ERECTA Modulates Seed Germination and Fruit Development via Auxin Signaling in Tomato.

Tomato (Solanum lycopersicum) breeding for improved fruit quality emphasizes selecting for desirable taste and characteristics, as well as enhancing disease resistance and yield. Seed germination is the initial step in the plant life cycle and directly affects crop productivity and yield. ERECTA (ER) is a receptor-like kinase (RLK) family protein known for its involvement in diverse developmental processes. We characterized a Micro-Tom EMS mutant designated as a knock-out mutant of sler. Our research reveals that SlER plays a central role in controlling critical traits such as inflorescence development, seed number, and seed germination. The elevation in auxin levels and alterations in the expression of ABSCISIC ACID INSENSITIVE 3 (ABI3) and ABI5 in sler seeds compared to the WT indicate that SlER modulates seed germination via auxin and abscisic acid (ABA) signaling. Additionally, we detected an increase in auxin content in the sler ovary and changes in the expression of auxin synthesis genes YUCCA flavin monooxygenases 1 (YUC1), YUC4, YUC5, and YUC6 as well as auxin response genes AUXIN RESPONSE FACTOR 5 (ARF5) and ARF7, suggesting that SlER regulates fruit development via auxin signaling.

Synchronization of Arabidopsis flowering time and vegetative growth stage via FT overexpression can reveal inherent heterosis due to heterozygosity in intraspecific hybrids.

Intraspecific hybrids of Arabidopsis sometimes display heterosis. However, allelic variation of flowering repressor genes causes late flowering in F1, which might distort the potential heterosis effect due to prolonged vegetative growth. Here, overexpression of flowering gene FT synchronized flowering and eliminated growth differentials between parental and F1. These findings indicate the possibility of quantitatively demonstrating the inherent heterosis caused by heterozygosity.

Comparative effects of ethylene inhibitors on Agrobacterium-mediated transformation of drought-tolerant wild watermelon.

Ethylene (C2H4), a phytohormone that is produced in response to both abiotic and biotic stresses, is an important factor influencing the efficiency of Agrobacterium-mediated transformation. In this study, effects of various ethylene inhibitors on the efficiency of Agrobacterium-mediated genetic transformation in drought-tolerant wild watermelon was comparatively examined. Consequently, in comparison to the application of chemical inhibitors such as AgNO3 and aminoethoxyvinylglycine (AVG), lower ethylene level was observed when the infecting Agrobacterium contained a gene for 1-aminocyclopropane-carboxylic acid (ACC) deaminase (acdS), which cleaves ethylene precursor ACC into α-ketobutyrate and ammonia. GUS histochemical and spectrophotometric enzyme assays showed that acdS was more effective in enhancing gene transfer than the chemical ethylene inhibitors. Efficiency of transgenic shoots formation was higher in acdS- and AVG-treated explants. These observations demonstrated that controlling the ethylene level during co-cultivation and shoot formation, particularly using the acdS-harboring Agrobacterium, is advantageous for enhancing the transformation efficiency in this plant.

Trans-acting small RNA determines dominance relationships in Brassica self-incompatibility.

A diploid organism has two copies of each gene, one inherited from each parent. The expression of two inherited alleles is sometimes biased by the effects known as dominant/recessive relationships, which determine the final phenotype of the organism. To explore the mechanisms underlying these relationships, we have examined the monoallelic expression of S-locus protein 11 genes (SP11), which encode the male determinants of self-incompatibility in Brassica. We previously reported that SP11 expression was monoallelic in some S heterozygotes, and that the promoter regions of recessive SP11 alleles were specifically methylated in the anther tapetum. Here we show that this methylation is controlled by trans-acting small non-coding RNA (sRNA). We identified inverted genomic sequences that were similar to the recessive SP11 promoters in the flanking regions of dominant SP11 alleles. These sequences were specifically expressed in the anther tapetum and processed into 24-nucleotide sRNA, named SP11 methylation inducer (Smi). Introduction of the Smi genomic region into the recessive S homozygotes triggered the methylation of the promoter of recessive SP11 alleles and repressed their transcription. This is an example showing sRNA encoded in the flanking region of a dominant allele acts in trans to induce transcriptional silencing of the recessive allele. Our finding may provide new insights into the widespread monoallelic gene expression systems.

Cytoplasmic Ca2+ changes dynamically during the interaction of the pollen tube with synergid cells.

The directional growth of the pollen tube from the stigma to the embryo sac in the ovules is regulated by pollen-pistil interactions based on intercellular communication. Although pollen tube growth is regulated by the cytoplasmic Ca(2+) concentration ([Ca(2+)](cyt)), it is not known whether [Ca(2+)](cyt) is involved in pollen tube guidance and reception. Using Arabidopsis expressing the GFP-based Ca(2+)-sensor yellow cameleon 3.60 (YC3.60) in pollen tubes and synergid cells, we monitored Ca(2+) dynamics in these cells during pollen tube guidance and reception under semi-in vivo fertilization conditions. In the pollen tube growing towards the micropyle, pollen tubes initiated turning within 150 µm of the micropylar opening; the [Ca(2+)](cyt) in these pollen tube tips was higher than in those not growing towards an ovule in assays with myb98 mutant ovules, in which pollen tube guidance is disrupted. These results suggest that attractants secreted from the ovules affect Ca(2+) dynamics in the pollen tube. [Ca(2+)](cyt) in synergid cells did not change when the pollen tube grew towards the micropyle or entered the ovule. Upon pollen tube arrival at the synergid cell, however, [Ca(2+)](cyt) oscillation began at the micropylar pole of the synergid, spreading towards the chalazal pole. Finally, [Ca(2+)](cyt) in the synergid cell reached a maximum at pollen tube rupture. These results suggest that signals from the pollen tube induce Ca(2+) oscillations in synergid cells, and that this Ca(2+) oscillation is involved in the interaction between the pollen tube and synergid cell.

Dominance relationships between self-incompatibility alleles controlled by DNA methylation.

In crucifers, the pollen S-determinant gene, SP11, is sporophytically expressed in the anther tapetum, and the pollen self-incompatibility phenotype is determined by the dominance relationships between the two S-haplotypes it carries. We report here that 5' promoter sequences of recessive SP11 alleles are specifically methylated in the tapetum before the initiation of SP11 transcription. These results suggest that tissue-specific monoallelic de novo DNA methylation is involved in determining the dominance interactions that determine the cruciferous self-incompatibility phenotype.

Multivariate Profiling of Metabolites and Volatile Organic Compounds in Citrus depressa Hayata Fruits from Kagoshima, Okinawa, and Taiwan.

Citrus depressa Hayata is a small-fruit citrus species; it is indigenous to Kagoshima, Okinawa, and Taiwan. The metabolites and volatile organic compounds (VOCs) that affect the flavor of its fruits have not been investigated based on geographical origin. In the present study, we investigated the metabolite and VOC profiles of 18 C. depressa cultivation lines from these regions. Multivariate analysis revealed differences in the metabolites of C. depressa based on its cultivation origins; variations in sugar, sugar alcohol, and amino acid contents were also observed. Fruits from Kagoshima and Okinawa had higher galactinol, trehalose, xylose, glucose, and sucrose intensities than fruits from Taiwan (log2-fold change; 2.65-3.44, 1.68-2.13, 1.37-2.01, 1.33-1.57, and 1.07-1.43, respectively), whereas the Taiwanese lines contained higher leucine, isoleucine, serine, and alanine. In contrast to the Taiwanese Nantou line, other cultivation lines had comparable total VOC contents, and the VOCs of all lines were dominated by limonene, γ-terpinene, and p-cymene. Accordingly, the highest VOC intensities were recorded in the Nantou line, which was followed by Shikunin sweet (Kagoshima) and Taoyuan (Taiwan) (log10 normalize concentration; 5.11, 3.08, and 3.01, respectively). Moreover, multivariate analysis plots elucidated the difference in the VOCs of Ishikunibu (Okinawa), Shikunin sweet, and Taoyuan and between those of most Kagoshima and Okinawa cultivation lines. These results suggest that both the cultivation line and origin influence the metabolites and VOCs of C. depressa, thus possibly affecting its flavor quality; the data provide a valuable insight for utilizing C. depressa of different cultivation lines and origins to produce foods and beverages.

Morphological and metabolomics profiling of intraspecific Arabidopsis hybrids in relation to biomass heterosis.

Heterosis contributes greatly to the worldwide agricultural yield. However, the molecular mechanism underlying heterosis remains unclear. This study took advantage of Arabidopsis intraspecific hybrids to identify heterosis-related metabolites. Forty-six intraspecific hybrids were used to examine parental effects on seed area and germination time. The degree of heterosis was evaluated based on biomass: combinations showing high heterosis of F1 hybrids exhibited a biomass increase from 6.1 to 44% over the better parent value (BPV), whereas that of the low- and no-heterosis hybrids ranged from - 19.8 to 9.8% over the BPV. Metabolomics analyses of F1 hybrids with high heterosis and those with low one suggested that changes in TCA cycle intermediates are key factors that control growth. Notably, higher fumarate/malate ratios were observed in the high heterosis F1 hybrids, suggesting they provide metabolic support associated with the increased biomass. These hybrids may produce more energy-intensive biomass by speeding up the efficiency of TCA fluxes. However, the expression levels of TCA-process-related genes in F1 hybrids were not associated with the intensity of heterosis, suggesting that the post-transcriptional or post-translational regulation of these genes may affect the productivity of the intermediates in the TCA cycle.

Epigenetic regulation of monoallelic gene expression.

Monoallelic expression from biallelic genes is frequently observed in diploid eukaryotic organisms. Classic examples of this phenomenon include the well-characterized cases of genomic imprinting and X-chromosome inactivation. However, recent studies have shown that monoallelic expression is widespread in autosomal genes. This discovery was met with great interest because it represents another mechanism to generate diversity in gene expression that can affect cell fate and physiology. To date, the molecular mechanisms underlying this phenomenon are largely unknown. In our original study describing the dominant / recessive relationships of pollen- determinant alleles in Brassica self-incompatibility, we found that the recessive allele was specifically methylated and silenced through the action of small RNA derived from the dominant allele. In this review, we focus on recent studies of monoallelic expression in autosomal genes, and discuss the possible mechanisms driving this form of monoallelic gene suppression.

Straight Back Syndrome Presented with Chest and Back Pain: A Case Report.

A 17-year-old female adolescent presented with her mother to our clinic with a two-month history of left-sided chest pain and a one-week history of middle back pain. We diagnosed straight back syndrome based on the chest and thoracic radiographic findings and symptoms of chest pain, palpitations, and dyspnea. We reassured the patient that the disease was benign and advised her to start and continue chiropractic therapy. All symptoms, including back pain, disappeared in three weeks. Straight back syndrome is under-diagnosed, and back pain is less recognized as a symptom of the disease.

The prognostic factors of in-hospital death among patients with pneumonic COPD acute exacerbation.

BACKGROUND: Pneumonic acute exacerbation of chronic obstructive pulmonary disease (COPD-AE) is associated with worse outcomes compared with non-pneumonic COPD-AE. We aimed to explore prognostic factors among patients with pneumonic COPD-AE. METHODS: This multicentered retrospective cohort study was conducted across five hospitals in Japan. Hospitalized patients ≥40 years of age with pneumonic COPD-AE who were administered systemic corticosteroids during hospitalization were included. Patients with other causes of respiratory failure, daily systemic steroid users, and patients who were not treated with systemic steroids were excluded. Based on existing clinical prediction models, the following potential prognostic factors were selected in advance: age, blood eosinophil count, blood urea nitrogen, respiratory rate, diastolic blood pressure, and altered mental status. Multivariate logistic regression was conducted to determine the association between potential prognostic factors and in-hospital death. RESULTS: After excluding 897 patients based on the exclusion criteria, 669 patients with pneumonic COPD-AE who were administered systemic corticosteroids were included. The in-hospital mortality rate was 5.1%. Altered mental status was associated with mortality (odds ratio, 4.47; 95% confidence intervals, 2.00 to 10.00), and eosinophilia was associated with a lower risk of mortality (odds ratio, 0.19; 95% confidence intervals: 0.06 to 0.56). CONCLUSIONS: Altered mental status may be a prognostic factor for in-hospital death among patients with pneumonic COPD-AE who were administered systemic corticosteroids. Moreover, eosinophilia may be a prognostic factor for lower in-hospital mortality rate among these patients.

Inappropriate Evaluation of Effect Modifications Based on Categorical Outcomes: A Systematic Review of Randomized Controlled Trials.

Our meta-epidemiological study aimed to describe the prevalence of reporting effect modification only on relative scale outcomes and inappropriate interpretations of the coefficient of interaction terms in nonlinear models on categorical outcomes. Our study targeted articles published in the top 10 high-impact-factor journals between 1 January and 31 December 2021. We included two-arm, parallel-group, interventional superiority randomized controlled trials to evaluate the effects of modifications on categorical outcomes. The primary outcomes were the prevalence of reporting effect modifications only on relative scale outcomes and that of inappropriately interpreting the coefficient of interaction terms in nonlinear models on categorical outcomes. We included 52 articles, of which 41 (79%) used nonlinear regression to evaluate effect modifications. At least 45/52 articles (87%) reported effect modifications based only on relative scale outcomes, and at least 39/41 (95%) articles inappropriately interpreted the coefficient of interaction terms merely as indices of effect modifications. The quality of the evaluations of effect modifications in nonlinear models on categorical outcomes was relatively low, even in randomized controlled trials published in medical journals with high impact factors. Researchers should report effect modifications of both absolute and relative scale outcomes and avoid interpreting the coefficient of interaction terms in nonlinear regression analyses.

Predicting in-hospital death in pneumonic COPD exacerbation via BAP-65, CURB-65 and machine learning.

INTRODUCTION: There is no established clinical prediction model for in-hospital death among patients with pneumonic COPD exacerbation. We aimed to externally validate BAP-65 and CURB-65 and to develop a new model based on the eXtreme Gradient Boosting (XGBoost) algorithm. METHODS: This multicentre cohort study included patients aged ≥40 years with pneumonic COPD exacerbation. The input data were age, sex, activities of daily living, mental status, systolic and diastolic blood pressure, respiratory rate, heart rate, peripheral blood eosinophil count and blood urea nitrogen. The primary outcome was in-hospital death. BAP-65 and CURB-65 underwent external validation using the area under the receiver operating characteristic curve (AUROC) in the whole dataset. We used XGBoost to develop a new prediction model. We compared the AUROCs of XGBoost with that of BAP-65 and CURB-65 in the test dataset using bootstrap sampling. RESULTS: We included 1190 patients with pneumonic COPD exacerbation. The in-hospital mortality was 7% (88 out of 1190). In the external validation of BAP-65 and CURB-65, the AUROCs (95% confidence interval) of BAP-65 and CURB-65 were 0.69 (0.66-0.72) and 0.69 (0.66-0.72), respectively. XGBoost showed an AUROC of 0.71 (0.62-0.81) in the test dataset. There was no significant difference in the AUROCs of XGBoost versus BAP-65 (absolute difference 0.054; 95% CI -0.057-0.16) or versus CURB-65 (absolute difference 0.0021; 95% CI -0.091-0.088). CONCLUSION: BAP-65, CURB-65 and XGBoost showed low predictive performance for in-hospital death in pneumonic COPD exacerbation. Further large-scale studies including more variables are warranted.

Integrated transcript and metabolite profiling reveals coordination between biomass size and nitrogen metabolism in Arabidopsis F1 hybrids.

Heterosis refers to the improved agronomic performance of F1 hybrids relative to their parents. Although this phenomenon is widely employed to increase biomass, yield, and stress tolerance of plants, the underlying molecular mechanisms remain unclear. To dissect the metabolic fluctuations derived from genomic and/or environmental differences contributing to the improved biomass of F1 hybrids relative to their parents, we optimized the growth condition for Arabidopsis thaliana F1 hybrids and their parents. Modest but statistically significant increase in the biomass of F1 hybrids was observed. Plant samples grown under the optimized condition were also utilized for integrated omics analysis to capture specific changes in the F1 hybrids. Metabolite profiling of F1 hybrids and parent plants was performed using gas chromatography-mass spectrometry. Among the detected 237 metabolites, 2-oxoglutarate (2-OG) and malate levels were lower and the level of aspartate was higher in the F1 hybrids than in each parent. In addition, microarray analysis revealed that there were 44 up-regulated and 12 down-regulated genes with more than 1.5-fold changes in expression levels in the F1 hybrid compared to each parent. Gene ontology (GO) analyses indicated that genes up-regulated in the F1 hybrids were largely related to organic nitrogen (N) process. Quantitative PCR verified that glutamine synthetase 2 (AtGLN2) was upregulated in the F1 hybrids, while other genes encoding enzymes in the GS-GOGAT cycle showed no significant differences between the hybrid and parent lines. These results suggested the existence of metabolic regulation that coordinates biomass and N metabolism involving AtGLN2 in F1 hybrids.

Effectiveness of empirical anti-pseudomonal antibiotics for recurrent COPD exacerbation: a multicenter retrospective cohort study.

Although frequent chronic obstructive pulmonary disease (COPD) exacerbation has been associated with the isolation of Pseudomonas aeruginosa (PA) in sputum cultures, it remains unknown whether the empirical use of anti-pseudomonal antibiotics can improve outcomes in patients with frequent COPD exacerbations. This multicenter retrospective cohort study evaluated whether the empirical use of anti-pseudomonal antibiotics improves the length of the hospital stay in patients with recurrent COPD exacerbation (≥ 2 admissions from April 1, 2008 to July 31, 2020). For statistical analysis, a log-linked Gamma model was used. Parameters were estimated using a generalized estimating equation model with an exchangeable correlation structure accounting for repeated observations from a single patient. Covariates included age, body mass index, home oxygen therapy use, respiratory rate, heart rate, oxygen use on admission, mental status, systemic steroid use, activities of daily living, and the number of recurrences. Hospital-specific effects were specified as fixed effects. In total, 344 patients and 965 observations of recurrent COPD exacerbations were selected. Anti-pseudomonal antibiotics were used in 173 patients (18%). The estimated change in the length of the hospital stay between anti-pseudomonal and non-anti-pseudomonal antibiotics groups was 0.039 days [95% confidence interval; - 0.083, 0.162]. Anti-pseudomonal antibiotics could not shorten the length of the hospital stay.

Novel self-compatible lines of Brassica rapa L. isolated from the Japanese bulk-populations.

Self-incompatibility (SI) in Brassicaceae is sporophytically controlled by a single S-locus with multi allelic variety. The male S determinant, SP11/SCR (S-locus protein 11/S-locus cysteine-rich protein), is a small cysteine-rich protein, and the female S determinant, SRK (S-locus receptor kinase), functions as a receptor for SP11 at the surface of stigma papilla cells. Although a few of the following downstream factors in the SP11-SRK signaling cascade have been identified, a comprehensive understanding of the SI mechanism still remains unexplained in Brassicaceae. Analysis of self-compatible (SC) mutants is significant for understanding the molecular mechanism in SI reactions, thus we screened SC lines from a variety of Japanese bulk-populations of B. rapa vegetables. Two lines, TSC4 and TSC28, seem to have disruptions in the SI signaling cascade, while the other line, TSC2, seems to have a deficiency in a female S determinant, SRK. In TSC4 and TSC28, known SI-related factors, i.e. SRK, SP11, MLPK (M-locus protein kinase), THL (thioredoxin-h-like), and ARC1 (arm repeat containing 1), were expressed normally, and their expression levels were comparable with those in SI lines. On a B. rapa genetic linkage map, potential SC genes in TSC4 and TSC28 were mapped on linkage groups A3 and A1, respectively, whereas MLPK, ARC1, and THL were mapped on A3, A4, and A6, respectively. Although potential SC genes of TSC4 and MLPK were on the same linkage group, their positions were apparently independent. These results indicate that the SC genes of TSC4 and TSC28 are independent from the S-locus or known SI-related genes. Thus, the SC lines selected here have mutations in novel factors of the SI signaling cascade, and they will contribute to fill pieces in a signal transduction pathway of the SI system in Brassicaceae.

Effectiveness of Steroid Therapy on Pneumonic Chronic Obstructive Pulmonary Disease Exacerbation: A Multicenter, Retrospective Cohort Study.

Purpose: To date, no consensus exists on the effects of systemic steroid use on pneumonic chronic obstructive pulmonary disease (COPD) exacerbation owing to trial design issues in previous trials involving these conditions. This multicenter study aimed to evaluate more precisely the effectiveness of the use of systemic steroids in treating pneumonic COPD exacerbation in a larger sample by adjusting for confounding factors. Patients and Methods: This multicenter, retrospective, observational study was conducted across five acute general hospitals in Japan. We analyzed the association between parenteral/oral steroid therapy and time to clinical stability in pneumonic COPD exacerbation. We used a validated algorithm derived from the 10th revision of the International Classification of Diseases and Related Health Problems (ICD-10) to include patients with pneumonic COPD exacerbation. We excluded patients with other hypoxia causes (asthma exacerbation, pneumothorax, heart failure) and complicated pneumonia (obstructive pneumonia, empyema), those who required tracheal intubation/vasopressors, and those who were clinically stable on day of admission. The primary outcome was the time to clinical stability. Multiple imputation was used for missing data. Propensity scores within each imputed dataset were calculated using potential confounding factors. The Fine and Gray model was used within each dataset to account for the competing risk of death and hospital discharge without clinical stability, and we combined the results. Results: Altogether, 1237 patients were included. Systemic steroid therapy was administered to 658 patients (53%). The pooled estimated subdistribution hazard ratio of time to clinical stability in steroid vs non-steroid users was 0.89 (95% confidence interval, 0.78 to 1.0). Conclusion: This study revealed that systemic steroid therapy may not improve the time to clinical stability in patients with pneumonic COPD exacerbation of mild to moderate severity. Further randomized controlled trials including more severe patients will be needed to evaluate the effectiveness of systemic steroid therapy accurately.

Association analysis of phenotypic and metabolomic changes in Arabidopsis accessions and their F1 hybrids affected by different photoperiod and sucrose supply.

Photoperiod and sucrose (Suc) assimilation play important roles in the regulation of plant growth and development. However, it remains unclear how natural variation of plants could contribute to metabolic changes under various growth conditions. Here, we investigated the developmental and metabolomic responses of two natural accessions of Arabidopsis thaliana, Columbia (Col) and C24, and their reciprocal F1 hybrids grown under four carbon source regimens, i.e., two different photoperiods and the presence or absence of exogenous Suc supply. The effect of exogenous Suc clearly appeared in the growth of Col and the F1 hybrid but not in C24, whereas long-day conditions had significant positive effects on the growth of all lines. Comparative metabolite profiling of Col, C24, and the F1 hybrid revealed that changes in metabolite levels, particularly sugars, were highly dependent on genotype-specific responses rather than growth conditions. The presence of Suc led to over-accumulation of seven metabolites, including four sugars, a polyamine, and two amino acids in C24, whereas no such accumulation was observed in the profiles of Col and the F1 hybrid. Thus, the comparative metabolite profiling revealed that the two parental lines of the hybrid show a distinct difference in sugar metabolism.

Multiplex exome sequencing reveals genome-wide frequency and distribution of mutations in the 'Micro-Tom' Targeting Induced Local Lesions in Genomes (TILLING) mutant library.

While the 'Micro-Tom' TILLING mutant library is used for a wide range of purposes, including both basic research of gene function and breeding of commercial cultivars, genome-wide distribution and frequency of mutations have not yet been thoroughly elucidated on a population scale. In this study, we developed a 96-plex exome sequencing method to identify and analyze mutations within the TILLING mutants that were developed in the University of Tsukuba. First, an Illumina paired-end sequencing coupled with 96-plex exome capture resulted in the acquisition of an exome sequence dataset with an average read count of 5.6 million for the 95 mutants. Over 98% of the capture target region could be covered by the short reads with an averaged read depth of 12.8, which enabled us to identify single nucleotide polymorphisms and Indels in a genome-wide manner. By subtracting intra-cultivar DNA variations that are present between wild-type 'Micro-Tom' lines, we identified 241,391 mutation candidates in 95 mutant individuals. Of these, 64,319 and 6,480 mutations were expected to cause protein amino acid substitutions or premature stop codon, respectively. Based on the exome mutation dataset, a mutant line designated 'TOMJPW601' was found to carry a premature stop codon mutation (W261*) in a putative auxin influx carrier gene SlLAX1 (Solyc09G014380), consistent with our previous report of its curly leaf phenotype. Our results suggested that a population-scale mutation database developed by multiplexed exome sequencing could be used for in silico mutant screening, which in turn could contribute to both gene function research and breeding programs.