Project description:Arabidopsis seedlings, of both wild-type and an ARF7/ARF19 double knockout mutant, were grown to 7 days post-germination. The roots were then dissected into 5 developmental zones, the meristem, early elongation zone, late elongation zone, mature root and lateral root zone. The sections then underwent transcriptional profiling to identify processes and regulatory events specific and in common to the zones.
Project description:Transcriptome analysis in nodules of Medicago truncatula with customn 2.3K cDNA arrays.<br><br>Study of different nodule developmental stages in wild type.<br><br>Study of various mutants forming non-functional nodules.
Project description:RNA was sequenced from meristems excised from dormant and non-dormant potato tubers harvested from four different harvest years. Expression based on mapped RNA-sequences was accomplished from excised meristems from fall harvested (dormant tubers) and the same harvested tubers were stored under standard commercial conditions until sprouting was present (non-dormant). The experiment was replicated for four different harvest years.
Project description:Delayed implantation occurs in many mammals, but the underlying mechanisms that direct this process remain largely unknown. In mice, ovariectomy prior to the preimplantation ovarian estrogen secretion on day 4 of pregnancy initiates blastocyst dormancy, which can be maintained for more than 200 days by continued progesterone treatment. An injection of estrogen activates blastocysts rapidly and makes them to implant in the progesterone-primed uterus. Recent establishment of a 60-mer oligo microarray platform, enriched for genes expressed in stem cells and early embryos including preimplantation embryos (7), fulfills this objective. With an optimized labeling reaction for a small amount of RNA with two rounds of cRNA linear amplification, we compared gene expression differences between dormant and activated blastocysts with validation of microarray data of several key genes at protein expression level using immunohistochemistry.
Project description:The goal of this project is to characterize the ECM composition of actively proliferative and dormant head and neck squamous cell carcinoma xenografts and identify components of the ECM niche instructing tumor cell dormancy.
Project description:Dormant cells of Mycobacterium tuberculosis, in addition to low metabolic activity and a high level of drug resistance, are characterized by ‘non-culturability’ – a specific reversible state of the inability of the cells to grow on solid media. The biochemical characterization of this physiological state of the pathogen is only superficial, pending clarification of the metabolic processes that may exist in such cells. In this study, applying LC-MS proteomic profiling, we report the analysis of proteins accumulated in dormant, ‘non-culturable’ M. tuberculosis cells in an in vitro model of self-acidification of mycobacteria in the post-stationary phase, simulating the in vivo persistence conditions. This approach revealed the preservation of 1379 proteins in cells after 5 months of storage in dormancy; among them, 468 proteins were statistically different from those in the actively growing cells and bore a positive fold change (FC). Differential analysis revealed the proteins of the pH-dependent regulatory system PhoP and allowed the reconstruction of the reactions of central carbon/glycerol metabolism, as well as revealing the salvaged pathways of mycothiol and UMP biosynthesis, establishing the cohort of survival enzymes of dormancy. The annotated pathways mirror the adaptation of the mycobacterial metabolic machinery to life within lipid-rich macrophages: especially the involvement of the methyl citrate and glyoxylate pathways. Thus, the current in vitro model of M. tuberculosis self-acidification reflects the biochemical adaptation of these bacteria to persistence in vivo. Comparative analysis with published proteins displaying antigenic properties makes it possible to distinguish immunoreactive proteins among the proteins bearing a positive FC in dormancy, which may include specific antigens of latent tuberculosis. Additionally, the biotransformatory enzymes (oxidoreductases and hydrolases) capable of prodrug activation and stored up in the dormant state were annotated. These findings may potentially lead to the discovery of immunodiagnostic tests for early latent tuberculosis and trigger the discovery of efficient drugs/prodrugs with potency against non-replicating, dormant populations of mycobacteria.
Project description:The objective of this study was to obtain expression profiles of proliferative T-HEp3-GFP and dormant D-HEp3-GFP cells after one week in vivo. The second objective was find tumor cells quiescence associated genes in dormant D-HEp3 cells that are only quiescent when injected in vivo. In this case we compared cells one week growing vs. dormant for the indicated cells in chick embryo CAMs. After one week 5 embryos per cell line carrying the indicated cells were isolated, tumors collagenased as described below and sorted for GFP-high cells usig a MoFlo machine. The sorted cells > 5x10^4 were used to extract RNA and the pure RNA was used to perform expression profiling using the Affymetrix HG-u133plus2 arrays. Because of the low amount of D-HEp3 (dormant) cells recovered all tumor cells from the dormant nodules were pooled. The same was done for proliferative-sorted T-HEp3-GFP cells to allow comparisons. Arrays were performed in triplicate. 5 T-HEp3-GFP tumors and 5 D-HEp3-GFP nodules were processed for preparation of single cells suspensions, RNA extracted and then pools of T-HEp3-GFP and D-HEp3-GFP sorted cells were analyzed in triplicate arrays
Project description:We experimentally generated a genome-wide gene expression data. To this end, we first collected samples of three important haploid developmental stages, specifically germinating spores (gametophyte_1), protonemata (gametophyte_2) and young gametophores (gametophyte_3) (four biological replicates each). We also collected three developmental stages of the diploid phase (sporophyte), specifically sporophytes shorter than 5mm (sporophyte_1), elongated needle-like sporophytes (sporophyte_2), and sporophytes with swollen capsules (sporophyte_3)
Project description:Roswell Park Human 19K Array CGH<br><br>the format of the data is:<br> <br>Reporter Identifier<br>Band<br>Count - number of replicate spots the data represents (some spots are excluded in image analysis, usually because they are too dim to be reliable)<br>chr - Chromosome<br>Start - Start location in base pairs<br>Stop - Stop Location in Base pairs<br>Center - Center in base pairs<br>g_loc - graphing location this is the location of the center in base pairs if the chromosomes were laid end to end<br>Log2 ratio - log2 ratio (test/control)<br>Ratio - linear version of the ratio above <br>A - Measure of brightness A=(log2 cy3 + log2 cy5)/2 <br>Flag - Used to color code spots<br> 3 - red probably mismapped<br> 4 - green potentially polymorphic<br> 5 - light blue Shows a high degree of duplication with other area in the genome (see UCSC genome browser) <br>reference - Reference for why the clone was flagged <br>Pub Med link - Pub Med ID for why clone was flagged