title: Transcriptional Profiling of the Anterior Pituitary Gland of Genetically Selected Fat and Lean Chickens

city: College Park

first: Tom

middle: Eric

last: Porter

address: Building #142

department: Animal and Avian Sciences

institute: University of Maryland

summary: Chickens divergently selected for either high abdominal fat content (fat genotype) or low abdominal fat content (lean genotype) at SRA-INRA, France were used to profile pituitary gland gene expression during juvenile development (1 to 7 weeks of age) and to identify differentially expressed genes associated with genotype and age. The fat line (FL) and lean line (LL) chickens are different in various phenotypic and metabolic measurements, including abdominal fatness, plasma glycemia, and T3. The FL and LL chickens represent unique models for characterizing biomedical and agricultural traits. The Del-Mar 14K Chicken Integrated Systems microarrays were used for a transcriptional scan in the pituitary gland during juvenile development using a reference design for the hybridization of total RNA from the pituitary gland. A reference RNA pool was made from an equal amount of high-quality total RNA extracted from all of the samples. Each of the microarrays was co-hybridized with Cy3-labeled cDNA targets from one of the pituitary samples and Cy5-labled cDNA targets from the reference pituitary RNA pool. Log2-transformed fluorescence intensities were analyzed with a mixed model.  Two-way ANOVA (SAS) of log2 ratios was used to detect significant (p<0.05) differences by line, age, and the line-by-age interaction. There were 1150 significantly different genes between the two lines, and 339 of these genes exhibited greater than 0.68-fold differences in their log2 ratios (highest group mean at least 160% of the lowest group mean). One thousand four hundred twenty nine genes were significantly different by age and of these, 583 exhibited fold changes greater than 0.68 in the log2 ratio.  There were 145 genes that significantly differed in their line-by-age interaction, and 62 of these exhibited greater than 0.68-fold differences. There were 386 genes with significant differences by line or for line-by-age interaction with at least a 0.68-fold change in log2 ratio and n ≥ 2 for each experimental group.

overall_design: Four biological replicates were analyzed, each consisting of a complete set of individual samples from pituitary glands of Fat and Lean line chickens at week 1, week 3, week 5, or week 7 of age.  Amplified antisense RNA from each sample was analyzed using Del-Mar 14 K array in a reference design. Each experimental sample (Fat and Lean Weeks 1, 3, 5, and 7) was labeled with Cy3 and hybridized with an aliquot of the Cy5 reference pool, which was generated from all 32 RNA samples.

first: M

last: Muchow

first: T

middle: E


title: Physiological and molecular characterization of genetic competence in Streptococcus sanguinis

status: Public on Jan 21 2011

city: Richmond

first: Alejandro

last: Rodriguez

state: VA

address: 521 North 11th Street

department: Dentistry

country: USA

institute: Virginia Commonwealth University

summary: Streptococcus sanguinis is a major component of the oral flora and an important cause of infective endocarditis. The genome sequence of S. sanguinis strain SK36 was recently determined. A number of foreign genes acquired by natural transformation were detected, as well as orthologs of competence genes previously identified in other species. However, significant differences in the S. sanguinis competence system relative to that of other streptococci were noted. We sought to examine S. sanguinis genetic competence, to characterize the global transcriptional response to competence induction, and to compare our results with those obtained from previous analyses of other streptococci. A mutant possessing an in-frame deletion in the comC gene encoding the competence-stimulating peptide was created and confirmed to have the expected phenotype. Studies indicated that competence could be induced in this strain by addition of competence-stimulating peptide, and determined the optimal conditions to employ for this purpose. Expression was monitored by microarray analysis at multiple time points from 2.5 to 30 min after induction. Over 200 genes were identified whose expression was altered at least two-fold in at least one time point, with the majority upregulated. The “late” response was typical of that seen in previous studies. However, comparison of the “early” response in S. sanguinis with that of other streptococci revealed unexpected heterogeneity with regard to the number of genes induced, the nature of these genes, and their putative upstream regulatory sequences. S. sanguinis possesses a comparatively limited early response, which may define a minimal competence regulatory circuit.

overall_design: Transcriptional analysis of S. sanguinis strain JFP41 cells 0 to 30 min after treatment with CSP. Biological replicates: 3 replicates each independently grown and harvested. 4 technical replicates per array

middle: M

first: Jill

last: Callahan

first: Paul

last: Fawcett

first: Xiuchun

last: Ge

first: Ping

last: Xu

first: Todd

last: Kitten


title: PBRM1 Knockdown in RCC Cell Lines

status: Public on Jan 20 2011

city: Grand Rapids

first: Karl

last: Dykema

state: MI

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

summary: PBRM1 was found to be mutated in a high percentage of clear cell RCCs. We performed knockdown of PBRM1 via siRNA and compared with scrambled control in three different RCC cell lines.

overall_design: PBRM1 siRNA and mock treated cell lines were normalized together with 'hypoxic' clear cell renal tumors and normal renal tissue samples from GSE17818.


title: Paternally-induced transgenerational environmental reprogramming of metabolic gene expression in mammals (dye swap)

status: Public on Jan 14 2011

city: Jerusalem

first: naomi

last: habib

address: Givat-Ram

department: Computer Scince

country: Israel

institute: Hebrew University

summary:
Epigenetic information can be inherited through the mammalian germline, and represents a plausible transgenerational carrier of environmental information. To test whether transgenerational inheritance of environmental information occurs in mammals, we carried out an expression profiling screen for genes in mice that responded to paternal diet.
Characterizing the RNA exression changes in livers of offspring mice in response to the paternal diet, comparing between low-protein diet and control-diet.

overall_design: Examination of the effect of 2 different paternal diets, control diet and low-protein diet, on the mRNA expression in the liver of the offsprinngs. 26 samples: including Control diet vs. Low-protein (with dye swap), and Control diet vs. Low-protein after fasting the mice.

first: Benjamin

middle: R

last: Carone

first: Lucas

last: Fauquier

first: Naomi

last: Habib

first: Jeremy

last: Shea

first: Caroline

last: Hart

first: Ruowang

last: Li

first: Christoph

last: Bock

first: Chengjian

first: Phillip

middle: D

last: Zamore

first: Alexander

last: Meissner

first: Zhiping

last: Weng

first: Hans

middle: A

last: Hofmann

first: Nir

last: Friedman

first: Oliver

middle: J

last: Rando


title: Transcritptome of a revR deletion mutant during Clostridium perfringens exponential phase growth.

status: Public on Jan 17 2011

city: Clayton

first: Julian

middle: I

last: Rood

state: Victoria

address: Wellington Road

department: Microbiology

country: Australia

institute: Monash University

summary: RevR is a putative orphan response regulator with a high degree of similarity to YycF from Bacilus subtilis and PhoB from Clostridium kluyveri.  A revR deletion mutant of C. perfringens strain 13 was generated and the transcriptome analysed using microarrays.

overall_design: Total RNA was isolated from exponentially growing cells from the revR mutant and the wild-type control.  Gene expression levels were compared between the revR mutant and wild-type strain 13

first: Thomas

last: Hiscox

first: Jackie

middle: K

last: Cheung

first: Anjana

last: Chakravorty

first: Jocelyn

last: Choo

first: Kaori

last: Ohtani

first: Tohru

last: Shimizu


status: Public on Jan 15 2011

city: Houston

first: Delphine

last: Saulnier

state: TX

address: Feigin Center, Suite 830, 1102 Bates Avenue

department: Pathology

institute: Baylor College of Medicine

summary: Gene expression comparison of L. reuteri ATCC PTA 6475 and cyclopropane-fatty-acyl-phospholipid synthase mutant in MRS medium in anaerobic condition at 37C

overall_design: Include 3 biological replicate and dye-swap for each comparison. Reference time point = L. reuteri ATCC PTA 6475


title: Transcriptome response to different carbon sources in Acetobacter aceti

city: Bunkyo-ku

first: Hiroyuki

last: Arai

state: Tokyo

address: Yayoi 1-1-1

department: Department of Biotechnology

country: Japan

institute: The University of Tokyo

summary: Acetic acid bacteria are obligately aerobic alphaproteobacteria that have a unique ability to incompletely oxidize various alcohols and sugars to organic acids. The ability of these bacteria to incompletely oxidize ethanol to acetate has been historically utilized for vinegar production. The mechanism of switching between incomplete oxidation and assimilatory oxidation and the control of energy and carbon metabolism in acetic acid bacteria are not fully understood. To understand the physiology and molecular biology of acetic acid bacteria better, we determined the draft genome sequence of Acetobacter aceti NBRC 14818, which is the type strain of the genus. Based on this draft genome sequence, the transcriptome profiles in A. aceti cells grown on ethanol, acetate, glucose, or mix of ethanol and glucose was determined by using NimbleGen Prokaryotic Expression array (4x72K).

overall_design: Acetobacter aceti NBRC14818 was cultivated in the medium containing ethanol, acetate, glucose, or mix of ethanol and glucose as carbon sources in Erlenmeyer flask with rotary shaking. Total RNA was extracted when optical density at 600 nm was 0.3-0.4. The experiment was performed in duplicate independent cultures.

first: Kenta

last: Sakurai


title: Multi-omics approach to study the growth efficiency and amino acid metabolism in Lactococcus lactis at various specific growth rates

status: Public on Jan 11 2011

city: Tallinn

first: Ranno

last: Nahku

address: Akadeemia tee 15b

country: Estonia

institute: TFTAK

summary: Background  Lactococcus lactis is recognised as a safe (GRAS) microorganism and has hence gained interest in numerous biotechnological approaches. As it is fastidious for several amino acids, optimization of processes which involve this organism requires a thorough understanding of its metabolic regulations during multisubstrate growth.    Results  Using glucose limited continuous cultivations, specific growth rate dependent metabolism of L. Lactis including utilization of amino acids was studied based on extracellular metabolome, global transcriptome and proteome analysis. A new growth medium was designed with reduced amino acid concentrations to increase precision of measurements of consumption of amino acids. Consumption patterns were calculated for all 20 amino acids and measured carbon balance showed good fit of the data at all growth rates studied. It was observed that metabolism of L. lactis became more efficient with rising specific growth rate in the range 0.10 – 0.60 h-1, indicated by 30% increase in biomass yield based on glucose consumption, 50% increase in efficiency of nitrogen use for biomass synthesis, and 40% reduction in energy spilling. The latter was realized by decrease in the overall product formation and higher efficiency of incorporation of amino acids into biomass. L. lactis global transcriptome and proteome profiles showed good correlation supporting the general idea of transcription level control of bacterial metabolism, but the data indicated that substrate transport systems together with lower part of glycolysis in L. lactis were presumably under allosteric control.     Conclusions   The current study demonstrates advantages of the usage of strictly controlled continuous cultivation methods combined with multi-omics approach for quantitative understanding of amino acid and energy metabolism of Lactococcus lactis which is a valuable new knowledge for development of balanced growth media, gene manipulations for desired product formation etc. Moreover, collected dataset is an excellent input for developing metabolic models.

overall_design: For microarray analysis, steady state chemostat culture of L. lactis IL1403 was used as reference (μ = 0.10 1/h). Subsequent quasi steady state points from A-stat experiment at specific growth rates 0.52 ± 0.03; 0.42 ± 0.02; 0.29 ± 0.01 1/h in biological duplicates and 0.17 1/h were compared to the reference sample.

first: Petri-Jaan

last: Lahtvee

first: Kaarel

last: Adamberg

first: Liisa

last: Arike

first: Kadri

last: Aller

first: Raivo

last: Vilu


title: Genomic profiling of human Tert/shp53/Ras mesenchymal cells isolated from several xenografted tumors and their non-transformant epithelial counterparts

city: MONTPELLIER cedex 5

first: Beatrice

last: ORSETTI

address: 208 rue des apothicaires- CRLC Val d'Aurelle

department: Tumoral Plasticity and Identity

country: France

institute: INSERM-U896 IRCM

type: Genome variation profiling by genome tiling array

summary: The epithelial-mesenchymal transition (EMT) is an embryonic transdifferentiation program which consists of the conversion of polarized epithelial cells into a motile mesenchymal phenotype. EMT is aberrantly reactivated during tumor progression, promoting metastatic dissemination. Herein, we demonstrate that EMT-permissive conditions also favor tumor initiation by minimizing the number of events required for neoplastic transformation. We further demonstrated that even the partial commitment of human mammary epithelial cells into an EMT program is sufficient to confer malignant properties, suggesting that the reactivation of embryonic EMT inducers participates to the primary tumor growth long before the initiation of the invasion-metastasis cascade.

overall_design: arrayCGH profiles analysis of Tert/shp53/Ras epithelial HMEC derivatives and 3 different tumors generated after injection of mesenchymal Tert/shp53/Ras/ HMEC derivatives in fad pads of nude mice

first: Anne-Pierre

last: MOREL

first: Béatrice


title: Monocyte-derived macrophages stimulated with the TLR8 agonist 3M-002 at 10 microM show a prominent activation of TLR-dependent genes as assessed b "Human Toll-like Receptor PCR array pathway" over time

city: Zurich

first: Roberto

middle: F

last: Speck

state: Zurich

address: Raemistrasse 100

department: Division of Infectious Diseases and Hospital Epidemiology

country: Switzerland

institute: University Hospital of Zurich

summary: We were interested in the effects of TLR8 triggering of human monocyte-derived macrophages. We observed a striking upregulation of those genes. This work was done in the context of examining the effects of TLR8 triggering for the activation of HIV.

overall_design: We generated monocyte-derived macrophages (MDM) by initially isolating monocytes and subsequently culturing them in RPMI supplemented with human AB serum. MDM were stimulated for 18 h with the TLR8 agonist 3M-002, and subsequently harvested for extraction of total RNA. Total RNA was then used to quantify the TLR-dependent genes using a PCR array pathway.

first: Erika

last: Schlaepfer


title: U1 cells stimulated with the TLR8 agonist 3M-002 at 10 microM show a prominent activation of TLR-dependent genes as assessed by "Human toll-like Receptor PCR array pathway" over time

summary: We investigated the effects of the TLR8 agonist 3M-002 on latently HIV infected U1 cells. We found a prominent upregulation of TLR-dependent genes. Notably, the TLR8 agonist resulted in a marked activation of HIV.

overall_design: We stimulated U1 cells for 6 or 10 hours with 3M-002 and subsequently harvested the cells, extracted total RNA. RNA was then used for quantifiying TLR-dependent gene upregulation using a commercial PCR array pathway


title: Transcriptomic responses to salinity stress in invasive and native blue mussels (genus Mytilus)

status: Public on Jan 10 2011

city: Pacific Grove

first: Brent

middle: L

last: Lockwood

state: CA

address: 120 Oceanview Blvd.

department: Biology

institute: Hopkins Marine Station of Stanford University

summary: The invasive marine mussel Mytilus galloprovincialis has displaced the native congener Mytilus trossulus from central and southern California, but the native species remains dominant at more northerly sites that have high levels of freshwater input. To determine the extent to which interspecific differences in physiological tolerance to low salinity might explain limits to the invasive species’ biogeography, we used an oligonucleotide microarray to compare the transcriptional responses of these two species to an acute decrease in salinity. Among 6,777 genes on the microarray, 117 genes showed significant changes that were similar between species, and 12 genes showed significant species-specific responses to salinity stress. Osmoregulation and cell cycle control were important aspects of the shared transcriptomic response to salinity stress, whereas the genes with species-specific expression patterns were involved in mRNA splicing, polyamine synthesis, exocytosis, translation, cell adhesion, and cell signaling. Forty-five genes that changed expression significantly during salinity stress also changed expression during heat stress, but the direction of change in expression was typically opposite for the two forms of stress. These results (i) provide insights into the role of changes in gene expression in establishing physiological tolerance to acute decreases in salinity, and (ii) indicate that transcriptomic differences between M. galloprovincialis and M. trossulus in response to salinity stress are subtle and involve only a minor fraction of the overall suite of gene regulatory responses.

sample_organism:
Mytilus trossulus
Mytilus galloprovincialis

platform_organism:
Mytilus californianus
Mytilus galloprovincialis

overall_design:
Two species (Mytilus galloprovincialis, Mytilus trossulus), hypo-osmotic shock for four hours (850 mOs/kg), one control group (1000 mOs/kg) sampled at the end of the treatment exposure (850 mOs/kg), one control group (1000 mOs/kg) sampled at the beginning. Biological replicates: 6 in each treatment group, 6 in each control group. Heterologous and homologous hybridization to a microarray constructed from Mytilus californianus and Mytilus galloprovincialis sequences. A reference design that used separate pools of reference RNA for each species was employed. Reference amplified RNA (aRNA) was created for each species by pooling RNA before and after amplification. The reference pool was made up of RNA from six different samples: two base-line control samples from the beginning of the experiment, two treatment samples from the end of the four-hour hypo-osmotic exposure, and two time-control samples from the end of the four-hour exposure time.

To accurately compare the transcriptomes of Mytilus galloprovincialis and M. trossulus, we chose to develop a common microarray format that could be used for both species. This microarray design consisted of probe sequences generated from the out-group species, M. californianus. M. trossulus and M. galloprovincialis are approximately 7.5 million years divergent from M. californianus, yet only 3.5 million years divergent from each other (Seed, 1992). Therefore, heterologous hybridization to the microarray allowed us to compare transcriptional responses of M. galloprovincialis and M. trossulus without the inherent sequence biases that would result from a microarray that was designed from sequences of either M. galloprovincialis or M. trossulus. A limited number of sequences (556) from ESTs from M. galloprovincialis that matched M. californianus ESTs were included on the microarray to test for the effects of sequence mismatches. Only probes that performed well for both M. galloprovincialis and M. trossulus were used in our analyses. In order to determine significant changes in expression, we conducted a two-way ANOVA, in which salinity and species were modeled as fixed effects, and focused on genes that were significant for the salinity effect or the species x temperature interaction. We ignored the species term from the ANOVA as this effect could have highlighted genes that differentially bound to probes on the microarray due to differences in sequence homology, thus not reflecting true differences in gene expression. In accordance with statistical convention, all genes with a significant species x temperature interaction were deemed not to have significant temperature effects, even if the temperature term from the ANOVA had a low P-value. All genes with FDR-corrected (Benjamini and Hochberg, 1995) P-values less than 0.05 were considered significant. Analyses were conducted in the R statistical programming environment (R Development Core Team, 2009).

first: George

middle: N

last: Somero


title: Secreted bacterial effectors that inhibit host protein synthesis are critical for induction of the innate immune response to virulent Legionella pneumophila [exp2]

status: Public on Jan 08 2011

city: Berkeley

first: Russell

last: Vance

address: 415 Life Science Addition

institute: UC Berkeley

summary: The intracellular bacterial pathogen Legionella pneumophila causes an inflammatory pneumonia called Legionnaires’ Disease.  For virulence, L. pneumophila requires a Dot/Icm type IV secretion system that translocates bacterial effectors to the host cytosol.  L. pneumophila lacking the Dot/Icm system is recognized by Toll-like receptors (TLRs), leading to a canonical NF-κB-dependent transcriptional response.  In addition, L. pneumophila expressing a functional Dot/Icm system potently induces unique transcriptional targets, including proinflammatory genes such as Il23a and Csf2. Here we demonstrate that this Dot/Icm-dependent response, which we term the effector-triggered response (ETR), requires five translocated bacterial effectors that inhibit host protein synthesis.  Upon infection of macrophages with virulent L. pneumophila, these five effectors caused a global decrease in host translation, thereby preventing synthesis of IκB, an inhibitor of the NF-κB transcription factor.  Thus, macrophages infected with wildtype L. pneumophila exhibited prolonged activation of NF-κB, which was associated with transcription of ETR target genes such as Il23a and Csf2.  L. pneumophila mutants lacking the five effectors still activated TLRs and NF-κB, but because the mutants permitted normal IκB synthesis, NF-κB activation was more transient and was not sufficient to fully induce the ETR.  L. pneumophila mutants expressing enzymatically inactive effectors were also unable to fully induce the ETR, whereas multiple compounds or bacterial toxins that inhibit host protein synthesis via distinct mechanisms recapitulated the ETR when administered with TLR ligands. Previous studies have demonstrated that the host response to bacterial infection is induced primarily by specific microbial molecules that activate TLRs or cytosolic pattern recognition receptors. Our results add to this model by providing a striking illustration of how the host immune response to a virulent pathogen can also be shaped by pathogen-encoded activities, such as inhibition of host protein synthesis.

overall_design: Three-condition experiment: macrophages left uninfected (negative control), or infected with wildtype Legionella pneumophila, or the mutant Δ5, which lacks five bacterial effectors involved in inhibition of host protein synthesis (lgt1, lgt2, lgt3, sidI, sidL) (two experimental conditions).  Biological replicates: two, independently infected, harvested, and hybridized to arrays.  One technical replicate per array.

first: Mary

last: Fontana

first: Simran

last: Banga

first: Kevin

middle: C

last: Barry

first: Xihui

last: Shen

first: Yunhao

last: Tan

first: Zhao-Qing

last: Luo


title: Secreted bacterial effectors that inhibit host protein synthesis are critical for induction of the innate immune response to virulent Legionella pneumophila [exp1]

overall_design: Four-condition experiment: macrophages left uninfected (negative control), or infected with wildtype Legionella pneumophila, the flagellin-deficient mutant ΔflaA, or the secretion-deficient mutant ΔdotA (three experimental conditions).  Biological replicates: two, independently infected, harvested, and hybridized to arrays.  One to two technical replicates per array, as indicated in file titles.


title: Human Peripheral blood monocytes untreated or treated with CXCL12

status: Public on Jan 13 2011

city: Madrid

first: Lorena

last: Sánchez-Martín

address: C/ Dr Esquerdo 46

department: Inmunología

country: Spain

institute: Hospital General Gregorio Marañon

summary: Total mRNA expression of CXCL12-treated monocytes was compared with control untreated monocytes

overall_design: Human Peripheral blood monocytes from three different healthy donors were isolated by anti-CD14-labeled magnetic microbeads. CD14+ monocytes were cultured in teflon dishes for 1h in RPMI 10% FCS and then, were treated or not with CXCL12 for 6h. Total RNA from each condition was extracted and purified using the RNasey kit (Qiagen). Labelled RNA was used as hybridization probes on human Codelink Whole genome Bioarray. All experimental procedures were performed following manufacturer instructions. Microarrays were scanned with a GenePix 4000B (Axon Instruments) scanner. Scanned images and raw data were processed using the Codelink Expression Software.

last: Sanchez-Martin

first: Paloma

last: Sanchez-Mateos


title: Identification of Genes and Networks Driving Cardiovascular and Metabolic Phenotypes in a Mouse F2 Intercross

city: Seattle

first: Jonathan

last: Derry

state: WA

address: 1100 Fairview Ave N

institute: Sage Bionetworks

summary: To identify the genes and pathways that underlie cardiovascular and metabolic phenotypes we performed an integrated analysis of a mouse C57BL/6J x A/J F2 (B6AF2) cross by relating genome-wide gene expression data from adipose, kidney, and liver tissues to physiological endpoints measured in the population. We have identified a large number of trait QTLs including loci driving variation in cardiac function on chromosomes 2 and 6 and a hotspot for adiposity, energy metabolism, and glucose traits on chromosome 8. Integration of adipose gene expression data identified a core set of genes that drive the chromosome 8 adiposity QTL. This chromosome 8 trans eQTL signature contains genes associated with mitochondrial function and oxidative phosphorylation and maps to a subnetwork with conserved function in humans that was previously implicated in human obesity. In addition, human eSNPs corresponding to orthologous genes from the signature show enrichment for association to type II diabetes in the DIAGRAM cohort, supporting the idea that the chromosome 8 locus perturbs a molecular network that in humans senses variations in DNA and in turn affects metabolic disease risk. We functionally validate predictions from this approach by demonstrating metabolic phenotypes in knockout mice for three genes from the trans eQTL signature, Akr1b8, Emr1, and Rgs2. In addition we show that the transcriptional signatures for knockout of two of these genes, Akr1b8 and Rgs2, map to the F2 network modules associated with the chromosome 8 trans eQTL signature and that these modules are in turn very significantly correlated with adiposity in the F2 population. Overall this study demonstrates how integrating gene expression data with QTL analysis in a network-based framework can aid in the elucidation of the molecular drivers of disease that can be translated from mice to humans.

overall_design:
An F2 population was derived from a C57BL/6J x A/J mouse cross (B6AF2) and tissues were collected in 360 male and female progeny for microarray analysis. RNA extraction, probe preparation, and array hybridizations were all carried out at the Rosetta Inpharmatics Gene Expression Laboratory (Seattle, WA). Mouse tissues (gonadal adipose, kidney medulla, kidney cortex, hypothalamus) were pulverized prior to homogenization in a solution of GITC/BME (1:50 ratio) using a Covaris S2 cryo-prep (Covaris, Inc, Woburn, MA), followed by addition of a TRIzol water solution (4:1 ratio). 100% Chloroform was added to the TRIzol/GITC lysate (1:5 ratio) to facilitate separation of the organic and aqueous components using the phaselock (Eppendorf) system. The aqueous supernatant was further purified using a Promega SV-96 total RNA kit (Promega, Madison, WI), incorporating a DNase treatment. Total RNA samples were assayed for quality using an Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA) and for yield using Ribogreen (Ambion, Austin, TX) metrics prior to amplification.  All samples, with the exception of kidney medulla, were amplified and labeled using a custom automated version of a 5 µg RT/IVT protocol and hybridizations to custom Agilent microarrays were performed as described [58].
The custom ink-jet microarrays used in this study were manufactured by Agilent Technologies and consisted of 4,732 control probes and 39,558 non-control oligonucleotides derived from mouse Unigene clusters, combined with RefSeq sequences and RIKEN full-length cDNA clones. For each individual animal tissue sample, labeled complementary RNA (cRNA) was hybridized against a pool of labeled cRNAs constructed from equal aliquots of RNA for that specific tissue from at least 200 individuals.

first: Cliona

last: Molony

first: Debraj

last: Guhathakurta

first: John

last: Mudgett

first: Kersten

last: Small

first: Lahcen

last: El Fertak

first: Alain

last: Guimond

first: Mohammed

last: Selloum

first: Marie

last: Champy

first: Laurent

last: Monassier

first: Tom

last: Vogt

first: Doris

last: Cully

first: Andrew

last: Kasarskis

first: Eric

last: Schadt


title: Gene expression data from treated LNCaP prostate cells.

status: Public on Jan 07 2011

city: Philadelphia

first: Clay

last: Comstock

state: PA

department: Dept Cancer Biology

institute: Thomas Jefferson University/Kimmel Cancer Center

summary:
Prostate cancer is dependent on androgen receptor (AR) signaling at all stages of the disease and cyclin D1 has been shown to negatively modulate the expression of the AR-dependent gene prostate specific antigen (KLK3/PSA).
Unbiased gene expression profiling was performed to determine the androgen-regulated geneset that is sensitive to cyclin D1.

overall_design: Androgen-sensitive LNCaP cells were straved of androgen, then transduced with control green fluorescent protein (GFP) or cyclin D1 (CCND1) adenovirus, then subsequently stimulated with control (Ethanol) or dihydrotestosterone (DHT).

first: Karen

last: Knudsen


title: Gene expression of immortalized cystic fibrosis and non-cystic fibrosis airway epithelial cells

city: La Jolla

first: Steven

last: Head

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

summary: Our laboratory has held a long interest in the glycosylation changes seen on the surface of airway epithelia of patients with the disease cystic fibrosis (CF). Experiments from our laboratory have detailed a CF glycosylation phenotype of increased Fuca1,3/4 and decreased Fuca1,2 and sialic acid on the surfaces of immortalized and primary CF cells compared to non-CF cells. Further, we have shown that gene transfer and subsequent expression of a wild type CF plasmid in CF airway cells results in correction or reversal of this glycosylation phenotype. We hypothesize that the changes in glycosylation seen in CF cells are key in the pathophysiology of the cystic fibrosis airway disease. For example, it has been shown that Pseudomonas aeruginosa, a bacterium that has a predilection for colonizing CF airways, adheres to asialylated glycolipids and glycoconjugates with terminal Fuca1,3/4. One focus of our laboratory is to elucidate the etiology of the glycosylation changes seen in CF cells and the mechanism by which these changes are reversed by wild type CFTR gene transfer.

platform_organism:
Homo sapiens
Mus musculus

overall_design:
We propose to study the gene expression of immortalized and primary CF and non-CF airway epithelial cells: 1. CF/T43 vs. BEAS-2B cells. These are two widely used immortalized airway cell lines that we have used extensively in the past.  2. C38 cells;  C38 cells are IB3 cells expressing wtCFTR.
The experimental focus is to elucidate the etiology of the glycosylation changes seen in Cystic Fibrosis (CF) cells and the mechanism by which these changes are reversed by wild type CFTR gene transfer. To do so, the gene expression of immortalized and primary CF and non-CF airway epithelial cells were compared and studied. Cell lines used were CF/T43 and BEAS-2B, both widely used immortalized airway cell lines. Other cell lines studied included C38 cell lines (clonal derivatives of IB3 cells expressing wtCFTR).

first: Thomas

last: Scanlin


title: Hepatocellular carcinoma (HCC) tumors and cell lines

city: WOODBURY

first: jack

last: zhang

state: NY

address: 500 sunnyside blvd

department: genome research center

institute: cold spring harbor laboratory

summary: DNA copy number profiling for all primary tumor samples and HCC cell lines was performed by ROMA, a form of comparative genomic hybridization.  The aim was to identify commonly amplifiied and deleted regions across human HCC.

overall_design: 88 primary HCC samples and 12 human HCC cell lines were analyzed.

first: Scott

last: Powers

first: Ken

last: Nguyen

first: Jack

last: Zhang

first: Jinyu

last: Li


title: Lamin binding profiles in the ENCODE regions

city: Palo Alto

first: Ghia

last: Euskirchen

address: 1501 S. California Ave.

department: Genetics

institute: Stanford University

type: Genome binding/occupancy profiling by genome tiling array

summary: A systems understanding of nuclear organization and events is critical for determining how cells divide, differentiate and respond to stimuli and for identifying the causes of diseases. Chromatin remodeling complexes such as SWI/SNF have been implicated in a wide variety of cellular processes including gene expression, nuclear organization, centromere function and chromosomal stability, and mutations in SWI/SNF components have been linked to several types of cancer. To better understand the biological processes in which chromatin remodeling proteins participate we globally mapped binding regions for several components of the SWI/SNF complex throughout the human genome using ChIP-Seq. SWI/SNF components were found to lie near regulatory elements integral to transcription (e.g. 5’ ends, RNA Polymerases II and III and enhancers) as well as regions critical for chromosome organization (e.g. CTCF, lamins and DNA replication origins). To further elucidate the association of SWI/SNF subunits with each other as well as with other nuclear proteins we also analyzed SWI/SNF immunoprecipitated complexes by mass spectrometry. Individual SWI/SNF factors are associated with their own family members as well as with cellular constituents such as nuclear matrix proteins, key transcription factors and centromere components implying a ubiquitous role in gene regulation and nuclear function. We find an overrepresentation of both SWI/SNF-associated regions and proteins in cell cycle and chromosome organization. Taken together the results from our ChIP and immunoprecipitation experiments suggest that SWI/SNF facilitates gene regulation and genome function more broadly and through a greater diversity of interactions than previously appreciated.

overall_design: ChIP-chip analysis of lamin A/C and lamin B in HeLa S3 cells

first: Raymond

last: Auerbach

first: Eugene

last: Davidov

first: Tara

last: Gianoulis

first: Joel

last: Rozowsky

first: Guoneng

last: Zhong

first: Nitin

last: Bhardwaj

first: Mark

middle: B

last: Gerstein

first: Michael

middle: P

last: Snyder


title: Kinetics of glycosyltransferase expression during the T-cell response to lymphocytic choriomeningitis virus

summary: This lab investigates how protein-carbohydrate interactions affect cell fate in the immune system. The specific focus is on the mechanism of galectin-1 mediated death of T lymphocytes, and the role of galectin-1 in immune development, lymphocyte homeostasis, response to pathogens, autoimmunity and tumor cell evasion of the immune response.

overall_design:
T cell memory, the ability of T cells to respond to recall antigens rapidly and effectively, is a critical component of the adaptive immune response and the essential target of vaccine development. After naive T cells are exposed to a new antigen (or pathogen), expansion of antigen-specific T cells creates an effector population; the majority of effector T cells die once the antigen or pathogen is cleared. A small subset of T cells remains after antigen is cleared, the memory T cells. These memory cells can respond more rapidly than naive cells to recall antigen, and are also capable of homeostatic self-renewal. During the development of T cell memory, there are dramatic changes in gene transcription, protein expression and post-translational modification of proteins, compared to naive and effector T cells. Our labs have described some of these changes at the phenotypic level, and have found important distinctions in the glycotypes of naive, effector and memory T cells. However, there has not been a systematic examination of differential glycosyltransferase expression among these T cell populations.
Gene expression during the development of T-cell memory: After naive T cells are exposed to a new antigen (or pathogen), expansion of antigen-specific T cells creates an effector T cell population, the majority of which dies once antigen is cleared. A small subset, the memory T cells, remains after antigen is cleared. Using the LCMV system in P14 TCR transgenic mice specific for the DbGP33-41 epitope of LCMV, RNA (triplicate samples) was isolated from FACS-sorted virus-specific CD8+ T-cell populations during a time course following viral infection. The time points are day 0, day 8 (the peak of T-cell expansion following viral infection), day 15 (during the contraction or apoptotic phase), day 22 (during the transitional phase), and day 40 or later (the stable memory phase). The RNA samples were analyzed by Glyco-gene Chip analysis.

first: Linda

last: Baum


title: Mouse lymphocyte study

first: Steven

last: Head

summary: Dr. Paulson's group investigates the roles of carbohydrate-binding proteins involved in immune regulation and human disease, through their interaction with carbohydrate groups expressed on cell surface glycoconjugates. This laboratory is currently focused on how sialoside ligands modulate Siglec functions and on understanding the molecular basis of glycosylation changes following differentiation and activation of leukocytes.

overall_design:
Evaluation of Glycosyltransferases and CBP expression in B cells, CD4+ and CD8+ T cells following activation. The overall goal of this study is to understand the molecular regulation of cell surface glycosylation in mouse lymphocytes before and after activation. Initial studies using lectins and antibodies showed differences in glycan expression following activation, which included a marked increase in PNA binding. Interestingly, this increase was observed in B, CD4+ and CD8+ cells after 72h of activation. Our aim is to elucidate the molecular basis for such changes in B and T lymphocytes (CD4+ and CD8+), focusing on the mRNA expression of glycogenes before and after activation of mixed spleenocytes.
In brief, the experimental protocol is as follows: splenocytes are isolated from C57Bl/6 mice (6-10 wks old) and cultured for 0, 24, 48 and 72 hrs. Cultures containe either anti-CD3/IL2/IL4 or anti-IgM/IL4 to activate T cells and B cells respectively. At each time point, B, CD4+ and CD8+ cells are purified by positive selection using magnetic beads and total RNA is prepared from each cell type.

first: James

last: Paulson


title: Glycosyl-T expression in NB cells

summary: Dr. Ladisch's work focuses on the establishment of the biological significance of gangliosides that are shed by tumor cells, particularly those involved in pediatric cancers, including brain tumors and neuroblastoma. These studies are directed toward illuminating the hypothesis that shed gangliosides enhance tumor formation, possibly both by inhibiting the antitumor immune response and by enhancing growth factor-induced signaling and proliferation of fibrobalsts and vascular endotheilial cells in the tumor microenvironment. Delineation of the signaling pathways affected by ganglioside exposure is currently under study.

overall_design:
The effect of retinoic acid on the mRNA levels of ganglioside glycosyltransferases in neuroblastoma cells in vitro
Experiment to determine mRNA expression for ganglioside glycosyltransferases in NB cells (untreated versus treated with ATRA) using the Glyco-gene Chip by the Consortium for Functional Glycomics. Human NB cell lines LAN-5 were incubated with 10 µM of all-trans retinoic acid or untreated as control, and total RNA harvested after 24 hours, 72 hours and 120 hours of exposure to retinoic acid. We performed three independent experiments on either cell line so that for each cell line and each time point three replicates were be obtained (total: 18 chips). Glycosyltransferases of particular interest are LacCer synthase, GlucCer synthase, GM3 synthase, GD3 synthase, GM2/GD2 synthase, GD1b/GM1a synthase, GT1b/GD1a synthase and GQ1b/GT1a synthase.

first: Stephen

last: Ladisch


title: Human gliomatosis cerebri vs. non-neoplastic adult brain tissue

city: Lecce

first: Oscar

middle: Fernando

last: D'Urso

state: Lecce

address: provinciale Monteroni

department: Department of biological science

country: Italy

institute: Salento University

summary:
We report the results of a molecular study in  thirty-seven cases of gliomatosis cerebri, correlating these results with prognosis. The well-known prognostic factors of gliomas, i.e., age, KPS, histology (Grade 2 vs. 3), or contrast enhancement, was predictive of response or outcome only in a percentage of patients but not in all patients. We identified an 8 miRNA signature able to predict patient prognosis with microarray gene expression profiling. The 8 gene features were used to built a prediction method able to distinguish patients with good prognosis (more likely to be responsive to therapy) from patients with a poor prognosis (less likely to be responsive to therapy).

Keywords: miRNA expression profile

overall_design: Fifty-nine patients, between 12- and  73-years-old, with clinical signs of increased intracranial pressure were admitted to our institutions between January 2000 to September 2005. Pre-operative neuroradiological studies (CT scan and MRI) showed diffuse infiltrative processes involving more than two different lobes, no identifiable focal mass, and contrast enhancement absent or less than 1 cm in diameter. Written informed consent and tumour DNA were obtained for molecular analysis. Other eligibility criteria included a Karnofsky Performance Scale index (KPS) >50, normal bone marrow function (white blood cell count >3.0X109/l, neutrophil count >1.5X109/l, platelet count >100X109/l, and haemoglobin >10g/dL), normal liver function (aspartate aminotransferase or alanine aminotransferase <2 times the upper limit of laboratory normal, normal bilirubin, and alkaline phosphatase < 2 times the upper limit of normal), and normal renal function (serum creatinine <1.5 mg/dL). The patients received chemotherapy with temozolamide and radiotherapy. The TMZ schedule consisted of 150 to 200 mg/m2 was orally administered once daily on days 1  to 5. Treatment cycles were repeated every 28 days, with a maximum of 24 months. All patients had a monthly neurological and performance status evaluation and a radiological (MRI) evaluation every 2 to 3 months. Responses were evaluated according to previously described criteria (8): a clinical response was defined as an improvement of a neurological deficit or cognitive function evaluated by Mini-Mental Status Examination, an improvement of at least 75% in seizure frequency, or the disappearance of intracranial hypertension. When radiological MRI scans showed a reduction of more than 50% in the hyper intense area it was considered a partial response (PR), and a <50% regression or an objective regression of mass effect, was considered a minor response (MR). Disease was considered as stable when no clinical or radiological changes were seen for at least 6 months, whereas neurological deterioration, a need to increase corticosteroids, or evidence of tumour progression on MRI (an increase in the T2 or the appearance of contrast enhancement) indicated tumour progression.

first: Pietro


title: A transcriptomic approach to elucidate apricot fruit development using an oligonucleotide peach microarray

status: Public on Jan 12 2011

city: Legnaro

first: claudio

last: Bonghi

state: Padova

address: Viale dell'UNiversità, 16

institute: University of Padova

summary: The aim of this study was to elucidate the potential use of microarray technology, developed in model species, in related, yet phenotypically distinct, species where few or no information are available. Considering the high degree of sequence conservation within the Rosaceae family and, in particular, among the Prunus species we employed the first available peach oligonucleotide microarray (µPEACH 1.0) for studying the transcrptomic profile during apricot fruit development (Prunus armeniaca L., cv. 'Goldrich'). Fruit material was harvested at three distinct stages, corresponding to immature-green stage (6 weeks before fully-ripe stage), mature-firm-ripe stage (change of peel color, 1 week before fully-ripe stage) and at fully-ripe stage and designated as S1, S2 and S3 stages, respectively.  Apricot targets cDNA, when applied the  µPEACH1.0, were showing significant hybridization with an average of 43% of spotted targets validating the use of μPEACH1.0 to profile the transcriptome of apricot fruit during development and ripening.  Microarray analysis carried out on immature and ripe peach and apricot  fruit separately pointed out that 70% of genes differentially expressed was detectable the same pattern of expression in both species. This result indicates that the transcriptome of immature and ripe fruit are quite similar in apricot and peach, but also highlighted the presence of transcript changes specie-specific. When μPEACH1.0 was used to profile apricot developing fruit were identified 400 and 74 genes differetially expressed  during the transition from S1 to S2 stage and from S2 to S3 stage, respectively.  Intriguingly, a considerable number of auxin action regulators (AUX/IAA) and of genes coding heat shock proteins (hsp) were highly up-regulated at the onset and late of ripening phase, respectively.The comparison between the expression profiles of these apricot genes and their peach hortologues showed a similar pattern for AUX/IAA and quite different for hsps. This result suggests a similar role for AUX/IAA in both species and a more important involvement for hsps in the apricot fruit ripening.

sample_organism:
Prunus persica
Prunus armeniaca

overall_design: A direct comparison approach has been used to investigate changes at the transcriptional level in immature (S1, 45 days after full bloom), mature-firm ripe (S2, 80 DAFB) and fully ripe (S3, 87 DAFB) fruit of apricot (Prunus armeniaca, cv Goldrich). The comparison was carried out also for immature (S1) and ripe (S4) fruit of peach (Prunus persica cv Fantasia).  RNA has been extracted from fruit harvest at above mentionated stages of development.  At least four hybridization have been conducted for a total of four technical replicates (with dye-swap).

first: Claudio

first: George

last: Manganaris

first: Angela

last: Rasori

first: Daniele

last: Bassi

last: Tonutti

first: Angelo

last: Ramina


title: Asf1/HIRA facilitate global histone deacetylation and associate with HP1 to promote nucleosome occupancy at heterochromatic loci (MNase)

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

summary: Nucleosome occupancy (NO) profiling in fission yeast Schizosaccharomyces pombe

overall_design: Agilent 60mer array was used to analyze mononucleosomal DNA recovered by MNase treatment from asynchronous culture of fission yeast.

first: Kenichi

last: Yamane

first: Takeshi

last: Mizuguchi

first: Bowen

last: Cui

first: Martin

last: Zofall

first: Ken-ichi

last: Noma


title: Oxygen exposure increases resistance of Desulfovibrio vulgaris Hildenborough to hydrogen peroxide inactivation

status: Public on Jan 05 2011

city: Calgary

first: Sean

middle: Michael

last: Caffrey

state: Alberta

address: 2500 University Dr NW

department: Biological Scineces

country: Canada

institute: University of Calgary

summary: Differences in gene expression between a mutant D. vulgaris strain missing the PerR transcriptional regulator gene and the wild-type strain.

sample_organism: Nitratidesulfovibrio vulgaris str. Hildenborough

overall_design:
For each condition (PerR_cDNA_vrs_gDNA, wild-type_cDNA_vrs_gDNA) 2 unique biological samples were hybridized to 4 arrays that each contained duplicate spots. Genomic DNA was used as universal reference. Log2 PerR mutant versus wild-type gene expresson with growth on WP-lactate.

SUPPLEMENTARY FILES:
* Log2 gene expression ratios of PerR mutant/wild-type (PerR/gDNA/ wildtype/gDNA) and q-values.
* Wild type raw data.
* PerR mutant raw data.

first: Gerrit

last: Voordouw

first: Janine

last: Wildschut

first: Johanna


title: Gene microarray experiments on RNA samples isolated from murine B cells

first: Steven

last: Head

summary: This laboratory studies 1) enzymes which are involved in selectin ligand formation in leukocytes, 2) how expression of those enzymes is controlled, and 3) basic cell biology of FucT-VII.

overall_design:
B cells vs. plasma cells. Study of primary IgG plasma cells. Plasma cells constitute the final stage of B-cell differentiation, and their migration from the lymph nodes and spleen to bone marrow is thought to be an important step in the maintenance of a long-term antibody response to a pathogen. Dr. Kansas has purified primary IgG plasma cells from E-selectin/P-selectin double knockout mice by a negative selection technique and compared their gene expression profile to that of murine B cells using Affymetrix murine oligonucleotide microarray analysis. Highly distinct gene expression profiles were revealed (see Underhill GH et al, Blood. 2003;101:4013-4021). As a follow-up to that experiment, the same probes (in triplicate) derived from primary murine IgG plasma cells and normal B cells were used to probe Glyco-gene Chips.
As a follow-up to that experiment, the same probes (in triplicate) derived from primary murine IgG plasma cells and normal B cells were used to probe Glyco-gene Chips.

first: Geoffrey

last: Kansas


title: Expression analysis of Mycobacterium smegmatis delta-MSMEG_0166 mutant

status: Public on Jan 06 2011

city: Portland

first: Melissa

middle: Suzan

last: Standley

state: OR

address: 3181 SW Sam Jackson Park Rd.

institute: Oregon Health & Science University

summary:
Investigation of whole genome gene expression level changes in a Mycobacterium smegmatis mc2 155 delta-MSMEG_0166 mutant, compared to the wild-type strain. MSMEG_0166 is a transcriptional regulator in the gntR family.
Mutations in MSMEG_0166 result in hypersensitivity to the bactericidal ubiquitin peptide Ub2, as well as oxidative stress caused by either organic or inorganic agents

overall_design: A three chip study using total RNA recovered from three separate wild-type cultures of Mycobacterium smegmatis mc2 155 and three separate cultures of a MSMEG_0166 mutant strain, Mycobacterium smegmatis mc2 155 delta-MSMEG_0166, in which MSMEG_0166 is interupted by the insertion of a hygromycin resistance cassette.  Each chip measures the expression level of 6,588 genes from Myobacterium smegmatis with five 60-mer probes per transcript and two replicates of each probe for a total of 65,880 experimental probes.

first: Georgiana

last: Purdy

first: Cathy

last: Kim

first: S

last: Rosato

middle: S


title: Expression analysis of phenol degradation in the hyperthermophilic archaeon Ferroglobus placidus

city: Amherst

first: Dawn

middle: E

last: Holmes

state: Massachusetts

address: 639 N Pleasant St Morrill IVN 422C

institute: University of Massachusetts Amherst

summary: Investigation of whole genome gene expression level changes in Ferroglobus placidus grown on phenol versus acetate as electron donors, with ferric citrate as electron acceptor.

overall_design: A six chip study using total RNA recovered from three separate cultures of Ferroglobus placidus DSM 10642 grown with 0.5 mM phenol and three separate cultures of Ferroglobus placidus DSM 10642 grown on 10 mM acetate.  Each chip measures the expression level of 2613 genes from Ferroglobus placidus DSM 10642 with nine 45-60-mer probe pairs (PM/MM) per gene, with three-fold technical redundancy.

first: Carla

last: Risso

first: Derek

last: Lovley


title: LIF-Dependent, Pluripotent Stem Cells Established from Inner Cell Mass of Porcine Embryos

city: Columbia

first: Bhanu

last: Telugu

state: MO

address: 1201 E.Rollins St

department: Animal Sciences

institute: University of Missouri

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary:
The pig is important for agriculture and as an animal model in human and veterinary medicine, yet, despite over 20 years of effort, it has proved a difficult species from which to generate pluripotent stem cells analogous to those derived from mouse embryos. Here we report the production of LIF-dependent, so called naïve type, pluripotent stem cells from the inner cell mass of porcine blastocysts by up-regulating expression of KLF4 and POU5F1. These cells resemble mouse ES cells and are distinct from the FGF2-dependent, induced pluripotent cell type derived from porcine somatic cells.
High throughput SNP chip genotyping was conducted on Illumina's Porcine SNP60 BeadChip (WG-410, a service provided by Geneseek, NE, http://www.neogen.com/GeneSeek/). The results exhibited that the two lines pluripotent stem cells from the inner cell mass of porcine blastocysts were porcine origin and genetically distinct.

overall_design: Porcine pluripotent stem cells were derived from the inner cell mass with transduction with human KLF4 by lentiviral transduction.

first: R

middle: M

last: Roberts


title: Expression analysis of melanoma harvested from GFP versus SETDB1 transgenic zebrafish (Danio rerio)

city: Karp 7

first: Yariv

last: Houvras

state: MA

address: 1 Blackfan Circle

institute: Childrens Hospital Boston

summary: Investigation of expression differences between melanomas harvested from MiniCoopR-GFP versus MiniCoopR-SETDB1 transgenic zebrafish.

overall_design: An eight-chip study using total RNA prepared from four distinct melanomas from zebrafish injected with MiniCoopR-GFP (control) transposon and four distinct melanomas from zebrafish injected with MiniCoopR-SETDB1 transposon.  Injected animals carried a p53 loss-of-function mutation, a mutation in nacre, and an mitf:BRAF-V600E transgene.  Each chip measures the expression level of 32,292 genes.

first: Craig

last: Ceol


title: Whole-genome analysis of heat shock factor binding sites in Drosophila melanogaster at room temperature

city: Mississauga

first: Zak

last: Razak

state: Ontario

address: 3359 Mississauga Rd

institute: Canadian Drosophila Microarray Centre

summary: Whole-genome analysis of heat shock factor binding sites in Drosophila melanogaster. Heat shock factor IP DNA from non-shock (room temperature) Kc 167 cells compared to whole cell extract on Agilent 2x244k tiling arrays.

overall_design: Heat Shock Factor IP vs whole cell extract from non-shock (room temperature) Kc cells.

first: Sarah

last: Gonsalves


title: Gene expression analysis during heat shock in Drosophila melanogaster 3rd instar hsf4 cn bw larvae

summary: Gene expression analysis of Drosophila melanogaster 3rd instar hsf4 cn bw larvae, under heat shock and non-heat shock conditions (room temperature) using Nimblegen arrrays (GPL8443)

overall_design: total RNA recovered from heat shocked or non-heat shocked (room temperature) samples in hsf4 larvae, 3 biological replicates for each treatment


title: Arabidopsis floral initiator SKB1 confers high salt tolerance by regulating transcription and pre-mRNA splicing through altering histone H4R3 and small nuclear ribonucleoprotein LSM4 methylation

status: Public on Jan 04 2011

city: Beijing

first: Zhaoliang

last: Zhang

state: Beijing

address: datun road

country: China

institute: Institute of Genetics and Developmental Biology, Chinese Academy of sciences

summary: This study examines how histone modification confers salt stress in Arabidopsis. The floral initiator SKB1 is found to mediate the plant’s response to salt stress by altering the methylation status of histone H4R3 and of the small nuclear ribonucleoprotein (snRNP) LSM4, and thereby affecting the expression of stress-responsive genes.

overall_design: Total RNA was isolated with Trizol reagent (Invitrogen) from eleven11-day-old seedlings of the wild type and skb1-1 mutant without or with 200 mM NaCl for 6 hrs. 29k Arabidopsis Genome Array hybridization was carried out by CapitalBio Corporation (Beijing, China).

first: Shupei

first: Shilai

last: Bao


title: Gene expression analysis during heat shock in Drosophila melanogaster KC167 cells and 3rd instar dp cn bw larvae

summary: Gene expression analysis of Drosophila melanogaster Kc167 cells and 3rd instar dp cn bw larvae, under heat shock and non-heat shock conditions  (room temperature) using Nimblegen arrrays (GPL8443)

overall_design: A 12 chip study using total RNA recovered from heat shocked or non-heat shocked (room temperature) samples in either cells or larvae, 3 biological replicates for each treatment


title: Leishmania RNA Virus controls the severity of muco-cutaneous leishmaniasis

status: Public on Jan 03 2011

city: Lausanne

first: Frédéric

last: Schütz

address: Batiment Amphipole

institute: Swiss Institute of Bioinformatics

summary: Comparison of the transcriptome of bone marrow derived macrophages infected with either metastasizing (M+, Lg13) or non-metastasizing (M-, Lg17) parasites after 24 hours of infection.

overall_design: 3 experimental conditions; M+ infected BMMf vs. uninfected BMMf, M- infected BMMf vs. uninfected BMMf, M+ infected BMMf vs. M- infected BMMf, BMMf from 3 biologically independant infection experiments were used where BMMf were infected for 24hrs at a ratio of 1 BMMf to 10 parasites. Total RNA was extracted reverse transcribed into cDNA with either a Cy3 or Cy5 fluorescent tag and hybridized on to mouse 17k chip. Slides were scanned and differential BMMf gene expression was determined above 1.5 fold change and p less than 0.05. 6 slides per biological independant experiment were used including the dye swap, with 18 slides used in total.

first: Annette

last: Ives

first: Catherine

last: Ronet

first: Florence

last: Prével

first: Giulia

last: Ruzzante

first: Silvia

last: Fuertes-Marraco

first: Fréderic

first: Haroun

last: Zangger

first: Mélanie

last: Revaz-Breton

first: Lon-Fye

last: Lye

first: Suzanne

last: Hickerson

first: Stephen

last: Beverley

first: Hans

last: Acha-Orbea

first: Pascal

last: Launois

first: Nicolas

last: Fasel

first: Slavica

last: Masina


title: Human primary meningioma vs. non-neoplastic adult meningeal tissue

status: Public on Jan 02 2011

first: Oscar

last: D'Urso

summary:
Meningiomas are common brain tumors that are classified into three World Health Organization grades (Grade I: benign, Grade II: atypical and Grade III: malignant) and are molecularly ill-defined tumors. The purpose of this study was identify microRNA (miRNA) molecular signatures unique to the different grades of meningiomas correlating them to prognosis.

We have used a miRNA expression microarray to show that meningiomas of all three grades fall into two main molecular groups designated “benign” and “malignant” meningiomas. While all typical meningiomas fall into the benign group and all anaplastic meningiomas fall into the malignant group, atypical meningiomas distribute into either one of these groups. We have identified a miRNA signature that distinguishes benign meningiomas from malignant meningiomas.

overall_design: We studied the gene expression profiles of 340 mammalian miRNAs in 37 primary meningioma tumors by means of DNA microarrays.

first: Pietro

first: Pasqualino

last: Ciappetta


title: Expression analysis of benzoate degradation in the hyperthermophilic archaeon Ferroglobus placidus

first: Dawn

last: Holmes

summary: Insight into the mechanisms for the anaerobic metabolism of aromatic compounds by the hyperthermophilic archaeon Ferroglobus placidus is expected to improve understanding of the degradation of aromatics in hot (> 80 °C) environments and to identify enzymes that might have biotechnological applications.  Analysis of the F. placidus genome revealed genes predicted to encode enzymes homologous to those previously identified as playing a role in benzoate and phenol metabolism in mesophilic bacteria.  Surprisingly, F. placidus lacks genes for an ATP-independent class II benzoyl-CoA reductase found in all strictly anaerobic bacteria, but instead has two sets of genes for ATP-consuming class I benzoyl-CoA reductases, similar to those found in facultative bacteria.   The lower portion of the benzoate degradation pathway appears to be more similar to that found in the phototroph Rhodopseudomonas palustris, than the pathway reported for all heterotrophic anaerobic benzoate degraders.  Many of the genes predicted to be involved in benzoate metabolism were found in one of two gene clusters.  Genes for a phenol carboxylation proceeding through a phenylphosphate intermediate and for conversion of p-hydroxybenzoate to benzoyl-CoA were identified in a single gene cluster.  Analysis of transcript abundance with a whole-genome microarray and quantitative PCR demonstrated that most of the genes predicted to be involved in benzoate or phenol metabolism had higher transcript abundance during growth on those substrates versus growth on acetate.  These results suggest that the general strategies for benzoate and phenol metabolism may be highly conserved between microorganisms living in moderate and hot environments, and that anaerobic metabolism of aromatic compounds might be analyzed in a wide range of environments with similar molecular targets.

overall_design: A four chip study using total RNA recovered from two separate cultures of Ferroglobus placidus DSM 10642 grown with 1 mM sodium benzoate (experimental condition) and two separate cultures of Ferroglobus placidus DSM 10642 grown on 10 mM acetate (control condition).  Each chip measures the expression level of 2613 genes from Ferroglobus placidus DSM 10642 with nine 45-60-mer probe pairs (PM/MM) per gene, with three-fold technical redundancy.

first: Carla

last: Risso

first: Jessica

last: Smith

first: Derek

last: Lovley


title: Mode of action studies of the novel bisquaternary bisnaphthalimide MT02 against Staphylococcus aureus

city: Geneva

first: FRANCOIS

last: Patrice

state: Ge 4

address: Rue Gabrielle-Perret-Gentil, 4

department: Service of Infectious Diseases

institute: Genomic Research Laboratory

summary: Screening of various bisquaternary bisnaphthalimides against a variety of human pathogens revealed one compound, designated MT02, with strong inhibitory effects against gram-positive bacteria. The minimal inhibitory concentrations ranged from 0.31 µg/ml against community-acquired methicillin resistant Staphylococcus aureus (MRSA) strain USA300 to 20 µg/ml against Streptococcus pneumonia. DNA-microarray studies generated a transcriptional signature characterized by a strong increase of genes involved in DNA-metabolism, DNA-replication, SOS-response and transport of positively charged compounds. Radioactive whole cell labeling experiments indicated a strong impact of MT02 on bacterial DNA-replication. Furthermore, surface plasmon resonance and gel retardation experiments demonstrated direct binding of MT02 to DNA in a concentration dependent, reversible and sequence-unspecific manner. The data presented suggest that the bisquaternary bisnaphthalimide MT02 exerts anti-gram-positive activity by binding to DNA and thereby prohibiting appropriate DNA-replication.

platform_organism: Staphylococcus aureus subsp. aureus NCTC 8325

platform_organism: Staphylococcus aureus subsp. aureus Mu50

platform_organism: Staphylococcus aureus subsp. aureus N315

platform_organism: Staphylococcus aureus subsp. aureus MRSA252

platform_organism: Staphylococcus aureus subsp. aureus MSSA476

platform_organism: Staphylococcus aureus subsp. aureus USA300

overall_design: WT strain exposed to MT02 for 60 minutes in rich medium

first: Thomas

last: Menzel

first: Maximilian

last: Tischer

first: Patrice

last: François

first: Joachim

last: Nickel

first: Jacques

last: Schrenzel

first: Heike

last: Bruhn

first: Annette

last: Albrecht

first: Leane

last: Lehmann

first: Ulrike

last: Holzgrabe

first: Knut

last: Ohlsen


title: Epigenetic regulation of transcription and virulence of Trypanosoma cruzi

status: Public on Jan 01 2011

city: Athens

first: Dilrukshi

last: Ekanayake

state: GA

address: 120, Green Street

department: Biochemistry and Molecular Biology

institute: University of Georgia

summary: Trypanosoma cruzi, a flagellated protozoan, is the causative agent of Chagas’ disease, a chronic and potentially fatal disease that causes irreversible damage to heart and digestive tract in humans. Like all trypanosomes, the protein coding genes of T. cruzi are arranged into large polycistronic gene clusters transcribed by polymerase II (Pol II). Therefore, trypanosomes presumably rely on post-transcriptional process to regulate gene expression. Pol II promoters have not been identified and there is no evidence for regulated gene expression at the transcriptional level. However, the presence of the hyper-modified DNA base J, Beta-D-glucosyl hydroxymethyluracil, at regions flanking the polycistronic units (PTU) in T. brucei suggested its involvement in regulating Pol II transcription. We now demonstrate that base J is localized at PTU flanking regions in T. cruzi and levels are differentially regulated by the thymidine hydroxylases, JBP1 and JBP2, involved in J biosynthesis. Microarray analysis of the JBP1dKO and JBP2dKO indicate the up and down regulation of several hundred genes distributed throughout the genome. We show a large increase in Pol II transcription rate following the decrease in base J at the PTU flanks. Changes in gene expression include virulence genes and parasites are defective in host cell invasion and egress. There is a direct correlation between the reduction in base J levels, number of genes affected and strength of the virulence phenotype. These studies indicate that base J represents an epigenetic factor regulating Pol II transcription initiation in kinetoplastids and provides a biological role of the only hyper-modified DNA base in eukaryotes.

overall_design: J1 and J2 null mutant trypomastigotes were each compared to wild type trypomastigotes.  There were 3 biological replicates for each comparison.

first: Todd

last: Minning

first: D

last: Weatherly

first: Rick

last: Tarleton

first: Robert

last: Sabatini


title: Fathead minnow pharmaceuticals

city: Alachua

first: Barbara

middle: Joan

last: Carter

state: FL

address: 12085 Research Drive

department: R&D

institute: Applied Food Technologies

summary: Gene expression profiles of fathead minnow brain tissue following treatment to fluoxetine (Prozac), carbamazepine, venlafaxine, and a mixture of all three; compared to untreated controls.

overall_design: Two-condition experiment, treated vs. controls. Biological replicates of 4 treatment and a control.  Additional alcohol control (solvent carrier) has only one array.

first: Michael

last: Thomas

first: Rebecca

last: Klaper


title: Early response of Coxiella burnetii to temperature stress

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

summary: Transcriptional profiling of Coxiella burnetii phase I (RSA 493) submitting either to Cold and Heat shock comparing to control untreated Coxiella burnetii phase I (RSA 493) grown at 35°C.

overall_design:
Four experiments : Cold shock 30 min Vs 35°C; Cold shock 60 min Vs 35°C; Heat shock 30 min Vs 35°C; Heat shock 60 min Vs 35°C
3 biological replicates, independently grown and harvested. Four replicate per array.

first: Quentin

last: Leroy

first: Pascal

last: Barbry

first: Richard

last: Thiéry

first: Didier

last: Raoult


title: Chromatin immunoprecipitation of Rok-myc and Hbs-myc in Bacillus subtilis

city: Cambridge

first: Alan

middle: D.

last: Grossman

email: clee2@mit.edu, adg@mit.edu

address: 31 Ames Street, 68-530

institute: MIT

type: Genome binding/occupancy profiling by array

summary: The Rok protein of Bacillus subtilis was identified as a negative regulator of competence development. Here we show that Rok binds to extended areas of the B. subtilis genome that are characterized by a high A+T content and are known or believed to have been acquired by horizontal gene transfer, e.g. mobile elements. A deletion of rok results in higher excision of one such element, ICEBs1. The preferential association of Rok with DNA with a high A+T content is also observed in a Gram-negative host, E. coli, and depends on a conserved C-terminal region of the protein. Based on our findings, we propose that Rok is a nucleoid-associated protein that fulfills a function analogous to H-NS, a protein absent from most Gram-positive bacteria.

sample_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design:
The genome-wide binding profile of the transcription factor Rok and the nucleoid-binding protein HBsu were determined.
Three biological replicates were analyzed per strain (one per array). Binding profiles were determined in exponentially growing cells. Enrichment in immunoprecipitated samples versus total genomic DNA were determined.

first: Wiep

last: Smits

middle: D


title: Effects of diet and age on canine liver gene expression

city: Urbana

first: Kelly

middle: Scott

last: Swanson

state: IL

address: 1207 W. Gregory Dr.

institute: University of Illinois

summary: The liver is the central organ in the regulation of nutrient metabolism, xenobiotic metabolism, and detoxification.  Aging leads to a marked change in liver structure and function, characterized by a decline in weight, blood flow, regeneration rate, and detoxification.  However, the mechanisms that contribute to these changes are poorly described.  Global gene expression profiles of aged versus young adult dogs have not been compared previously.  Thus, we used canine microarrays to compare gene expression profiles of liver tissue from geriatric and young adult dogs fed 2 different diets.  Liver tissue samples were collected from 6 geriatric (12 yr-old) and 6 young adult (1 yr-old) female beagles after being fed one of two diets (animal protein-based versus plant-protein based) for 12 months.  RNA samples were hybridized to Affymetrix GeneChip Canine Genome Arrays.  Statistical analyses indicated that age had the greatest impact on gene expression, with 234 gene transcripts differentially expressed in geriatric dogs.  Although not as robust as age, diet affected mRNA abundance of 137 gene transcripts.  The effect of age was most notable, with increased expression in genes related to inflammation, oxidative stress, and glycolysis and decreased expression in genes associated with regeneration, xenobiotic metabolism, and cholesterol trafficking in senior dogs.  The effect of diet on gene expression was not consistent, but led to more changes in young adult dogs.

overall_design: Six geriatric (11.1 yr old) and 6 weanling (8 wk old) female beagles were used.  Three dogs of each age were assigned to one of two dietary treatments and fed for 12 months.  Diets tested in this experiment were previously shown to manipulate energy metabolism.  One diet was an animal-protein based diet (APB) and was composed primarily of highly digestible ingredients and animal-derived protein and fat sources (brewer’s rice, poultry by-product meal, poultry fat) and was formulated to contain 28% protein, 23% fat, and 5% dietary fiber.  The other diet was a plant-protein based diet (PPB) and was composed primarily of moderately digestible plant-derived ingredients (corn, soybean meal, wheat middlings, and meat and bone meal) and was formulated to contain 26% protein, 11% fat, and 15% dietary fiber.  Although the two diets were very different in terms of ingredient and chemical composition, both were formulated to meet or exceed all nutrient requirements for canine growth according to the Association of American Feed Control Officials.  Young dogs were fed ad libitum to allow for adequate growth, while geriatric dogs were fed to maintain baseline BW throughout the experiment.  To produce the desired metabolic effects, the PPB diet was formulated to contain a lower caloric density (APB = 5.38 kcal/g; PPB = 4.75 kcal/g) and have a lower nutrient digestibility than the APB diet.  Thus, dogs fed the PPB diet needed to consume a greater (P<0.05) quantity of food (237 g/d; 1123 kcal/d) than dogs fed the APB diet (166 g/d; 893 kcal/d) to grow (young) or maintain BW (geriatrics).  Even though metabolic indices were altered, mean BW among dietary treatments was not different at any time over the course of the study for young or geriatric dogs.  After 12 months on experiment, animals were fasted for 12 hr and then given a lethal dose (130 mg/kg BW) of sodium pentobarbital (Euthasol, Virbac Corp., Fort Worth, TX) intravenously into the left forearm.  Death was confirmed by lack of respiration and a corneal reflex, and absence of a heartbeat detected with a stethoscope placed under the left elbow.  Liver samples were collected immediately after death was confirmed, flash frozen using liquid nitrogen, and stored at -80oC until further analysis.

first: Lawrence

last: Schook


title: Gene expression profile analysis in the mid-gestation human intestine discloses greater immaturity of the colon as compared to ileum

city: Sherbrooke

first: Jean-François

last: Beaulieu

state: Québec

address: 3001, 12ème avenue nord

department: Anatomie & biologie cellulaire

institute: Université de Sherbrooke

summary: The occurrence of many neonatal inflammatory intestinal diseases in preterm infants highlights the susceptibility of the immature intestine to respond inadequately to nutrient and microbes. A better understanding of the functional intestinal development is essential for the design of optimal treatments ensuring survival and growth of premature infants. The purpose of this study was to evaluate the gene expression profiles of the developing human ileum and colon at mid-gestation. Our results showed that more than 11% of the genes were differentially expressed between ileum and colon. Pathway analysis revealed an even higher level of transcriptional dissimilarity between the developing ileum and the colon including 35% of the significant cellular, molecular and physiological functions and 85% of the canonical pathways. Segment-specific/over-expressed functions in the ileum included a number of amino acid, vitamin and mineral metabolisms and lymphoid tissue structure and development reflecting the high level of maturity of the small intestine as compared to the colon in which cell cycle, cell morphology and actin cytoskeleton, integrin and ERK/MAPK signaling were the predominant functions. All together, functional clustering analysis of the differentially expressed genes revealed important functional difference between the two segments namely to an unexpected relative immaturity of the colon.

overall_design: Two-condition experiment: three human fetal small intestines vs. three human fetal large intestines.

first: Eric

last: Tremblay

first: Emanuela

last: Ferretti

first: Babakissa

last: Corentin

first: Ernest

last: Seidman

first: Emile

last: Levy

first: Daniel

last: Ménard

first: Jean-FranÃ§ois


title: Response of Candida glabrata to low pH

city: Hyderabad

first: Rupinder

last: Kaur

address: Building 7, Gruhakalpa, 5-4-399/B, Nampally

country: India

institute: Centre for DNA Fingerprinting & Diagnostics

summary:
To examine the role of a glycosylphosphatidylinositol-linked aspartyl protease, CgYps1, in the regulation of pH homeostasis in Candida glabrata, transcriptional profiling analysis was carried out on wild-type and Cgyps1∆ cells grown in YNB medium (pH 5.5) and in YNB medium adjusted to pH 2.0. Genes involved in carbohydrate and amino acid metabolism, protein folding and stress response pathways were found to be differentially regulated in response to acidic environment in both the strains.
To examine the role of a glycosylphosphatidylinositol-linked aspartyl protease, CgYps1, in the regulation of pH homeostasis in Candida glabrata, transcriptional profiling analysis was carried out on wild-type and Cgyps1∆ delta cells grown in YNB medium (pH 5.5) and in YNB medium adjusted to pH2.0. Genes involved in carbohydrate and amino acid metabolism, protein folding and stress response pathways were found to be differentially regulated in response to acidic environment in both the strains

overall_design: Agilent one-color experiment,Organism: Yeast ,Agilent-026378 Genotypic designed Custom Candida glabrata 8x15k   , Labeling kit: Agilent Quick-Amp labeling

first: Kaur

last: Rupinder

first: Bairwa

last: Gaurav


title: MeJA-induced gene expression in rice plants

city: Seoul

first: Ju-Seok

last: Seo

department: Dept. of Applied Biology & Chemistry

country: South Korea

institute: Seoul National University

summary: To understand signal transduction mechanism by MeJA in rice, we have analyzed transcription profile with 60K Rice Whole Genome Microarray after MeJA treatment. Gene transcripts were extracted from ten individual rice plants treated with 100 uM MeJA for 6 hrs. RNA samples from these plants were used to generate cyanine-3 (Cy3) and Cy5-labeled complementary DNA (cDNA) probes, which were then hybridized to the microarray. Each data set was obtained from three biological repeats independently.

overall_design: Preparation of fluorescence labeled probes and microarray hybridization was performed as procedures provided by Genisphere 3DNA Array Detection Array 50 kit (v. 2, Genisphere, Hatfield, PA). The microarray was scanned with Genepix 4000B (Axon Instruments, Union City, CA) and the quality of the chip data was analyzed with statistical R language and sma package in Bioconductor project (http://www.bioconductor.org/) implemented on Linux platform. Noncorrelation of signal and background intensities were confirmed by plotting base 2 log background intensity in x axis and base 2 log intensity subtracted with background intensity in y axis. Prior to normalization, normal distribution of Cy3 and Cy5 intensities were tested by qqplot function in R statistical language. The spatial effects on the chip during the hybridization process were checked with spatial func in sma package. The variance difference between Cy3 and Cy5 intensities within microarray was tested by the Student's t test under the assumptions firstly uniform and then nonuniform variances. The ANOVA difference of signal intensities between microarrays was performed by one-way ANOVA. Block-by-block Lowess normalization (Yang et al., 2002) and multivariate statistics such as clustering, principal component analysis, multidimensional scaling, etc. were analyzed with Acuity 3.1 (Axon Instruments). Spots with flag of 0 and a diameter greater than 51 pixel size were used for the analysis. Cy3 significant spots were determined when its log ratio is less than –0.67 [2**(–0.67) = 1.6-fold decrease] and its background subtracted intensity is higher than 500. On the contrary, Cy5 significant spots was determined when its log ratio is greater than 0.67 [2**0.67 = 1.6-fold increase] and its intensity is higher than 500. A preliminary microarray experiment using nontreated wild-type RNA labeled Cy3 and Cy5, respectively, gave less than 0.5% false positive signals in the analysis. To assess the reproducibility of the microarray analysis, we repeated the experiment three times with independently prepared total RNA

first: Yang

last: Choi


title: Differences in major bacterial taxa in three high Arctic soils lead to different CO2 production rates

city: Montreal

first: Martineau

last: Christine

state: Qc

address: 6100 Royalmount Ave.

department: Environmental Microbiology

institute: NRC-BRI

summary: The melting of permafrost and its potential impact on greenhouse gas emissions is a major concern in the context of global warming. The fate of the carbon trapped in permafrost will largely depend on soil physico-chemical characteristics, among which are the quality and quantity of organic matter, pH and water content, and on microbial community composition. In this study, we used microarrays and real-time PCR (qPCR) targeting 16S rRNA genes to characterize the bacterial communities in three different soil types representative of various Arctic settings. The microbiological data were linked to soil physico-chemical characteristics and CO2 production rates. Microarray results indicated that soil characteristics, and especially the soil pH, were important parameters in structuring the bacterial communities at the genera/species levels. Shifts in community structure were also visible at the phyla/class levels, with the soil CO2 production rate being positively correlated to the relative abundance of the Alphaproteobacteria, Bacteroidetes, and Betaproteobacteria. These results indicate that CO2 production in Arctic soils does not only depend on the environmental conditions, but also on the presence of specific groups of bacteria that have the capacity to actively degrade soil carbon.

sample_organism:
environmental samples
environmental samples
environmental samples
environmental samples
environmental samples
environmental samples

platform_organism: Bacteria Archaea

overall_design: Three different soil types from the Canadian high Arctic were sampled at two depths within the active layer of soil and at two sampling dates (winter and summer conditions), for a total of 20 samples.

first: Christine

last: Martineau

first: Etienne

last: Yergeau

first: Lyle

middle: G

last: Whyte

first: Charles

middle: W

last: Greer


title: Expression data from Sinorhizobium meliloti strains Rm8530 and Rm8530 mucR.

city: Richardson

first: Juan

last: González

state: TX

address: 800 West Campbell Rd. RL 11

department: Molecular and Cell Biology

institute: University of Texas at Dallas

summary: We used microarrays to analyze the effects of the disruption of mucR in planktonic S. meliloti strain Rm8530.

platform_organism:
Sinorhizobium meliloti
Medicago sativa
Medicago truncatula

overall_design: S. meliloti were grown in minimal low-phosphate media to OD600 = 1.2 for RNA extraction and hybridization on Affymetrix microarrays.

first: Konrad

last: Mueller


title: Bile stress response in probiotic Lactobacillus rhamnosus GG

city: Helsinki

first: Kati

last: Laakso

address: Meijeritie 4

country: Finland

institute: Valio Ltd

summary: Transcriptional profiling of probiotic Lactobacillus rhamnosus strain GG mid-exponential pH-controlled bioreactor cultures before and after exposure to bovine bile (0.2% ox gall). Keywords: bile, stress response

overall_design: Cell samples from four biological replicates were harvested right before (time point 0 min) and 10, 30 and 120 min after bile treatment. Each sample was compared to a common reference sample (time point 0 min, mid-exponential growth phase Lactobacillus rhamnosus GG cultures). A total of 12 hybridizations were performed using balanced dye-swap design. Dyes were balanced between compared sample pairs and between biological replicates.

first: Kerttu

last: Koskenniemi

first: Johanna

last: Koponen

first: Matti

last: Kankainen

first: Dario

last: Greco

first: Petri

last: Auvinen

first: Kirsi

last: Savijoki

first: Tuula

middle: A

last: Nyman

first: Anu

last: Surakka

first: Tuomas

last: Salusjärvi

first: Willem

last: de Vos

first: Soile

last: Tynkkynen

first: Nisse

last: Kalkkinen

first: Pekka

last: Varmanen


title: Genome-Wide Gene Expression Profiling Of Chicken Spleen Responding To Campylobacter jejuni Infection In Broilers

city: College Station

first: Huaijun

last: Zhou

address: Rm 418D Kleberg Center,Texas A&M University

institute: Texas A&M University

summary: Campylobacter jejuni (C. jejuni) is a zoonotic pathogen that causes human diarrhea worldwide. Chickens are a natural reservoir of C. jejuni. Understanding the host response to C. jejuni infection at the molecular level will lay the foundation to control human campylobacterosis by reducing food contamination. Two distinct genetic lines, resistant (line A) and susceptible (line B) to C. jejuni colonization, were utilized to profile the host response to C. jejuni infection using an Agilent chicken 44K microarray. Day-old chickens were challenged orally with C. jejuni and spleens collected for total RNA 7 days post-challenge. Twenty infected samples with highest (a) or lowest bacterial number (b) in cecal content and twenty non-infected (c) in each line were randomly pooled into four biological replicates. The pair comparisons among these three groups within each line were analyzed. The signal intensity of each gene was normalized using LOWESS method. A mixed model was used to identify differentially expressed genes by SAS (P < 0.001). This was opposite to previous cecal tonsil microarray result. There were 468, 743, and 939 genes differentially expressed between groups a and c, groups a and b, and groups b and c in line A, respectively, and 201, 37, 126 genes in line B, respectively. More differentially expressed genes in spleen in line A than in line B were found. The results indicated that significantly different response to C. jejuni infection occurred between resistant and susceptible chicken lines, and the effects of interaction between genetics and tissue should be considered.

overall_design: Chickens in two broiler lines were inoculated with 10^5 cfu C. jejuni on one day after hatch. The cecal content and cecal tonsil was collected and bacterial number in cecal content was counted on day 7 after inoculation. Twenty samples were separated into 3 groups (high burden, low burden, and control) based on bacterial burden of cecal content in each line, 5 samples were mixed randomly into one pool. A dual color, balanced design was carried on for all samples. Three comparisons were used in each line, non-infected/susceptible, susceptible/resistant, resistant/non-infected, totally, four biological replicates in each line. A Dye swap was used in each pair of comparisons including AN/AS, AS/AR, AR/AN; BN/BS, BS/BR, and BR/BN. Background subtracted signal intensity were collected from 24 arrays and normalized for data analysis.

first: Xianyao

last: Li

first: Christina

middle: L

last: Swaggerty

first: Michael

middle: H

last: Kogut

first: Hsin-I

last: Chiang

first: Ying

last: Wang

first: Kenneth

last: Genovese

first: Haiqi

last: He

first: Igal

last: Pevzner


title: Expression profiling analysis of thymus and brain from EMP3 mutant mice

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum München GmbH

summary:
Background: Epithelial membrane protein 3 (EMP3) was previously reported to be involved in immunological reactions and in tumor as potential suppressor, as well as a candidate gene for cardiac dystrophic calcification (DCC). Given its assumed role in different disorders, we aimed to generate and perform a generalized phenotypic screening of EMP3-knockout mice. Materials and Methods: TaconicArtemis used knockout-targeting strategy and generated knockout mice for EMP3. Large-scale phenotype screens were performed at the German Mouse Clinic (GMC) to obtain a standardized and comprehensive way of phenotype. The phenotype screens involved tests for nearly 320 parameters in different screening areas such as: dysmorphology, behavior, neurology, eye, nociception, energy metabolism, clinical chemistry and hematology, immunology, allergy, steroid metabolism, cardiovascular and lung function and pathology. For DCC, screening was performed in our laboratory using the freeze-thaw injury method.

Results: Here, we report on the phenotype of EMP3 knockout. EMP3-KO mice are viable and fertile. Under baseline conditions, an aberrant immunological phenotype was found with nearly 70% penetrance in mutant male mice. Specifically, a lower frequency of T cells and an inverse trend in B cells was observed. Also a higher frequency of B cells was seen in female mutant mice. For all the remaining screening, no genotype-specific differences were found. Also no calcification deposits were found in the EMP3-KO mice as response to injury. In addition we reviewed and discussed the strong role of EMP3 in apoptosis and tumor. Therefore, further analysis of EMP3 as tumor suppressor gene in EMP3-KO mice required investigation under challenging conditions.

Conclusion: Large-scale phenotypic screening suggests a role of EMP3 under basal conditions in immunity. Differences in the proportion of various leukocyte subsets from the corresponding wild type were found. Further investigation is ongoing to demonstrate the role of EMP3 as tumor suppressor in a sensitized model. Finally, we excluded the EMP3 gene as candidate gene for DCC on the C57BL/6 genetic background.

overall_design: Thymus and brain of four mutant animals of the EMP3 mutant mice versus a pool of four reference (wildtype) mice; two technical replicates for each mutant mouse including a dye swap experiment - in total 8 chip hybridisations for each of the analysed organs

first: Johannes

middle: J

last: Beckers

first: Marion

last: Horsch

first: Z

middle: Z

last: Aherrahrou


title: Dll1 mice cloned by nuclear transfer

summary:
Production of viable and fertile mice have been reported by nuclear replacement, however, the reasons behind the frequent deformations among foetuses and progeny are not well understood. Activation and in vitro culture methods are also important. Origin of the nuclear donor cells affects success rates, and their survival in culture varies. It has been reported that offspring of nuclear replacement parental mice were normal and fertile. All epigenetic problems in the parents seem to be erased when cell nuclei go through the germ line.
cDNA microarray analysis compared expression patterns of Dll1 ko versus Dll1 ko NT (NT = nuclear transfer) and wt versus wt NT of liver and spleen. The aim of this study was analysis of possible epigenetic effects by cloning in the offspring of the 3rd generation.
If the 3rd generation cloned animals are indeed phenotypically equivalent to conventional transgenic mouse models then this would open the possibility to develop novel techniques of genetic engineering based on somatic gene targeting and nuclear replacement.

overall_design: four male animals of each cohort (Dll1 conventional transgenic mouse, Dll1 nuclear transfer mouse, wildtype, wildtye nuclear transfer mouse). Two technical replicates including a colour flip experiment. For each analysed organ (liver, spleen) eight experiments including four biological replicates. As reference RNA pools were used

first: Andras

last: Dinnyes


title: Gene expression of two-week old seedlings of OsCc1:OsbHLH148 transgenic rice plants

first: Ju-Seok

last: Seo

type: Expression profiling by genome tiling array

summary: To understand downstream genes affected by overexpression of OsbHLH148, the Rice 3’-Tiling Microarray analysis (GreenGene Biotech, Yongin, Korea) was carried out to profile gene expression of OsCc1:OsbHLH148 transgenic plants in comparison with wild-type plants under normal growth conditions. RNA samples from these plants were used to generate cyanine-3 (Cy3)-labeled complementary DNA (cDNA) probes, which were then hybridized to the microarray. Each data set was obtained from two biological repeats with independent transgenic lines.

overall_design: Expression profiling was conducted using a Rice 3’-Tiling Microarray. Information on the microarray can be found at http://www.ggbio.com (GreenGene Biotech). The Rice 3’-Tiling Microarray was designed from 27,448 genes deposited at IRGSP, RAP1 database (http://rapdb.lab.nig.ac.jp). Among these, 20,507 genes were from representative RAP1 sequences with cDNA/EST supports and 6,941 genes were predicted without cDNA/EST supports. Ten 60-nt long probes were designed from each gene starting 60 bp ahead the end of stop codon with 10 bp shifts in position so that 10 probes covered 150 bp in the 3' region of the gene. In total, 270,000 probes were designed (average size, 60-nt) to have Tm values of 75 to 85 °C. The microarray was manufactured by NimbleGen Inc. (http://www.nimblegen.com/). Random GC probes (38,000) were used to monitor the hybridization efficiency and fiducial markers at the four corners (225) were included to assist with overlaying the grid on the image. The microarray was used to profile gene expression in OsCc1:OsbHLH148 transgenic and wild-type rice plants. Cy3-labeled target cDNA fragments were synthesized from two-week old seedlings using a Cy3-9mer primer. For normalization, data were processed with cubic alpine normalization using quartiles to adjust signal variation between chips and with Rubust Multi-Chip Analysis using a median polish algorithm implemented in NimbleScan (Workman et al., 2002; Irizarry et al., 2003). To assess the reproducibility of the microarray analysis, we repeated the experiment two times with independent transgenic lines, T-2 and T-9, and analyzed each data set statistically using one-way ANOVA.

first: Yang

last: Choi


title: CovR-regulated genes in Streptococcus mutans strain UA159

city: Kansas City

first: Alexander

middle: V

last: Dmitriev

state: KS

address: 3901 Rainbow Boulevard

institute: Kansas University Medical Center

summary: The goal of the study was to identify subsets of the genes, which are up-regulated and down-regulated by CovR regulator in UA159 strain.

overall_design: Two independently isolated RNA samples from each of the wild-type UA159 strain and its covR mutant strain grown until mid-exponential phase were analyzed. Each sample was hybridized with 5 blocks of NimbleGen arrays.

first: Indranil

last: Biswas


title: MicroRNA expression profiling using microRNA microarrays on NCI-60 cell lines.

status: Public on Dec 31 2010

city: Lund

first: Rolf

last: Søkilde

address: Scheelevägen 2

department: Department of Oncology

country: Sweden

institute: Lund University, Sweden

overall_design: RNA samples containing small RNA fraction were profilled


title: Gene expression analysis of four conditions for Puccinia graminis f. sp. tritici

first: Christina

last: Cuomo

address: 7 Cambridge Center

institute: Broad Institute

summary:
Puccinia graminis f. sp. tritici is the cause of wheat stem rust.  A microarray was designed from genes predicted from the P. graminis f. sp. tritici genome assembly, and gene expression measured for four conditions which include wheat or barley infecting growth stages initiated by urediniospores. mRNA was prepared from fresh urediniospores, uredinospores germinated for 24 hr, wheat seedlings infected with urediniospores for 8 days, and barley seedlings infected with urediniospores for 8 days. The asexual uredinial infection cycle on wheat produces additional urediniospores, which can start new cycles of wheat infection and are readily spread by aerial transport.
This expression data is further described in Duplessis et al, Obligate Biotrophy Features Unraveled by the Genomic Analysis of the Rust Fungi, Melampsora larici-populina and Puccinia graminis f. sp. tritici

overall_design: A total of 12 samples were analyzed, including three biological replicates of the four conditions.

first: Les

last: Szabo