title: Supiculisporic Acid treatment with 0.16 % for 2 h

status: Public on Nov 01 2007

city: Tsukuba

first: Emiko

last: Kitagawa

state: Ibaraki

address: Onogawa 16-1

institute: National Institute of Advanced Industrial Science and Technology

summary:
The number and type of synthetic chemicals that are being produced worldwide continues to increase significantly. While these industrial chemicals provide numerous benefits, there is no doubt that some have potential to damage the environment and health. Toxicity must be evaluated and use must be carefully controlled and monitored in order to minimize potential damage. DNA microarray technology has become an important new technique in toxicology. We are using the yeast Saccharomyces cerevisiae as a model organism for toxicological study because it is a simple, fast-growing eukaryote that has been thoroughly characterized. In order to evaluate toxicity by newly synthesized or mixture chemicals, toxicity-induced gene expression alteration profiles by known chemicals should be collected. In our study, cells need to be exposed with same experimental cellular condition, semi lethal (IC50), respectively. In the case of supiculisporic acid, one of bio-surfactants, the exposure dose was decided as 0.16 % by growth curve with continuously diluted exposure.
Keywords: stress response

overall_design: Series contains 6 hybridization results from independent biological samples respectively.

first: Sakiko

last: Kurita

first: Hitoshi

last: Iwahashi


title: Chemical toxicity of thorium in Saccharomyces cerevisiae

country: Japan

summary:
Thorium (232Th), an actinoide element, is among the most common and naturally occurring radioactive materials distributed in our environment. Thorium has been used as a radiographic contrast agent (thorotrast) from 1930 to 1955, and many studies on its effects to the human body have been reported. Once thorium is injected in the body, the risk of cancer is increased by the direct bombardment from alpha-particle with high linear energy transfer during decay of Thorium. However, these many reports focus on the irradiation damage by long-term exposure of thorium. The acute toxicity of thorium is greater risk from the chemical toxicity than from the radiological toxicity. Here, we evaluated the effect of thorium from the stand point of chemical toxicity using yeast DNA microarray. In this experiment, genes that contribute to “C-compound and carbohydrate metabolism”, “energy”, and “cell rescue, defense and virulence” were significantly induced. These genes were classified into oxidative stress, glycogen and trehalose metabolism, sugar transport, and cell wall damage. On the contrary, only one gene related to DNA damage was detected. These results indicate that thorium causes the damage of cell wall and induces the oxidative stress. In order to overcome oxidative stress, yeast cells promote the glycogen and trehalose metabolisms and shift to anaerobic fermentation.
Keywords: stress response

overall_design: Series containes 3 hybridization results from independent biological samples, and each experiment have high and low power scanned data respectively.

first: Satomi

middle: M

last: Murata


title: Paraquat treatment with 35 ppm for 2 h

summary:
The number and type of synthetic chemicals that are being produced worldwide continues to increase significantly. While these industrial chemicals provide numerous benefits, there is no doubt that some have potential to damage the environment and health. Toxicity must be evaluated and use must be carefully controlled and monitored in order to minimize potential damage. DNA microarray technology has become an important new technique in toxicology. We are using the yeast Saccharomyces cerevisiae as a model organism for toxicological study because it is a simple, fast-growing eukaryote that has been thoroughly characterized. In order to evaluate toxicity by newly synthesized or mixture chemicals, toxicity-induced gene expression alteration profiles by known chemicals should be collected. In our study, cells need to be exposed with same experimental cellular condition, semi lethal (IC50), respectively. In the case of paraquat (CAS; 1910-42-5), IC 50 was decided as 1250 ppm by growth curve with continuously diluted exposure, however, we had chosen 35 ppm for this experimental series because the reaction with low dose should be explored. Paraquat is used as a quaternary ammonium herbicide, and suspected to be a carcinogen, cardiovascular or blood toxicant, gastrointestinal or liver toxicant, kidney toxicant, neurotoxicant, reproductive toxicant, respiratory toxicant, skin or sense organ toxicant.
Keywords: stress response

overall_design: Series contains 3 hybridization results from independent biological samples, and each experiment have high and low power scanned data respectively.

first: JooMyung

last: Ahn


title: Characterization of ST-4821 complex, a unique Neisseria meningitidis clone

status: Public on Nov 28 2007

city: Beijing

first: Junping

last: Peng

address: No 6, Rongjing Eastern Street, BDA

country: China

institute: Chinese center for disease control and prevention

summary:
Neisseria meningitidis is the leading cause of bacterial meningitis and septicemia worldwide. The novel ST-4821 clonal complex caused several serogroup C meningococcal outbreaks unexpectedly during 2003–2005 in China. We fabricated a whole-genome microarray of Chinese N. meningitidis serogroup C representative isolate 053442 and characterized 27 ST-4821 complex isolates which were isolated from different serogroups using comparative genomic hybridization (CGH) analysis. This paper provides important clues which are helpful to understand the genome composition and genetic background of different serogroups isolates, and possess significant meaning to the study of the newly emerged hyperinvasive lineage.
Keywords: comparative genomic hybridization

overall_design: To further understand the genome diversity of ST-4821 complex isolates, CGH analysis was employed to compare the genomic content of 053442 with those of 27 ST-4821 complex isolates which were isolated from 14 provinces of China during 1977–2005.

first: Li

last: Yang

first: Qi

last: Jin


title: Supress under 40 MPa 25 C

summary:
Hydrostatic pressure is one of the physical factors affecting cellular physiology. Hydrostatic pressure of a few hundred MPa decreases the viability of yeast cells, and pressure of a few tens MPa decreases the growth rate. To understand the effect of hydrostatic pressure, we employed yeast, Saccharomyces cerevisiae, DNA microarrays and analyzed genome-wide mRNA expression profiles under hydrostatic pressures. In this experiment, we selected a hydrostatic pressure of 40 MPa at 25 degrees C because the condition is not lethal for yeast cells but the growth was suppressed.
Keywords: stress response

overall_design: Series contains triplicate hybridization results from independent biological samples respectively. From 1st to 3th hybridization data have single scanned data, on the other hand, 4th data have high and low power scanned data.

first: Hisayo

last: Shimizu

first: Mine

last: Odani


title: Recovery from 30 MPa 25 C

summary:
Hydrostatic pressure is one of the physical factors affecting cellular physiology. Hydrostatic pressure of a few hundred MPa decreases the viability of yeast cells, and pressure of a few tens MPa decreases the growth rate. To understand the effect of hydrostatic pressure, we employed yeast, Saccharomyces cerevisiae, DNA microarrays and analyzed genome-wide mRNA expression profiles under hydrostatic pressures. In this experiment, we selected a hydrostatic pressure of 30 MPa at 25 degrees C because yeast cells are able to grow with this condition.
Keywords: stress response

overall_design: Series contains triplicate hybridization results from independent biological samples respectively. 1st and 2nd hybridization data have high and low power scanned data, respectively. On the other hand, 3rd hybridization has single scanned data.

first: Emi

last: Kojima


title: Recovery from freezing

summary:
Screening of genes that respond to cryopreservation stress using yeast DNA microarray.:
We studied the response of yeast cells after cryopreservation treatment using DNA microarray technology. Genes that contribute to "Cell rescue, defense and virulence," "energy," and "metabolism," were significantly induced. These genes were classified as encoding heat shock proteins, oxidative stress scavenger, and enzymes involved in glucose metabolism. The expression profile of mRNA after cryopreservation treatment was calculated to be closer to that following treatment with detergent or plant oils rather than by other stress factors such as heavy metals and agricultural chemicals. These results suggest that the cryopreservation treatment caused damage to the structure of the cell wall and cellular organelles. This was supported by the localization of the products of the induced genes at the cell wall and within cellular organelles.
Keywords: stress response

overall_design: Series contains triplicate hybridization in each time-point from independent biological samples respectively.


title: Sodium dodecyl sulfate treatment with 0.01% for 2 h

summary:
The number and type of synthetic chemicals that are being produced worldwide continues to increase significantly. While these industrial chemicals provide numerous benefits, there is no doubt that some have potential to damage the environment and health. Toxicity must be evaluated and use must be carefully controlled and monitored in order to minimize potential damage. DNA microarray technology has become an important new technique in toxicology. We are using the yeast Saccharomyces cerevisiae as a model organism for toxicological study because it is a simple, fast-growing eukaryote that has been thoroughly characterized. In order to evaluate toxicity by newly synthesized or mixture chemicals, toxicity-induced gene expression alteration profiles by known chemicals should be collected. In our study, cells need to be exposed with same experimental cellular condition, semi lethal (IC50), respectively. In the case of SDS (CAS; 151-21-3), the exposure dose was decided as 0.01% by growth curve with continuously diluted exposure. SDS is an anionic surfactant that is suspected to be gastrointestinal or liver toxicant.
//
Toxicity of anionic detergents determined by Saccharomyces cerevisiae microarray analysis:
Sodium n-dodecyl benzene sulfonate (LAS) and sodium dodecyl sulfate (SDS) are popular anionic detergents (surfactants) that are used worldwide and the toxicities of these chemicals have been characterized. We applied these chemicals in a DNA microarray bioassay and determined that the microarray data reflects previous findings and also provides some new information about anionic detergent toxicity. The mRNA expression profiles suggest that LAS and SDS cause damage to membranes and alterations in carbon metabolism, and induce the oxidative stress response. We also found that LAS and SDS induce the pleiotropic drug-resistance network, and that LAS and SDS may be pumped out of yeast cells by this network. Hierarchical clustering of the expression profiles showed that LAS and SDS cause similar features of toxicity and that the toxicity is similar to that of capsaicin but different from that of cadmium and mercury.
Keywords: stress response

overall_design: Series contains triplicate hybridization results from independent biological samples respectively.

first: Sophon

last: Sirisattha

first: Yuko

last: Momose


title: Transcriptional profiling of Loc1 knockout

status: Public on Nov 02 2007

city: Boston

first: Suzanne

last: Komili

state: MA

address: 44 Binney St.

country: USA

institute: Harvard University

summary:
Duplicated genes escape gene loss by conferring a dosage benefit or evolving diverged functions. The yeast Saccharomyces cerevisiae contains many duplicated genes encoding ribosomal proteins. Prior studies have suggested that these duplicated proteins are functionally redundant and affect cellular processes in proportion to their expression. In contrast, through studies of ASH1 mRNA in yeast, we demonstrate paralog-specific requirements for the translation of localized mRNAs. Intriguingly, these paralog-specific effects are limited to a distinct subset of duplicated ribosomal proteins. Moreover, transcriptional and phenotypic profiling of cells lacking specific ribosomal proteins reveals differences between the functional roles of ribosomal protein paralogs that extend beyond effects on mRNA localization. Finally, we show that ribosomal protein paralogs exhibit differential requirements for assembly and localization. Together, our data indicate complex specialization of ribosomal proteins for specific cellular processes, and support the existence of a ribosomal code.
Keywords: genetic modification

overall_design: Four biological replicates processed independently, two with each dye configuration

first: Natalie

middle: G

last: Farny

first: Frederick

middle: P

last: Roth

first: Pamela

middle: A

last: Silver


title: Vitamin E treatment for 2 h

first: Emiko

last: Kitagawa

summary:
The number and type of synthetic chemicals that are being produced worldwide continues to increase significantly. While these industrial chemicals provide numerous benefits, there is no doubt that some have potential to damage the environment and health. Toxicity must be evaluated and use must be carefully controlled and monitored in order to minimize potential damage. DNA microarray technology has become an important new technique in toxicology. We are using the yeast Saccharomyces cerevisiae as a model organism for toxicological study because it is a simple, fast-growing eukaryote that has been thoroughly characterized. In order to evaluate toxicity by newly synthesized or mixture chemicals, toxicity-induced gene expression alteration profiles by known chemicals should be collected. In our study, cells need to be exposed with same experimental cellular condition, semi lethal (IC50), respectively. Vitamin E (alpha-tocopherol) (CAS; 59-02-9) is a fat-soluble antioxidant.
Keywords: stress response


title: Gingerol treatment with 400 ppm for 2 h

summary:
The number and type of synthetic chemicals that are being produced worldwide continues to increase significantly. While these industrial chemicals provide numerous benefits, there is no doubt that some have potential to damage the environment and health. Toxicity must be evaluated and use must be carefully controlled and monitored in order to minimize potential damage. DNA microarray technology has become an important new technique in toxicology. We are using the yeast Saccharomyces cerevisiae as a model organism for toxicological study because it is a simple, fast-growing eukaryote that has been thoroughly characterized. In order to evaluate toxicity by newly synthesized or mixture chemicals, toxicity-induced gene expression alteration profiles by known chemicals should be collected. In our study, cells need to be exposed with same experimental cellular condition, semi lethal (IC50), respectively. In the case of gingerol (CAS; 23513-14-6), the exposure dose was decided as 400 ppm by growth curve with continuously diluted exposure. Gingerol is the active constituent of fresh ginger.
Keywords: stress response

first: Sakiko

last: Kurita


title: Capsaicin treatment with 250 ppm for 2 h

summary:
The number and type of synthetic chemicals that are being produced worldwide continues to increase significantly. While these industrial chemicals provide numerous benefits, there is no doubt that some have potential to damage the environment and health. Toxicity must be evaluated and use must be carefully controlled and monitored in order to minimize potential damage. DNA microarray technology has become an important new technique in toxicology. We are using the yeast Saccharomyces cerevisiae as a model organism for toxicological study because it is a simple, fast-growing eukaryote that has been thoroughly characterized. In order to evaluate toxicity by newly synthesized or mixture chemicals, toxicity-induced gene expression alteration profiles by known chemicals should be collected. In our study, cells need to be exposed with same experimental cellular condition, semi lethal (IC50), respectively. In the case of capsaicin (CAS; 404-86-4), the exposure dose was decided as 250 ppm by growth curve with continuously diluted exposure. Capsaicin, active component of chilli peppers, is an irritant for mammals, including humans, and produces a sensation of burning in any tissue with which it comes into contact.
//
Studies on the antimicrobial mechanisms of capsaicin using yeast DNA microarray:
Capsaicin is a pungent element in a variety of red peppers that are widely used as food additives and considered to be an antimicrobial factor. For our tests, we used yeast DNA micro-array methods to understand the mechanisms of inhibitory effects of capsaicin. The capsaicin treatment significantly induced 39 genes from approximately 6,000 genes. These induced genes were classified as multi-drug resistance transporter genes, membrane biosynthesis genes, genes encoding stress proteins, and uncharacterized genes. The growth abilities of the strains with the deletion of the induced genes suggest that capsaicin is pumped out of the yeast cells by the PDR5 transporter.
Keywords: stress response

first: Hitoshi

last: Iwahashi


title: Lindane treatment with 1.25 mM for 2 h

summary:
The number and type of synthetic chemicals that are being produced worldwide continues to increase significantly. While these industrial chemicals provide numerous benefits, there is no doubt that some have potential to damage the environment and health. Toxicity must be evaluated and use must be carefully controlled and monitored in order to minimize potential damage. DNA microarray technology has become an important new technique in toxicology. We are using the yeast Saccharomyces cerevisiae as a model organism for toxicological study because it is a simple, fast-growing eukaryote that has been thoroughly characterized. In order to evaluate toxicity by newly synthesized or mixture chemicals, toxicity-induced gene expression alteration profiles by known chemicals should be collected. In our study, cells need to be exposed with same experimental cellular condition, semi lethal (IC50), respectively. In the case of lindane (gamma-hexachlorocyclohexane) (CAS; 58-89-9), the exposure dose was decided as 2 ppm by growth curve with continuously diluted exposure. Lindane is a organochlorine pesticides that is recognized as a carcinogen and suspected to be cardiovascular or blood toxicant, developmental toxicant, endocrine toxicant, gastrointestinal or liver toxicant, immunotoxicant, kidney toxicant, neurotoxicant, reproductive toxicant, respiratory toxicant and skin or sense organ toxicant.
Keywords: stress response

first: Parveen

last: Meher


title: Fluazinam treatment with 1.5 uM for 2 h

summary:
The number and type of synthetic chemicals that are being produced worldwide continues to increase significantly. While these industrial chemicals provide numerous benefits, there is no doubt that some have potential to damage the environment and health. Toxicity must be evaluated and use must be carefully controlled and monitored in order to minimize potential damage. DNA microarray technology has become an important new technique in toxicology. We are using the yeast Saccharomyces cerevisiae as a model organism for toxicological study because it is a simple, fast-growing eukaryote that has been thoroughly characterized. In order to evaluate toxicity by newly synthesized or mixture chemicals, toxicity-induced gene expression alteration profiles by known chemicals should be collected. In our study, cells need to be exposed with same experimental cellular condition, semi lethal (IC50), respectively. In the case of fluazinam (CAS; 79622-59-6), the exposure dose was decided as 1.5 uM by growth curve with continuously diluted exposure. Fluazinam is a pesticide (fungicides) that is suspected to be immunotoxicant and skin or sense organ toxicant.
Keywords: stress response


title: 2-Aminobenzimidazole treatment with 5 mM for 2 h

summary:
The number and type of synthetic chemicals that are being produced worldwide continues to increase significantly. While these industrial chemicals provide numerous benefits, there is no doubt that some have potential to damage the environment and health. Toxicity must be evaluated and use must be carefully controlled and monitored in order to minimize potential damage. DNA microarray technology has become an important new technique in toxicology. We are using the yeast Saccharomyces cerevisiae as a model organism for toxicological study because it is a simple, fast-growing eukaryote that has been thoroughly characterized. In order to evaluate toxicity by newly synthesized or mixture chemicals, toxicity-induced gene expression alteration profiles by known chemicals should be collected. In our study, cells need to be exposed with same experimental cellular condition, semi lethal (IC50), respectively. In the case of 2-aminobenzimidazole (CAS; 934-32-7), the exposure dose was decided as 5 mM by growth curve with continuously diluted exposure. 2-Aminobenzimidazole is one of the hydrolyzed substrate from benomyl. Benomyl is a fungicide that has a selectively toxic to micro-organisms and to invertebrates, especially earthworms. Benomyl binds to microtubules, interfering with cell functions such as meiosis and intracellular transportation. The selective toxicity of benomyl as a fungicide is possibly due to its heightened effect on fungal rather than mammalian microtubules.
Keywords: stress response


title: Maneb treatment with 2 ppm for 2 h

summary:
The number and type of synthetic chemicals that are being produced worldwide continues to increase significantly. While these industrial chemicals provide numerous benefits, there is no doubt that some have potential to damage the environment and health. Toxicity must be evaluated and use must be carefully controlled and monitored in order to minimize potential damage. DNA microarray technology has become an important new technique in toxicology. We are using the yeast Saccharomyces cerevisiae as a model organism for toxicological study because it is a simple, fast-growing eukaryote that has been thoroughly characterized. In order to evaluate toxicity by newly synthesized or mixture chemicals, toxicity-induced gene expression alteration profiles by known chemicals should be collected. In our study, cells need to be exposed with same experimental cellular condition, semi lethal (IC50), respectively. In the case of maneb (CAS; 12427-38-2), the exposure dose was decided as 2 ppm by growth curve with continuously diluted exposure. Maneb is a pesticide (fungicides) that is recognized as a carcinogen and suspected to be developmental toxicant, endocrine toxicant, gastrointestinal or liver toxicant, immunotoxicant, neurotoxicant, reproductive toxicant and skin or sense organ toxicant.
Keywords: stress response


title: TPN treatment with 10 uM for 2 h

summary:
The number and type of synthetic chemicals that are being produced worldwide continues to increase significantly. While these industrial chemicals provide numerous benefits, there is no doubt that some have potential to damage the environment and health. Toxicity must be evaluated and use must be carefully controlled and monitored in order to minimize potential damage. DNA microarray technology has become an important new technique in toxicology. We are using the yeast Saccharomyces cerevisiae as a model organism for toxicological study because it is a simple, fast-growing eukaryote that has been thoroughly characterized. In order to evaluate toxicity by newly synthesized or mixture chemicals, toxicity-induced gene expression alteration profiles by known chemicals should be collected. In our study, cells need to be exposed with same experimental cellular condition, semi lethal (IC50), respectively. In the case of TPN (chlorothalonil) (CAS; 1897-45-6), the exposure dose was decided as 10 uM by growth curve with continuously diluted exposure. TPN is a pesticide (fungicides) that is recognized as a carcinogen and suspected to be immunotoxicant, neurotoxicant , respiratory toxicant and skin or sense organ toxicant.
Keywords: stress response


title: Dimethylsulfoxide treatment with 10 % for 2 h

summary:
The number and type of synthetic chemicals that are being produced worldwide continues to increase significantly. While these industrial chemicals provide numerous benefits, there is no doubt that some have potential to damage the environment and health. Toxicity must be evaluated and use must be carefully controlled and monitored in order to minimize potential damage. DNA microarray technology has become an important new technique in toxicology. We are using the yeast Saccharomyces cerevisiae as a model organism for toxicological study because it is a simple, fast-growing eukaryote that has been thoroughly characterized. In order to evaluate toxicity by newly synthesized or mixture chemicals, toxicity-induced gene expression alteration profiles by known chemicals should be collected. In our study, cells need to be exposed with same experimental cellular condition, semi lethal (IC50), respectively. In the case of Dimethylsulfoxide (DMSO) (CAS; 67-68-5), the exposure dose was decided as 10 % by growth curve with continuously diluted exposure.

Me2SO (DMSO) is a polar solvent that is widely used in biochemistry, pharmacology, and industry. Although there are several reports in the literature concerning the biological effects of Me2SO, the total cellular response remains unclear. In this paper, DNA microarray technology combined with the hierarchical clustering bioinformatics tool was used to assess the effects of Me2SO on yeast cells. We found that yeast exposed to Me2SO increased phospholipid biosynthesis through up-regulated gene expression. It was confirmed by Northern blotting that the level of INO1 and OPI3 gene transcripts, encoding key enzymes in phospholipid biosynthesis, were significantly elevated following treatment with Me2SO. Furthermore, the phospholipid content of the cells increased during exposure to Me2SO as shown by conspicuous incorporation of a lipophilic fluorescent dye (3,3'-dihexyloxacarbocyanine iodide) into the cell membranes. From these results we propose that Me2SO treatment induces membrane proliferation in yeast cells to alleviate the adverse affects of this chemical on membrane integrity.
Keywords: stress response

first: Yoshinori

last: Murata


title: Cycloheximide treatment with 15 uM for 2 h

summary:
The number and type of synthetic chemicals that are being produced worldwide continues to increase significantly. While these industrial chemicals provide numerous benefits, there is no doubt that some have potential to damage the environment and health. Toxicity must be evaluated and use must be carefully controlled and monitored in order to minimize potential damage. DNA microarray technology has become an important new technique in toxicology. We are using the yeast Saccharomyces cerevisiae as a model organism for toxicological study because it is a simple, fast-growing eukaryote that has been thoroughly characterized. In order to evaluate toxicity by newly synthesized or mixture chemicals, toxicity-induced gene expression alteration profiles by known chemicals should be collected. In our study, cells need to be exposed with same experimental cellular condition, semi lethal (IC50), respectively. In the case of cycloheximide (CAS; 66-81-9), the exposure dose was decided as 15 uM by growth curve with continuously diluted exposure. Cycloheximide is an inhibitor of protein biosynthesis in eukaryotic organisms that is recognized as a developmental toxicant and suspected to be a kidney toxicant.
Keywords: stress response


title: Thiuram treatment with 75 uM for 2 h

summary:
The number and type of synthetic chemicals that are being produced worldwide continues to increase significantly. While these industrial chemicals provide numerous benefits, there is no doubt that some have potential to damage the environment and health. Toxicity must be evaluated and use must be carefully controlled and monitored in order to minimize potential damage. DNA microarray technology has become an important new technique in toxicology. We are using the yeast Saccharomyces cerevisiae as a model organism for toxicological study because it is a simple, fast-growing eukaryote that has been thoroughly characterized. In order to evaluate toxicity by newly synthesized or mixture chemicals, toxicity-induced gene expression alteration profiles by known chemicals should be collected. In our study, cells need to be exposed with same experimental cellular condition, semi lethal (IC50), respectively. In the case of thiuram (CAS; 137-26-8), the exposure dose was decided as 75 uM by growth curve with continuously diluted exposure. Thiuram is a pesticide (fungicides) that is suspected to be cardiovascular or blood toxicant, developmental toxicant, endocrine toxicant, gastrointestinal or liver toxicant, immunotoxicant, neurotoxicant, respiratory toxicant and skin or sense organ toxicant.
Keywords: stress response


title: Recovery from 40 or 180 MPa 4C

summary:
Piezophysiology of genome wide gene expression levels in the yeast Saccharomyces cerevisiae:
Hydrostatic pressure is one of the physical factors affecting cellular physiology. Hydrostatic pressure of a few hundred MPa decreases the viability of yeast cells, and pressure of a few tens MPa decreases the growth rate. To understand the effect of hydrostatic pressure, we employed yeast DNA microarrays and analyzed genome-wide gene-expression levels after the pressure treatment with 180 MPa (immediate) at 4 degrees C and recovery incubation for 1 h and 40 MPa (16 h) at 4 degrees C and recovery incubation for 1 h. The transcription of genes involved in energy metabolism, cell defense, and protein metabolism was significantly induced by the pressure treatment. Genome-wide expression profiles suggested that high pressure caused damage to cellular organelles, since the induced gene products were localized in the membrane structure and/or cellular organelles. Hierarchical clustering analysis suggested that the damage caused by the pressure was similar to that caused by detergents, oils, and freezing/thawing. We also estimated the contribution of induced genes to barotolerance using some strains that have the deletion in the corresponding genes.
Keywords: stress response

overall_design: In the experiment that used 40 MPa, triplicate hybridization from independent biological samples were done, respectively. In the experiment that used 180 MPa, hybridization result was obtained from 5 independent biological samples, respectively. 5th data in 180 MPa have high and low power scanned data, on the other hand, others have single scanned data, respectively.


title: Zineb treatment with 2 ppm for 2 h

summary:
The number and type of synthetic chemicals that are being produced worldwide continues to increase significantly. While these industrial chemicals provide numerous benefits, there is no doubt that some have potential to damage the environment and health. Toxicity must be evaluated and use must be carefully controlled and monitored in order to minimize potential damage. DNA microarray technology has become an important new technique in toxicology. We are using the yeast Saccharomyces cerevisiae as a model organism for toxicological study because it is a simple, fast-growing eukaryote that has been thoroughly characterized. In order to evaluate toxicity by newly synthesized or mixture chemicals, toxicity-induced gene expression alteration profiles by known chemicals should be collected. In our study, cells need to be exposed with same experimental cellular condition, semi lethal (IC50), respectively. In the case of zineb (CAS; 12122-67-7), the exposure dose was decided as 2 ppm by growth curve with continuously diluted exposure. Zineb is a pesticide (fungicides) that is suspected to be endocrine toxicant, gastrointestinal or liver toxicant, immunotoxicant, neurotoxicant, reproductive toxicant and skin or sense organ toxicant.
Keywords: stress response


title: Nitrophenol (m-nitrophenol) treatment with 5 mM for 2 h

summary:
The number and type of synthetic chemicals that are being produced worldwide continues to increase significantly. While these industrial chemicals provide numerous benefits, there is no doubt that some have potential to damage the environment and health. Toxicity must be evaluated and use must be carefully controlled and monitored in order to minimize potential damage. DNA microarray technology has become an important new technique in toxicology. We are using the yeast Saccharomyces cerevisiae as a model organism for toxicological study because it is a simple, fast-growing eukaryote that has been thoroughly characterized. In order to evaluate toxicity by newly synthesized or mixture chemicals, toxicity-induced gene expression alteration profiles by known chemicals should be collected. In our study, cells need to be exposed with same experimental cellular condition, semi lethal (IC50), respectively. In the case of m-nitrophenol (CAS; 554-84-7), the exposure dose was decided as 5 mM by growth curve with continuously diluted exposure. m-Nitrophenol is one of the nitrogen compounds.
Keywords: stress response

first: Hyun-Ju

last: Kim


title: Nitrophenol (o-nitrophenol) treatment with 3 mM for 2 h

summary:
The number and type of synthetic chemicals that are being produced worldwide continues to increase significantly. While these industrial chemicals provide numerous benefits, there is no doubt that some have potential to damage the environment and health. Toxicity must be evaluated and use must be carefully controlled and monitored in order to minimize potential damage. DNA microarray technology has become an important new technique in toxicology. We are using the yeast Saccharomyces cerevisiae as a model organism for toxicological study because it is a simple, fast-growing eukaryote that has been thoroughly characterized. In order to evaluate toxicity by newly synthesized or mixture chemicals, toxicity-induced gene expression alteration profiles by known chemicals should be collected. In our study, cells need to be exposed with same experimental cellular condition, semi lethal (IC50), respectively. In the case of o-nitrophenol (CAS; 88-75-5), the exposure dose was decided as 3 mM by growth curve with continuously diluted exposure. o-Nitrophenol is one of the nitrogen compounds, and 2-nitrophenol is reported to be less toxic than 4-. This substrate is suspected to be cardiovascular or blood toxicant, neurotoxicant.
Keywords: stress response


title: Tetrachloroethylene treatment with 3.3 mM for 2 h

summary:
The number and type of synthetic chemicals that are being produced worldwide continues to increase significantly. While these industrial chemicals provide numerous benefits, there is no doubt that some have potential to damage the environment and health. Toxicity must be evaluated and use must be carefully controlled and monitored in order to minimize potential damage. DNA microarray technology has become an important new technique in toxicology. We are using the yeast Saccharomyces cerevisiae as a model organism for toxicological study because it is a simple, fast-growing eukaryote that has been thoroughly characterized. In order to evaluate toxicity by newly synthesized or mixture chemicals, toxicity-induced gene expression alteration profiles by known chemicals should be collected. In our study, cells need to be exposed with same experimental cellular condition, semi lethal (IC50), respectively. In the case of tetrachloroethylene (CAS; 127-18-4), the exposure dose was decided as 3.3 mM by growth curve with continuously diluted exposure. Tetrachloroethylene is a manufactured chemical compound that is widely used for the dry cleaning of fabrics and for metal-degreasing. This substrate is recognized as a carcinogen and suspected to be developmental toxicant, gastrointestinal or liver toxicant, kidney toxicant, neurotoxicant, reproductive toxicant, respiratory toxicant and skin or sense organ toxicant.
Keywords: stress response

first: Yoshiteru

last: Suzuki


title: Agricultural fungicides to gene expression in Saccharomyces cerevisiae upon exposure to toxic doses

summary:
Correlations between the chemical structures of agricultural fungicides and mRNA expression levels following exposure of Saccharomyces cerevisiae to toxic doses of thiuram, zineb, maneb, TPN, and PCP were examined. Structurally, thiuram, zineb, and maneb are dithiocarbamate fungicides, whereas TPN and PCP are not. To characterize chemical toxicity, genes expression was classified according to the functional groups used by the MIPS database. However, no correlations between the classification scheme and chemical structures were found. Hierarchical clustering of gene expression profiles was performed to characterize the effects of the five chemicals. According to this analysis the similarity of gene expression profiles depended on the similarity of chemical structures. These results suggest that DNA microarray technology has potential for predicting the major chemicals which will cause environmental toxicity and will provide information on new biomonitoring methods.

Keywords: stress response

overall_design: This series contains 5 kinds of chemical-induced gene expression profiles. Triplicates hybridization was done in each chemical exposure condition. All biological samples were collected independently.


title: Global Transcriptional Analysis of Mycoplasma hyopneumoniae Following Exposure to Hydrogen Peroxide

city: Ames

first: Chris

last: Minion

state: IA

address: 1130 Vet Med

department: VMPM

institute: Iowa State University

summary:
Mycoplasma hyopneumoniae, the causative agent of swine enzootic pneumonia, colonizes the cilia of swine lungs, causing ciliostasis and cell death. Mycoplasma hyopneumoniae is a component of the porcine respiratory disease complex (PRDC) and is especially problematic for the finishing swine industry, causing the loss of hundreds of millions of dollars in farm revenues worldwide. For successful infection, M. hyopneumoniae must effectively resist oxidative stresses due to the release of oxidative compounds from neutrophils and macrophages during the host’s immune response. However, the mechanism M. hyopneumoniae uses to avert the host response is still unclear. To gain a better understanding of the transcriptional responses of M. hyopneumoniae under oxidative stress, cultures were grown to early exponential phase and exposed to 0.5% percent hydrogen peroxide for 15 minutes. RNA samples from these cultures were collected and compared to RNA samples from control cultures using two-color PCR-based M. hyopneumoniae microarrays. This study revealed significant down-regulation of important glycolytic pathway genes and gene transcription proteins, as well as a protein known to activate oxidative stressor cascades in neutrophils. This study has also contained significantly differentially expressed genes common to other environmental stress responses, and merits further study of universal stress response genes of M. hyopneumoniae.
Keywords: Mycoplasma hyopneumoniae, RNA microarray

overall_design: Six independent RNA samples from hydrogen peroxide-exposed cultures were paired with six independent RNA samples from control cultures for hybridization to six two-color microarrays. For three arrays, the control RNA sample was labeled with Cy3 dye and the experimental RNA sample was labeled with Cy5 dye, the dyes were reversed for the other three arrays to account for any possible dye bias.

first: Erin

middle: R

last: Schafer

first: Michael

middle: J

last: Oneal

first: Melissa

middle: L

last: Madsen

first: F

middle: C


title: Pentachlorophenol treatment with 50 uM for 2 h

summary:
The number and type of synthetic chemicals that are being produced worldwide continues to increase significantly. While these industrial chemicals provide numerous benefits, there is no doubt that some have potential to damage the environment and health. Toxicity must be evaluated and use must be carefully controlled and monitored in order to minimize potential damage. DNA microarray technology has become an important new technique in toxicology. We are using the yeast Saccharomyces cerevisiae as a model organism for toxicological study because it is a simple, fast-growing eukaryote that has been thoroughly characterized. In order to evaluate toxicity by newly synthesized or mixture chemicals, toxicity-induced gene expression alteration profiles by known chemicals should be collected. In our study, cells need to be exposed with same experimental cellular condition, semi lethal (IC50), respectively. In the case of pentachlorophenol (CAS; 87-86-5), the exposure dose was decided as 50 uM by growth curve with continuously diluted exposure. Pentachlorophenol is a pesticide (fungicides) that is recognized as a carcinogen and suspected to be cardiovascular or blood toxicant, developmental toxicant, endocrine toxicant, gastrointestinal or liver toxicant, immunotoxicant, kidney toxicant, neurotoxicant, reproductive toxicant, respiratory toxicant and skin or sense organ toxicant.
Keywords: stress response


title: Design and testing of genome-proxy microarrays to profile marine microbial communities

status: Public on Oct 31 2007

city: Tucson

first: Virginia

middle: Isabel

last: Rich

state: AZ

address: 1041 E. Lowell St.

institute: University of Arizona

summary:
Microarrays are useful tools for detecting and quantifying specific functional and phylogenetic genes in natural microbial communities. In order to track uncultivated microbial genotypes and their close relatives in an environmental context, we designed and implemented a “genome proxy” microarray that targets microbial genome fragments recovered directly from the environment. Fragments consisted of sequenced clones from large-insert genomic libraries from microbial communities in Monterey Bay, the Hawaii Ocean Time-series station ALOHA, and Antarctic coastal waters. In a prototype array, we designed probe sets to thirteen of the sequenced genome fragments and to genomic regions of the cultivated cyanobacterium Prochlorococcus MED4. Each probe set consisted of multiple 70-mers, each targeting an individual ORF, and distributed along each ~40-160kbp contiguous genomic region. The targeted organisms or clones, and close relatives, were hybridized to the array both as pure DNA mixtures and as additions of cells to a background of coastal seawater. This prototype array correctly identified the presence or absence of the target organisms and their relatives in laboratory mixes, with negligible cross-hybridization to organisms having ≤~75% genomic identity. In addition, the array correctly identified target cells added to a background of environmental DNA, with a limit of detection of ~0.1% of the community, corresponding to ~10^3 cells/ml in these samples. Signal correlated to cell concentration with an R2 of 1.0 across six orders of magnitude. In addition the array could track a related strain (at 86% genomic identity to that targeted) with a linearity of R2=0.9999 and a limit of detection of ~1% of the community. Closely related genotypes were distinguishable by differing hybridization patterns across each probe set. This array’s multiple-probe, “genome-proxy” approach and consequent ability to track both target genotypes and their close relatives is important for the array’s environmental application given the recent discoveries of considerable intra-population diversity within marine microbial communities.
Keywords: target addition experiment, proof-of-concept for GPL6012

sample_organism: Prochlorococcus marinus subsp. pastoris str. CCMP1986

platform_organism: uncultured marine gamma proteobacterium EBAC31A08

platform_organism: uncultured marine group II euryarchaeote 37F11

platform_organism: uncultured gamma proteobacterium eBACHOT4E07

platform_organism: uncultured marine group II euryarchaeote EF100_57A08

overall_design:
***Overall Array design***

The prototype microarray targeted thirteen BAC or fosmid genome fragments (20-160kb) from both bacteria and archaea, recovered from a variety of marine habitats, as well as the cyanobacterium Prochlorococcus MED4. These clones were originally sequenced because of the presence of taxonomic marker or specific functional genes. This array consisted of sets of 70-bp oligonucleotides targeting each genome or genome fragment (Fig. 1), dispersed along the target sequences with no more than one probe per gene, and excluding rRNA genes as targets. The probes were selected solely based on theoretical thermodynamic properties and GC content (~40%); that is, probe selection did not focus on specific genes or regions, but simply produced the “optimal” probes for each genome proxy based on the probes’ predicted hybridization properties. rRNA genes were excluded, because this probe design approach, which avoids sequence alignments and considerations of RNA secondary structure, would be unlikely to result in useful rRNA probes. Furthermore, rRNA probes of traditional design could not be included on the array because their appropriate hybridization conditions would be very different from those of this array’s probes.

***Microarray probe design***

Microarray 70-mer probes were designed using the program ArrayOligoSelector (Zhu et al., 2003) with the following settings: target %GC = 40%, 1 probe/gene, with the ORFs for each genome fragment as both the input and the database file. The output candidate 70mers were then sorted based on their %GC and those closest to 40% were chosen. In the case of more than the target number of probes having 40%GC, the subset with the lowest free energy of hybridization were selected as probes. Generally, 20 probes were selected per organism. Prochlorococcus MED4 was represented by 60 probes total, 20 each for three different 80kb “genome-proxy” regions: 0-80kb, 1.29-1.37Mbp, and 1.58 to 1.66Mbp.

Using the same method, a set (n=20) of positive control probes were designed to the genome of the halophillic archaeon Halobacterium salinarum NRC-1. Negative control probes (n=28) were designed to a set of 49 random 1000-base sequences (Stothard, 2000).

***Microarray construction and hybridization***

Oligonucleotides were synthesized (Illumina, San Diego, California), suspended in 3XSSC to a concentration of 40pmol/μl, and spotted on homemade poly-L-lysine-coated glass slides using a QArray 2 microarraying robot (Genetix, Hampshire, England). Six replicates of each probe were spotted.

***Microarray data analysis***

Hybridized arrays were scanned using an Axon Instruments 4000B scanner (Foster City, CA) and the data was normalized and filtered using perl scripts written for the purpose, by the following steps. (1) Signal intensities for each spot were calculated by subtracting the local background (mean F532 – median B532, as calculated by GenePix Pro 5.1 software, Axon Instruments). (2) The median value across replicates was calculated for each probe. (3) For each probe set, the number of probes greater than twice the mean negative control signal was calculated, before further processing. (4) Filter I: Arrays with less than half their positive control probes exceeding twice the mean negative control signal were considered poor quality, low dynamic range, arrays and were excluded from further analysis. (5) Each probe signal was corrected for non-specific binding by subtracting the mean negative control spot signal. (6) The data was then normalized for array-to-array variations in brightness by dividing each probe signal by the mean positive control signal. This positive control signal was the mean signal across the Halobacterium salinarum probes in each hybridization, with identical amounts of H. salinarum DNA having been added to each reaction prior to amplification and labeling. (7) Filter II: In order for a genotype to be considered “present”, at least 45% of its probes had to exceed twice the mean negative control signal. (8) Finally, each genotype signal was calculated as either the MEAN or TUKEY BIWEIGHT across its probe set.

***Experimental Design***

The array was hybridized to laboratory mixtures of cloned environmental genomic DNA targeted by the array, in varying ratios. The use of multiple probes to target many genes from each organism helped to normalize probe-to-probe heterogeneity, by averaging across all probes in a set (as described below). The evenness of probe response across each genotype’s set was also used to evaluate the relatedness of hybridizing DNA.

To more precisely define the array’s phylogenetic range and specificity, it was tested against DNA from Prochlorococcus MED4 and related strains, spanning the known range of Prochlorococcus phylogenetic diversity.

To test the effects of hybridization stringency on the specificity and signal of the MED4 probes, Prochlorococcus strains were hybridized at a range of conditions.

To test whether the specificity results for Prochlorococcus were comparable for other targeted clades, two genome fragments recovered from closely related phylotypes within the SAR86 clade of the gamma-proteobacteria were represented on the array, and were tested for specificity.

To understand the equivalence of probe sets targeting different regions of the same organism’s genome, we targeted three 80kb “genome proxy” regions of the Prochlorococcus MED4 genome. One of the regions fell in a genomic “island” where inter-strain variability is concentrated (“ISL5” in Coleman et al., 2006).

To test the array in a complex environmental context, we collected coastal seawater (lacking detectable Prochlorococcus cells by flow cytometry) and added Prochlorococcus cells from strains MED4, MIT9515, MIT9312 and MIT9313 over a range of concentrations from ~101 – 106 cells/ml (Fig. 3). The seawater was then filtered and the DNA extracted, amplified, labeled, and hybridized to the array.

middle: I

first: Konstantinos

last: Konstantinidis

first: Edward

middle: F

last: DeLong


title: Nitrophenol (p-nitrophenol) treatment with 1.5 mM for 2 h

summary:
The number and type of synthetic chemicals that are being produced worldwide continues to increase significantly. While these industrial chemicals provide numerous benefits, there is no doubt that some have potential to damage the environment and health. Toxicity must be evaluated and use must be carefully controlled and monitored in order to minimize potential damage. DNA microarray technology has become an important new technique in toxicology. We are using the yeast Saccharomyces cerevisiae as a model organism for toxicological study because it is a simple, fast-growing eukaryote that has been thoroughly characterized. In order to evaluate toxicity by newly synthesized or mixture chemicals, toxicity-induced gene expression alteration profiles by known chemicals should be collected. In our study, cells need to be exposed with same experimental cellular condition, semi lethal (IC50), respectively. In the case of p-nitrophenol (CAS; 100-02-7), the exposure dose was decided as 1.5 mM by growth curve with continuously diluted exposure. p-Nitrophenol is one of the nitrogen compounds, and 4-nitrophenol is reported to be more toxic than 2-. This substrate is reported to cause methemoglobinemia and suspected to be cardiovascular or blood toxicant, neurotoxicant, skin or sense organ toxicant.
Keywords: stress response


title: Gene expression profiles by 3 types of nitrophenol isomers

summary:
The number and type of synthetic chemicals that are being produced worldwide continues to increase significantly. While these industrial chemicals provide numerous benefits, there is no doubt that some have potential to damage the environment and health. Toxicity must be evaluated and use must be carefully controlled and monitored in order to minimize potential damage. DNA microarray technology has become an important new technique in toxicology. We are using the yeast Saccharomyces cerevisiae as a model organism for toxicological study because it is a simple, fast-growing eukaryote that has been thoroughly characterized. In order to evaluate toxicity by newly synthesized or mixture chemicals, toxicity-induced gene expression alteration profiles by known chemicals should be collected.
Nitrophenols belong to the family of nitro compounds. There are three isomers, depending upon position of the functional groups at the aromatic ring: o- (CAS; 88-75-5), m- (CAS; 554-84-7) and p- (CAS; 100-02-7). It was reported that 4-nitrophenol is reported to be more toxic than 2- in animal test. In our yeast result, IC50 of o-, m- and p-nitrophenol was 3 mM, 5 mM, 1.5 mM, respectively, indicating highest toxic isomer was p-. p-Nitrophenol is reported to cause methemoglobinemia, and all isomers are suspected to be cardiovascular or blood toxicant, neurotoxicant.
Keywords: stress response

overall_design: Each chemical exposure was done with 3 hybridization results from independent biological samples, and each experiment have high and low power scanned data respectively.


title: Lon Protease Promotes Survival of Escherichia coli During Anaerobic Glucose Starvation

city: Bethesda

first: Timothy

last: Myers

state: MD

address: 50 South Drive, Room 5509

department: Research Technologies Branch

institute: National Institute of Allergy and Infectious Diseases

summary:
In Escherichia coli, Lon is an ATP-dependent protease which degrades misfolded proteins and certain rapidly-degraded regulatory proteins. Given that oxidatively damaged proteins are generally degraded rather than repaired, we anticipated that Lon deficient cells would exhibit decreased viability during aerobic, but not anaerobic, carbon starvation.  We found that the opposite actually occurs.  Wild-type and Lon deficient cells survived equally well under aerobic conditions, but Lon deficient cells died more rapidly than the wild-type under anaerobiosis.  Microarray analysis revealed that genes of the Clp family of ATP-dependent proteases were induced during aerobic growth but not during anaerobic growth.  Thus, Clp may compensate for loss of Lon when cells are in an oxygen containing atmosphere.  Under anaerobic carbon starvation conditions, Lon must be active to support survival.
Keywords: Other

overall_design:
Three aliquots of isolated total RNA, drawn from one of four cultures containing 3E+9 cells, were each divided in half. The first half was labeled with Cy5 and the second half was added to a reference pool of RNA. The reference pool, containing an equal amount of RNA from each pooled culture sample, was labeled with Cy3. Triplicate samples yielded three expression measurements per gene for each experimental condition. Five arrays of lower quality, as determined by within-group correlation of log(base 2) ratio (cy5/cy3) measurements of all array features, were excluded from further analysis. Data from the remaining nineteen arrays were grouped as follows:
Group A: day 1, anaerobic, lon(+) (wild-type)
Group B: day 1, anaerobic, lon(-)
Group C: day 1, aerobic, lon(+)
Group D: day 1, aerobic, lon(-)
Group E: day 3, anaerobic, lon(+)
Group F: day 3, anaerobic, lon(-)
Group G: day 3, aerobic, lon(+)
Group H: day 3, aerobic, lon(-).

first: Shen

last: Luo

first: Megan

last: McNeill

first: Robert

last: Hohman

first: Rodney

last: Levine


title: Short RNA profiling of ES cells with and without Dicer

city: Cambridge

first: J. Mauro

last: Calabrese

address: 40 Ames Street

department: Biology

institute: MIT

type: Expression profiling by high throughput sequencing

summary:
To better understand Dicer function, and the potential mechanisms by which RNAi contributes to pluripotency, short RNA expression was profiled from 4 ES cell libraries: 2 made from a Dicer-conditional ES cell line before and several months after deletion of Dicer, and 2 made before and 5 days after demethylation of J1 ES cells with 5-aza-deoxycytidine.  Contributed here are the unannotated sequence data from each library, including those sequences that did not match the mouse genome or any known non-coding RNAs.
Keywords: 454 sequencing, miRNA, dicer, demethylation

overall_design: cDNA libraries were made as described in Neilson et al. Genes and Development, 2007 Mar 1;21(5):578-89.

first: J

first: A

last: Seila

first: G

middle: W

last: Yeo

first: P

last: Sharp


title: Genome-wide transcriptional changes in Streptococcus gordonii in response to competence signaling peptide

status: Public on Oct 30 2007

city: Buffalo

first: M

last: Vickerman

state: NY

address: 3435 Main St.

department: Oral Biology

institute: University at Buffalo

summary:
Streptococcus gordonii is a primary colonizer of the multispecies biofilm on tooth surfaces forming dental plaque, and a potential agent of endocarditis.  The recent completion of the genome sequence of the naturally competent strain Challis allowed the design of a spotted oligonucleotide microarray to examine a genome-wide response of this organism to environmental signals.  Based on temporal responses to synthetic competence signaling peptide (CSP) as indicated by transformation frequencies, the S. gordonii transcriptome was monitored at increments after CSP exposure.  Microarray analysis identified 35 candidate early genes and 127 candidate late genes that were up-regulated at 5 and 15 minutes, respectively; these genes were often grouped in clusters.  Findings supported published literature on the S. gordonii competence response, with up-regulation of most, but not all, genes that have been reported to affect this species' transformation frequencies.  The CSP-induced transcriptomes of S. gordonii were compared to those of published S. pneumoniae strains.  Both conserved and species-specific genes were identified.  Putative intergenic regulatory sites such as the conserved combox sequence thought to be a binding site for competence sigma factor, were found preceding S. gordonii late responsive genes.  In contrast, S. gordonii early CSP-responsive genes were not preceded by S. pneumoniae conserved direct repeats.  These studies provide the first insights into a genome-wide transcriptional response of an oral commensal organism.  They offer an extensive analysis of transcriptional changes that accompany competence in S. gordonii and form a basis for future intra- and inter-species comparative analyses of this ecologically important phenotype.
Keywords: gene expression design

overall_design: 6 samples were analyzed.  The quality controls were biological replicate and technical replicate

last: Jesionowski

first: S

last: Iobst

last: Gill


title: NFkB in multiple myeloma - EJM IkBa super-repressor

status: Public on Oct 29 2007

first: Christina

last: Annunziata

address: 10 Center Drive

department: Metabolism Branch

institute: Center for Cancer Research

summary:
Mechanisms of constitutive NF-kappaB signaling in multiple myeloma are unknown. An inhibitor of IkappaB kinase beta (IKKbeta), targeting the classical NF-kappaB pathway, was lethal to many myeloma cell lines. Several had elevated expression of NIK due to genomic alterations or enhanced protein stability while others had inactivating mutations or deletion of TRAF3. Both abnormalities triggered the classical and alternative NF-kappaB pathways. A majority of primary myeloma patient samples and cell lines had elevated NF-kappaB target gene expression, often associated with genetic and epigenetic alteration of NIK, TRAF3, CYLD, BIRC2/BIRC3, CD40, NFKB1, and NFKB2. These genetic and functional data demonstrate that addiction to the NF-kappaB pathway is a frequent feature of myeloma and suggest that IKKbeta inhibitors hold promise for the treatment of this disease.
Keywords: time series design

overall_design: EJM cells were treated with doxycycline to induce the IkappaBalpha super-repressor for 1-4 days. A total of 4 samples were analyzed in comparison to uninduced cells.


title: Recurrent DNA copy number variation in the laboratory mouse

status: Public on Oct 28 2007

city: Cold Spring Harbor

first: Ira

last: Hall

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

type: Genome variation profiling by genome tiling array

summary:
We have conducted a genome-wide analysis of spontaneous copy number variation (CNV) in the laboratory mouse. We used high resolution microarrays to identify 38 CNVs between 14 colonies of the C57BL/6 strain spanning ~967 generations of inbreeding, and examined these loci in 12 additional strains.  It is clear from our results that many CNVs arise through a highly non-random process: 18 of 38 were the product of recurrent mutation, and rates of change vary roughly four orders of magnitude across different loci. These recurrent CNVs are distributed throughout the genome, affect 43 genes, and fluctuate in copy number over mere hundreds of generations, observations that raise questions about their contribution to natural variation.
Keywords: comparative genomic hybridization, DNA copy number variation, structural variation, inbred mice, spontaneous mutation rate

overall_design: IIn order to verify, precisely map, and accurately score spontaneous copy number mutations identified by our previous analysis using representational oligonucleotide microarray analysis (ROMA, see related submission), we performed comparative genome hybridization (CGH) for each strain using high resolution oligonucleotide microarrays (tiling arrays).  These arrays contain 385,213 probes placed at high density (~1 per 46 bp) across each locus identified by ROMA.  We performed at least two independent experiments for each of 25 strains, each compared to a single pedigreed individual of the C57BL6/J strain.

first: Chris

last: Egan

first: Srinath

last: Sridhar

first: Michael

last: Wigler


title: NFkB in multiple myeloma - L363 IKK inhibitor

overall_design: L363 cells were treated with IKKb inhibitor MLN120b for 8h, 12h, 24h. Three timecourses, a total of 8 samples, were analyzed in comparison to cells treated with DMSO (solvent) alone.


title: Gene expression level during L-threonine production

status: Public on Oct 26 2007

city: Daejeon

first: Sang Yup

last: Lee

address: Dept. of Chemical & Biomolecular Engineering, KAIST, 373-1 Guseong-dong, Yuseong-gu

country: South Korea

institute: KAIST

summary:
The comparative transcriptome profiling of L-threonine producing strain (TH07 strain harboring pBRThrABC) and control W3110 (lacI-deleted) strain harboring pKK223-3 has been analyzed using oligo nucleotide microarray.
Keywords: comparative transcriptome analysis (between L-threonine producing strain and the control strain)

overall_design: Samples for transcriptome profiling were taken at the OD600 of 5.13 (TH07 harboring pBRThrABC) and 5.21 (control strain), replicate = 2


title: NIA15k screen.  Pax5 +/+, Pax5 -/-, and Rag1-/- pro B cell lines.

city: Parkville

first: Stephen

last: Nutt

state: Vic

address: 1G Royal Pde

department: Molecular Medicine

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

summary:
The transcription factor Pax5 is essential for B cell commitment in the mouse, where it represses lineage-inappropriate gene expression, while simultaneously activating the B cell gene expression program. We have performed a global gene expression screen of wild type and Pax5-deficient pro-B cells in an attempt to identify the crucial Pax5 targets in early B-lymphopoiesis. We have also included Rag1-/- and wild type (+/+) proB cells starved of the cytokine IL-7 for 4 hours as controls. Rag1-/- proB cells are incapable of further differentiation due to an absence of immunoglobulin recombination and IL-7 is the major cytokine regulating proB cell growth.
Keywords: comparison of genetically modified cell-lines

overall_design: Twelve arrays were used to compare a single Pax5+/+ proB cell line grown in the presence or abscence of IL-7 for 4 hours.  3 independently derived Pax5-/- proB cells lines and a single Rag1-/- pro B cell line were also analysed. cDNA were hybridised  in a saturated loop design using dye swaps for each comparison, such that all samples were compared twice.

first: Clare

last: Pridans

first: Melissa

last: Holmes

first: Matthew

last: Polli

first: James

last: Wettenhall

first: Aleksandar

last: Dakic

first: Lynn

last: Corcoran

first: Gordon

middle: K

last: Smyth


title: Iodine treatment (dose-response, time course)

first: Emiko

last: Kitagawa

summary:
The number and type of synthetic chemicals that are being produced worldwide continues to increase significantly. While these industrial chemicals provide numerous benefits, there is no doubt that some have potential to damage the environment and health. Toxicity must be evaluated and use must be carefully controlled and monitored in order to minimize potential damage. DNA microarray technology has become an important new technique in toxicology. We are using the yeast Saccharomyces cerevisiae as a model organism for toxicological study because it is a simple, fast-growing eukaryote that has been thoroughly characterized. In order to evaluate toxicity by newly synthesized or mixture chemicals, toxicity-induced gene expression alteration profiles by known chemicals should be collected. In our study, cells need to be exposed with same experimental cellular condition, semi lethal (IC50), respectively. In the case of iodine (CAS; 7553-56-2), the IC50 was 1 mM by growth curve with continuously diluted exposure.
// Effects of Iodine on Global Gene Expression in Saccharomyces cerevisiae :
It is well documented that iodine kills microorganisms with broad spectrum. However, a systematic study of its mechanism of action has not yet been reported. Here we have demonstrated the action of iodine on gene expression level, using the yeast Saccharomyces cerevisiae with a DNA microarray. It was found that like antimicrobial activity, iodine causes an immediate and dose-dependent (0.5 mM, 0.75 mM and 1 mM) transcriptional alteration on yeast cells. The effects of iodine continued after the first immediate response. Genes for C-compound and carbohydrate metabolism, for energy, and for cell rescue were continuously up-regulated. On the other hand, genes related to protein fate were induced especially at 0.5 h. The gene expression profile at 0.5 h was significantly different from other longer iodine exposed condition. The main reaction at 0.5 h after iodine addition may be due to the oxidative toxicity, and the profile at 0.5 h was similar to agricultural bactericide.
Keywords: stress response

overall_design: In each condition except the data at 2.5 h, there are 2 hybridization results from independent biological samples, respectively. The data at 2.5 h has one hybridization data, only. 2nd hybridization in dose-response experiments and both hybridization in all time course experiments have high and low power scanned data, respectively. On the other hand, 1st hybridization in dose-response experiments have single scanned data.

first: Kuniko

last: Akama

first: Hitoshi

last: Iwahashi


title: Global transcriptional profiling of Saccharomyces cerevisiae treated with p-anisaldehyde

status: Public on Oct 24 2007

city: Changchun

first: Xuming

last: Deng

address: Xi'an Street 5333#

institute: College of Animal Science and Veterinary Medicine, Jilin University

summary:
We employed CapitalBio Corporation to investigate the global transcriptional profiling of Saccharomyces cerevisiae  treated with p-anisaldehyde.
Keywords: response to p-anisaldehyde

overall_design: 3 replicates analyzed.


title: Genome-Wide Transcriptional Responses of Nitrosomonas europaea to Zinc

city: Corvallis

first: Sunhwa

last: Park

state: OR

address: 116 Gilmore

department: Biological & Ecological Eng.

institute: Oregon State University

summary:
Nitrosomonas europaea is a Gram-negative obligate chemolithoautotroph that derives energy for growth through oxidation of ammonia and participates in the process of nitrification in global nitrogen cycling. The physiological, proteomic, and transcriptional responses of N. europaea to zinc stress were studied. The nitrite production rate and ammonia-dependent oxygen uptake rate of the cells exposed to 3.4 uM ZnCl2 decreased about 61 % and 69 % within 30 minutes, respectively. Two proteins were notably up regulated in zinc treatment and the mRNA levels of their encoding genes started to increase by one hour after the addition of zinc. A total of 27 genes were up regulated and 30 genes were down regulated. Up-regulated genes included mercury resistance genes (merACDPT), inorganic ion transport genes, oxidative stress genes, toxin-antitoxin genes (TA) and two-component signal transduction systems genes. The merACDPT  was the highest up regulated operon (46-fold). Down-regulated genes included the RuBisCO operon (cbbO), carbohydrate transporter (mrsA and mnxG) and amino acid transporter.
Keywords: zinc, stress response, global transcription, mercury resistance genes, inorganic ion transport genes, oxidative stress genes

overall_design: The 3.4 uM ZnCl2 caused 50 % inhibition in physiological response for 1 hour incubation. Transcriptional levels of the cells inhibited by zinc were compared with the cells under control condition.

first: Roger

last: Ely


title: Effects of the pesticide thiuram: genome-wide screening of indicator genes by yeast DNA microarray.

summary:
Although there have been studies on the toxicity of the pesticide thiuram, the present study is the first one to attempt to integrate a whole genomic response using microarray technology. From the DNA microarray experiment it was found that exposure to thiuram led to alterations of gene expression in yeast cells and that many genes involved in detoxification and stress response were highly induced. The induced genes were classified according to the MIPS yeast database. The induction of genes concerned with folding and proteolysis reflects the protein denaturing and degradation effects of the thiuram treatment The induction of genes involved in redox and defense against reaction oxygen species also suggests that thiuram has other effects, such as oxidative stress. Genes classified for carbohydrate metabolism and energy were also highly induced, and these gene products may play the role of providing the energy for the detoxification mechanism. In addition, in view of the induction of some genes involved in DNA repair, thiuram potentially causes DNA damage. Therefore, as stated in previous reports, thiuram is a potential positive toxic chemical. On the other hand, YKL071W, YCR102C, YLR303W, and YLL057C were selected based on the result of a DNA microarray experiment and used for the promoter activity assay. Thiuram treatment affected the promoter of these genes, indicating that this technique could be used for the selection of biomarker candidates.

Keywords: stress response

overall_design: This series contains 3 time-points data with triplicate hybridization results from independent biological samples, respectively.

first: Junko

last: Takahashi

first: Yuko

last: Momose


title: Subpopulation array data, Veening et al.

status: Public on Oct 23 2007

city: Groningen

first: Jan-Willem

last: Veening

address: Nijenborgh 7

country: Netherlands

institute: University of Groningen

summary:
The transcriptome profiles of sporulating vs non-sporulating cells, within an isogenic culture were compared.
Keywords: isogenic subpopulation comparison Bacillus subtilis sporulation

overall_design: RNA was isolated from endospore containing cells which were separated from non-spore forming cells using buoyant density gradient centrifugation within an isogenic culture (details in Veening et al, submitted).

first: Oleg

last: Igoshin

first: Robyn

middle: T

last: Eijlander

first: Leendert

last: Hamoen

first: Reindert

last: Nijland

first: Oscar

last: Kuipers


title: Euchromatic chromatin modifications on chromosome 2L

status: Public on Oct 27 2007

city: Basel

first: Oliver

last: Bell

address: Maulbeerstr. 66

department: Epigenetics

country: Switzerland

institute: Friedrich Miescher Institute

type: Genome binding/occupancy profiling by genome tiling array

summary:
Chromosome-wide analysis of the distribution of H3K4me3, H3K36me2 and H3K36me3 on chromosome 2L.
Keywords: ChIP-chip

overall_design:
Input and antibody-bound DNA were separately amplified and labeled as described (Schübeler et al. 2004) except using indirect labeling via aminoallyl-modified nucleotides. Labeled DNA was co-hybridized to a chromosomal tiling array representing chromosome 2L of the Drosophila genome in a 2kb tiling resolution as described (Macalpine et al., 2004). Two repeats (including dye swap) starting from independent ChIP experiments were carried out. After hybridization and washing slides were scanned (Axon) and fluorescent reads were analyzed according to standard normalization and filtering criteria in the GenePix software package (Axon).
Repeats showed high reproducibility (H3K4me3 R=0.98, H3K36me2 R=0.91, H3K36me3 R=0.92) so that average value from two experiments could be used in further analysis.

first: Christiane

last: Wirbelauer

first: Michaela

last: Schwaiger

first: David

last: MacAlpine

first: Stephen

first: Dirk

last: Schubeler


title: Differential gene expression in resting human skeletal muscle of sedentary and highly-trained individuals.

city: Clayton

first: Nigel

middle: Keith

last: Stepto

state: VIC

address: Wellington Road

department: Physiology

institute: Monash University

summary:
We used gene microarray analysis to compare the global expression profile of genes involved in adaptation to exercise training in skeletal muscle from chronically strength/resistance trained (ST), endurance trained (ET) and untrained control subjects (Con).

Resting skeletal muscle samples (~100mg) were obtained from the vastus lateralis of 20 subjects (Con n=7, ET n=7, ST n=6; trained groups >8 years specific training). Total RNA was extracted from tissue and microarrays completed, with test samples compared with standard human reference RNA. Subjects were characterised by performance measures of maximal oxygen uptake (VO2max) on a cycle ergometer and maximal concentric and eccentric leg strength on an isokinetic dynamometer.

263 genes were differentially expressed in trained (TR collectively ET + ST) subjects compared with Con (P<0.05) while 21 genes were different between ST and ET (P<0.05). Manual cluster analyses revealed significant regulation of genes involved in muscle structure and development in TR subjects compared with Con (P<0.05), and expression of these correlated significantly with measures of performance (P<0.05). ET had increased and ST decreased expression of gene clusters related to mitochondrial/oxidative capacity (P<0.05), and these mitochondrial gene clusters correlated significantly with VO2max (P<0.05). VO2max also correlated with expression of gene clusters that regulate fat and carbohydrate oxidation (P<0.05).

We have demonstrated that chronic training has marked effects on basal gene expression by regulating levels of multiple mRNAs that transcribe genes for important functional groups in human skeletal muscle. Some specific gene clusters are expressed regardless of the training stimulus, whereas others exhibit divergent expression patterns as a result of specific training stimuli.
Keywords: Comparative, cluster analysis, endurance training, strength training, muscle phenotype

overall_design:
This was a crossectional study examining basal gene expression profiles of the human vastus lateralis. Twenty healthy males volunteered for this investigation. Seven were endurance trained cyclists (ET), who had been participating in endurance training for 8 yr. These subjects had no history of resistance training. Six subjects were strength trained power-lifters (ST) who had been participating exclusively in strength/resistance training for 9 yr.  The final seven subjects were healthy controls (CON) that did not participate in any formal exercise.  The study was approved by the Human Research Ethics Committee of RMIT University and Monash University Standing Committee on Ethics Research on Humans.
After RNA extraction, amplification and indirect labelling, a dual colour micro-array analysis was conducted by hybridizing a test (muscle RNA; Cy5) sample and a reference (Universal human RNA; Cy3) sample on the AGRF glass slide human 8K micro-array.  After data capture with the Genepix scanner and associated software data was normalised and the three populations compared using GeneSpring and simplified cluster analysis.

first: Andrew

last: Carey

first: Vernon

last: Coffey

first: Anna

last: Ponnampalam

first: Benedict

last: Canny

last: Powell

first: John

last: Hawley


title: Genome-wide location map of Polycomb in prostate cancer

city: Chicago

first: Jindan

last: Yu

state: IL

address: 303 E. Superior St.

department: Medicine - Hem/Onc

institute: Northwestern University

summary:
We used chromatin immunoprecipitation (ChIP) in combination with human promoter microarrays to idnetify SUZ12 and H3K27me3-occupied gene promoters in prostate cancer cells and tissues. We observed a common set of SUZ12 and H3K27me3-occupied genes in LNCaP cells, and metastatic prostate cancer tissues across individuals as well as tissue types of the metastatic sites. We also found significant overlap of cancer polycomb targets with previously published embryonic stem cell polycomb targets. In addition, a strong association between cancer polycomb targets with prostate cancer outcome was observed. We developed a cancer Polycomb Repression Signature, comprised direct targets of PRC2 silencing in cancer, that is predictive of cancer outcome in multiple expression profling datasets of tumors.
Keywords: protein-DNA interaction

overall_design: SUZ12 and H3K27me3 occupancy were tested in LNCaP cells as well as 3 metastatic prostate cancer tissues from independent patients. Using the proximal promoter arrays, we are assaying binding in -1.0kb to 0.3kb promoter regions of over 17,000 human genes. We first tested the co-ocupancy of SUZ12 and H3K27me3 in LNCaP prostate cancer cell lines, then extended to 2 metastatic prostate cancer tissue (to the liver). We lastly examined H3K27me3 occupancy in another metastatic prostate cancer tissue from different metasatic site (to the lung) of an independent patient.

first: Arul

last: Chinnaiyan


title: Chloroacetaldehyde treatment with 25 ppm for 2 h

city: Tsukuba

first: Emiko

last: Kitagawa

address: Onogawa 16-1

institute: National Institute of Advanced Industrial Science and Technology

summary:
The number and type of synthetic chemicals that are being produced worldwide continues to increase significantly. While these industrial chemicals provide numerous benefits, there is no doubt that some have potential to damage the environment and health. Toxicity must be evaluated and use must be carefully controlled and monitored in order to minimize potential damage. DNA microarray technology has become an important new technique in toxicology. We are using the yeast Saccharomyces cerevisiae as a model organism for toxicological study because it is a simple, fast-growing eukaryote that has been thoroughly characterized. In order to evaluate toxicity by newly synthesized or mixture chemicals, toxicity-induced gene expression alteration profiles by known chemicals should be collected. In our study, cells need to be exposed with same experimental cellular condition, semi lethal (IC50), respectively. In the case of chloroacetaldehyde (CAS; 107-20-0), the exposure dose was decided as 25 ppm by growth curve with continuously diluted exposure. Chloroacetaldehyde is one of the toxic gases and vapors. This substrate is suspected to be respiratory toxicant and skin or sense organ toxicant.
Keywords: stress response

overall_design: Series containes 3 hybridization results from independent biological samples, and each experiment have high and low power scanned data respectively.

first: Hyun-Ju

last: Kim

first: Hitoshi

last: Iwahashi


title: NF-κB Activation Controls Phagolysosome Fusion-Mediated killing of Mycobacteria by Macrophages

city: Heidelberg

first: Bibhuti

middle: Bhusan

last: Mishra

state: Heidelberg

department: Cell Biology and Biophysics

country: Germany

institute: EMBL-Heidelberg

summary:
Mycobacterium smegmatis is a model non-pathogenic mycobacterium that is efficiently killed by macrophages. Here, we explore the role of NF-κB in the innate immune response, focusing in detail on the mechanisms of the first killing period (1-4h) of M. smegmatis which coincides with phagosome-lysosome fusion. We show that infection of macrophages with M. smegmatis induces an activation of NF-κB and this activation is required for killing since treatment of macrophages with NF-κB inhibitors or siRNA silencing of the NF-κB subunit p65 increases bacterial survival. NF-κB induced proteins were thus hypothesized to be essential during the first phase of M. smegmatis killing. We therefore identified, using RNA microarray, the genes that were regulated during infection in the absence and presence of NF-κB inhibitors. By subtraction this provided a list of pro-inflammatory proteins that were under the control of NF-κB and putatively involved in the killing response. Among these category of genes were those for lysosomal enzymes and membrane trafficking regulators, including Cathepsins, LAMP-2 and Rab34, are regulated by NF-κB. Moreover, inhibition of NF-κB signaling retarded the delivery of v-ATPase, LAMP-2, CtsZ and CtsH thereby impairing the maturation of mycobacterial phagosomes. Collectively; our data provide the first compelling evidence that the innate immune response via NF-κB activation is linked to phagosome fusion with lysosomes that is essential for killing of mycobacteria.
Keywords: NFkB inhibitor treated vs untreated

overall_design: The study includes J774 macrophage cell lines which are infected with Mycobacterium smegmatis in the presence and absense of NFkB inhibitor SC-514.Total RNA was isolated from individual samples and each sample was hybridised to CodeLink Mouse whole genome bioarray slides.This study was intended to know the role of NFkB regulated genes in killing non-pathogenic mycobacteria during 4 hour post infection of macrophages.

middle: B

first: Maximilliano

last: Gutierrez

first: Gareth

last: Griffiths

first: Elsa

last: Anes


title: Genome-scale RNAi profiling of cell division in human tissue culture cells

city: Carlsbad

first: Aimee

last: Jackson

state: CA

address: 1896 Rutherford Rd

institute: Regulus Therapeutics

summary:
Cell division is a fundamental process for multicellula organisation.  Here we report a genome-scale RNAi screen in HeLa cells designed to identify human genes important for cell division.  We utilized a library of endoribonuclease-prepared siRNAs (esiRNAs) for gene-silencing and used DNA content analysis to uncover genes that induced cell cycle arrest or altered ploidy upon knockdown.  Rigorous validation and secondary assays were preformed to generate a nine-parameter fingerprint for each of the genes.  These phenotypic signatures allowed the assignment of genes to specific functional classes by combining hierarchical clustering, cross-species analysis and proteomic data mining.  We highlight the richness of our dataset by describing novel functions to genes in mitosis and cytokinesis.  In particular, we identified two evolutionarily conserved transcriptional regulatory networks that govern cytokinesis in mammalian cells.  Our work provides an experimental framework from which the systematic analysis of novel genes necessary for cell division in human cells can begin.
Keywords: time course

overall_design: An esiRNA targeting LIN54 was transfected into HCT116 cells.  RNA was harvested at 24, 48, and 72 hours post-transfection for microarray analysis.  Transcripts regulated at least 1.5-fold, and with a p-value<0.01 were identified as signature transcripts.

first: Ralf

last: Kittler

first: Laurence

last: Pelletier

first: Anne-Kristine

last: Heninger

first: Mikolaj

last: Slabicki

first: Mirko

last: Theis

first: Lukasz

last: Miroslaw

first: Ina

last: Poser

first: Hannes

last: Grabner

first: Karol

last: Kozak

first: Jan

last: Wagner

first: Vineeth

last: Surendranath

first: Constance

last: Richter

first: Wayne

last: Bowen

first: Bianca

last: Habermann

first: Anthony

last: Hyman

first: Frank

last: Buchholz


title: Detection of novel amplification units in prostate cancer

first: Sean

last: Davis

address: 37 Convent Drive, Room 6138

institute: National Cancer Institute

summary:
Genome-wide screening for regions of genetic gains and losses on nine prostate cancer cell lines (PC3, DU145, LNCaP, CWR22, and derived sublines) was carried out using comparative genomic hybridization on a 35 K longmer oligonucleotide microarray (arrayCGH). Compared to conventional chromosomal CGH more deletions and small regions of gains, particularly in pericentromeric regions and regions next to the telomers, were detected. As a proof for the high-resolution of arrayCGH we further analyzed a small amplification unit of 1.7 MB at 9p13.3, which was found in CWR22 and CWR22-Rv1. Increased copy number was confirmed by fluorescence in situ hybridization using the BAC clone RP11-165H19 from the amplified region comprising the two genes interleukin 11 receptor alpha (IL11-RA) and dynactin 3 (DCTN3). Using quantitative real time PCR (qPCR) we could demonstrate that IL11-RA is the gene with the highest copy number gain in the cell lines compared to DCTN3 suggesting IL11-RA to be the amplification target. Screening of 20 primary prostate carcinomas by qPCR revealed a high frequency of IL11-RA copy number gain in 75% of the tumors analyzed. Gain of DCTN3 was only found in two cases together with a gain of IL11-RA. Thus, IL11-RA is a frequently amplified gene in prostate cancer with amplification being supposed to be one mechanism of IL11-RA overexpression in this tumor type.
Keywords: comparative genomic hybridization

overall_design: whole genome array comparative genomic hybridization

first: Joern

last: Kamradt

first: Volker

last: Jung

first: Kerstin

last: Wahrheit

first: Laura

last: Tolosi

first: Joerg

last: Rahnenfuhrer

first: Claudia

last: Rubie

first: Robert

last: Walker

first: Michael

last: Stoeckle

first: Paul

last: Meltzer

first: Bernd

last: Wullich


first: Ira

middle: M

last: Hall

summary:
We have conducted a genome-wide analysis of spontaneous copy number variation (CNV) in the laboratory mouse. We used high resolution microarrays to identify 38 CNVs between 14 colonies of the C57BL/6 strain spanning ~967 generations of inbreeding, and examined these loci in 12 additional strains.  It is clear from our results that many CNVs arise through a highly non-random process: 18 of 38 were the product of recurrent mutation, and rates of change vary roughly four orders of magnitude across different loci. These recurrent CNVs are distributed throughout the genome, affect 43 genes, and fluctuate in copy number over mere hundreds of generations, observations that raise questions about their contribution to natural variation.
Keywords: Representational oligonucleotide microarray analysis, comparative genomic hybridization, DNA copy number variation, structural variation, inbred mice, spontaneous mutation rate

overall_design: We performed ROMA for both liver and tail DNA from a single pedigreed mouse from each of 13 different C57BL/6 substrains.  For each substrain we performed at least 3 independent dye-swap experiments against the C57BL/6J reference strain, and we performed at least 1 dye-swap experiment against a third strain. We then used ROMA to assess relative DNA copy number at each locus in 13 additional inbred strains for which we analyzed at least two individuals with at least 1 dye-swap experiment per individual  These included four unpedigreed individuals from the C57BL/6Crl substrain, as well as two individuals from each of 12 inbred strains.  We also performed ROMA on tail DNA from 6 different C57BL/6 families comprising 12 parental individuals and 41 progeny.  We verified CNVs using a custom-designed tiling array (see related submission).  We performed three types of replicates: biological replicates involved either separate individuals from the same inbred strain or separate tissues from the same individual (numbers signify individuals, L=Liver, T=Tail); ROMA replicates entailed independently-constructed genomic representations from the same DNA sample, and are indicated in the experiment title (rep1, rep2, etc.); hybridization replicates entailed independent labeling and hybridization of the same genomic representation from the same DNA sample, and are indicated in the experiment title (hyb1, hyb2, etc.)

first: Chris

last: Egan

first: Srinath

last: Sridhar

last: Wigler


title: Phenotype-directed analysis of genotype in early-onset, familial breast cancers using arrayCGH

city: Brisbane

first: Gareth

last: Price

state: Queensland

address: Carmody Road

institute: Queensland Facility for Advanced Bioinformatics

summary:
Summary: Considerable heterogeneity of morphology and disease outcome exists within breast cancers (BC), which likely reflects variable molecular pathogeneses within this broad clinical group. Aim: To evaluate the underlying genomic alterations associated with familial, early-onset BC (EOBC) phenotypes, in order to improve the management of this disease.

Methods: Using hierarchical clustering of morphological and immunophenotypical parameters, 116 EOBC were stratified into six groups. Conventional and array-based comparative genomic hybridisation was used to analyse the genomic alterations.

Results: Specific areas of genomic imbalance were associated with individual phenotypes. The largest phenotypical group was high grade, oestrogen receptor and HER-2 negative. This group contained the majority of BRCA1 germline mutation-associated tumours and commonly showed loss of chromosomal regions 5cent-5q13, 5q14–22 and 4q28–32. High mitotic rate, an important indicator of tumour cell proliferation and poor prognosis, was associated with gain of 19p, mapped within 7 Mb of the telomere. This region contains the candidate oncogene CDC34, the protein product of which is involved in ubiquitin-mediated degradation of the cyclin-dependent kinase inhibitor, p27Kip1.

Conclusion: Phenotype-based analysis can be used to determine the genetic changes important in subtypes of BC. Further, the different morphological phenotypes could act as a cost-effective surrogate for genotypical stratification to facilitate optimal management of this disease.
Keywords: comparative genomic hybridisation, breast cancer, aCGH

overall_design:
aCGH data was produced for 27 cases within a cohort of 116 Early Onset Breast Cancers (Phenotype-directed analysis of genotype in early-onset, familial breast cancers. Pathology 2006 GARETH R. PRICE, JANE E. ARMES, SUSAN J. RAMUS, ELENA PROVENZANO, BEENA KUMAR, TIFFANY F. COWIE, JOHN CICIULLA, ANNE-MARIE HUTCHINS, MERVYN THOMAS AND DEON J. VENTER). Cases were chosen to represent each of 6 phenotypic cluster represented in Price et al, 2006. DNA was extracted from formalin-fixed paraffin embedded tissue and subjected to amplification and labelling using a modified cCGH procedure detailed in Price et al, 2006.

The normalized data matrix below was generated as follows:

All following steps refer to Spot Ratio generated as:
[(F653-B635) / (F532-B532)]

1) Spot Ratio normalised across entire sample to Median = 1
2) Spots removed where either 635nm or 532nm Feature/Background ratio was <1.2
3) Spots removed where either 635nm or 532nm Feature signal was <0.66 of whole slide Background median signal for corresponding nm channel
4) Removed individual spots where Flag status did not equal 0
5) BAC spot pairs were averaged by Meta_Row position (BAC spots duplicated in Blocks 1 and 2, corresponding to Meta_Row positions 1 and 2), therefore a BAC represented more than twice on the slide will only be averaged within its Meta_Row pairing, not averaged across all instances on the slide
6) Individual spot data rows were removed if SPOT_ID = “Control” or “Empty”

Original file contains:
3840 Total Spots
- 96 Control Spots
- 640 Empty Spots
= 3104 BAC spots /2 (average)
= 1552 individual BAC IDs

first: Jane

middle: E

last: Armes

first: Susan

last: Ramus

first: Elena

last: Provenzano

first: Beena

last: Kumar

first: Tiffany

last: Cowie

first: John

last: Ciciulla

first: Anne-Marie

last: Hutchins

first: Mervyn

last: Thomas

first: Deon

last: Venter


title: Global assessment of the acute phase response in channel catfish after infection with a Gram negative bacterium

city: Auburn

first: Eric

last: Peatman

state: AL

address: 203 Swingle Hall

department: Fisheries and Allied Aquacultures

institute: Auburn University

summary:
The acute phase response (APR) is a set of metabolic and physiological reactions occurring in the host in response to tissue infection or injury and is a crucial component of the larger innate immune response.  The APR is best characterized by dramatic changes in the concentration of a group of plasma proteins known as acute phase proteins (APP) which are synthesized in the liver and which function in a wide range of immunity-related activities.  Utilizing a second generation high-density in situ oligonucleotide microarray for catfish, we have surveyed for the first time the APR in channel catfish liver following infection with Edwardsiella ictaluri, a fast-acting bacterial pathogen that causes enteric septicemia of catfish.  Our catfish microarray design (28K) builds upon a previous 19K channel catfish array by adding recently sequenced immune transcripts from channel catfish along with 7159 unique sequences from closely-related blue catfish. Analysis of microarray results using a traditional two-fold change in gene expression cutoff and a 10% false discovery rate revealed a well-developed APR in catfish, with particularly high up-regulation (>50-fold) of genes involved in iron homeostasis (i.e. intelectin, hemopexin, haptoglobin, ferritin, and transferrin).  Other classical APP upregulated greater than two-fold included coagulation factors, proteinase inhibitors, transport proteins, and complement components.  Up-regulation of the majority of the complement cascade including the membrane attack complex components and complement inhibitors was observed.  A number of pathogen recognition receptors (PRRs) and chemokines were also differentially expressed in the liver following infection.  Validation with real-time PCR confirmed microarray results.
Keywords: Disease state analysis

platform_organism:
Ictalurus punctatus
Ictalurus furcatus

overall_design: Global gene expression in the channel catfish liver 3 days after infection with virulent Edwardsiella ictaluri was measured utilizing a new 28K catfish microarray.  Three replicate pools of RNA (n=25) for control fish and three replicate pools (n=25) for infected fish were analysed on 6 separate arrays.  Gene calls from at least 6 probe pairs/transcript were generated in RMA, and normalized values from treatment and control replicates were compared in SAM to identify differentially expressed genes.  Criteria of two-fold expression change and a 10% FDR rate were used to determine a set of significantly up- and down-regulated genes.  Representative results were confirmed by real-time RT-PCR.

first: Puttharat

last: Baoprasertkul

first: Jefferey

last: Terhune

first: Rex

last: Dunham

first: Zhanjiang

last: Liu


status: Public on Oct 20 2007

city: Livermore

first: Anu

last: Chakicherla

address: 7000 East Avenue, Mail Stop: L-446

institute: Lawrence Livermore National Lab

summary:
Comparative transcriptome analysis of Methylibium petroleiphilum PM1 exposed to the fuel-oxygenates methyl-tert-butyl ether and ethanol

High-density whole genome cDNA microarrays were used to investigate substrate-dependent gene expression of Methylibium petroleiphilum PM1, one of the best-characterized aerobic methyl tert-butyl ether (MTBE)-degrading bacteria. Differential gene expression profiling was conducted with PM1 grown on MTBE and ethanol as sole carbon sources. Based on microarray high scores and protein similarity analysis, an MTBE regulon located on the megaplasmid was identified for further investigation. Putative functions for enzymes encoded in this regulon are described with relevance to the predicted MTBE degradation pathway. A new unique dioxygenase enzyme system that carries out the hydroxylation of TBA to 2-methyl-2-hydroxy-1-propanol in M. petroleiphilum PM1 was discovered. Based on the expression data, hypotheses regarding the acquisition and evolution of MTBE genes as well as the involvement of IS elements in these complex processes were formulated. The pathways for toluene, phenol, and alkane oxidation via toluene monooxygenase, phenol hydroxylase, alkane monooxygenase as well as propane monooxygenase, respectively, were upregulated in MTBE-grown cells compared to ethanol-grown cells. Four out of nine putative cyclohexanone monooxygenases were also upregulated in MTBE-grown cells. The global transcriptome response revealed the link between metabolism of MTBE and aromatic compounds (e.g. benzene, toluene) present in gasoline mixtures. The expression data aids our understanding of the regulation of metabolic processes that may occur in response to pollutant mixtures and perturbations in the environment.
Keywords: bacterial metabolism

overall_design: After growth with MTBE or ethanol as sole carbon source under aerobic conditions, cells from three biological replicates for each treatment were harvested at mid-exponential phase.  RNA was extracted from each replicate for microarray analysis.

first: Krassimira

last: Hristova

first: Radomir

last: Schmidt

middle: Y

first: Tina

last: Legler

first: Janice

last: Wu

first: Patrick

middle: S

last: Chain

first: Kate

last: Scow

first: Staci

last: Kane