Systematic analysis of Heat Shock Protein 70 (HSP70) gene family in radish and potential roles in stress tolerance.

The 70 kD heat shock proteins (HSP70s) represent a class of molecular chaperones that are widely distributed in all kingdoms of life, which play important biological roles in plant growth, development, and stress resistance. However, this family has not been systematically characterized in radish (Raphanus sativus L.). In this study, we identified 34 RsHSP70 genes unevenly distributed within nine chromosomes of R. sativus. Phylogenetic and multiple sequence alignment analyses classified the RsHSP70 proteins into six distinct groups (Group A-F). The characteristics of gene structures, motif distributions, and corresponding cellular compartments were more similar in closely linked groups. Duplication analysis revealed that segmental duplication was the major driving force for the expansion of RsHSP70s in radish, particularly in Group C. Synteny analysis identified eight paralogs (Rs-Rs) in the radish genome and 19 orthologs (Rs-At) between radish and Arabidopsis, and 23 orthologs (Rs-Br) between radish and Chinese cabbage. RNA-seq analysis showed that the expression change of some RsHSP70s were related to responses to heat, drought, cadmium, chilling, and salt stresses and Plasmodiophora brassicae infection, and the expression patterns of these RsHSP70s were significantly different among 14 tissues. Furthermore, we targeted a candidate gene, RsHSP70-23, the product of which is localized in the cytoplasm and involved in the responses to certain abiotic stresses and P. brassicae infection. These findings provide a reference for further molecular studies to improve yield and stress tolerance of radish.

Transcriptional and physiological data revealed cold tolerance in a photo-thermo sensitive genic male sterile line Yu17S.

BACKGROUND: Rice is highly sensitive to chilling stress during the seedling stage. However, the adaptable photo-thermo sensitive genic male sterile (PTGMS) rice line, Yu17S, exhibits tolerance to low temperatures. Currently, the molecular characteristics of Yu17S are unclear. RESULTS: To evaluate the molecular mechanisms behind cold responses in rice seedlings, a comparative transcriptome analysis was performed in Yu17S during seedling development under normal temperature and low temperature conditions. In total, 9317 differentially expressed genes were detected. Gene ontology and pathway analyses revealed that these genes were involved mostly in photosynthesis, carotenoid biosynthesis, carbohydrate metabolism and plant hormone signal transduction. An integrated analysis of specific pathways combined with physiological data indicated that rice seedlings improved the performance of photosystem II when exposed to cold conditions. Genes involved in starch degradation and sucrose metabolism were activated in rice plants exposed to cold stress treatments, which was accompanied by the accumulation of soluble sugar, trehalose, raffinose and galactinol. Furthermore, chilling stress induced the expression of phytoene desaturase, 15-cis-ζ-carotene isomerase, ζ-carotene desaturase, carotenoid isomerase and ß-carotene hydroxylase; this was coupled with the activation of carotenoid synthase activity and increases in abscisic acid (ABA) levels in rice seedlings. CONCLUSIONS: Our results suggest that Yu17S exhibited better tolerance to cold stress with the activation of carotenoid synthase activity and increasing of ABA levels, and as well as the expression of photosynthesis-related genes under cold condition in rice seedlings.

Identification, systematic evolution and expression analyses of the AAAP gene family in Capsicum annuum.

BACKGROUND: The amino acid/auxin permease (AAAP) family represents a class of proteins that transport amino acids across cell membranes. Members of this family are widely distributed in different organisms and participate in processes such as growth and development and the stress response in plants. However, a systematic comprehensive analysis of AAAP genes of the pepper (Capsicum annuum) genome has not been reported. RESULTS: In this study, we performed systematic bioinformatics analyses to identify AAAP family genes in the C. annuum 'Zunla-1' genome to determine gene number, distribution, structure, duplications and expression patterns in different tissues and stress. A total of 53 CaAAAP genes were identified in the 'Zunla-1' pepper genome and could be divided into eight subgroups. Significant differences in gene structure and protein conserved domains were observed among the subgroups. In addition to CaGAT1, CaATL4, and CaVAAT1, the remaining CaAAAP genes were unevenly distributed on 11 of 12 chromosomes. In total, 33.96% (18/53) of the CaAAAP genes were a result of duplication events, including three pairs of genes due to segmental duplication and 12 tandem duplication events. Analyses of evolutionary patterns showed that segmental duplication of AAAPs in pepper occurred before tandem duplication. The expression profiling of the CaAAAP by transcriptomic data analysis showed distinct expression patterns in various tissues and response to different stress treatment, which further suggest that the function of CaAAAP genes has been differentiated. CONCLUSIONS: This study of CaAAAP genes provides a theoretical basis for exploring the roles of AAAP family members in C. annuum.

OsSLC1 Encodes a Pentatricopeptide Repeat Protein Essential for Early Chloroplast Development and Seedling Survival.

BACKGROUND: The large family of pentatricopeptide repeat (PPR) proteins is widely distributed among land plants. Such proteins play vital roles in intron splicing, RNA editing, RNA processing, RNA stability and RNA translation. However, only a small number of PPR genes have been identified in rice. RESULTS: In this study, we raised a mutant from tissue-culture-derived plants of Oryza sativa subsp. japonica 'Zhonghua 11', which exhibited a lethal chlorosis phenotype from germination to the third-leaf stage. The mutant was designated seedling-lethal chlorosis 1 (slc1). The slc1 mutant leaves showed extremely low contents of photosynthetic pigments and abnormal chloroplast development, and were severely defective in photosynthesis. Map-based cloning of OsSLC1 revealed that a single base (G) deletion was detected in the first exon of Os06g0710800 in the slc1 mutant, which caused a premature stop codon. Knockout and complementation experiments further confirmed that OsSLC1 is responsible for the seedling-lethal chlorosis phenotype in the slc1 mutant. OsSLC1 was preferentially expressed in green leaves, and encoded a chloroplast-localized PPR protein harboring 12 PPR motifs. Loss-of-function of OsSLC1 affected the intron splicing of multiple group II introns, and especially precluded the intron splicing of rps16, and resulted in significant increase in the transcript levels of 3 chloroplast ribosomal RNAs and 16 chloroplast development-related and photosynthesis-related genes, and in significant reduction in the transcript levels of 1 chloroplast ribosomal RNAs and 2 chloroplast development-related and photosynthesis-related genes. CONCLUSION: We characterized a novel chloroplast-localized PPR protein, OsSLC1, which plays a vital role in the intron splicing of multiple group II introns, especially the rps16 intron, and is essential for early chloroplast development and seedling survival in rice.

Malignancy risk stratification of thyroid nodules: comparisons of four ultrasound Thyroid Imaging Reporting and Data Systems in surgically resected nodules.

To compare the efficiency of four different ultrasound (US) Thyroid Imaging Reporting and Data Systems (TI-RADS) in malignancy risk stratification in surgically resected thyroid nodules (TNs). The study included 547 benign TNs and 464 malignant TNs. US images of the TNs were retrospectively reviewed and categorized according to the TI-RADSs published by Horvath E et al. (TI-RADS H), Park et al. (TI-RADS P), Kwak et al. (TI-RADS K) and Russ et al. (TI-RADS R). The diagnostic performances for the four TI-RADSs were then compared. At multivariate analysis, among the suspicious US features, marked hypoechogenicity was the most significant independent predictor for malignancy (OR: 15.344, 95% CI: 5.313-44.313) (P < 0.05). Higher sensitivity was seen in TI-RADS H, TI-RADS K, TI-RADS R comparing with TI-RADS P (P < 0.05 for all), whereas the specificity, accuracy and area under the ROC curve (Az) of TI-RADS P were the highest (all P < 0.05). Higher specificity, accuracy and Az were seen in TI-RADS K compared with TI-RADS R (P = 0.003). With its higher sensitivity, TI-RADS K, a simple predictive model, is practical and convenient for the management of TNs in clinical practice. The study indicates that there is a good concordance between TI-RADS categories and histopathology.

Virtual touch tissue imaging and quantification (VTIQ) in the evaluation of thyroid nodules: the associated factors leading to misdiagnosis.

To evaluate the associated factors leading to misdiagnosis with VTIQ for differentiation between benign from malignant thyroid nodules (TNs). The study included 238 benign TNs and 150 malignant TNs. Conventional ultrasound (US) features and VTIQ parameters were obtained and compared with the reference standard of histopathological and/or cytological results. Binary logistic regression analysis was performed to select independent variables leading to misdiagnosis. The maximum shear wave speed (SWS) (SWS-max), mean SWS (SWS-mean), SWS-ratio and standard deviation of SWS (SWS-SD) were significantly higher for malignant TNs compared with benign TNs (all P < 0.001). SWS-mean achieved the highest diagnostic performance with a cut-off value of 3.15 m/s. False positive rate was 13.4% (32/238) while false negative rate was 35.3% (53/150). Intranodular calcification (OR: 1.715) was significantly associated with false positive VTIQ findings, while nodule size (OR: 0.936) and echotexture of the thyroid gland (OR: 0.033) were negatively associated with them. Nodule depth (OR: 0.881) and TI-RADS category (OR: 0.563) were negatively associated with false negative VTIQ findings. These US characteristic of TNs should be taken into consideration when interpreting the results of VTIQ examinations.

The De-Etiolated 1 Homolog of Arabidopsis Modulates the ABA Signaling Pathway and ABA Biosynthesis in Rice.

DEETIOLATED1 (DET1) plays a critical role in developmental and environmental responses in many plants. To date, the functions of OsDET1 in rice (Oryza sativa) have been largely unknown. OsDET1 is an ortholog of Arabidopsis (Arabidopsis thaliana) DET1 Here, we found that OsDET1 is essential for maintaining normal rice development. The repression of OsDET1 had detrimental effects on plant development, and leaded to contradictory phenotypes related to abscisic acid (ABA) in OsDET1 interference (RNAi) plants. We found that OsDET1 is involved in modulating ABA signaling in rice. OsDET1 RNAi plants exhibited an ABA hypersensitivity phenotype. Using yeast two-hybrid (Y2H) and bimolecular fluorescence complementation assays, we determined that OsDET1 interacts physically with DAMAGED-SPECIFIC DNA-BINDING PROTEIN1 (OsDDB1) and CONSTITUTIVE PHOTOMORPHOGENIC10 (COP10); DET1- and DDB1-ASSOCIATED1 binds to the ABA receptors OsPYL5 and OsDDB1. We found that the degradation of OsPYL5 was delayed in OsDET1 RNAi plants. These findings suggest that OsDET1 deficiency disturbs the COP10-DET1-DDB1 complex, which is responsible for ABA receptor (OsPYL) degradation, eventually leading to ABA sensitivity in rice. Additionally, OsDET1 also modulated ABA biosynthesis, as ABA biosynthesis was inhibited in OsDET1 RNAi plants and promoted in OsDET1-overexpressing transgenic plants. In conclusion, our data suggest that OsDET1 plays an important role in maintaining normal development in rice and mediates the cross talk between ABA biosynthesis and ABA signaling pathways in rice.