Gene expression profiles in black soybean sprouts: 0.5 cm long vs 5 cm long
ABSTRACT: To explore the mechanism underlying antioxidant activity of extracts from black soybean sprouts 0.5 cm long, Agilent-016772 G. max (Soybean) Oligo Microarray 4x44K was used to compare mRNA expression between the black soybean sprouts 0.5 cm long (n=4) and the black soybean sprouts 5 cm long (n=4). GO term enrichment analysis showed ten up-regulated genes (BE823689.1_567, GMFL01-02-F14-R_381, GMFL01-03-G22-R_364, GMFL01-14-M12-R_553, GMFL01-51-M23-R_265, AW757007.1_297, AW761420.1_260, BI788389.1_501, BQ273202.1_332 and GMFL01-10-I14-F_701) in the 0.5 cm seedlings were associated with response to oxidative stress. qRT-PCR assay confirmed the up-regulation of these ten genes in sprouts 0.5 cm long. In conclusion, these ten genes may contribute to antioxidant activity of sprout extract. Gene expressions in black soybean sprouts were measured using Agilent-016772 G. max (Soybean) Oligo Microarray 4x44K. Four independent experiments were performed in each group using different sprout sample.
Project description:Soybean sprout, a kind of year-round vegetable in Asia, is perceived as a part of a healthy diet. We found that supplemental Ca2+ could increase soybean sprout yield and improve its nutrition qualities. Ca2+-treated sprouts had higher yield than water-treated ones. Metabolism of selected anti-nutritional factors and bioactive substances in soybean sprouts was strengthened by Ca2+. To investigate the role of Ca2+ in soybean during germination, proteomic changes were analyzed. Total protein from soybean sprouts that treated with deionized water or with 6 mM Ca2+ were analyzed.
Project description:The seed coat of black (iRT) soybean with the dominant R allele begins to accumulate cyanic pigments at the transition stage of seed development (300 – 400 mg fresh seed weight), whereas the brown (irT) nearly-isogenic seed coat with the recessive r allele lacks cyanic pigments at all stages of seed development. We used microarrays to determine global gene expression differences between black (iRT) and brown (irT) soybean seed coats at the transition stage of seed development (300 – 400 mg fresh seed weight). To identify the complete set of gene transcripts that are differentially expressed between the seed coats of black (iRT) and brown (irT) Clark isolines, seed coats were dissected at the transition stage of seed development (300 – 400 mg fresh seed weight) for microarray analysis using the Affymetrix Soybean GeneChip. To ensure seed coats were of the same stage of development, the days post anthesis, pod length, pod color, embryo morphology, and transcript levels of the developmental marker gene Gm-r1083-1191, a putative cutin biosynthesis gene, and DFR1 were ensured to be equivalent between black (iRT) and brown (irT) isolines.
Project description:Dormant/sprouting bud or eye tissue was collected from field grown Russet Burbank tubers using melon baler. These tubers after harvest washed with 5% Clorox, dried and stored at room temperature and allowed to sprout. Tissue samples were collected from dormant and sprouting eye at different physiological stages (based on length of the sprout) of sprouting. RNA was extracted using a hot phenol method and treated with DNAse. RNA extracted from different stages of sprouting potato tubers was used as query samples. RNA collected from non-sprouting eyes of potato tubers was used as reference samples Information on RNA samples. Plant species: S. tuberosum CV Russet Burbank. Tissue harvested: Tissue was harvested from the dormant/sprouting bud/eye using ½ inch melon baler. Time points: Dormant eyes –Stage 1 Initiating buds/sprouts – Stage 2 Sprouts (1/8 inch) – Stage 3 Sprouts (1/4 inch) – Stage 4 Sprout callus (1/4 inch) – Stage 5 Sprouts (1/2 inch) – Stage 6. Growth conditions: Field grown. Replicate information: Biological replicates; A, B and C Keywords: Direct comparison Overall design: 15 hybs total
Project description:Soybean root hair transcriptional response to their inoculation by the symbiotic bacteria B. japonicum involved in soybean nodulation. We used the first generation of an Affymetrix microarray to quantify the abundance of the transcripts from soybean root hair cells inoculated and mock-inoculated by B. japonicum. This experiment was performed on a time-course from 6 to 48 hours after inoculation. Soybean seeds were sowed on sterile agar medium and grown for 3 days in a growth chamber before being treated with H2O (mock-inoculated) or B. japonicum (inoculated). Soybean root hair cells were isolated at different time points (6hr, 12hr, 18hr, 24hr, 36hr, 48hr) after treatment. For each time point and condition, 3 or 4 independent biological replicates were produced.
Project description:We want to obtained miRNA-seq from 4 day-old broccoli sprouts by deep sequencing and identified the binding sites of the those miRNAs in human target genes. Meanwhile, we extracted the human target genes from published paper that were regulated by broccoli and compared those genes with the predicted human targets of 4-day broccoli sprouts.
Project description:Ayu, Plecoglossus altivelis, is an economically important amphidromous fish species cultured in East Asia. LECT2 is a liver derived cytokine and involved in many pathologic conditions, especially in immune regulation. To understand cellular and molecular mechanisms of LECT2 in immune response of ayu, macrophages were isolated from ayu head kidney. After treatment with 0, 0.5 or 5 μg/ml of LECT2 for 3.5 hour, gene expression profile in ayu macrophages was measured using gene expression array. Results showed that LECT2 treatment led to the altered expression of immune related genes in ayu macrophages. Gene expression in ayu macrophages isolated from head kidney were measured after exposure to 0, 0.5 or 5 μg/ml LECT2 for 3.5 hours using gene expression array. Three independent experiments were performed using different ayu for each experiment for gene expression array analysis.
Project description:Soybean's productivity is significantly compromised by soil salinity, but, like most plants, it has evolved a variety of mechanisms to aid its survival under environmental stress. The expression of many plant genes is altered by salinity stress. We used microarrays to detail the global programme of gene expression and identified distinct up or down-regulated genes between salinity stressed and non stressed soybean Seedlings of the soybean cultivar Williams 82 were grown in vermiculite under a 16h photoperiod at 25 ºC for 14 days. RNA were isolated from the mock (M0, M1, M3, M6, M12, M24) and salinity treated (S0, S1, S3, S6, S12, S24) seedlings. 0.5 µg RNA that extracted from each time point of the mock and salinity-stressed seedlings were mixed respectively to obtain the mock and salinity-stressed RNA pools, and then they were used to synthesize the cDNA. The cDNA was labeled with biotin, and then hybridized to an Affymetrix soybean Genome Array.
Project description:GmMYB176, an R1 MYB transcription factor regulates isoflavonoid biosynthesis in soybean. In the current experiment, GmMYB176 was silenced (GmMYB176-Si) or overexpressed (GmMYB176-OE) in soybean hairy roots and their effect on transcriptome was studied. RNA-Seq analyses of GmMYB176-Si and GmMYB176-OE along with control non-transformed soybean hairy roots revealed that alteration of gene expression of GmMYB176 affects gene regulation of hundreds of genes in soybean.
Project description:To investigate the molecular mechanism of nonhost resistance of M. truncatula against soybean rust, we performed integrated tanscriptome and metabolome analyses using samples derived from M. truncatula leaves inoculated with soybean rust. To identify host signaling pathways triggered by soybean rust infection, we carried out microarray analysis to monitor the expression profiles associated with nonhost resistance including pre-invasive (12 hai) and apoplastic defense (24 hai) using Affymetrix GeneChip® Medicago Genome Array (Affymetrix).