title: Mitochondrial beta-cyanoalanine synthase is essential for root hair formation in Arabidopsis thaliana

status: Public on Oct 01 2010

city: Sevilla

first: Cecilia

last: Gotor

address: Avda. Américo Vespucio, 49

country: Spain

institute: Instituto de Bioquímica Vegetal y Fotosíntesis

summary: Cyanide is stoichiometrically produced as a co-product of the ethylene biosynthesis pathway, and it is detoxified by the b-cyanoalanine synthase enzyme. The molecular and phenotypical analysis of T-DNA insertional mutants of the mitochondrial b-cyanoalanine synthase CYS-C1 suggests that discrete accumulation of cyanide is not toxic for the plant and does not alter mitochondrial respiration rates, but does act as a strong inhibitor of root hair development. The cys-c1 null allele is defective in root hair formation and accumulates cyanide in root tissues. The root hair defect is phenocopied in wild type plants by the exogenous addition of cyanide to the growth medium and is reversed by the addition of hydroxocobalamin. Hydroxocobalamin not only recovers the root phenotype of the mutant, but also the formation of ROS at the initial step of the root hair tip. Transcriptional profile analysis of the cys-c1 mutant reveals that cyanide accumulation acts as a repressor signal for several genes encoding enzymes involved in cell wall rebuilding and the formation of the root hair tip, as well as genes involved in ethylene signaling and metabolism. Our results demonstrate that mitochondrial b-cyanoalanine synthase activity is essential to maintain a low level of cyanide for proper root hair development.

overall_design: Using Affymetrix ATH1 GeneChips, we performed a comparative transcriptomic analysis of the cys-c1 and wild type plants. Total RNA was extracted from of roots or leaves of 14-days-old plants grown under identical conditions on MS medium (three biological replicates for each genotype), and these samples were used to prepare complementary RNA and and analyzed using the Affymetrix-Arabidopsis ATH1GeneChip array.

first: Irene

last: García

first: Luis

last: Romero

first: Roberto

last: Solano


title: Gene expression changes in differentiated cortical neurospheres pre-exposed to ethanol

status: Public on Sep 30 2006

city: Bryan

first: Rajesh

last: Miranda

address: 8447 Riverside Parkway

country: USA

institute: Texas A&M University

summary:
Cerebral cortical-derived neurosphere cultures were exposed to ethanol to model heavy alcohol exposure during the period of cortical neurogenesis
Keywords: Compared differentiated neurospheres pre-exposed to ethanol to untreated differentiated neurospheres

overall_design: We analyzed 8, dual labeled, 22K Mouse arrays where 4 arrays correspond to one channel (Ch1) that represents the control (no ethanol) and the other channel (Ch2) represents the treatment (ethanol exposed), and the other 4 arrays were 'dye-flips' so Ch1 corresponds to the treatment (ethanol exposed) and Ch2 corresponds to the control (no ethanol)"

first: Cynthia

last: Camarillo

middle: C


title: Gene expression changes in fetuses exposed to ethanol in utero

status: Public on Oct 31 2006

summary:
Timed pregnant C57Bl6 mice were exposed to ethanol during a critical period, gestational day 15 to 18, of cerebral cortical development to identify gene expression changes in the cerebral cortex of developing fetus due to this ethanol exposure
Keywords: Compared animals exposed to ethanol (alcohol fed group) to a pair-fed control group and both groups were normalized to a control group (animals fed adlibitum)

overall_design: We analyzed 14, dual labeled, 22K Mouse arrays where one channel (Ch1) represents the sample for animals fed with alcohol (alcohol fed group) or to animals fed with maltose dextrose (pair-fed group) and the other channel (Ch2) corresponds to universal control (total RNA from 7 animals fed adlibitum with food and water; control)

first: Leena

last: Kumar


title: Transcription profiling of CD133/Prominin positive neurospheres

status: Public on Oct 01 2006

summary:
To identify expression of hematopoetic stem cell antigens in cerebral cortical derived neurospheres
Keywords: Compared CD133 positive neurospheres to control GFP-positive neurospheres

overall_design: We analyzed 12, dual labeled, 23K Mouse arrays where one channel (Ch1) represents the treatment (GFP or prominin positive neurospheres) and the other channel (Ch2) represents the universal embryonic mouse control "

first: Daniel

middle: R

last: Santillano

middle: S

first: Henry

last: Thomas

first: Terasa

middle: L

last: Prock

first: Diana

last: Yang


title: Rheumatoid arthritis and anti-TNF treatment

status: Public on Jan 28 2010

city: Amsterdam

first: Lisa

last: van Baarsen

address: Meibergdreef 9

department: Div. of Clinical Immunology and Rheumatology

country: Netherlands

institute: EULAR & FOCIS Center of Excellence

summary:
In 15 patients with rheumatoid arthritis the baseline expression (t=0) of type I IFN-regulated genes was determined in peripheral blood cells (PAXgene) using cDNA-microarrays and compared to levels one month after (t=1) anti-TNF treatment (infliximab). Therefore, we used 43K cDNA microarrays from the Stanford Functional Genomics Facility (http://microarray.org/sfgf/) printed on aminosilane-coated slides containing ~20.000 unique genes. Only one batch of arrays was used for all experiments. First DNA spots were UV-cross linked to the slide using 150-300 mJoules. Sample preparation and microarray hybridization were performed as described previously (1,2). Data storage and filtering was performed using the Stanford Microarray Database (http://genome-www5.stanford.edu//) as described previously.   1. van der Pouw Kraan TC, Wijbrandts CA, van Baarsen LG, Voskuyl AE, Rustenburg F, Baggen JM et al.: Rheumatoid arthritis subtypes identified by genomic profiling of peripheral blood cells: assignment of a type I interferon signature in a subpopulation of patients. Ann Rheum Dis 2007, 66: 1008-1014. 2. van der Pouw Kraan TC, van Baarsen LG, Rustenburg F, Baltus B, Fero M, Verweij CL: Gene expression profiling in rheumatology. Methods Mol Med 2007, 136: 305-327.  Abbreviations: - Bnrs are the different patients analyzed - PAX or Paxgene indicates the total RNA was isolated from peripheral blood obtained in PAXgene tubes - CRS: common reference sample: We made a common reference that consisted of a mixture of mRNAs isolated from 11 different cell lines (Perou CM, Jeffrey SS, van de RM et al. Distinctive gene expression patterns in human mammary epithelial cells and breast cancers. Proc Natl Acad Sci U S A. 1999; 96:9212-9217) supplemented with RNA from rheumatoid synovial tissue, fibroblasts, and activated peripheral blood mononuclear cells (PBMCs). - PMT: photomultiplier tube: the sensitivity/intensity of the scanner can be adjusted to prevent spot saturation.
Compound Based Treatment: anti-TNF (infliximab)

first: Cornelis

last: Verweij


title: Mouse Fetal Cortical-derived Neurosphere cultures transfected with null control or miRNA-153 mimetic

status: Public on Aug 01 2014

summary: The expression of the mciroRNA, miR-153 is significantly altered in neural stem cells (NSCs) following exposure to the teratogens, alcohol and nicotine (PMIDs:22458409, 17687032). To better understand how miR-153 may mediate teratogenesis, we first needed to identify miR153 targets in fetal NSCs. Gestational day 12.5 fetal mouse cortical neural epithelium was isolated and grown as neurospheres in defined medium for studies. We overexpressed miR-153 in fetal NSCs for 24 hours in a transient transfection assay, and profiled mRNA expression using a microarray platform (codelink array) to identify potential target genes. Over expression of pre-miR-153 resulted in a ~32-fold induction of miR-153 compared to the transfection control. Transcript profiles were assessed from RNA samples (6 independent replicates in each condition) hybridized to codelink microarrays according to manufacturer's protocols. Data analysis showed that miR-153 overexpression resulted in statistically significant down-regulation of 102 genes (at a false discovery rate α=0.1, of a total of 860 transcripts down-regulated by ≥1.3-fold). These data suggested the role of this miRNA in moderately controlling expression hundreds of gene transcripts. These regulated genes may be important in controlling neural stem cell differentiation and downstream signaling pathways.

overall_design: Six independent replicates were performed for control and treatment groups, and twelve independent single channel intensity values were uploaded after normalization for analysis  independent single channel intensity values were uploaded after normalization

first: Pai-Chi

last: Tsai


title: Identification of downstream effectors of retinoic acid specifying the zebrafish pancreas by integrative genomics [RNA-seq]

status: Public on Mar 16 2021

city: Pamplona

first: Ana

middle: Rosa

last: López-Pérez

address: Calle Irunlarrea, 3

institute: Navarrabiomed - Fundacion Migues Servet

type: Expression profiling by high throughput sequencing

summary: Retinoic acid (RA) is a key signal for the specification of the pancreas. Still, the gene regulatory cascade triggered by RA in the endoderm remains poorly characterized. In this study, we investigated this regulatory network in zebrafish by combining RNA-seq, RAR ChIP-seq and ATAC-seq assays. By analysing the effect of RA and of the RA receptor (RAR) antagonist BMS439 on the transcriptome and on the chromatin accessibility of endodermal cells, we identified a large set of genes and regulatory regions regulated by RA signalling. RAR ChIP-seq further defined the direct RAR target genes including the known hox genes as well as several pancreatic regulators like mnx1, insm1b, hnf1ba and gata6. Comparison of our zebrafish data with available murine RAR ChIP-seq data highlighted conserved direct target genes and revealed that some RAR sites are under strong evolutionary constraints. Among them, a novel highly conserved RAR-induced enhancer was identified downstream of the HoxB locus and driving expression in the nervous system and in the gut in a RA-dependant manner. Finally, ATAC-seq data unveiled the role of the RAR-direct targets Hnf1ba and Gata6 in opening chromatin at many regulatory loci upon RA treatment.

overall_design: Combination of 24 RNA-seq samples. Non endodermal cells and endodermal cells (sox17:GFP +) from zebrafish embryos at 3 and 8 somites stage treated with DMO (control), retionic acid and BMS493 (RA antagonist)  were generated in triplicates.

first: Piotr

middle: J

last: Balwierz

first: Boris

last: Lenhard

first: Ferenc

last: Muller

first: Fiona

last: Wardle

first: Isabelle

last: Manfroid

first: Marianne

last: Voz

first: Bernard

last: Peers