Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Time course IAA treatment Arabidopsis seedlings

ABSTRACT: 7-days-old Arabidopsis seedlings of wildtype (Col-0) were treated with 1 μM IAA for 15 minutes or 3 hours and gene expression of whole plant was analyzed using Affymetrix Gene 1.1 ST Array strips. Arabidopsis seedling (Col-0) 25 plants were grown in each plate (1/2 MS medium) under continuous light at 22 °C for 6 or 7 days. Ten seedlings were cultured in 50 ml plastic tube containing liquid medium (1/2 MS medium), and incubated with shaking. After 24 hours, samples were treated with 0.1% DMSO for 15 minutes or 3 hours (Mock treatments) and with 1 μM indole-3-acetic acid dissolved in DMSO for 15 minutes or 3 hours (IAA tretments). The plants were wiped on papertowels and sampled. Immediately after sampling of the plants, these plants were soaked in liquid nitrogen and stored at -80 °C. The experiment was repeated 3 times in 3 different days. Total RNA was extracted from the frozen samples using RNeasy Plant Mini Kit (Qiagen) following the protocol supplied by manufacturer. The quality of RNA was checked by 2100 Bioanalyzer system (Agilent) and 100 ng RNA of each experiment was applied to microarray analysis. The microarray analysis was carried out using Affymetrix gene 1.1 ST array strips and GeneAtlas (Affymetrix) following the protocol supplied manufacturer.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Yukihisa Shimada

PROVIDER: E-GEOD-58063 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

AtCAST3.0 update: a web-based tool for analysis of transcriptome data by searching similarities in gene expression profiles.

Kakei Yusuke Y Shimada Yukihisa Y

Plant & cell physiology 20141209 1

In transcriptome experiments, the experimental conditions (e.g. mutants and/or treatments) cause transcriptional changes. Identifying experimental conditions that induce similar or opposite transcriptional changes can be useful to identify experimental conditions that affect the same biological process. AtCAST (http://atpbsmd.yokohama-cu.ac.jp) is a web-based tool to analyze the relationship between experimental conditions among transcriptome data. Users can analyze 'user's transcriptome data' o ...[more]

PMID: 25505006

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Project description:Human ingestion of microplastics (MPs) is common and inevitable due to the widespread contamination of food items, but implications on the gastric digestion of food proteins are still unknown. In this study, the interaction between pepsin and polystyrene (PS) MPs was uncovered by investigating its effect on enzyme activity and conformation while in a simulated human gastric environment. The impact on food digestion was also determined by monitoring the kinetics of protein hydrolysis through static in vitro gastric digestion of cow’s milk contaminated with PS. The binding of pepsin to PS showed that surface chemistry of MPs dictates binding affinity. The key contributor to pepsin adsorption seems to be π−π interactions between the aromatic residues and the PS phenyl rings. During quick exposure (10 minutes) of pepsin to increasing concentrations (222, 2219, 22188 particles/mL) of 10 μm PS (PS10) and 100 μm PS (PS100), total enzymatic activities were not affected remarkably. However, upon prolonged exposure at 1 and 2 hours, preferential binding of pepsin to the small, low zeta-potential PS caused structural changes in the protein which led to a significant reduction of its activity. Digestion of cow’s milk mixed with PS10 resulted in transient accumulation of larger peptides (10-35 kDa) and reduced bioavailability of short peptides (2-9 kDa) in the gastric phase. This, however, was only observed at extremely high PS10 concentration (0.3 mg/mL or 5.46E+05 particles/mL). The digestion of milk peptides, bound preferentially over pepsin on the hard corona around PS10, was delayed up to 15 minutes in comparison to bulk protein digestion. Intact caseins, otherwise rapidly digested, remained bound to PS10 in hard corona for up to 15 minutes. This work presents valuable insights regarding the interaction of MPs, food proteins, and pepsin, and their dynamics during gastric digestion which provides new knowledge and understanding on the potential risks of MPs to human health.

Dataset Information

Time course IAA treatment Arabidopsis seedlings

Publications

AtCAST3.0 update: a web-based tool for analysis of transcriptome data by searching similarities in gene expression profiles.

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