title: Spatial Coupling of mTOR and Autophagy Augments Secretory Phenotypes

status: Public on May 05 2011

first: Shamith

last: Samarajiwa

address: Robinson way

institute: Cambridge Research Institute

summary: Protein synthesis and autophagic degradation are regulated in an opposite manner by mammalian target of rapamycin (mTOR), whereas under certain conditions it would be beneficial if they occured in unison to handle rapid protein turnover. We observed a distinct cellular compartment at the trans-side of the Golgi apparatus, the ‘TOR-autophagy spatial coupling compartment’ (TASCC), where (auto)lysosomes and mTOR accumulated during Ras-induced senescence. mTOR recruitment to the TASCC was amino acid- and Rag guanosine triphosphatase (GTPase)-dependent, and disruption of mTOR localization to the TASCC suppressed interleukin-6/8 synthesis. TASCC-formation was observed during macrophage differentiation and in glomerular podocytes; both displayed increased protein secretion. The spatial coupling of cells’ catabolic and anabolic machinery could augment their respective functions and facilitate the mass synthesis of secretory proteins.

overall_design: To compare gene expression profile between growing and oncogenic Ras induced senescence, 4OHT inducible ER:H-RasV12 was stably expressed in IMR90 human diploid fibroblasts. Total RNA was isolated from day 0 and day 4 after 4OHT addition. There were 3 biological replicates for each of day0 and day 4 timepoints.

first: Masashi

last: Narita

first: Masako


title: Real-time quantitative PCR analysis of human dendritic cells

status: Public on May 08 2011

city: Boston

first: Attila

last: Szanto

state: MA

address: 185 Cambridge St.

department: Molecular Biology

country: USA

institute: Massachusetts General Hospital

summary: Human CD14 positive monocytes were purified from healthy volunteers' blood and were differentiated to immature dendritic cells in vitro by culturing for five days in the presence of interleukin-4 (IL-4 100 ng/ml) and GM-CSF (75 ng/ml). Immature dendritic cells were activated three different ways for 24 hours: 1. Double-stranded DNA poly(dA:dT) (2.5 μg/ml) complexed with LyoVec transfection reagent. 2. LPS (500 ng/ml) 3. Inflammatory cocktail containing 10 ng/ml TNF, 5 ng/ml IL-1β, 20 ng/ml IL-6, 75 ng/ml GM-CSF and 1 μg/ml PGE2. We used SA Biosciences Antigen Presenting and Toll-like Receptor Pathway PCR Arrays to quantitate gene expression of immunologically relevant genes from the immature and the differently activated cells.

overall_design: Monocytes from three donors were used and treated separately as indicated in the summary. Equal amount total RNA from each donor was pooled prior to gene expression analysis.

first: Katalin

last: Kis-Toth

first: George

last: Tsokos


title: Ammonia exposures on the endangered delta smelt

city: Davis

first: Richard

middle: Edward

last: Connon

state: CA

address: One Shields Avenue

department: Anatomy, Physiology and Cell Biology

institute: University of California at Davis

summary: The delta smelt (Hypomesus transpacificus) is a pelagic fish species endemic to the Sacramento-San Joaquin Estuary in Northern California, listed as endangered under both the USA Federal and Californian State Endangered Species Acts and acts as an indicator of ecosystem health in its habitat range. Interrogative tools are required to successfully monitor effects of contaminants upon the delta smelt, and to research potential causes of population decline in this species. We used microarray technology to investigate genome-wide effects in 57-day old larvae after a 4-day exposure to ammonia; one of multiple contaminants arising from wastewater treatment plants and agricultural runoff. Genomic assessments were carried out between larvae exposed to 10 mg/L total ammonium; the lowest observed effect concentration (LOEC), and controls.

overall_design: Microarray assessments were conducted on larvae exposed for 4-days to 10 mg/L (nominal) ammonium chloride and controls. Assessments were carried out in quadruplicate, using 5 fish per treatment. RNA was extracted from frozen whole, individual organisms, using Trizol Reagent (Invitrogen) as per manufacturer's guidelines. Total RNA from 5 fish was pooled per treatment and cDNA was synthesized from a total of 500ng total RNA, amplified using a SuperScripttm Indirect RNA Amplification System (Invitrogen). Resulting cDNA was labeled with Alexa fluor dyes (Invitrogen) as per manufacturer’s instructions. Two color microarray assessments were carried out on quadruplicate treatments, using 1µg of amplified cDNA for each control vs exposed sample, incorporating dye swaps for each (total 8 samples). Microarray hybridizations were performed using an automated Tecan HS4800 hybridization station. Slides were scanned using a GenePix 4000B scanner (Axon Instruments). Data was analyzed using LIMMA GUI (Linear model for microarray analysis graphical user interface) (Smyth, 2005), written in the R-programming language available through Bioconductor http://www.Bioconductor.org. Data was normalized within using print-tip Lowess and between arrays applying average intensity quantile (Aquantile) normalization methods with background correction (Smyth, 2005). A linear model fit was computed using the duplicates on the arrays and the least-squares method, with Benjamin Hochberg false discovery rate adjustment.

middle: E

first: Linda

middle: A

last: Deanovic

first: Erika

middle: B

last: Fritsch

first: Leandro

middle: S

last: D'Abronzo

first: Inge

last: Werner


title: Virulence differences in Toxoplasma mediated by amplification of polymorphic pseudokinases.

status: Public on May 03 2011

city: St Louis

first: Michael

middle: Sean

last: Behnke

state: MO

address: 660 S. Euclid Ave

department: Molecular Microbiology

institute: Washington University School of Medicine

summary: The population structure of Toxoplasma gondii includes three highly prevalent clonal lineages, types I, II, and III, which differ greatly in virulence in the mouse model.  Previous studies have implicated a family of serine threonine protein kinases found in rhoptries (ROPs) as important in mediating virulence differences between types I vs. III and II vs. III.  Here, we explored the genetic basis of differences in virulence between the highly virulent type I lineage and moderately virulent type II based on a new genetic cross and linkage mapping.  Genome-wide association revealed a single quantitative trait locus controls the > 4 log difference in lethality between these strains.  Neither ROP16 nor ROP18, previously implicated in virulence differences in T. gondii, were found to contribute to differences between types I and II.  Instead, the major virulence locus contained a cluster of pseudokinases denoted as rhoptry protein 5 (ROP5); this locus contains a tandem cluster of polymorphic alleles that differed in expression levels between strains.  ROP5 alleles contained only part of the catalytic triad of canonical S/T kinases, and consistent with this they lack demonstrable kinase activity in vitro.  Genetic disruption of the rop5 locus in the type I lineage lead to a > 5 log increase in the lethal dose, and surviving mice developed lasting immunity and were protected from an otherwise lethal challenge.  These findings reveal that amplification of a polymorphic cluster of pseudokinases plays an important role in pathogenesis of toxoplasmosis in the mouse model.

overall_design: We used a new genotyping protocol based on hybridization of parental and recombinant progeny genomic DNA (gDNA) to Affymetrix gene arrays constructed for T. gondii (http://ancillary.toxodb.org/docs/Array-Tutorial.html).  We identified 1,603 single feature polymorphisms (SFP) based on probes that successfully discriminated perfect match (type II) from mismatch (type I) hybridization across all clones and provided reliable SFP markers for this cross.

first: Asis

last: Khan

first: John

middle: C

last: Wootton

first: J

middle: P

last: Dubey

first: L

middle: D

last: Sibley


title: cps wild type vs cps mgtA mutant

city: Groningen

first: Jetta

last: Bijlsma

address: Hanzeplein 1

department: Medical Microbiology

country: Netherlands

institute: University Medical Center Groningen

summary: Comparison of the Streptococcus pneumoniae D39 cps mgtA mutant vs cps wild type

overall_design: One condition design comparison of two strains including a dye swap

middle: J

first: Oscar

last: Kuipers

first: Jolanda

last: Neef

first: Vahid

middle: F

last: Andisi

first: Kwang

last: Kim


title: Haemophilus ducreyi 35000HPcpxA gene expression relative to 35000HP

city: Dallas

first: Eric

last: Hansen

state: TX

address: 5323 Harry Hines Blvd

department: Microbiology

institute: University of Texas Southwestern Medical Center

summary: Comparative analysis of the global gene expression of a Haemophilus ducreyi 35000HP cpxA deletion mutant relative to the wild type strain

overall_design: After the cpxA mutant was generated, both strain were grown in Columbia Broth.  After 8 hr of growth RNA wa isolated and processed for DNA microarray analysis.  This study includes three biological replicates (paired samples), and all three were subjected to dye swap.

first: Maria

last: Labandeira-Rey


title: Gene expression profiling of high (HAB) vs. low (LAB) and normal (NAB) anxiety-related behavior mice in five laser microdissected brain regions.

status: Public on May 04 2011

city: München

first: Ludwig

last: Czibere

address: Kraepelinstrasse 2

country: Germany

institute: Max Planck Institute of Psychiatry

summary:
Investigating the molecular basis and correlates of anxiety-related and depression-like behaviors, we generated a mouse model consisting of high (HAB), normal (NAB) and low (LAB) anxiety-related behavior mice. We utilized the elevated plus-maze for testing the genetic predisposition to anxiety-related behavior and, consequently, used this as selection criterion for the inbreeding of our animals. In depression-related tests, HAB mice display a more passive, depression-like coping strategy than LAB mice, resembling clinical comorbidity of anxiety and depression as observed in psychiatric patients.
Using a microarray approach, the hypothalamic paraventricular nucleus (PVN), the basolateral (BLA) and central amygdala (CeA), the cingulate cortex (Cg) and the dentate gyrus (DG) – centers of the central nervous anxiety and fear circuitries – were investigated and screened for differences between HAB, NAB and LAB mice.

overall_design: Analysis was performed from four to six animals per line (HAB, NAB and LAB from generation 25, respectively) per brain region, giving a total of 78 individual arrays analyzed. The LAB mouse line is referred to as reference.

first: Peter

last: Weber

first: Benno

last: Pütz

first: Claudia

last: Kühne

first: Gabriele

last: Rieder

first: Florian

last: Holsboer

first: Jan

middle: M

last: Deussing

first: Rainer

last: Landgraf


title: affy_ams_maize-Cell wall maize mutant during arbuscular mycorrhizal symbiosis

city: evry

first: stephanie

last: huguet

address: 2 rue gaston cremieux

country: France

institute: inra

summary:
affy_ams_maize - aafy_ams_maize - Main objectives of this study: - role of plant cell wall during AM symbiosis - regulation pattern during AM symbiosis - understanding of the original mycorrhizal phenotype of bm4 - search of candidate-genes to study AM symbiosis-After 7 days in phytochambers, plantlets were transplanted in 2L of humidified bedrock with 3000 spores for inoculation conditions or without spore for mock conditions then plants have grown in greenhouse. Maize roots have been sampled 7 weeks post-inoculation and freezed in liquid nitrogen then stocked at -80°C. Total RNA was isolated from frozen root tissue by using the RNeasy Plant Mini Kit (Qiagen) following the manufacturer’s instructions.

Keywords: treated vs untreated comparison

overall_design: 8 arrays - maize

first: Magalie

last: Pichon

first: Stephanie

last: Huguet

first: CHRISTOPHE

last: ROUX

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Salmonella Typhimurium LT2: Control versus naringenin

city: College Station

first: Bhimanagouda

last: Patil

address: 1500 Research Pkwy, Ste A120

institute: Texas A&M University

summary: Salmonellosis is one of the leading health problems worldwide. With the rise of drug resistance strains it has become imperative to identify alternative strategies. Naringenin, a flavonone, is present predominantly in grapefruit. Previously we have demonstrated that naringenin is potent inhibitor of cell-cell signaling. In the present study, we provide evidence that naringenin specifically represses 24 genes in the Salmonella pathogenicity island 1, and down-regulates 17 genes involved in flagellar and motility; thereby, attenuating virulence and cell motility, respectively. This is the first molecular evidence to demonstrate effect of naringenin on bacterial virulence and cell motility.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

overall_design: One condition experiment, naringenin treated versus DMSO treated. Biological replicates: 3 control, 3 treatment, hybridized in dye-swapped design

first: Amit

last: Vikram

first: Palmy

middle: R

last: Jesudhasan

first: G

middle: K

last: Jayaprakasha

first: Suresh

last: Pillai

first: Arul

last: Jayaraman


title: microRNA expression in salt-tolerant and salt-sensitive cotton cultivars under normal and salt-stressed conditions

city: Anyang

first: Zujun

last: Yin

state: Henan

address: 38 Huanghe Dadao, Anyang 455000, Henan, China

department: Cotton Research Institute

country: China

institute: Chinese Academy of Agricultural Sciences

summary: To detect salt-tolerance-related miRNAs, comparative analysis of miRNA expression profiles was performed between the salt-tolerant and -sensitive cotton cultivars in control and salt-stressed conditions (treated with 300 mM NaCl for 24 h) using microRNA microarray

overall_design: Total RNA was extracted from (1) the seedling of salt-tolerant cotton cultivar in normal growth conditions, (2) the seedling of salt-tolerant cotton cultivar in salt-stressed growth conditions, (3) the seedling of salt-sensitive cotton cultivar in normal growth conditions, and (4) the seedling of salt-sensitive cotton cultivar in salt-stressed growth conditions. Then, the low-molecular-weight RNA (LMW-RNA) was isolated using the PEG solution precipitation method and used to hybridization.

first: Chunhe

last: Li

first: Fafu

last: Shen


title: Environment-responsive transcription factors bind proto-silencer elements and regulate subtelomeric silencing

city: Seattle

first: Jennifer

middle: Joy

last: Smith

state: WA

address: 1441 North 34th Street

institute: Institute for Systems Biology

type: Genome binding/occupancy profiling by genome tiling array

summary:
Subtelomeric chromatin is subject to evolutionarily conserved complex epigenetic regulation and is implicated in numerous aspects of cellular function including formation of heterochromatin, regulation of different stress response pathways, and control of lifespan.  Subtelomeric DNA is characterized by the presence of specific repeated segments that serve to propagate silencing activities or to protect chromosomal regions from spreading epigenetic control.  Using condition-specific genome wide chromatin immunoprecipitation and expression data, we show that several yeast transcription factors regulate subtelomeric silencing in response to various environmental stimuli through conditional association with proto-silencing regions called X elements.  In this context, some factors control the propagation of silencing toward centromeres in response to stimuli affecting stress responses and metabolism, whereas others appear to influence boundaries of silencing, regulating telomere-proximal genes in Y’ elements.  The factors implicated here have previously been shown to control adjacent genes at intrachromosomal positions, suggesting dual functionality of the factors and a possible mechanism of coordinating intrachromosomal gene expression with subtelomeric silencing.  These data suggest a fundamental mechanism to coordinate telomere biology related to aging and adaptation with cellular environment and the activities of other cellular processes.
These are Chip-CHIP data for myc tagged Oaf1p transcription factor from S. cerevisiae grown in the presence or absence of the fatty acid oleate.

overall_design: ChIP-CHIP analysis was performed to determine the genomic distribution of Oaf1p transcription factor in the BY4742 yeast strain after growth in 0.1% glucose, or in the presence of the fatty acid oleate.  Three biological replicates for each growth condition (in the presence of low glucose or 5 h after a shift to medium containing oleate as a carbon source).  ChIP samples were amplified by PCR, labelled and hybridized to 50-mer tiling arrays covering both strands of the entire yeast genome at a 64 bp resolution.

first: Leslie

last: Miller

first: Laura

last: Vazquez

first: Yakun

last: Wan

first: John

last: Aitchison


title: Transcriptomes profile of Solanum tuberosum (St) and Solanum commersonii (Sc) under cold stress and AtCBF3 overexpression.

status: Public on May 01 2011

city: East Lansing

first: Marcela

last: Carvallo

state: MI

address: 310 Plant Biology bldg

department: Plant Research Laboratory

institute: Michigan State University

summary: St (common potato) is a freezing sensitive species unable to cold acclimate. The close wild relative Sc is freezing tolerant and able to cold acclimate. Here we compare the cold transcriptome of these two species with different levels of freezing tolerance. We also identify the putative CBF regulons by comparing the transcriptomes of wild type plants with that of 35S::AtCBF3 transgenic lines in both species.

sample_organism:
Solanum commersonii
Solanum tuberosum

overall_design: Plants were grown in 16:8 photoperiod. Eight hours after dawn, plants were either transfered to cold or kept in the warn. Wild type S. tuberosum and S. commersonii were grown at 2oC for 2h, 24h and 7 days. Wild type plants grown under warm temperatures for 2h was used as control for 2h cold samples; wild type warm grown plants for 24h were used as controls for 24h and 7 days cold samples. Under warm conditions, S. commersonii 35S::AtCBF3 lines were compared to S. commersonii wild type plants (same thing was done for S. tuberosum).

first: Michael

last: Thomashow

first: Maria

middle: T

last: Pino

first: Zoran

last: Jeknic

first: Tony

last: Chen


title: Schistosoma mansoni developmental stages

status: Public on Apr 30 2011

city: São Paulo

first: Katia

middle: Cristina Pereira

last: Oliveira

state: O

address: Av Prof lineu prestes 748

department: Centro de Parasitologia e Micologia

country: Brazil

institute: Instituto Adolfo Lutz

summary: Transcriptional profiling using two subsequent developmental stages of Schistosoma mansoni (Egg vs. Miracidium; Cercaria vs. 7-days-old Schistosomulum; 7-days-old Schistosomulum vs. Adult worms

overall_design: Two conditions experiment; Developmental Stage 1 vs. Developmental Stage 2

first: Sergio

last: Verjovski-Almeida


title: Expression data of rhabdomyosarcoma cells and spheres

city: Zurich

first: Dagmar

last: Walter

address: August-Forel Str 1

department: Oncology

country: Switzerland

institute: University Children's Hospital

summary:
Rhabomyosarcoma cells can be cultured in stem cell medium over several passages and form spheres being enriched in putative cancer stem cell markers and expressing high levels of stem cell genes.
In this dataset, we include RNA samples from 2 rhabdomyosarcoma cell lines and 3 different sphere passages of each cell line.

overall_design: 16 samples were analyzed and all sphere passages were compared to the expression level of their corresponding adherent cell line. We wanted to see an up- or downregulation of genes in the spheres to identify new potential cancer stem cell marker.

first: Beat

middle: W

last: Schäfer


title: Comparing the transcriptional profiles of a Caulobacter crescentus CB15N (NA1000) wild-type to a SpoT null in carbon starvation.

first: Sean

last: Crosson

state: Michigan

address: 567 Wilson Rd

department: Dept. Microbiology and Molecular Genetics

summary:
SpoT is an Rsh (Rel / Spo homolog) protein, which synthesizes the alarmone ppGpp in response to starvation.
This experiment is quantifying transcription in two Caulobacter strains after 5 minutes of glucose starvation:  one strain is wild-type CB15N (NA1000); the other strain is NA1000 which has a chromosomal in-frame deletion of the spoT gene.  The wild-type strain can synthesize the alarmone ppGpp in response to starvation and the spoT null strain cannot.  Both strains were cultured in M2 defined medium with glucose as the sole carbon source, and then washed and incubated in M2 medium lacking glucose for 5 minutes before RNA isolation.

overall_design: Triplicate cultures of: 1) C. crescentus strain CB15N , and 2) CB15N ∆SpoT, cultured in M2-glucose media, then starved for glucose for 5 minutes.


title: Gene expression in aerial hyphae in response to rep1 deletion in Ustilago maydis

city: Utrecht

first: Wieke

middle: R.

last: Teertstra

address: Padualaan 8

department: Biology

institute: University of Utrecht

summary: The rep1 gene of the maize pathogen Ustilago maydis encodes a pre-pro-protein that is processed in the secretory pathway into 11 peptides. These so-called repellents form amphipathic amyloid fibrils at the surface of aerial hyphae. Strains in which the rep1 gene is inactivated (∆rep1 strain) are affected in aerial hyphae formation. This makes these strains instrumental to assess changes in global gene expression as a consequence of aerial growth. Microarray analysis revealed that only 31 genes in the ∆rep1 SG200 strain had a fold change in expression of >= 2. Twenty-two of these genes are up-regulated and half of them encode small secreted proteins (SSP’s) with unknown functions. Seven of the SSP genes and two other genes that are over-expressed in the ∆rep1 SG200 strain encode secreted cysteine-rich proteins (SCRP’s). Interestingly, most of the SCRP’s are predicted to form amyloids. The SCRP gene um00792 showed the highest up-regulation in the ∆rep1 strain. Using GFP as a reporter, it was shown that this gene is over-expressed in the layer of hyphae at the medium-air interface. Taken together, it is concluded that only minor changes occur in the expression profile when U. maydis forms aerial structures.  Key words: aerial hypha, repellent, hydrophobin-like protein, Ustilago maydis, SSP, SCRP, fungal pathogenicity.

overall_design: To analyze expression changes in aerial hyphae upon deletion of the rep1 gene, strains SG200 and SG200∆rep1 were grown on charcoal nitrate minimal array media supplemented with vitamins and 1% glucose at 22 C for 48 h. For each experiment three biological replicates were performed.

first: W

first: H

last: Wösten


title: Transcriptional profiling of intracellular F. tularensis Type A and Type B strains following infection of human monocyte derived macrophage (hMDM).

city: Rockville

last: Braisted

state: MD

address: 9704 Medical Center Dr

department: PFGRC

institute: J Craig Venter Institute

summary:
Francisella tularensis is one of just three bacterial species designated as a Category A select agent by the Centre for Disease Control (CDC), a category indicating agents most likely to be employed as a biological weapon. F. tularensis can be divided into four different subspecies, and it is well known that the type, severity and duration of the disease can differ substantially depending on what subspecies is responsible for the infection. Of the four subspecies, subsp. tularensis (Type A) and subsp. holartica (Type B) are of primary clinical significance, and account for nearly all recorded incidences of the disease in humans. Though Type A is considered to be much more virulent than Type B, recent reports have shown that Type A can be further subdivided into two genetically distinct populations, termed A.I and A.II, which differ with respect to geographical location, disease outcome and source of recovered isolates. Of these two subpopulations, clinical data suggests that Type A.I strains are much more virulent than Type A.II, and Type A.II strains appear to have a disease outcome similar to infections with Type B. During natural infections, host mononuclear phagocytes appear to be the primary target of all F. tularensis subsp. Despite the differences in disease outcome between different subspecies, the mechanisms involved in phagosomal escape, the modulation of phagosomal biogenesis, phagosomal disruption and bacterial egress appears to be indistinguishable between subspecies, at least at a physiological level. However, recent reports suggest that at the molecular level there appears to be significant differences between subspecies during infection, and this may account for the dramatically different disease outcome associated with different subspecies.
	Our long-term goal is to identify unique molecular markers associated with the more virulent Type A.I strains with the potential for use as vaccine or therapeutic targets, and to provide a greater insight into the molecular differences associated with F. tularensis infection. Our overall objective of this application, which is the next step in the pursuit of that goal, is to obtain a full transcriptional profile of Type A.I, Type A.II and Type B strains following infection of human monocyte derived macrophage (hMDM) using a novel full genome quantitative real time PCR array (qRT-PCR). The central hypothesis of the application is that Type A.I, Type A.II and Type B strains activate different transcriptional networks during the course of infection of macrophage, and that these differences are at least partially responsible for the observed differences in disease outcome between the subspecies. This hypothesis has been formulated on the basis of preliminary data obtained at our laboratory that shows significant differences in the global transcriptional profiles of Type A and Type B strains exposed to environmental stimuli that mimic the intracellular environment (see Preliminary studies).The rationale for the proposed research is that by investigating differences in the transcriptional profiles of the three subspecies, we can identify unique pathogen-associated molecules or networks that can be targeted for future therapeutic research. Complementary to our supportive preliminary data, we are particularly well prepared to undertake the proposed research, with the recent development of a full genome qRT-PCR array that will allow accurate and comprehensive detection of transcriptional changes from pictogram quantities of starting RNA.
This is a pilot study

overall_design: We examined global transcriptome changes in F. tularensis LVS (attenuated Type B), Schu S4 (Type A.I) and B38 (attenuated Type A.II) exposed to a variety of environmental conditions including growth phase, temperature change, acid exposure, oxidative and energy stress, and identified juxtaposing genes that display identical transcription regulation under all the conditions tested. From this data, we generated a list of 1,068 orthologous genes that represent the transcriptional network of Francisella tularensis Type A and Type B strains. Orthologous genes from Type A and B strains were compared and regions of 100% homology selected to generate a list of unique primers for each of the 1,068 genes. Using these primers, a real time two-step RT-PCR using a SYBR Green assay using a Light Cycler 480 Real-Time PCR system (Roche Diagnostics, Indianapolis, IN, USA) in a 384-well format was performed on 5 F. tularensis strains : LVS (typeB), FRAN050 (typeB) 2827G (typeB), Schu S4 (typeA1) and WY-96 (typeA2) in a 384-well format.

first: Patrick

last: Mc Gann

first: Mark

last: Wolcott

first: Marcus

last: Jones

first: Tatiana

last: Dracheva


title: Differential expression of innate immune and metabolic genes in LPS-challenged chickens

city: Ste Anne de Bellevue

first: Bushansingh

middle: Shyam

last: Baurhoo

state: Quebec

address: 21111, Lakeshore Road

department: Animal Science

country: Canada

institute: McGill University

summary: Salmonella causes inflammation in infected hosts. Inflammation is a well-characterized defensive mechanism of innate immunity. The recognition and engagement of lipopolysaccharide (LPS) endotoxins in the outer membranes of Salmonella to Toll-like receptor 4 of immune cells (macrophages and dendritic cells) trigger inflammatory responses characterized by secretion of pro-inflammatory cytokines, including TNF-beta, IL-1 and IL-6. These cytokines cause fever, anorexia, bodyweight losses, and catabolism of skeletal muscles and adipose tissues. However, molecular events underlying innate immune responses and metabolic activities during the later stage of inflammation are poorly understood. Additionally, the effects of prebiotics and antibiotics on innate immunity and nutrient metabolism are not yet reported. The objective of this study is to investigate the effects of a mannanoligosaccharide (MOS) prebiotic and virginiamycin (VIRG) sub-therapeutic antibiotic on innate immunity and glucose metabolism during late inflammation. We induced Salmonella LPS-systemic inflammation in a chicken model. Differentially regulated gene expressions were measured using 2 colour focussed oligonucleotide chicken-specific microarrays.  Microarray analysis was performed on liver, intestinal and skeletal muscle tissues. We found that late inflammation was principally modulated by interleukin 3 (IL 3) and that glucose was mobilized from gluconeogenesis occurring in the intestines only. MOS and VIRG modulated innate immunity and metabolic genes differently. In contrast to VIRG, MOS terminated inflammatory responses earlier. Our results indicate IL 3 gene up-regulation in VIRG-fed chickens. To meet the higher energy requirements of VIRG chickens, genes for intestinal gluconeogenesis and liver glycolysis were respectively induced.  Our study reveals the potential mechanisms by which prebiotic and antibiotic modulated innate immunity and glucose metabolism during late inflammation.

overall_design:
14-day old chickens were injected i.p. with saline or LPS. For each tissue and experimental conditions (saline or LPS challenge), a total of 12 microarrays (6 MOS birds + 6 VIRG birds) were used in a 2 x 2 factorial design and complete interwoven loop arrangement.  We compared gene expression from prebiotic-fed birds with antibiotic-fed birds without including reference RNA.
LPS challenge, antibiotic or prebiotic, innate immunity, glucose metabolism

first: Peter

last: Ferket

first: Christopher

last: Ashwell

first: Jean

middle: E

last: de Oliveira

first: Xin

last: Zhao


title: To analyze expression in the conjunctival epithelium of patients with severe dry eye disease

status: Public on Apr 29 2011

city: La Jolla

first: Steven

last: Head

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

summary: In 2005, we determined the glyco-gene expression profile of three normal subjects ( www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE27593). This led to information on the biosynthesis of mucin O-glycans and glycoproteins that may be involved in the protection of the ocular surface. The interaction of the most highly expressed glycoprotein identified by the glyco-gene chip, galectin-3, with other ligands at the ocular surface (i.e., mucin O-glycans), is now under intense study in our laboratory, and has lead to a collaboration with another group in the glycobiology field.

overall_design:
Patients with dry eye disease have an alteration of mucin O-glycans at the ocular surface, but the molecular mechanism(s) leading to this alteration remain unknown. In this experiment we (i) pooled three pathological samples per chip to reduce variability, and (ii) used three additional chips to include pooled control samples (normal subjects).
Currently, we have RNA from 9 patients with dry eye disease, which have been divided it in 3 groups (D1, D2, and D3)—each group containing RNA pooled from 3 patients. We request three additional chips to include control samples (normal subjects). At this moment, we have RNA from 9 normal subjects, which have been divided it in 3 groups (N1, N2, and N3)—each group containing RNA pooled from 3 normal subjects. RNA was extracted in Trizol, purified using RNeasy column, and dissolved in water were sent to Microarray Core (E).  The RNA was amplified, labeled, and hybridized to the GLYCOv3 microarrays.  Data Analysis was done by Microarray Core (E).

first: Pablo

last: Argueso


title: Global gene expression profile of Haemophilus ducreyi 35000HPcpxRpML125 relative to 35000HPcpxRpLS88

first: Eric

last: Hansen

summary: Haemophilus ducreyi 35000HPcpxRpML125 which over-expresses CpxR in a CpxR deletion background, was compared to it vector alone counterpart (35000HPcpxRpLS88) in hopes to elucidate members of the CpxRA regulon.

overall_design: Haemophilus ducreyi 35000HPcpxRpML125 and 35000HPcpxRpLS88 were grown in Columbia broth.  After 8 hr of growth, total RNA was isolated and processed for DNA microarray analysis.  This study includes 3 biological replicates (paired samples), two of which were selected for dye swap.


title: Structural variation of the gorilla genome

first: Tomas

last: Marques-Bonet

address: 1705 NE Pacific St,

department: Genome Sciences

institute: University of Washington

type: Genome variation profiling by genome tiling array

summary: Structural variation has played an important role in the evolutionary restructuring of human and great ape genomes. We generated approximately 10-fold genomic sequence coverage from a western lowland gorilla and integrated these data into a physical and cytogenetic framework to develop a comprehensive view of structural variation. We discovered and validated over 7,665 structural changes within the gorilla lineage including sequence resolution of inversions, deletions, duplications and retrotranspositions. A comparison with human and other ape genomes shows that the gorilla genome has been subjected to the highest rate of segmental duplication. We show that both the gorilla and chimpanzee genomes have experienced independent yet parallel patterns of structural mutation that have not occurred in humans, including the formation of subtelomeric heterochromatic caps, the hyperexpansion of segmental duplications and bursts of retroviral integrations. Our analysis suggests that the chimpanzee and gorilla genomes are structurally more derived than either orangutan or human.

sample_organism:
Gorilla gorilla
Pan troglodytes
Homo sapiens

platform_organism:
Gorilla gorilla
Homo sapiens

overall_design: all combinations of human, chimpanzee and gorilla are used in 2 different arrayCGH designs. First, a standard 2.1 was used to detected CNVs, and second, we used a custom designed arrayCGH to validate gorilla specific duplications and deletions

first: Mario

last: Ventura

first: Claudia

last: Catacchio

first: Can

last: Alkan

first: Saba

last: Sajjadian

first: Tina

last: Graves

first: Fereydoun

last: Hormozdiari

first: Maika

last: Malig

first: Carl

last: Baker

first: Lee

last: Choli

first: Emily

last: Turner

first: Lin

last: Chen

first: Jeff

last: Kidd

first: Nicoletta

last: Archidicacono

first: Jay

last: Shendure

first: Richard

last: Wilson

first: Evan

last: Eichler


title: Examination of glycan-related gene expression in the livers of three groups of mice: wild-type, ad-lib-fed type 2 diabetic mice (db/db), and calorically restricted db/db mice

first: Steven

last: Head

summary: Assembly of HSPGs in the liver is defective in diabetes mellitus.  A major consequence is impaired clearance of post-prandial lipoproteins, which ordinarily depends on the binding of these particles to hepatic HSPGs.  Impaired clearance leads to prolonged exposure of the arterial wall to these harmful lipoproteins.  We pin-pointed suppression of NDST-1 in livers of type 1 diabetic rats as at least a partial explanation for defective HSPG assembly.

overall_design:
Dr. Williams' lab examined glycan-related gene expression in the livers of three groups of mice: wild-type, ad-lib-fed type 2 diabetic mice (db/db), and calorically restricted db/db mice (caloric restriction was shown several years ago to correct their clearance of atherogenic post-prandial lipoproteins). The results will indicate the molecular basis for defective HSPG assembly in type 2 diabetes, which is a question of considerable medical importance.
RNA preparations from mice livers (wild-type, ad-lib-fed type 2 diabetic mice, and calorically restricted mice) were sent to Microarray Core (E).  The RNA was amplified, labeled, and hybridized to GLYCO_v3 microarrays.

first: Kevin

last: Williams


title: Assessment of RNA samples from macrophages infected or non-infected with HIV to determine the effect of HIV infection on the gene expression

summary: We previously looked the differences in glyco genes using the CFG microarray in normal macrophages and T cells, in conjunction with our studies on effects of glycosylation on HIV/SIV infectivity. In the review of a submitted manuscript, the question arose on the effect of HIV infection on the gene expression.

overall_design:
To address this interesting question, we looked at RNA samples derived from macrophages (derived from the sample donor), either infected or not with HIV (in vitro) at different time points.
RNA preparations of infected and un-infected Human macrophage at three different time points (5, 7, and 10 days)were sent to the Microarray Core (E). The RNA was amplified, labeled, and hybridized to the GLYCOv3 microarrays.

first: Howard

middle: S

last: Fox


title: To investigate the role of cell surface glycans in CIK cell homing from the bloodstream to the tumor tissue

summary:
Dr. Christopher Contag lab's aim is to, investigate the molecular interactions that underlie CIK cell homing from the bloodstream to tumor tissue using a combination of gene expression profiling, flow cytometry, and in vivo molecular imaging. Collectively, these proposed experiments will define the repertoire of molecules employed in CIK cell recognition of the tumor vasculature and guide the development of improved CIK cell therapies for use in cancer patients.
A promising new direction in cancer therapy is the use of cytokine-induced killer (CIK) cells as broadly active tumoricidal agents.  CIK cells derive from blood samples stimulated ex vivo, and these activated immune cells are capable of recognizing and destroying a plethora of tumor targets in vivo.  In fact, CIK cells have demonstrated efficacy in clinical trials to treat patients with hepatoma, renal cell cancer, and hematological malignancies.  Despite the remarkable clinical promise of this therapy, little is known about the mechanisms that govern CIK cell migration to tumor tissue in vivo.  Understanding the trafficking patterns of these potent immune cells is of critical importance to advancing their use in humans.  I aim to investigate the molecular interactions that underlie CIK cell homing from the bloodstream to tumor tissue using a combination of gene expression profiling, flow cytometry, and in vivo molecular imaging.  Collectively, these proposed experiments will define the repertoire of molecules employed in CIK cell recognition of the tumor vasculature and guide the development of improved CIK cell therapies for use in cancer patients.

overall_design: RNA from three groups (1,2,3) were sent to Microarray Core E.  Group one samples: Splenocytes were obtained from BALB/c mice, and the T cells were isolated using a negative isolation kit (magnetic bead separation).  For group 2 and 3 samples: The isolated splenocytes were treated with IFN-gamma overnight.  The cells were then added to anti-CD3 coated flasks and stimulated with IL-2.  Fresh IL-2 was added to the media every 3 days, and the cells were harvested 12 days post-isolation.  The RNA was labeled and hybridized to Glyco_v3 arrays.

first: Christopher

last: Contag


title: Evaluation and comparison of the glyco-gene expression profile of endothelial cells stimulated with VEGF, bFGF and galectin-3

summary:
Dr. Panjwani's laboratory is focusing on the mechanism by which galectins-3 and 7 mediate corneal epithelial cell migration.
Recently published studies, that we have confirmed and expended on in our laboratory, clearly demonstrate that galectin-3 mediates angiogenesis in vitro and in vivo.  More interestingly we have found that bFGF- and VEGF-mediated angiogenesis can be inhibited by galectin-3 inhibitors, which suggests an important role of carbohydrate recognition systems in the process of angiogenesis.  In an effort to characterize the role of carbohydrate recognition system in angiogenesis, we are interested to evaluate and compare the glyco-gene expression profile of endothelial cells stimulated with VEGF, bFGF and galectin-3 at time and concentration at which, the compounds stimulate angiogenesis in vitro.

overall_design: RNA preparations of Galectin-3, VEGF, bFGF, Media Control biological replicates were sent to Microarray Core (E).  The RNA was amplified, labeled, and hybridized to GLYCO_v3 microarrays.

first: Noorjahan

last: Panjwani


title: Analysis of the gene expression pattern of the human corneal epithelial cells to prove the changing medium induces (suppresses) expression

summary:
Dr. Fukuda's laboratory is interested in determining how changing medium induces or suppresses expression of genes involved in keratan sulfte production in the corneal cells.  Human corneal epithelial cells can be induced for keratan sulfate production by replacing culture medium to a serum free medium.
We speculate that changing medium induces (or suppress) expression of gene involved in keratan sulfate production in the corneal cells.  A microarray experiment is ideal for analyzing gene expression pattern of the cells.

overall_design: RNA preparations from human corneal epithelial cells under normal culture condition (control) and under induced condition for keratan sulfate production (target) were sent to the Microarray Core (E). The RNA was amplified, labeled, and hybridized to the GLYCOv3 microarrays. Data was analyzed by Core E and also provided to Dr. Fukuda's laboratory for analysis.

first: Michiko

middle: N

last: Fukuda


title: Analysis of the purified RNA samples to confirm that Notch pathway activation inhibits apoptosis in uterine leiomyomas leading to fibroid growth

summary:
Uterine leiomyomas are the most common benign tumor in humans causing significant morbidity with vaginal bleeding, pelvic pressure and pain.  Histologically, leiomyomas show a large degree of extracellular matrix disorganization.   I am working with a colleague who recently found Notch pathway gene expression were clearly altered in fibroids (“Differential expression of the Notch signal transduction pathway: ligands, receptors and Numb in uterine leiomyomas vs. myometrium,” G. Christman, H. Tang, I. Ahmad, J. Stribley,  Fertility and Sterility, Volume 88, Supp 1, S72, September 2007). Glycosaminoglycan expression was found to be over-expressed in uterine leiomyomas compared to myometrial samples (Fertility and Sterility, Vol 88 Supp 1, S106, September, 2007), but glycosyltransferase and glycosidase expression has not been reported.  We have purified RNA samples from paired uterine leiomyoma and normal myometrium from a previous clinical study.
Dr. Domino's laboratory hypothesis is that Notch pathway activation inhibits apoptosis in uterine leiomyomas leading to fibroid growth. Notch ligands are fucosylated glycans. The bulk of a fibroid is the extracellular matrix yet little has been studied on leiomyocyte expression of enzymes that model glycans in the extracellular matrix.

overall_design: RNA preparations of paired samples of excess human tissues from hysterectomies, with two different groups normal myometrium, and leiomyoma tumors were sent to Microarray Core (E).  The RNA was amplified, labeled, and hybridized to GLYCO_v3 microarrays.

last: Domino


title: Glycogene expression during maturation of human antigen-presenting cells

summary: Dr. van Kooyk's laboratory is exploring the function of antigen presenting cells, such as dendritic cells (DC), that regulate viral-antigen recognition, DC trafficking and T cell binding--all processes that initiate immunity or tolerance. Essential in this is the recognition of ligands by C-type lectins and the functional consequences of differential terminal glycosylation that may regulate DC function.

overall_design:
In this study, the gene expression profile of glycosylation-related genes is examined in relation to the maturation of human antigen-presenting cells.
Two pooled RNA samples, one each from immature and mature human monocyte-derived dendritic cells, were prepared and sent to Microarray Core (E). The RNA was amplified, labeled, and hybridized to the GLYCOv3 microarrays.

first: Yvette

last: van Kooyk


title: Changes in glycogene expression during maturation of dendritic cells

summary:
Dr. van Kooyk's laboratory is interested in investigating the expression of glycosyltransferases in dendritic cells and the changes in expression associated with maturation.
Dr. van Kooyk's laboratory is exploring the function of antigen presenting cells, such as dendritic cells (DC), that regulate viral-antigen recognition, DC trafficking and T cell binding--all processes that initiate immunity or tolerance. Essential in this is the recognition of ligands by C-type lectins and the functional consequences of differential terminal glycosylation that may regulate DC function.

overall_design: RNA preparations from monocytes and dendritic cells (DC) from Ai and Bi (immature DC), Am and Bm (mature DC), and C (monocyte) from healthy human donors were sent to the Microarray Core (E).  The RNA was amplified, labeled, and hybridized to the GLYCOv3 microarrays

last: Van Kooyk


title: Gene microarray screening to identify glycosylation genes that are regulated during the formation of osteoclast cells

summary: Bone remodeling is a tightly regulated process that engages degradation and biogenesis of the bone matrix. The process is controlled by two major cell types, bone forming cells-osteoblasts and bone-degrading cells-osteoclasts. We are interested in the bone-resorption mechanism mediated by osteoclasts and wish to identify glycosylation genes that are regulated during the formation of osteoclast cells and determine the function of glycosylation and glycan-binding proteins in the osteoclastogenesis.

overall_design:
We propose to examine the gene expression patterns that are altered during the osteoclastogenesis using mouse glyco-chips and RNA samples isolated from osteoclast precursors and mature osteoclasts prepared from mouse bone marrows. 6 chips are requested for the analysis.
RNA preparations from mouse bone marrow MG2, MG4, MG6 (mature osteoclasts) and MG1, MG3, MG5 osteoclasts precursors (control) were sent to the Microarray Core (E). The RNA was amplified, labeled, and hybridized to the GLYCOv3 microarrays.

first: Hui

last: Wu


title: Identify changes in gene expression during overexpression of the glycosyltransferase LARGE

summary: alpha-dystroglycan is a component of the dystrophin associated glycoprotein complex that binds components of the extracellular matrix (including laminin, perlecan and neurexin) via its carbohydrate groups. Recently, a group of muscular dystrophies have been identified due to the aberrant glycosylation of this molecule (dystroglycanopathies). The overexpression of the glycosyltransferase LARGE in several cell lines results in alpha-dystroglycan hyperglycosylation and enhanced ligand binding. The glycan structures induced by LARGE overexpression are unknown.

overall_design:
We have injected into mouse legs two LARGE constructs, one wild type and the second in which a DxD motif has been mutated to NNN as a control. We aim to identify genes unregulated during LARGE induced hyperglycosylation in order to gain insight into the enzymes involved in this process and ultimatley the nature of the glycans responsible for ligand binding.
RNA preparations from two LARGE constructs, were sent to Microarray Core (E).  One wild type and the second in which a DxD motif has been mutated to NNN as a control.  The aim is to identify genes unregulated during LARGE induced hyperglycosylation in order to gain insight into the enzymes involved in this process and ultimatley the nature of the glycans responsible for ligand binding.  The RNA was amplified, labeled, and hybridized to teh GLYCOv3 microarrays.

first: Francesco

last: Muntoni


title: Glycan and gene chip analysis of purified osteoclast cell populations

summary: Osteoclast derived from macrophage lineage cells are responsible for bone resorption and important in bone remodeling. Emerging of a new discipline-osteoimmunology highlights the important connection between immunology and bone biology.

overall_design:
We had mouse osteoclast's RNA samples analyzed by the consortium’s gene microarray and identified a number of significant changes in expression of genes involved in glycan biosynthesis. Osteoclasts were treated with: control, Rankl (Receptor activator of nuclear factor kappa-B ligand (RANKL), tunicamycin, and both rankl and tunicamycin.
RNA preparations from osteoclasts purified from mice: control (1,2,3), Rankl (1,2,3), tunicamycin (1,2,3), and both rankl and tunicamycin (1,2,3) were sent to the Microarray Core (E). The RNA was amplified, labeled, and hybridized to the GLYCOv3 microarrays.


title: Detection of de novo and homozygous copy number variants in 99 autism simplex trios

city: Houston

first: Patricia

middle: Borges

last: Celestino

address: One Baylor Plaza, T613

department: Molecular and Human Genetics

institute: Baylor College of Medicine

summary: Comparison of whole genome exome array CGH to a commercial SNP array for detection of de novo and homozygous copy number variants in 99 autism simplex trios. Will update once manuscript is prepared.

overall_design:
Agilent custom designed array comparative genomic hybridization (CGH) was performed on 100 samples with a diagnosis of autism. Unaffected parents of the 100 probands were also tested.  A common male reference was used for all samples and parents.  Samples  were obtained from the Simons Simplex Collection.

Three samples (11154_P1, 11154_Mo, 11154_Fa) were removed from the final analysis for quality control.

first: Arthur

last: Beaudet

middle: B

first: Chad

middle: A

last: Shaw


summary: To investigate the expression of glycosyltransferases in dendritic cells and the changes in expression associated with maturation.

overall_design: Healthy normal donor RNA preparations from Resting macrophages (Macro), LPS-mature dendritic cells (LPSMDC), IL-15 immature dendritic cells (IL15DC), Dexamethasone immature dendritic cells (DxMDC) from 2 different donors.


title: Glycogene expression in control and tumor-bearing mouse muscles

summary: We have observed aberrant glycosylation in membrane proteins in mouse skeletal muscles undergoing cachexia ( muscle wasting) in a tumor bearing condition. Since multiple proteins were glycosylated in this tumor state, we are interested in looking at the glycochip array that includes glycosyltransferases to observe any possible induction of these transferases.

overall_design:
RNA from control (PBS treated) and tumor bearing mouse muscles, at 12 and 22 days, was isolated and prepared in triplicate.
RNA was labeled and hybridized to the GLYCOv3 array.  Gene expression patterns were analyzed with special interest on possible induction of these transferases.

first: Denis

last: Guttridge


title: Microarray screening of RNA samples from low-, intermediate- and high-passage human prostate LNCaP cells

summary:
This laboratory studies the structures, biosynthesis, and functions of mucin glycans
The low-(<33) and high-(>80)passage human prostate LNCaP cells developed by Dr. Ming-Fong Lin (Lin et al, Urology 166:1943, 2001) have been considered as the best in vitro model that reflects the progression of prostate cancer from androgen-dependent to androgen-independent stage (Parajuli et al, Cancer Res. 61:8227, 2001; Demeade et al, The Prostate 54:249, 2003; Unni et al, Cancer Res. 64:7156, 2004). The high-passage cells are metastatic while the low-passage cells are not. RT-PCR analysis of these two cell clones for 25 glycogenes among 8 different groups of glycogenes showed that only high-passage cells expressed two (isozymes 1 and 5) of the five known GlcNAc6ST genes. In addition, P-selectin blot analysis showed qualitative and quantitative differences between these clones. They included 3 higher intensity bands and 3 lower intensity bands in high-passage cells as compared to low-passage cells. The difference in P-selectin-specific glycoconjugates between low and high-passage LNCaP cells should help identify the glycans that distinguish high- from low-passage LNCaP cells.

overall_design: RNA preparations from low-, intermediate-, and high-passage human prostate LNCaP cells were sent to Microarray Core (E). *Concurrent analysis of glycan profiles in these cells was performed in Core C*. Three replicate samples from each condition were used in the study. The RNA was amplified, labeled, and hybridized to the GLYCOv3 microarrays. Data was analyzed to identify the glycogenes, glycans, and/or carbohydrate binding proteins responsible for the difference in metastatic property between low- and high-passage LNCaP cells. The intermediate-passage cells were used for identifying changes in glycogene, glycan, and/or carbohydrate binding protein expression that may be responsible for the earliest change of the metastatic property.

first: Pi-Wan

last: Cheng


title: Screening RNA from human uninfected macrophages, activated macrophages and T cells

summary:
The Fox laboratory studies the SIV infection of rhesus monkeys as a model for HIV/AIDS, focusing on central nervous system infection, immunity, and brain dysfunction that develops following infection.
Previous Fox lab data shows that virions derived from macrophages and T-cells differ in infectivity in a manner based solely on their cellular origin, and that these differences can be influenced by the removal of various glycans from the surface proteins present on the virion. This study examines the glycosylation pathways functioning in human macrophages and T-cells, in the context of examining how differences in the glycosylation pathways in these cell types might influence the infectivity of viral particles derived from macrophages vs. those derived from T-cells.

overall_design: RNA was prepared from uninfected, activated a) human macrophages and b) T-cells and sent to Microarray Core (E). Samples were prepared in triplicate, with 3 biological replicates from each cell type. The RNA was amplified, labeled, and hybridized to the GLYCOv3 microarrays. Data was analyzed to determine the active glycosylation pathways in these cell types.


title: Glyco-gene expression in human breast cancer MDA-MB-231 cells treated with ManNAc analogs

summary:
Analogs of ManNAc, the committed precursor of sialic acid, decrease metastatic potential and trigger apoptosis in cancer cells.   Adding Lev to ManNAc analogs increases their toxicity due to an ill-understood mechanism.  Comparing gene expression profiles of cells treated with Ac4ManNLev and Ac4ManNAc will provide insight into the similarities and differences of these analogs.
Specifically, MDA-MB-231 human breast cancer cells will be treated with Ac4ManNLev and Ac4ManNAc at doses that inhibit cell growth and induce the cell to undergo apoptosis later.  RNA will be harvested in the early stage of cell arrest in order to identify genes altered by Ac4ManNLev and Ac4ManNAc.

overall_design: RNA preparations from three conditions, were sent to Microarray Core (E). One as control (Ethanol), and two experimental groups: high concentration Ac4ManNAc (100 uM) and high concentration Ac4ManNLev (100 uM). The aim is to gain insight into apoptosis and cell cycle arrest. Specifically, the Ac4ManNLev samples will be comprared to a less potent ManNAc analog. The RNA was amplified, labeled, and hybridized to the GLYCOv3 microarrays.

last: Yarema


title: Breast tumors from CHEK2 1100delC mutation carriers: genomic landscape and clinical implications (CGH)

status: Public on May 10 2011

city: Helsinki

first: Taru

last: Muranen

address: Haartmaninkatu

department: Department of Obstetrics and Gynecology

country: Finland

institute: Helsinki University Central Hospital

summary:
Introduction: CHEK2 is a moderate penetrance breast cancer risk gene, whose truncating mutation 1100delC increases the risk about two fold. We pursued to investigate gene copy number aberrations and gene expression profiles that are typical for breast tumors of CHEK2 1100delC mutation carriers.

Materials and methods: A total of 126 breast tumor tissue specimens including 32 samples from patients carrying CHEK2 1100delC were studied in array comparative genomic hybridization (aCGH) and gene expression experiments (GEX). After dimensionality reduction with CGHregions R package, CHEK2 1100delC associated regions in the aCGH data were detected by Wilcoxon rank sum test. Linear model was fitted to GEX data with R package limma. Genes whose expression levels were associated with CHEK2 1100delC mutation were detected by Bayesian method.

Results: We discovered four lost and three gained CHEK2 1100delC related loci. These include losses of 1p13.3-31.3, 8p21.1-2, 8p23.1-2 and 17p12-13.1 as well as gains of 12q13.11-3, 16p13.3 and 19p13.3. Twenty-eight genes located on these regions showed differential expression between CHEK2 1100delC and other tumors nominating them as candidates for CHEK2 1100delC associated tumor progression drivers. These included CLCA1 on 1p22 as well as CALCOCO1, SBEM and LRP1 on 12q13. Altogether 188 genes were differentially expressed between CHEK2 1100delC and other tumors. Of these, 144 had elevated and 44 lowered expression levels.
Our results suggest WNT pathway as a driver of tumorigenesis in breast tumors of CHEK2 1100delC mutation carriers and a role for the olfactory receptor protein family in cancer progression. Differences in the expression of the 188 CHEK2 1100delC associated genes divided breast tumor samples from three independent datasets into two groups that differed in their relapse-free survival time.

Conclusions: We have shown that copy number aberrations of certain genomic regions are associated with CHEK2 mutation 1100delC. On these regions we have identified potential drivers of CHEK2 1100delC associated tumorigenesis, whose role in cancer progression is worth investigating. Furthermore, poorer survival related to the CHEK2 1100delC gene expression signature highlights pathways that are likely to have a role in the development of metastatic disease in carriers of CHEK2 1100delC mutation.

overall_design:
79 samples from breast tumors: 22 tumors from CHEK2 1100delC mutation carriers, 57 other tumors

Five files attached represent segmented values, copy number calls, gain, loss and normal copy number probabilities.

first: Dario

last: Greco

first: Rainer

last: Fagerholm

first: Outi

last: Kilpivaara

first: Kati

last: Kampjarvi

first: Kristiina

last: Aittomaki

first: Carl

last: Blomqvist

first: Paivi

last: Heikkila

first: Ake

last: Borg

first: Heli

last: Nevanlinna


title: Glyco-gene expression in DP thymic T cells from control and mutant mice that carry a mutation in the ligand binding domain of Notch1

first: Steven

last: Head

summary:
Dr. Stanley's laboratory is interested in determining how O-fucose glycans function in Notch receptor signaling and in modulating the interactions of Notch receptors with their ligands.
We have generated mice carrying a point mutation in the ligand binding domain of Notch1 that reduces Notch ligand binding to mutant T cells. We wish to identify Notch target genes including glycosylation genes with altered expression in DP thymic T cells from mutant and control mice.

overall_design: DP cells were prepared from the thymus of 3 control and 3 mutant mice at ~8 weeks of age and RNA extracted from each prep will be analysed. RNA preparations from CD4+CD8+ double positive (DP) T cells from F+2323, F+2324, F+2329 (control) and FF2330, FF2332, FF2333 (Notch1 with a point mutation to prevent fucosylation in EGF12) mice of ~8 weeks were sent to the Microarray Core (E). The RNA was amplified, labeled, and hybridized to the GLYCOv3 microarrays.

first: Pamela

last: Stanley


title: Analysis of expression of genes involved in glycan and GBP synthesis in control and differentiated dendritic cells

summary: Analysis of expression of genes involved in glycan and glycan-binding molecule synthesis in dendritic cells.

overall_design:
Gene expression patterns for unstimulated dendritic cells, macrophages, and monocytes were compared. Also, gene expression patterns for dendritic cells and macrophages stimulated with LPS for 4 and 18 hours were compared to unstimulated cells.
Three replicate samples of RNA were taken from human cells, one sample per donor. Samples were prepared and hybridized to the GLYCOv3 array.

first: Philippe

last: Delannoy


title: Study of differential gene expression in the thymus, spleen and lymphatic nodes of susceptible and resistant mice during T. cruzi infection

summary: This is a time course study of differential gene expression in the thymus and spleen of susceptible (Balb/c) and resistant (C57BL/6) mice during experimental Trypanosoma cruzi infection. There is a special interest in the expression of galectins, glycosyltransferases, neuraminidases and chemokines in the gene expression patterns.

overall_design:
Mice were infected with 1000 trypomastigotes of T. cruzi strain Y i.p. Organs (thymus and spleen) were removed aseptically at days 0, 7, 14, 21 and 28 post-infection. The time points have been selected as they allow the following of the acute phase of the disease with the peak of parasitemia (between 7 and 14 days), and the chronic phase (more than 21 days post infection).
RNA from at least three animals from the same data point was pooled to normalize internal variability. Total RNA was isolated as per recommended protocol and shipped to the Core E site. Samples were hybridized to the GLYCOv3 array.

first: Pedro

last: Bonay


title: Examine differential expression of sulf-1 and sulf-2, enzymes involved in heparan sulfate biosynthesis

summary:
Our specific aim is to examine differential expression of sulf-1 and sulf-2, enzymes involved in heparan sulfate biosynthesis, as well as Wnt ligands and Wnt signaling mediators during corneal wound healing using a mouse corneal scratch model.
The specific structural features of heparan sulfate underlie its role in modulating cellular responses to growth factors such as the Wnts. Heparan sulfate 6-O-endosulfatases (sulf-1 and sulf-2) remove 6-O sulfate group from trisulfated disaccharides present on heparan sulfate chains. Our preliminary results suggest that sulf-1 is upregulated at the protein level in the epithelial cells of wounded mouse corneas, as compared to the undamaged contralateral eye.  Modulation of heparan sulfate proteoglycan expression and/or structural modifications of its chains might be an important aspect of the regulation of epithelial cell migration and proliferation during wound healing.

overall_design: RNA preparations from four different conditions, were sent to Microarray Core (E).  Gene expression was examined in triplicates at 2 time points (8 and 24 hrs post-wounding: 6 arrays), using the contralateral eye as a control at one time point as a control (3 arrays). To account for a systemic response (i.e. bilateral inflammation) to the corneal wounding, corneas of non-wounded mice (3 arrays) were used.  The RNA was amplified, labeled, and hybridized to the GLYCOv3 microarrays.

last: Rosen


title: Resistance to Plasmopara viticola in a grapevine segregating population is associated with stilbenoid accumulation and with specific host transcriptional responses

status: Public on Apr 28 2011

city: S. Michele a/Adige

first: Giulia

last: Malacarne

state: Trento

address: Via Edmund Mach,1

department: Genomics and Biology of Fruit Crops Department

country: Italy

institute: Edmund Mach Foundation

summary:
Downy mildew, caused by the oomycete Plasmopara viticola, is a serious disease in Vitis vinifera, the most commonly cultivated grapevine species. Several wild Vitis species have instead shown resistance to this pathogen and they have been used as a source to introgress resistance into a V. vinifera background. Stilbenoids represent the major phytoalexins in grapevine, and their toxicity has been strictly related to the specific compound. The aim of this study was to assess the resistance response to P. viticola of the Merzling x Teroldego cross by profiling the stilbenoid content of the leaves of the entire population and the transcriptome of resistant and susceptible individuals following infection. A three-year analysis of the population?s response to artificial inoculation showed that individuals were distributed in nine classes ranging from total resistance to total susceptibility. In addition, quantitative metabolite profiling of stilbenoids in the population, carried out using HPLC-DAD-MS, identified three distinct groups differing according to the concentrations present and the complexity of their profiles. The high producers were characterized by the presence of trans-resveratrol, trans-piceid, trans-pterostilbene and up to thirteen different viniferins, nine of them new in grapevine. Accumulation of these compounds is consistent with a resistant phenotype and suggests that they may contribute to the resistance response.
A preliminary transcriptional study using cDNA-AFLP selected a set of genes modulated by the oomycete in a resistant genotype. The expression of this set of genes in resistant and susceptible genotypes of the progeny population was then assessed by comparative microarray analysis. A group of 57 genes was found to be exclusively modulated in the resistant genotype suggesting that they are involved in the grapevine-P. viticola incompatible interaction. Functional annotation of these transcripts revealed that they belong to the categories defense response, photosynthesis, primary and secondary metabolism, signal transduction and transport.This set of genes should be taken into account in future breeding programs.

overall_design:
Leaves from one resistant (F1 21/66) and two susceptible (F1 22/73 and Teroldego) genotypes were infected with Plasmopara viticola, and transcriptome changes were investigated at 12h and 96h after infection (treated samples) and at 0h after spraying with water (control samples)
Two biological replicates were considered and each hybridization was performed three times. One color labeling was performed.

first: Urska

last: Vrhovsek

first: Luca

last: Zulini

first: Alessandro

last: Cestaro

first: Marco

last: Stefanini

first: Fulvio

last: Mattivi

first: Massimo

last: Delledonne

first: Riccardo

last: Velasco

first: Claudio

last: Moser


title: Chromosome-biased binding and gene reguation by the C. elegans DRM complex [ChIP-chip]

status: Public on Apr 27 2011

city: Worcester

first: Kirsten

last: Hagstrom

address: 377 Plantation street

department: Molecular Medicine

institute: University of Massachusetts, Medical School

summary: DRM is a conserved transcription factor complex that includes E2F/DP and pRB  family proteins and plays important roles in development and cancer. Here we analyze genome-wide binding and function of the C. elegans DRM subunit LIN-54. We demonstrate that LIN-54 DNA-binding activity is required for the DRM  complex to efficiently bind and regulate target genes containing adjacent putative  E2F/DP and LIN-54 binding sites. We show that LIN-54 binds to the promoters of  genes involved in cell division, development, and reproduction, and acts  differently in the germline versus the soma. The E2F/DP-LIN-54 binding motif,  individual target genes, and overall DRM function are conserved among worms,  flies, and humans. Despite this conservation, we discovered one striking feature  of C. elegans DRM not shared in flies or humans: it is depleted from X  chromosomes. We show that DRM binding, the E2F-LIN-54 hybrid motif, and  LIN-54-regulated genes are all autosome-enriched.

overall_design: Chromatin-immunoprecipitation of mixed staged wild-type C.elegans (N2, Bristol strain) was performed using non-commercial anti-LIN-54 antibody raised in guinea pig (Harrison et at. 2006).

first: Bart

last: Deplancke

first: Inmaculada

last: Barrasa

first: Tomoko

last: Tabuchi

first: Albertha


title: Mouse peripheral blood leukocytes cyclophosphamide treated vs untreated

city: Roma

first: Federica

last: Moschella

address: Viale Regina Elena 299

department: Cell Biology and Neurosciences

institute: Istituto Superiore di Sanità

summary:
Analysis of the effect of cyclophosphamide on peripheral blood leukocyte gene expression.
Certain chemotherapeutic drugs such as cyclophosphamide can enhance the antitumor efficacy of immunotherapy because of their capacity to modulate innate and adaptive immunity. Indeed, it has been argued that this capacity may be more significant to chemotherapeutic efficacy in general than is presently appreciated. To gain insights into the core mechanisms of chemoimmunotherapy, we methodically profiled the effects of cyclophosphamide on gene expression in bone marrow, spleen and peripheral blood, and on cytokine expression in plasma and bone marrow of tumor-bearing mice. Gene and protein expression were modulated early and transiently by cyclophosphamide, leading to upregulation of a variety of immunomodulatory factors, including danger signals, pattern recognition receptors, inflammatory mediators, growth factors, cytokines, chemokines and chemokine receptors. These factors are involved in sensing cyclophosphamide myelotoxicity and activating repair mechanisms, which, in turn, stimulate immunoactivation events that promote efficacy. In particular, cyclophosphamide induced a T helper 17 (Th17)-related gene signature associated with an increase in Th17, Th1 and activated CD25+CD4+Foxp3- T lymphocytes and a slight recovery of regulatory T-cells. By analyzing gene and protein expression kinetics and their relationship to the antitumor efficacy of different therapeutic schedules of combination, we determined that optimal timing for performing adoptive immunotherapy is approximately 1 day after cyclophosphamide treatment. Together, our findings highlight factors that may propel the efficacy of chemoimmunotherapy, offering a mechanistic glimpse of the important immune modulatory effects of cyclophosphamide

overall_design: Four-condition experiment, Untreated mice - Cyclophosphamide-treated mice 1 day - Cyclophosphamide-treated mice 2 days - Cyclophosphamide-treated mice 5 days. Biological replicates: 4, controls: 4, independently harvested. Two replicates per array.

first: Mara

last: Valentini


title: Examine how the absence of prion protein expression could affect the cellular glycosylation enzymes during development

first: Steven

last: Head

summary: Dr. Wong's laboratory is interested in examining if and how the absence of prion protein expression could affect the cellular glycosylation enzymes during development.

overall_design:
Prion protein is a glycoprotein and changes in glycosylation on the protein have been implicated in the pathogenic process. Our objective is to examine if and how the absence of prion protein expression could affect the cellular glycosylation enzymes during development. To do this, we proposed to compare and contrast the expression profile of the glycosylation enzymes in control and prion protein knockout mouse brain at the age of 2 and 82 weeks (n=3).
RNA preparations from control and prion protein knockout mice brain of age ~2 and 82 weeks were sent to the Microarray Core (E).  The RNA was amplified, labeled, and hybridized to GLYCOv3 microarrays.

first: Boon-Seng

last: Wong


title: Mouse bone marrow cyclophosphamide treated vs untreated

summary:
Analysis the effect of cyclophosphamide on bone marrow gene expression.
Certain chemotherapeutic drugs such as cyclophosphamide can enhance the antitumor efficacy of immunotherapy because of their capacity to modulate innate and adaptive immunity. Indeed, it has been argued that this capacity may be more significant to chemotherapeutic efficacy in general than is presently appreciated. To gain insights into the core mechanisms of chemoimmunotherapy, we methodically profiled the effects of cyclophosphamide on gene expression in bone marrow, spleen and peripheral blood, and on cytokine expression in plasma and bone marrow of tumor-bearing mice. Gene and protein expression were modulated early and transiently by cyclophosphamide, leading to upregulation of a variety of immunomodulatory factors, including danger signals, pattern recognition receptors, inflammatory mediators, growth factors, cytokines, chemokines and chemokine receptors. These factors are involved in sensing cyclophosphamide myelotoxicity and activating repair mechanisms, which, in turn, stimulate immunoactivation events that promote efficacy. In particular, cyclophosphamide induced a T helper 17 (Th17)-related gene signature associated with an increase in Th17, Th1 and activated CD25+CD4+Foxp3- T lymphocytes and a slight recovery of regulatory T-cells. By analyzing gene and protein expression kinetics and their relationship to the antitumor efficacy of different therapeutic schedules of combination, we determined that optimal timing for performing adoptive immunotherapy is approximately 1 day after cyclophosphamide treatment. Together, our findings highlight factors that may propel the efficacy of chemoimmunotherapy, offering a mechanistic glimpse of the important immune modulatory effects of cyclophosphamide

overall_design: Four-condition experiment, Untreated mice - Cyclophosphamide-treated mice 1 day - Cyclophosphamide-treated mice 2 days - Cyclophosphamide-treated mice 5 days. Biological replicates: 5, controls: 5, independently harvested. Two replicates per array.


title: Glyco-gene expression induced by IL-4 macrophage activation

summary: Evaluation of the changes in glycosylation induced by IL-4 alternative macrophage activation

overall_design:
Thioglycolate elicited murine peritoneal macrophages where incubated with and with out IL4 for 24 hours.
Mouse RNA from macrophages incubated in OptiMEM10 and incubated in OptiMEM10 plus IL4, for 24 hours, was isolated and prepared in triplicate.  RNA was labeled and hybridized to the GLYCOv3 array. Resulting Gene expression patterns were analyzed.

first: Siamon

last: Gordon


title: Mouse spleen cyclophosphamide treated vs untreated

summary:
Analysis the effect of cyclophosphamide on splenocytes gene expression.
Certain chemotherapeutic drugs such as cyclophosphamide can enhance the antitumor efficacy of immunotherapy because of their capacity to modulate innate and adaptive immunity. Indeed, it has been argued that this capacity may be more significant to chemotherapeutic efficacy in general than is presently appreciated. To gain insights into the core mechanisms of chemoimmunotherapy, we methodically profiled the effects of cyclophosphamide on gene expression in bone marrow, spleen and peripheral blood, and on cytokine expression in plasma and bone marrow of tumor-bearing mice. Gene and protein expression were modulated early and transiently by cyclophosphamide, leading to upregulation of a variety of immunomodulatory factors, including danger signals, pattern recognition receptors, inflammatory mediators, growth factors, cytokines, chemokines and chemokine receptors. These factors are involved in sensing cyclophosphamide myelotoxicity and activating repair mechanisms, which, in turn, stimulate immunoactivation events that promote efficacy. In particular, cyclophosphamide induced a T helper 17 (Th17)-related gene signature associated with an increase in Th17, Th1 and activated CD25+CD4+Foxp3- T lymphocytes and a slight recovery of regulatory T-cells. By analyzing gene and protein expression kinetics and their relationship to the antitumor efficacy of different therapeutic schedules of combination, we determined that optimal timing for performing adoptive immunotherapy is approximately 1 day after cyclophosphamide treatment. Together, our findings highlight factors that may propel the efficacy of chemoimmunotherapy, offering a mechanistic glimpse of the important immune modulatory effects of cyclophosphamide


title: Preferential localization of human origins of DNA replication at the 5' end of expressed genes

status: Public on May 13 2011

city: Bethesda

first: Yuelin

middle: Jack

last: Zhu

address: 9000 Rockville Pike

department: Genetics Branch, Center for Cancer Research

institute: NCI

summary:
Human DNA replication relies on the activation of thousands of origins distributed along the genome. Their organization and the functional significance of their distribution remains unknown. To map large number of origins in human cells, we have localized the distribution of short nascent DNA using a high-resolution DNA tiling array platform covering 33.9Mb.  Results with three different cell lines reveal that origins are very closely spaced (average interval 3-5kb), and that their positions are largely conserved among the cell lines studied. Origins are non-randomly distributed, being preferentially enriched at the 5’-end of expressed genes and at evolutionary intergenic sequences. In MCF7 cells, a strong correlation is also found between origin positioning and histone H3K4me3 and of PolII binding to chromatin. This study provides a large scale view of the organization of DNA replication origins in human chromosomes and suggests a link between this distribution and underlying chromatin features related to chromosome structure, and gene expression
Keywords: nascent strand DNA, histone, Pol-II ChIP-chip.

overall_design: To map initiation sites for DNA replication and the position of both H3K4Me3 and Pol-II chromatin binding sites in human cell lines  on a custom made high density tiling DNA microarray covering 33.9 Mb of the human genome.

first: Manuel

last: Valenzuela

first: Yidong

last: Chen


title: Transcriptome profiling of immune responses to cardiomyopathy syndrome (CMS) in Atlantic salmon

status: Public on Apr 26 2011

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

summary: Cardiomyopathy syndrome (CMS) is a disease associated with severe myocarditis in adult Atlantic salmon (Salmo salar L.), which is presumably caused with a double-stranded RNA virus (piscine myocarditis virus; PMCV). This study addressed the host immune response in Atlantic salmon during experimentally induced CMS as assessed by microarray transcriptome profiling. Post-smolts were infected by intraperitoneal injection of PMCV and developed cardiac pathology consistent with CMS. From analysis of heart samples at several time points and different tissues at early and clinical stages by oligonucleotide microarrays, six gene sets representing a broad range of immune responses were identified. Histopathological examination of cardiac tissue showed myocardial lesions from 6 weeks post infection (wpi) that peaked at 8-9 wpi and was followed by a recovery. Viral RNA was detected in all organs from 2 wpi. The highest and equal viral load was observed in heart, spleen and kidney, peaking at 8-9 wpi. Strong and systemic induction of antiviral and IFN-dependent genes from 2 wpi that leveled off during infection, was followed by a biphasic activation of pathways for B cells and MHC antigen presentation, both peaking at clinical pathology. This was preceded by a distinct cardiac activation of complement at 6 wpi. Most severe cardiac pathology and peak viraemia coincided with a cardiac-specific activation of T cell responses dominated by genes involved in effector CD8 cell responses and splenic induction of complement. These changes preceded the reduction in viral load and pathology, suggesting an important role of cytotoxic T cells for viral elimination in infected heart.

platform_organism:
Oncorhynchus mykiss
Salmo salar

overall_design: Atlantic salmon post-smolts (average weight 50g) were challenged with the putative CMS-causing pathogen (PMCV). Hearts were sampled from challenged and control fish at 2, 4, 6, 8, 9 and 10 wpi. Pools of equal amounts of total RNA from three fish hearts each were combined and hybridized against control pools of 8 to 10 fish hearts per time point. Spleen, liver, mid-kidney, red blood cells (RBC) and peripheral blood leukocytes (PBL) were analyzed at 4 wpi (latest time point before clinical stage) and 8 wpi (peak pathology). The samples of infected fish were labeled with Cy5 and hybridized to control samples from the same time-points labeled with Cy3. Competitive hybridization to the arrays was followed by washing, scanning, image analysis, and data analysis. Selected genes were analyzed with RT-qPCR.

first: Gerrit

last: Timmerhaus

first: Sven

last: Jørgensen

first: Sergey

last: Afanasyev

first: Harald

last: Takle


title: Expression data from 5 day old Arabidopsis thaliana seedlings

status: Public on Apr 21 2011

city: Vienna

first: Gudrun

last: Boehmdorfer

address: Dr. Bohr-Gasse 3

country: Austria

institute: GMI – Gregor Mendel Institute of Molecular Plant Biology

summary: Upon induction of DNA damage Arabidopsis thaliana plants initiate a transcriptional response program governed by signalling cascades which are activated by the ATM and ATR kinases

overall_design: To analyse if the ATM dependent gene GMI1 (At5G24280) is involved in the regulation of the transcriptionl response, we compared the gene expression profiles of wildtype and gmi1 deficient plants upon gamma-irradiation

first: Reinhard

last: Brunmeir

first: David

middle: P

last: Kreil

first: Dieter

last: Schweizer


title: Transcriptional responses to chronic oxidative stress in skeletal muscle

city: Winter Park

first: Hui

last: Xie

state: FL

address: 2566 Lee Rd.

department: TRI

institute: Florida Hospital

summary: We measured gene expression differences in the extensor digitorum longus (edl) skeletal muscle between wild-type and mice lacking Cu, Zn-superoxide dismutase to determine the effect of chronic oxidative stress on skeletal muscle.

overall_design: We analyzed 4 edl samples from WT mice and 4 samples from the SOD1 knockouts.

middle: J

last: Marcinek

last: Smith


title: FlhC mediated gene regulation In E. coliO157:H7 on meat

city: Fargo

first: Birgit

middle: Magdalene

last: Pruess

state: North Dakota

address: 1523 Centennial Blvd.

department: Veterinary and Microbiological Sciences

institute: North Dakota State University

summary: The study aimed at investigating FlhC mediated gene regulation in E. coli O157:H7 on surface of meat. It also aimed at investigating the phenotypic effect of such a regulation.

overall_design: Two strains WT and FlhC mutant used. FlhC mutant had a 12 base pair deletion. 3 biological replicates . Wt labeled with Alexa 555, FlhC mutant with Alexa 647

first: Sule

last: Preeti

first: Shelley

middle: M

last: Horne

first: Catherine

last: Logue

last: Prüß


title: Expression profiles of microRNAs in gastric cancer

city: Taipei

first: Chien-Wei

last: Tseng

address: No. 1, Sec. 4, Roosevelt Road

country: Taiwan

institute: National Taiwan University

summary: We analyzed expression profiles of microRNAs from 22 paired gastric cancer and normal tissues and identified differentially expressed microRNAs.

overall_design: RNA from paired normal and tumor specimens in 22 gastric cancer patients were extracted and treated for microRNA microarray analysis.

first: Chiung-Nien

last: Chen

first: Hsueh-Fen

last: Juan


title: Microarray screening of RNA samples from the olfactory epithelium from wild type and beta3GnT1 mutant mice

first: Steven

last: Head

summary:
Dr. Schwarting's research is focused on the analysis of developmentally regulated cell surface molecules and their role in axon guidance and neuronal migration, using the olfactory system as a model. The interaction of cell surface glycans with endogenous lectins in the extracellular matrix provides one mechanism by which axons can utilize specific pathways as they grow towards their targets.
Beta3GnT1 mutant mice lose lactosamine expression and have an olfactory axon guidance phenotype (Henion et al, 2005). Olfactory neurons are capable of regeneration and we know that when these neurons regenerate in beta3GnT1 mutant they synthesize lactosamine by a secondary mechanism. By comparing RNA from the olfactory epithelium from wild type and mutant mice, we would expect to see the upregulation of glycosyltransferases that could produce lactosamine in the absence of beta3GnT1. In a preliminary experiment carried out by the CFG staff, we saw that radical fringe, a beta 3GnT, was upregulated in the olfactory epithelium, although it is probably not responsible for the new lactosamine expression. beta3GnT1 Knock out. Strain info: The b3GnT1 mice were generated on a mixed 129Ola-C57BL/6 background and backcrossed to C57BL/6 for four generations. They were then crossed to I7-Internal ribosomal entry site (IRES)-tau greeen fluorescent protein (GFP) mice generated by Dr. Peter Mombaerts.

overall_design: RNA preparations from wild type and beta3GnT1 mutant mouse olfactory epithelium were sent to Microarray Core (E). Three replicate samples from each condition were used in the study. The RNA was amplified, labeled, and hybridized to the GLYCOv3 microarrays. Data was analyzed to determine glycosyltransferase expression changes in beta3GnT1 mutant mice, with specific interest on glycosyltransferases that could produce lactosamine in the in the absence of beta3GnT1.

first: Gerald

last: Schwarting

middle: R


title: EMT is the dominant program in human colon cancer (Agilent)

status: Public on Apr 25 2011

city: West Point

first: Michael

last: Nebozhyn

state: PA

address: Mail Stop WP53B-120, 770 Sumneytown Pike, Building 53, P.O. Box 4

department: GpGx/Computational System biology

institute: Merck, Inc

summary: mRNA profiles on 129 colorectal tumors

overall_design: 129 colorectal tumors profiled on Agilent array using pool of individual tumors as common reference

first: Andrey

last: Loboda

middle: V

first: James

last: Watters

first: Carolyne

last: Buser-Doepner

first: Peter

last: Shaw

first: Pearl

last: Huang

first: Laura

last: Van't Veer

first: Rob

last: Tollenaar

last: Jackson

first: Deepak

last: Agrawal

first: Hongyue

last: Dai

first: Timothy

last: Yeatman


title: Gene expression in natural killer cells specifically recruited to lymph nodes by tumors

summary: Dr. Fukuda's laboratory focuses on the cellular and molecular biology of cell surface glycoproteins in development and cancer with a secial emphasis on immune and neural systems.

platform_organism:
Homo sapiens
Mus musculus

overall_design:
Experiment to determine the genes upregulated in natual killer cells specifically recruited to lymph nodes by tumors
Genes upregulated in natual killer cells specifically recruited to lymph nodes by tumors were determine via gene expression analysis Mouse RNA from control mouse NK cell, isolated from spleen, and NK cells isolated from B16 melanoma-bearing lymph nodes, was isolated and prepared in 5 paired samples. RNA was labeled and hybridized to the GLYCOv2 array. Resulting Gene expression patterns were analyzed.

first: Minoru

last: Fukuda


title: Genomic profiling of hereditary epithelial ovarian cancer using tiling resolution array CGH

city: Lund

first: Katarina

last: Bartuma

address: Barn garan 2b

country: Sweden

institute: department of Oncology

summary: Heredity is a major risk factor for ovarian cancer, but many families escape detection. Refined diagnosis of ovarian cancers linked to the breast and ovarian cancer (HBOC) syndrome and the hereditary nonpolyposis colorectal cancer (HNPCC) syndrome would allow cancer prevention in high risk families. In order to delineate genetic profiles of hereditary ovarian cancer, we applied genome wide array comparative genomic hybridization to 24 sporadic tumors, 12 HBOC associated tumors (BRCA1 mutations) and eight HNPCC associated tumors (mismatch repair gene mutations). Unsupervised cluster analysis identified two distinctive clusters related to genetic complexity. Most sporadic and HBOC associated tumors had complex genetic profiles with multiple gains and losses with an average of 41% of the genome altered, whereas mismatch repair defective tumors had stable genetic profiles, with an average of 18% of the genome altered. Losses of 4q34, 13q12-q32 and 19p13 were overrepresented in the HBOC subset, gains of chromosomes 17 and 19 characterized the HNPCC tumors and gains of 20q11 were more common in the sporadic tumors. The genetic distinction between HBOC and HNPCC associated ovarian cancer suggests that genetic profiles can be applied for refined classification of hereditary cases and reflects tumor development along different genetic pathways.

overall_design: DNA was extracted from formalin fixed, paraffin embedded tumor tissue according to protocols from the UCSF Waldman Laboratory, San Francisco, CA, USA (http://cc.ucsf.edu/people/waldman/Protocols/paraffin.html), with an additional purification step using Phase Lock Gel tubes (Eppendorf AG, Hamburg, Germany). DNA quality was assessed using a Ready-To-Go RAPD analysis kit (GE Healthcare, Little Chalfont, UK) with primers 5’-AATCGGGCTG-3’ and 5’-GAACGGGTG-3’. PCR products were validated on a Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Tiling 32k BAC microarrays, with contiguous genome wide coverage, were produced at the Microarray DNA Resource Centre, SCIBLU Genomics, Department of Oncology, Lund University, Sweden (http://www.lth.se/sciblu). Labeling and hybridization were performed in short, 2-8 μg tumor DNA and 2 µg reference DNA (Promega Corporation, Madison, WI, USA) were labeled with Cy3-dCTP and Cy5-dCTP, using BioPrime Array CGH Genomic Labeling System (Invitrogen Life Technologies, Carlsbad, CA, USA). Tumor and reference DNA were pooled and mixed with Human COT-1 DNA (Invitrogen). Hybridizations were conducted using the MAUI® Hybridization System (BioMicro systems Inc, Salt Lake City, UT, USA) and the slides were scanned in an Agilent Microarray Scanner (Agilent Technologies).

last: Domanska

first: Susanne

last: Malander

first: Johan

last: Staaf

first: Anna

last: Karlsson

first: Ake

last: Borg

first: Göran

last: Jönsson

first: Mef

last: Nilbert


title: medium vs cell miRNA

status: Public on Apr 23 2011

city: Seattle

first: Shile

last: Zhang

address: 1441 N 34th Street

institute: Institute for systems biology

summary: To investigate the inside and exported miRNA in cell culture system.

overall_design: We characterized the miRNA spectra of cell lines when deprived of serum. The absence of miRNAs present in bovine serum is a distinct advantage of using serum depletion to study extracellular miRNA as it removes potential source of interference.

first: Kai

last: Wang

first: Ji-Hoon

last: Cho

first: David

last: Galas


title: Gene expression analysis of an endometrial cell line

first: Steven

last: Head

summary:
This group is studying the role of glycoproteins in embryo implantation and development of the maternal-fetal interface.
The Aplin lab is developing an embryo implantation model in which blastocysts attach to human endometrial cells. The project aims to investigate the molecular interactions mediating attachment and subsequent events including trophoblast invasion and displacement of maternal cells. In the present phase of the project, the lab is using the Ishikawa (human endometrial) cell line with mouse embryos.

overall_design: RNA from three replicate samples from the Ishikawa cell line were prepared and sent to Microarray Core (E). The RNA was amplified, labeled, and hybridized to the GLYCOv3 microarrays.

first: John

last: Alpin


title: Gene expression based on an oligonucleotide microarray for Dicentrarchus labrax

city: Chile

first: Sebastian

last: Boltana

state: Bio BIO

address: Edmundo Larenas s/n, Barrio Universitario. Biotechnology Center

department: Oceanografia

country: Chile

institute: Universidad de Concepcion

summary:
Fish respond to stressors by means of an array of changes that involve many biological compartments including molecular, cellular, metabolic, physiological and behavioral acclimation. Among these changes, the immune system also experiences significant alterations that are characterized by an induction of the innate non-specific responses and changes in the acquired specific response. The present investigation was undertaken to check whether the innate response of the complement system is affected after a combination of an immune challenge and a husbandry stressor.  In European seabass, two different transcripts of the complement C3 protein, which correspond to two tissue-specific isoforms, have been detected in liver. They may come from post-transcriptional modifications at the pre-mRNA level or from alternative splicing in order to generate a diversified repertoire of protein isoforms in some fish species according to the tissue were they are located. After cloning the hepatic C3, the quantification of seabass isoforms showed specific responses, thus confirming the possible specialized roles of the C3 different isoforms in terms of defence immunity. On one hand, a stronger esbC3_2 expression was observed in front to the viral challenge, suggesting a specific participation of this molecule in front to viruses. This observation is in agreement with previous studies in trout macrophages in our lab, demonstrating that the immune response to viral infections was stronger than to bacterial ones. On the other hand, the esbC3_1 expression appeared stronger after bacterial challenge, especially under high density conditions. Our results confirm the hypothesis of an immune-activation of specific isoforms of the C3 protein of the complement system as a non-specific response in front to either immune or other type of stressors.
In order to confirm our hypothesis, we created an oligonucleotide microarray (Agilent Technologies) containing 6275 annotated transcripts, each with x3 specific probes, and 4516 ESTs with 1 probe/target sequence. Gene expression profiles obtained from the livers of fish held under high density culture conditions highlighted a significant contrast in the liver response. In total, 54 transcripts were differentially expressed (GDE; fold change FC >2) in treatment over the control (p<0.01)/201 (p<0.05).

overall_design: Oligonucleotide probes were used to construct a high-density seabass microarray based on the Agilent 4 × 44 K design format (http://www.agilent.com/), which covers 13,199 unique transcripts of Dicentrarchus labrax. Oligonucleotides, 60-mer plus a “linker”, are synthesized directly on glass slides using the Agilent’s SurePrint Tecnology; oligo design was carried out by Agilent and three or more non-overlapping probes were designed for each EST cluster. The number of transcripts represented by three is 6,275, while 6,924 targets EST have only one probe.

last: Boltaña

first: Simon

last: Mackenzie


title: EMT is the dominant program in human colon cancer (lung)

first: Michael

last: Nebozhyn

summary:
mRNA profiling of 93 lung cancer cell lines
supporting data for PMID: 21251323

overall_design: 93 lung cancer cell lines profiled at baseline


title: Dissecting Stages of the Notch signaling pathway during Kidney Development by Oligonucleotide Array Sequence Analysis

status: Public on Apr 20 2011

city: Hangzhou

first: Jiang

last: Hong

state: Zhe Jiang

address: Yuhangtang Road,NO.388

department: life science

institute: Zhejiang University

summary: Samples E12/E13/E14/E16/E18: We aims to screen out different gene expression profile in Embryo kidney on different gestation stages of the Notch signaling pathway  Results from the various study components can help to screening important candidate genes during embryonic kidney development.   Keywords: Embryo kidney, Development, Notch signaling pathway, Oligonucleotide Array Sequence Analysis

overall_design: The Oligo GEArray Assay comprises various components: RNA isolation,Assesing RNA yield and quality,cRNA labeling and synthesis,Hybridization,Chemiluminescent detection and Image acquisition and data analysis. Samples E12: This study has been accomplished with Embryo kidney on gestation 12,  3 techinical replicates.  Samples E13: This study has been accomplished with Embryo kidney on gestation 13, 3 techinical replicates. Samples E14: This study has been accomplished with Embryo kidney on gestation 14, 2 techinical replicates.  Samples E16: This study has been accomplished with 1Embryo kidney on gestation 16, 2 techinical replicates. Samples E18: This study has been accomplished with Embryo kidney on gestation 18, 2 techinical replicates.

first: Hong

last: Jiang


title: Gene expression in eosinophils from IL-5 transgenic mice

city: La Jolla

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

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:
Three RNA preparations from IL-5 transgenic C567/B1 adult mouse eosinophils were sent to Microarray Core (E). The RNA was amplified, labeled, and hybridized to the GLYCOv3 microarrays.
Data was analyzed to determine glycosyltransferase expression on mouse eosinophils, with specific interest in a cis-ligand of Siglec-F on eosinophils

first: James

last: Paulson