibits the infection of these three pathogens. Collectively, for the first time, we identified theNHLgenes in pepper and demonstrated thatCaNHL4is involved in the production of ROS and that it also regulates the expression of JA-related and SA-related genes in response to different pathogens, suggesting that members of the CaNHL family play an essential role in the disease resistance of pepper.
Novel stepwise and combined stepwise–piece‐wise linear tripping characteristics for coordinating numerical overcurrent relays
Authors: Azari Mehdi , Mazlumi Kazem , Ojaghi Mansour 
Published: June 2020

Technological developments in protective devices have established the basis for appearance of numerical overcurrent relays (OCRs), which enable the users to apply their desired time‐current characteristics (TCCs). This study propounds novel stepwise and combined stepwise–piece‐wise linear TCCs and presents clear procedure to utilise them for coordinating OCRs in large meshed power systems. The TCCs keep constant time interval between the main/backup relay pairs within entire fault current range. They are examined first by coordinating the OCRs in a 4‐bus power system and by coordinating the ground fault OCRs in a practical 60 kV looped power system. Then, the OCRs of the IEEE 14‐bus test system, which is a rather large meshed power system with 39 OCRs and 102 main/backup pairs, are coordinated by using the novel TCCs. The same relays in the aforesaid power systems are coordinated using some non‐standard TCCs recently introduced in the literature. The comparison verifies that the lowest operating times are achieved by using the novel TCCs. The devised TCCs are simply formed as look‐up tables to be exactly set on the existing industrial relays. This fact is verified by setting them on an industrial OCR, and then, by testing the relay through the current injection method.
Flood risk assessment using the CV-TOPSIS method for the Belt and Road Initiative: an empirical study of Southeast Asia
Authors: An Yan , Tan Xianchun , Gu Baihe , Zhu Kaiwei 
Published: May 2020

ABSTRACT

Instruction

The countries along the Belt and Road Initiative remain high exposure and vulnerability to climate extremes. Southeast Asia, a significant part of the Belt and Road Initiative, suffers a lot from flood disasters. This study assessed the flood disaster risk from 1990–2015 in all 11 Southeast Asian countries. A model integrating the coefficient of variation approach and the Technique for Order Preference by Similarity to Ideal Solution method was introduced to analyze the flood disaster data. Considering that populations living in areas where elevation is below 5 m and land area where elevation is below 5 m have reached 11.86% and 3.54% (2015), respectively, the two indicators were opted for to propose new metrics for flood disaster risk assessment.
Outcomes
: Our findings show that the flood disaster risk in Southeast Asia appeared very high during most of the study period. Indonesia had an extremely high flood disaster risk, followed by Vietnam, whereas Laos, Malaysia, Brunei, and Timor Leste had lower flood risks. The model introduced in this paper is quite simple and easy to understand, providing accessible flood risk information for decision makers.
Conclusion
: The results we obtained have practical implications for land use and investment activities in Southeast Asia.
Influence of process parameters on quality of copper in electron-beam melting
Authors: Vassileva V , Vutova K 
Published: June 2020

Abstract
Results are presented and discussed obtained by experimental and theoretical investigation concerning the influence of process parameters (melting power and refining time) on the quality of copper metal ingots in electron-beam melting. The thermodynamic and kinetic conditions are analyzed. Possible refining process mechanisms under different technological conditions are investigated. Appropriate processing regimes are proposed for efficient refining of copper and for obtaining high-quality metal after e-beam melting.
Influence of post-polymerization processing on the mechanical characteristics of 3D-printed occlusal splints
Authors: Taneva I , Uzunov T 
Published: June 2020

Abstract
Occlusal splints are the most common devices for preventing bruxism and its consequences. Their application significantly reduces the pathologies of the dental and periodontal structures. Apart from the well-known technologies of manufacturing occlusal splints – thermo-vacuum forming, wax elimination and CAD/CAM machining, three-dimensional (3D) printing is a novel promising technique. It makes use of stereolithography, whereby the splint is built layer-by-layer through consecutive polymerization of a liquid photo-polymer by ultraviolet laser light. A very important stage in stereolithography following the 3D-printing is the post polymerization processing. It is a key moment in achieving biocompatibility and the final mechanical parameters – hardness, elasticity modulus, and strength. The process comprises two steps – washing with isopropyl alcohol (IPA) followed by post-curing in a polymerization device with an ultraviolet light source. The aim of the present study is determining the influence of the polymerization device’s light source on the mechanical characteristics of the occlusal splint.
Synthesis and characterization of 2D platinum diselenide
Authors: Buchkov K , Dimitrov D , Mickovski J , Dikov Ch , Goovaerts E , Petrova D , Babeva T , Marinova V 
Published: June 2020

Abstract
Two-dimensional (2D) materials have been intensively studied due to their outstanding chemical, physical, electronic and optical properties potentially offering a breakthrough in the search of a direct integration of these materials with the silicon (Si) technology. Among them, platinum diselenide (PtSe2) is of significant interest for applications in electronics, spintronics, sensors, catalysis, etc. In this paper, we report a large-scale synthesis of PtSe2-layers by thermally-assisted selenization of pre-deposited platinum films in a horizontal quartz-tube chemical vapor deposition (CVD) reactor. The overall structural information and quality of the PtSe2-films is analyzed by Raman spectroscopy and Raman active modes identification. The electrical characterization via V-I characteristics reveals sheet resistance values in the range of ~103 Ω.
Deposition of SiOx thin films using hexamethyldisiloxane in atmospheric pressure plasma enhanced chemical vapor deposition
Authors: Krueger T , Hansen L , Kersten H 
Published: June 2020

Abstract
The atmospheric pressure plasma enhanced chemical vapor deposition method was used to study the enhancement of the particle growth and thin layer deposition. For this purpose, an atmospheric pressure plasma jet was used to deposit silicon oxide compounds on a (100)-silicon wafer substrate. In this parametric study, hexamethyldisiloxane (HMDSO) was dissociated under different plasma jet parameters. It was found that by varying the working gas, the treatment time and jet parameters, such as nozzle-to-substrate distance and input energy, it is possible to influence the particles size and the morphology of the thin film. The choice of the working gas plays a major role in the formation of nanoparticles and the surface texture. This study was focused on the particles growth and how the growth can be controlled by tuning the parameters mentioned. Particles size of up to 100 nm was achieved under optimized conditions.
Carbon nanostructures on capacitor electrodes
Authors: Marinov S , Vachkov V , Djermanova N , Kiss’ovski Zh 
Published: June 2020

Abstract
Carbon nanostructures, such as carbon nanowires, nanotubes, nanosheets, have found applications in many areas – from electronics to medicine. Recently, they attracted particular attention as materials for energy storage due to their large aspect ratios, specific surface areas, and electrical conductivity. An efficient method for their deposition on metallic surfaces at atmospheric pressure is microwave plasma-enhanced chemical vapor deposition (MPECVD). In this study, metallic surfaces with deposited carbon nanostructures were used for preparation of capacitor electrodes. The capacitance of an electrolytic capacitor with metal electrodes without and with deposited carbon nanostructures was measured by an electronic system. The resulting high value of the capacitance of a capacitor with electrodes with deposited carbon nanostructures is discussed on the basis of these structures morphology as studied by SEM.
Mechanical properties dependence on the modulation period in multilayered TiN/ZrN coatings
Authors: Cholakova T M , Kolaklieva L P , Bahchedjiev Hr P , Kakanakov R D , Ranguelov B , Hristeva N T 
Published: June 2020

Abstract
This article presents results from a study on the properties of nanostructured multilayered TiN/ZrN coatings with different modulation periods deposited by cathodic-arc evaporation from Ti and Zr targets in nitrogen atmosphere on high-speed steel substrates. The thickness of the TiN-ZrN bilayers varied from 12 nm to 52 nm depending on the rotation speed of the holder. In order to investigate the effect of heat treatment on the mechanical and structural properties, the multilayer ZrN/TiN coatings were annealed in Ar atmosphere at different temperatures for two hours. The surface morphology, elemental composition, nano-hardness and adhesion strength of the as-deposited and annealed coatings were analyzed by scanning electron microscopy complemented with energy dispersive X-ray spectroscopy analysis, and nanoindentation and micro-scratch tests. The results obtained show that the mechanical properties of multilayer TiN/ZrN coatings are considerably improved in comparison to those of the monolayer ZrN and TiN coatings.