Priming-induced alterations in histone modifications modulate transcriptional responses in soybean under salt stress.

Plants that have experienced certain abiotic stress may gain tolerance to a similar stress in subsequent exposure. This phenomenon, called priming, was observed here in soybean (Glycine max) seedlings exposed to salt stress. Time-course transcriptomic profiles revealed distinctively different transcriptional responses in the primed seedlings from those in the non-primed seedlings under high salinity stress, indicating a stress response strategy of repressing unhelpful biotic stress responses and focusing on the promotion of those responses important for salt tolerance. To identify histone marks altered by the priming salinity treatment, a genome-wide profiling of histone 3 lysine 4 dimethylation (H3K4me2), H3K4me3, and histone 3 lysine 9 acetylation (H3K9ac) was performed. Our integrative analyses revealed that priming induced drastic alterations in these histone marks, which coordinately modified the stress response, ion homeostasis, and cell wall modification. Furthermore, transcriptional network analyses unveiled epigenetically modified networks which mediate the strategic downregulation of defense responses. Altering the histone acetylation status using a chemical inhibitor could elicit the priming-like transcriptional responses in non-primed seedlings, confirming the importance of histone marks in forming the priming response.

The chromatin accessibility landscape of pistils and anthers in rice.

Transcription activation is tightly associated with the openness of chromatin and allows direct contact between transcriptional regulators and their targeted DNA for gene expression. However, there are limited studies on the annotation of open chromatin regions (OCRs) in rice (Oryza sativa), especially those in reproductive organs. Here, we characterized OCRs in rice pistils and anthers with an assay for transposase-accessible chromatin using sequencing. Despite a large overlap, we found more OCRs in pistils than in anthers. These OCRs were enriched in gene transcription start sites (TSSs) and showed tight associations with gene expression. Transcription factor (TF) binding motifs were enriched at these OCRs as validated by TF chromatin immunoprecipitation followed by sequencing. Pistil-specific OCRs provided potential regulatory networks by binding directly to the targets, indicating that pistil-specific OCRs may be indicators of cis-regulatory elements in regulating pistil development, which are absent in anthers. We also found that open chromatin of pistils and anthers responded differently to low temperature (LT). These data offer a comprehensive overview of OCRs regulating reproductive organ development and LT responses in rice.

Identification of the accessible chromatin regions in six tissues in the soybean.

Accessible chromatin regions (ACRs) are tightly associated with gene expressions in the genome. Conserved non-coding cis-regulatory elements, such as transcription factor binding motifs, are usually found in ACRs, indicating an essential regulatory role of ACRs in the plant genome architecture. However, there have been few studies on soybean ACRs, especially those focusing on specific tissues. Hence, in this study, with the convenient ATAC-seq, we identified the ACRs in six soybean tissues, including root, leaf bud, flower, flower bud, developing seed, and pod. In total, the ACRs occupied about 3.3% of the entire soybean genome. By integrating the results from RNA-seq and transcription factor (TF) ChIP-seq, ACRs were found to be tightly associated with gene expressions and TF binding capacities in soybean. Together, these data provide a comprehensive understanding of the genomic features of ACRs in soybean. As a collection of essential genomic resources, these processed data are made available at datahub.wildsoydb.org.

QTL analyses of soybean root system architecture revealed genetic relationships with shoot-related traits.

KEY MESSAGE: The genetic basis of soybean root system architecture (RSA) and the genetic relationship between shoot and RSA were revealed by integrating data from recombinant inbred population grafting and QTL mapping. Variations in root system architecture (RSA) affect the functions of roots and thus play vital roles in plant adaptations and agricultural productivity. The aim of this study was to unravel the genetic relationship between RSA traits and shoot-related traits in soybean. This study characterized RSA variability at seedling stage in a recombinant inbred population, derived from a cross between cultivated soybean C08 and wild soybean W05, and performed high-resolution quantitative trait locus (QTL) mapping. In total, 34 and 41 QTLs were detected for RSA-related and shoot-related traits, respectively, constituting eight QTL clusters. Significant QTL correspondence was found between shoot biomass and RSA-related traits, consistent with significant correlations between these phenotypes. RSA-related QTLs also overlapped with selection regions in the genome, suggesting the cultivar RSA could be a partial consequence of domestication. Using reciprocal grafting, we confirmed that shoot-derived signals affected root development and the effects were controlled by multiple loci. Meanwhile, RSA-related QTLs were found to co-localize with four soybean flowering-time loci. Consistent with the phenotypes of the parental lines of our RI population, diminishing the function of flowering controlling E1 family through RNA interference (RNAi) led to reduced root growth. This implies that the flowering time-related genes within the RSA-related QTLs are actually contributing to RSA. To conclude, this study identified the QTLs that determine RSA through controlling root growth indirectly via regulating shoot functions, and discovered superior alleles from wild soybean that could be used to improve the root structure in existing soybean cultivars.

Genome-wide characterization of nuclear factor Y transcription factors in Fagopyrum tataricum.

The nuclear factor Y (NF-Y) is an important transcription factor family that regulates plant developmental processes and abiotic stress responses. Currently, genome-wide studies of the NF-Y family are limited in Fagopyrum tataricum, an important economic crop. Based on the released genome assembly, we predicted a total of 38 NF-Y encoding genes (FtNF-Ys), including 12 FtNF-YAs, 18 FtNF-YBs, and eight FtNF-YCs subunits, in F. tataricum. Phylogenetic tree and sequence alignments showed that FtNF-Ys were conserved between F. tataricum and other species. Tissue expressions and network analyses suggested that FtNF-Ys might be involved in regulating developmental processes in different tissues. Several FtNF-YAs and FtNF-Ybs were also potentially involved in light response. In addition, FtNF-YC-like1 and FtNF-YC-like2 partially rescued the late flowering phenotype in nf-yc1 nf-yc3 nf-yc4 nf-yc9 (ycQ) mutant in Arabidopsis thaliana, supporting a conserved role of FtNF-Ys in regulating developmental processes. Together, the genomic information provides a comprehensive understanding of the NF-Y transcription factors in F. tataricum, which will be useful for further investigation of their functions in F. tataricum.

An expedient survey and characterization of the soybean JAGGED 1 (GmJAG1) transcription factor binding preference in the soybean genome by modified ChIPmentation on soybean protoplasts.

ChIP-seq is widely used for mapping the transcription factor (TF) binding sites throughout the genome in vivo. In this study, we adopted and modified ChIPmentation, a fast, robust, low-input requirement ChIP-seq method, to a transient expression system using soybean protoplasts to expedite the exploration of TF binding sites. To test this new protocol, we expressed a tagged version of a C2H2-type zinc finger TF, JAGGED1 (GmJAG1), in soybean protoplasts and successfully identified its binding sites in the soybean genome. Furthermore, valuable genomic features such as a novel GmJAG1-binding motif, and the epigenetic characteristics as well as an enhancer-like function of GmJBSs were also found via coupling ATAC-seq and H3K27me3 ChIP-seq data. The application of the modified ChIPmentation protocol in this study using soybean protoplasts provided a new approach for rapid elucidation of how a TF binds to the various target genes in the soybean genome, as illustrated here using GmJAG1.

OsTPP1 regulates seed germination through the crosstalk with abscisic acid in rice.

Seed germination is essential for direct seeding in rice. It has been demonstrated that trehalose-6-phosphate phosphatase 1 (OsTPP1) plays roles in improving yield and stress tolerance in rice. In this study, the roles of OsTPP1 on seed germination in rice were investigated. The tpp1 mutant germinated slower than the wild-type (WT), which can be restored by exogenous trehalose. tpp1 seeds showed higher ABA content compared with WT seeds. The tpp1 mutant was hypersensitive to ABA and ABA catabolism inhibitor (Dinicozanole). Furthermore, two ABA catabolism genes were downregulated in the tpp1 mutant which were responsible for increased ABA concentrations, and exogenous trehalose increased transcripts of ABA catabolism genes, suggesting that OsTPP1 and ABA catabolism genes acted in the same signaling pathway. Further analysis showed that a transcription factor of OsGAMYB was an activator of OsTPP1, and expression of OsGAMYB was decreased by both the exogenous and endogenous ABA, subsequently reducing the expression of OsTPP1, which suggested a new signaling pathway required for seed germination in rice. In addition, ABA-responsive genes, especially OsABI5, were invoved in OsTPP1-mediated seed germination. Overall, our study provided new pathways in seed germination that OsTPP1 controlled seed germination through crosstalk with the ABA catabolism pathway.

Ectopic expression of Torenia fournieri TCP8 and TCP13 alters the leaf and petal phenotypes in Arabidopsis thaliana.

Teosinte branched1/cycloidea/proliferating cell factor (TCP) transcription factors (TFs) are essential for regulating plant developmental processes, which is still largely unknown in Torenia fournieri (T. fournieri), a widely used horticultural flower. In this study, we used a de novo transcriptome assembly method to predict the TCP transcription factors in T. fournieri. In total, 15 out of 21 predicted T. fournieri TCPs (TfTCPs) were isolated and verified with Sanger sequencing. Phylogenetic analysis showed that these 15 TfTCPs could be classified into two major classes. Most of these TfTCPs were expressed in floral buds, flowers, or leaves, suggesting an important role in developmental regulation in these tissues. Moreover, TfTCP8 and TfTCP13, the homologues of the Arabidopsis thaliana TCP5-like transcription factor, were able to bind to the conserved Class II TCP binding motifs and are localized to the nucleus, indicating that TfTCP8 and TfTCP13 act as transcriptional regulators. In agreement with the overexpression phenotype of AtTCP5, ectopic expression of TfTCP8 and TfTCP13 resulted in narrow leaves and the small petal phenotype in Arabidopsis, suggesting that these two TfTCPs potentially regulate leaf or flower shape in T. fournieri.

Visual hallucinations in 246-km mountain ultra-marathoners: An observational study.

Ultra-marathons are typically held over harsh terrains such as mountains, deserts, or other wilderness, and place severe demands on the physical and psychological capabilities of participants. Adventure-race competitors commonly report hallucinations. The goal of this study was to gain insight into visual hallucinations (VHs) during a mountain ultra-marathon. Thirty-one Taiwanese runners who participated in the 2018 Run Across Taiwan Ultra-Marathon, which spans 246 km with an altitude difference of 3266 m and an overall cut-off time of 44 h, volunteered for this study. Self-reported questionnaires on sleep duration, hallucinatory experiences, clinical symptoms of cold- and heat-related illnesses, and the 2018 Lake Louise Acute Mountain Sickness (AMS) Score were recorded prerace, during the summit, immediately postrace, and 3-days postrace. Hematological samples were collected 1 week before, immediately after, and 3 days after the race. Eight ultra-marathoners (six males and two females; seven finishers and one withdrawer) were recruited. Three out of eight (37.5%) subjects (two males and one female) reported experiencing VHs during the last 60 km. Three out of five (60%) lower-ranked subjects experienced VHs. All eight runners slept for <30 min during the race. None of the runners presented with headache either during or after the race to meet the criteria for AMS. None of the runners suffered an abnormal thermoregulatory response or a hypoglycemic episode throughout the ultra-marathon. The changes in blood osmolality immediately postrace were subclinical, despite being statistically significant. Among the three runners with VHs, none presented with severe dehydration or dysnatremia immediately postrace. High-altitude exposure, hyper/hypothermia, dehydration, dysnatermia, or hypoglycemia did not seem to contribute to hallucination onset in our subjects during the event. VHs of ultra-marathoners may be associated with excessive physical exertion and sleep deprivation.

The genome of the medicinal plant Andrographis paniculata provides insight into the biosynthesis of the bioactive diterpenoid neoandrographolide.

Andrographis paniculata is a herbaceous dicot plant widely used for its anti-inflammatory and anti-viral properties across its distribution in China, India and other Southeast Asian countries. A. paniculata was used as a crucial therapeutic treatment during the influenza epidemic of 1919 in India, and is still used for the treatment of infectious disease in China. A. paniculata produces large quantities of the anti-inflammatory diterpenoid lactones andrographolide and neoandrographolide, and their analogs, which are touted to be the next generation of natural anti-inflammatory medicines for lung diseases, hepatitis, neurodegenerative disorders, autoimmune disorders and inflammatory skin diseases. Here, we report a chromosome-scale A. paniculata genome sequence of 269 Mb that was assembled by Illumina short reads, PacBio long reads and high-confidence (Hi-C) data. Gene annotation predicted 25 428 protein-coding genes. In order to decipher the genetic underpinning of diterpenoid biosynthesis, transcriptome data from seedlings elicited with methyl jasmonate were also obtained, which enabled the identification of genes encoding diterpenoid synthases, cytochrome P450 monooxygenases, 2-oxoglutarate-dependent dioxygenases and UDP-dependent glycosyltransferases potentially involved in diterpenoid lactone biosynthesis. We further carried out functional characterization of pairs of class-I and -II diterpene synthases, revealing the ability to produce diversified labdane-related diterpene scaffolds. In addition, a glycosyltransferase able to catalyze O-linked glucosylation of andrograpanin, yielding the major active product neoandrographolide, was also identified. Thus, our results demonstrate the utility of the combined genomic and transcriptomic data set generated here for the investigation of the production of the bioactive diterpenoid lactone constituents of the important medicinal herb A. paniculata.

Arabidopsis LEAFY COTYLEDON1 Mediates Postembryonic Development via Interacting with PHYTOCHROME-INTERACTING FACTOR4.

Plants undergo postembryonic growth during the developmental transition from germinating seeds to seedlings. Recent studies suggest LEAFY COTYLEDON1 (LEC1), initially identified as a central regulator in embryogenesis and seed maturation in Arabidopsis thaliana, plays a distinct role in postembryonic development. However, the mechanism by which LEC1 regulates nonembryonic development still remains elusive. In this study, we observed etiolation-related phenotypes in early seedlings of lec1 mutants and inducible LEC1 overexpression transgenic lines. Consistent with this, LEC1 promotes the expression of hypocotyl elongation-related genes in a darkness-dependent manner in spite of the comparable LEC1 transcript levels in the light- and dark-grown seedlings. Furthermore, we show that LEC1 interacts with PHYTOCHROME-INTERACTING FACTOR4 (PIF4), a major transcription modulator in postgermination development, to interdependently regulate hypocotyl elongation-related genes via direct binding to G-box element in the dark. Moreover, loss of LEC1 function suppresses the elongated hypocotyl phenotype of PIF-overaccumulating plants; conversely, inducible overexpression of LEC1 does not rescue the short hypocotyl in pif4 mutants. Our findings reveal that LEC1 acts as a coactivator of PIFs in transcriptional regulation during postembryonic growth, providing a possible mechanism by which plants fine-tune morphological development for their survival during the transition from the embryonic phase to seedling establishment.

Concurrent changes in methyl jasmonate emission and the expression of its biosynthesis-related genes in Cymbidium ensifolium flowers.

Methyl jasmonate (MeJA) is one of most abundant scent compounds in Cymbidium ensifolium flowers. In this study, the emission of MeJA and its regulation mechanism were investigated. Our results showed that emission of MeJA in C. ensifolium flowers was controlled developmentally and rhythmically. It occurred in a tissue-specific manner, and high MeJA emission was found in sepals and petals. A group of vital genes involved in the MeJA biosynthesis via the octadecanoid pathway were isolated from C. ensifolium flowers, including CeLOX, CeAOS, CeAOC and CeJMT. MeJA emission was at very low levels in unopened or half-opened C. ensifolium flowers and reached its maximal level between day 4 and 6 and declined from day 7 to 10 postanthesis. The expression of CeLOX, CeAOS, CeAOC and CeJMT increased from day 1 to day 6, and then declined from day 7 to 10 postanthesis, corresponding to the change in MeJA emission. Moreover, the expression of CeLOX, CeAOS, CeAOC and CeJMT oscillated in a rhythmic manner could reach the maximum level between 8:00 h and 16:00 h, which coincided with the MeJA emission. The high level of MeJA emission in sepals and petals coincided with the high transcript levels. The results suggest that MeJA emission in C. ensifolium flower might be directly regulated at the transcription levels. Moreover, the recombinant protein of CeJMT could specifically catalyze the jasmonic acid to form the corresponding ester MeJA.

The enhanced responsivity and response speed of SnO2 visible-blind transparent photodetectors via the SiO2 passivation layer.

Recently, transparent ultraviolet (UV) photodetectors have gained wide attention for their giant potential in integrated transparent electronics applications. SnO2 films as a common candidate for visible-blind transparent ultraviolet photodetectors have attracted increasing attention. In this work, high-performance visible-blind transparent UV photodetectors based on SnO2 thin film and a SiO2 passivation layer were successfully synthesized by the sol-gel spin coating method for the first time. The obtained SnO2/SiO2 hybrid device has a transmittance of nearly 80% in the visible band at 400-700 nm and demonstrates a high responsivity of 769 mA W-1 and a detection sensitivity of 1.24 × 1014 Jones under UV light illumination. The UV-C/UV-A rejection ratio is greater than 106, indicating that the device has good photo-selectivity. In addition, after the introdution of the SiO2 layer, the response speed is 2 times higher than that of pure SnO2. The presence of the SiO2 layer reduces the exposed area of SnO2, passivates the oxygen vacancies on the surface of SnO2 and inhibits the surface chemical adsorption. The above results provide a new perspective for improving the performance of SnO2 thin film for visible-blind transparent ultraviolet photodetectors.

Identification of the New GmJAG1 Transcription Factor Binding Motifs Using DAP-Seq.

Interaction between transcription factors (TFs) and motifs is essential for gene regulation and the subsequent phenotype formation. Soybean (Glycine max) JAGGEED 1 (GmJAG1) is a key TF that controls leaf shape, seed number and flower size. To understand the GmJAG1 binding motifs, in this study, we performed the GmJAG1 DNA affinity purification sequencing (DAP-seq) experiment, which is a powerful tool for the de novo motif prediction method. Two new significant GmJAG1 binding motifs were predicted and the EMSA experiments further verified the ability of GmJAG1 bound to these motifs. The potential binding sites in the downstream gene promoter were identified through motif scanning and a potential regulatory network mediated by GmJAG1 was constructed. These results served as important genomic resources for further understanding the regulatory mechanism of GmJAG1.

High myopia at high altitudes.

Background: Optic nerve sheath diameter (ONSD) increases significantly at high altitudes, and is associated with the presence and severity of acute mountain sickness (AMS). Exposure to hypobaria, hypoxia, and coldness when hiking also impacts intraocular pressure (IOP). To date, little is known about ocular physiological responses in trekkers with myopia at high altitudes. This study aimed to determine changes in the ONSD and IOP between participants with and without high myopia (HM) during hiking and to test whether these changes could predict symptoms of AMS. Methods: Nine participants with HM and 18 without HM participated in a 3-day trek of Xue Mountain. The ONSD, IOP, and questionnaires were examined before and during the trek of Xue Mountain. Results: The ONSD values increased significantly in both HM (p = 0.005) and non-HM trekkers (p = 0.018) at an altitude of 1,700 m. In the HM group, IOP levels were greater than those in the non-HM group (p = 0.034) on the first day of trekking (altitude: 3,150 m). No statistically significant difference was observed between the two groups for the values of ONSD. Fractional changes in ONSD at an altitude of 1,700 m were related to the development of AMS (r pb = 0.448, p = 0.019) and the presence of headache symptoms (r pb = 0.542, p = 0.004). The area under the ROC curve for the diagnostic performance of ONSD fractional changes at an altitude of 1,700 m was 0.859 for predicting the development of AMS and 0.803 for predicting the presence of headache symptoms. Conclusion: Analysis of changes in ONSD at moderate altitude could predict AMS symptoms before an ascent to high altitude. Myopia may impact physiological accommodation at high altitudes, and HM trekkers potentially demonstrate suboptimal regulation of aqueous humor in such environments.

Defect detection and identification for aircraft cable insulation layer based on deep forest.

Due to the special internal environment of aircraft, cable damage is inevitable, which usually starts from insulation layer defects and may cause major economic losses, and even seriously threaten the life of people on board. According to the above issue, a defect detection system for aircraft cable insulation layer based on ultrasonic guided waves (UGWs) is built in this paper. In order to ensure the complete coupling between the sensor and the insulation layer of the aircraft cable, the macro fiber composite (MFC) flexible sensor is employed in the system. Both simulation and experimental results show that this method can simultaneously monitor four different types (abrasion, cut, semi-stripping and full-stripping) of cable insulation layer defects at different locations on the same cable. The reflection signals of different types of defects are extremely similar and difficult to distinguish directly. In this paper, a classification method for four types of defects based on the deep forest method is proposed. This method requires a small sample size, and the classification performance is not affected by network structure and parameters. The recognition accuracy can reach 100%, avoiding the problem of traditional deep learning classification relying on a large number of samples and requiring parameter adjustment. The proposed method in this paper is proven to be able to effectively carry out online monitoring and accurately classify defect types, which has guiding significance for aircraft maintenance personnel to take corresponding measures in time.

Comprehensive metabolome and transcriptome analyses demonstrate divergent anthocyanin and carotenoid accumulation in fruits of wild and cultivated loquats.

Eriobotrya is an evergreen fruit tree native to South-West China and adjacent countries. There are more than 26 loquat species known in this genus, while E. japonica is the only species yet domesticated to produce fresh fruits from late spring to early summer. Fruits of cultivated loquat are usually orange colored, in contrast to the red color of fruits of wild E. henryi (EH). However, the mechanisms of fruit pigment formation during loquat evolution are yet to be elucidated. To understand these, targeted carotenoid and anthocyanin metabolomics as well as transcriptomics analyses were carried out in this study. The results showed that ß-carotene, violaxanthin palmitate and rubixanthin laurate, totally accounted for over 60% of the colored carotenoids, were the major carotenoids in peel of the orange colored 'Jiefangzhong' (JFZ) fruits. Total carotenoids content in JFZ is about 10 times to that of EH, and the expression levels of PSY, ZDS and ZEP in JFZ were 10.69 to 23.26 folds to that in EH at ripen stage. Cyanidin-3-O-galactoside and pelargonidin-3-O-galactoside were the predominant anthocyanins enriched in EH peel. On the contrary, both of them were almost undetectable in JFZ, and the transcript levels of F3H, F3'H, ANS, CHS and CHI in EH were 4.39 to 73.12 folds higher than that in JFZ during fruit pigmentation. In summary, abundant carotenoid deposition in JFZ peel is well correlated with the strong expression of PSY, ZDS and ZEP, while the accumulation of anthocyanin metabolites in EH peel is tightly associated with the notably upregulated expressions of F3H, F3'H, ANS, CHS and CHI. This study was the first to demonstrate the metabolic background of how fruit pigmentations evolved from wild to cultivated loquat species, and provided gene targets for further breeding of more colorful loquat fruits via manipulation of carotenoids and anthocyanin biosynthesis.

A pilot study of digital bedside cards in the emergency room of a medical centre in Taiwan.

The emergency room (ER) digital bedside card is a simple and important invention. It can be directly connected to the hospital information system to display important patient information in real time, reduce the workload of ER staff, improve their satisfaction, and provide useful information for patients and their families. We conducted a prospective study of ER staff using questionnaires and conducted Wilcoxon signed-rank test to compare before and after ER digital bedside card implementation in the Tamsui MacKay Memorial Hospital. Sixty participants of the ER staff joined the study before and after digital card implementation. After the ER digital bedside card was set up, the number of round trips from the nursing station to the ER bedside and the number of common questions asked by patients and their family members were significantly reduced. The cards reduced the response time for frequently asked questions by patients and their family members and significantly improved the satisfaction of ER staff. Our study showed that ER digital bedside cards reduced the workload of ER staff, provided patients and their families with useful information, and greatly improved ER staff satisfaction. This marks an important milestone in the future development of smart ER.