Project description:The growth behavior of plant roots on tilted, hard agar surfaces is determined by many basic cellular processes, including microtubule dynamics and cell wall expansion. Among Arabidopsis thaliana accessions there is natural variation for these behaviors, including one known as skewing or slanting. The root skewing pattern on hard, tilted agar surfaces may be a clue to adaptations of an accession to its environment. Here, we compare expression profiles of two accessions with diverse skewing behavior grown on the wave assay, which consists of seedlings growing two days vertically and 3 days tilted on hard agar plates. Cvi has a strong skew on tilted, hard agar sufaces, and Ler-2 has a weaker one. We also include a near isogenic line, 170G-55-16 a.k.a HGI2.1, that is mostly Ler-2 in background but has a segment of Cvi introgressed into chromosome 2. This line has an intermediate skew between its two parents. 3 biological replicates of each of 3 genotypes (Cvi, Ler-2, and 170G-55-16/HGI2.1) were subjected to the wave assay. After the assay, approximately 600 root tips from each biological replicate were pooled for RNA extraction and hybridization on the Affymetrix ATH1 microarray.
Project description:The growth behavior of plant roots on tilted, hard agar surfaces is determined by many basic cellular processes, including microtubule dynamics and cell wall expansion. Among Arabidopsis thaliana accessions there is natural variation for these behaviors, including one known as skewing or slanting. The root skewing pattern on hard, tilted agar surfaces may be a clue to adaptations of an accession to its environment. Here, we compare expression profiles of two accessions with diverse skewing behavior grown on the wave assay, which consists of seedlings growing two days vertically and 3 days tilted on hard agar plates. Cvi has a strong skew on tilted, hard agar sufaces, and Ler-2 has a weaker one. We also include a near isogenic line, 170G-55-16 a.k.a HGI2.1, that is mostly Ler-2 in background but has a segment of Cvi introgressed into chromosome 2. This line has an intermediate skew between its two parents.
Project description:To investigate effects of carbon nanotubes (CNTs) om total expression profile of tomato plants we introduced CNTs in MS agar medium in concentrationd 0, 50, 100, 200 ug/ml Objectives for this study included the identification of genes that were up or down-regulated at the transcriptional level in tomato seedlings in response to carnom nanotubes (CNTs). 10 day old root tips and first two leaves of wild type tomato seedlings (cv. Micro-Tom) growing on regular MS agar medium or MS medium supplemented with carbon nanotubes (50, 100, 200 ug/ml) or MS medium supplemented with activated carbon (50 ug/ml) were selected for RNA extraction and hybridization on Affymetrix microarrays.
Project description:Plant roots located in the upper soil layers are prone to experience high temperatures. To gain insight into the effect of high temperature on root development and functioning, we exposed five-day-old Arabidopsis thaliana seedlings grown on agar plates to 30 °C for 48 hours, and compared the gene expression profile in the root tip with that from seedlings that remained at 22 °C.
Project description:The purpose of the present study is to determine the effect of Phosphorus deficiency on gene expression level using microarray analysis to identify genes responsible for root hair development. Phosphorus deficiency induced the formation of root hairs to explore a greater soil volume but molecular mechanisms were unknown. Therefore, microarray experiments were performed using root tips of Brassica carinata cultivars Bale and Bacho, respectively differing in root hair length during Phosphorus deficiency. Experimental design was carried out in nutrient solution in a climate chamber with controlled environmental conditions (20°C, 16h day/8h night cycle, 70% relative humidity) in a randomized design. 25 root tips from 10 day old seedlings grown without Phosphorus of 1cm length were harvested and immediately frozen in liquid nitrogen. Gene expression analyses were performed
Project description:Calcium deficiency response in liverwort, Arabidopsis and lettuce: (1) Marchantia polymorpha: M. polymorpha wildtype and Gβ-null mutant plants (Tak-1, gpb1-2) were grown in control liquid Yamagami media (2 mM Ca) for 6 days. For RNA-seq experiments, 6 day old gemmalings were transferred to calcium deficiency (0 mM Ca) media. Samples were collected at 48 h after the transfer. The transcriptomic profiles were collected from two independent batches. In total four biological replicates were used for each condition and each genotype for a total of 16 samples. (2) Arabidopsis thaliana: For Arabidopsis RNA-seq experiment, 6-day old seedlings grown on ½ strength MS media with sucrose were transferred to Yamagami media with 2 mM or 0 mM CaCl2 and treated for 7 days. (3) Lactuca Sativa: For lettuce RNA-seq, 4-day old seedlings grown on water agar (1%) were transferred to Yamagami media with 2 mM or 0.15 mM CaCl2 and treated for 7 days. In total four and three biological replicates were used for each condition for a total of 8 and 6 samples respectively for Arabidopsis and lettuce.
Project description:Our objective is to study root stem cell niche. We isolated total RNA from the roots tips of 5-day-old Col-0,arf2-7 and stop1 seedlings. New genes after responding to NAA treatment, during the root development, are discovered.
Project description:An Arabidopsis mutant showing an altered ability to green on illumination after extended periods of darkness has been isolated in a screen for genomes uncoupled (gun) mutants. Following illumination for 24 h, 10-day-old dark-grown mutant seedlings accumulated 5 times more chlorophyll than wild-type seedlings and this was correlated with differences in plastid morphology observed by transmission electron microscopy. The mutant has been named greening after extended darkness 1 (ged1). We used microarrays to detail the global profiles of transcript abundances in the mutant in comparison to the wild type. Microarray analysis showed much lower amounts of transcripts of genes encoding seed storage proteins, oleosins and late embryogenesis abundant (LEA) proteins in 7-day-old seedlings of ged1 compared to wild type. RNA-gel-blot analyses confirmed very low levels of transcripts of seed protein genes in ged1 seedlings grown for 2-10 days in the dark, and showed higher amounts of transcripts of photosynthesis-related genes in illuminated 10-day-old dark-grown ged1 seedlings compared to wild type. Keywords: Genotype
Project description:Transcript profiling analysis of csn4-1 light grown mutant seedlings compared to wild type using Arabidopsis ATH1 GeneChip array Keywords: 7 day old light grown seedlings, wild type and mutant