MADS-box gene family in rice: genome-wide identification, organization and expression profiling during reproductive development and stress

<p>Abstract</p> <p>Background</p> <p>MADS-box transcription factors, besides being involved in floral organ specification, have also been implicated in several aspects of plant growth and development. In recent years, there have been reports on genomic localization, protein motif structure, phylogenetic relationships, gene structure and expression of the entire MADS-box family in the model plant system, <it>Arabidopsis</it>. Though there have been some studies in rice as well, an analysis of the complete MADS-box family along with a comprehensive expression profiling was still awaited after the completion of rice genome sequencing. Furthermore, owing to the role of MADS-box family in flower development, an analysis involving structure, expression and functional aspects of MADS-box genes in rice and <it>Arabidopsis </it>was required to understand the role of this gene family in reproductive development.</p> <p>Results</p> <p>A genome-wide molecular characterization and microarray-based expression profiling of the genes encoding MADS-box transcription factor family in rice is presented. Using a thorough annotation exercise, 75 MADS-box genes have been identified in rice and categorized into MIKC^c, MIKC*, Mα, Mβ and Mγ groups based on phylogeny. Chromosomal localization of these genes reveals that 16 MADS-box genes, mostly MIKC^c-type, are located within the duplicated segments of the rice genome, whereas most of the M-type genes, 20 in all, seem to have resulted from tandem duplications. Nine members belonging to the Mβ group, which was considered absent in monocots, have also been identified. The expression profiles of all the MADS-box genes have been analyzed under 11 temporal stages of panicle and seed development, three abiotic stress conditions, along with three stages of vegetative development. Transcripts for 31 genes accumulate preferentially in the reproductive phase, of which, 12 genes are specifically expressed in seeds, and six genes show expression specific to panicle development. Differential expression of seven genes under stress conditions is also evident. An attempt has been made to gain insight into plausible functions of rice MADS-box genes by collating the expression data of functionally validated genes in rice and <it>Arabidopsis</it>.</p> <p>Conclusion</p> <p>Only a limited number of MADS genes have been functionally validated in rice. A comprehensive annotation and transcriptome profiling undertaken in this investigation adds to our understanding of the involvement of MADS-box family genes during reproductive development and stress in rice and also provides the basis for selection of candidate genes for functional validation studies.</p

A Pharmaceutico-Analytical and Antimicrobial Study of Trivargtrityadi Yoga (TTY)

In current scenario herbal formulations containing natural ingredients is more acceptable in public belief than chemical based synthetic formulations due to their safety and efficacy in reducing dental caries, pyorrhoea and preventing other dental and oral issues to which this generation is prone to. Clinically more effective and tolerable treatments should improve patient compliance with oral hygiene practices, further supporting medical professionals' efforts to avoid disease. Controlling the creation of dental plaque is the most efficient method of preventing the onset of dental disease. Microbes have an impact on its formation. Ayurveda recommends some daily use therapeutic procedures for the prevention and maintenance of oral health. These include: Pratisarana (gentle massage over tissue), Dant Dhavani (brushing), Jivha Lekhana (tongue scrapping) and Gandoosha (gargling) or oil pulling.&nbsp;The present study focused on preparation and validation of the classical formulation Trivargtrityadi yoga (TT yoga) which mentioned in Ashtang Sangraha by Acharya Vagbhata described in Dantadhawanacharya. It Contains Triphala, Trikatu, Trijatak and Kuth. These extracts have a variety of beneficial characteristics, including those that are anti-cancer, anti-fungal, and anti-ulcer, anti-caries, anti-bacterial and wound healing. The preparation of the formulation in accordance with traditional references and evaluation of its analytic and antibacterial properties are the objectives of this study

A Comparative Pharmaceutical Study on Tiladi Churna and Tiladi Granules

Bhaishajya Kalpana- the pharmaceutical science of Ayurveda mainly deals with the planning and preparation of medicines. As per Ayurveda, an ideal drug is that one which can process into different forms. Though Ayurveda claims that no material is incapable of being utilized as medicine, none of them can be employed in the form in which they are available because they are not appetizing or easily absorbed by the human system. In this modern era, society prefers medicines which are more palatable, available, less dose and with more shelf life. In this view, as per the need of time, there is a need to modify the classical formulations in order to improve its characters and to make more acceptable. In this present study, Tiladi churna, a pure herbal formulation having minimum ingredients and its granules were prepared in departmental pharmacy. Churna Kalpana is considered as an Upakalpana of Kalka Kalpana which is one among the basic Panchavidha Kashaya Kalpana mentioned in classical texts while Khanda Kalpana or granules are the preparations added after 20th century which have more palatability and acceptance. Here both Tiladi Churna and granules were then compared to determine the efficiency in terms of method, duration of preparation and also in terms of organoleptic and physical parameter

Genome-wide identification and characterization of gene family for RWP-RK transcription factors in wheat (Triticum aestivum L.).

RWP-RKs represent a small family of transcription factors (TFs) that are unique to plants and function particularly under conditions of nitrogen starvation. These RWP-RKs have been classified in two sub-families, NLPs (NIN-like proteins) and RKDs (RWP-RK domain proteins). NLPs regulate tissue-specific expression of genes involved in nitrogen use efficiency (NUE) and RKDs regulate expression of genes involved in gametogenesis/embryogenesis. During the present study, using in silico approach, 37 wheat RWP-RK genes were identified, which included 18 TaNLPs (2865 to 7340 bp with 4/5 exons), distributed on 15 chromosomes from 5 homoeologous groups (with two genes each on 4B,4D and 5A) and 19 TaRKDs (1064 to 5768 bp with 1 to 6 exons) distributed on 12 chromosomes from 4 homoeologous groups (except groups 1, 4 and 5); 2-3 splice variants were also available in 9 of the 37 genes. Sixteen (16) of these genes also carried 24 SSRs (simple sequence repeats), while 11 genes had targets for 13 different miRNAs. At the protein level, MD simulation analysis suggested their interaction with nitrate-ions. Significant differences were observed in the expression of only two (TaNLP1 and TaNLP2) of the nine representative genes that were used for in silico expression analysis under varying levels of N at post-anthesis stage (data for other genes was not available for in silico expression analysis). Differences in expression were also observed during qRT-PCR, when expression of four representative genes (TaNLP2, TaNLP7, TaRKD6 and TaRKD9) was examined in roots and shoots of seedlings (under different conditions of N supply) in two contrasting genotypes which differed in NUE (C306 with low NUE and HUW468 with high NUE). These four genes for qRT-PCR were selected on the basis of previous literature, level of homology and the level of expression (in silico study). In particular, the TaNLP7 gene showed significant up-regulation in the roots and shoots of HUW468 (with higher NUE) during N-starvation; this gene has already been characterized in Arabidopsis and tobacco, and is known to be involved in nitrate-signal transduction pathway

MADS-box gene family in rice: genome-wide identification, organization and expression profiling during reproductive development and stress-0

<p><b>Copyright information:</b></p><p>Taken from "MADS-box gene family in rice: genome-wide identification, organization and expression profiling during reproductive development and stress"</p><p>http://www.biomedcentral.com/1471-2164/8/242</p><p>BMC Genomics 2007;8():242-242.</p><p>Published online 18 Jul 2007</p><p>PMCID:PMC1947970.</p><p></p>are written at the top. Genes belonging to five groups have been marked by different colors (MIKC, red; MIKC*, yellow; Mα, purple; Mβ, green and Mγ, blue). Genes lying on duplicated segments of genome have been joined by dashed lines. Tandemly duplicated genes are joined with vertical lines. (* The duplicated segment between chromosome 1 and 9 containing and , respectively, could be detected only in segmental duplication database with 500 kb and not with 100 kb distance allowed between collinear genes in TIGR, for details experimental procedures)

MADS-box gene family in rice: genome-wide identification, organization and expression profiling during reproductive development and stress-6

<p><b>Copyright information:</b></p><p>Taken from "MADS-box gene family in rice: genome-wide identification, organization and expression profiling during reproductive development and stress"</p><p>http://www.biomedcentral.com/1471-2164/8/242</p><p>BMC Genomics 2007;8():242-242.</p><p>Published online 18 Jul 2007</p><p>PMCID:PMC1947970.</p><p></p>Differential expressions shown by seven MADS-box genes in response to various abiotic stress conditions. Left panel shows four genes up regulated and right panel shows down regulated genes more than 2 folds with p value less than 0.05 in response to three abiotic stress conditions. X-axis represents seedling followed by stress samples (CS, cold stress; DS, dehydration stress; SS, salt stress). Y-axis represents average expression values obtained using microarrays. Error bars represent standard error for data obtained in three biological replicates

MADS-box gene family in rice: genome-wide identification, organization and expression profiling during reproductive development and stress-3

<p><b>Copyright information:</b></p><p>Taken from "MADS-box gene family in rice: genome-wide identification, organization and expression profiling during reproductive development and stress"</p><p>http://www.biomedcentral.com/1471-2164/8/242</p><p>BMC Genomics 2007;8():242-242.</p><p>Published online 18 Jul 2007</p><p>PMCID:PMC1947970.</p><p></p>xpression and red signifies high level expression). . (Color bar at the base represents logexpression values, thereby blue color representing low level expression, yellow shows medium level expression and red signifies high level expression). Developmental stages used for expression profiling are mentioned on top of each column. Panicle and seed stages have been listed in the temporal order of development. On the left side of expression map, cluster dendrogram is shown. On the right side, eight groups have been made for the genes showing discrete expression patterns (Figure 5). Symbol * represents accumulative expression profiles of duplicated genes, , , and . Genes belonging to the different groups have been marked by a symbol (m, MIKC; m*, MIKC*; α, Mα; β, Mβ and γ, Mγ). . Expression profiles of and using QPCR. X-axis represents the developmental stages as given in Table 2. Y-axis represents relative expression values obtained after normalizing against maximum expression value. Error bars show the standard error for two biological replicates performed

MADS-box gene family in rice: genome-wide identification, organization and expression profiling during reproductive development and stress-5

<p><b>Copyright information:</b></p><p>Taken from "MADS-box gene family in rice: genome-wide identification, organization and expression profiling during reproductive development and stress"</p><p>http://www.biomedcentral.com/1471-2164/8/242</p><p>BMC Genomics 2007;8():242-242.</p><p>Published online 18 Jul 2007</p><p>PMCID:PMC1947970.</p><p></p>ained using both the techniques. Y-axis represents raw expression values obtained using microarays, QPCR data has been normalized to ease profile matching with that of microarrays. X-axis depicts developmental stages as explained in table 2

MADS-box gene family in rice: genome-wide identification, organization and expression profiling during reproductive development and stress-2

<p><b>Copyright information:</b></p><p>Taken from "MADS-box gene family in rice: genome-wide identification, organization and expression profiling during reproductive development and stress"</p><p>http://www.biomedcentral.com/1471-2164/8/242</p><p>BMC Genomics 2007;8():242-242.</p><p>Published online 18 Jul 2007</p><p>PMCID:PMC1947970.</p><p></p>motif is represented by a number in colored box. Length of box does not correspond to length of motif. Order of the motifs corresponds to position of motifs in individual protein sequence. For detail of motifs refer to supplementary material

MADS-box gene family in rice: genome-wide identification, organization and expression profiling during reproductive development and stress-8

<p><b>Copyright information:</b></p><p>Taken from "MADS-box gene family in rice: genome-wide identification, organization and expression profiling during reproductive development and stress"</p><p>http://www.biomedcentral.com/1471-2164/8/242</p><p>BMC Genomics 2007;8():242-242.</p><p>Published online 18 Jul 2007</p><p>PMCID:PMC1947970.</p><p></p>Y-axis represents the raw expression values obtained using microarrays. Chromosome numbers on the left of each graph represent the duplicated segments on which the duplicated genes were identified. Homology for each duplicated gene pair is given in brackets