A label-free quantitative shotgun proteomics analysis of rice grain development

<p>Abstract</p> <p>Background</p> <p>Although a great deal of rice proteomic research has been conducted, there are relatively few studies specifically addressing the rice grain proteome. The existing rice grain proteomic researches have focused on the identification of differentially expressed proteins or monitoring protein expression patterns during grain filling stages.</p> <p>Results</p> <p>Proteins were extracted from rice grains 10, 20, and 30 days after flowering, as well as from fully mature grains. By merging all of the identified proteins in this study, we identified 4,172 non-redundant proteins with a wide range of molecular weights (from 5.2 kDa to 611 kDa) and <it>pI </it>values (from pH 2.9 to pH 12.6). A Genome Ontology category enrichment analysis for the 4,172 proteins revealed that 52 categories were enriched, including the carbohydrate metabolic process, transport, localization, lipid metabolic process, and secondary metabolic process. The relative abundances of the 1,784 reproducibly identified proteins were compared to detect 484 differentially expressed proteins during rice grain development. Clustering analysis and Genome Ontology category enrichment analysis revealed that proteins involved in the metabolic process were enriched through all stages of development, suggesting that proteome changes occurred even in the desiccation phase. Interestingly, enrichments of proteins involved in protein folding were detected in the desiccation phase and in fully mature grain.</p> <p>Conclusion</p> <p>This is the first report conducting comprehensive identification of rice grain proteins. With a label free shotgun proteomic approach, we identified large number of rice grain proteins and compared the expression patterns of reproducibly identified proteins during rice grain development. Clustering analysis, Genome Ontology category enrichment analysis, and the analysis of composite expression profiles revealed dynamic changes of metabolisms during rice grain development. Interestingly, we detected that proteins involved in glycolysis, TCA-cycle, lipid metabolism, and proteolysis accumulated at higher levels in fully mature grain compared to grain developing stages, suggesting that the accumulation of these proteins during the desiccation stage may be associated with the preparation of proteins required in germination.</p

Comparison of Sasang Constitutional Medicine, Traditional Chinese Medicine and Ayurveda

Sasang constitutional medicine (SCM), traditional Chinese medicine (TCM) and Ayurveda are three different forms of Asian traditional medicine. Although these traditions share a lot in common as holistic medicines, the different philosophical foundations found in each confer distinguishing attributes and unique qualities. SCM is based on a constitution-based approach, and is in this way relatively more similar to the Ayurvedic tradition than to the TCM, although many of the basic SCM theories were originally derived from TCM, a syndrome-based medicine. SCM and TCM use the same botanical materials that are distributed mainly in the East Asian region, but the basic principles of usage and the underlying rationale are completely different from each other. Meanwhile, the principles of the Ayurvedic use of botanical resources are very similar to those seen in SCM, but the medicinal herbs used in Ayurveda generally originate from the West Asian region which displays a different spectrum of flora

EVALUASI KANDUNGAN PROTEIN DAN SIFAT PASTA BERAS JAPONICA DENGAN MARKA DNA

An evaluation of protein content and pasting properties of rice using molecular markers approach is still limited. This study was aimed to evaluate protein content and pasting properties of japonica rice using DNA marker in complement to conventional tools. This study was further analysis based on the data of protein content and pasting properties of 22 japonica varieties and genotyping data using 30 DNA markers. Multiple regression analysis was performed to formulate equations to estimate the protein content and pasting properties. As a result, the protein content and Rapid Visco Analyzer (RVA) pasting properties values of 22 varieties demonstrated in the range of japonica rice with high variation. Correlation between protein content and RVA pasta properties showed differential profiles. Several type of DNA markers tested in this study showed allele variation among varieties. To estimate the protein content and several parameters of pasting properties of japonica rice, six marker sets in the form of model equations were successfully developed. High resolutions of equations with signifikant R2 in range of 0.95 - 0.99 showed their potency to predict rice physicochemical properties. These developed marker sets are an initial step which needs further validation in order to be able for evaluation of thephysicochemical properties in early generation of breeding and germplasm collection of japonica rice in the future

Prediction of Physicochemical Properties of Indonesian Indica Rice Using Molecular Markers

Physicochemical properties determine the palatability and cooking quality of rice, which must be determined efficiently in order to satisfy consumer demand. To date, little information exists on the use of molecular markers to predict physicochemical properties of the “indica” rice varieties found in Indonesia. The objective of this study was to investigate physicochemical properties and genetic variation of Indonesian rice varieties, and to formulate regression equations to analyze sets of DNA markers which could predict  amylose content (AC), protein content (PC) and pasting properties of the varieties. A total of 24 Indonesian indica rice varieties were chosen based on their genetic background and agricultural characteristics. We then measured selected physicochemical properties, and genotyped the varieties using 30 DNA markers. The chosen varieties showed favorable values for PC, AC, and six rapid viscosity analyzer (RVA) pasting properties, which was supported by molecular data. As demonstrated by principal component analysis (PCA), markers could provide a complementary method for differentiating rice varieties, as an alternative to measuring physicochemical properties. PCA analysis also allowed us to establish marker sets using multiple regression analysis. We formulated eight model regression equations comprising data regarding 15 to 19 markers with high coefficients (R2=0.98-0.99). The formulas provided results that consistently correlated and therefore predicted the physicochemical properties of indica rice. Further validation of these marker sets may provide rapid and efficient means for predicting the physicochemical properties of Indonesian-bred indica rice in the future

Transcriptional changes in the developing rice seeds under salt stress suggest targets for manipulating seed quality

Global sea-level rise, the effect of climate change, poses a serious threat to rice production owing to saltwater intrusion and the accompanying increase in salt concentration. The reclaimed lands, comprising 22.1% of rice production in Korea, now face the crisis of global sea-level rise and a continuous increase in salt concentration. Here, we investigated the relationship between the decrease in seed quality and the transcriptional changes that occur in the developing rice seeds under salt stress. Compared to cultivation on normal land, the japonica rice cultivar, Samgwang, grown on reclaimed land showed a greatly increased accumulation of minerals, including sodium, magnesium, potassium, and sulfur, in seeds and a reduced yield, delayed heading, decreased thousand grain weight, and decreased palatability and amylose content. Samgwang showed phenotypical sensitivity to salt stress in the developing seeds. Using RNA-seq technology, we therefore carried out a comparative transcriptome analysis of the developing seeds grown on reclaimed and normal lands. In the biological process category, gene ontology enrichment analysis revealed that the upregulated genes were closely associated with the metabolism of biomolecules, including amino acids, carboxylic acid, lignin, trehalose, polysaccharide, and chitin, and to stress responses. MapMan analysis revealed the involvement of upregulated genes in the biosynthetic pathways of abscisic acid and melatonin and the relationship of trehalose, raffinose, and maltose with osmotic stress. Interestingly, many seed storage protein genes encoding glutelins and prolamins were upregulated in the developing seeds under salt stress, indicating the negative effect of the increase of storage proteins on palatability. Transcription factors upregulated in the developing seeds under salt stress included, in particular, bHLH, MYB, zinc finger, and heat shock factor, which could act as potential targets for the manipulation of seed quality under salt stress. Our study aims to develop a useful reference for elucidating the relationship between seed response mechanisms and decreased seed quality under salt stress, providing potential strategies for the improvement of seed quality under salt stress

COMPARATIVE GENETICS OF APODEMUS AGRARIUS (RODENTIA: MAMMALIA) FROM INSULAR AND CONTINENTAL EURASIAN POPULATIONS: CYTOCHROME B SEQUENCE ANALYSES

To reexamine genetic divergence of Apodemus agrarius in insular Taiwan and the Korean Jeju from other populations in continental Eurasia, we obtained 91 cytochrome b complete sequences of A. agrarius across Eurasia, and these sequences were compared to eight corresponding sequences of A. agrarius, obtained from GenBank. We first found that the two insular populations are two clades, and that each of them is divergent from continental Eurasian populations, clustered into another clade. Each of the two insular clades appeared to be isolated in spite of land connection to nearby continent during the last glacial period, and we considered the two insular forms as A. a. insulaemus and A. a. chejuensis and one continental Eurasian form as A. a. agrarius, although further analyses are needed to confirm our present findings. Additionally, the Taiwan clade seemed to be composed of two subclades (western and eastern), separated by Taiwan’s central mountain range

Proteomic and biochemical analyses reveal the activation of unfolded protein response, ERK-1/2 and ribosomal protein S6 signaling in experimental autoimmune myocarditis rat model

<p>Abstract</p> <p>Background</p> <p>To investigate the molecular and cellular pathogenesis underlying myocarditis, we used an experimental autoimmune myocarditis (EAM)-induced heart failure rat model that represents T cell mediated postinflammatory heart disorders.</p> <p>Results</p> <p>By performing unbiased 2-dimensional electrophoresis of protein extracts from control rat heart tissues and EAM rat heart tissues, followed by nano-HPLC-ESI-QIT-MS, 67 proteins were identified from 71 spots that exhibited significantly altered expression levels. The majority of up-regulated proteins were confidently associated with unfolded protein responses (UPR), while the majority of down-regulated proteins were involved with the generation of precursor metabolites and energy metabolism in mitochondria. Although there was no difference in AKT signaling between EAM rat heart tissues and control rat heart tissues, the amounts and activities of extracellular signal-regulated kinase (ERK)-1/2 and ribosomal protein S6 (rpS6) were significantly increased. By comparing our data with the previously reported myocardial proteome of the Coxsackie viruses of group B (CVB)-mediated myocarditis model, we found that UPR-related proteins were commonly up-regulated in two murine myocarditis models. Even though only two out of 29 down-regulated proteins in EAM rat heart tissues were also dysregulated in CVB-infected rat heart tissues, other proteins known to be involved with the generation of precursor metabolites and energy metabolism in mitochondria were also dysregulated in CVB-mediated myocarditis rat heart tissues, suggesting that impairment of mitochondrial functions may be a common underlying mechanism of the two murine myocarditis models.</p> <p>Conclusions</p> <p>UPR, ERK-1/2 and S6RP signaling were activated in both EAM- and CVB-induced myocarditis murine models. Thus, the conserved components of signaling pathways in two murine models of acute myocarditis could be targets for developing new therapeutic drugs or methods aimed at treating enigmatic myocarditis.</p

Reinterpretation of anthocyanins biosynthesis in developing black rice seeds through gene expression analysis

The biosynthesis of anthocyanins is still questionable in regulating the quantities of anthocyanins biosynthesized in rice seeds and the expression levels of transcription factors and the structural genes involved in the biosynthetic pathway of anthocyanins. We herein investigated the relationship between the accumulated anthocyanin contents and the expression levels of genes related to the biosynthesis of anthocyanins in rice seeds. Liquid chromatography/mass spectrometry-mass spectrometry analysis of cyanidin 3-glucoside (C3G) in rice seeds showed no accumulation of C3G in white and red rice cultivars, and the differential accumulation of C3G among black rice cultivars. RNA-seq analysis in rice seeds, including white, red, and black rice cultivars, at twenty days after heading (DAH) further exhibited that the genes involved in the biosynthesis of anthocyanins were differentially upregulated in developing seeds of black rice. We further verified these RNA-seq results through gene expression analysis by a quantitative real-time polymerase chain reaction in developing seeds of white, red, and black rice cultivars at 20 DAH. Of these genes related to the biosynthesis of anthocyanins, bHLHs, MYBs, and WD40, which are regulators, and the structural genes, including chalcone synthase (CHS), flavanone 3-hydroxylase (F3H), flavonoid 3´-hydroxylase (F3´H), dihydroflavonol 4-reductase (DFR), and anthocyanidin synthase (ANS), were differentially upregulated in black rice seeds. The correlation analysis revealed that the quantities of C3G biosynthesized in black rice seeds were positively correlated to the expression levels of bHLHs, MYBs and WD40, CHS, F3H, F3´H, DFR, and ANS. In addition, we present bHLH2 (LOC_Os04g47040) and MYBs (LOC_Os01g49160, LOC_Os01g74410, and LOC_Os03g29614) as new putative transcription factor genes for the biosynthesis of anthocyanins in black rice seeds. It is expected that this study will help to improve the understanding of the molecular levels involved in the biosynthesis of anthocyanins in black rice seeds