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.

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.

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.

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.

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.

The changes of electroencephalography in mountaineers on Mount Jade, Taiwan: An observational study.

BACKGROUND: The diagnosis of acute mountain sickness, which lacks a reliable and objective diagnostic tool, still depends on the clinical symptoms and signs and remains a major threat and unpredictable disease affecting millions of mountaineers. OBJECTIVES: To record electroencephalography signals with small, convenient, wireless equipment and to test whether electroencephalography parameters, which are more sensitive and reliable markers, could predict the symptoms of acute mountain sickness. METHODS: Twenty-five participants were enrolled and separated into two groups to climb Mount Jade in Taiwan. We collected electrocardiography signals and arterial oxygen saturation data at ground, moderate (2,400 m), and high altitude (3,400 m). A spectral analysis of the electrocardiography was performed to assess the study subjects' electroencephalography activity at different frequencies (α, ß, θ, δ) and the mean power frequency of electrocardiography. The clinical symptoms and Lake Louise Acute Mountain Sickness scores of the subjects were recorded for comparison. RESULTS: A significant change in the δ power of electroencephalography was recorded in subjects ascending from the ground to a high altitude of 3,400 m in a 4-day itinerary. In addition, between the two groups of subjects with and without acute mountain sickness (Lake Louise Acute Mountain Sickness scores < 3 and ≥ 3), the δ power of electroencephalography at the fronto-parietal 1 and parietal 3 electrodes at moderate altitude as well as the changes of δ power and mean power frequency of electrocardiography over parietal 4 at high altitude showed a significant difference. At moderate altitude, the increasing δ power of electroencephalography at the parietal 4 electrode was related to the headache symptom of acute mountain sickness before ascending to high altitude. CONCLUSION: At moderate altitude, the δ power increase of electroencephalography at the P4 electrode could be a predictor of acute mountain sickness symptoms before ascending to high altitude. Thus, electroencephalography had the potential to identify the risk of acute mountain sickness.

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.

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.

Optimization of an Efficient Protoplast Transformation System for Transient Expression Analysis Using Leaves of Torenia fournieri.

Torenia fournieri (T. fournieri) is one of the most widely used horticultural flowers and is considered a potential model plant for the genetic investigation of ornamental traits. In this study, we optimized an efficient protocol for high efficiency preparation and transformation of T. fournieri protoplast. The transformation rate reached ~75% when a 35S:GFP construct was used for the transformation. Using this system, we characterized the subcellular localization of several TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR (TCP) transcription factors (TFs), and found a distinct localization pattern between the CIN and CYC classes of TCP TFs. Furthermore, we also demonstrated the feasibility of the expression of dual luciferase assay system in T. fournieri protoplasts for the measurement of the activity of cis-regulatory elements. Taken together, a well-optimized transient expression system in T. fournieri protoplasts would be crucial for rapid exploration of the gene function or cis-regulatory elements.

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.

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.

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.

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.

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.

How noncoding open chromatin regions shape soybean domestication.

Open chromatin regions (OCRs), a generally conserved genomic feature amongst plant species, contain noncoding cis-regulatory elements for gene regulation. Wang et al. recently investigated how OCR structures and noncoding regions might have influenced the domestication of soybean. This knowledge could guide genome editing on future improvements of agronomic traits.