title: Temperature acclimation in rainbow trout heart

status: Public on Feb 19 2005

summary:
In this project, effects of chronic temperature changes on the transcriptome of the rainbow trout heart (Oncorhynchus mykiss) were examined. Ectothermic animals of north-temperate latitudes experience large seasonal changes in temperature which strongly affect the rate of body functions. To compensate for the effects of temperature changes ectotherms can respond to chronic temperature changes by increasing the quantity of tissue or enzyme needed for different physiological tasks, or by expressing proteins isoforms which are more appropriate for the new thermal conditions. On the other hand, proteins which are needed in lesser amounts in the new thermal regime could be depressed or down-regulated. Although expression of proteins can be changed by multiple mechanisms during synthesis and degradation, temperature dependent changes in transcription of genes is probably the most important factor in modifying the proteome of the tissues. Rainbow trout are active throughout their thermal tolerance range (0-25°C). Maintenance of adequate cardiac function at different thermal conditions requires a thorough change of the cardiac phenotype which appears as compensatory changes in relative heart mass, energy metabolism, nervous and humoral control of cardiac contractility and in electrical and mechanical properties of the trout heart. Such an extensive structural and functional remodeling of the heart probably necessitates both qualitative and quantitative changes among the numerous macromolecules which constitute the cardiac phenotype and cannot, therefore, be solely based on posttranslational modification of proteins but is expected to require differential gene expression. As a power supply of the circulatory system, the heart is in the focal point of physiological plasticity and sets limits for the activity level of the animal in different thermal conditions. Although several aspects of heart function have been studied in thermally acclimated fish and a number of structural changes have been noticed on exposure to different temperatures, the cellular and molecular mechanisms involved in chronic thermal stress of the fish heart are only partially elucidated. An interesting and poorly examined feature of the cold-acclimated phenotype of the trout heart is the increased heart mass which attenuates the depressive effect of low temperature on cardiac pump function. The heart is a complex organ composed of multiple tissues which together provide the system all necessary qualifications for cardiac pump function. In addition to the contractile and metabolic machinery of the cardiac myocytes, the amount and quality of the extracellular matrix also contribute to the properties of the heart as a muscular pump. Due to the complexity of the heart an enormous amounts of research efforts are needed to find out and examine all crucial aspects of cardiac plasticity required for thermal acclimation. In this regard the screening of gene expression by cDNA micro arrays might provide a broader view to genomic basis of cardiac remodeling under changing temperatures and aid to reveal the candidate genes which are important for thermal acclimation and which might remain unnoticed by traditional biochemical and physiological methods. In the present study we the steady-state effects of temperature acclimation on gene expression of the rainbow trout heart were screened by micro array analysis.
Keywords: parallel sample

first: Matti

last: Vornanen


title: Gene expression analysis of testicular DLBCL: ABC or GCB subtype?

status: Public on May 01 2006

city: Groningen

first: Marije

last: Booman

department: Pathology

country: Netherlands

institute: University Medical Center Groningen

summary:
Diffuse large B cell lymphomas (DLBCL) constitute a heterogeneous group of lymphomas in which germinal center B cell-like and activated B cell-like subtypes can be discerned based on pathology, clinical presentation and gene expression patterns. Testicular DLBCL form an immune-privileged site-related subgroup of DLBCL with an unfavorable prognosis. We used cDNA microarray analysis, immunohistochemistry for CD10, Bcl6 and MUM1, and somatic hypermutation analysis of the immunoglobulin heavy chain gene rearrangements to determine the subtype of primary testicular DLBCL. Immunohistochemistry revealed 14/22 testicular DLBCL with an activated B cell-like immunophenotype and 8/22 with an ambiguous immunophenotype co-expressing CD10 and high levels of MUM1. cDNA microarray analysis of these 22 and 4 additional cases showed a uniform activated B cell-like gene expression pattern in both immunophenotypes. Somatic hypermutation analysis showed a very high mutation load in 7 cases tested, but intraclonal heterogeneity was found at low level in only one of these cases. We conclude that primary testicular DLBCL have uniform activated B cell-like subtype characteristics despite a number of cases showing an ambiguous immunophenotype.
Keywords: Gene expression

overall_design:
Twenty-six primary testicular DLBCL and 10 primary nodal DLBCL were analyzed using an 18k cDNA microarray. Hierarchical clustering was done based on a set of 21 genes and a set of 201 genes, both discriminative for ABC/GCB subtypes, to classify cases. Gene expression profiles were compared between testicular DLBCL of ambiguous and activated B cell-like immunophenotype.

Immunophenotype classification of Nodal DLBCL and Testicular DLBCL samples: see Table 1 in PMID 16823896.

first: Jenny

last: Douwes

first: Annuska

middle: M

last: Glas

first: Daphne

last: de Jong

first: Ed

last: Schuuring

first: Philip

last: Kluin


title: Toxicogenomic Response of Staphylococcus aureus to Peracetic Acid

status: Public on May 31 2006

city: Singapore

first: Matthew

middle: Wook

last: Chang

address: 62 Nanyang Drive

department: School of Chemical and Biomedical Engineering

country: Singapore

institute: Nanyang Technological University

summary:
In the present study, we employed Affymetrix Staphylococcus aureus GeneChip arrays to investigate the dynamics of global gene expression profiles during the cellular response of Staphylococcus aureus to peracetic acid, which involved initial growth inhibition and subsequent partial recovery.
Keywords: Time course

overall_design: We conducted three independent microarray experiments (biological replicates) in the absence (control) and the presence (experimental) of peracetic acid. We calculated fold change as the ratio between the signal averages of three untreated (control) and three peracetic acid-treated (experimental) cultures for 10 and 20 min exposures.

first: Wook

first: Freshteh

last: Toghrol

first: William

middle: E

last: Bentley


title: Response to stress in brain and kidney

status: Public on May 13 2004

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

summary:
Rainbow trout was stressed with netting and confinement, samples were collected after 1, 3 and 5 days. 4 individuals were pooled in each sample, hybridization followed dye-swap design
Keywords: time-course


title: Global Transcriptome Analysis of Staphylococcus aureus Response to Hydrogen Peroxide

status: Public on Dec 31 2005

summary:
In the present study, we employed Affymetrix Staphylococcus aureus GeneChip arrays to investigate the dynamics of global gene expression profiles during the cellular response of Staphylococcus aureus to hydrogen peroxide-induced oxidative stress, which involved initial growth inhibition and subsequent recovery.
Keywords: Time course

overall_design: We conducted three independent microarray experiments (biological replicates) in the absence (control) and the presence (experimental) of hydrogen peroxide. We calculated fold change as the ratio between the signal averages of three untreated (control) and three hydrogen peroxide-treated (experimental) cultures for 10 and 20 min exposures.

first: David

middle: A

last: Small


title: Alpha-amanitin treatment effect on intronic transcription

status: Public on Mar 29 2007

city: SÃO PAULO

first: Helder

middle: I.

last: Nakaya

state: SÃO PAULO

address: AVENIDA PROFESSOR LINEU PRESTES, 580, Block 17

country: Brazil

institute: Universidade de São Paulo

summary:
We compared the gene expression profiles of prostate carcinoma cells, LNCaP, treated or not with an inhibitor of RNA Polymerase II (RNAP II), alpha-amanitin. These experiments pointed to a fraction of intronic messages that seems to be insensitive to alpha-amanitin or up-regulated in cells with blocked RNAP II transcription.
Keywords: RNA-polymerase II inhibition experiments

overall_design: Two samples of RNA isolated from alpha-amanitin-treated cells and two samples of control LNCaP cells were used in the hybridization experiments, performing a total of 4 hybridizations.

middle: I

first: Paulo

middle: P

last: Amaral

first: Rodrigo

last: Louro

first: Eduardo

last: Reis

first: Sergio

middle: V

last: Almeida


title: Molecular profiles(HG-U95B,C,D,E) of dystrophin-deficient and normal human skeletal muscle

status: Public on Feb 04 2004

city: Boston

first: Judith

last: Haslett

state: MA

country: USA

institute: Harvard Medical School

summary:
molecular profiles (HG-U95B,C,D,E) of biopsy skeletal muscle samples obtained from 10 normal individuals and 10 DMD patients
Keywords = gene expression profiles of normal human skeletal muscles
Keywords = gene expression profiles of DMD patients' skelatal muscle samples
Keywords = Affymetrix HG-U95B
Keywords = Affymetrix HG-U95C
Keywords = Affymetrix HG-U95D
Keywords = Affymetrix HG-U95E
Keywords: other

middle: N

first: Despina

last: Sanoudou

first: Alvin

middle: T

last: Kho

first: Mei

last: Han

first: Richard

middle: R

last: Bennett

first: Isaac

middle: S

last: Kohane

first: Alan

middle: H

last: Beggs

first: Louis

last: Kunkel


title: The Frequency Dependent Response of the Vascular Endothelium to Pulsatile Shear Stress

status: Public on Feb 22 2006

city: Durham

first: Heather

middle: Anne

last: Himburg

state: NC

address: PO Box 90281

department: Biomedical Engineering

institute: Duke Univeristy

summary:
The objective of this study was to advance the understanding of how in vivo arterial shear forces affect vascular endothelial gene expression.  Complicated blood flow patterns at arterial branches create small regions that experience fluctuations in shear stress at frequencies higher than the heart rate.  To assess whether such temporal variations in shear stress can affect endothelial gene expression, a series of in vitro microarray experiments was performed.  The effects of three sinusoidal waveforms (1, 2, and 3 Hz) and one physiological waveform were compared to the expression profiles under steady flow.  At each frequency, three levels of mean shear stress (0, 7.5, and 15 dyn/cm2) were used.  Porcine aortic endothelial cells were exposed for 24 hours to each combination, replicated four times.  Following shear exposure, phase contrast images of the cells were acquired, and RNA was extracted for microarray analysis against about 10,000 porcine oligonucleotides.  Cell alignment with the flow was positively correlated with mean shear (p < 0.001) and independent of frequency.  A two-way ANOVA identified 232 genes that were differentially regulated by frequency.  The frequency sensitive genes were clustered to identify groups of genes exhibiting similar frequency responses.   The largest response was seen at 2 Hz.  At this frequency, several inflammatory molecules were upregulated, including VCAM, CTGF, TGF-beta2, c-jun, and IL-8, indicating a potential endothelial atherosusceptibility at this frequency.   Mean shear significantly affected the expression of ~3,000 genes.  Purely oscillatory flow (zero mean shear) enhanced the expression of several growth factors and adhesion molecules (E-selectin, VCAM, MCP-1, IL-8, c-jun), relative to non-reversing flow (15 dyn/cm2 mean shear).  The 2 Hz upregulation of certain atherogenic molecules such as VCAM, c-jun, and IL-8 was enhanced as the mean shear was reduced.  Thus, the inflammatory response evoked at certain frequencies appears to be exacerbated by low, oscillatory shear.
Keywords: Shear stress response

overall_design: Endothelial cells were exposed to 3 levels of mean shear stress: 0, 7.5, and 15 dyn/cm^2.  At each mean level, 5 shear stress waveforms were tested: steady, 1 Hz, 2 Hz, 3 Hz, and a physiological waveform.  The amplitude of oscillation in each case was +/- 15 dyn/cm^2.  Four replicates of each condition were performed for a total of 60 experiments.  Each experimental sample was hybridized to an oligonucleotide array along with a standard reference sample.

first: Morton

last: Friedman


title: Tissue-specific signature

summary:
The experiments described here aim to generate a set of gene expression profiles from prostate, liver and kidney tissues using a custom-designed oligo-array platform enriched in messages that map to intronic regions of known human genes. Expression profiles of these tissues were combined in order to find a tissue-specific signature of intronic transcripts.
Keywords: Tissue-specific, Intronic transcripts

overall_design: Equal amounts of 300ng of DNase-treated total RNA of each tissue sample (detailed below in section 2.3) were used to create amplified cyanine 3- and cyanine 5-labeled cRNA. Next, cRNA solutions were mixed and hybridized to oligo-array slide for 17 hours. Using this approach, we labeled 2 liver pool samples and 2 prostate samples, obtaining a total of 4 sets of microarray intensities from each tissue. Four sets of microarray intensities were also obtained by labeling 2 kidney pool samples with cy3 and 2 kidney pool samples with cy5.


title: Hepatocyte growth factor time course

status: Public on Nov 04 2003

city: Philadelphia

last: Johnson

state: PA

address: 415 Curie Blv

department: Medicine

institute: University of Pennsylvania

summary:
Cultured Madin-Darby canine kidney (MDCK) cells treated with hepatocyte growth factor (HGF) for 0, 3 and 24 hours.  Each time point in triplicate.
Keywords: time-course

first: Joshua

last: Lipschutz