title: Profile comparisons of stored mRNA in dry maize seeds from two closely-related geneotypes varying in aflatoxin accumulation

status: Public on Jul 30 2012

city: New Orleans

first: Meng

last: Luo

state: LA

address: 1100 Robert E Lee Blvd

department: FFS

country: USA

institute: SRRC, USDA-ARS

summary: Aflatoxin contamination occurring after infection by Aspergillus flavus is a major concern in maize production both pre- and post-harvest. A recent gene expression study of imbibed kernels highlighted induced resistance and gene regulation in kernels. In the present study, stored mRNA was profiled using oligo-nucleotide array. This comparison of stored mRNAs would enhance our understanding of the difference between resistant and susceptible lines at the kernel storage phase. To minimize the effect of different genetic backgrounds on the differential genes between resistant and susceptible lines, two closely related inbred lines were used. Of the two lines, Eyl25 is aflatoxin-resistant (R), and Eyl31 is –susceptible (S). These were derived from a cross between two resistant lines, 1368 and GT-MASK:gk, in the IITA and USDA- ARS collaborative breeding project.

overall_design: Direct comparisons were designed between Eyl25 and Eyl31. Dry kernels from the two lines were selected randomly into four groups to extract total RNA. Four biological replications were performed in the comparison including two dye-swaps.

first: Robert

middle: L

last: Brown

first: Zhiyuan

last: Chen

first: Abebe

last: Menkir

first: Deepak

last: Bhatnagar


title: P. falciparum (lab strain DD2) treated with ionomycin vs untreated [CGH]

status: Public on Jul 15 2012

city: Singapore

first: Ramya

last: Ramadoss

address: 60 Nanyang Drive, 04n-18, School of Biological Sciences

country: Singapore

institute: Nanyang Technological University, School of Biological Sciences

summary: Calcium is a universal second messenger molecule which plays a significant role in several biological processes. Presence of calcium sensors (calmodulins) and calcium-dependent protein kinases in Plasmodium species suggests an important role of calcium-dependent signaling pathways in the regulation of cellular processes in the malaria parasites. Evidence for the transcriptional response of Plasmodium falciparum asexual blood stages to the well-known calcium ionophore ionomycin has been presented here.

overall_design: Comparative genomic hybridization (CGH) was carried out with total DNA isolated from the untreated parasites and the parasites treated with the calcium ionophores (ionomycin 5 μM concentration) at 1 hour, 4 hours and 6 hours post treatment. Genomic DNA from the isolates was extracted by phenol chloroform. 3 μg of the total DNA from each of the isolate was subjected to klenow(NEB) reaction as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5. Treated DNA labeled with Cy3 was then hybridized against untreated DNA labeled with Cy5.

first: Sabna

last: Cheemadan

first: Zbynek

last: Bozdech


title: APJ1 and GRE3 Homologs Work in Concert to Allow Growth in Xylose in a Genetically Intractable Natural Saccharomyces sensu stricto Hybrid Yeast

status: Public on Jul 19 2012

city: Stanford

first: Barbara

last: Dunn

state: CA

department: Genetics

institute: Stanford University

summary: Creating Saccharomyces yeasts capable of efficient fermentation of pentoses such as xylose remains a key challenge in the production of ethanol from lignocellulosic biomass.  Metabolic engineering of industrial Saccharomyces cerevisiae strains has yielded xylose-fermenting strains, but these strains have not yet achieved industrial viability due largely to xylose fermentation being prohibitively slower than that of glucose.  Recently, it has been shown that naturally occurring xylose-utilizing Saccharomyces species exist.  Uncovering the genetic architecture of such strains will shed further light on xylose metabolism, suggesting additional engineering approaches or possibly even the development of xylose-fermenting yeasts that are not genetically modified.  We previously identified a hybrid yeast strain, the genome of which is largely Saccharomyces uvarum, which has the ability to grow on xylose as the sole carbon source.  Despite the sterility of this hybrid strain, we were able to develop novel methods to genetically characterize its xylose utilization phenotype, using bulk segregant analysis in conjunction with high-throughput sequencing.  We found that its growth in xylose is governed by at least two genetic loci: one of the loci maps to a known xylose-pathway gene, a novel allele of the aldo-keto reductase gene GRE3, while a second locus maps to an allele of APJ1, a chaperonin gene not previously connected to xylose metabolism. Our work demonstrates that the power of sequencing combined with bulk segregant analysis can also be applied to a non-genetically-tractable hybrid strain that contains a complex, polygenic trait, and it identifies new avenues for metabolic engineering as well as for construction of non-genetically modified xylose-fermenting strains.

overall_design: comparative genomic hybridization by array


title: Gene expression profile after oral vaccination against infectious pancreatic necrosis virus (IPNV)

city: Madrid

first: Julio

middle: M

last: Coll

state: Madrid

address: crt Coruna km7

department: Biotechnology

country: Spain

institute: INIA

summary: Oral immunization of trout against infectious pancreatic necrosis virus (IPNV) have been recently reported by using a DNA vector coding the viral capsid VP2 gene encapsulated in alginate microspheres. We report here an study of the transcripts in head kidney and pyloric ceca 7 days after oral vaccination of rainbow trout by using a newly designed rainbow trout 60-mer oligo microarray focused in their immune-related genes.

overall_design: Trout were obtained from 4 different farms, one group of trout was defined as belonging to one of the farms. Each of the trout 4 groups were divided into two subgroups of 6 trout for each subgroup. Subgroup I was orally vaccinated with 10 µl of suspension of the vaccine microspheres each containing 10 µg of pcDNA-VP2 diluted in 10µl of PBS, while subgroup II received similar microspheres suspension but pcDNA. Head kidney and pyloric ceca  were collected from each subgroup and RNA was extracted.


title: Identification of LMO2 transcriptome and interactome in diffuse large B-cell lymphoma

status: Public on Jul 13 2012

first: Andrew

last: Gentles

address: 1201 Welch Road

summary: LMO2 regulates gene expression facilitating the formation of multipartite DNA-binding complexes. In B cells, LMO2 is specifically up-regulated in the Germinal Center (GC) reaction and is expressed in GC-derived non-Hodgkin’s lymphomas. LMO2 is one of the most powerful prognostic indicators in DLBCL patients. However, its function in GC B cells and DLBCL is currently unknown. In the present study we characterized the LMO2 transcriptome and interactome in DLBCL cells. LMO2 regulates genes implicated in kinetochore function, chromosome assembly and mitosis. Overexpression of LMO2 in DLBCL cell lines results in centrosome amplification. In DLBCL, the LMO2 complex contains some of the traditional partners such as LDB1, E2A, HEB, Lyl1, ETO2 and SP1, but not TAL1 or GATA proteins. Furthermore, we identified novel LMO2 interacting partners: ELK1, NFATc1 and LEF-1 proteins. Reporter assays revealed that LMO2 increases transcriptional activity of NFATc1 and decreases transcriptional activity of LEF-1 proteins. Overall, our studies identified a novel LMO2 transcriptome and interactome in DLBCL and provide a platform for future elucidation of LMO2 function in GC B-cells and DLBCL pathogenesis.

overall_design: RCK8 DLBCL cell lines were stably transfected with control plasmid or plasmid+LMO2

middle: J


title: microRNA profiling of human healthy liver and hepatocellular carcinoma

status: Public on Jul 22 2012

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

summary: microRNA profiling of 10 human healthy liver and 9 human hepatocellular carcinoma tissues using bead-based technology

overall_design:
microRNA expression profiling was performed using freshly frozen healthy liver and hepatocellular carcinoma tissues obtained at the time of surgical treatment.
keywords: healthy liver, hepatocellular carcinoma, expression array, microRNA

first: Sara

last: Toffanin

first: Todd

middle: R

last: Golub

first: Vincenzo

last: Mazzaferro

first: Josep

last: Llovet


title: Chemosensitization of DLBCL cells in vitro and in vivo by demethylating nucleoside analogues [methylation]

city: New-York

first: thomas

last: clozel

state: NY

address: 1300 York Avenue

department: Hematology-Oncology

institute: Weill Cornell Medical College

type: Methylation profiling by genome tiling array

summary: Silencing of genes that suppress the malignant phenotype by DNA methylation spurred an interest in the clinical use of epigenetic reprogramming agents. Single therapy is unlikely to be curative in the context of a heterogeneous disease such as Diffuse Large B cell Lymphomas (DLBCL). The combination of DNA demethylating drugs could increase the chance to respond to classical and new treatments. We found that DLBCL cell lines respond heterogeneously to DNA demethylating agents. In sensitive cell lines, 5-aza-2’-deoxycytidine induced a genomic signature similar to that of doxorubicin, the most important drug of the combinatorial chemotherapy regimen for DLBCL treatment. Accordingly, the combination of 5-aza-2’-deoxycytidine and doxorubicin proved to be synergistic in cell killing in vitro and in vivo for DLBCL cell lines individually responsive to these drugs. In doxorubicin resistant cell lines, long-term exposure to low-dose of 5-aza-2’-deoxycytidine induces DNA demethylation and subsequent doxorubicin sensitization in vitro and in vivo. This later effect correlates with SMAD1 demethylation. SMAD1 is epigenetically silenced in doxorubicin-resistant DLBCL cells and DLBCL patients with poor prognostic. In addition, we found that DNA demethylating agents can sensitize primary DLBCL cells to doxorubicin. Primary cells obtained from a DLBCL patient treated with 5-azacytidine shows SMAD1 demethylation and ex vivo sensitization to multiple drugs. Therefore, DNA demethylating drugs can reprogram otherwise resistant DLBCL cells to respond to chemotherapy agents without increasing the toxicity to normal tissues. Our data also indicate that DNA methylation and consequent suppression of SMAD1 expression represent a previously undescribed molecular mechanism of chemoresistance in DLBCL that can be further exploit for therapy.

overall_design: A microarray study using genomic DNA from different DLBCL cell lines before any treatment. Two to four biological replicates by cell line. The HELP data wil be used to find genes hypermethylated in resistant cell lines compared to sensitive cell lines to doxorubicin and other drugs.

first: Leandro

last: Cerchietti

first: Maria

last: Figueroa

first: Rita

last: Shaknovich

first: Shao-Ning

last: Yang


title: P. falciparum (lab strain DD2) treated with A23187 vs untreated [CGH]

summary: Calcium is a universal second messenger molecule which plays a significant role in several biological processes. Presence of calcium sensors (calmodulins) and calcium-dependent protein kinases in Plasmodium species suggests an important role of calcium-dependent signaling pathways in the regulation of cellular processes in the malaria parasites. Evidence for the transcriptional response of Plasmodium falciparum asexual blood stages to the well-known calcium ionophore A23187 has been presented here.

overall_design: Comparative genomic hybridization (CGH) was carried out with total DNA isolated from the untreated parasites and the parasites treated with the calcium ionophore (A23187 5 μM concentration) at 1 hour, 4 hours and 6 hours post treatment. Genomic DNA from the isolates was extracted by phenol chloroform. 3 μg of the total DNA from each of the isolate was subjected to klenow(NEB) reaction as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5. Treated DNA labeled with Cy3 was then hybridized against untreated DNA labeled with Cy5.


title: P. falciparum (lab strain 3d7) schizonts treated with A23187 vs P. falciparum (lab strain 3d7) reference RNA pool

overall_design: P. falciparum 3D7 strain was cultured as described by Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5. Calcium ionophore treatment was done as follows. Parasites at schizont stage were treated with 5 μM of calcium ionophore, A23187 for 30 minutes, 1 hour, 2 hours, 4 hours and 6 hours. Total RNA from each of the time points was isolated and aminoallyl-cDNA was synthesized using reverse transcriptase system (Fermentas). cDNA made from the treated parasites were labeled with Cy5 (GE-Amersham). A reference pool was made by mixing equal amount of cDNA from the parasites collected at 6 hours interval throughout the 48 hours life cycle and was labeled with Cy3 (GE-Amersham). The samples were then hybridized on a spotted cDNA chip platform comprising 10166 MOEs representing 5363 coding sequences as described in Hu G, Cabrera A, Kono M, Mok S, Chaal BK, Haase S, Engelberg K, Cheemadan S, Spielmann T, Preiser PR, Gilberger TW, Bozdech Z: Transcriptional profiling of growth perturbations of the human malaria parasite Plasmodium falciparum. Nat Biotechnol, 2009. 28(1): p. 91-8. The data was normalized and filtered with the condition, signal intensity>background intensity + 2 SD of background intensity) using NOMAD.


title: P. falciparum (lab strain 3d7) schizonts untreated control vs P. falciparum (lab strain 3d7) reference RNA pool

summary: Calcium is a universal second messenger molecule which plays a significant role in several biological processes. Presence of calcium sensors (calmodulins) and calcium-dependent protein kinases in Plasmodium species suggests an important role of calcium-dependent signaling pathways in the regulation of cellular processes in the malaria parasites. Evidence for the transcriptional response of control Plasmodium falciparum asexual blood stages not treated with the calcium ionophores, A23187 and ionomycin has been presented here.

overall_design: P. falciparum 3D7 strain was cultured as described by Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5. Total RNA from each of the time points was isolated and aminoallyl-cDNA was synthesized using reverse transcriptase system (Fermentas). cDNA made from the untreated parasites were labeled with Cy5 (GE-Amersham). A reference pool was made by mixing equal amount of cDNA from the parasites collected at 6 hours interval throughout the 48 hours life cycle and was labeled with Cy3 (GE-Amersham). The samples were then hybridized on a spotted cDNA chip platform comprising 10166 MOEs representing 5363 coding sequences as described in Hu G, Cabrera A, Kono M, Mok S, Chaal BK, Haase S, Engelberg K, Cheemadan S, Spielmann T, Preiser PR, Gilberger TW, Bozdech Z: Transcriptional profiling of growth perturbations of the human malaria parasite Plasmodium falciparum. Nat Biotechnol, 2009. 28(1): p. 91-8. The data was normalized and filtered with the condition, signal intensity>background intensity + 2 SD of background intensity) using NOMAD.


title: extracellular calcium chelation experiment_P. falciparum (lab strain 3d7) schizonts untreated vs P. falciparum (lab strain 3d7) reference RNA pool

summary: Calcium is a universal second messenger molecule which plays a significant role in several biological processes. Presence of calcium sensors (calmodulins) and calcium-dependent protein kinases in Plasmodium species suggests an important role of calcium-dependent signaling pathways in the regulation of cellular processes in the malaria parasites. Evidence for extracellular calcium chelation of the control Plasmodium falciparum asexual blood stages not treated with the calcium ionophore ionomycin and EGTA has been presented here.


title: extracellular calcium chelation experiment_P. falciparum (lab strain 3d7) schizonts treated with EGTA and ionomycin vs P. falciparum (lab strain 3d7) reference RNA pool

summary: Calcium is a universal second messenger molecule which plays a significant role in several biological processes. Presence of calcium sensors (calmodulins) and calcium-dependent protein kinases in Plasmodium species suggests an important role of calcium-dependent signaling pathways in the regulation of cellular processes in the malaria parasites. Evidence for extracellular calcium chelation of the control Plasmodium falciparum asexual blood stages treated with the calcium ionophore EGTA ans later with ionomycin has been presented here.

overall_design: P. falciparum 3D7 strain was cultured as described by Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5. Total RNA from each of the time points was isolated and aminoallyl-cDNA was synthesized using reverse transcriptase system (Fermentas). cDNA made from the parasites treated with 3 mM of EGTA and later with 5 μM ionomycin were labeled with Cy5 (GE-Amersham). A reference pool was made by mixing equal amount of cDNA from the parasites collected at 6 hours interval throughout the 48 hours life cycle and was labeled with Cy3 (GE-Amersham). The samples were then hybridized on a spotted cDNA chip platform comprising 10166 MOEs representing 5363 coding sequences as described in Hu G, Cabrera A, Kono M, Mok S, Chaal BK, Haase S, Engelberg K, Cheemadan S, Spielmann T, Preiser PR, Gilberger TW, Bozdech Z: Transcriptional profiling of growth perturbations of the human malaria parasite Plasmodium falciparum. Nat Biotechnol, 2009. 28(1): p. 91-8. The data was normalized and filtered with the condition, signal intensity>background intensity + 2 SD of background intensity) using NOMAD.


title: Regulation of the Arabidopsis Transcriptome by Oxidative Stress

status: Public on Jul 24 2012

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

summary: Oxidative stress, resulting from an imbalance in the accumulation and removal of reactive oxygen species such as hydrogen peroxide (H2O2), is a challenge faced by all aerobic organisms. In plants, exposure to various abiotic and biotic stresses results in accumulation of H2O2 and oxidative stress. Increasing evidence indicates that H2O2 functions as a stress signal in plants, mediating adaptive responses to various stresses. To analyze cellular responses to H2O2, we have undertaken a large-scale analysis of the Arabidopsis transcriptome during oxidative stress. Using cDNA microarray technology, we identified 175 non-redundant expressed sequence tags that are regulated by H2O2. Of these, 113 are induced and 62 are repressed by H2O2. A substantial proportion of these expressed sequence tags have predicted functions in cell rescue and defense processes. RNA-blot analyses of selected genes were used to verify the microarray data and extend them to demonstrate that other stresses such as wilting, UV irradiation, and elicitor challenge also induce the expression of many of these genes, both independently of, and, in some cases, via H2O2.

first: Steven

last: Neill


title: Response of Methicillin-resistant Staphylococcus aureus to Amicoumacin A

status: Public on Jul 31 2012

city: Greifswald

first: Jan

last: Pané-Farré

address: F.-L.-Jahn-Str. 15

department: Department of Microbial Physiology

country: Germany

summary: Methicillin resistant Staphylococcus aureus (MRSA) infection is becoming refractory to existing antibiotic therapy owing to the inherent ability of S. aureus to develop rapid resistance and is considered a major threat to public health.  We found that a natural isolate of Bacillus pumilus from the Columbia River Estuary produces a strong anti-MRSA compound, amicoumacin A.  As amicoumacin A has been reported to exhibit anti-microbial, anti-inflammatory, and anti-ulcer activities, we sought to uncover its mechanism of action.  Genome-wide transcriptome analysis of S. aureus COL in response to amicoumacin A showed alteration in the expression of genes involved in several cellular processes including cell envelope turnover, cross-membrane transport, virulence, metabolism, and general stress response.  The most highly induced gene was lrgA, encoding an antiholin-like product, which has been shown to be induced in response to a collapse of membrane potential.  In order to gain further insight into the mechanism of action of amicoumacin A, a whole genome comparison of wild-type COL and amicoumacin A-resistant mutants isolated by serial passage method was carried out.  Single point mutations resulting in codon substitutions were uncovered in several distinct genes: ksgA, RNA dimethyltranferase; fusA, elongation factor G; dnaG, primase, ; lacD, tagatose 1,6-bisphosphate aldolase, ; and SACOL0611, encoding a putative glycosyl transferase gene.  Based on these results, a candidate approach was undertaken to recreate the same amino acid substitution individually in FusA and KsgA, each of which resulted in two-fold resistance towards amicoumacin A.  The fusA gene is known as the site for fusidic acid- resistant mutations; however the codon substitutions in EF-G that cause amicoumacin A resistance and fusidic acid resistance occur in separate domains and do not bring about cross resistance.  Taken together, these results suggest that amicoumacin A might cause perturbation of the cell membrane and lead to energy dissipation.  Decreased rates of cellular metabolism including protein synthesis and DNA replication in resistant strains might allow cells to compensate for membrane dysfunction and thus increase cell survivability.

platform_organism: Staphylococcus aureus subsp. aureus NCTC 8325

platform_organism: Staphylococcus aureus subsp. aureus Mu50

platform_organism: Staphylococcus aureus subsp. aureus N315

platform_organism: Staphylococcus aureus subsp. aureus MRSA252

platform_organism: Staphylococcus aureus subsp. aureus MSSA476

platform_organism: Staphylococcus aureus subsp. aureus USA300

overall_design: Amicoumacin A, isolated from Bacillus pumilus, was added to exponentially growing cultures (OD600 =0.5) of Staphylococcus aureus COL at concentrations leading to around 12% and 20% reduction of OD600 after 10 min and 40 min, respectively. Total RNA was isolated from three biological replicates. Labeled cDNA from treated and control cultures (Cy5) was hybridized against a common reference cDNA pool (Cy3). The reference pool was prepared from a mixture of equal amounts of total RNA isolated from all stress and control samples in the experiment.

first: Amrita

last: Lama

first: Tai

last: Huang

first: Anna

last: Wiersma

first: Clarissa

last: Sit

first: John

middle: C

last: Vederas

first: Michael

last: Hecker

first: Michiko

last: Nakano


title: P. falciparum (lab strain 3d7) schizonts treated with ionomycin vs P. falciparum (lab strain 3d7) reference RNA pool

first: Ramya

last: Ramadoss

overall_design: P. falciparum 3D7 strain was cultured as described by Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5. Calcium ionophore treatment was done as follows. Parasites at schizont stage were treated with 5 μM of calcium ionophore, ionomycin for 30 minutes, 1 hour, 2 hours, 4 hours and 6 hours. Total RNA from each of the time points was isolated and aminoallyl-cDNA was synthesized using reverse transcriptase system (Fermentas). cDNA made from the treated parasites were labeled with Cy5 (GE-Amersham). A reference pool was made by mixing equal amount of cDNA from the parasites collected at 6 hours interval throughout the 48 hours life cycle and was labeled with Cy3 (GE-Amersham). The samples were then hybridized on a spotted cDNA chip platform comprising 10166 MOEs representing 5363 coding sequences as described in Hu G, Cabrera A, Kono M, Mok S, Chaal BK, Haase S, Engelberg K, Cheemadan S, Spielmann T, Preiser PR, Gilberger TW, Bozdech Z: Transcriptional profiling of growth perturbations of the human malaria parasite Plasmodium falciparum. Nat Biotechnol, 2009. 28(1): p. 91-8. The data was normalized and filtered with the condition, signal intensity>background intensity + 2 SD of background intensity) using NOMAD.

first: Sabna

last: Cheemadan

first: Zbynek

last: Bozdech


title: Comparison of gene expression and mutant fitness in Zymomonas mobilis ZM4

city: Berkeley

first: Morgan

middle: N

last: Price

address: 1 Cyclotron Road Mailstop 977-152

department: Physical Biosciences Division

institute: Lawrence Berkeley Lab

sample_organism: Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821

overall_design: Expression data from diverse conditions

first: Jordan

middle: S

last: Mar

first: Jeffrey

last: Skerker

first: Adam

middle: P

last: Arkin


title: Gene Expression Changes Associated With TLR2 Mediated Inhibition of Allergen Specific TH2 Response In Vitro

city: Brisbane

first: Antonia

last: Pritchard

state: QLD

address: Level 3, R Wing, Princess Alexandra Hospital, Ipsiwch Road

department: School of Medicine

country: Australia

institute: The University of Queensland

summary: Investigation of the gene expression changes associated with TLR2 adjuvant (lipoteichoic acid; LTA) inhibition of allergic TH2 responses in peripheral blood mononuclear cell cultures (derived from house dust mite allergic individuals) stimulated with house dust mite extract.

overall_design: Pooled samples from 5 individuals were analysed by microarray; qPCR validation was carried out in a larger cohort of 23 individuals.

first: Rebecca

last: Taylor

first: Kathy

last: McKenna

first: Olivia

last: White

first: Anthony

last: Bosco

first: Stephanie

middle: T

last: Yerkovich

middle: W

last: Upham


title: Comprehensive profiling of DNA methylation in colorectal cancer reveals subgroups with distinct clinicopathological and molecular features

status: Public on Jul 18 2012

first: Marie

last: Loh

address: 14 Medical Drive

institute: National University of Singapore

summary: The Illumina GoldenGate® methylation array was used to evaluate DNA methylation at 1,505 CpG sites in 807 cancer-related genes in 91 consecutive CRC samples and 28 matched normal colonic mucosa.

overall_design: Bisulphite converted DNA from the 119 samples (91 CRC, 28 matched normals) were hybridised to the Illumina GoldenGate® methylation array.

first: Pei

last: Ang

first: Natalia

last: Liem

last: Lim

first: Fabienne

last: Grieu

first: Aparna

last: Vaithilingam

first: Cameron

last: Platell

first: Wei

last: Yong

first: Barry

last: Iacopetta

first: Richie

last: Soong


title: Expression analysis of genes in the legume endosymbiont Sinorhizobium meliloti with reference to Hydroxyproline Catabolism

status: Public on Jul 17 2012

city: Hamilton

first: Turlough

last: Finan

state: Ontario

address: 1280 Main Street West

department: Biology

country: Canada

institute: McMaster University

summary: Hydroxyproline in decaying organic matter and root exudates and is a source of carbon and nitrogen to soil-dwelling microorganisms.  A bacterial pathway for hydroxyproline catabolism was elucidated over 30 years ago however genes and gene function relationships were not established.  In that pathway, trans-4-hydroxy-L-proline (4-L-Hyp) is epimerized to cis-4-hydroxy-D-proline (4-D-Hyp), and then, in three enzymatic reactions, the D-diastereomer is converted via 1-pyrroline-4-hydroxy-2-carboxylate and alpha-ketoglutaric semialdehyde to alpha-ketoglutaric acid.  Here we report on the regulation and functions of several genes from a hydroxyproline catabolism locus on the pSymB megaplasmid of the legume endosymbiont Sinorhizobium meliloti.  The hydroxyproline catabolism genes (hyp) are negatively regulated by hypR and are organized as four single transcripts (hypR, hypD, hypS and hypH) and a 9 gene transcript (hypMNPQ(RE)XYZ).  Transcription of these genes was induced in the presence of either 4-L-Hyp and 4-D-Hyp, and was not subject to nitrogen source regulation.    The hypRE gene is shown to encode 4-hydroxyproline 2-epimerase (HypRE) responsible for the reversible isomerization of 4-L-Hyp and 4-D-Hyp, whereas a hypRE mutant grew with 4-D-Hyp but not of 4-L-Hyp as carbon source.  hypO, hypD and hypH are predicted to encode the 4-D-Hyp oxidase, the 1-pyrroline-4-hydroxy-2-carboxylate deaminase and alpha-ketoglutaric semialdehyde dehydrogenase respectively.  No epimerase activity was detected for the HypY (Smb20270), a predicted racemase, and activities from four other genes (designated hypS, hypX and hypZ) remain to be determined.  In summary, the 4-hydroxyproline (4-Hyp) catabolic pathway for S. meliloti is similar to that previously elucidated for Pseudomonas however the presence of additional genes at the hyp locus suggests that additional metabolic steps still remain to be elucidated.

overall_design:
Investigation of whole genome (three replicons) changes in gene expression in minimal (M9) media plus glycerol and galactitol and/or hydroxyproline.
Part of an investigation of the pathway for catabolism of hydroxyproline in Sinorhizobium meliloti.
RNA expression was measured for  S. meliloti in exponential phase, minimal mediaa under 4 growth conditions (2 replicates: total 8 arrays):  1) Glyceol, 2) Galactitol, 3) 4-L-hydroxyproline, 4) 4-L-hydroxyproline plus NH3

first: Catharine

middle: E

first: Jennilee

last: Gavina

first: Philip

last: Britz-McKibbin

first: Richard

middle: A

last: Morton


title: The oncoprotein v-Myb activates transcription of Gremlin 2 during differentiation of the chicken neural crest to melanoblasts

status: Public on Jul 14 2012

city: Prague

first: Vladimir

last: Cermak

address: Videnska 1083

country: Czech Republic

institute: Institute of Molecular Genetics, Czech Academy of Sciences

summary: The neural crest (NC) is a transient dynamic structure of ectodermal origin, found in early vertebrate embryos. The multipotential NC cells migrate along well defined routes, differentiate to various cells types including melanocytes and participate in the formation of various permanent tissues. Abnormal development of NC cells causes several human diseases – neurocristopathies. As there is only limited information about the molecular mechanisms controlling early events in melanocyte specification and development, we exploited the AMV v-Myb transcriptional regulator, which directs differentiation of in vitro chicken NC cells to the melanocyte lineage. This activity is strictly dependent on v-Myb specifically binding to the Myb recognition DNA element (MRE). The two tamoxifen-inducible v-myb alleles were constructed, one which recognizes the MRE and one which does not. These were activated in ex-ovo NC cells, and the expression profiles of resulting cells were analyzed using Affymetrix microarrays and RT-PCR. These approaches revealed up-regulation of the BMP antagonist gremlin 2 mRNA, and down-regulation of mRNAs encoding several epithelial genes including KRT19 as very early events following the activation of melanocyte differentiation by v-Myb.

overall_design: Comparison of gene expression profiles of chicken neural crest cells constitutively expressing 4-OH-tamoxifen inducible v-myb with mutated leucine zipper region or a version with an additional point mutation (N118D) in the DNA-binding domain. Three biological replicates were analyzed for each group.

first: Michaela

last: Starostova

first: Marta

last: Dvorakova

first: Vit

last: Karafiat

first: Michal

last: Dvorak


title: Real-time quantitative PCR analysis of mouse natural killer cells isolated from the bone marrow

status: Public on Jul 25 2012

city: Ann Arbor

first: Yasmina

last: Laouar

state: Michigan

address: 1150 West Medical Center Drive

department: Microbiology and Immunology

institute: University of Michigan

summary: A large gap in our understanding of infant immunity is why natural killer (NK) cell responses are deficient, which makes infants more prone to viral infection. Here we demonstrate that transforming growth factor-beta (TGF-beta) was responsible for NK cell immaturity during infancy. We found more fully mature NK cells in CD11cdnR mice, whose NK cells lack TGF-beta receptor (TGF-beta R) signaling. Ontogenic maturation of NK cells progressed faster in the absence of TGF-beta signaling, which results in the formation of a mature NK cell pool early in life. As a consequence, infant CD11cdnR mice efficiently controlled viral infections. These data thus demonstrate an unprecedented role for TGF-beta in ontogeny that can explain why NK cell responses are deficient early in life.

overall_design: Bone marrow cells were isolated from CD11cdnR (TG) and wild-type (WT) mice, and NK cells were sorted at different stages of development (stages D, E, and F) using BD Biosciences FACSAria.  mNK cells from stages D, E, and F were obtained from three cell sorting analyses with samples pooled from n = 12 CD11cdnR and 25 WT mice. Equal amounts of total RNA from each stage was pooled prior to gene expression analysis. RNA was prepared using the RNeasy Micro kit (Qiagen), and cDNA was obtained using the standard protocol of reverse transcription. A customized StellARay cell cycle qPCR array (Lonza) was used. Quantitative gene expression analysis (quantitative PCR) was conducted on an ABI Prism 7900 instrument (Applied Biosystems).

first: Alexandra

last: McCubbrey


title: ChIP-chip from DAOY cells stably expressing HA-MXD3 with anti-HA

city: Sacramento

first: Gustavo

middle: A.

last: Barisone

department: Internal Medicine

institute: University of California Davis Health System

type: Genome binding/occupancy profiling by genome tiling array

summary:
A subset of medulloblastomas, the most common brain tumor in children, is hypothesized to originate from granule neuron precursors (GNPs) in which the sonic hedgehog (SHH) pathway is over-activated. MXD3, a basic helix-look-helix zipper transcription factor of the MAD family, has been reported to be upregulated during postnatal cerebellar development and to promote GNP proliferation and MYCN expression. Mxd3 is upregulated in mouse models of medulloblastoma as well as in human medulloblastomas. Therefore, we hypothesize that MXD3 plays a role in the cellular events that lead to medulloblastoma biogenesis.
The purpose of this study was to identify MXD3 target genes.

overall_design: Stable cell line overexpressing HA tagged MXD3 immunoprecipitated with anti-HA; 2 biological replicates on 2 promoter arrays

first: Elva

last: Díaz


title: Acropora millepora adult samples: Control vs medium and high ocean acidification treatment

city: St Lucia

first: Paulina

last: Kaniewska

address: Gehrman Building

department: School of Biological Sciences

institute: University of Queensland

summary: In this study we investigated how changes in pH and ocean chemistry consistent with the scenarios of the Intergovernmental Panel on Climate Change (IPCC) drive major changes in gene expression, respiration, photosynthesis and symbiosis of the coral, Acropora millepora, long before they affect biomineralization.  Changes in gene expression were consistent with metabolic suppression, an increase in oxidative stress, apoptosis and symbiont loss.  Other expression patterns demonstrated up-regulation of membrane transporters, as well as the regulation of genes involved in membrane cytoskeletal interactions and cytoskeletal remodeling. These widespread changes in gene expression emphasize the need to expand future studies of ocean acidification to include a wider spectrum of cellular processes, many of which may occur well before impacts on calcification.

overall_design: We applied a reference microarray design for the experiment outlined in the study, which was a three condition experiment of ocean acidification: control pH 8.0-8.2, medium pH 7.8-7.9 and high pH 7.6-7.7, and across three time points: time zero, day 1 and day 28. Samples from time zero and control treatments were used to generate the reference sample for the microarray hybridization experiments. A total of 27 microarrays were used in the entire experiment, 3 biological replicates per treatment and timepoint. Reference samples in each array was labeled with Cy3, and the actual experimental samples with Cy5.

first: Paul

last: Campbell

first: David

last: Kline

first: Mauricio

last: Rodriguez-Lanetty

last: Miller

first: Sophie

last: Dove

first: Ove

last: Hoegh-Guldberg


title: Vaccination against yersiniosis induces a specific gill transcriptome biosignature in Atlantic salmon

city: Launceston

first: Andrew

last: Bridle

state: Tasmania

address: Old School Road

department: NCMCRS

institute: University of Tasmania

summary: Simple cost-effective bacterins are the earliest and most successfully used commercial vaccines in fish. In particular, those prepared from Yersinia ruckeri have proven effective at controlling Enteric Red Mouth Disease (ERM) and yersiniosis in rainbow trout and Atlantic salmon, respectively. However, the emergence of outbreaks of ERM caused by atypical biotypes of Y. ruckeri and reports of vaccine failure resulting in mass mortality of hatchery Atlantic salmon has reinvigorated interest in vaccines against fish bacterial diseases. Therefore the objective of this study was to identify surrogates of protection against yersiniosis using cDNA microarray to characterise the response of host genes in the gills of unvaccinated and vaccinated Atlantic salmon challenged with Y. ruckeri. Differentially expressed genes were identified using two-way ANOVA and restricted to those with >2.5-fold change at P<0.05. Using cDNA microarray we identified the expression of 6 genes in response to infection and 4 genes associated with the protective host response to yersiniosis. Analysis by real-time PCR confirmed that three immunologically relevant genes, namely a cathelicidin (47-fold) and a C-type lectin (19-fold) increased in response to yersiniosis. Including collagenase (17-fold increase), an important tissue remodelling and repair enzyme, these genes represent 3 of 6 non-protective and/or pathological responses to yersiniosis. Genes associated with the protective host response included an immunoglobulin gene and a selenoprotein that showed significant fold changes (15-fold increases each), highlighting the importance of antibody-mediated protection against yersiniosis. These findings provide much needed knowledge of the host-pathogen interaction in response to bacterial infection and immunisation in fish. Significantly, we identified a transcriptional biosignature consisting of predominantly immune-relevant genes (14 up and 3 down-regulated) in the gills of Atlantic salmon after immersion vaccination and before bacterial challenge. This biosignature may be used as a surrogate of protection and therefore as a predictor of vaccine success against yersiniosis.

platform_organism:
Oncorhynchus mykiss
Salmo salar

overall_design: 36 microarray slides representing 6 individual fish (biological replicates) at 0 h (pre-challenge), 8 h, and 72 h post-challenge from both vaccinated and unvaccinated fish. Two-colour array using sample cDNA labelled with Cy5 and a common reference aRNA labelled with Cy3 hybridized to each slide.

first: Ben

middle: F

last: Koop

first: Barbara

last: Nowak


title: Substrate phosphorylation of protein microarray by leucine-rich repeat kinase 2

city: Philadelphia

first: Jason

last: Covy

state: PA

address: 3620 Hamilton Walk

institute: University of Pennslyvania

summary: Numerous leucine-rich repeat kinase 2 mutations identified throughout the protein are associated with Parkinson disease, however the activating G2019S kinase domain mutation is currently regarded as the most common cause of familial and sporadic forms of this disorder.  Despite studies demonstrating the prominent role that its kinase activity plays in the pathobiology of leucine-rich repeat kinase 2, few substrates have been identified and only a subset of these have been linked to disease.  Therefore, we utilized protein microarrays to screen over 9,000 human proteins in an unbiased radiometric assay for potential targets of the kinase.

overall_design: ProtoArray™ Human Protein Microarrays v5.0 (Invitrogen, Carlsbad, CA, USA) were used following the manufacture’s protocol (ProtoArray Kinase Substrate Identification Kit).  Briefly, slides were equilibrated at 4C for 15 min before blocking in 1% BSA in PBS for 1 h at 4oC with gentle shaking.  Recombinant G2019S or D1994A  glutathione-S-transferase (GST)-LRRK2 (970-2527) (Invitrogen) was diluted to 50nM in 20mM Tris (pH 7.5), 10mM MgCl2, 1mM EGTA, 1mM Na3VO4, 5mM beta-glycerophosphate, 2mM DTT, 0.02% polysorbate 20, and 10 mCi /mL of  [gamma- 33P]ATP (33 nM final concentration) in a total volume of 120uL. Slides were overlayed with buffer alone, or buffer containing G2019S or D1994A LRRK2, then covered with a coverslip and placed in a 50 mL conical tube for 1 h at 30oC. Afterwards, slides were washed with 0.5% SDS buffer and water followed by centrifugation. Dried slides were exposed to a PhosphorImager plate (Amersham Biosciences, Piscataway, NJ, USA), and scanned on a Storm 840 (Molecular Dynamics, Inc., Sunnyvale, CA, USA) at 50 microns.


title: Novel Lung Cancer-Related Genes Identified by a Non-Gapped Array-Comparative Genomic Hybridization Microarray  in Asian and Caucasian Populations

city: Tainan

first: Yi-Ching

last: Wang

address: No.1, University Road, Tainan 70101, Taiwan, R. O. C.

department: Department of Pharmacology, College of Medicine

country: Taiwan

institute: National Cheng Kung University

type: Genome variation profiling by genome tiling array

summary: This study constructed a non-gapped bacterial artificial chromosomes (BAC) array containing 3604 BAC clones covering 18 lung cancer-related chromosome imbalance hotspot regions. Using this specialized array, DNA from tumor and normal tissues of 40 Asian and 20 Caucasian non-small cell lung cancer (NSLCL) patients was analyzed by array-comparative genomic hybridization (array-CGH). Block-wise normalization and a Bayes regression approach were used to refine the chromosomal imbalance regions identified by array-CGH. The array-CGH results then analyzed by MetaCore software to identify potential cancer-related genes. Finally, 273 genes showing significantly associated with molecular pathway, cancer biomarker, and gene ontology database, such as ZNF322A on 6p22.1, ARHGAP19 on 10q24.1, FRAT2 on 10q24.1, and PAFAH1B1 on 17p13.3 functioning in MAPK, Rho GTPase, and Wnt, and motility control pathways with frequent copy number gain were selected. This study mapped concisely the novel oncogenes or tumor suppressor genes in lung cancer and revealed insights of difference on chromosomal imbalance between lung cancer from Asian and Caucasian.

overall_design:
Clinical samples preparation and DNA extraction: Tissues were collected after obtaining appropriate institutional review board permission and informed consent from the recruited patients. Surgically resected tumor tissue and corresponding normal tissue were collected from 40 patients diagnosed with primary NSCLC admitted to Taipei Veterans General Hospital, Taiwan and 20 Caucasian NSCLC tumor tissues from University of Chicago, USA. Histological classification was determined according to the WHO classification and the tumor-node-metastasis system. Information on the age, sex, tumor type, tumor stage and smoking history of the patients was obtained from hospital records. The genomic DNA was prepared using proteinase K digestion and phenol-chloroform extraction.
Array-CGH: The genomic microarray used containing 3604 BAC clones representing the human genome at 18 non-gap chromosome regions. Clone mapping was analyzed using the BAC end pairs database of UCSC Genome Bioinformatics (http://genome.ucsc.edu/). The BAC library used was RP-11, which was provided from Genome Research Center, University of Yang-Ming. The extracted BAC DNA was amplified to 10 μg by Phi29 DNA polymerase reaction (TempliPhi DNA Sequencing Template Amplification Kit, Amersham, Princeton, NJ), and digested by DNaseI (New England Biolabs, Ipswich, MA), and purified by MultiScreen-PCR Plates (Millipore, Danvers, MA). After digestion, the DNA fragments were resolved by gel electrophoresis and the fragment size were optimized to within 0.5–3 kb. Finally, the purified BAC DNA fragments were dotted triplicate in 72 blocks on the glass slides (Corning, NY, USA) with spotting solution (50% DMSO, 50% D2H2O). In brief, approximately 500 ng of tumor genomic DNA and reference DNA (for Asian samples: 28 matched-normal genomic DNA pool; for Caucasian samples: commercial human genomic DNA, Invitrogen) were labeled by random priming using BioPrime DNA Labeling System (Invitrogen) with Cy3-dCTP (tumor) or Cy5-dCTP (reference). Labeled tumor and reference DNA were combined together with 100 μg human Cot-1 DNA (Invitrogen). Hybridization was performed using MAUI hybridization system (BioMcro Systems, Salt Lake City, UT), agitating the hybridization solution for 50 hours at 50℃. The arrays were scanned using scanner GenePix4000B (Axon Instruments, Foster City, CA) and the images were segmented and transformed to Cy3-Cy5 log ratio using GenePix software by Axon Instruments, Inc. (http://www.axon.com). Further data processing, a normalization method called “block-wise normalization”, which normalized the array-CGH data by the log ratio of the self-self hybridization of reference DNA according to the mean and the standard deviations of each array block, was established.

first: Fang-Yi

last: Lo

first: Jer-Wei

last: Chang

first: I-Shou

first: Ravi

last: Salgia

first: Yann-Jang

last: Chen

first: Han-Shui

last: Hsu

first: Shiu-Feng

middle: K

last: Huang

first: Hsiung-Ting

first: Fang-Yu

last: Tsai

first: Shih-Sheng

last: Jiang

first: Rajani

last: Kanteti

first: Suvobroto

last: Nandi

first: Guey-Jen

last: Lee-Chen


title: CP001: Modulation of glutamine metabolism by the PI3K-PKB/c-akt-FOXO network regulates autophagy

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

country: Netherlands

institute: Princess Maxima Center for Pediatric Oncology

summary: The PI3K-PKB/c-akt-FOXO signalling network provides a major intracellular hub for regulation of cell proliferation, survival and stress resistance1. Here we report a novel function for FOXO transcription factors in regulating autophagy through modulation of intracellular glutamine levels. To identify novel transcriptional targets of this module we performed an unbiased microarray analysis after conditional activation of the key components PI3K, PKB, FOXO3 and FOXO4. Utilising this global pathway approach we identified glutamine synthetase (GS) as being transcriptionally regulated by PI3K-PKB-FOXO signalling. FOXO-mediated increase in GS expression specifically induced glutamine production independently of cell type, and this was evolutionary conserved. FOXO activation resulted in mTOR inhibition by preventing the translocation of mTOR to lysosomal membranes, which was dependent on GS activity. Increased GS activity resulted in increased autophagosome turnover as measured by LC3 lipidation, p62 degradation, and confocal imaging of LC3, p62, WIPI-1, ULK2 and Atg12. Inhibition of FOXO3-mediated autophagy resulted in increased apoptosis, suggesting that the induction of autophagy by FOXO3-mediated upregulation of GS is important for cellular survival. These findings reveal a novel signalling network that can directly modulate autophagy through regulation of glutamine metabolism.

overall_design: conditional activation of pkb and pi3k were followed in a timeseries. Each timepoint consists of 4 independent replicates, labeled with either cy3 or cy5 and put on array against time0.

first: Kristan

last: van der Vos

first: Pernilla

last: Eliasson

first: Tassula

last: Proikas-Cezanne

first: Stephin

last: Vervoort

first: Ruben

last: van Boxtel

first: Marrit

last: Putker

first: Iris

last: van Zutphen

first: Mario

last: Mauthe

first: Sebastian

last: Zellmer

first: Cornelieke

last: Pals

first: Liesbeth

last: Verhagen

first: Koen

last: Braat

first: Tobias

middle: B

last: Dansen

first: Frank

last: Holstege

first: Rolf

last: Gebhardt

first: Boudewijn

last: Burgering

first: Paul

last: Coffer


title: extracellular calcium chelation experiment_P. falciparum (lab strain 3d7) schizonts treated with ionomycin vs P. falciparum (lab strain 3d7) reference RNA pool

city: Singapore

first: Ramya

last: Ramadoss

address: 60 Nanyang Drive, 04n-18, School of Biological Sciences

institute: Nanyang Technological University, School of Biological Sciences

summary: Calcium is a universal second messenger molecule which plays a significant role in several biological processes. Presence of calcium sensors (calmodulins) and calcium-dependent protein kinases in Plasmodium species suggests an important role of calcium-dependent signaling pathways in the regulation of cellular processes in the malaria parasites. Evidence for extracellular calcium chelation of the control Plasmodium falciparum asexual blood stages treated with the calcium ionophore ionomycin has been presented here.

overall_design: P. falciparum 3D7 strain was cultured as described by Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5. Total RNA from each of the time points was isolated and aminoallyl-cDNA was synthesized using reverse transcriptase system (Fermentas). cDNA made from the parasites treated with 5 μM ionomycin were labeled with Cy5 (GE-Amersham). A reference pool was made by mixing equal amount of cDNA from the parasites collected at 6 hours interval throughout the 48 hours life cycle and was labeled with Cy3 (GE-Amersham). The samples were then hybridized on a spotted cDNA chip platform comprising 10166 MOEs representing 5363 coding sequences as described in Hu G, Cabrera A, Kono M, Mok S, Chaal BK, Haase S, Engelberg K, Cheemadan S, Spielmann T, Preiser PR, Gilberger TW, Bozdech Z: Transcriptional profiling of growth perturbations of the human malaria parasite Plasmodium falciparum. Nat Biotechnol, 2009. 28(1): p. 91-8. The data was normalized and filtered with the condition, signal intensity>background intensity + 2 SD of background intensity) using NOMAD.

first: Sabna

last: Cheemadan

first: Zbynek

last: Bozdech


title: Tissue-enriched expression profiles in Aedes aegypti identify hemocyte-specific transcriptome responses to infection

status: Public on Jul 23 2012

city: Madison

first: Bruce

last: Christensen

state: WI

address: 1656 Linden Drive

department: Pathobiological Sciences

institute: University of Wisconsin-Madison

summary: We present a microarray study of hemocyte-enriched transcriptome in Aedes aegypti. We directed our efforts to critically assess the transcriptomic features distinctive of hemocytes, and discussed our findings in relation to infection-responsive genes and immune-relate gene families. Specifically, our analysis examined how tissue-enriched expression patterns change with the immune status of the host, and resolved patterns of transcriptional change unique to hemocytes from those that are likely shared by other immune responsive tissues.

overall_design: We profiled the transcriptome of circulating hemocytes and the remaining carcass in both naïve and bacteria-challenged adult female mosquitoes. To examine transcriptional changes associated with hemocoelic infection in distinct tissue samples, we adopted a linear model-based framework for analyzing dual-channel hybridizations (i.e., two-color microarrays) as separate single-channels (Smyth, 2004). The biological and technical dye-swap replicates of the 2×3 experimental conditions consisted of forty separate single-channel intensity profiles. For each biological replication, hemolymph perfusate and the remaining carcass were collected as paired samples at 24 hours post intra-hemocoelic injection of either Escherichia coli or Micrococcus luteus overnight culture (0.5 µl) in parallel with an age-matched naïve group from the same cohort. Concomitantly-collected hemocyte and carcass samples were co-hybridized on microarrays. Material for each experimental condition was generated from three (bacterial challenge) or four (naïve) separate generations of mosquitoes, and four separate microarray hybridizations using carcass and hemocyte material were performed. The first hybridization compared naïve and E. coli-challenged conditions, the second compared naïve and M. luteus-challenged conditions, and the third and fourth compared all three conditions.

first: Young-Jun

last: Choi

first: Jeremy

last: Fuchs

first: George

last: Mayhew

first: Helen

last: Yu


title: Mycobacterium tuberculosis whiB4 mutant expression

city: New Delhi

first: Amit

last: Singh

state: Delhi

address: Aruna Asaf Ali Marg

department: Immunology

country: India

institute: International Center for Genetic Engineering and Biotechnology

summary:
Comparison of gene expression profile of the whiB4 mutant strain of Mycobacterium tuberculosis with the wild type Mycobacterium tuberculosis H37RV
Mtb WhiB4 mutant mRNA was compared with the mRNA of wtMtb H37RV under aerobic conditons

overall_design: Aerbic conditions OD600 nm of 0.4, MtbWhiB4KO vs wtMtb, biological replicates: 3 wt Mtb H37RV and 3 MtbWhiB4 KO

first: Singh

last: Amit


title: Transcriptomic analysis of porcine muscle Longissimus dorsi (LD) exposed to a single bout of endurance exercise

city: Aarhus

first: Lene

middle: Nagstrup

last: Conley

state: Denmark

address: Langelandsgade 140

department: Department of Chemistry

country: Denmark

institute: University of Aarhus

summary: Acute physical exercise elicits changes in gene expression in skeletal muscles to promote metabolic changes and to repair exercise-induced muscle injuries. Here, we investigated the impact of a single bout of running exercise until exhaustion on global transcriptional profiles in porcine skeletal muscles. Using a combined microarray and candidate gene approach, we identified a suite of genes that are differentially expressed in muscles during post-exercise recovery. Thus, several members of the heat shock protein family and proteins associated with proteolytic events were significantly up-regulated, suggesting that protein breakdown, prevention of protein aggregation and stabilization of unfolded proteins are important processes for restoring cellular homeostasis. We also detected an up-regulation of genes, which have been reported to be associated with muscle cell proliferation and differentiation, possibly reflecting an activation, differentiation and fusion of satellite cells to facilitate repair of muscle damage. In addition, exercise increased expression of the nuclear hormone receptors, which regulates metabolic functions associated with lipid, carbohydrate and energy homeostasis. Finally, we observed an unanticipated involvement of long non-coding RNA transcripts, which have been implicated in RNA processing and nuclear retention of adenosine-to-inosine edited mRNAs. These findings expand the complexity of pathways affected by acute contractile activity of skeletal muscle, contributing to a better understanding of the molecular processes that occur in muscle tissue in the recovery phase.

overall_design: Gene expression study of the porcine muscle Longissimus dorsi in regard to exercise, pigs allowed to rest for 0 hours, 1 hour and 3 hours after exercise were compared with pigs that had not been exercising, using in-house printed porcine two-colour oligonucleotide microarrays.

first: Jeanette

middle: H

last: Jensen

first: Jakob

last: Hedegaard

first: Bo

last: Thomsen


title: Transcriptomic analysis of porcine muscle Biceps femoris (BF) exposed to a single bout of endurance exercise

overall_design: Gene expression study of the porcine muscle Biceps femoris in regard to exercise, pigs allowed to rest for 0 hours, 1 hour and 3 hours after exercise were compared with pigs that had not been exercising, using in-house printed porcine two-colour oligonucleotide microarrays.


title: Oligoarray comparative genomic hybridisation-mediated mapping of suppressors of an essential receptor tyrosine kinase generated in a deletion-biased mutagenesis screen

city: Vancouver

first: Martin

middle: Richard

last: Jones

state: BC

address: Room 419 NCE Building 2125 East Mall

department: Medical Genetics

institute: University of British Columbia

summary:
We have used oligoarray comparative genomic hybridization (aCGH) to identify novel suppressors generated in a UV-TMP based suppressor screen. This approach is suitable for detecting single gene mutations as well as copy number variations.

Keywords: C.elegans Suppressor screen array CGH

overall_design:
[1] 2 test samples from homozygous rol-3 suppressor strains mapped to chromosome II individually hybridized to reference DNA from BC6637 (rol-3(s1040ts) conditional strain), using a high density tiling array for chromosome II.
[2] 4 test samples from homozygous rol-3 suppressor strains individually hybridized to reference DNA from BC6637 (rol-3(s1040ts) conditional strain).

first: Ann

last: Rose

first: David

middle: L

last: Baillie


title: Gene Transcription Abnormalities in Canine Atopic Dermatitis

status: Public on Jul 12 2012

city: Rochester

first: Douglas

last: Plager

state: MN

address: 200 First Street SW

department: Dermatology

institute: Mayo Clinic Rochester

summary: Canine atopic dermatitis (AD) is clinically similar to human AD, implicating it as a useful model of human eosinophilic allergic disease.  To identify cutaneous gene transcription changes in relatively early inflammation of canine AD, microarrays were used to monitor transcription in normal skin (n=13) and in acute lesional AD (ALAD) and nearby visibly nonlesional AD (NLAD) skin (n=13) from dogs.  Scanning the putative abnormally-transcribed genes, several potentially relevant genes, some abnormally transcribed in both NLAD and ALAD (e.g. IL6, NFAM1, MSRA, and SYK), were observed.  Comparison for abnormally-transcribed genes common to two related human diseases, human AD and asthmatic chronic rhinosinusitis with nasal polyps (aCRSwNP), further identified genes or gene sets likely relevant to eosinophilic allergic inflammation.  These included 1) genes associated with alternatively-activated monocyte-derived cells, including members of the monocyte chemotactic protein (MCP) gene cluster, 2) members of the IL1 family gene cluster, 3) eosinophil-associated seven transmembrane receptor EMR1 and EMR3 genes, 4) interferon-inducible genes, and 5) keratin genes associated with hair and nail formation.  Overall, numerous abnormally-transcribed genes were observed only in canine AD; however, many others are common to related human eosinophilic allergic diseases and represent therapeutic targets testable in dogs with AD.

overall_design: Total RNA from skin biopsy specimens from 13 Healthy (i.e. Normal) dogs were compared to total RNA from acute lesional skin biopsy specimens (i.e. ALAD) and nearby visibly nonlesional skin biopsy specimens (i.e. NLAD) from 13 dogs with atopic dermatitis.

first: Sheila

middle: M

last: Torres

first: Sandra

last: Koch

first: Hirohito

last: Kita


title: Genomic copy-number analysis in Alveolar capillary dysplasia (ACD) patient samples

status: Public on Jul 11 2012

city: Houston

first: Pawel

last: Stankiewicz

address: One Baylor Plaza

department: Molecular Human Genetics

institute: Baylor College of Medicine

summary: Non-coding copy number changes in 16q24.1 upstream of FOXF1 were identified in two patients with ACD. An unanticipated and tremendous amount of the non-coding sequences of the human genome are transcribed. Long non-coding RNAs (lncRNAs) are non-protein coding transcripts longer than 200 nucleotides and their functions remain enigmatic. We demonstrate that deletions of lncRNA genes cause a lethal lung developmental disorder, Alveolar Capillary Dysplasia with Misalignment of Pulmonary Veins (ACD/MPV), with parent of origin effects. We identify non-coding overlapping deletions 250 kb upstream to FOXF1 in nine patients with ACD/MPV that arose de novo specifically on the maternally inherited chromosome and delete a fetal lung-specific EST, part of an lncRNA. These deletions define distant cis-regulatory region that harbors a differentially methylated CpG island, binds GLI2 depending on the methylation status of this CpG island, and physically interacts with and up-regulates the FOXF1 promoter, consistent with the absence of the fetal lung-transcribed lncRNA perturbing FOXF1 regulation. LncRNA-mediated chromatin interactions may be responsible for position effect phenomenon and potentially cause many disorders of human development.

overall_design: CNVs were identified by array CGH using 4.2M whole genome tiling arrays from Nimblegen in 3 ACD patients

first: Katarzyna

last: Kolodziejska

first: Przemyslaw

last: Szafranski


title: Comparative analysis of bacterial transcriptome using DNA microarray and next generation sequencing technologies

status: Public on Jul 10 2012

city: Ede

first: Michiel

last: Wels

address: Kernhemseweg 2

institute: NIZO food research

summary: Validation of Lactobacillus plantarum WCFS1 transcriptome profile using RNA sequencing (direct cDNA sequencing and 3'-UTR sequencing) in comparison with DNA microarray as a reference platform.

overall_design:
Transcriptome analysis was performed on total RNA and enriched mRNA of L. plantarum WCFS1 grown in CDM or MRS media. Samples were hybridized in a loop design, hybridizing each sample twice, once for each dye
This Series represents the DNA microarray experiments only.

first: Milkha

last: Leimena

first: Roger

last: Bongers

first: Eddy

middle: J

last: Smid

last: Kleerebezem


title: Effect of polyglutamine expanded TBP on microRNA expression in Neuro2A cells

city: NEW DELHI

first: REEMA

last: ROSHAN

address: A-93/94, IGIB, NARAINA INDUSTRIAL AREA, NARAINA

department: FGU

institute: INSTITUTE OF GENOMICS AND INTEGRATIVE BIOLOGY

summary: The study was carried out to identify changes in expression of microRNAs in Neuro2A cells transfected with TATA binding protein (TBP) containing a polyglutamine expansion (59 glutamine-59Q) compared to normal TBP.

overall_design: Neuro2A cells were transfected in triplicate with either 16Q-TBP-GFP fusion or 59Q TBP-GFP Fusion and total RNA collected at 24 hours, 36 hours and 60 hours post-transfection.  Each sample was subjected to microRNA microarray analysis as per manufacturer's (Agilent) instructions.

first: Tanay

last: Ghosh

first: Reema

last: Roshan

first: Beena

last: Pillai


title: Sequential stage specific reporter line analysis (SSRLA) of 3 BAC transgenic mESC lines

city: New York

first: Jeffrey

last: Zhao

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

summary: FACS purified cells from differentiation day 14-15  cells from 3 BAC transgenic mESC lines: Hes::GFP (early), Nurr1::GFP (mid), and Pitx3::YFP (late) DA neuron development reporter lines

overall_design: All three lines were differentiated towards the midbrain dopamine phenotype, and FACS purification was performed at D14-15, and then subject to global transcriptome analysis

first: Yosif

last: Ganat

first: Lorenz

last: Studer


title: Infection of bone marrow derived macrophages with M. tuberculosis CDC1551

city: Ithaca

first: Kyle

middle: Herman

last: Rohde

address: Vet. Med. Center, C5 101

institute: Cornell University

summary:
I infected 8 flasks of resting murine bone marrow derived macrophages with M. tuberculosis CDC1551.  Individual samples of intracellular Mtb were collected at 2hr, and days 2,4,6,8,10,12, and 14 post-infection using the GTC (guanidine thiocyanate) method as previously published.  A 2hr "no macrophage" control was used as a common denominator in the two-color hybridizations.  I have two independent biological replicates of this experiment.
Groups of assays that are related as part of a time series.
Time: culture time post-infection

first: David

last: Russell


status: Public on Jul 07 2012

city: Guangzhou

first: bijun

last: huang

address: 651#Dongfeng East Road

department: State Key Laboratory of Oncology in Southern China

country: China

institute: Cancer Center, Sun Yat-Sen University, Guangzhou, China

summary:
Comprehensive Profiling of Epstein-Barr Virus-Encoded miRNAome Associated with Specific Latent Type in Tumor Cells
Epstein-Barr virus (EBV) is an etiological cause of many human lymphocytic and epithelial malignancies. EBV expressed different genes associated with three latent types. So far as many as 44 EBV-encoded miRNA species have been found but their comprehensive and comparative profiling is not well documented in three latent infection states linked to various tumor cells. In this study, we utilized the polyA-tailed quantitative real time RT-PCR procedure to measure the relative abundance of viral miRNA species that linked to individual viral genome locations in combination with microarray evaluation in a subset of representative lymphoid and epithelial tumor cells undergoing various types of EBV latent infection. The results showed that miR-BHRF1 family and miR-BART family are expressed differentially in a tissue-dependent and latency-dependent manner. In particular, in NPC tissue and the only EBV consistently harboring cell line C666-1 with latency type II, there were highly abundant miR-BART family but not miR-BHRF1 family members that accounted for more than 10% of the whole known human miRNA library, implicating their important roles in maintaining EBV latent infection and driving NPC tumorigenesis. In addition, EBV miRNAome-based clustering analysis could classify three distinct EBV latency types, meanwhile, for the first time, we found and subsequently evaluated a novel secret latent switch in BL cell line Daudi from type I to III, which was unable to be identified by traditional latent biomarkers. Together, our data provided an in-depth and comparative profiling of EBV miRNA transcriptome in correspondence with three EBV latent infections, suggesting that different viral miRNA species were involved in divergent host cell carcinogenesis. Finally, EBV miRNAome, as a cluster of novel latency biomarkers expressed variedly in tumor cells, greatly complements and improves the classical typing criteria in conjunction with other latently expressed marker genes.

platform_organism:
Homo sapiens
human gammaherpesvirus 4

overall_design: 2 NPC tissue samples and 2 NPC cell lines and 5 lymphocytic cell lines

first: Hong-jie

last: Yang

first: Hui-yun

last: Wang

first: Bi-jun

last: Huang


title: Motility gene expression in L. ruminis ATCC25644 vs L. ruminis ATCC27782 during motile and non-motile growth in MRS media

city: Cork

first: Paul

last: O'Toole

address: Western Rd.

department: Microbiology

country: Ireland

institute: Univeristy College Cork

summary: The genus Lactobacillus contains over 100 different species that were traditionally considered to be uniformly non-motile.  However, at least twelve motile species are known to exist in the L. salivarius clade of this genus.  Of these, Lactobacillus rumnis is the only motile species that is also autochthonous to the mammalian gastrointestinal tract.  The genomes of two L. ruminis strains, ATCC25644 (human isolate, non-motile) and ATCC27782 (bovine isolate, motile) were sequenced and annotated to identify the genes responsible for flagellum biogenesis and chemotaxis in this species.  Transcriptome analysis revealed that motility genes were transcribed at a significantly higher level in motile L. ruminis ATCC27782 than in non-motile ATCC25644 during the motile growth phase.

sample_organism:
Ligilactobacillus ruminis ATCC 25644
Ligilactobacillus ruminis ATCC 27782

overall_design:
In preparation for RNA isolation from L. ruminis ATCC27782 and ATCC25644 cultures in the motile phase, 20 ml aliquots of MRS broth were inoculated (0.25 % inoculum) with a turbid culture of the desired strain.  The cultures were incubated anaerobically at 37 °C for 15 hr.

In preparation for RNA isolation from L. ruminis ATCC27782 and ATCC25644 cultures in the non-motile growth phase, 20 ml aliquots of MRS broth were inoculated (1 % inoculum) with a turbid culture of the desired strain.  The cultures were incubated anaerobically at 37 °C for 16-20 hrs.

RNAprotect Bacteria reagent (Qiagen) was used to stabilize gene expression in the target cultures, and total RNA was isolated according to the protocol for enzymatic and mechanical disruption of bacteria as described in the RNAprotect Bacteria Reagent handbook.  RNA isolation was completed with the RNeasy Mini kit, and contaminating DNA was removed with the Turbo DNA-free kit (Ambion).

An Oligo aCGH/ChIP-on chip hybridization kit (Agilent) was used for hybridization of the labelled cDNA to the microarrays.  Probe hybridization took place at 65 °C for 20 hrs with constant rotation (10 rpm).  Microarrays were scanned using the Agilent Microarray Scanner System (G2505B) and the scanned files were converted to data files with Feature Extraction software (Agilent).

Three microarrays, (three biological replicates) were used to examine gene transcription during the motile growth phase.  One microarray was used to examine gene transcription during the non-motile growth phase.

first: Anne

last: Neville

first: Brian

last: Forde


title: Developmental features of DNA methylation during activation of the embryonic zebrafish genome

status: Public on Jul 06 2012

city: Oslo

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo

summary: Zygotic genome activation (ZGA) occurs at the mid-blastula transition (MBT) in zebrafish and is a period of chromatin remodeling. Genome-scale gametic demethylation and remethylation occurs after fertilization, during blastula stages, but how ZGA relates to promoter DNA methylation states is unknown. Using methylated DNA immunoprecipitation coupled to high-density microarray hybridization (MeDIP-ChIP), we characterize genome-wide promoter DNA methylation dynamics before, during and after ZGA onset, in relation changes in post-translational histone modification and gene expression (Series GSE22830). A Kolmogorov-Smirnov (KS) test was applied with P <= 0.01 to identify methylation peaks.

overall_design: MeDIP-chip experiments were performed on24 hpf zebrafish embryos and sperm. Samples were lysed and proteins digested by proteinase k treatment. DNA was extracted with phenol-chloroform-isoamylalcohol and ethanol precipitation. The DNA was RNAse treated and sonicated to fragment lengths between 300-1000 bp. From each stage, duplicate immuneoprecipitations were performed using anti-5-methylcytosine antibody (10 ng/µl; Mab-006-100; Diagenode) coupled to Dynabeads M-280 sheep anti-mouse IgG (Invitrogen).  MeDIP and input DNA (150 ng each) were amplified (WGA-2; Sigma-Aldrich), cleaned up, eluted and processed for array hybridization. MeDIP and input DNA were labeled and co-hybridized onto the Nimbegen promoter arrays. The array covers 15 kb of upstream regulatory sequence and 5 kb downstream of the TSS of all zebrafish genes. A Kolmogorov-Smirnov (KS) test was applied with P <= 0.01 to identify methylation peaks.

first: P

first: A

last: Reiner


title: Gene expression profiling data from sooty mangabeys treated with interferon alpha

city: Atlanta

first: Gregory

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

summary:
In contrast to pathogenic HIV and SIV infection of humans and macaques, SIV infection of sooty mangabeys (SMs) is typically non-pathogenic despite high virus replication.
A key feature of primary SIV infection of SMs is a strong type I interferon (IFN-I) response, characterized by massive up-regulation of interferon-stimulated genes (ISG), followed by rapid resolution during the acute-to-chronic phase transition and establishment of an immune quiescent state that persists throughout the chronic infection. Based on these observations we hypothesized that low levels of IFN-I signaling may be instrumental in preventing chronic immune activation and disease progression in SIV-infected SMs. We used microarrays to characterize gene expression changes induced by IFNalpha treatment.

overall_design: To directly assess the effects of an experimentally-induced augmentation of IFN-I signaling in chronically SIV-infected SMs, we administered recombinant rhesus macaque IFNalpha2-IgFc (rmIFNα2) to eight naturally SIV-infected SMs weekly for 16 weeks and longitudinally monitored viral load, lymphocyte counts, immune activation, SIV-specific CD8+ T-cell responses, and gene expression profile. Administration of rmIFNα2 was bioactive in vivo with gene expression profiling revealing a strong upregulation of numerous ISGs in the blood of treated animals.

first: Thomas

last: Vanderford

first: Guido

last: Silvestri

first: Steven

last: Bosinger

first: Francois

last: Villinger

first: Chloe

last: Schlicter

first: Benton

middle: O

last: Lawson

first: Obaede

last: Rend

first: Greg


title: Adult bovine serum (10%) alters the expression of Pseudomonas aeruginosa genes

status: Public on Jul 09 2012

city: Lubbock

first: Jane

last: Colmer-Hamood

state: Texas

address: 3601 4th Street  STOP 6591

department: Microbiology & Immunology

institute: Texas Tech University Health Sciences Center

summary: As production of virulence factors by Pseudomonas aeruginosa is influenced by the host environment, we examined the effect of 10% adult bovine serum (ABS) on the global transcription with P. aeruginoas PAO1 at different phases of growth.  At early exponential phase (4 h), serum significantly enhanced expression of 138 genes, most of which are repressed by iron and carry binding sequences for the ferric uptake regulator or the Fur-regulated extracytoplasmic function sigma factor PvdS.  The expression of another 40 genes was reduced at 4h.  However, the expression of only a few genes was significantly altered (reduced) at the early stationary phase of growth (8 h).  Transcriptional fusion analyses confirmed serum enhances the expression of toxA, regA, and their regulatory genes regA and pvdS, yet does not interfere with the repression of these genes by iron.

overall_design: The P. aeruginosa strain PAO1 was grown in the iron-limited medium TSB-DC with or without 10% (v/v) ABS.  The presence of 10% ABS reduced PAO1 growth, but despite this reduction, the cultures reached early exponential phase at 4 h and early stationary phase at 8 h in both media.  Accordingly, we determined the PAO1 transcriptome in both media at these two specific time points.  To standardize the comprison, we adjusted the cultures to the same optical density at 600 nm (biomass) by diluting with fresh TSB-DC PAO1 grown in TSB-DC to the same OD as PAO1 grown in TSB-DC/ABS.  We obtained the transcriptome profile of 5,552 genes representing the complete P. aeruginosa PAO1 genome.

first: Cassandra

last: Kruczek

first: Mitchell

last: Wachtel

first: Madgy

middle: S

last: Alabady

first: Paxton

middle: R

last: Payton

first: Abdul

middle: N

last: Hamood


title: Evaluation of microRNAs in urine samples as indicators of prostate cancer occurrence

city: Mexico City

first: Mauricio

last: Rodriguez-Dorantes

state: Distrito Federal

address: Periferico Sur 4124

country: Mexico

institute: National Institute Of Genomic Medicine

summary: miRNAs have been proven to be very useful biomarkers, readily detectable in body fluids, particularly urine may be a valuable source to identify changes in miRNA levels that contribute to better differentiate prostate cancer (PCa) from benign prostate hyperplasia (BPH) cases. In order to characterize microRNA expression in urine samples from PCa, we analyzed expression of 376 microRNAs in 9 samples of PCa and 9 of BPH. The Normalized Ct values were compared between PCa and BPH. Statistical comparisons were made using Mann-Whitney U test, considering two different distributions. We found statiscally differences n expression for 21 miRNAs (Fold change >2 and P value<0.05).

overall_design: For the initial screening of all the studied samples, we selected only those with a concentration above 100 ng/ml, for a total of 9 samples of group of PCa and 9 BPH group. The isolated RNA was evaluated by measuring the absorbance at 260 nm and 280 nm. RNA aliquots from specimens were pooled and reverse transcription (RT) reaction was pweformed. In total, we formed 3 pools from BPH specimens and 3 from PCa ones. The RT product was used to perform a preamplification reaction. The product of preamplification teaction was loaded into the Taqman Homo sapiens microRNA Low density arrays (TLDA) panel A and amplification signal  was detected using the 7900 FAST real time thermal cycler (ABI).

first: Alberto

middle: I

last: Salido-Guadarrama

first: Jorge

middle: G

last: Morales-Montor

first: Samuel

last: Ahumada-Tamayo

first: Dorian

middle: V

last: Saavedra-Briones

first: Carlos

last: Pacheco-Gabhler

first: Eros

last: Balam-Ortiz

first: Claudia

last: Rangel-Escareño


title: FOXF1 promoter-putative enhancer chromatin looping

first: Pawel

last: Stankiewicz

summary:
To determine if there is a physical interaction between the FOXF1 promoter and putative enhancer sequences ~250kb upstream of the promoter chromosome conformation capture-on-chip (4C) analysis was performed.
An unanticipated and tremendous amount of the non-coding sequences of the human genome are transcribed. Long non-coding RNAs (lncRNAs) are non-protein coding transcripts longer than 200 nucleotides and their functions remain enigmatic. We demonstrate that deletions of lncRNA genes cause a lethal lung developmental disorder, Alveolar Capillary Dysplasia with Misalignment of Pulmonary Veins (ACD/MPV), with parent of origin effects. We identify non-coding overlapping deletions 250 kb upstream to FOXF1 in nine patients with ACD/MPV that arose de novo specifically on the maternally inherited chromosome and delete a fetal lung-specific EST, part of an lncRNA. These deletions define distant cis-regulatory region that harbors a differentially methylated CpG island, binds GLI2 depending on the methylation status of this CpG island, and physically interacts with and up-regulates the FOXF1 promoter, consistent with the absence of the fetal lung-transcribed lncRNA perturbing FOXF1 regulation. LncRNA-mediated chromatin interactions may be responsible for position effect phenomenon and potentially cause many disorders of human development.

overall_design: 4C analysis using 16q24.1 specific 3x720K arrays demonstrated physical interaction between the FOXF1 promoter and distant putative regulatory sequences, about 250 kb upstream in human pulomonary microvascular endothelial cells; 2 biological replicates performed; this chromatin looping was not detected in lymphoblasts that do not express FOXF1 and hence serve as a negative control.

first: Przemyslaw

last: Szafranski

first: Avinash

last: Dharmadhikari


title: Transcriptomic response of 6 Propionibacterium freudenreichii strains during cold storage

city: Fermoy

first: Marion

last: Dalmasso

address: Moorepark

department: Food Safety

institute: Teagasc

summary: Propionibacterium freudenreichii is used as a ripening culture in Swiss cheese manufacture. It produces flavor compounds over the whole ripening period. During cheese ripening, P. freudenreichii is exposed to a temperature downshift, especially when cheeses are transferred from warm temperature (about 24°C) to cold temperature (about 4°C). The cold adaptation of the type strain was studied previously. The aim of this study was to investigate the adaptation of 6 other P. freudenreichii strains at cold temperature by means of a global gene expression profile. The temporal transcriptomic response of 6 P. freudenreichii strains was analyzed at 2 times of growth, during growth at 30°C then after 3 days 4°C, in the constant presence of lactate as the main carbon source.

sample_organism: Propionibacterium freudenreichii subsp. shermanii

overall_design: Six strains were used: CIRM-BIA9, CIRM-BIA118, CIRM-BIA122, CIRM-BIA123, CIRM-BIA472, CIRM-BIA482. Gene expression was measured in the middle of exponential growth phase at 30°C (20h, OD650 ≈ 0.5), and after 3days of incubation at 4°C. Three independent biological experiments were performed for each strain and at each time, and were labelled A, B, C. Five technical repetitions were performed using the  RNA of 3J_122B, 3J_123A, 3J_472C, 20H_9A and 20H_482C samples. These technical repetitions were labelled  3J_122Bii, 3J_123Aii, 3J_472Cii, 20H_9Aii and 20H_482Cii respectively. The transcriptomic data for 20H_122A and 3J_123C samples were abberant and were thus not considered for further analysis.

first: Julie

last: Aubert

first: Hélène

last: Falentin

first: Sandrine

last: Parayre

first: Sergine

last: Even

first: Marie-Bernadette

last: Maillard

first: Jarna

last: Tanskanen

first: Anne

last: Thierry


title: miRNA measurements in wildtype and Eri1-deficient Th cells

city: San Francisco

first: Andrea

last: Barczak

state: CA

address: 1550 4th St Rock Hall 545

institute: UCSF Sandler Center Functional Genomics Core Facility

summary: Natural killer (NK) cells play a critical role in early host defense to infected and transformed cells. Here we show that mice deficient in Eri1, a conserved 3’-to-5’ exoribonuclease that represses RNA interference, have a cell-intrinsic defect in the homeostasis and terminal maturation of NK cells. Eri1–/– NK cells show delayed acquisition of Ly49 receptors in the bone marrow and a selective reduction in Ly49D and Ly49H activating receptors in the periphery. Furthermore, antigen-specific Ly49H+ NK cells deficient in Eri1 fail to expand efficiently in mouse cytomegalovirus (MCMV) infection. Consequently, we find that Eri1 is required for immune-mediated control of MCMV titers. In contrast to NK cells, T cells deficient in Eri1 differentiate into effectors that produce high levels of Th2 cytokines. Here we identify miRNAs as the major endogenous small RNA target of Eri1 in mouse lymphocytes. NK and T cells deficient in Eri1 display an approximately two-fold increase in all miRNAs. In Eri1-deficient T cells, ectopic expression of wildtype Eri1 is sufficient to rescue defects in both miRNA homeostasis and Th2 cytokine production. Thus mouse Eri1 negatively regulates miRNA homeostasis and is required to promote normal lymphocyte effector functions.

platform_organism:
Caenorhabditis elegans
Drosophila melanogaster
Danio rerio
Gallus gallus
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: One sample; one color design. These are six arrays from a study investigating the microRNA profile of wildtype and Eri1-deficient Th cells that is to published separately.

first: Molly

last: Thomas

first: K

last: Ansel


title: cirDNA methylome analysis in prostate cancer

city: Toronto

first: Rene

last: Cortese

address: 250 College St.

department: The Krembil Family Epigenetics Laboratory

institute: CAMH

summary:
DNA modification profiling of circulating DNA (cirDNA) from plasma samples from prostate cancer patients (T2-3N0Mx), benign prostatic hyperplasia and control individuals
Epigenetic differences are a common feature of many diseases, including cancer, and disease-associated changes have even been detected in bodily fluids. DNA modification studies in circulating DNA (cirDNA) may lead to the development of specific non-invasive biomarkers.

overall_design: Three-conditions experiment: Prostate cancer (n=19), bening prostatic hyperplasia (n=20), controls without any know prostatic disease (n=20). cirDNA was isolated and the modified fraction of the genome was enriched using DNA-modification-sensitive digestion and adaptor-mediated PCR. Enriched fraction was labelled with Cy3. DNA samples extracted from white blood cells (WBC) of 20 individuals unrelated to this project were pooled and used as reference (Cy5-labelled).

first: Andrew

last: Kwan

first: Emilie

last: Lalonde

first: Olga

last: Bryzgunova

first: Anna

last: Bondar

first: Ying

last: Wu

first: Juozas

last: Gordevicius

first: Mina

last: Park

first: Gabriel

last: Oh

first: Zachary

last: Kaminsky

first: Juste

last: Tverkuviene

first: Arvydas

last: Laurinavicius

first: Feliksas

last: Jankevicius

first: Dorota

last: Sendorek

first: Syed

last: Haider

first: Sun-Chong

last: Wang

first: Sonata

last: Jarmalaite

first: Pavel

last: Laktionov

first: Paul

middle: C

last: Boutros

first: Arturas

last: Petronis


title: Multiple roles for CodY in the type strain Bacillus cereus ATCC 14579

status: Public on Jul 05 2012

city: Jena

first: Akos

middle: T

last: Kovacs

address: Neugasse 23

department: Institute of Microbiology

institute: Friedrich Schiller University of Jena

summary: Comparison of the B cereus codY deletion mutant with wild type strain (ATCC 14579)

overall_design: One condition design comparision of mutant vs wild type including a dye swap, 4 biological replicate

first: Toril

last: Lindback

first: Per

middle: E

last: Granum

first: Oscar

middle: P

last: Kuipers


title: The DNA Methylomes of a Newborn and a Centenarian

city: L'Hospitalet de Llobregat

first: Antonio

last: Gómez

state: Barcelona

address: Av. Gran Vía s/n km. 2,7.

department: Epigenetics and Biology of Cancer Program

institute: IDIBELL

summary: Examination of two DNA methylomes at the most extreme points of their lives to see differences that might contribute to explain the aged phenotype

overall_design:
We have performed Whole Genome Bisulfite Sequencing (WGBS) and methylation array technology of newborn and a centenarian samples to address the Epigenetic drifts in Human aging, which might be an alternative pathway to explain the age-associated alterations. In addition, we used SNP array platforms to exclude an influence of copy number changes with age and SNPs on the identification of differentially methylated regions.
This Series represents the methylation array data. The WGBS data are available in GSE31263.

first: Heyn

last: Holger

first: Esteller

last: Manel


title: Profiling proteome-scale antibody responses to M. tuberculosis proteins in sera of macaques infected with M. tuberculosis

city: Bronx

first: Shajo

last: Kunnath-Velayudhan

state: NY

address: 1300 Morris Park Ave

department: Microbiology and Immunology

institute: Albert Einstein College of Medicine

summary: Human infection with Mycobacterium tuberculosis results in a continuum of ill-defined, clinical manifestations with stable latent M. tuberculosis infection (LTBI) and severe active disease at the ends.  Identifying different states of infection is of importance to tuberculosis (TB) control since risk of developing active disease varies among different asymptomatic states while infectiousness varies among patients with different bacterial burden.  We investigated changes in proteome-scale antibody responses during disease progression in a non-human primate model of tuberculosis.  We probed M. tuberculosis proteome microarrays with serial sera collected from three infection-outcome groups (active, reactivation, and latent).  We found that each infection outcome is associated with characteristic changes in the antibody levels and number of antigenic targets, which suggested an association between antibody responses and bacillary burden.  Additional proteome-scale serological profiling of > 400 human TB suspects established that antibody responses are positively associated with bacterial load.  Thus tuberculosis-specific antibody levels and number of antigenic targets increases with disease progression.

overall_design: To investigate antibody responses during the course of infection, we probed M. tuberculosis proteome microarrays with serial sera collected from experimentally infected cynomolgus macaques.  Based on infection outcome, the macaques were grouped into three classes; A) active disease (n = 4), B) latent infection (n=5) and C) reactivation disease (n = 5).  Note that the macaques in the reactivation class developed signs of disease spontaneously without any experimental intervention.  For each animal, we tested one pre-infection time point and approximately ten post-infection time points at one-month intervals.

first: Maria

last: Gennaro


title: Pseudomonas putida KT2440 cells: control vs. 2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one (DIMBOA)

city: Harpenden

first: Andrew

last: Neal

state: Herts

address: West Common

country: United Kingdom

institute: Rothamsted Research

summary: Transcriptome profiling of Pseudomonas putida KT2440 comparing cells exposed for 1 hour to DIMBOA from maize (Zea mays) to unexposed cells

overall_design: Two-condition experiment, unexposed vs. exposed, three biological replicates independantly grown and harvested. A dye swap was performed on each biological replicate for a total of six hybridizations. Each GEO Sample represents the data after merging of the technical (dye swap) replicates.


title: Profiling proteome-scale antibody responses to M. tuberculosis proteins in TB suspect's sera

overall_design: Serum samples collected from adult patients with suspected tuberculosis during a multi-site study was used to probe whole proteome microarrays. Subject recruitment was conducted under uniform protocols approved by the institutional ethics committee at each site.  Final diagnosis of active TB was based on positive M. tuberculosis culture results.  The active TB patients were further subdivided into smear-positive and negative disease based on results of Ziehl-Neelsen staining of sputum smears for acid fast bacilli. Active TB was excluded as a diagnosis (Non-TB Disease [NTBD] patients) based on having negative M. tuberculosis culture and smear results and on having an alternate diagnosis.  All subjects were presumably negative for HIV infection given the very low incidence of HIV infection in the study sites.  Sera from 169 TB and 242 NTBD patients were selected for microarray probing. The control sera (n = 14) which was used to generate negative control distribution for each protein were negative to latent M. tuberculosis infection, as indicated by negative results to tuberculin skin test.


title: Identification of expression quantitative trait loci (eQTL) in human liver (SNP)

status: Public on Jul 03 2012

city: Tuebingen

first: Michael

last: Bonin

state: BW

address: CAlwerstr. 7

institute: University Tuebingen

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

summary: We genotyped 149 human surgical liver samples from Caucasian donors with detailed medical documentation. The overall purpose of the study was to identify expression quantitative trait loci (eQTL) in human liver.....

overall_design: 149 liver samples of Caucasian origin were included in the study on the analysis of RNA expression (Illumina Human_WG6_V2) and genotype (HumanHap_300_V2)

first: Adrian

last: Schröder

first: Kathrin

last: Klein

first: Stefan

last: Winter

first: Matthias

last: Schwab

first: Andreas

last: Zell

first: Ulrich

last: Zanger


title: Synthetic lethality between Rb, p53 and miR-17~92 in retinal progenitors suppresses retinoblastoma formation_human data

city: Gent

first: Pieter

last: mestdagh

address: De Pintelaan 185

country: Belgium

institute: Center for Medical Genetics

summary: Although Dicer1 functions as a haploinsufficient tumour suppressor its complete loss of function is selected against during tumourigenesis. Here we show that homozygous loss of Dicer1 prevents retinoblastoma formation in mice by synthetic lethality with combined inactivation of the p53 and Rb tumor suppressor pathways. We show that Dicer1 deficiency is tolerated in Rb-deficient retinal progenitor cells harbouring an intact p53 pathway, but not in absence of p53. The synthetic lethal interaction is mediated by the oncogenic miR-17∼92 cluster since its deletion phenocopies Dicer1 loss in this context. Accordingly, miR-17∼92- inactivation suppresses retinoblastoma formation in mice and co-silencing of miR17/20a and p53 cooperatively decrease the viability of pre-formed human retinoblastoma cells. These data provide important insights into what underlies selective pressure against loss of Dicer1 during tumorigenesis and indicate that targeting Dicer or miR-17-20a family members should be explored as a potential selective therapeutic approach for retinoblastoma prevention and/or treatment.

overall_design: 36 human samples

first: Jean-Christophe

last: Marine

last: Mestdagh


title: Synthetic lethality between Rb, p53 and miR-17~92 in retinal progenitors suppresses retinoblastoma formation_murine data

overall_design: 23 murine samples


title: Comparative analysis of gene expression changes upon overexpression of activated Thickveins in the Drosophila wing at larval vs. pupal stages

status: Public on Jul 04 2012

city: Seattle

first: Laura

last: Buttitta

state: WA

address: 1100 Fairview Ave. N.

country: USA

institute: Fred Hutchinson Cancer Research Center

summary: Investigation of whole genome gene expression changes in dissected Drosophila wings at the wandering L3 larval stage and 24h after pupa formation, expressing UAS-activated Thickveins Q-D under control of apterous-gal4 with a tubulin driven temperature sensitive gal80 transgene, compared to the parental strain lacking the UAS-Thickveins transgene

overall_design: A 20 chip study using total RNA recovered from five independently isolated samples of 10 dissected Drosophila wings at the indicated developmental stages expressing UAS-activated thickveins or the non-UAS containing matched control strain.

middle: A

first: David

middle: D

last: O'Keefe

first: Bruce

last: Edgar


title: Expression profile of Chicken Early Yolksac Endodermal Tissues

city: Kobe

first: Fumie

last: Nakazawa

address: 2-2-3 Minatojima-minamimachi, Chuo-ku

country: Japan

institute: Center for Developmental Biology, RIKEN

summary: A major role of yolk sac endoderm is the uptake of lipids and other constituents from the yolk and transfer of these components into the embryonic circulation. The molecular basis of the initial step of this regionalization has largely remained unclear. Using chick as a model system, we generated high-quality transcriptomic datasets of different stages of the yolksac endoderm and analyzed their molecular heterogeneity.

overall_design: Two independent samples of total RNA were isolated from yolk sac endodermal tissues on embryonic day 1, 2, 3, and 4.  5 μg of RNA from each sample (total of 8 samples) were used to screen Affymetrix Chicken Genome Array without an amplification step.

first: Alev

last: Cantas

first: Martin

last: Jakt

first: Sheng

last: Guojun


title: Thermotoga maritima wild type minimal media expression analysis

city: Logan

first: Daniel

last: Hyduke

state: UT

address: 4105 Old Main Hill ENGR 402S

department: Biological Engineering

institute: Utah State University

type: Expression profiling by genome tiling array

summary: An eight chip study using total RNA recovered from separate wild-type cultures of Thermotoga maritima at mid-log with 3 different minimal sugar media.

overall_design: A eight-chip study using total RNA recovered from separate wild-type cultures of Thermotoga maritima at mid-log with 3 different minimal sugar media. 4 biological replicates maltose, 2 biological replicates L-arabinose, 2 biological replicates cellobiose.

first: Joshua

last: Lerman

first: Haythem

last: Latif


title: Adaptive mutations that prevent cross-talk enable the expansion of paralogous signaling protein families

status: Public on Jul 02 2012

city: Cambridge

first: Emily

last: Capra

state: MA

address: 31 Ames Street, 68-570

department: Biology

institute: Massachusetts Institute of Technology

summary: Orthologous proteins often harbor numerous substitutions, but whether these differences result from neutral or adaptive processes is usually unclear. To tackle this challenge, we examined the divergent evolution of a model bacterial signaling pathway comprising the kinase PhoR and its cognate substrate PhoB. We show that the specificity-determining residues of these proteins are typically under purifying selection, but have, in α-proteobacteria, undergone a burst of diversification followed by extended stasis. By reversing mutations that accumulated in an α-proteobacterial PhoR, we demonstrate that these substitutions were adaptive, enabling PhoR to avoid cross-talk with a paralogous pathway that arose specifically in α-proteobacteria. Our findings demonstrate that duplication and the subsequent need to avoid cross-talk strongly influence signaling protein evolution. These results provide a concrete example of how system-wide insulation can be achieved post-duplication through a surprisingly limited number of mutations. Our work may help explain the apparent ease with which paralogous protein families expanded in all organisms.

overall_design: Two-condition experiment, mutant vs. WT in given growth media

first: Barrett

last: Perchuk

first: Jeffrey

last: Skerker

first: Michael

last: Laub