OsRLR4 binds to the OsAUX1 promoter to negatively regulate primary root development in rice.

Root architecture is one of the most important agronomic traits that determines rice crop yield. The primary root (PR) absorbs mineral nutrients and provides mechanical support; however, the molecular mechanisms of PR elongation remain unclear in rice. Here, the two loss-of-function T-DNA insertion mutants of root length regulator 4 (OsRLR4), osrlr4-1 and osrlr4-2 with longer PR, and three OsRLR4 overexpression lines, OE-OsRLR4-1/-2/-3 with shorter PR compared to the wild type/Hwayoung (WT/HY), were identified. OsRLR4 is one of five members of the PRAF subfamily of the regulator chromosome condensation 1 (RCC1) family. Phylogenetic analysis of OsRLR4 from wild and cultivated rice indicated that it is under selective sweeps, suggesting its potential role in domestication. OsRLR4 controls PR development by regulating auxin accumulation in the PR tip and thus the root apical meristem activity. A series of biochemical and genetic analyses demonstrated that OsRLR4 functions directly upstream of the auxin transporter OsAUX1. Moreover, OsRLR4 interacts with the TRITHORAX-like protein OsTrx1 to promote H3K4me3 deposition at the OsAUX1 promoter, thus altering its transcription level. This work provides insight into the cooperation of auxin and epigenetic modifications in regulating root architecture and provides a genetic resource for plant architecture breeding.

Loci and natural alleles for cadmium-mediated growth responses revealed by a genome wide association study and transcriptome analysis in rice.

BACKGROUND: Cadmium (Cd) is a toxic heavy metal that is harmful to the environment and human health. Cd pollution threatens the cultivation of rice (Oryza sativa L.) in many countries. Improving rice performance under Cd stress could potentially improve rice productivity. RESULTS: In this study, 9 growth traits of 188 different cultivated rice accessions under normal and Cd stress conditions were found to be highly variable during the seedling stage. Based on ~3.3 million single nucleotide polymorphisms (SNPs), 119 Cd-mediated growth response (CGR) quantitative trait loci (QTL) were identified by a genome-wide association study (GWAS), 55 of which have been validated by previously reported QTL and 64 were new CGR loci. Combined with the data from the GWAS, transcriptome analysis, gene annotations from the gene ontology (GO) Slim database, and annotations and functions of homologous genes, 148 CGR candidate genes were obtained. Additionally, several reported genes have been found to play certain roles in CGRs. Seven Cd-related cloned genes were found among the CGR genes. Natural elite haplotypes/alleles in these genes that increased Cd tolerance were identified by a haplotype analysis of a diverse mini core collection. More importantly, this study was the first to uncover the natural variations of 5 GST genes that play important roles in CGRs. CONCLUSION: The exploration of Cd-resistant rice germplasm resources and the identification of elite natural variations related to Cd-resistance will help improve the tolerance of current major rice varieties to Cd, as well as provide raw materials and new genes for breeding Cd-resistant varieties.

Rice EARLY SENESCENCE 2, encoding an inositol polyphosphate kinase, is involved in leaf senescence.

BACKGROUND: Early leaf senescence influences yield and yield quality by affecting plant growth and development. A series of leaf senescence-associated molecular mechanisms have been reported in rice. However, the complex genetic regulatory networks that control leaf senescence need to be elucidated. RESULTS: In this study, an early senescence 2 (es2) mutant was obtained from ethyl methanesulfonate mutagenesis (EMS)-induced mutational library for the Japonica rice cultivar Wuyugeng 7 (WYG7). Leaves of es2 showed early senescence at the seedling stage and became severe at the tillering stage. The contents of reactive oxygen species (ROS) significantly increased, while chlorophyll content, photosynthetic rate, catalase (CAT) activity significantly decreased in the es2 mutant. Moreover, genes which related to senescence, ROS and chlorophyll degradation were up-regulated, while those associated with photosynthesis and chlorophyll synthesis were down-regulated in es2 mutant compared to WYG7. The ES2 gene, which encodes an inositol polyphosphate kinase (OsIPK2), was fine mapped to a 116.73-kb region on chromosome 2. DNA sequencing of ES2 in the mutant revealed a missense mutation, ES2 was localized to nucleus and plasma membrane of cells, and expressed in various tissues of rice. Complementation test and overexpression experiment confirmed that ES2 completely restored the normal phenotype, with chlorophyll contents and photosynthetic rate increased comparable with the wild type. These results reveal the new role of OsIPK2 in regulating leaf senescence in rice and therefore will provide additional genetic evidence on the molecular mechanisms controlling early leaf senescence. CONCLUSIONS: The ES2 gene, encoding an inositol polyphosphate kinase localized in the nucleus and plasma membrane of cells, is essential for leaf senescence in rice. Further study of ES2 will facilitate the dissection of the genetic mechanisms underlying early leaf senescence and plant growth.

Development of nutritious rice with high zinc/selenium and low cadmium in grains through QTL pyramiding.

Enriching zinc (Zn) and selenium (Se) levels, while reducing cadmium (Cd) concentration in rice grains is of great benefit for human diet and health. Large natural variations in grain Zn, Se, and Cd concentrations in different rice accessions enable Zn/Se-biofortification and Cd-minimization through molecular breeding. Here, we report the development of new elite varieties by pyramiding major quantitative trait loci (QTLs) that significantly contribute to high Zn/Se and low Cd accumulation in grains. A chromosome segment substitution line CSSLGCC7 with the PA64s-derived GCC7 allele in the 93-11 background, exhibited steadily higher Mn and lower Cd concentrations in grains than those of 93-11. This elite chromosome segment substitution line (CSSL) was used as the core breeding material to cross with CSSLs harboring other major QTLs for essential mineral elements, especially CSSLGZC6 for grain Zn concentration and CSSLGSC5 for grain Se concentration. The CSSLGCC7+GZC6 and CSSLGCC7+GSC5 exhibited lower Cd concentration with higher Zn and Se concentrations in grains, respectively. Our study thus provides elite materials for rice breeding targeting high Zn/Se and low Cd concentrations in grains.

Nalmefene combined noninvasive positive-pressure ventilation in Chinese patients with chronic obstructive pulmonary disease coupled with type II respiratory failure: A meta-analysis.

BACKGROUND: Nalmefene is an opioid system modulator with antagonist activity at the µ and δ receptors and partial agonist activity at the κ receptor. Previous studies have suggested that nalmefene could improve respiratory function in patients with chronic obstructive pulmonary disease (COPD). However, there is no comprehensive systematic review published regarding the clinical efficacy of nalmefene. METHODS: We explored the following electronic bibliographic databases: EMBASE, Web of Science, PubMed, Wanfang, and Chinese national knowledge infrastructure. To collect data from randomized controlled trials on the therapy of COPD coupled with type II respiratory failure and nalmefene + noninvasive ventilator treatment. The retrieved articles were screened to determine the final inclusion criteria and to extract relevant data, such as the clinical efficacy rate, pulmonary function, blood gas analysis, and adverse reactions. In our study, we used relative risk and weighted mean deviation, as well as a 95% confidence interval for describing nalmefene effectiveness and safety while treating COPD with type II respiratory failure. RESULTS: The outcomes of the meta-analysis demonstrated that the clinical efficacy rate of the nalmefene + noninvasive ventilation group was higher than that of the naloxone + noninvasive ventilation and noninvasive ventilation groups. Moreover, the improvement indices of pH value, partial pressure and saturation of blood oxygen, partial pressure of carbon dioxide, and pulmonary function of the nalmefene + noninvasive ventilation group were better than those of the noninvasive ventilation group, and there was no increase in the occurrence of adverse drug reactions. CONCLUSION: Nalmefene combined with noninvasive ventilation can significantly improve the blood gas index and lung function in patients with COPD combined with type II respiratory failure.

Hypoxia Affects Mitochondrial Stress and Facilitates Tumor Metastasis of Colorectal Cancer Through Slug SUMOylation.

BACKGROUND: Colorectal cancer (CRC) is a malignant tumor. Slug has been found to display a key role in diversified cancers, but its relevant regulatory mechanisms in CRC development are not fully explored. OBJECTIVE: Hence, exploring the function and regulatory mechanisms of Slug is critical for the treatment of CRC. METHODS: Protein expressions of Slug, N-cadherin, E-cadherin, Snail, HIF-1α, SUMO1, Drp1, Opa1, Mfn1/2, PGC-1α, NRF1, and TFAM were measured through western blot. To evaluate the protein expression of Slug and SUMO-1, an immunofluorescence assay was used. Cell migration ability was tested through transwell assay. The SUMOylation of Slug was examined through CO-IP assay. RESULTS: Slug displayed higher expression and facilitated tumor metastasis in CRC. In addition, hypoxia treatment was discovered to upregulate HIF-1α, Slug, and SUMO-1 levels, as well as induce Slug SUMOylation. Slug SUMOylation markedly affected mitochondrial biosynthesis, fusion, and mitogen-related protein expression levels to trigger mitochondrial stress. Additionally, the induced mitochondrial stress by hypoxia could be rescued by Slug inhibition and TAK-981 treatment. CONCLUSION: Our study expounded that hypoxia affects mitochondrial stress and facilitates tumor metastasis of CRC through Slug SUMOylation.

Isolation of TSCD11 Gene for Early Chloroplast Development under High Temperature in Rice.

BACKGROUND: Chloroplasts are essential for photosynthesis and play key roles in plant development. High temperature affects structure of chloroplasts and metabolism in plants. The seryl-tRNA synthetase plays an important role in translation of proteins. Although seryl-tRNA synthetase has been widely studied in microbes and animals, few studies have reported about its role in chloroplast development under high temperature in rice. RESULTS: In this study, we isolated a novel temperature-sensitive chlorophyll-deficient 11 (tscd11) mutant by ethyl methane sulfonate (EMS) mutagenesis of japonica variety Wuyujing7. The tscd11 mutant developed albino leaves at the 3-leaf stage under high temperature (35 °C), but had normal green leaves under low temperature (25 °C). Consistent with the albino phenotype, impaired chloroplasts, decreased chlorophyll content and increased ROS accumulation were found in the tscd11 mutant at 35 °C. Fine mapping and DNA sequencing of tscd11 revealed a missense mutation (G to A) in the eighth exon of LOC_Os11g39670 resulted in amino acid change (Glu374 to Lys374). The TSCD11 gene encodes a seryl-tRNA synthetase localized to chloroplast. Complementation test confirmed that the point mutation in TSCD11 is responsible for the phenotype of tscd11. TSCD11 is highly expressed in leaves. Compared with the wild type (WT), mutation in TSCD11 led to significant alteration in expression levels of genes associated with chlorophyll biosynthesis, photosynthesis and chloroplast development under high temperature. CONCLUSIONS: TSCD11, encoding a seryl-tRNA synthetase localized to chloroplast, is vital to early chloroplast development at high temperature in rice, which help to further study on the molecular mechanism of chloroplast development under high temperature.

Genetic Analysis for Cooking and Eating Quality of Super Rice and Fine Mapping of a Novel Locus qGC10 for Gel Consistency.

Rice (Oryza sativa L.) is an important cereal that provides food for more than half of the world's population. Besides grain yield, improving grain quality is also essential to rice breeders. Amylose content (AC), gelatinization temperature (GT) and gel consistency (GC) are considered to be three indicators for cooking and eating quality in rice. Using a genetic map of RILs derived from the super rice Liang-You-Pei-Jiu with high-density SNPs, we detected 3 QTLs for AC, 3 QTLs for GT, and 8 QTLs for GC on chromosomes 3, 4, 5, 6, 10, and 12. Wx locus, an important determinator for AC and GC, resided in one QTL cluster for AC and GC, qAC6 and qGC6 here. And a novel major QTL qGC10 on chromosome 10 was identified in both Lingshui and Hangzhou. With the BC4F2 population derived from a CSSL harboring the segment for qGC10 from 93-11 in PA64s background, it was fine mapped between two molecular markers within 181 kb region with 27 annotated genes. Quantitative real-time PCR results showed that eight genes were differentially expressed in endosperm of two parents. After DNA sequencing, only LOC_Os10g04900, which encodes a F-box domain containing protein, has 2 bp deletion in the exon of PA64s, resulting in a premature stop codon. Therefore, LOC_Os10g04900 is considered to be the most likely candidate gene for qGC10 associated with gel consistency. Identification of qGC10 provides a new genetic resource for improvement of rice quality.

Exploiting and integrating rich features for biological literature classification.

BACKGROUND: Efficient features play an important role in automated text classification, which definitely facilitates the access of large-scale data. In the bioscience field, biological structures and terminologies are described by a large number of features; domain dependent features would significantly improve the classification performance. How to effectively select and integrate different types of features to improve the biological literature classification performance is the major issue studied in this paper. RESULTS: To efficiently classify the biological literatures, we propose a novel feature value schema TF*ML, features covering from lower level domain independent "string feature" to higher level domain dependent "semantic template feature", and proper integrations among the features. Compared to our previous approaches, the performance is improved in terms of AUC and F-Score by 11.5% and 8.8% respectively, and outperforms the best performance achieved in BioCreAtIvE 2006. CONCLUSIONS: Different types of features possess different discriminative capabilities in literature classification; proper integration of domain independent and dependent features would significantly improve the performance and overcome the over-fitting on data distribution.

Immobilization of powdery calcium silicate hydrate via PVA covalent cross-linking process for phosphorus removal.

Calcium silicate hydrate (CSH) is a popular material used for phosphorus removal in recent years. In this work, a novel immobilized material, polyvinyl alcohol-CSH (PVA-CSH), was prepared using a 1:10 weight ratio of CSH powder to 8% PVA solution and then used for phosphorus removal. Samples were characterized by scanning electron microscopy (SEM), energy dispersive spectroscopy (EDS), X-ray diffraction (XRD) and Fourier transform infrared spectroscopy (FTIR). The adsorption mechanism and practical application properties of phosphorus wastewater were studied by sequential batch and continuous flow experiment. The results showed PVA-CSH possessed a porous network structure and an average pore diameter of 24.94 ±â€¯0.11 nm. Furthermore, the CSH functional groups were unaffected by PVA immobilization. Compared with CSH, PVA-CSH did not easily lose CSH after being immobilized by PVA, and the duration of efficient phosphorus removal stage was approximately 20 h longer than that of CSH. In addition, the effluent turbidity of PVA-CSH was 0.11 ±â€¯0.03 NTU during the continuous operation period, which was significantly lower than CSH. In summary, this research study demonstrated the significant potential of PVA-CSH for practical phosphorus removal.

[Correlation between traditional chinese medicine syndrome differentiation and urodynamic parameters in benign prostate hyperplasia].

OBJECTIVE: To explore the correlation between the Traditional Chinese Medicine (TCM) syndrome differentiation and urodynamic parameters in benign prostate hyperplasia (BPH). METHODS: Urodynamic examination was conducted for 152 BPH patients, who were divided by TCM syndrome differentiation into seven types, namely, kidney-yin deficiency, kidney-yang deficiency, aqueduct stagnancy, spleen-qi deficiency, lung-heat and qi stagnancy, wetness-heat down-flow and phlegm-wetness stagnancy. RESULTS: Of the total number of the BPH cases, 71 (46.71%) were differentiated as the type of kidney-yang deficiency, 40 (26.31%) as aqueduct stagnancy, and 14 (9.21%) as kidney-yin deficiency. Fifty-eight cases of Grade III-IV bladder outflow obstruction fell into the type of kidney-yang deficiency, and another 38 cases of the same grade along with 26 cases of Grade V-VI came under the type of aqueduct stagnancy. Of the 12 patients with very weak contractility of detrusor urine, 4 (33.33%) were attributed to the type of kidney-yang deficiency and 7 (58.33%) the type of aqueduct stagnancy. Among the 48 with weak contractility of detrusor urine, 27 (56.25%) fell under the type of kidney-yang deficiency and 17 (35.42%) the type of aqueduct stagnancy. CONCLUSION: The TCM syndrome differentiation of BPH is correlated with bladder outflow obstruction and detrusor urine contractility, which has provided corresponding evidence for the quantization and objectification of the TCM syndrome differentiation of BPH.

Mining physical protein-protein interactions from the literature.

BACKGROUND: Deciphering physical protein-protein interactions is fundamental to elucidating both the functions of proteins and biological processes. The development of high-throughput experimental technologies such as the yeast two-hybrid screening has produced an explosion in data relating to interactions. Since manual curation is intensive in terms of time and cost, there is an urgent need for text-mining tools to facilitate the extraction of such information. The BioCreative (Critical Assessment of Information Extraction systems in Biology) challenge evaluation provided common standards and shared evaluation criteria to enable comparisons among different approaches. RESULTS: During the benchmark evaluation of BioCreative 2006, all of our results ranked in the top three places. In the task of filtering articles irrelevant to physical protein interactions, our method contributes a precision of 75.07%, a recall of 81.07%, and an AUC (area under the receiver operating characteristic curve) of 0.847. In the task of identifying protein mentions and normalizing mentions to molecule identifiers, our method is competitive among runs submitted, with a precision of 34.83%, a recall of 24.10%, and an F1 score of 28.5%. In extracting protein interaction pairs, our profile-based method was competitive on the SwissProt-only subset (precision = 36.95%, recall = 32.68%, and F1 score = 30.40%) and on the entire dataset (30.96%, 29.35%, and 26.20%, respectively). From the biologist's point of view, however, these findings are far from satisfactory. The error analysis presented in this report provides insight into how performance could be improved: three-quarters of false negatives were due to protein normalization problems (532/698), and about one-quarter were due to problems with correctly extracting interactions for this system. CONCLUSION: We present a text-mining framework to extract physical protein-protein interactions from the literature. Three key issues are addressed, namely filtering irrelevant articles, identifying protein names and normalizing them to molecule identifiers, and extracting protein-protein interactions. Our system is among the top three performers in the benchmark evaluation of BioCreative 2006. The tool will be helpful for manual interaction curation and can greatly facilitate the process of extracting protein-protein interactions.