Transgenic AhNF-YC-OE vs Wild type Col 0 Arabidopsis plants
ABSTRACT: Transcriptional profiling of Arabidopsis rossette leaves comparing WT Col-0 with a transgenic lines overexpressing AhNF-YC gene from Amaranthus hypochondriacus in three different conditions. Three-condition experiment WT vs AhNF-YC OE plant leaves. The analyzed conditions were: normal growth conditions, water stress for 5 days and 24 hrs of recovery after normal watering was reestablished to 8-day water stressed plants.
Project description:Transcriptional profiling of Arabidopsis rossette leaves comparing WT Col-0 with a transgenic line overexpressing Ah24 gene from Amaranthus hypochondriacus. One-condition experiment WT vs Ah24 OE plant leaves.
Project description:Transcriptional profiling of Arabidopsis rossette leaves comparing WT Col-0 with a transgenic line overexpressing AhERF or AhDOF genes from Amaranthus hypochondriacus under different conditions. Three-condition experiment of WT vs AhERF OE plant leaves. The analyzed conditions were: normal growth conditions, 5 days of water stress (no irrigation) and 24 hrs of recovery after watering water-stressed plants. Besides, a two-condition experiment where WT vs AhDOF OE plant leaves were compared. The experimental conditions were: normal growth conditions and plants watered with 40mL of 400mM NaCl solution for three straight days to produce salt stress.
Project description:Taurine was previously reported to increase the proliferation of neural precursor cells (NPCs) from subventricular zone of the mouse brain. The results of a study that aimed to understand the mechanisms of this effect are presented here. A gene expression profile analysis indicated that genes regulated by taurine have roles in proliferation, cellular adhesion, cell survival, and mitochondrial functioning. Together with additional functional analyses, the results suggest that taurine provides more favorable conditions for cell proliferation by improving mitochondrial functioning. The total RNA from the control and taurine NPC cultures was used to produce tagged complementary DNA (cDNA) probes. Hybridation analysis used the mouse 65-mer oligo library from Sigma-Genosys to compare the expression of 23,232 gene-specific oligonucleotide probes for mouse.
Project description:Cross-species hybridization analysis of mammary glands during pregnancy and lactation. Results provide insight into putative conserved molecular mechanisms regulating mammary gland development. This study was performed to identify orthologous transcripts that are differentially co-expressed in the mammary gland at 2 stages of development (pregnancy and lactation) in wild type Sprague-Dawley rats. Key points are examined in a time series of Sprague Dawley rat mammary gland development, secretory activation and lactation. Triplicate rat (three biological replicates) at each time point were used for statistical power totalling 12 individual arrays in this study. Rats were as staged pregnant day 1 the day that post coital plug was observed, and similarly, lactation day 1 was the first day after birth. Whole mammary glands No. 4 (inguinal) were obtained from female rats at stages of development: virgin (adulthood, 14 wks of age), Pregnant (5 and 14 days of pregnancy) and Lactating (day 1 and 12 postpartum). The two-color (Cy5/Cy3) microarray experiment was designed to hybridize samples from each group against a common reference, a pool of RNA from mammary gland of three parous or virgin female rats.
Project description:One of the most regulated steps of translation initiation is the recruitment of an mRNA by the translation machinery. In eukaryotes, this step is mediated by the 5´end cap-binding factor eIF4E bound to the bridge protein eIF4G and forming the eIF4F complex. In plants, different isoforms of eIF4E and eIF4G form the antigenically distinct eIF4F and eIF(iso)4F complexes proposed to mediate selective translation. Using a microarray analysis of polyribosome- and non-polyribosome-purified mRNAs from 15 day-old Arabidopsis thaliana wild type [WT] and eIF(iso)4E knockout mutant [AteIF(iso)4E-1] seedlings we found 79 transcripts shifted from polyribosomes toward non-polyribosomes, and 47 mRNAs with the opposite behavior in the mutant. The translationally decreased mRNAs were overrepresented in root-preferentially expressed genes and proteins from the endomembrane system, including several transporters such as the phosphate transporter PHOSPHATE1 (PHO1), Sucrose transporter 3 (SUC3), the ABC transporter-like with ATPase activity (MRP11) and five electron transporters, as well as signal transduction-, protein modification- and transcription-related proteins. For transcriptional analysis used total RNA of AteIF(iso)4E-1 seedlings of 15 days old to known the changes on transcripts leves by the eIF(iso)4E absence, using as control Wt seedlings. The experiments were performed in duplicate, and swap analysis were done. For translational analysis, used non-polysomal and polysomal RNA of AteIF(iso)4E-1 seedlings of 15 days old in order to known the transcripts that are modified in their translational levels by the eIF(iso)4E absence, using as control non polysomal and polysomal RNA of Wt seddlings.
Project description:Transcriptional responses to CYP78A9 activity in Arabidopsis thaliana. Microarray experiment comparing es1-D (Arabidopsis activation tagging mutant that overexpress a P450 named CYP78A9) and wild type (Ws-3)closed floral buds from young primary inflorescences.
Project description:Growth inhibition of Rhizobium etli and other organisms by exogenous OA has not been previously reported. We conducted genome-wide transcriptomic analysis to determine the possible mechanism by which OA exerts its growth-inhibitory effect on R. etli CE3. The observed changes fall into several broad categories. First, the decreased expression of genes involved in protein synthesis (including ribosomal genes), replication and energy production indicates that the cells arrest or at least slow their growth, which agrees with the observed growth arrest induced by OA. The upregulation of a key enzyme (PrsAch) for 5'-phosphoribosyl-1'-pyrophosphate (PRPP) synthesis suggests that cells exposed to OA suffer PRPP deprivation. We hypothesized that the PRPP pools were depleted as a result of an increase in the synthesis of OMP stimulated by exogenous OA. PRPP depletion would result in a marked decrease in purine synthesis, which would lead to an imbalance between purine and pyrimidine nucleotides, causing arrest of DNA synthesis and a lack of energetic nucleotides (ADP, ATP). Three independent biological materials with one dyeswap were performed.
Project description:JNK is a member of the mitogen-activated protein kinase (MAPK) family and there are three genes that encode for JNK1, JNK2 and JNK3 respectively. JNK3 is mainly expressed in the central nervous system and it plays a crucial role in neuronal death in several neurodegenerative diseases, including epilepsy, Alzheimer’s disease, Parkinson’s disease and Huntington’s disease. By contrast, the isoforms JNK1 and JNK2 seem to be involved in brain development. The lack of Jnk3 gene confers neuroprotection, although the specific mechanism underlying this has yet to be elucidated. The present study analyze the gene expression profiling in mice lacking Jnk3, comparing them to wild-type mice. The microarray analysis showed that 22 genes are differentially expressed in Jnk3 null mice. Of these we focused in pik3cb, since it is directly related to the pro-survival PI3K/AKT pathway. Results from Jnk3 null mice showed an increase in pik3cb transcript, together with an increase in PI3K activity and hyperphosphorylation of AKT. By contrast, these changes were not observed in Jnk1 null mice, indicating that activation of PI3K/AKT pathway is specifically related to the lack of JNK3. The data obtained in this study demonstrates activation of the PI3K/AKT pathway in Jnk3 null mice through the increase of pik3cb transcript. We performed arrays from Jnk3 null mice respect wilde-type mice. For each experiment (sample) a RNA pool from hippocampus form three different mice were used. Moreover, a second independent hybridization were done with new sample of RNA (sample 2). The genes differentially expressed were determined based on the results from both samples.
Project description:Transcriptional profiling of human dendritic cells (DC) comparing control (DC generated with GM-CSF plus IL-4) with three different treatments of tolerogenic (DC generated with GM-CSF plus IL-4 and IL-10, or IL-4, IL-10, and IL-6, or IL-4, IL-10, and TGF-b1) Three two-condition experiments, control (N) vs tolerogenic DC with three different treatments. Pool of 4 indivuduals for each condition. One replicate per array.
Project description:Increasing atmospheric CO2 concentrations are causing decreased pH over vast expanses of the ocean. This decreasing pH may alter biogeochemical cycling of carbon and nitrogen via the microbial process of nitrification, a key process that couples these cycles in the ocean, but which is often sensitive to acidic conditions. Recent reports indicate a decrease in oceanic nitrification rates under experimentally lowered pH. How composition and abundance of ammonia oxidizing bacteria (AOB) and archaea (AOA) assemblages respond to decreasing oceanic pH, however, is unknown. We sampled microbes from two different acidification experiments and used a combination of qPCR and functional gene microarrays for the ammonia monooxygenase gene (amoA) to assess how acidification alters the structure of ammonia oxidizer assemblages. We show that despite widely different experimental conditions, acidification consistently altered the community composition of AOB by increasing the relative abundance of taxa related to the Nitrosomonas ureae clade. In one experiment this increase was sufficient to cause an increase in the overall abundance of AOB. There were no systematic shifts in the community structure or abundance of AOA in either experiment. These different responses to acidification underscore the important role of microbial community structure in the resiliency of marine ecosystems. amoA gene diversity from two ocean acidification experiments, Monterey Bay experiment (two time points, ambient and acidified) and Vineyard Sound experiment (ambient and acifidied, with and without nutrients) examined with 2 two-color arrays (Cy3 and Cy5): the universal standard 20-mer oligo is printed to the slide with a 70-mer oligo (an archetype). Environmental DNA sequences (fluoresced with Cy3) within 15% of the 70-mer conjugated to a 20-mer oligo (fluoresced with Cy5) complementary to the universal standard will bind to the oligo probes on the array. Signal is the ratio of Cy3 to Cy5.