title: Transcriptional responses of Saccharomyces cerevisiae to carbon limitation in aerobic chemostat cultures

summary:
Zinc is indispensable for the catalytic activity and structural stability of many proteins, and its deficiency can have severe consequences for microbial growth in natural and industrial environments. For example, Zn depletion in wort negatively affects beer fermentation and quality. Several studies have investigated yeast adaptation to low Zn supply, but were all performed in batch cultures, where specific growth rate depends on Zn availability. The transcriptional responses to growth-rate and Zn availability are then intertwined, which obscures result interpretation. In the present study, transcriptional responses of Saccharomyces cerevisiae to Zn availability were investigated at a fixed specific growth rate under Zn limitation and excess in chemostat culture. To investigate the context-dependency of this transcriptional response, yeast was grown under several chemostat regimes resulting in various carbon (glucose), nitrogen (ammonium) and oxygen supplies. A robust set of genes that responded consistently to Zn limitation was identified and enabled the definition of a Zn-specific Zap1 regulon comprising of 26 genes and characterized by a broader ZRE consensus (MHHAACCBYNMRGGT) than so far described. Most surprising was the Zn-dependent regulation of genes involved in storage carbohydrate metabolism. Their concerted down-regulation was physiologically relevant as revealed by a substantial decrease in glycogen and trehalose cellular content under Zn limitation. An unexpectedly large amount of genes were synergistically or antagonistically regulated by oxygen and Zn availability. This combinatorial regulation suggested a more prominent involvement of Zn in mitochondrial biogenesis and function than hitherto identified
Keywords: Chemostat-based transcriptome analysis


title: Physiological and transcriptional responses of Saccharomyces cerevisiae to zinc limitation in chemostat cultures

status: Public on Oct 16 2007

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

country: Netherlands

institute: Delft University of Technology

summary:
Zinc is indispensable for the catalytic activity and structural stability of many proteins, and its deficiency can have severe consequences for microbial growth in natural and industrial environments. For example, Zn depletion in wort negatively affects beer fermentation and quality. Several studies have investigated yeast adaptation to low Zn supply, but were all performed in batch cultures, where specific growth rate depends on Zn availability. The transcriptional responses to growth-rate and Zn availability are then intertwined, which obscures result interpretation. In the present study, transcriptional responses of Saccharomyces cerevisiae to Zn availability were investigated at a fixed specific growth rate under Zn limitation and excess in chemostat culture. To investigate the context-dependency of this transcriptional response, yeast was grown under several chemostat regimes resulting in various carbon (glucose), nitrogen (ammonium) and oxygen supplies. A robust set of genes that responded consistently to Zn limitation was identified and enabled the definition of a Zn-specific Zap1 regulon comprising of 26 genes and characterized by a broader ZRE consensus (MHHAACCBYNMRGGT) than so far described. Most surprising was the Zn-dependent regulation of genes involved in storage carbohydrate metabolism. Their concerted down-regulation was physiologically relevant as revealed by a substantial decrease in glycogen and trehalose cellular content under Zn limitation. An unexpectedly large amount of genes were synergistically or antagonistically regulated by oxygen and Zn availability. This combinatorial regulation suggested a more prominent involvement of Zn in mitochondrial biogenesis and function than hitherto identified.
Keywords: Chemostat-based transcriptome analysis

first: Lucie

last: Hazelwood

first: Jack

middle: T

last: Pronk

first: Pascale

last: Daran-lapujade

first: Jean-marc


title: SKN-1-dependent oxidative stress response in C. elegans

status: Public on Nov 01 2007

city: Boulder

first: Sang-Kyu

last: Park

state: CO

department: IBG

country: USA

institute: University of Colorado at Boulder

summary:
Oxidative stress may play a role in normal aging. SKN-1 is a transcription factor necessary for intestine development in Caenorhabditis elegans, which also regulates the response to oxidative stress post-embryonically. Using DNA microarrays, we found that oxidative stress induces the antioxidant response, the heat shock response, and detoxification genes, while the expression of genes involved in homeostasis, development, and reproduction were decreased. Both up-regulated and down-regulated genes can be wholly, partially, or not at all dependent on SKN-1 action. However, induction of the heat shock response by oxidative stress was not affected by SKN-1 removal.
Keywords: stress response

overall_design: TJ1060 was grown at 16°C. Eggs were collected by hypochlorite, hatched overnight at 20°C (Emmons, 1979 #52) and first-stage larvae (L1) were placed onto 2 % peptone plates (1.7 % agar, 20 g/l peptone, 25 mM NaCl, 50 mM KH2PO4 pH 6.0, 5 ug/ml cholesterol, 1 mM CaCl2, 1 mM MgSO4) at 25°C.  Sterile 3 day old young adult animals on peptone plates were treated with 99 % O2 at 40 PSI for 6 hours at 20°C in a hyperbaric O2 chamber.  Half of the worms were untreated and served as a control population.  A small plate of strain CL2166 [dvIs19 pAF15(gst-4::GFP::NLS)]  was used as an indicator strain and checked for GFP induction in both control and experimental conditions. Worms were harvested by washing off plates with S-basal and quick frozen in liquid nitrogen.  Total RNA was prepared using TRIZOL reagent and standard protocols and cleaned up on Qiagen RNeasy columns.  The Affymetrix labeling kit was used to prepare labeled cRNA as a target for the Affymetrix GeneChip C.elegans Genome Array. Gene chip hybridization and scanning were done at Genome Explorations (Memphis, MN) and the University of Colorado at Boulder Gene Chip Core Facility (Boulder, CO).

first: Patricia

middle: M

last: Tedesco

first: Thomas

middle: E

last: Johnson


title: Expression data from Saccharomyces cerevisiae treated with gentamicin

status: Public on Oct 14 2007

city: Indianapolis

first: Mark

last: Wagner

state: IN

address: 950 West Walnut Street

department: Medicine/Nephrology

institute: Indiana University Medical Ctr

summary:
Gentamicin is a highly efficacious antibiotic against gram-negative bacteria.  However, its usefulness in treating infection is compromised by its poorly understood renal toxicity.  This toxic effect is seen in a variety of organisms.  While the yeast Saccharomyces cerevisiae is relatively insensitive to gentamicin, mutations in any one of 20 or so genes causes a dramatic increase in sensitivity.  Many of these genes encode proteins important for translation termination or specific protein trafficking complexes.  Here, we demonstrate by microarray analysis that gentamicin treatment leads to dramatic decreases in genes under the control of the MADS box protein Mcm1, including genes encoding products involved in mating, nitrogen utilization, and ribosome biogenesis.  Furthermore, microarray analysis also demonstrates an increase in a Rlm1-dependent set of genes involved in maintaining the structure of the cell wall that are also induced by the antifungal agents caspofungin and calcofluor white.  Subsequent inspection of the physical and genetic interactions of the remaining gentamicin sensitive mutants revealed a network centered around chitin synthase and the Arf Pathway.  Furthermore, conditional arf1 mutants are hypersensitive to gentamicin even under permissive conditions. These results suggest that gentamicin may act as a cell wall stress, possibly by disrupting Arf-dependent trafficking of proteins involved in forming the cell wall.
Keywords: disease state analysis, comparative genomic analysis +/- gentamicin treatment

overall_design: The yeast strain 4073 was grown to mid-log with and without gentamicin (500 mg/ml) (n=4 for each condition).  Yeast cells were pelleted and snap frozen. Total RNA was isolated using the Epicentre Masterpure Yeast RNA Purification kit.  RNA samples were brought to the Indiana University Center for Medical Genomics who performed the microarray analysis using Affymetrix GeneChip Scanner 3000 and the Affymetrix Yeast arrays.

middle: G

last: Goebl

first: Maureen

last: Harrington

first: Lin

last: Lin

first: Elizabeth

last: Molnar

first: Bruce

middle: A

last: Molitoris

middle: C


title: Control of glycolytic enzyme fluxes in Saccharomyces cerevisiae

status: Public on Oct 17 2007

summary:
Metabolic fluxes may be regulated "hierarchically," e.g., by changes of gene expression that adjust enzyme capacities (V(max)) and/or "metabolically" by interactions of enzymes with substrates, products, or allosteric effectors. In the present study, a method is developed to dissect the hierarchical regulation into contributions by transcription, translation, protein degradation, and posttranslational modification. The method was applied to the regulation of fluxes through individual glycolytic enzymes when the yeast Saccharomyces cerevisiae was confronted with the absence of oxygen and the presence of benzoic acid depleting its ATP. Metabolic regulation largely contributed to the approximately 10-fold change in flux through the glycolytic enzymes. This contribution varied from 50 to 80%, depending on the glycolytic step and the cultivation condition tested. Within the 50-20% hierarchical regulation of fluxes, transcription played a minor role, whereas regulation of protein synthesis or degradation was the most important. These also contributed to 75-100% of the regulation of protein levels.
Keywords: Condition comparison

overall_design: To quantify the regulation of the Vmax values and the fluxes at the different levels of gene expression, we measured how the fluxes through the glycolytic enzymes, the Vmax values, and the concentrations of these enzymes and their corresponding mRNA concentrations change when yeast is exposed to aerobic and anaerobic (with and without challenges.

last: Daran-Lapujade


title: Histone H2A K4,7G

status: Public on Oct 11 2007

city: Pullman

first: John

middle: J.

last: Wyrick

state: WA

address: Biotechnology Life Sciences 241

department: School of Molecular Biosciences

institute: Washington State University

summary:
Total RNA from three replicate cultures of wild-type and mutant strains was isolated and the expression profiles were determined using Affymetrix arrays. Comparisons between the sample groups allow the identification of genes regulated by the histone H2A K4,7G mutant.
Keywords: histone H2A mutant, repeat

overall_design: Comparison of genes whose mRNA levels are affected in a histone H2A K4,7G mutant yeast strain compared to wild-type yeast strain.

first: Michael

last: Parra

middle: J


title: Histone H2A^4-20

summary:
Total RNA from three replicate cultures of wild-type and mutant strains was isolated and the expression profiles were determined using Affymetrix arrays. Comparisons between the sample groups allow the identification of genes regulated by histone H2A^4-20 mutant.
Keywords: histone H2A mutant, repeat

overall_design: Comparison of genes whose mRNA levels are affected in a histone H2A^4-20 mutant yeast strain compared to wild-type yeast strain.


title: Analysis of gene expression during neurite outgrowth and regeneration (MG-U74B)

status: Public on Dec 04 2007

city: Princeton

first: Moriah

last: Szpara

state: NJ

address: 301 Schultz

department: Molecular Biology

institute: Princeton University

summary:
We have undertaken a genome-wide study of transcriptional activity in embryonic superior cervical ganglia (SCG) and dorsal root ganglia (DRG) during a time course of neurite outgrowth in vitro.  Gene expression observed in these models likely includes both developmental gene expression patterns and regenerative responses to axotomy, which occurs as the result of tissue dissection.  Comparison across both models revealed many genes with similar gene expression patterns during neurite outgrowth.  These patterns were minimally affected by exposure to the potent inhibitory cue Semaphorin3A, indicating that this extrinsic cue does not exert major effects at the level of nuclear transcription.  We also compared our data to several published studies of DRG and SCG gene expression in animal models of regeneration, and found the expression of a large number of genes in common between neurite outgrowth in vitro and regeneration in vivo.
Keywords: time course

overall_design: We wished to determine the transcriptional profiles of neurons undergoing neurite outgrowth in vitro. We were particularly interested in finding genes whose expression is generally associated with the process of neurite outgrowth, rather than with cell type-specific effects. Thus, in order to avoid focusing on transcripts unique to one tissue type versus another, we used a comparative strategy to look for effects that were common to two tissue types and therefore more likely to be involved in the general process of neurite outgrowth.  While these explants contain multiple cell types, we felt this was preferable to the more disruptive conditions required to dissociate neurons or obtain a pure neuron population.  To this end, we monitored gene expression in cultured explants from SCG and DRG using DNA microarrays.  We initiated our studies by culturing embryonic day 13 (E13) mouse SCG in vitro and harvesting tissue for RNA isolation at time points from 2 to 65 hours.  Time points were selected to detect both fast, short-term responses (2, 5 and 12 hours), as well as sustained, long-term changes (24, 40, and 65 hours).  Samples were hybridized to Affymetrix MG-U74v2 A and B microarrays, with RNA from acutely dissected explants serving as a baseline reference.  We followed these experiments with a parallel analysis of a more heterogeneous tissue type, the DRG, which is more frequently used than SCG for in vivo studies of neurite regeneration.  Cervical and upper thoracic DRG from E12 embryos were cultured with NGF (the same trophic support as in SCG cultures), harvested at time points from 2 to 40 hours, and hybridized to Affymetrix MOE 430A microarrays.

middle: L

first: Karen

last: Vranizan

first: Yu

last: Tai

first: Corey

middle: S

last: Goodman

first: Terence

middle: P

last: Speed

last: Ngai


title: Overexpression of transcriptional factors Kin28 and Pog1 suppresses the stress sensitivity caused by the rsp5 mutation

status: Public on Sep 07 2007

city: Tsukuba

first: Yoshinori

last: Murata

state: Ibaraki

address: 1-1 Ohwashi

department: Post-harvest Science and Technology Division

country: Japan

institute: Japan International Research Center for Agricultural Science

summary:
Rsp5 is an essential and multi-functional E3 ubiquitin ligase in Saccharomyces cerevisiae. We previously isolated the Ala401Glu rsp5 mutant, which is hypersensitive to various stresses. To understand the function of Rsp5 in stress responses, suppressor genes whose overexpression allows rsp5A401E cells to grow at high temperature were screened. The KIN28 and POG1 genes, encoding a subunit of the transcription factor TFIIH and a putative transcriptional activator, respectively, were identified as multicopy suppressors of not only high temperature but also LiCl stresses. The overexpression of Kin28 and Pog1 in rsp5A401E cells caused an increase in the transcriptional level of some stress proteins when exposed to temperature up-shift. DNA microarray analysis under LiCl stress revealed that the transcriptional level of some proteasome components was increased in rsp5A401E cells overexpressing Kin28 or Pog1. These results suggest that the overexpression of Kin28 and Pog1 enhances the protein refolding and degradation pathways in rsp5A401E cells.
Keywords: mutant analysis, stress response

overall_design:
Total RNA from S. cerevisiae was isolated by the method of Köhrer and Domdey (1991). Poly A mRNA was enriched from total RNA by Oligotex dT30 mRNA purification kit (Takara Bio). The Affimetrix yeast genome S98 arrays (YGS98 GeneChip, Affymetrix, Santa Clara, CA) were used as DNA microarray in this study. The biotinyated cRNA (15 μg) probe was hybridized to DNA microarray at 45°C for 18 h according to Affymetrix user’s manual.
The washing and staining of arrays were performed using the GeneChip Fluidics Station 400.
The scanning of arrays was carried out using the GeneArray scanner (Agilent technologies, Palto Alto, CA).

first: Mika

last: Demae

first: Hiroshi

last: Takagi

first: Jun

last: Shima


title: Comparison between mRNAs of how germ-line clones embryos and WT embryos at 3-5 h AEL

status: Public on Sep 24 2007

city: Rehovot

first: Talila

last: Volk

address: Hertzel street

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

summary:
Mutant embryos lacking maternal and zygotic HOW exhibit defects in mesoderm development. How is an RNA binding protein that regulates the levels of mRNAs by controling RNA metabolism.
To gain an insight as to the profile of mRNAs regulated by HOW during early mesoderm development we analyzed the array of mRNAs whose levels are altered in the how mutant embryos.
Keywords: Genetic modification

overall_design: Embryos lacking both maternal and zygoic HOW were selected using a GFP balancer. The mRNA of 5 collections of 3-5 hrs old WT or how mutant embryos were pooled and used for each microarray experiment. Two microarray experiments were performed from independent samples.

first: Hila

last: Toledano-Katchalski


title: Prolonged selection in aerobic, glucose-limited chemostat cultures of Saccharomyces cerevisiae

status: Public on Aug 31 2007

first: Jean-Marc

last: Daran

summary:
Prolonged cultivation of Saccharomyces cerevisiae in aerobic, glucose-limited chemostat cultures (dilution rate, 0·10 h–1) resulted in a progressive decrease of the residual glucose concentration (from 20 to 8 mg l–1 after 200 generations). This increase in the affinity for glucose was accompanied by a fivefold decrease of fermentative capacity, and changes in cellular morphology. These phenotypic changes were retained when single-cell isolates from prolonged cultures were used to inoculate fresh chemostat cultures, indicating that genetic changes were involved. Kinetic analysis of glucose transport in an ‘evolved’ strain revealed a decreased Km, while Vmax was slightly increased relative to the parental strain. Apparently, fermentative capacity in the evolved strain was not controlled by glucose uptake. Instead, enzyme assays in cell extracts of the evolved strain revealed strongly decreased capacities of enzymes in the lower part of glycolysis. This decrease was corroborated by genome-wide transcriptome analysis using DNA microarrays. In aerobic batch cultures on 20 g glucose l–1, the specific growth rate of the evolved strain was lower than that of the parental strain (0·28 and 0·37 h–1, respectively). Instead of the characteristic instantaneous production of ethanol that is observed when aerobic, glucose-limited cultures of wild-type S. cerevisiae are exposed to excess glucose, the evolved strain exhibited a delay of 90 min before aerobic ethanol formation set in. This study demonstrates that the effects of selection in glucose-limited chemostat cultures extend beyond glucose-transport kinetics. Although extensive physiological analysis offered insight into the underlying cellular processes, the evolutionary ‘driving force’ for several of the observed changes remains to be elucidated
Keywords: evolution

overall_design: A crucial feature of bakers' yeast is its capacity to produce CO2, referred to as fermentative capacity (van Hoek et al., 1998). After prolonged glucose-limited cultivation of S. cerevisiae, in addition to an increased affinity for glucose, we observed a dramatic decrease in fermentative capacity. Consequently, the aim of the present study was to perform an integral analysis of the long-term adaptation of S. cerevisiae during prolonged glucose-limited, aerobic cultivation in chemostat cultures, with special emphasis on the regulation of glucose transport and glycolytic capacity. To this end, we applied an integrated approach that combined transcriptome analysis, measurement of fermentative capacity and activities of glucose transport and glycolytic enzymes, and characterization of cellular morphology.

first: M

last: Jansen

first: P

first: J

last: Pronk

first: JM


title: Prolonged Maltose-Limited Cultivation of Saccharomyces cerevisiae

summary:
Prolonged cultivation (>25 generations) of Saccharomyces cerevisiae in aerobic, maltose-limited chemostat cultures led to profound physiological changes. Maltose hypersensitivity was observed when cells from prolonged cultivations were suddenly exposed to excess maltose. This substrate hypersensitivity was evident from massive cell lysis and loss of viability. During prolonged cultivation at a fixed specific growth rate, the affinity for the growth-limiting nutrient (i.e., maltose) increased, as evident from a decreasing residual maltose concentration. Furthermore, the capacity of maltose-dependent proton uptake increased up to 2.5-fold during prolonged cultivation. Genome-wide transcriptome analysis showed that the increased maltose transport capacity was not primarily due to increased transcript levels of maltose-permease genes upon prolonged cultivation. We propose that selection for improved substrate affinity (ratio of maximum substrate consumption rate and substrate saturation constant) in maltose-limited cultures leads to selection for cells with an increased capacity for maltose uptake. At the same time, the accumulative nature of maltose-proton symport in S. cerevisiae leads to unrestricted uptake when maltose-adapted cells are exposed to a substrate excess. These changes were retained after isolation of individual cell lines from the chemostat cultures and nonselective cultivation, indicating that mutations were involved. The observed trade-off between substrate affinity and substrate tolerance may be relevant for metabolic engineering and strain selection for utilization of substrates that are taken up by proton symport.
Keywords: Evolution

overall_design:
In a recent study (25) we analyzed glucose efflux upon exposure of S. cerevisiae to excess maltose, with yeast cells originating from “young” chemostat cultures (<20 generations). In these experiments no cell lysis was observed upon exposure to excess maltose. However, in further work on this subject, we observed an apparent effect of chemostat culture age on transport capacity. The aim of the present study was to further investigate the effect of prolonged maltose-limited chemostat cultivation on the physiology of S. cerevisiae. To this end we monitored the affinity for maltose, genome-wide transcript levels, activities of key enzymes, and physiological responses to maltose excess during long-term cultivation in maltose-limited chemostat cultures.

Jansen, M. L. A., J. H. de Winde, and J. T. Pronk. 2002. Hxt-carrier-mediated glucose efflux upon exposure of Saccharomyces cerevisiaeSaccharomyces cerevisiae to excess maltose. Appl. Environ. Microbiol. 68:4259-4265.

last: Daran-Lapujade


title: Histone H3,K4,79R and H3,K4,36,79R (at 0, 6, and 9 hours) Mutations

status: Public on Aug 01 2007

first: John

last: Wyrick

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Histone H3 K4,36,79R 9 hr

summary:
Total RNA from two replicate cultures of wild-type and mutant strains was isolated and the expression profiles were determined using Affymetrix arrays. Comparisons between the sample groups allow the identification of genes regulated by H3 K4,36,79R mutant.  Cells were grown in galactose media and then shifted to glucose media for 9 hours to give the 9 hour time point.
Keywords: repeat

overall_design: Histone H3 K4,36,79R time course. Cells were grown in galactose media and then shifted to glucose media, which repressed the expression of wild-type histone H3, leaving the histone H3 K4,36,79R mutant as the sole source of histone H3 protein in the cell. Total RNA was isolated from replicate cultures of wild-type and mutant histone H3 at various time points after the shift to glucose media (0, 6, and 9 hours). Expression profiles were determined using Affymetrix arrays. Comparisons between the sample groups allow the identification of genes regulated by H3 K4,36,79R mutant.

first: Amy

last: Rodriguez

first: Yi

last: Jin


title: Genome-wide transcriptional responses of Saccharomyces cerevisiae to high carbon dioxide concentrations

summary:
Physiological effects of carbon dioxide and impact on genome-wide transcript profiles were analysed in chemostat cultures of Saccharomyces cerevisiae. In anaerobic, glucose-limited chemostat cultures grown at atmospheric pressure, cultivation under CO2-saturated conditions had only a marginal (<10%) impact on the biomass yield. Conversely, a 25% decrease of the biomass yield was found in aerobic, glucose-limited chemostat cultures aerated with a mixture of 79% CO2 and 21% O2. This observation indicated that respiratory metabolism is more sensitive to CO2 than fermentative metabolism. Consistent with the more pronounced physiological effects of CO2 in respiratory cultures, the number of CO2-responsive transcripts was higher in aerobic cultures than in anaerobic cultures. Many genes involved in mitochondrial functions showed a transcriptional response to elevated CO2 concentrations. This is consistent with an uncoupling effect of CO2 and/or intracellular bicarbonate on the mitochondrial inner membrane. Other transcripts that showed a significant transcriptional response to elevated CO2 included NCE103 (probably encoding carbonic anhydrase), PCK1 (encoding PEP carboxykinase) and members of the IMD gene family (encoding isozymes of inosine monophosphate dehydrogenase
Keywords: Dose reponse

overall_design: Knowledge on the genome-wide transcriptional response of S. cerevisiae to high CO2 concentrations may provide a deeper insight into the molecular mechanisms of CO2 stress. Such insight is essential to develop metabolic-engineering strategies for improving CO2 tolerance. Furthermore, identification of ‘signature transcripts’ that uniquely respond to CO2 stress may be applicable for diagnosing the CO2 status of industrial fermentations. It has recently been demonstrated that the combination of chemostat cultivation with DNA-microarray-based transcriptome analysis offers a powerful and reproducible approach to identify the transcriptional responses of yeasts to environmental parameters For this reason, in the present study we used chemostat cultures of S. cerevisiae to quantify the effect of CO2 on respiring and fermenting cells, and to determine the genome-wide transcriptional responses of this yeast to high CO2 concentrations.

last: Aguilera


title: The embryonic muscle transcriptome of Caenorhabditis elegans

status: Public on Jul 13 2007

city: Nashville

first: David

last: Miller

state: TN

address: 465 21st Avenue South

department: Cell and Developmental Biology

institute: Vanderbilt University

summary:
Background:  The force generating mechanism of muscle is evolutionarily ancient; the fundamental structural and functional components of the sarcomere are common to motile animals throughout phylogeny. Recent evidence suggests that the transcription factors that regulate muscle development are also conserved. Thus, a comprehensive description of muscle gene expression in a simple model organism should define a basic muscle transcriptome that is also expressed in animals with more complex body plans. To this end, we have applied Micro-Array Profiling of Caenorhabditis elegans Cells (MAPCeL) to muscle cell populations extracted from developing Caenorhabditis elegans embryos.   Results:  Fluorescence Activated Cell Sorting (FACS) was used to isolate myo-3::GFP-positive muscle cells, and their cultured derivatives, from dissociated early Caenorhabditis elegans embryos.  Microarray analysis identified 6,693 expressed genes, 1,305 of which are enriched in the myo-3::GFP positive cell population relative to the average embryonic cell.  The muscle-enriched gene set was validated by comparisons to known muscle markers, independently derived expression data, and GFP reporters in transgenic strains.  These results confirm the utility of MAPCeL for cell type-specific expression profiling and reveal that 60% of these transcripts have human homologs.
Conclusions:  This study provides a comprehensive description of gene expression in developing Caenorhabditis elegans embryonic muscle cells. The finding that over half of these muscle-enriched transcripts encode proteins with human homologs suggests that mutant analysis of these genes in Caenorhabditis elegans could reveal evolutionarily conserved models of muscle gene function with ready application to human muscle pathologies.
Keywords: embryonic muscle, myo-3::GFP

overall_design: Our goal is to profile gene expression in the major excitable tissues of Caenorhabditis elegans. As part of this effort, we profiled embryonic muscle cells at two timepoints: 0hr and 24hr.. To isolate transcripts from these cells we utilized the MAPCeL (Microarray Profiling Caenorhabditis elegans Cells) technique, which our lab previously developed (Fox et al 2005) in which myo-3::GFP+ cells are captured by FACS for RNA isolation. We verified these data by bioinformatic means and by in vivo validation by creating GFP reporters for a random set of genes in our enriched gene list.

first: Rebecca

last: Fox

first: Joseph

middle: D

last: Watson

first: Stephen

last: Von Stetina

first: Joan

last: McDermott

first: Thomas

last: Brodigan

first: Tetsunari

last: Fukushige

first: Michael

last: Krause

last: Miller III


title: Histone H3 K4,36,79R 0 hr

summary:
Total RNA from two replicate cultures of wild-type and mutant strains was isolated and the expression profiles were determined using Affymetrix arrays. Comparisons between the sample groups allow the identification of genes regulated by H3 K4,36,79R mutant.  Cells were grown in galactose media to give the 0 hour timepoint.
Keywords: repeat


title: Histone H3 K4,36,79R 6 hr

summary:
Total RNA from two replicate cultures of wild-type and mutant strains was isolated and the expression profiles were determined using Affymetrix arrays. Comparisons between the sample groups allow the identification of genes regulated by H3 K4,36,79R mutant.  Cells were grown in galactose media and then shifted to glucose media for 6 hours to give the 6 hour time point.
Keywords: repeat


title: Histone H3 K4,79R

summary:
Total RNA from three replicate cultures of wild-type and mutant strains was isolated and the expression profiles were determined using Affymetrix arrays. Comparisons between the sample groups allow the identification of genes regulated by H3 K4,79R mutant.
Keywords: repeat

overall_design: Comparison of genes whose mRNA levels are affected in a histone H3 K4,79R mutant yeast strain compared to wild-type yeast strain.


title: Stb3 deletion affects gene expression within 10 minutes of glucose addition

status: Public on Jul 06 2007

city: Madison

first: Warren

last: Heideman

state: WI

address: 777 Highland Ave

department: Pharmacy

institute: University of Wisconsin

summary:
Microarrays were conducted to asses the effect of Stb3 deletion in immediate transcriptional induction in response to glucose
Keywords: Stb3, immediate glucose induction, growth genes.

overall_design: Response of Stb3 delete cells was compared to that of wild type (BY4742) in cells grown for 3 days in YPD and cells that received 2% glucose for 10 minutes after the 3 day growth period. Two repetitive samples were done for each timepoint.

first: Dritan

last: Liko

first: Matthew

last: Slattery


title: Role of Transcriptional Regulation in Controlling Fluxes in Central Carbon Metabolism of Saccharomyces cerevisiae

first: Jean-Marc

last: Daran

summary:
In contrast to batch cultivation, chemostat cultivation allows the identification of carbon source responses without interference by carbon-catabolite repression, accumulation of toxic products, and differences in specific growth rate. This study focuses on the yeast Saccharomyces cerevisiae, grown in aerobic, carbon-limited chemostat cultures. Genome-wide transcript levels and in vivo fluxes were compared for growth on two sugars, glucose and maltose, and for two C2-compounds, ethanol and acetate. In contrast to previous reports on batch cultures, few genes (180 genes) responded to changes of the carbon source by a changed transcript level. Very few transcript levels were changed when glucose as the growth-limiting nutrient was compared with maltose (33 transcripts), or when acetate was compared with ethanol (16 transcripts). Although metabolic flux analysis using a stoichiometric model revealed major changes in the central carbon metabolism, only 117 genes exhibited a significantly different transcript level when sugars and C2-compounds were provided as the growthlimiting nutrient. Despite the extensive knowledge on carbon source regulation in yeast, many of the carbon source-responsive genes encoded proteins with unknown or incompletely characterized biological functions. In silico promoter analysis of carbon source-responsive genes confirmed the involvement of several known transcriptional regulators and suggested the involvement of additional regulators. Transcripts involved in the glyoxylate cycle and gluconeogenesis showed a good correlation with in vivo fluxes. This correlation was, however, not observed for other important pathways, including the pentose-phosphate pathway, tricarboxylic acid cycle, and, in particular, glycolysis. These results indicate that in vivo fluxes in the central carbon metabolism of S. cerevisiae grown in steadystate, carbon-limited chemostat cultures are controlled to a large extent via post-transcriptional mechanisms.
Keywords: medium composition

overall_design:
Cultivation of microorganisms in chemostats offers numerous advantages for studying the structure and regulation of metabolic networks (11). In chemostat cultures, individual culture parameters can be changed, while keeping other relevant physical and chemical culture parameters (composition of synthetic medium, pH, temperature, aeration, etc.) constant. An especially important parameter in this respect is the specific growth rate, which, in a chemostat, is equal to the dilution rate, which can be accurately controlled. This allows the experimenter to investigate the effects of environmental changes or genetic interventions at a fixed specific growth rate, even if these changes result in different specific growth rates in batch cultures. In a chemostat, growth can be limited by a single, selected nutrient. The very low residual concentrations of this growth-limiting nutrient in chemostat cultures alleviate effects of catabolite repression and inactivation. Furthermore, these low residual substrate concentrations prevent substrate toxicity, which, for example, occurs when S. cerevisiae is grown on ethanol or acetate as the carbon source in batch cultures .
The central goal of the present study is to assess to what extent carbon source-dependent regulation of fluxes through central carbon metabolism in S. cerevisiae is regulated at the level of transcription. To this end, we compare the transcriptome of carbon-limited, aerobic chemostat cultures grown on four different carbon sources: glucose, maltose, ethanol, and acetate. Data from the transcriptome analysis are compared with flux distribution profiles calculated with a stoichiometric metabolic network model. Questions that will be addressed are as follows: (i) does glucose-limited aerobic cultivation lead to a complete alleviation of glucose-catabolite repression; (ii) how (in)complete is our understanding of the genes involved in the transcriptional response of S. cerevisiae to four of the most common carbon sources for this yeast; and (iii) to what extent do transcriptome analyses with microarrays provide a reliable indication of flux distribution in metabolic networks?

first: Pascale

last: Daran-Lapujade

first: Jack

last: Pronk

first: Jean-marc


title: Transcriptional responses by alpha-emitting radioimmunoconjugate Bi-213-CD20-rituximab

status: Public on Jul 01 2007

city: Düsseldorf

first: Sascha

last: Raschke

address: Universitätsstraße 1

department: Klinik für Hämatologie, Onkologie und klinische Immunologie

country: Germany

institute: Heinrich-Heine Universität Düsseldorf


title: Transcript profiling of normal and transformed buccal keratinocytes

status: Public on Aug 21 2007

first: Roland

last: Grafström

address: Nobelsväg 13

department: Institute of Environmental Medicine

country: Sweden

institute: Karolinska Institutet

summary:
Normal and two transformed buccal keratinocyte lines were cultured under a standardized condition to explore mechanisms of carcinogenesis and tumor marker expression at transcript and protein level. An approach combining three bioinformatic programs allowed coupling of abundant proteins and large-scale transcript data to low-abundance transcriptional regulators. The analysis identified previously proposed, and suggested novel, protein biomarkers, Gene Ontology categories and molecular networks including functionally impaired key regulator genes for buccal/oral carcinoma.
Keywords: Cell type comparison

overall_design:
Analysis of differential expression in two transformed buccal keratinocyte lines (SVpgC2a and SqCC/Y1) relative to normal buccal keratinocytes. Both normal and transformed cells were cultured under a standardized serum-free condition.
Two replicates for all cell types were included.

first: Claudia

last: Staab

last: Ceder

first: Theres

last: Jägerbrink

first: Jan-Anders

last: Nilsson

first: Karin

last: Roberg

first: Hans

last: Jörnvall

first: Jan-Olov

last: Höög


title: Cell-specific microarray profiling of the C. elegans nervous system.

status: Public on Jun 25 2007

first: David

last: Miller

summary:
Background: With its fully sequenced genome and simple, well-defined nervous system, the nematode C. elegans offers a unique opportunity to correlate gene expression with neuronal differentiation.  The lineal origin, cellular morphology and synaptic connectivity of each of the 302 neurons are known. In many instances, specific behaviors can be attributed to particular neurons or circuits. Here we describe microarray-based methods that monitor gene expression in C. elegans neurons and thereby link comprehensive profiles of neuronal transcription to key developmental and functional attributes of the nervous system. Results: We employed complementary microarray-based strategies to profile gene expression in the embryonic and larval nervous systems.  In the MAPCeL (Micro-Array Profiling C. elegans Cells) method, we used Fluorescence Activated Cell Sorting (FACS) to isolate GFP-tagged embryonic neurons for microarray analysis. To profile the larval nervous system, we used the mRNA-tagging technique in which an epitope-labeled mRNA binding protein (FLAG-PAB-1) was transgenically expressed in neurons for immunoprecipitation of cell-specific transcripts. These combined approaches identified approximately 2,500 mRNAs that are highly enriched in either the embryonic or larval C. elegans nervous system. These data are validated in part by the detection of gene classes (e.g. transcription factors, ion channels, synaptic vesicle components) with established roles in neuronal development or function. In addition to utilizing these profiling approaches to define stage specific gene expression, we also applied the mRNA-tagging method to fingerprint a specific neuron type, the A-class group of cholinergic motor neurons, during early larval development. A comparison of these data to a MAPCeL profile of embryonic A-class motor neurons identified genes with common functions in both types of A-class motor neurons as well as transcripts with roles specific to each motor neuron type.
Conclusion: We describe microarray-based strategies for generating expression profiles of embryonic and larval C. elegans neurons. These methods can be applied to particular neurons at specific developmental stages and therefore provide an unprecedented opportunity to obtain spatially and temporally defined snapshots of gene expression in a simple model nervous system.
Keywords: nervous system, development

overall_design:
Our goal is to profile gene expression throughout the nervous system of the model organism Caenorhabditis elegans. As a first goal, we profiled the entire nervous system at two developmental timepoints. To isolate transcripts from embryonic neurons we employed the MAPCeL (Microarray Profiling C. elegans Cells) technique in which pan-neuronal GFP+ cells are captured by FACS for RNA isolation. Since postembryonic cells are unattainable via this method, we used mRNA-tagging to isolated pan-neural RNAs from larval animals. In short, an epitope tagged poly-A binding protein (FLAG-PAB-1) was driven in all neurons using the F25B3.3 promoter.  Following formaldehyde cross-linking, animals were passed through a French press and Dounce homogenized to isolate a cell-free extract. Anti-FLAG antibodies were incubated with the cell-free extract to capture FLAG-PAB bound RNAs. After elution and reversal of the crosslinks, RNAs are isolated by TriZOL extraction. We also identified transcripts enriched in a subset of C. elegans larval neurons, the A-class neurons (using unc-4::3xFLAG::PAB-1).

3 sets of experiments normalized separately by RMA

larval references of sets 2 and 3 originate from the same hybridizations (accompanying CEL files are identical)

first: Stephen

last: Von Stetina

first: Joseph

last: Watson

first: Rebecca

last: Fox

first: Kellen

last: Olszewski

first: W

last: Spencer

first: Peter

last: Roy


title: In vivo evidence of Pseudomonas aeruignosa nutrient acquisition and pathogenesis in the cystic fibrosis lung

status: Public on Aug 15 2007

city: Honolulu

first: Tung

last: Hoang

state: HI

address: 1800 East-West Road

department: Microbiology

institute: University of Hawaii at Manoa

summary:
One of the hallmarks of Pseudomonas aeruginosa cystic fibrosis (CF) infection is very high-cell-density (HCD) replication in the lung, allowing this bacterium to induce virulence controlled by HCD quorum-sensing systems.  However, the nutrient sources sustaining HCD replication in this chronic infection is largely unknown.  Hence, understanding the nutrient factors contributing to HCD in the CF lung will yield new insights into the 'metabolic pathogenicity' and potential treatment of CF infections caused by P. aeruginosa.  Herein, we performed microarray studies of P. aeruginosa directly isolated from the CF lung to demonstrate its metabolic capability and virulence in vivo.  Our in vivo microarray data, confirmed by real-time reverse-transcription-PCR, indicated P. aeruginosa expressed several genes for virulence, drug-resistance, and utilization of multiple nutrient sources (lung surfactant lipids and amino acids) contributing to HCD replication.  The data also indicates deregulation of several pathways, suggesting in vivo evolution by deregulation of a large portion of the transcriptome during chronic CF infection.  To our knowledge, this is the first in vivo transcriptome of P. aeruginosa in a natural CF infection, and it indicates several important aspects of pathogenesis, drug-resistance, and nutrient-utilization never before observed in vivo.
Keywords: in vivo gene induction

overall_design: The purpose of the experiment was to observe which genes are upregulated in P. aeruginosa during chronic CF lung infection as compared to PAO1.  All in vitro studies were grown in 1x M9 minimal media supplemented with 20 mM citrate and grown to mid-log phase prior to RNA isolation.  The in vivo RNA was isolated directly from CF sputum samples after TRIzol treatment.  Each in vitro sample (both for PAO1 and the CF sputum pool isolate) were processed individually and in triplicate.  Two in vivo isolations from sputum were conducted from the same patient but two different sputum samples.  After isolation of total RNA, samples were processed for microarrays (i.e. cDNA synthesis, fragmentation, labeling, etc) as recommended by Affymetrix, and processed on the GeneChip as recommended by Affymetrix.

first: Mike

last: Son

first: Wallace

last: Matthews

first: Yun

last: Kang

last: Nguyen


title: Transcriptional responses in primary CD19+ B-cells by the alpha-emitting radioimmunoconjugate Bi-213-CD20-rituximab

first: Sascha

last: Raschke

summary:
The possibility to deliver radioisotopes directly to tumor cells by using monoclonal antibodies has become a promising concept for the elimination of small tumor nodules or single disseminated tumor cells. The alpha-particle emitter Bismut-213 which has a high linear energy transfer and a very short path length appears to be able to kill cells by only few nuclear hits. Bismut-213 based alpha-immunotherapy treatment is currently proved in clinical trials for AML, NHL and preclinically for CLL and multiple myeloma.
Because little is known about the biological effects of alpha radiation we examined the molecular effects of the alpha emitter Bismut-213 in malignant and normal B-cells. In this study, we used the cell line Karpas 422 (K422) which had been derived from a malignant B-cell Non-Hodgkin’s lymphoma as well as normal primary CD19+ B-cells which had been selected immunomagnetically from peripheral blood. For the delivery and binding of the alpha emitter we used the monoclonal antibody rituximab which targets the CD20 receptor of malignant and normal B-cells.
The lymphoma cell line K422 was incubated in vitro with Bismut-213-CD20 with 100 µCi and 200 µCi respectively, for 46 min (1 half life time of the alpha emitter) or 24 h. Immunomagnetically isolated CD19+ cells from healthy donors were incubated in vitro with Bismut-213-CD20 with 100 µCi or 200 µCi, for 46 min. Gene expression profiles of irradiated cells were analysed using cDNA oligonucleotide arrays (Affymetrix Human Genome Focus Arrays) comprising 8,793 genes and compared with those from untreated control cells. Following normalization significantly altered genes were identified by using the variance stabilization normalization (VSN) method and the significance analysis of microarrays (SAM) algorithm.
Differentially expressed genes were defined to exhibit a fold change of 1,4 and higher or 0,7 and lower and a q-value of 5% or lower compared to the genes of the untreated control cells. Irradiated K422 cells with 100 µCi showed 42 differential expressed genes after 46 minutes (one half life time) and 451 deregulated genes after exposure of 24 hours. A similar response could be observed at an exposure of 200 µCi (50 differentially expressed genes after 46 min; 485 genes after 24 h). Hence, a severe radiation induced response could not be detected before 24 hours. 200 µCi irradiated CD19+ cells showed 67 differentially expressed genes after 46 minutes compared to the untreated CD19+ cells (for 100 µCi: 42 differentially expressed genes).

By performing cluster analyses the irradiated cells exhibited a distinct homogenous molecular phenotype in comparison to not irradiated cells. Alpha irradiated cells showed transcriptional activation of DNA repair genes. Furthermore, both examined cell types showed up-regulated genes which are known to play a role in general and oxidative stress response. Surprisingly, up-regulation of interferon-stimulated genes in K422 cells could be observed. Because of the transcriptional activation of genes regulating the G1-S- cell cycle transition the supposition came up that the irradiated K422 do progress into the S-phase of the cell cycle and arrest in the S- or G2/M-phase. In contrast to the K422 cells the primary CD19+ B-cells revealed transcriptional activation of cell cycle inhibitors which is an already known reaction following ionizing radiation but no apoptosis associated genes could be observed. In spite of the massive cytotoxic damages which are assumed referring to the gene expression data the K422 cells appear to be able to activate several defense mechanisms in a precise manner. Hence, the malignant K422 cells exhibit a larger amount as well as more various responses than the CD19+ cells. This might be due to the tumorigenic transformation of the malignant cells that exhibit probably more effective defense strategies than the CD19+ cells. The balance between the therapeutic effect of alpha radiation on malignant cells and the damaging effect on normal cells is an essential issue and it is of important clinical relevance concerning radioimmunotherapy with alpha radiation.
Keywords: time course and dose dependency

overall_design: Comparison of gene expression profiles of untreated and Bi-213-CD20 rituximab irradiated immunomagnetically selected primary CD19+ cells from healthy human donors

first: Simona

last: Martin

first: Michael

last: Rosskopf

first: Slawomir

last: Kliszewski

first: Christos

last: Apostolidis

first: Alfred

last: Morgenstern

first: Mirjam

last: Weis

first: Frank

last: Neumann

first: Arndt

last: von Haeseler

first: Rainer

last: Haas

first: Ralf

last: Kronenwett


title: Repression of pleiotrophic drug resistance genes in Saccharomyces cerevisiae using chimeric transcriptional repressors

status: Public on Jun 29 2007

city: Memphis

first: Geoffrey

last: Neale

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

summary:
Yeast is a powerful model system for studying the action of small molecule therapeutics. An important limitation has been low efficacy of many small molecules in yeast due to limited intracellular drug accumulation. We used the DNA binding domain of the pleiotropic drug resistance regulator Pdr1 fused in-frame to transcription repressors to repress Pdr1 regulated genes. Expression of these regulators conferred dominant enhancement of drug sensitivity and led to greatly diminished levels of Pdr1p regulated transcripts, including the yeast p-glycoprotein homologue Pdr5. Enhanced sensitivity was seen for a wide range of small molecules. Biochemical measurements demonstrated enhanced accumulation of rhodamine in yeast cells carrying the chimeras. These repressors of Pdr1p regulated transcripts can be introduced into large collections of strains such as the S. cerevisiae deletion set, and enhance the utility of yeast for studying drug action and for mechanism-based drug discovery.
Keywords: Comparison of genetic variants

overall_design: We determined the profiles of gene expression in yeast strains expressing dominant-negative Pdr1-fusion transcription factors. Yeast strains expressing different Pdr1-fusion repressors were analyzed by extracting total RNA and hybridization to Affymetrix GeneChip YG-s98 microarrays

first: John

last: Nitiss

first: Alexander

last: Stepanov

first: Karin


title: Gene expression profiling of hormone resistant prostate cancer

city: Kassel

first: Oliver

middle: Christoph

last: Stoss

department: Molecular Pathology

institute: Targos GmbH

summary:
In this study we performed transcriptional profiling of transurethral resections of hormone resistant prostate cancer and compared it with benign prostatic hyperplasia (BPH), untreated localized prostate cancer and hormone sensitive prostate cancer.
Keywords: time course; disease state analysis

overall_design:
Each sample (= Array) is derived from a different patient with the following subsequent disease states: 3x BPH, 7x localized prostate cancer samples, 2 horomone sensitive prostate cancer samples, one locally advanced prostate cancer, 4x hormone resistant prostate cancer early stage and 3x hormone resistant prostate cancer late stage.
Platform was Affymetrix

first: Peter

last: Albers

first: Meike

last: Werther

first: Dirk

last: Zielinski

first: Katja

last: Saur-Metz

last: Middel

first: Nico

last: Jost

first: Josef

last: Rueschoff

first: Thomas

last: Henkel


title: Expression data for whole adult tissue; Drosophila males of seven species

status: Public on May 23 2007

city: Ithaca

first: Jason

last: Mezey

state: NY

address: 101 Biotechnology Building, Cornell University

department: BSCB

institute: Cornell University

summary:
Co-expression of genes that physically cluster together is a common characteristic of eukaryotic transcriptomes.  Identifying these groups of co-expressed genes is important to the functional annotation of genomes and understanding the evolutionary fates of the clustered genes.
We used microarrays to measure gene expression in seven closely related Drosophila species, to identify domains clusters within a species of Drosophila (D. simulans) and that are evolving among species in the D. melanogater subgroup.
Keywords: species comparison

sample_organism:
Drosophila mauritiana
Drosophila melanogaster
Drosophila sechellia
Drosophila simulans
Drosophila teissieri
Drosophila yakuba
Drosophila santomea

overall_design: Assays were carried out on three independent (biological) replicates per species for a single line of the following five species: D.yakuba (Tuscon Stock Center Number: 14021-0261.00), D.santomea (TSCN: 14021-0271.00), D.teissieri (TSCN: 14021-0257.00), D.mauritiana (David 105, TSCN: 14021-0241.01), D.sechellia (Roberstson, TSCN: 14021-0248.21). Three biological replicates for D.melanogaster.  The samples assayed for D.melanogaster reflect an even genotypic contribution of 10 isogenic lines developed from a wild population (Winters, CA) and crossed in a round-robin design.For D. simulans, three replicate arrays were used to assay each of 10 round-robin crosses between 10 isogenic lines developed from the same population.  the entire data set therefore included a total of 48 independent transcript assays covering seven Drosophila species in the D.melanogaster subgroup

first: Sergey

last: Nuzhdin

first: Corbin

last: Jones


title: Unique Gene Expression Profiles of Donor-Matched Human Retinal and Choroidal Vascular Endothelial Cells

status: Public on May 25 2007

city: Portland

first: Justine

last: Smith

state: OR

address: 3181 SW Sam Jackson Park Road, Biomedical Research Building, Level 2

department: Casey Eye Institute

institute: Oregon Health & Science University

summary:
Consistent with clinical observations that posterior uveitis frequently involves the retinal vasculature and recent recognition of vascular heterogeneity, we hypothesized that retinal vascular endothelium was a cell population of unique molecular phenotype. Donor-matched cultures of primary retinal and choroidal endothelial cells from 6 human cadavers were incubated with either Toxoplasma gondii tachyzoites (10:1, parasite:cell) or Escherichia coli lipopolysaccharide (100 ng/mL); control cultures were simultaneously incubated with medium. Gene expression profiling of endothelial cells was performed using oligonucleotide arrays containing probes designed to detect 8747 human transcripts. After normalization, differential gene expression was assessed by the significance analysis of microarrays, with the false discovery rate set at 5 %. For selected genes, differences in level of expression between retinal and choroidal cells were evaluated by real-time RT-PCR. Graphical descriptive analysis demonstrated strong correlation between gene expression of unstimulated retinal and choroidal endothelial cells, but also highlighted distinctly different patterns of expression that were greater than differences noted between donors or between unstimulated and stimulated cells. Overall, 779 of 8,747 transcripts (8.9 %) were differentially represented. Notably, the 330 transcripts that were present at higher levels in retinal cells included a larger percentage of transcripts encoding molecules involved in the immune response. Differential gene expression was confirmed for 12 transcripts by RT-PCR. Retinal and choroidal vascular endothelial cells display distinctive gene expression profiles. Our findings suggest the possibility of treating posterior uveitis by targeting specific interactions between the retinal endothelial cell and an infiltrating leukocyte.
Keywords: Cell type comparison, stress response

overall_design: Retinal and choroidal vascular endothelial cells were isolated from both eyes of 6 human cadaver donors. Endothelial cells of each subtype from each donor were separately pooled and cultured. In a first series of experiments (Experiment 1), donor-matched cultures of retinal and choroidal endothelial cells derived from 3 donors were incubated with either T. gondii tachyzoites or medium alone. In a second set of experiments (Experiment 2), cultured retinal and choroidal endothelial cells derived from the other 3 donors were stimulated with LPS or medium alone. Whenever possible, 2 replicate dishes of endothelial cells were subjected to each set of conditions. Subsequent to incubations, mRNA was extracted from a cell lysate prepared from each dish of cells, and cRNA derived from each mRNA preparation was separately hybridized to one oligonucleotide expression array.

middle: R

first: Dongseok

last: Choi

first: James

last: Rosenbaum


title: Transcriptional responses in B-cell lymphomas by the alpha-emitting radioimmunoconjugate Bi-213-CD20-rituximab

first: Sascha

last: Raschke

overall_design: Comparison of gene expression profiles of untreated and Bi-213-CD20 rituximab irradiated K422 cells

first: Simona

last: Martin

first: Michael

last: Rosskopf

first: Slawomir

last: Kliszewski

first: Christos

last: Apostolidis

first: Alfred

last: Morgenstern

first: Mirjam

last: Weis

first: Frank

last: Neumann

first: Arndt

last: von Haeseler

first: Rainer

last: Haas

first: Ralf

last: Kronenwett


title: Differential expression in selected adult female Drosophila melanogaster

status: Public on Apr 16 2007

city: Aarhus

first: Morten

middle: Muhlig

last: Nielsen

address: Palle Juul-Jensens Bouleward 99

department: Department of Molecular Medicine

country: Denmark

institute: Aarhus University

summary:
A study evaluating the effect of stress resistance selection of Drosophila melanogaster.

Abstract
Here, we report a detailed analysis of changes in gene expression in Drosophila melanogaster selected for multiple eological relevant environmental stress resistance traits. We analyzed females from three biological replicates from seven selection regimes and one control regime using whole genome gene expression arrays. Replicated selection lines were selected for resistance to acute heat survival, high temperature knock down, constant 30°C during development, cold shock survival, desiccation and starvation, respectively. Additionally, a set of replicated lines was selected for increased longevity. When compared to gene expression profiles of control lines, we were able to detect consistent selection responses at the transcript level in each specific selection regime and also found a group of differentially expressed genes that were generally changed among all selected lines. Replicated selection lines clustered together, i.e. showed similar changes in gene expression (compared to controls) and thus showed that 10 generations of artificial selection gives a clear signal among gene expression profiles. The changes in gene expression in lines selected for increased longevity, desiccation and starvation resistance, respectively, showed high similarities. Cold resistance selected lines showed little differentiation from controls. Different methods of heat selection (heat survival, heat knock down and constant 30°C) showed little similarity verifying that different mechanism are involved in high temperature adaptation. The direction of change in gene expression in the selected lines showed a consistent pattern for each selection regime. For most selection regimes and in the comparison of all selected lines and controls exclusively up- or down regulation of gene expression among significant differentially expressed genes was found. The different responses to selection expressed in individual selection regimes and among all selected lines indicate that we have identified genes involved in stress specific and general stress response mechanisms.
Keywords: control versus selected

overall_design: gene expression was measured in biological triplicates of control flies and flies selected for resistance to various stressors.

first: Jesper

last: Sørensen

first: Volker

last: Loeschcke


title: Combined arrayCGH and SNP-loss of heterozygosity analysis in cervical cancer

status: Public on Jul 31 2007

city: Leiden

first: Jan

last: Oosting

address: Albinusdreef 2

department: Pathology

institute: Leiden University Medical Center

type: Genome variation profiling by genome tiling array

summary:
BACKGROUND: Cervical carcinoma develops as a result of multiple genetic alterations. Different studies investigated genomic alterations in cervical cancer mainly by means of metaphase comparative genomic hybridization (mCGH) and microsatellite marker analysis for the detection of loss of heterozygosity (LOH). Currently, high throughput methods such as array comparative genomic hybridization (array CGH), single nucleotide polymorphism array (SNP array) and gene expression arrays are available to study genome-wide alterations. Integration of these 3 platforms allows detection of genomic alterations at high resolution and investigation of an association between copy number changes and expression. RESULTS: Genome-wide copy number and genotype analysis of 10 cervical cancer cell lines by array CGH and SNP array showed highly complex large-scale alterations. A comparison between array CGH and SNP array revealed that the overall concordance in detection of the same areas with copy number alterations (CNA) was above 90%. The use of SNP arrays demonstrated that about 75% of LOH events would not have been found by methods which screen for copy number changes, such as array CGH, since these were LOH events without CNA. Regions frequently targeted by CNA, as determined by array CGH, such as amplification of 5p and 20q, and loss of 8p were confirmed by fluorescent in situ hybridization (FISH). Genome-wide, we did not find a correlation between copy-number and gene expression. At chromosome arm 5p however, 22% of the genes were significantly upregulated in cell lines with amplifications as compared to cell lines without amplifications, as measured by gene expression arrays. For 3 genes, SKP2, ANKH and TRIO, expression differences were confirmed by quantitative real-time PCR (qRT-PCR). CONCLUSION: This study showed that copy number data retrieved from either array CGH or SNP array are comparable and that the integration of genome-wide LOH, copy number and gene expression is useful for the identification of gene specific targets that could be relevant for the development and progression in cervical cancer.
Keywords: DNA copynumber RNA expression correlation

overall_design: Cervival cancer cell lines were hybridized to Affymetrix Focus arrays in duplicate. Correlations were made with copynumber profiles from arrayCGH and SNP arrays.

first: Judith

middle: N

last: Kloth

first: Tom

last: van Wezel

first: Karoly

last: Szuhai

first: Jeroen

last: Knijnenburg

first: Arko

last: Gorter

first: Gemma

last: Kenter

first: Gert-Jan

last: Fleuren

first: Ekaterina

last: Jordanova


title: Responses of Pseudomonas aeruginosa to low oxygen

status: Public on May 17 2007

city: Seattle

first: Carolina

last: Alvarez

address: 1959 NE Pacific St

institute: University of Washington

summary:
In order to understand how Pseudomonas aeruginosa responds to low oxygen we grew strain PAO1 with 3 different oxygen concentrations: 2%, 0.4% and 0% supplemented with nitrate as an electron acceptor. Gene expression under these conditions was compared to that of cells grown with 20% oxygen.
Keywords: Comparison of transcriptome profiles

overall_design: Transcriptome profiles of Pseudomonas aeruginosa cells grown with 20% oxygen were compared to transcriptome profiles obtained by growing cells with 2%, 0.4% and 0% oxygen (with nitrate as the electron acceptor).

last: Alvarez-Ortega

first: Caroline

last: Harwood


title: Regulation of presenilin genes (rogae-affy-c.ele-431660)

status: Public on Mar 23 2007

city: Phoenix

first: Winnie

last: Liang

state: AZ

address: 445 N. Fifth Street

institute: Translational Genomics

summary:
Regulation of presenilin genes. Presenilins are intramembrane aspartic proteases. These proteases are critical proteins in pathogenesis of Alzheimer's disease. The function of recently identified presenilin-homologous proteases (IMPAS or SPP)s is unknown. Our preliminary data in C.elegans model suggested the role of these proteins in early-development and , perhaps, in pathway related- to cholesterol -regulated signalling (Grigorenko et al, 2004, PNAS).
The overall goal is to determine pattern of gene expression alterations in cells with knock-out or knock-down presenilin related proteins (IMPAS). The cultured cells, C.elegans and mouse models are planned to be used in this study. Here , we will determine gene expression patterns in C.elegans strain NL2099, fed with bacteria HT115, producing dsRNA for Ce-imp-2 gene (knock-down of imp-2 gene by RNAi )or GFP gene as a control.
We hypothesize that novel family of presenilin-related proteases is important for cholesterol-regulated intracellular signalling and early development (including CNS/neuronal development and function).
C.elegans (strain  NL2099)  on L1 stage were placed  on agarose plates with bacteria HT115,  producing dsRNA for: 1) Ce-imp-2 gene; 2) GFP as a control gene. After 48 hours  at 20C , worms were washed in  M9 buffer and total RNA was isolated by TRIzol method.
Keywords: dose response

first: Evgeny

middle: I

last: Rogaev


title: Explaining Differences in Saturation Levels for Affymetrix GeneChip Arrays

status: Public on Jun 15 2007

city: Los Angeles

first: Diana

last: Abdueva

state: CA

address: 443 S San Pedro St, STE 403

institute: USC

summary:
The experimental spike-in studies of microarray hybridization conducted by Affymetrix demonstrate a nonlinear response of fluorescence intensity signal to target concentration. It was shown that the Langmuir adsorption isotherm recapitulates a general trend of signal response to concentration. However, this model fails to explain some key properties of the observed signal. In particular, according to the simple Langmuir isotherm, all probes should saturate at the same intensity level. However, this effect was not observed in the publicly available Affymetrix spike-in datasets. In our experimental study, we attempt to account for the unexplained variation in the observed probe intensities using customized fluidics scripts. We explore experimentally the effect of the stringent wash, target concentration, and hybridization time on the final microarray signal.
Keywords: hybridization condition effect

overall_design: The washing effect is assessed by scanning chips both prior to and after the stringent wash (Wash Condition). Selective labeling of both specific and non-specific targets allows the visualization and investigation of the washing effect for both specific and non-specific signal components. By varying the length of the hybridization cycle, the issue of attaining probe-target binding equilibrium can be addressed (Hybridization Time). To explore saturation potential, we performed hybridization experiments in which four clones are spiked-in and hybridized to two chips at a concentration of 1nM and 10nM respectively, each in the absence of complex background (Labeling Condition).

first: Dmitriy

last: Skvortsov

first: Christina

last: Curtis

first: Betty

last: Schaub

first: Simon

last: Tavare


title: Decline of Nucleotide Excision Repair Capacity in Aged Caenorhabditis elegans

status: Public on May 16 2007

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary:
We used gene expression profiling to address several specific questions that arose in a study of repair of ultraviolet C radiation in C elegans, as well as to generate hypotheses regarding the possible mechanism(s) of decreased DNA repair observed in old adults in that study. This analysis was performed in order to analyze gene expression in the strain (JK1107) and experimental conditions that we used for our DNA repair studies.
The supplementary file GSE4766_Resolver_all_data.txt includes  Resolver generated fold-changes and p values based on ratios built in Rosetta Resolver as described in the Rosetta Biosoftware Technical Note (Lee Weng, 2004), Data processing and analysis methods in the Rosetta Resolver system (http://www.rosettabio.com/tech/default.htm).
Keywords: C elegans, glp-1, age, nucleotide excision repair, ultraviolet radiation, DNA damage

overall_design: Gene expression data for glp-1 (strain JK1107) nematodes were obtained by comparing mRNA expression level in replicate pools of 2000-3000 mixed-stage embryos, young (1-day) adults, and old (6-day) adults raised at 25ºC. Three replicate pools of embryo and young adult samples were analyzed, but only two replicate pools of 6-day adults were analyzed due to low RNA recovery.

first: Joel

last: Meyer

first: Windy

last: Boyd

first: Greg

last: Azzam

first: Astrid

last: Haugen

first: Jonathan

middle: H

last: Freedman

first: Bennett

last: Van Houten


title: Pseudomonas aeruginosa PAO1 virulent genes in the poplar rhizosphere

status: Public on Mar 18 2007

city: College Station

first: Can

last: Attila

state: TX

address: 524 Jack E. Brown Bldg.

department: Chemical Eng

institute: Texas A&M University

summary:
Pseudomonas aeruginosa PAO1 contacted with and without poplar roots gene expression Poplar contacted with and without PAO1 gene expression. All samples cultured in 1 x hrp + 0.25 % sucrose
Keywords: Contact with different species

sample_organism:
Pseudomonas aeruginosa
Populus

platform_organism:
Pseudomonas aeruginosa
Populus sp.

overall_design:
Strains: P. aeruginosa PAO1 WT
Medium: 1 x hrp + 0.25 % sucrose
Biofilm grown on poplar root compared to biofilm grown on glasswool
Poplar roots grown

first: Thomas

middle: K

last: Wood

first: Akihiro

last: Ueda


title: Natural gene expression variation in the HapMap CEU and YRI samples

status: Public on Mar 14 2007

first: Joshua

middle: M

last: Akey

address: 1705 NE Pacific St

department: Genome Sciences

summary:
B lymphoblastoid cell lines were obtained from Coriell Cell Repositories. Cell lines were grown according to Coriell guidelines and total RNA was extracted, labeled, and hybridized to an Affymetrix Human Genome Focus Array as previously described. We found extensive variation in gene-expression levels and estimate that ~83% of genes are differentially expressed among individuals and that ~17% of genes are differentially expressed among populations. By decomposing total gene-expression variation into within- versus among-population components, we find that most expression variation is due to variation among individuals rather than among populations, which parallels observations of extant patterns of human genetic variation.
Keywords: resting expression levels in B lymphoblastoid cell lines

overall_design: We used microarrays to survey patterns of natural gene expression variation in 16 HapMap individuals derived from the CEU and YRI samples.

first: John

last: Storey

first: Mark

last: Wurfel

first: Jenny

last: Madeoy

first: Jeanna

last: Strout


title: Developmental transcriptome profiling of the C. elegans pocket protein ortholog, lin-35

status: Public on Apr 27 2007

city: Laramie

first: David

last: Fay

state: WY

address: 1000 E. University Dept. 3944

department: MOLB

institute: University of Wyoming

summary:
LIN-35 is the single C. elegans ortholog of the mammalian pocket protein family members, pRb, p107, and p130. To gain insight into the roles of pocket proteins during development, a microarray analysis was performed with lin-35 mutants. Stage-specific regulation patterns were revealed, indicating that LIN-35 plays diverse roles at distinct developmental stages. LIN-35 was found to repress the expression of many genes involved in cell proliferation in larvae, an activity that is carried out in conjunction with E2F. In addition, LIN-35 was found to regulate neuronal genes during embryogenesis and targets of the intestinal-specific GATA transcription factor, ELT-2, at multiple developmental stages. Additional findings suggest that LIN-35 functions in cell cycle regulation in embryos in a manner that is independent of E2F. A comparison of LIN-35-regulated genes with known fly and mammalian pocket-protein targets revealed a high degree of overlap, indicating strong conservation of pocket protein functions in diverse phyla. Based on microarray results and our refinement of the C. elegans E2F consensus sequence, we were able to generate a comprehensive list of putative E2F-regulated genes in C. elegans. These results implicate a large number of genes previously unconnected to cell cycle control as having potential roles in this process.
Keywords: time course

overall_design:
We compared transcriptom profiles of lin-35 mutants and control N2 worms at 3 developmental stages (embryonic, L1 and L4).
Each comparison was done in triplicate on independently grown and isolated animals.

first: Natalia

middle: V

last: Kirienko


title: A gene expression fingerprint of C. elegans embryonic motor neurons.

status: Public on Jun 18 2007

last: Miller

address: 465 21st Avenue South

institute: Vanderbilt University

summary:
Background: Differential gene expression specifies the highly diverse cell types that constitute the nervous system. With its sequenced genome and simple, well-defined neuroanatomy, the nematode C. elegans is a useful model system in which to correlate gene expression with neuron identity. The UNC-4 transcription factor is expressed in thirteen embryonic motor neurons where it specifies axonal morphology and synaptic function. These cells can be marked with an unc-4::GFP reporter transgene. Here we describe a powerful strategy, Micro-Array Profiling of C. elegans cells (MAPCeL), and confirm that this approach provides a comprehensive gene expression profile of unc-4::GFP motor neurons in vivo. Results: Fluorescence Activated Cell Sorting (FACS) was used to isolate unc-4::GFP neurons from primary cultures of C. elegans embryonic cells. Microarray experiments detected 6,217 unique transcripts of which ~1,000 are enriched in unc-4::GFP neurons relative to the average nematode embryonic cell. The reliability of these data was validated by the detection of known cell-specific transcripts and by expression in UNC-4 motor neurons of GFP reporters derived from the enriched data set. In addition to genes involved in neurotransmitter packaging and release, the microarray data include transcripts for receptors to a remarkably wide variety of signaling molecules. The added presence of a robust array of G-protein pathway components is indicative of complex and highly integrated mechanisms for modulating motor neuron activity. Over half of the enriched genes (537) have human homologs, a finding that could reflect substantial overlap with the gene expression repertoire of mammalian motor neurons.
Conclusion: We have described a microarray-based method, MAPCeL, for profiling gene expression in specific C. elegans motor neurons and provide evidence that this approach can reveal candidate genes for key roles in the differentiation and function of these cells. These methods can now be applied to generate a gene expression map of the C. elegans nervous system.
Keywords: expression profile

overall_design: Our goal is to profile gene expression throughout the nervous system of the model organism Caenorhabditis elegans. As a first goal, we profiled a single class of embryonic motor neurons. To isolate transcripts from thesec neurons we developed the MAPCeL (Microarray Profiling C. elegans Cells) technique in which unc-4::GFP+ cells are captured by FACS for RNA isolation. We verified these data by bioinformatic means and by in vivo validation by creating GFP reporters for a random set of genes in our enriched gene list.

first: Rebecca

last: Fox

first: Stephen

middle: E

last: Von Stetina

first: Susan

last: Barlow

first: Christian

last: Shaffer

first: Kellen

last: Olszewski

first: Jason

last: Moore

first: Denis

last: Dupuy

first: Marc

last: Vidal

last: Miller III


title: Expression data for filamentous-form yeast with genetic perturbations

status: Public on Mar 01 2007

city: Bar Harbor

first: Gregory

last: Carter

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

summary:
We construced combinations of genetic deletions to infer genetic interactions in genomic expression data.
Keywords: combinatorial genetic perturbations

overall_design: The yeast transciptome was measured in rich media for a wild-type strain as a reference. We then collected genomic expression data in filamentous-growth conditions for 16 strains: wild-type, TEC1 gene deletion, CUP9 gene deletion, SFL1 gene deletion, SOK2 gene deletion, SKN7 gene deletion, and all possible pairwise combinations of deletions.

middle: W

first: Susanne

last: Prinz

first: Timothy

last: Galitski


title: Gene expression changes induced by heavy metals and other chemicals

city: Sapporo

first: Akinobu

last: Ito

address: North-13, West-8, Kitaku

department: Graduate School of Engineering

institute: Hokkaido University

summary:
From the results of gene expression analyses of HepG2 under the exposure of 2,3-Dimethoxy-1,4-naphthoquinone (DMNQ), N-nitrosodimethylamine (DMN), phenol and six heavy metals We showed that biological action of six heavy metals were clearly related to that of DMNQ and distinguishable from the other chemicals. These results suggest that oxidative stress is major apparent biological action of high dose heavy metals, supporting the previous reports.
Keywords: other

overall_design: Using Affymetrix HG-Focus arrays, we compared the gene expression patterns of Hep G2 cells induced by six heavy metals (As, Cd, Ni, Sb, Hg or Cr) with that of DMNQ, DMN or phenol, and evaluated the toxicities of these heavy metals.

first: Koji

last: Kawata

first: Hiroyuki

last: Yokoo

first: Ryuhei

last: Shimazaki

first: Satoshi

last: Okabe


title: Expression data from wild type, mre11delta, rad50delta, and spo11Y135F at meiosis 0 hr and 4 hr.

status: Public on Apr 10 2007

city: Kisarazu

first: Kazuto

last: Kugou

state: Chiba

address: 2-6-7 KazusaKamatatri

department: Department of Frontier Research

institute: Kazusa DNA Research Institute

summary:
Mre11, together with Rad50 and Xrs2/NBS, plays pivotal roles in homologous recombination, repair of DNA double strand breaks (DSBs), activation of damage-induced checkpoint, and telomere maintenance. Using DNA microarray assays to analyze yeast mutants (mre11delta, rad50delta, and spo11Y135F) defective for meiotic DSB formation, we demonstrate that the absence of Mre11 in yeast causes specific effects on regulation of a class of meiotic genes for spore development. The transcriptional deficiency was not observed in other DSB mutants such as rad50delta and spo11Y135F, suggesting the transcriptional defect in mre11delta is due to neither lack of meiotic DSB formation, nor disintegrity of Mre11-Rad50-Xrs2 complex.These defects were confirmed by northern and lacZ reporter gene assays.
Keywords: mutant vs. wildtype strains

overall_design: Gene expression data from wild type, mre11delta, rad50delta, and spo11Y135F cells in premeiosis (meiosis 0 hr) and prophase (meiosis 4 hr). Affymetrix GeneChip YG-S98 was used. All strains used were SK1 background diploid cells.

last: Sasanuma

first: Kouji

last: Matsumoto

first: Katsuhiko

last: Shirahige

first: Kunihiro

last: Ohta


title: Expression data from select tissues harvested from C57BL6 mice

status: Public on Jan 23 2007

city: New York

first: Kevin

middle: Jon

last: Cheung

address: 1230 York Avenue

department: Molecular Genetics

institute: The Rockefeller University

summary:
Gene expression was studied from different mouse tissues
Keywords: tissue types

overall_design: Tissues were harvested from adult mice and processed for microarray analysis

first: J

last: Friedman


title: Expression data from C57BL6 tissues and 3T3-L1 fibroblasts

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Effect of Dorsal, Dif, and Relish mutation on Drosophila response to G- Bacteria

city: College Park

first: Subhamoy

last: Pal

state: MD

address: 5126 Plant Sciences Building

department: Center for Biosystems Research

institute: University of Maryland

summary:
 The abstract of the manuscript titled "Microarray analyses reveal possible new targets for the Rel protein Dif in Drosophila melanogaster " is given below:
The fruit fly Drosophila melanogaster express three closely related NF-κB-like transcription factors: Dorsal, Dif, and Relish. They share significant sequence identity in their DNA binding Rel homology domain and bind similar DNA sequence motifs. These factors play an important role in the transcription of Drosophila humoral immune proteins such as antimicrobial peptides during infection. To study their roles in vivo, we used microarrays to determine the effect of null mutations in individual Rel transcription factors on larval gene expression. Of the 188 genes that were significantly upregulated in wildtype larvae upon bacterial challenge, overlapping but distinct groups of genes were affected in the Rel mutants. We also ectopically expressed Dorsal or Dif and used cDNA microarrays to determine the genes that were up-regulated in the presence of these transcription factors. Combining this data, we identified novel genes that may be specific targets of Dif.
Keywords: genetic modification

overall_design: This study uses Affymetrix chips to study the effect on gene expression when third instar larvae are injected with PBS or E. coli bacteria.  Wildtype, Dorsal1 mutant, Dif1 mutant, and Relish E20 mutant larvae are used to determine the effect of the mutations on gene expression.

first: Junlin

last: Wu

first: Louisa


title: Pof mutant expression analysis

status: Public on Mar 22 2007

city: Umea

first: Jan

last: Larsson

address: Umea University

department: Molecular Biology

institute: Umea University

summary:
Analysis of expression in pof mutant and wt 1st instar larvae
Keywords: Mutant vs Wt expression

overall_design: 400 1st instar larvae were used for each of 4 biological replicates of pof mutants and 3 replicates of wt larvae.

first: Per

last: Stenberg


title: Analysis of expression of genes regulated by DAF-19

status: Public on Dec 21 2006

city: Vancouver

first: BCGSC

last: BC Cancer Agency

state: BC

address: 675 West 10th Avenue

department: Gene Expression

country: Canada

institute: Canada's Michael Smith Genome Sciences Centre

summary:
By screening for genes possessing canonical X-box sequences in promoters of three Caenorhabditis species, namely C. elegans, C. briggsae and C. remanei, we identified 93 genes (including known X-box regulated genes) that encode putative components of ciliated neurons in C. elegans and are subject to the same regulatory control. For many of these genes, restricted anatomical expression in ciliated cells was confirmed, and control of transcription by the ciliogenic DAF-19 RFX transcription factor was demonstrated by comparative transcriptional profiling of daf-19(+) and daf-19(-) animals.
Keywords: Microarry analysis; DAF-19; X-box motif; C. elegans; transcription; comparative genomics

overall_design: There 4 samples.

first: Michel

last: Leroux

first: Donald

middle: G

last: Moerman

first: Nansheng

last: Chen

first: Oliver

last: Blacque

first: Allan

last: Mah

first: Jeffery

last: Chu

first: Kiran

last: Phgra

first: Mathieu

last: Bakhoum

first: Rebecca

last: Newbury

first: Jaswinder

last: Khattra

first: Kim

last: Wong

first: Susanne

last: Chan

first: Anne

last: Go

first: Evgeni

last: Efimenko

first: Robert

last: Johnsen

first: Prasad

last: Phirke

first: Peter

last: Swoboda

first: Marco

last: Marra

first: Lincoln

last: Stein


title: Gene expression of Pseudomonas aeruginosa on reverse osmosis membranes

status: Public on Mar 16 2007

city: New Haven

first: Moshe

last: Herzberg

state: CT

address: 9 Hillhouse avenue

department: Chemical Engineering

institute: Yale University

summary:
The transcriptome of P. aeruginosa PA01 biofilm cells was compared to the associated suspended culture, upon growth on reverse osmosis membrane coupon under limited nutrient conditions.
Keywords: growth in reverse osmosis unit and on reverse osmosis membrane

overall_design: Cells were collected from the RO unit and from the membrane coupon after 20 hours of growth and biofouling of the membrane. A defined media was used, resembeling secondary wastewaters.

first: Menachem

last: Elimelech


title: Effect of LARK overexpression in CNS neurons

status: Public on Dec 30 2006

city: Boston

first: Yanmei

last: Huang

state: MA

address: 136 Harrison Ave, A305B

department: Neuroscience

institute: Tufts University School of Medicine

summary:
The goal of this study is to identify, in the head of adult flies, mRNA species whose expresson level are altered by overexpression of the Drosophila RNA-binding protein LARK in CNS neurons.
Keywords: genetic modification, gene experssion profile

overall_design: RNA samples from adult head of the LARK overexpression flies (elav-gal4; uas-lark/+) and control flies were compared. One total RNA sample was isolated from each genotype, of which three technical replicates (repeating the labeling and hybridization processes) were generated, respectively.

first: Rob

last: Jackson


title: The Influence of Human Respiratory Epithelia on Pseudomonas aeruginosa Gene Expression

status: Public on Dec 19 2006

first: S

last: Chugani

state: WA

address: 1959 NE Pacific St, HSB I-420, Box 357242

summary:
To gain insights into the initial phases of P. aeruginosa infections and to identify P. aeruginosa genes regulated in response to respiratory epithelia we exposed P. aeruginosa to cultured primary differentiated human airway epithelia. We used a P. aeruginosa strain (PAO1) that causes acute damage to the epithelia and a mutant (PAOSC11) with defects in Type III secretion and in rhamnolipid synthesis. The mutant did not cause rapid damage to epithelia as did the wildtype.
Keywords: Pseudomonas aeruginosa and respiratory epithelia

overall_design:
We performed three comparisons:
First comparison:To identify genes regulated in the initial phase of an acute P. aeruginosa infection, we performed transcriptome analyses of wildtype PAO1 co-incubated with respiratory epithelia. For a baseline comparison we used wildtype P. aeruginosa PAO1 grown in broth culture.
Second comparison:To identify genes regulated in the initial phase of a chronic P. aeruginosa infection (an infection that does not result in acute injury to the epithelium), transcriptome analyses were done with the TTSS, rhamnolipid synthesis mutant  (PAOSC11) co-incubated with respiratory epithelia in our in vitro infection model. For a baseline comparison we used PAOSC11 grown in broth culture.
Third comparison: We compared the transcript profiles of wildtype PAO1 exposed to epithelia and the PAOSC11 mutant exposed to epithelia.

first: Sudha

first: E

last: Greenberg


title: Allelic Differences Account for Gene Expression Differences Among Population.

status: Public on Jan 07 2007

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

summary:
Expression level of genes in lymphoblasts from individuals in three HapMap populations (CEU, CHB, JPT) were compared.  More than 1,000 genes were found to be significantly different (Pc<0.05) in mean expression level between the CEU and CHB+JPT samples.
Keywords: Comparison of Gene Expression Profiles from Lymphoblastoid cells

overall_design: Gene expression analysis using Affymetrix Human Focus arrays; comparison of expression levels of genes by t-test.

first: Richard

last: Spielman

first: Laurel

middle: A

last: Bastone

first: Joshua

middle: B

last: Burdick

first: Warren

middle: J

last: Ewens

first: Vivian

last: Cheung


title: The effects of IL-10 on the gene expression of LPS-activated activated dendritic cells

status: Public on Feb 22 2007

city: Davis

first: William

last: Chang

address: County Rd 98 and Hutchison Dr

department: Center for Comparative Medicine

institute: University of California, Davis

summary:
Gene expression profiels in the human monocyte-derived dendritic cells (DCs) from 4 different donors (A, B, C, and D) were studied. Cells were left untreated (Group 4), activated with LPS alone (Group 1) or activated in the presence cmv IL-10 (Group 2) or human IL-10 (Group 3) for 12 hours before subjected to RNA extraction.
Keywords: IL-10, LPS, dendritic cells

overall_design: Overall ranscriptional profiles of activated DCs and IL-10-exposed activated DCs were compared with untreaetd immature DCs as baseline control.


title: Temperature-dependent transcriptional response under anaerobic C and N limitations in Yeast

status: Public on Jan 20 2007

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

institute: Delft University of Technology

summary:
The global transcriptional response of Saccharomyces cerevisiae was investigated in low temperature chemostat cultures grown in carbon or nitrogen limitation. During steady state chemostats, the growth rates and in vivo fluxes were kept constant however the growth-limiting nutrient was significantly higher at 12oC than at 30oC and had significant effects on transcriptional responses. Growth at 12oC resulted in a rearrangement of transporters for the limiting nutrient, where hexose transporters (HXTs) and ammonium permeases (MEPs) were differentially expressed in cultures grown at 30oC in carbon and nitrogen limitations, respectively. In addition, we found repression of genes encoding proteins in reserve carbohydrates metabolism and metabolism of alternative carbon or nitrogen sources other than glucose or ammonia. However, there were also similar responses when the transcriptional response was evaluated regardless of the growth-limiting nutrient. In particular, induction of ribosome biogenesis genes emphasizes the significance of transcription and translational adaptation at low temperature. In contrast, genes encoding proteins during stress response were downregulated. This down-regulation of stress elements better known as environmental stress response (ESR) is in contradiction with previous low temperature transcriptome analyses. During continuous steady state low temperature cultivation, ESR no longer plays an integral role in S. cerevisiae’s response to temperature change. Similarly, trehalose accumulation, consistent with its gene expression, was not indispensable for growth at 12oC. This response, however, does not exclude that ESR may be required for transition phase in low temperature growth when cells are transferred from one temperature to another.
Keywords: chemostat temperature 12 degree celsuis 30 degree celsius

overall_design: The global transcriptional response of Saccharomyces cerevisiae was investigated in low temperature chemostat cultures grown in carbon or nitrogen limitation at a dilution rate of 0.03h-1

first: SiewLeng

last: Tai

first: Pascale

last: Daran-Lapujade

middle: C

last: Walsh

first: Jack

middle: T

last: Pronk


title: Transcriptional response to weak organic acids in chemostat cultures of Saccharomyces cerevisiae

status: Public on Feb 27 2007

summary:
Raw expression values (CHP data) for transcriptional profiling of the response of Saccharomyces cerevisiae to challenges with various weak organic acids
Keywords: response to weak organic acids

overall_design:
The laboratory reference strain CEN.PK 113-7D (MATa) was grown at 30 °C in 2-L chemostat fermentors (Applikon, Schiedam, The Netherlands) with a working volume of 1-L using an electronic level sensor to maintain a constant volume.  All cultures, including the reference, were fed with minimal medium as described by Verduyn et al. (1992) with 25 g L-1 glucose as the limiting nutrient and 0.15 ml L-1 silicone antifoam (BDH, Poole, England) to prevent excessive foaming.  The dilution rate was set to 0.10 h-1 and the pH was controlled at 5.0 with the automatic addition (ADI 1031 bio controller, Applikon) of 2 M KOH.  The stirrer speed was set at 800 RPM and anaerobicity was maintained by sparging the fermentor with N2 gas at 500 ml min-1.  To prevent diffusion of oxygen, the fermentor was equipped with Norprene tubing and Viton O-rings and the medium vessel was also flushed with N2 gas.  A comparable degree of weak acid uncoupling was ensured by decreasing the biomass yield to approximately 50% of the reference condition (no organic acids added) with the addition of the appropriate concentration of acetic acid, sodium benzoate, propionic acid or potassium sorbate to the reservoir media.  Triplicate cultivations and microarrays were performed for each condition.

Sampling of chemostat cultures, probe preparation and hybridization to Affymetrix GeneChip microarrays was performed as described previously (Piper et al., 2002), but with the following modifications.  Double-stranded cDNA synthesis was carried out using 15 μg of total RNA and the components of the One Cycle cDNA Synthesis Kit (Affymetrix).  The double-stranded cDNA was purified (Genechip Sample Cleanup Module, Qiagen) before in vitro transcription and labeling (GeneChip IVT Labeling Kit, Affymetrix).  Finally, labeled cRNA was purified (GeneChip Sample Cleanup Module) prior to fragmentation and hybridization of 15 μg of biotinylated cRNA.

Data acquisition was performed using the Affymetrix scanner 3000, quantification of array images and data filtering were performed with the Affymetrix software packages Microarray Suite v5.0, MicroDB v3.0 and Data Mining Tool v3.0.

first: Derek

last: Abbott

first: Theo

last: Knijnenburg

first: Linda

last: de Poorter

first: Marcel

last: Reinders

first: Antonius

last: van Maris


title: Aging and oxidative stress in fly heads

status: Public on Dec 03 2006

city: San Francisco

first: Sige

last: Zou

department: Physiology Department

institute: University of California, San Francisco


title: Transcriptional responses of yeast to preferred and non-preferred nitrogen sources in C-lim chemostat cultures

status: Public on Feb 28 2007

summary:
Aerobic, glucose-limited chemostat cultures of Saccharomyces cerevisiae grown with six different nitrogen sources were subjected to transcriptome analysis. The use of chemostats enabled an analysis of nitrogen-source-dependent transcriptional regulation at a fixed specific growth rate. A selection of preferred (ammonium and asparagine) and non-preferred (leucine, phenylalanine, methionine and proline) nitrogen sources was investigated. For each nitrogen source, distinct sets of genes were induced or repressed relative to the other five nitrogen sources. A total number of 131 of such ‘signature transcripts’ were identified in this study. In addition to signature transcripts, genes were identified that showed a transcriptional co-response to two or more of the six nitrogen sources. For example, 33 genes were transcriptionally up-regulated in leucine-, phenylalanine- and methionine-grown cultures, which was partly attributed to the involvement of common enzymes in the dissimilation of these amino acids. In addition to specific transcriptional responses elicited by individual nitrogen sources, their impact on global regulatory mechanisms such as nitrogen catabolite repression (NCR) could be monitored. NCR-sensitive gene expression in the chemostat cultures showed that, ammonia and asparagine were ‘rich’ nitrogen sources. By this criterion, leucine, proline and methionine were ‘poor’ nitrogen sources and phenylalanine showed an ‘intermediate’ NCR response.
Keywords: Response to growth on various nitrogen source transcriptome

overall_design:
Chemostat  based transcriptomics study.
Each growth condition was performed in triplicate.

first: Viktor

last: Boer

first: Siewleng

first: Jean-marc


title: Expression data from 3T3-L1 adipogenesis

first: Kevin

summary:
3T3-L1 fibroblasts are a commonly used in vitro model for adipogenesis.  When induced with hormones, they differentiate into mature fat cells.  Here, microarrays were used to study 3T3-L1 adipose differentiation through time.
Keywords: time course

overall_design: 3T3-L1 fibroblasts were cultured in vitro and induced to differentiate using standard MDI protocol.  At successive time-points, cells were collected, and processed for microarray analysis.

first: J

last: Friedman


title: Genes regulated by PMK-1 and DAF-16 in a daf-2(e1368) background.

status: Public on Feb 08 2007

city: La Jolla

first: Emily

last: Troemel

department: Cell and Developmental Biology

institute: University of California, San Diego

summary:
Analysis of genes differentially expressed between daf-2(e1368) and daf-2(e1368);pmk-1(km25) and between daf-2(e1368) and daf-2(e1368);daf-16(mgDf47).  These studies identified genes upregulated by wild-type PMK-1 and wild-type DAF-16.
Keywords: genetic modification

overall_design: Three independent biological replicates were isolated for each strain. All strains in a replicate were grown and harvested in parallel.

middle: R

first: Dennis

last: Kim

first: Siu

middle: S

last: Lee

first: Frederick

last: Ausubel