bluuebunny/crossref_metadata_2025_split huggingface dataset:
Test of the Effective Stress Law for Semibrittle Deformation Using Isostatic and Triaxial Load Paths
Authors: Ding J. , Chester F. M. , Chester J. S. 
Published: April 2021

AbstractFor brittle friction and rock deformation, the coefficient α in the general effective stress relation σe = σ − αPp can be approximated as unity with sufficient accuracy. However, it is uncertain if α deviates from unity for semibrittle flow when both brittle and intracrystalline‐plastic deformation is involved. We conducted triaxial and isostatic compression experiments on synthetic salt‐rocks (∼300 ppm water) at room temperature to test the effective stress relation in the semibrittle regime using silicone oil and argon gas as pore fluids. Confining and pore pressures were cycled while their difference (differential pressure) was kept constant, such that changes in the mechanical behavior would indicate deviation of α from unity. Microstructural observations were used to determine the dependence of α on true area of grain contact from asperity yielding. In triaxial compression experiments, semibrittle flow involves grain boundary cracking and sliding, and intragranular dislocation glide and cracking. Flow strength remains constant for changes in pore fluid pressure of more than two orders of magnitude. In isostatic compression experiments, samples show combined processes of microcracking, grain boundary sliding, dislocation glide, and fluid‐assisted grain boundary migration recrystallization. Volumetric strain depends directly on the differential pressures (i.e., α equals one). Analysis of grain‐contact area in both experiments indicates that α is independent of the true area of contact defined by plastic yielding at grain boundaries. The observation of α effectively equals one may be explained by operation of pressure‐independent intracrystalline‐plastic mechanisms and transmission of pore pressure at grain boundaries through thin fluid films.
Dart‐Leader and K‐Leader Velocity From Initiation Site to Termination Time‐Resolved With 3D Interferometry
Authors: Jensen Daniel P. , Sonnenfeld Richard G. , Stanley Mark A. , Edens Harald E. , da Silva Caitano L. , Krehbiel Paul R. 
Published: April 2021

AbstractSimultaneous data from two interferometers separated by 16 km and synchronized within 100 ns were collected for a thunderstorm near Langmuir Lab on October 23, 2018. Analysis via triangulation followed by a least squares fit to time of arrival across all six antennae produced a three‐dimensional interferometer (3DINTF) data set. Simultaneous Lightning Mapping Array data enabled an independent calculation of 3DINTF accuracy, yielding a median location uncertainty of 200 m. This is the most accurate verified result to date for a two‐station interferometer. The 3D data allowed profiling the velocity of multiple dart leaders and K leaders that followed the same channel. 3D velocities calculated from the in‐cloud initiation site to ground ranged from 3 × 106 to 20 × 106 m/s. Average velocity generally increased with subsequent leaders, consistent with increased conditioning of the channel. Also, all leaders showed a factor of 2–3 decrease in velocity as they proceeded over 15 km of channel. We speculate that the velocity decrease is consistent with energy lost in the reionization of the channel at the leader tip. This paper includes an appendix providing details of the triangulation technique used.
Pulse Coherent Doppler Profiler Measurement of Bedload Transport
Authors: Zedel Len , Hay Alex E. , Wilson Gregory W. , Hare Jenna 
Published: April 2021

AbstractPrior studies demonstrate that bottom velocity measurements from Doppler sonar systems are proportional to bedload transport rates. These observations suggest that acoustically based systems offer a capability for rapid sampling of bedload transport processes. Before these measurements can be fully utilized, validation and understanding of the sampling mechanism are essential. We explore the measurement mechanism through a series of laboratory trials with a field instrument, the multi‐frequency coherent Doppler profiler (MFDop). The MFDop system is a multi‐frequency (1.2–2.2 MHz), bistatic Doppler sonar that provides three‐component ensemble‐averaged velocity profiles over a ∼30 cm depth interval with up to 1 mm resolution at a rate of 50 profiles/sec. Tests of the MFDop system were carried out in the main flume in field‐scale conditions at the St. Anthony Falls Laboratory (SAFL) using 1 ms−1 mean flows over a mobile bed of sand with median grain size d50 = 0.4 mm. We find agreement between MFDop transport measurements and measurements based on bedform migration rates, and sediment traps built into the SAFL flume. Predictions using the Meyer‐Peter and Müller (1948) empirical equation closely match our observations while in contrast, predictions using the Nielsen (1992) equation are a factor of two higher.
Highly efficient THz four-wave mixing in doped silicon
Authors: Dessmann Nils , Le Nguyen H. , Eless Viktoria , Chick Steven , Saeedi Kamyar , Perez-Delgado Alberto , Pavlov Sergey G. , van der Meer Alexander F. G. , Litvinenko Konstantin L. , Galbraith Ian , Abrosimov Nikolay V. , Riemann Helge , Pidgeon Carl R. , Aeppli Gabriel , Redlich Britta , Murdin Benedict N. 
Published: April 2021

AbstractThird-order non-linearities are important because they allow control over light pulses in ubiquitous high-quality centro-symmetric materials like silicon and silica. Degenerate four-wave mixing provides a direct measure of the third-order non-linear sheet susceptibility χ(3)L (where L represents the material thickness) as well as technological possibilities such as optically gated detection and emission of photons. Using picosecond pulses from a free electron laser, we show that silicon doped with P or Bi has a value of χ(3)L in the THz domain that is higher than that reported for any other material in any wavelength band. The immediate implication of our results is the efficient generation of intense coherent THz light via upconversion (also a χ(3) process), and they open the door to exploitation of non-degenerate mixing and optical nonlinearities beyond the perturbative regime.
Strawberry sweetness and consumer preference are enhanced by specific volatile compounds
Authors: Fan Zhen , Hasing Tomas , Johnson Timothy S. , Garner Drake M. , Schwieterman Michael L. , Barbey Christopher R. , Colquhoun Thomas A. , Sims Charles A. , Resende Marcio F. R. , Whitaker Vance M. 
Published: April 2021

AbstractBreeding crops for improved flavor is challenging due to the high cost of sensory evaluation and the difficulty of connecting sensory experience to chemical composition. The main goal of this study was to identify the chemical drivers of sweetness and consumer liking for fresh strawberries (Fragaria × ananassa). Fruit of 148 strawberry samples from cultivars and breeding selections were grown and harvested over seven years and were subjected to both sensory and chemical analyses. Each panel consisted of at least 100 consumers, resulting in more than 15,000 sensory data points per descriptor. Three sugars, two acids and 113 volatile compounds were quantified. Consumer liking was highly associated with sweetness intensity, texture liking, and flavor intensity, but not sourness intensity. Partial least square analyses revealed 20 volatile compounds that increased sweetness perception independently of sugars; 18 volatiles that increased liking independently of sugars; and 15 volatile compounds that had positive effects on both. Machine learning-based predictive models including sugars, acids, and volatiles explained at least 25% more variation in sweetness and liking than models accounting for sugars and acids only. Volatile compounds such as γ-dodecalactone; 5-hepten-2-one, 6-methyl; and multiple medium-chain fatty acid esters may serve as targets for breeding or quality control attributes for strawberry products. A genetic association study identified two loci controlling ester production, both on linkage group 6 A. Co-segregating makers in these regions can be used for increasing multiple esters simultaneously. This study demonstrates a paradigm for improvement of fruit sweetness and flavor in which consumers drive the identification of the most important chemical targets, which in turn drives the discovery of genetic targets for marker-assisted breeding.
Preharvest long-term exposure to UV-B radiation promotes fruit ripening and modifies stage-specific anthocyanin metabolism in highbush blueberry
Authors: Li Taishan , Yamane Hisayo , Tao Ryutaro 
Published: April 2021

AbstractUltraviolet-B (UV-B) light (280–315 nm) is an important environmental signal that regulates plant development and photomorphogenesis, while also affecting the flavonoid pathway, including anthocyanin biosynthesis. Regarding the effects of UV-B radiation on fruits, the effects of a short-term or postharvest irradiation on fruit quality have been well-documented, but the effects of a long-term preharvest UV-B irradiation on fruit growth and coloration remain unclear. Thus, in this study, we investigated the effects of a long-term treatment involving an environmentally relevant UV-B dose on highbush blueberry (Vaccinium corymbosum) fruit. The preharvest UV-B treatment quickly promoted fruit growth and sugar accumulation, which is not commonly observed in other fruit tree species. The UV-B exposure also accelerated fruit ripening and coloration. The dual-luciferase assay proved that in blueberries, expression ofVcUFGTencoding anthocyanin biosynthesis key enzyme, is positively and negatively regulated byVcMYBA1andVcMYBC2, respectively. Throughout the fruit development stage, the UV-B treatment up-regulatedVcMYBPA1expression, which increasedVcUFGTexpression viaVcMYBA1. In the green fruit stage, the UV-B treatment increasedHY5encoding UV receptor, which up-regulatesVcMYBPA1and down-regulatesVcMYBC2, thereby promotes the accumulation of anthocyanins. On the other hand, excessive anthocyanin synthesis was inhibited by increasedVcMYBC2levels in mature fruits when exposed to UV-B light throughHY5-independent pathway. In conclusion, anthocyanin-related MYB activators and repressor may coordinately balance the accumulation of anthocyanins in blueberry fruits, with UV-B treatments possibly influencing their effects in a stage-specific manner. The potential utility of preharvest UV-B treatments for improving blueberry fruit quality is discussed herein.
Genome of a citrus rootstock and global DNA demethylation caused by heterografting
Authors: Huang Yue , Xu Yuantao , Jiang Xiaolin , Yu Huiwen , Jia Huihui , Tan Chunming , Hu Gang , Hu Yibo , Rao Muhammad Junaid , Deng Xiuxin , Xu Qiang 
Published: April 2021

AbstractGrafting is an ancient technique used for plant propagation and improvement in horticultural crops for at least 1,500 years. Citrus plants, with a seed-to-seed cycle of 5–15 years, are among the fruit crops that were probably domesticated by grafting. Poncirus trifoliata, a widely used citrus rootstock, can promote early flowering, strengthen stress tolerance, and improve fruit quality via scion–rootstock interactions. Here, we report its genome assembly using PacBio sequencing. We obtained a final genome of 303 Mb with a contig N50 size of 1.17 Mb and annotated 25,680 protein-coding genes. DNA methylome and transcriptome analyses indicated that the strong adaptability of P. trifoliata is likely attributable to its special epigenetic modification and expression pattern of resistance-related genes. Heterografting by using sweet orange as scion and P. trifoliata as rootstock and autografting using sweet orange as both scion and rootstock were performed to investigate the genetic effects of the rootstock. Single-base methylome analysis indicated that P. trifoliata as a rootstock caused DNA demethylation and a reduction in 24-nt small RNAs (sRNAs) in scions compared to the level observed with autografting, implying the involvement of sRNA-mediated graft-transmissible epigenetic modifications in citrus grafting. Taken together, the assembled genome for the citrus rootstock and the analysis of graft-induced epigenetic modifications provide global insights into the genetic effects of rootstock–scion interactions and grafting biology.
Involvement of ethylene receptors in the salt tolerance response of Cucurbita pepo
Authors: Cebrián Gustavo , Iglesias-Moya Jessica , García Alicia , Martínez Javier , Romero Jonathan , Regalado José Javier , Martínez Cecilia , Valenzuela Juan Luis , Jamilena Manuel 
Published: April 2021

AbstractAbiotic stresses have a negative effect on crop production, affecting both vegetative and reproductive development. Ethylene plays a relevant role in plant response to environmental stresses, but the specific contribution of ethylene biosynthesis and signalling components in the salt stress response differs between Arabidopsis and rice, the two most studied model plants. In this paper, we study the effect of three gain-of-function mutations affecting the ethylene receptors CpETR1B, CpETR1A, and CpETR2B of Cucurbita pepo on salt stress response during germination, seedling establishment, and subsequent vegetative growth of plants. The mutations all reduced ethylene sensitivity, but enhanced salt tolerance, during both germination and vegetative growth, demonstrating that the three ethylene receptors play a positive role in salt tolerance. Under salt stress, etr1b, etr1a, and etr2b germinate earlier than WT, and the root and shoot growth rates of both seedlings and plants were less affected in mutant than in WT. The enhanced salt tolerance response of the etr2b plants was associated with a reduced accumulation of Na+ in shoots and leaves, as well as with a higher accumulation of compatible solutes, including proline and total carbohydrates, and antioxidant compounds, such as anthocyanin. Many membrane monovalent cation transporters, including Na+/H+ and K+/H+ exchangers (NHXs), K+ efflux antiporters (KEAs), high-affinity K+ transporters (HKTs), and K+ uptake transporters (KUPs) were also highly upregulated by salt in etr2b in comparison with WT. In aggregate, these data indicate that the enhanced salt tolerance of the mutant is led by the induction of genes that exclude Na+ in photosynthetic organs, while maintaining K+/Na+ homoeostasis and osmotic adjustment. If the salt response of etr mutants occurs via the ethylene signalling pathway, our data show that ethylene is a negative regulator of salt tolerance during germination and vegetative growth. Nevertheless, the higher upregulation of genes involved in Ca2+ signalling (CpCRCK2A and CpCRCK2B) and ABA biosynthesis (CpNCED3A and CpNCED3B) in etr2b leaves under salt stress likely indicates that the function of ethylene receptors in salt stress response in C. pepo can be mediated by Ca2+ and ABA signalling pathways.
Tissue-specific signatures of metabolites and proteins in asparagus roots and exudates
Authors: Döll Stefanie , Djalali Farahani-Kofoet Roxana , Zrenner Rita , Henze Andrea , Witzel Katja 
Published: April 2021

AbstractComprehensive untargeted and targeted analysis of root exudate composition has advanced our understanding of rhizosphere processes. However, little is known about exudate spatial distribution and regulation. We studied the specific metabolite signatures of asparagus root exudates, root outer (epidermis and exodermis), and root inner tissues (cortex and vasculature). The greatest differences were found between exudates and root tissues. In total, 263 non-redundant metabolites were identified as significantly differentially abundant between the three root fractions, with the majority being enriched in the root exudate and/or outer tissue and annotated as ‘lipids and lipid-like molecules’ or ‘phenylpropanoids and polyketides’. Spatial distribution was verified for three selected compounds using MALDI-TOF mass spectrometry imaging. Tissue-specific proteome analysis related root tissue-specific metabolite distributions and rhizodeposition with underlying biosynthetic pathways and transport mechanisms. The proteomes of root outer and inner tissues were spatially very distinct, in agreement with the fundamental differences between their functions and structures. According to KEGG pathway analysis, the outer tissue proteome was characterized by a high abundance of proteins related to ‘lipid metabolism’, ‘biosynthesis of other secondary metabolites’ and ‘transport and catabolism’, reflecting its main functions of providing a hydrophobic barrier, secreting secondary metabolites, and mediating water and nutrient uptake. Proteins more abundant in the inner tissue related to ‘transcription’, ‘translation’ and ‘folding, sorting and degradation’, in accord with the high activity of cortical and vasculature cell layers in growth- and development-related processes. In summary, asparagus root fractions accumulate specific metabolites. This expands our knowledge of tissue-specific plant cell function.
Differential regulation of triterpene biosynthesis induced by an early failure in cuticle formation in apple
Authors: Falginella Luigi , Andre Christelle M. , Legay Sylvain , Lin-Wang Kui , Dare Andrew P. , Deng Cecilia , Rebstock Ria , Plunkett Blue J. , Guo Lindy , Cipriani Guido , Espley Richard V. 
Published: April 2021

AbstractWaxy apple cuticles predominantly accumulate ursane-type triterpenes, but the profile shifts with the induction of skin russeting towards lupane-type triterpenes. We previously characterised several key enzymes in the ursane-type and lupane-type triterpene pathways, but this switch in triterpene metabolism associated with loss of cuticle integrity is not fully understood. To analyse the relationship between triterpene biosynthesis and russeting, we used microscopy, RNA-sequencing and metabolite profiling during apple fruit development. We compared the skin of three genetically-close clones of ‘Golden Delicious’ (with waxy, partially russeted and fully russeted skin). We identified a unique molecular profile for the russet clone, including low transcript abundance of multiple cuticle-specific metabolic pathways in the early stages of fruit development. Using correlation analyses between gene transcription and metabolite concentration we found MYB transcription factors strongly associated with lupane-type triterpene biosynthesis. We showed how their transcription changed with the onset of cuticle cracking followed by russeting and that one factor, MYB66, was able to bind the promoter of the oxidosqualene cyclase OSC5, to drive the production of lupeol derivatives. These results provide insights into the breakdown of cuticle integrity leading to russet and how this drives MYB-regulated changes to triterpene biosynthesis.
Genomic analysis uncovers functional variation in the C-terminus of anthocyanin-activating MYB transcription factors
Authors: Rodrigues Jessica A. , Espley Richard V. , Allan Andrew C. 
Published: April 2021

AbstractMYB transcription factors regulate diverse aspects of plant development and secondary metabolism, often by partnering in transcriptional regulatory complexes. Here, we harness genomic resources to identify novel MYBs, thereby producing an updated eudicot MYB phylogeny with revised relationships among subgroups as well as new information on sequence variation in the disordered C-terminus of anthocyanin-activating MYBs. BLAST® and hidden Markov model scans of gene annotations identified a total of 714 MYB transcription factors across the genomes of four crops that span the eudicots: apple, grape, kiwifruit and tomato. Codon model-based phylogenetic inference identified novel members of previously defined subgroups, and the function of specific anthocyanin-activating subgroup 6 members was assayed transiently in tobacco leaves. Sequence conservation within subgroup 6 highlighted one previously described and two novel short linear motifs in the disordered C-terminal region. The novel motifs have a mix of hydrophobic and acidic residues and are predicted to be relatively ordered compared with flanking protein sequences. Comparison of motifs with the Eukaryotic Linear Motif database suggests roles in protein–protein interaction. Engineering of motifs and their flanking regions from strong anthocyanin activators into weak activators, and vice versa, affected function. We conclude that, although the MYB C-terminal sequence diverges greatly even within MYB clades, variation within the C-terminus at and near relatively ordered regions offers opportunities for exploring MYB function and developing superior alleles for plant breeding.
The histone variant Sl_H2A.Z regulates carotenoid biosynthesis and gene expression during tomato fruit ripening
Authors: Yang Xuedong , Zhang Xuelian , Yang Youxin , Zhang Hui , Zhu Weimin , Nie Wen-Feng 
Published: April 2021

AbstractThe conserved histone variant H2A.Z is essential for transcriptional regulation; defense responses; and various biological processes in plants, such as growth, development, and flowering. However, little is known about how H2A.Z affects the developmental process and ripening of tomato fruits. Here, we utilized the CRISPR/Cas9 gene-editing system to generate a sl_hta9 sl_hta11 double-mutant, designated sl_h2a.z, and found that these two mutations led to a significant reduction in the fresh weight of tomato fruits. Subsequent messenger RNA (mRNA)-seq results showed that dysfunction of Sl_H2A.Z has profound effects on the reprogramming of genome-wide gene expression at different developmental stages of tomato fruits, indicating a ripening-dependent correlation between Sl_H2A.Z and gene expression regulation in tomato fruits. In addition, the expression of three genes, SlPSY1, SlPDS, and SlVDE, encoding the key enzymes in the biosynthesis pathway of carotenoids, was significantly upregulated in the later ripening stages, which was consistent with the increased contents of carotenoids in sl_h2a.z double-mutant fruits. Overall, our study reveals a role of Sl_H2A.Z in the regulation of carotenoids and provides a resource for the study of Sl_H2A.Z-dependent gene expression regulation. Hence, our results provide a link between epigenetic regulation via histone variants and fruit development, suggesting a conceptual framework to understand how histone variants regulate tomato fruit quality.
Silencing MdGH3-2/12 in apple reduces drought resistance by regulating AM colonization
Authors: Huang Dong , Wang Qian , Zhang Zhijun , Jing Guangquan , Ma Mengnan , Ma Fengwang , Li Chao 
Published: April 2021

AbstractDrought leads to reductions in plant growth and crop yields. Arbuscular mycorrhizal fungi (AMF), which form symbioses with the roots of the most important crop species, alleviate drought stress in plants. In the present work, we identified 14 GH3 genes in apple (Malus domestica) and provided evidence that MdGH3-2 and MdGH3-12 play important roles during AM symbiosis. The expression of both MdGH3-2 and MdGH3-12 was upregulated during mycorrhization, and the silencing of MdGH3-2/12 had a negative impact on AM colonization. MdGH3-2/12 silencing resulted in the downregulation of five genes involved in strigolactone synthesis, and there was a corresponding change in root strigolactone content. Furthermore, we observed lower root dry weights in RNAi lines under AM inoculation conditions. Mycorrhizal transgenic plants showed greater sensitivity to drought stress than WT, as indicated by their higher relative electrolytic leakage and lower relative water contents, osmotic adjustment ability, ROS scavenging ability, photosynthetic capacity, chlorophyll fluorescence values, and abscisic acid contents. Taken together, these data demonstrate that MdGH3-2/12 plays an important role in AM symbiosis and drought stress tolerance in apple.