title: FOXM1 Orchestrates a Global Methylation Signature that Mimics the Cancer Epigenome

status: Public on Apr 19 2012

city: London

first: Muy-Teck

last: Teh

state: England

address: Blizard Building, 4, Newark Street,

department: Centre for Clinical & Diagnostic Oral Sciences

country: United Kingdom

institute: Queen Mary University of London

type: Methylation profiling by genome tiling array

summary:
Aberrant upregulation of a single oncogene FOXM1 in primary normal human oral epithelial cells orchestrated a cancer-like methylome landscape
This study have identified a unique FOXM1-induced epigenetic signature which may have potentials as biomarkers for early oral cancer screening, diagnostic and/or therapeutic interventions

overall_design: Comparisons of primary human normal oral keratinocytes transduced with either EGFP (control) or FOXM1B and a head and neck squamous cell carcinoma cell line SCC15

first: M

middle: T


title: Growth competition experiment on the Yeast Homozygous Diploid Deletion Pool to investigate which ORFs conferred an advantage/disadvantage when growing on both standard and high concentration of oleic acid

status: Public on Apr 26 2012

city: Segrate, Milano

first: Clelia

last: Peano

address: Via Fratelli Cervi 93

department: Institute of Biomedical Technologies

country: Italy

institute: National Research Council

summary: The combination of genetic analysis and genome-wide expression profiles make Saccharomyces cerevisiae the cradle of Systems Biology. The way S. cerevisiae uses carbon sources has long been a landmark for studies concerning cellular responses to environmental conditions. S. cerevisiae conserves the entire machinery for utilization of fatty acids, yet with a different compartmentalization compared to higher eukaryotes. We propose S. cerevisiae as a model to understand how perixosomal compartmentalization of oleate metabolism co-evolved with the transcriptional regulatory networks of FA metabolism. With this aim, we performed growth competition experiments in oleate on the pooled collection of all viable yeast null mutants. We integrated results of competitive fitness with transcriptional profiles in oleate, identifying two genes previously not directly associated to FA metabolism: OAR1 and FET3. For the first time we show the importance of iron metabolism not only in maintaining functional mitochondria, but also in influencing peroxisome wellness.

overall_design: An aliquot of the Yeast Homozygous Diploid Deletion Pool (95401.H1Pool, Invitrogen), containing equal amounts of each barcoded viable knock-out mutant from the Saccharomyces Genome Deletion project, was grown in the presence of G418 in YPD medium for 24h, then aliquots of 5x10^7 cells were harvested and stored at -80°C. From the same pooled culture, equal amounts of cells were washed and transferred to YP medium added with oleic acid 0.1% and 5%. We collected samples of cells 24h and 72h after carbon source metabolic shift, and genomic DNA was extracted.  Each experiment was performed in biological duplicate. The upTAG and downTAG regions were amplified separately in PCR reactions, one for each experimental condition, using specific primers. Amplified upTAG and downTAG sequences were combined in equal amounts and used to probe high-density oligonucleotide arrays (Affymetrix GeneChip_DNA_Tag3). Data analysis was performed as previously described (Pierce et al., 2007). In order to adapt this data analysis protocol to our experimental design, and to the use of  GeneChip_DNA_Tag3 arrays, some changes to the procedure have been improved.

first: Emmanuela

last: Marchi

first: Enrica

last: Calura

first: Marco

last: Severgnini

first: Cristina

last: Battaglia

first: Duccio

last: Cavalieri


title: Global Transcriptomic and Proteomic Responses of Dehalococcoides ethenogenes Strain 195 to Fixed Nitrogen Limitation

city: Berkeley

first: Patrick

last: Lee

state: CA

address: 209 O'Brien Hall

department: Civil and Environmental Engineering

country: USA

institute: University of California, Berkeley

summary: Bacteria of the genus Dehalococcoides play an important role in the reductive dechlorination of chlorinated ethenes. A systems level approach was taken in this study to examine the global transcriptomic and proteomic responses of exponentially growing D. ethenogenes strain 195 to fixed nitrogen limitation (FNL). As expected, the nitrogen-fixing (nif) genes were differentially up-regulated in the transcriptome and proteome of strain 195 during FNL. Aside from the nif operon, a putative methylglyoxal synthase-encoding gene (DET1576), which is predicted to catalyze the formation of the toxic electrophile methylglyoxal and implicated in the uncoupling of anabolism from catabolism in bacteria, was strongly up-regulated in the transcriptome and could potentially play a role in the observed growth inhibition during FNL. Carbon catabolism genes were generally down regulated in response to FNL and a number of transporters were differentially regulated in response to nitrogen limitation, with some playing apparent roles in nitrogen acquisition while others were associated with general stress responses. A number of genes related to the biological functions of nucleotide synthesis, replication, transcription, translation, and post-translational modifications were also differentially expressed. One gene coding for a putative reductive dehalogenase (DET1545) and a number coding for oxidoreductases, which have implications in energy generation and redox reactions, were also differentially regulated. Interestingly, most of the genes within the multiple integrated elements were not differentially expressed. Overall, this study elucidates the molecular responses of strain 195 to FNL and identifies differentially expressed genes that are potential biomarkers to evaluate cellular nitrogen status in the environment.

overall_design: Dehalococcoides ethenogenes strain 195 was grown with or without ammonium in batch cultures with trichloroethene as the electron acceptor, acetate as the carbon source, and hydrogen as the electron donor. Microarrays were used to compare the transcriptome during fixed nitrogen limitation and triplicate biological samples were prepared for each condition. Differentially expressed genes between the two growth conditions were identified using a two-tailed Student's t-test, a false discovery rate of less than 1%, an absolute hybridization signal intensity of 300 or greater in one of the two conditions, and an expression ratio of two-fold or greater.

middle: K

first: Brian

middle: D

last: Dill

first: Nathan

middle: C

last: VerBerkmoes

first: Tiffany

middle: S

last: Louie

first: Manesh

last: Shah

first: Gary

middle: L

last: Andersen

first: Stephen

middle: H

last: Zinder

first: Lisa

last: Alvarez-Cohen


title: Identification of stage-specific gene expression signatures in response to retinoic acid during the neural differentiation of mouse embryonic stem cells

status: Public on Apr 27 2012

city: tsukuba

first: Sone

last: Hideko

state: ibaraki

department: Center for Environmental Risk Research

country: Japan

institute: National Institute for Environmental Studies

summary: We analyzed gene expression profiling by an bioinformatic approach to identify the stage-specific gene sets associated with neural differentiation of mESCs. We exposed mESCs (B6G-2 cells) to titrated doses of retinoic acid (RA) for 4 days during embryoid body formation and then performed morphological analysis on day of differentiation (DoD) 8 and 29, or genomic microarray analysis on DoD 0, 2, 8 and 29. Microarray data were analyzed by clustering methods such as self-organizing map and principal component analysis. A gene network analysis for selected gene sets was then performed using Bayesian statistics to identify stage-specific gene expression signatures in response to RA.

overall_design: 9 total samples: 1 vehcle, 8 Retinoic acid and two or three doses of each developmental stage(Day) [Vehicle Control (0.1% dimethyl sulfoxide), estradiol (1nM and 10nM), dehydrotestosterone (1nM and 10nM) bisphenol A (1pM and 100pM), triiodothyronine (1nM and 10nM), dexamethasone (1nM and 10nM), 2,3,7,8-tetrachlorodibenzo-p-dioxin (1nM and 10nM), 4(OH)-2’3,3’4’-5’-pentachlo biphenyls (1nM and 10nM), thalidomide (100nM and 0.01mM), bis(2-ethylhexyl)phthalate (0.001mM and 0.1mM), permethrin (100nM and 0.01mM), cyclopamine (100nM and 0.01mM), methoprene acid (0.001mM and 0.1mM)]; 1 Timepoint [48 hours].

first: Hideko

last: Sone

first: Seiichiroh

last: Ohsako


title: Xenoestrogen-induced epigenetic repression of non-coding microRNA genes in breast epithelial cells

status: Public on Apr 16 2012

city: Columbus

first: Pei-Yin

last: Hsu

state: OH

address: BRT836, 460W 12th Ave

institute: OSU

summary: Early exposure to xenoestrogens may predispose to breat cancer risk later in adult life. The long-lived, self-regenerating epithelial progenitor cells are more susceptible to these exposure injuries and transmit the injured memory throught epigenetic mechanisms to their differentiated progeny. We have established a breast progenitor model for epigenetic study and our previous work demonstrated that DNA methylation profiling of epithelial progeny derived from progenitors exposed to estradiol detected hypermethylated loci in 0.5% of protein-coding genes. In this study, we extended this exposure study to non-coding microRNA genes.

overall_design: Three mammosphere-derived epithelial cell (MDEC) sample sets from three independent patients. Each sample set includes one DES-preexposed and one DMSO-preexposed MDEC.

first: Daniel

middle: E

last: Deatherage

first: Benjamin

middle: A

last: Rodriguez


title: Genome-wide Identification of Polycomb Target Genes Reveals a Functional Association of Pho with Scm in Bombyx mori

status: Public on Apr 18 2012

city: Fukuoka

first: zhiqing

last: li

address: Higashi-ku, Hakozaki 6-10-1

department: Department of Bioresource Sciences

institute: Kyushu University

summary: Polycomb group (PcG) proteins are involved in chromatin modifications for maintaining gene repression that play important roles in the regulation of gene expression, tumorigenesis, chromosome X-inactivation, and genomic imprinting in Drosophila melanogaster, mammals, and even plants. PcG proteins act together in three multimeric complexes, Polycomb repressive complex 1 (PRC1), Polycomb repressive complex 2 (PRC2), and Pleiohomeotic repressive complex (PhoRC), to repress transcription of the target genes. Here, we identified Polycomb target genes in Bombyx mori using genome-wide expression screening based on the knockdown of the BmSCE, BmESC, BmPHO, or BmSCM gene, which represent the distinct complexes. As a result, most genes were up-regulated after knocking down these four PcG genes, which indicated a potential epigenetic mechanism on the regulation of these genes expression by the PcG system. The further analysis of our data will provide some important information for the regulation mediated by PcG proteins in Bombyx mori.

overall_design: Transcription profiling experiments, knockdowns of four Polycomb genes (four samples) in  silkworm BmN4-SID1 cells, were analyzed. Dual-channel experiments, with test samples labeled by Cy5 and common reference samples labeled by Cy3. The common reference sample, knockdown of the EGFP gene in BmN4-SID1 cells, was used for data normalization. One biological replicate. No dye-swaps.

first: Zhiqing

last: Li

first: Daojun

last: Cheng

first: Hiroaki

last: Mon

first: Tsuneyuki

last: Tatsuke

first: Li

last: Zhu

first: Jian

last: Xu

first: JaeMan

first: Qingyou

last: Xia

first: Takahiro

last: Kusakabe


title: AB family 2

status: Public on Apr 17 2012

city: Singapore

first: Woei Chang

last: Liew

address: 1 Research Link, NUS

country: Singapore

institute: Temasek Life Sciences Laboratory

type: Genome variation profiling by genome tiling array

summary:
Array comparative genomic hybridization was used to identify genomic differences between male and female zebrafish.
No universal sex-linked CNVR was identified.

overall_design: AB strain of zebrafish were used.The family consist of the parents and 2 male and female offspring each (total 6 samples). Dad's gDNA was used as reference sample for each family.

first: Woei

first: Richard

last: Bartfai

first: Zijie

last: Lim

first: Rajini

last: Sreenivasan

first: Kellee

middle: R

last: Siegfried

first: Laszlo

last: Orban


title: Ketogulonigenium vulgare cells: co-culture mode vs. mono-culture mode

city: Wuxi

first: Zhu

last: Yibo

state: Jiangsu

address: Lihu Road 1800#

country: China

institute: Jiangnan University

summary: Transcriptional profiling of K. vulgare cells co-cultured with Bacillus megaterium compared to K. vulgare mono-cultured cells. Differentially expressed genes in co-cultured and mono-cultured K. vulgare cells were analyzed. The aim was to investigate the mechanisms of B. megaterium stimulating K. vulgare propagation on global gene expression.

sample_organism:
Priestia megaterium
Ketogulonicigenium vulgare WSH-001

overall_design: Two-condition experiment: co-cultured K. vulgare and B. megaterium cells vs. mono-cultured K. vulgare cells. Biological replicates: 3 co-cultured replicates, 3 mono-cultured replicates.

first: Yibo

first: Jingwen

last: Zhou

last: Chen


title: INK4A expression in leukemic cells transformed by the v-Myb oncoprotein depends on the integrity of the v-Myb leucine zipper region

status: Public on Apr 12 2012

city: Prague

first: Vladimir

last: Cermak

address: Videnska 1083

country: Czech Republic

institute: Institute of Molecular Genetics, Czech Academy of Sciences

summary: The AMV v-Myb oncoprotein causes oncogenic transformation of myelomonocytic cells in vivo and in vitro. Its transforming capacity is strictly dependent upon the N-terminal DNA binding domain, the central transactivation region, and on the C-terminal domain containing a putative leucine zipper motif. While deletions in the central part of the leucine zipper region or point mutations of critical leucine residues abolish the leukemogenicity of the protein, a small deletion within the N-terminal part (deltaP mutant) preserves almost full in vitro transforming ability and only weakens the leukemogenic potential in vivo. We analyzed the gene expression profiles of ex vivo cultures transformed with either wild type or deltaP mutant of v-Myb. A few tens of genes were found to be significantly and reproducibly differentially expressed between the two cultures. Among them, the transcript of the CDKN2A gene, which is critically involved in the cell cycle progression regulation, showed higher expression in the deltaP mutant transformed cells. In mammals and also some avian species, there are two different mRNAs - ARF and INK4A – transcribed from the CDKN2A locus. It is known that in chickens the locus had been rearranged in evolution and only one mRNA is transcribed. We found that this mRNA encodes both ARF and INK4A and that the INK4A protein translation starts with a GUG codon downstream of the ARF AUG initiation codon and proceeds in a different reading frame. INK4A protein thus exists in chicken cells as well and its negative regulation by v-Myb is a part of the leukemic transformation mechanism.

overall_design: Comparison of expression profiles of chicken monoblasts transformed either by wild type v-myb or its mutated version designated deltaP. Three biological replicates were analyzed for each group.

first: Marta

last: Dvorakova

first: Michal

last: Dvorak


title: ChIP-chip from human liver cancer cells with HIF-2a

city: Shanghai

first: Haixiang

last: Sun

address: Fenglin Road, 180

institute: Zhongshan Hospital

type: Genome binding/occupancy profiling by genome tiling array

summary:
The transcription factor HIF-2a play an important role in the tumor progress, the aim is to explore the target genes of HIF-2a in liver cancer cell line.
Chromatin immunoprecipitation (ChIP) of HIF-2a together with chromatin profiling by ChIP-on-chip analysis demonstrated that  HIF-2a directly activates many target genes.

overall_design: Analyze the target genes in a liver cancer cell line MHCC97H

first: Hai-Xiang

first: Xin-Rong

last: Yang


title: Multidrug Resistance-Linked Gene Signature Predicts Overall Survival of Patients with Primary Ovarian Serous Carcinoma

city: Namur

first: jean-pierre

last: gillet

address: 61 Rue de Bruxelles

department: URPhyM

country: Belgium

institute: University of Namur

summary: This study assesses the ability of multidrug resistance (MDR)-associated gene expression patterns to predict survival in patients with newly diagnosed carcinoma of the ovary. The scope of this research differs substantially from that of previous reports, as a very large set of genes was evaluated whose expression has been shown to affect response to chemotherapy.

overall_design: We applied a customized TaqMan Low-Density Array, a highly sensitive and specific assay, to study the expression profiles of 380 MDR-linked genes in 80 tumor specimens collected at initial surgery to debulk primary serous carcinoma of Mullerian origin. The RNA expression profiles of these drug resistance genes were correlated with clinical outcomes.

first: Jean-Pierre

last: Gillet

first: Anna

middle: M

last: Calcagno

first: Sudhir

last: Varma

first: Ben

last: Davidson

first: Mari

middle: B

last: Elstrand

first: Ram

last: Ganapathi

first: Aparna

last: Kamat

first: Anil

last: Sood

first: Suresh

middle: V

last: Ambudkar

first: Michael

last: Seiden

first: Bo

last: Rueda

last: Gottesman


title: Expression analysis of Aspergillus nidulans AN1599 (PbcR) overexpression mutant

city: Espoo

first: Kirsi

last: Bromann

address: Tietotie 2

department: TK402, Cell Factory

country: Finland

institute: VTT Technical Research Centre of Finland

summary:
Investigation of whole genome gene expression level changes in Aspergillus nidulans AN1599 (PbcR) overexpression mutant, compared to the FGSC A4 wild-type strain.
Overexpression of the Zn(II)2Cys6 –type transcription factor, AN1599.4 (PbcR, pimaradiene biosynthetic cluster regulator), activates a secondary metabolite gene cluster in Aspergillus nidulans. Activation of the pathway in Aspergillus nidulans lead to a production of ent-pimara-8(14),15-diene.

overall_design: 12x135K array of two separate cultures of FGSC A4 and two separate cultures of oe:AN1599(PbcR) with three separate RNA extractions from each culture. Each 135K array measures expression level of 10,546 genes with 6 probes/transcript. In addition, the array format contains tiling probes for 36 longer transcripts. All probes are in duplicates, giving the total number of 137,562 probes per array.


title: MiRNA profiling during infection with H7N7 influenza A virus (A/Ck/Germany/R28/H7N7/2003)

status: Public on Apr 10 2012

city: Vancouver

first: Victoria

last: Svinti

address: 2350 Health Sciences Mall

country: Canada

institute: University of British Columbia

summary: MicroRNAs (miRNAs) repress the expression levels of genes by binding to mRNA transcripts, acting as master regulators of cellular processes. Differential expression of miRNAs has been linked to viral-associated diseases involving members of the hepacivirus, herpesvirus, and retrovirus families. In contrast, limited biological and molecular information has been reported on the potential role of cellular miRNAs in the lifecycle of influenza A viruses (infA). In this study, we hypothesize that elucidating the miRNA expression signatures induced by low-pathogenic swine-origin influenza A virus (S-OIV) pandemic H1N1 (2009) and highly pathogenic avian-origin (A-OIV) H7N7 (2003) infections could reveal temporal and strain-specific miRNA fingerprints during the viral lifecycle, shedding important insights into the potential role of cellular miRNAs in host-infA interactions. Using a microfluidic microarray platform, we profiled cellular miRNA expression in human A549 cells infected with S- and A-OIVs at multiple time-points during the viral lifecycle, including global gene expression profiling during S-OIV infection. Using target prediction and pathway enrichment analyses, we identified the key cellular pathways associated with the differentially expressed miRNAs and predicted mRNA targets during infA infection, including immune system, cell proliferation, apoptosis, cell cycle, and DNA replication and repair. By identifying the specific and dynamic molecular phenotypic changes (microRNAome) triggered by S- and A-OIV infection in human cells, we provide experimental evidence demonstrating a series of temporal- and strain-specific host molecular responses involving different combinatorial contributions of multiple cellular miRNAs. Our results also identify novel potential exosomal miRNA biomarkers associated with pandemic S-OIV and deadly A-OIV-host infection.

overall_design: Control (mock-infected) samples: 12, Infected samples: 6, for each time-point (0, 4, 8, 24, 48 and 72 hours post infection). Seven replicates for each miRNA were found on the microarray chips, for which the median has been retained. The experiment was performed in six replicates.

first: Emma-Kate

last: Loveday

first: Sandra

last: Diederich

first: John

last: Pasick

first: François

last: Jean


title: Regulation of monocyte functional heterogeneity by miR-146a

status: Public on Apr 06 2012

city: Boston

first: Martin

last: Etzrodt

state: MA

address: 185 Cambridge Street

department: Center for Systems Biology

institute: Massachusetts General Hospital

summary: Monocytes and their lineage descendants serve as a central defense system against infection and injury but if uncontrolled can also promote an excessive pathological inflammatory response. Therefore a current research goal is to understand how the organism controls the number and function of monocytes and how these variables can be tailored in therapy. Considering the evidence that monocytes are heterogeneous and exist in at least two subsets committed to divergent functions, we investigated whether distinct factors regulate the balance between monocyte subset responses in vivo. We identified a microRNA (miRNA), miR-146a, which is differentially regulated both in mouse (Ly-6Chi and Ly-6Clo) and human (CD14hi and CD14lo CD16+) monocyte subsets. The single miRNA was found to significantly control the amplitude of the Ly-6Chi monocyte response during inflammatory challenge whereas it did not affect Ly-6Clo cells. miR-146a–mediated regulation was cell-intrinsic and depended on Relb, a member of the non-canonical NF-κB/Rel family, which is identified here as a novel miR-146a target. These observations provide novel mechanistic insights into the molecular events that regulate monocyte functional heterogeneity and identify therapeutic targets that can influence the quality and quantity of monocyte responses.

overall_design: 4 samples of splenic Ly-6Chi monocytes,  4 samples of splenic Ly-6Clo monocytes; both isolated from C57BL/6 mice. Each sample was generated by fluorecsence activated cell sorting from the pooled spleens of 10 mice.

first: Virna

last: Cortez-Retamozo

first: Andita

last: Newton

first: Jimmy

last: Zhao

first: Aylwin

last: Ng

first: Moritz

last: Wildgruber

first: Thomas

last: Wurdinger

first: Ramnik

last: Xavier

first: Frederic

last: Geissmann

first: Etienne

last: Meylan

first: Matthias

last: Nahrendorf

first: Fillip

last: Swirski

first: David

last: Baltimore

first: Ralph

last: Weissleder

first: Mikael

middle: J

last: Pittet


title: Genome-wide Mapping of the Ozone-responsive Transcriptomes of Rice Panicle and Seed Tissues Reveals Novel Insight into their Regulatory Events

status: Public on Apr 25 2012

city: Tsukuba

first: RANDEEP

last: RAKWAL

state: Ibaraki

address: 1-1-1 Tennodai

department: Institute of Health and Sport Sciences

institute: University of Tsukuba

summary: The ‘O3-responsive transcriptome’ behavior in the panicles and grains of rice plant was studied individually through high-throughput oligo-DNA microarray technique. Obtained results showed that O3 differentially regulated 620 and 130 genes in the panicles and grains separately, by at least two-fold changes. However, only five genes were found to be common in both the tissues, suggesting towards the tissue specific O3-sensitivity in rice plants. Among the O3-responsive genes, 176 and 444 genes were up- and down-regulated in rice panicle; whereas, 24 and 106 genes in rice grain, respectively. Further mapping onto various regulatory events revealed that, the majority of differentially expressed genes were mainly involved in signaling, hormonal, cell wall, transcription, proteolysis, and defense events. Many previously unknown O3-responsive novel genes were identified, including the brassinosteroid insensitive-1 receptor kinase, wall-associated kinase like receptor, calcium-dependent protein kinases, phosphatidylinositol kinases, G-protein components, ethylene insensitive-3, cellulose synthases, pectatelyase, etc. Inventory of 745 O3-responsive genes and their mapping will surely expand our knowledge on novel regulatory processes in both panicles and grains of rice; and, serve as a resource towards the designing of rice crops for future high-O3 world.

overall_design: Comparison between healthy rice plant panicles and ozone treated plant panicles (for 8 h)  and seed (grain) of healthy rice plants and of rice plants grown under ozone for their lifeftime was performed. Three biological replicates (panicle or seed; pooled) were used, and dye-swaped.

first: Kyoungwon

last: Cho

first: Junko

last: Shibato

first: Akihiro

last: Kubo

first: Yoshihisa

last: Kohno

first: Kouji

last: Satoh

first: Shoshi

last: Kikuchi

first: Ganesh

last: Agrawal

first: Abhijit

last: Sarkar

first: Randeep

last: Rakwal


title: A transcriptome study of DSF-mediated quorum sensing in Xanthomonas axonopodis pv. citri

city: Lake Alfred

first: Yinping

last: Guo

state: FL

address: 700 Experiment station road

department: Microbiology and cell science; Citrus research and education center

institute: Xanthomonas axonopodis pv. citri

summary: Quorum sensing (QS) in Xanthomonas axonopodis pv. citri, the causal agent of citrus canker, is mediated by a diffusible signal factor (DSF). QS is required for the full virulence of X. axonopodis pv. citri in planta. Mutations in rpfF, rpfC and rpfG, the core genes of QS, decreased the production of extracellular proteases and bacterial motility. Comparison of the transcriptomes of QS mutants with that of the wild type stain revealed that QS temporally regulates the expression of a large set of genes, including genes involved in chemotaxis and flagellar biosynthesis, genes related to metabolism, genes encoding virulence traits such as type II secretion system substates, type III secretion system and effectors. Cross talk between the QS regulon and the HrpG regulon has also been identified by 62 common genes shared by both regulons. The temporal regulation of the QS regulon and cross talk with the HrpG regulon suggest the important role of QS in citrus canker infection, including attachment, invasion and growth in host apoplast.

sample_organism:
Xanthomonas citri
Xanthomonas citri pv. citri str. 306

overall_design: Three mutants and two time-points experiment. Four biological and dye-swap replicates of each strain per each time-point were used. In total, there were two datasets of the rpfF mutant: 1) rpfF mutant vs. wild type strain at 11 h, and 2) rpfF mutant vs. wild type strain at 25 h; two datasets of the rpfC mutant: 1) rpfC mutant vs. wild type strain at 11 h, and 2) rpfC mutant vs. wild type strain at 25 h; and two datasets of the rpfG mutant:  1) rpfG mutant vs. wild type strain at 11 h, and 2) rpfG mutant vs. wild type strain at 25 h.

first: Nian

last: Wang


title: Differential gene expression in human myeloid dendritic cells interacting with different knockout strains of Aspergillus fumigatus in vitro

city: Wuerzburg

first: Susanne

middle: Elma

last: Kneitz

address: Biozentrum, Am Hubland

department: Physiologigcal Chemistry

country: Germany

institute: University of Wuerzburg

summary: Dendritic cells (DC) are the most important antigen presenting cells and play a pivotal role in host immunity to infectious agents by acting as a bridge between the innate and adaptive immune systems.  Myeloid DCs (mDC) were isolated from peripheral blood and co-cultured with conidia (con) and germlings (ks) of Aspergillus fumigatus knockout (mitA, mnt1, rodA) and wildtype (wt) strains for 6 hours at an MOI of 1. RNA was extracted and hybridised to microarrays. Microarrays contain probes for approximately 110 selected human immune-relevant genes, including cytokine and chemokine genes, their receptors and downstream innate immunity genes.

overall_design: We used microarrays to detail the gene expression of human myeloid dendritic cells after 6h of co-cultivation with Aspergillus fumigatus wildtype and knockout mutants

first: Juergen

last: Loeffler

first: Oliver

last: Morton

first: Helga

last: Sennefelder

first: Ruth

last: Bauer

first: Jasmin

last: Kungl


title: Transcriptomic responses of juvenile Pacific whiteleg shrimp, Litopenaeus vannamei, to hypoxia and hypercapnic hypoxia

status: Public on Apr 30 2012

city: Charleston

first: Karen

last: Burnett

state: SC

address: 205 Fort Johnson Road

department: Biology

institute: College of Charleston

summary: Here we  used microarrays to characterize changes in global gene expression in the hepatopancreas of Pacific white shrimp, Litopenaeus vannamei, exposed to short term (4 h) hypoxia (H) or hypercapnic hypoxia (HH) or long term (24 h) H or HH, compared to animals in air-saturated water (normoxia).  The transcriptomes of crustaceans exposed to low O2 and high CO2 contained both shared and treatment-specific signature genes (q ≤ 0.01, FC ≥ 1.5), with shifts characteristic of metabolic depression rather than anaerobic metabolism.  Down-regulated signature genes dominated the transcript profile in three of the four treatments (H 4 h, H 24 h, 4 h HH); many of these genes were involved in amino acid or RNA metabolism or in translation, including several tRNA synthetases.  Unique patterns of gene expression such as increased lipid metabolism and hemocyanin synthesis (H 24 h) and initiation of apoptosis (24 h HH) were tied to specific treatments.  This work contributes insight to the effects that human perturbations might have on estuarine organisms, and the importance of examining the impacts of environmentally relevant combinations of hypoxia and hypercapnia on estuarine populations.

overall_design: L. vannamei were exposed for 4 or 24 hours to one of the following conditions: normoxia, hypoxia or hypercapnic hypoxia.  Hepatopancreas tissue from individual animals was dissected, total RNA extracted, labelled and hybridized to oligonucleotide microarrays with probes for 21,864 L. vannamei unigenes.  Treatments were repeated until a total of 7 biological replicates was obtained for each time:treatment combination, except for the 24 h normoxia group, represented by 6 replicates.

first: Charles

last: Rathburn

first: Natasha

last: Sharp

first: James

last: Ryan

first: Marion

last: Beal

first: Matthew

last: Cook

first: Robert

middle: W

last: Chapman

first: Louis

middle: G


title: Gsr1 in Arabidopsis thaliana: A locus inferred to regulate gene expression in response to exogenous glutamine

status: Public on Apr 13 2012

city: Stanford

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

summary:
An altered response to methylamine (MA) has been used to identify genes involved in nitrogen metabolism in many microbes and as an uncoupler of proton motive force in both prokaryotes and eukaryotes. The aim of this study was to attempt the use of MA to identify critical genes for response to exogenous nitrogen sources in Arabidopsis thaliana (thale cress). EMS mutagenesis and selection on MA were used to identify a series of mutants that showed increased sensitivity to MA but failed to identify any MA resistant mutants. The eight sensitive mutants were allelic as judged by segregation and map location so one mutant, gsr1-1, was selected for intensive analysis. Co-segregation of gsr1 with DNA markers showed the gene was on chromosome 5 between markers CA72 and nga151, an interval of about 0.42 Mbp. The co-segregating mutant phenotypes associated with gsr1 included; yellow color caused by a reduction in chloroplast number; reduced chlorophyll content; decreased nitrate reductase (EC 1.7.1.3) activity in the root; and increased glutamate dehydrogenase (EC 1.4.1.2) activity in root and shoot. Decreased transcripts included those encoding several nitrogen metabolism enzymes. In contrast, the mutation increased only 4 and 7 transcript abundances by more than two fold. RT-PCR showed that in the dark, regulation of transcript abundance by exogenously applied glutamine and to a lesser extent sucrose were altered. Gene action of the gsr1 mutant was recessive for chloroplast number but co-dominant for transcript abundances and co-dominant for enzyme activities. Supplementary data from the analysis of preliminary microarray data from AFGC used 10,560 targets and two reverse labeled slides to show that more than 351 ESTs were increased in transcript abundance by more than 2 fold in the green plants. In yellow plants only seventy-three ESTs were up-regulated in transcript abundance by more than 2 fold. Therefore, the gsr1 locus may regulate responses to endogenous and exogenous glutamine in an organ-specific fashion that could coordinately regulate the activity of genes enzymes and metabolic pathways that determine cellular nitrogen, carbon and bioenergetic (redox) status.
A replicate experimental design type is where a series of replicates are performed to evaluate reproducibility or as a pilot study to determine the appropriate number of replicates for a subsequent experiments.

first: David

last: Lightfoot


title: Genes differentially expressed Haloferax mediterranei strains: control wild-type strain vs ΔphaA1 strain

status: Public on Apr 20 2012

city: Beijing

first: Jing

last: Han

address: NO.1 West Beichen Road, Chaoyang District

institute: Institute of Microbiology, Chinese Academy of Sciences

summary: Transcriptional profiling of Haloferax mediterranei comparing control wild-type strain with ΔphaA1 strain, in which phaA1 gene are knockouted. ΔphaA1 strain can accumulate PHB only. Goal was to explore the PHA biosynthetic pathway and to determine their impact on primary metabolism in H. mediterranei.

overall_design: Total RNA from the control Haloferax mediterranei and its ΔphaA1 strain were used to generate target cDNA, and then hybridized to 8*15K Haloferax mediterranei genome array genechips, representing about 3800 genes.

first: Bo

last: Feng


title: AB family 1

first: Woei Chang

last: Liew

first: Woei

first: Richard

last: Bartfai

first: Zijie

last: Lim

first: Rajini

last: Sreenivasan

first: Kellee

last: Siegfried

first: Laszlo

last: Orban


title: Effects of 20 months Dietary Methionine Restriction on Hepatic Gene Expression in Fischer 344 Rats

status: Public on Apr 08 2012

city: Baton Rouge

first: Kirsten

middle: P

last: Stone

address: 6400 Perkins Rd

institute: Pennington Biomedical Research Center

summary: Dietary methionine restriction (MR)  has been shown to increase lifespan and decrease adiposity in rodents. This study was designed to examine the transcriptional effects of MR in metabolically relevant tissues. This experiment contains data from the liver.

overall_design: We analyzed MR-induced changes in gene expression using pooled RNA from liver of rats fed either a control purified amino acid diet (DL-methionine content of 0.86%) (CON) or a methionine-restricted diet (DL-methionine content of 0.172%)(MR). Rats were fed Purina rodent diet 5001 until 32 days of age and were then randomly assigned to be fed CON diet or MR diet  for 20 months.

first: A

last: Boudreau

first: E

last: Plaisance

first: B

last: Hasek

first: N

last: Lenard

first: L

last: Stewart

first: T

last: Henagan

last: Gettys


title: A plasma membrane calcium ATPase functions in FLS2-mediated immunity

city: Cologne

first: Bruno

last: Huettel

address: Carl-von-Linne-Weg 10

department: MPI Plant Breeding

institute: Max Planck Genome Centre Cologne

summary:
Pattern recognition receptors (PRRs) at the plasma membrane promote plant immunity through the detection of conserved microbe-associated molecular patterns (MAMPs). In plants, the PRR for bacterial flagellin (flg22) is encoded by the receptor kinase FLS2. One of the earliest MAMP responses is the rapid and transient increase of cytosolic calcium (Ca2+) ions, which is required for many of the well-described downstream responses, e.g. generation of reactive oxygen species (ROS) and the transcriptional activation of defence-associated genes. Despite its relevance, the molecular components regulating the Ca2+ burst remain largely unknown. Here, we show that the plasma membrane P2B-type Ca2+ ATPase ACA8 forms a dynamic complex with the PRR FLS2. ACA8 and its closest homologue ACA10 are required for immunity against virulent bacteria. Mutant aca8 aca10 plants are reduced in the flg22-induced Ca2+ burst, show reduced ROS production and exhibit altered transcriptional reprogramming. In particular, flg22-induced gene expression is elevated downstream of signalling mitogen-activated protein (MAP) kinases, but reduced downstream of the calcium-dependent protein (CDP) kinase cascade. These results demonstrate that the fine regulation of Ca2+ fluxes in the cytosol is critical for the coordination of the downstream MAMP responses and provide for the first time a link between the FLS2 receptor complex and signalling kinases via the secondary messenger Ca2+. ACA8 also interacted with the BRI1 and CLV1 receptor kinases, which correlated with the developmental phenotypes of aca8 aca10 mutants suggesting a broader role for Ca2+ ATPases in receptor-mediated signalling.
We used Affymetrix Arabidopsis Tiling 1.0R Array to compare global transcript levels in 7 days-old sterile grown seedlings.

overall_design: Steady-state mRNA levels in total RNA samples of 7 days old sterile seedlings

first: Nicolas

middle: F

last: dit Frey

first: Silke

last: Robatzek


title: MicroRNA analysis unravels the molecular basis of bleomycin induced lung fibrosis in mouse

city: Los Angeles

first: ting

last: Xie

address: 127 San Vicente Blvd

department: Pulmonary

institute: Cedars-Sinai Medical Center

summary: The molecular mechanisms of lung injury and fibrosis are incompletely understood. microRNAs (miRNAs) are crucial biological regulators by suppression of their target genes and are involved in a variety of pathophysiologic processes. To gain insight into miRNAs in the regulation of lung fibrosis, total RNA was isolated from lung samples harvested at different days after bleomycin treatment, and miRNA array was performed thereafter. miRNAs expressed in lungs with bleomycin treatment at different time points were compared to miRNAs expressed in lungs without bleomycin treatment, resulting in 161 miRNAs differentially expressed. Furthermore, miRNA expression patterns regulated in initial and late periods after bleomycin were identified. Target genes were predicted in silico for differentially expressed miRNAs, including miR-7f, miR-7g, miR-196b, miR-16, miR-195, miR-25, miR-144, miR-351, miR-34a, miR-499, miR-704, miR-717, miR-10a, miR-211, miR-34a, miR-367 and miR-21, and then cross-referenced to molecular pathways including apoptosis, Wnt, Toll-like receptor, and TGF-β signaling, which are involved in different pathological phenotypes such as apoptosis, inflammation, and fibrosis. Our study demonstrated relative abundance of miRNA levels in bleomycin-induced lung fibrosis. The miRNAs and their potential target genes identified herein contribute to the understanding of the complex transcriptional program of lung fibrosis.

overall_design: Under anesthesia, 2.5 U/kg bleomycin dissolved in sterile PBS was administered via trachea as previously described. Lung tissues were harvested at the time point of day 0, 3, 7, 14, and 21 post bleomycin challenges. 3 sample in specific time point, except for day 14 where nday14 = 2.

first: Ting

first: Jiurong

last: Liang

first: Rishu

last: Guo

first: Ningshan

last: Liu

first: Paul

last: Noble

first: Dianhua

last: Jiang


title: The gene expression difference in strain AT01, a mutant of Trichoderma reesei, with high ability of copper accumulation

city: Shanghai Municipality

first: Kehe

last: Fu

address: Rd.800 Dongchuan,Minhang district, shanghai municipality,China

institute: Shanghai Jiao Tong University

summary: The gene expression profile of AT01 was compared with a wild-type T. reesei strain in medium containing 0.7 mM Cu2+. A total of 627 genes were up-regulated and 305 genes were down-regulated under copper stress. The expression analysis showed that amino acid transport- and metabolism-related genes are up-regulated, which is associated with adenine metabolism. Furthermore, inorganic ion transport- and metabolism-associated genes, such as superoxide dismutase and copper transporters, were also up-regulated.

overall_design: Strain AT01 and wild-type strain were inoculated into YPD medium containing 1 mM CuSO4, and cultured at 25 °C for 5 d. Each sample was carried out with two repetitions.

first: Jie

last: Chen


title: A gene expression profile that predicts circulating tumor cell presence in breast cancer patients

city: Amsterdam

last: Roepman

address: Science Park 406

country: Netherlands

institute: Agendia

summary: Development of a primary tumor gene expression profile that can predict the presence of circulating tumor cells in the blood of breast cancer patients. The detection of circulating tumor cells (CTCs) in the peripheral blood and microarray gene expression profiling of the primary tumor are two promising new technologies able to provide valuable prognostic data for patients with breast cancer. In the current study, we aimed to develop a novel profile which provided independent prognostic data by building a signature predictive of CTC status rather than outcome.

overall_design: Seventy-two primary breast cancer tumor have been analyzed against a breast cancer reference pool.


title: Toh family 2

city: Singapore

first: Woei Chang

last: Liew

address: 1 Research Link, NUS

institute: Temasek Life Sciences Laboratory

summary:
Array comparative genomic hybridization was used to identify genomic differences between male and female zebrafish.
No universal sex-linked CNVR was identified.

overall_design: AB strain of zebrafish were used.The family consist of the parents and 2 male and female offspring each (total 6 samples). Dad's gDNA was used as reference sample for each family.

first: Woei

first: Richard

last: Bartfai

first: Zijie

last: Lim

first: Rajini

last: Sreenivasan

first: Kellee

last: Siegfried

first: Laszlo

last: Orban


title: Study of microRNA associated with metformin’s anti-tumor effect

status: Public on Apr 05 2012

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: The miRNAs expression was markedly altered with the treatment of metformin in vitro and in vivo and various miRNAs induced by metformin also may contribute to tumor growth in vitro and in vivo.

overall_design: Using a custom microarray platform, we analyzed the expression levels of 985 human miRNA probes in the cell lines in vitro and tumorous tissues in vivo that were treated with and without metformin.

first: Kiyohito

last: Kato

first: Tsutomu

last: Masaki


title: Streptomyces griseus transcriptome analysis in liquid culture with delta adpA, encoding a global transcriptional regulator involved in morphological differentiation and secondary metabolism

status: Public on Apr 04 2012

city: Bunkyo-ku, Tokyo

first: Yasuo

last: Ohnishi

department: Department of Biotechnology

institute: Graduate School of Agriculture and Life Science, The University of Tokyo

summary: To identify genes regulated by AdpA in liquid culture, transcriptome profiles between delta adpA strains with his-adpA and control delta adpA strains were analyzed.

overall_design: Analysis used control delta adpA strain RNA as control samples for comparison to the his-adpA expressing delta adpA mutant strain.

first: Akiyoshi

last: Higo


title: Streptomyces griseus transcriptome analysis in solid culture with delta adpA, encoding a global transcriptional regulator involved in morphological differentiation and secondary metabolism

summary: To identify genes regulated by AdpA in solid culture, transcriptome profiles between delta adpA strains with his-adpA and control delta adpA strains were analyzed.


title: MpeR regulation in Neisseria gonorrhoeae (F19) through an iron-responsive mechanism

city: Oklahoma City

first: Lydgia

last: Jackson

state: OK

address: 975 NE 10th Street

department: Microbiology and Immunology

institute: University of Oklahoma Health Sciences Center

summary: Previous studies have shown that the MpeR transcriptional regulator produced by Neisseria gonorrhoeae represses expression of mtrF, which encodes a putative inner membrane protein that works with the MtrC-MtrD-MtrE efflux pump to allow gonococci to resist high levels of multiple hydrophobic antimicrobials.  Regulation of mpeR has been reported to occur by an iron-dependent mechanism involving Fur (Ferric uptake regulator).  Collectively, these observations suggest the presence of an interconnected regulatory system in gonococci that modulates expression of drug efflux pump protein-encoding genes in an iron-responsive manner.  Herein, we describe this connection and report that levels of gonococcal resistance to a substrate of the mtrCDE-encoded efflux pump can be modulated by MpeR and the availability of free iron.  Using microarray analysis, we found that the mtrR gene, which encodes the direct transcriptional repressor (MtrR) of mtrCDE, is an MpeR-repressed determinant in the late-logarithmic phase of growth when free iron levels would be reduced due to bacterial consumption.  MpeR-mediated repression of mtrR appeared to be direct, as judged by DNA-binding analyses, and was enhanced by conditions of iron-limitation, which resulted in increased expression of the mtrCDE efflux pump operon.  Taken together, our results indicate that both genetic and physiologic parameters can influence expression of the mtr efflux system and that these can modulate levels of gonococcal susceptibility to efflux pump substrates.

overall_design: two strains, two growth phases, three replicates each.

first: Alexandra

middle: D

last: Mercante

last: Johnson

first: Virginia

last: Stringer

first: David

last: Dyer

first: William

last: Shafer


title: Rybp ChIP-chip in mouse ES cells

city: Yokohama

first: Takaho

middle: A.

last: Endo

address: 1-7-22 Suehiro, Tsurumi

department: IMS

institute: RIKEN

type: Genome binding/occupancy profiling by array

summary: Rybp binding in wild-type, Eed-KO, and Dnmt1-KO ES cells

overall_design: ChIP on chip analysis was carried out using the Mouse Promoter ChIP-on-chip Microarray Set (G4490A, Agilent-014716 and Agilent-014717, Palo Alto, Calif., USA). ESCs were subjected to ChIP assay using a Rybp antibody (Santa Cruz; H-115). Purified immunoprecipitated and input DNA was subjected to T7 RNA polymerase-based amplification as described previously (van Bakel et al., 2008). Labeling, hybridization and washing were carried out according to the Agilent mammalian ChIP-on-chip protocol (ver.9.0). Scanned images were quantified with Agilent Feature Extraction software under standard conditions.

first: Kaori

last: Hisada

first: Mitsuhiro

last: Endoh

first: Miguel

last: Vidal


title: Monitoring of functional gene responses to biostimulation from a TCE-contaminated site

status: Public on Apr 03 2012

city: AUBIERE

first: Peyret

last: Pierre

address: 24, avenue des landais

country: France

institute: CNRS - Blaise Pascal University

summary: A functional microarray targeting 24 genes involved in chlorinated solvent biodegradation pathways has been developed and used to monitor the gene expression in a contaminated site (site B) under ERD (enhanced reductive dechlorination) treatment. The microarray format provided by NimbleGen and used in this study is 12x135K. 4 µg of labelled antisense mRNA from 3 groundwater samples were hybridized on the microarray.

platform_organism: Shewanella Pseudomonas Methylosinus Nitrosomonas Mycobacterium Geobacter Thauera Desulfitobacterium Dehalobacter Sulfurospirillum Dehalococcoides

overall_design:
A 3-chip study was performed, each corresponding to hybridization with 4 µg of labelled antisense mRNA retrieved from a monitoring well of a contaminated site (site B). Each probe (760nt) on the microarray was synthesized in eight replicates, and a total of 5,707 random probes was used to determine the background noise.

Groundwater samples were collected from a contaminated site (site B) from three monitoring wells (P1, P2 and P3). P1: well located upstream to the contamination source. P2: well in the contamination source. P3 : well located downstream to the contamination source.

first: Eric

last: Dugat-Bony

first: Corinne

last: Biderre-Petit

first: Faouzi

last: Jaziri

first: Jérémie

last: Denonfoux

first: Delphine

last: Boucher

last: Peyretaillade

first: Pierre

last: Peyret


title: Gene expression in Longissimus lumborum in pig using the GenmascqChip (custom 15K Agilent microarray)

city: saint-gilles

first: marie

last: damon

address: domaine de la prise

institute: INRA

summary: Genetic variability of transcript abundance in pig skeletal muscle at slaughtering.

overall_design: The 325 pigs (females and barrows) used in gene expression analyses are part of a larger F2 population of 1,000 animals, setup within the framework of a QTL detection program. These animals were produced as a second generation intercross between two commercial sire lines (F016, Pietrain type line, and FH019, synthetic line from Hampshire, Duroc and Large-White founders, FRANCE-HYBRIDES, St Jean de Braye, France).

last: Cherel

first: Annie

last: Vincent

first: Marie

last: Damon


title: Identification of high temperature and daylength responsive genes in barley

city: Canberra

first: Megan

middle: Natalie

last: Hemming

state: ACT

address: GPO Box 1600

country: Australia

institute: CSIRO Division of Plant Industry

summary: High temperature influences plant development and can reduce crop yields. We used the Agilent Barley Gene Expression Microarray to identify high temperature responsive genes in cereals. In temperate cereals, such as wheat and barley, high temperature results in rapid progression through reproductive development in long-days but inhibits early stages of reproductive development in short-days. We examined the transcriptome of barley plants grown at two different temperatures, 15°C or 25°C, in either long or short-days. Under these conditions early reproductive development was accelerated by high temperature in long-days but inhibited by high temperature in short-days. To control for the effect of temperature on vegetative growth, plants were sampled at the same stage of vegetative development (leaf emergence) in all treatments. Transcriptome analysis identified genes that show changed transcript levels in response to daylength (long versus short-days), genes that show changed transcript levels in response to temperature (15°C versus 25°C), and small groups of genes that show changed transcript levels only in response to specific combinations of daylength and temperature. For example, genes that are upregulated only under long-days and high temperature: conditions in which early reproductive development proceeds rapidly. The temperature responsive genes identified here offer potential candidates for developmental regulators controlling the developmental response of cereal crops to high temperatures.

overall_design: Gene expression was assayed in vernalized barley plants grown at 15°C or 25°C in short or long-days until leaf 4 was visible on the main stem. Three replicate samples, consisting of 3 plants per sample, were assayed for each treatment.

middle: N

first: Sally

last: Walford

first: Sarah

last: Fieg

first: Elizabeth

middle: S

last: Dennis

first: Ben

last: Trevaskis


title: The IRF3 dependent response of macrophages to M. tuberculosis infection

status: Public on Apr 01 2012

city: San Francisco

first: Paolo

last: Manzanillo

institute: University of California at San Francisco

summary: Transcriptional profiling of macrophages (wild-type and IRF3-/- ) infected with various M.tuberculosis strains (wild-type and ESX-1 mutant)

overall_design: Comparison of the global gene expression of wild-type BMDM macrophages and IRF3-/- macrophages infected with either wild-type M.tuberculosis or ESX-1 mutant M.tuberculosis, with two biological replicates per group

first: P

first: J

last: Cox

first: M

last: Shiloh

first: D

last: Portnoy


title: Transcriptomic analysis of mature Desulfovibrio vulgaris biofilm

city: Bozeman

first: Matthew

last: Fields

state: MT

address: 366 EPS Bldg

department: Center for Biofilm Engineering

institute: Montana State University

summary: Background.  Desulfovibrio vulgaris Hildenborough is a sulfate-reducing bacterium (SRB) that is intensively studied in the context of metal corrosion and heavy-metal bioremediation, and SRB populations are commonly observed in pipe and subsurface environments as surface-associated populations.  In order to elucidate physiological changes associated with biofilm growth at both the transcript and protein level, transcriptomic and proteomic analyses were done on mature biofilm cells and compared to both batch and reactor planktonic populations. The biofilms were cultivated with lactate and sulfate in a continiouslly fed biofilm reactor, and compared to both batch and reactor planktonic populations.  The functional genomic analysis demonstrated that biofilm cells were different compared to planktonic cells, and the majority of altered abundances for genes and proteins were annotated as hypothetical (unknown function), energy conservation, amino acid metabolism, and signal transduction. Genes and proteins that showed similar trends in detected levels were particularly involved in energy conservation such as increases in an annotated ech hydrogenase, formate dehydrogenase, pyruvate:ferredoxin oxidoreductase, and rnf oxidoreductase, and the biofilm cells had elevated formate dehydrogenase activity.  Several other hydrogenases and formate dehydrogenases also showed an increased protein level, while decreased transcript and protein levels were observed for putative coo hydrogenases as well as a lactate permease and hyp hydrogenases for biofilm cells.  Genes annotated for amino acid synthesis and nitrogen utilization were also predominant changers within the biofilm state.  Ribosomal transcripts and proteins were notably decreased within the biofilm cells compared to exponential-phase cells but were not as low as levels observed in planktonic, stationary-phase cells.  Several putative, extracellular proteins (DVU1012, 1545) were also detected in the extracellular fraction from biofilm cells.  Even though both the planktonic and biofilm cells were oxidizing lactate and reducing sulfate, the biofilm cells were physiologically distinct compared to planktonic growth states due to altered abundances of genes/proteins involved in carbon/energy flow and extracellular structures.  In addition, average expression values for multiple rRNA transcripts and respiratory activity measurements indicated that biofilm cells were metabolically more similar to exponential-phase cells although biofilm cells are structured differently.  The characterization of physiological advantages and constraints of the biofilm growth state for sulfate-reducing bacteria will provide insight into bioremediation applications as well as microbially-induced metal corrosion.

sample_organism: Nitratidesulfovibrio vulgaris str. Hildenborough

overall_design: Biofilms grown in reactors were compared to reference samples of reactor, planktonic and batch, planktonic.  Each sample had a biological triplicate.

first: Melinda

middle: E

last: Clark

first: Zhili

last: He

first: Marcin

last: Joachimiak

first: Jay

last: Keasling

first: Jizhong

last: Zhou

first: Adam

last: Arkin

first: Aindrila

last: Mukhopadhyay


title: Monitoring of functional gene responses to ERD (enhanced reductive dechlorination) from four TCE-contaminated sites

first: Peyret

last: Pierre

summary: A functional microarray targeting 24 genes involved in chlorinated solvent biodegradation pathways has been developed and used to monitor the gene diversity present in four trichloroethylene (TCE) contaminated sites under ERD (enhanced reductive dechlorination) treatment. The microarray format provided by NimbleGen and used in this study is 12x135K. 2 µg of labelled gDNA from 30 groundwater samples were hybridized on the microarrays.

overall_design:
A 30-chip study was performed, each chip corresponding to hybridization with 2 µg of labelled gDNA retrieved from a monitoring well from one of the four contaminated sites. Each probe (760nt) on the microarray was synthesized in eight replicates, and a total of 5,707 random probes was used to determine the background noise.

Groundwater samples were collected from four contaminated sites (B, F, G and H), four monitoring wells per site (P1, P2, P3 and P4). P1: well located upstream to the contamination source. P2: well in the contamination source. P3 and P4: wells located downstream to the contamination source. For site B, the monitoring of ERD demonstration was performed through a total of 5 sampling campaigns: C1 (T=0), C2 (T=104 days), C3 (T=231 days), C4 (T=291 days) and C5 (T=378 days). For the three other sites (F, G and H), only one sampling campaign was performed after the treatment.

first: Eric

last: Dugat-Bony

first: Corinne

last: Biderre-Petit

first: Faouzi

last: Jaziri

first: Jérémie

last: Denonfoux

first: Delphine

last: Boucher

last: Peyretaillade

first: Pierre

last: Peyret


title: FREP3 is a determinant of resistance to schistosome infection in snails (part 2)

city: Albuquerque

first: Michelle

last: Forys

state: NM

address: MSC03 2020, 1 University of New Mexico

institute: University of New Mexico

summary: Transcriptional profile of BS-90 snails injected with a cocktail of four FREP3 specific 27-mer DSiRNA oligos and two hours later exposed to S. mansoni miricidia.  Compared to BS-90 snails injected with a cocktail of three GFP specific DSiRNA oligos and two hours later exposed to S. mansoni miricidia.  Experiments were done over the course of 49 days. Snails were collected (10each) at 2 and 4 dpe to S. mansoni for comparison.

overall_design: Each replicate is comprised of 1 individual snail from the specified treatment group.  Ten replicates of each treatment were analyzed on the Snail oligo array.

middle: A

first: Patrick

middle: C

last: Hanington


title: Genome-wide methylation in paired lung tumor/non-tumor samples using the HELP assay

city: Bronx

first: Miao

last: Shi

state: NY

address: 1301 Morris Park ave

institute: Albert einstein College of Medicine

summary:
In lung cancer, hypermethylation of specific gene promoters has been found during the progressive carcinogenesis. The identification of common methylation events will aid in the understanding of molecular events during neoplastic transformation and help develop biomarkers for cancer with high predictive and diagnostic value. To explore common methylation events on a genome-wide scale in lung cancer, we analyzed the methylation profiles of paired NSCLC tumor and far adjacent non-tumor samples using the HELP-microarray assay, which yields information on 1.2 million fragments throughout the genome. In this study, 24 pairs of tumor and adjacent non-tumor samples were analyzed using the HELP assay. At p = 5E-6, we identified 26,138 differentially methylated fragments (corresponding to 2 CpG sites each) in tumor versus non-tumor. The overall trend was consistent with genome-wide hypomethylation and locus specific hypermethylation (localized to CG-island containing promoters). We could identify both known and novel regions of the genome as well as specific gene-promoters that are hypermethylated in tumor versus non-tumor.
The HELPassay:  HpaII tiny fragment enrichment by ligation-mediated polymerase chain reaction [PCR] assay

overall_design: 24 pairs of NSCLC subjects, tumor and paired non-tumor samples from each subject were analyzed. Individual HpaII restriction digest profiles were compared to an internal MspI digest control, to yield differentially methylated fragments for every sample. Samples were compared intra-subject between tumor and adjacent non-tumor for these differential methylation profiles and the overall significant changes across 24 subjects were identified.

first: Nandita

last: Mullapudi

first: Masako

last: Suzuki

first: Melissa

last: Fazzari

first: John

last: Greally

first: Simon

last: Spivack


title: Gene expression profiling of Acute Myeloid Leukemia (AML) samples

city: Cantanhede

first: Jacek

middle: Dariusz

last: Marzec

address: Biocant Park

country: Portugal

institute: CoLAB AccelBio

summary: The aim was to analyze the expression of genes in cytogenetically distinct cases of AML.

overall_design: We used total RNA obtained from 6 AML samples, consisting of 3 cytogenetically distinct subtypes, to establish the expression levels of 27,868 individual human genes. Expression data from the ABI Human Genome Survey Microarray were filtered, quantile-normalized and subjected to significance analysis of microarrays. Established gene expression profiles were further compared with corresponding DNA methylation in analyzed AML patients.

first: Jun

last: Wang

first: Marwa

last: Saied

first: Bryan

last: Young

first: Silvana

last: Debernardi


title: Transcriptome Analysis Of Bovine Expanded Blastocysts Produced In Vivo Vs In Vitro Sof Opu

city: Quebec

first: Claude

last: Robert

state: Quebec

address: Pavillon Comtois

department: Animal Sciences

institute: Laval University

summary: Comparison of gene expression from expanded bovine blastocysts collected 7 days after fertilization and produced in vivo vs in vitro-SOF-OPU

overall_design: Two  kinds of 7 days post fertilization bovine embryos, in-vivo 7 days blastocysts vs. In vitro 7 days blastocysts, Biological replicates: 4 in-vitro, 4 in-vivo, protocol,extract and semen shared. Dye swap.

first: Dany

last: Plourde

first: Christian

last: Vigneault

first: Isabelle

last: Laflamme

last: Blondin


title: The Effect of copper stress on the gene expression, metabolism and bacteriophage activity of biocontrol Pseudomonas fluorescens strain Pf-5

city: Sydney

first: amy

middle: k

last: cain

state: NSW

address: Building E8A

department: CBMS

institute: Macquarie University

summary: Pf-5 is an important biocontrol strain of Pseudomonas fluorsecens, that improves plant growth, mainly via the production of secondary metabolites and growth/colonisation competition. Copper is a broad-spectrum antimicrobial that is effective against bacteria, fungi and even viruses in soluble forms such as copper sulfate and to a lesser extent in solid form, such as copper surfaces. Copper sulfate is commonly sprayed on food crops to increase yield and is becoming more routinely used due to the increasing problem of resistance to standard pesticides. Thus, an obvious question that remains is: what effect is this introduced copper having on these important biocontrol strains?    First, the phenotypic effects of copper on carbon utilisation and pH tolerance was tested using Biolog. Interestingly, the ability of Pf-5 to utilise amino acids as a sole carbon source was largely unaltered, but the presence of copper completely eliminated the utilisation of carbohydrates or fatty acids, and diminished the use of carboxylic acids and amines. This could be explained by copper-mediated disruptions of enzymes in metabolic pathways, such as the TCA cycle. The effect on gene expression was examined using reverse transcriptomics, which established molecular bases for the phenotypic results, and confirmed some known mechanisms for copper resistance, efflux and transporter proteins, and highlighted the delicate interplay with cellular control of iron, as well as uncovered the interesting relationship between integrated bacteriophage and copper as a molecular switch. The integrated phage, Prophage 01, was downregulated in the presence of copper and when this phage was activated with Mitomycin C, the copper appeared to stop the phage from going into lytic cycle and protected lysis of the cells. Prophage 01 is integrated between the housekeeping genes mutS and cinA and is conserved throughout many Pseudomonas. However, only Pf-5, out of the 10 strains tested seemed to be protected from cell lysis by copper, indicating that Prophage 01 in Pf-5 has unique features that interact with Cu.

overall_design: Two-condition experiment, where normal culture in rich medium versus cell treated with CuSO4. 3 biological replicates including 3 technical replicates for one of the biological replicates and 2 technical replicates for another of biological replicates. Swap-dye experiments were performed.

first: Amy

last: Cain

first: Karl

last: Hassan

first: Chee

middle: K

last: Lim

first: Joyce

last: Loper

first: Ian

middle: T

last: Paulsen


title: M. catarrhalis Gene Expression in the Chinchilla Nasopharynx

city: Dallas

first: Todd

middle: C.

last: Hoopman

state: TX

address: 5323 Harry Hines Blvd.

department: Microbiology

institute: University of Texas Southwestern Medical Center

summary: M. catarrhalis strain O35E.rpsl was inoculated into the nasopharynx of healthy, male adult chinchillas.  24 hours later the nasopharyngeal tissues were extracted and homogenized.  Total RNA was extracted from these tissue samples.  Subsequently, M. catarrhalis genome directed primers were utilized to synthesize cDNA from the total RNA sample.  As a control, M.catarrhalis strain O35E.rpsl was grown in BHI broth to a Klett density of 200 units and underwent RNA extraction per standard protocols.  The genome directed primers mentioned above were utilized to synthesize cDNA.  Both cDNA samples were subsequently labelled with either Cy3 or Cy5 and hybridized to a custom Microarrays, Inc. gene chip and scanned after 16 hours.  Differential gene expression was measured utilizing the broth grown cells as the baseline and the chinchilla isolated cells as the experimental variable.

overall_design: There are 5 individual sample results included in this series.  These represent the data from four individual biological replicates (i.e. 4 different sets of inoculated animals).  For each replicate the control samples are simultaneously grown broth samples.  Three dye swap experiments were performed.

first: Eric

middle: J

last: Hansen


title: Loss of DNA methylation affects recombination landscape in Arabidopsis

status: Public on Mar 12 2012

city: Beaucouzé

first: Etienne

last: Bucher

address: 42 rue Georges Morel

institute: IRHS

summary: During sexual reproduction half of the genetic material is deposited in gametes and a complete set of chromosomes is restored upon fertilisation. Reduction of the genetic information prior gametogenesis occurs in meiosis where crossovers (COs) between homologous chromosomes secure an exchange of their genetic information. COs are not evenly distributed along chromosomes and are suppressed in chromosomal regions encompassing compact, hypermethylated centromeric and pericentromeric DNA. Therefore, it has been postulated that DNA hypermethylation is inhibitory to COs. Here by analysing meiotic recombination in mutant plants with hypomethylated DNA we observed unexpected and counterintuitive effects of the DNA methylation losses on COs distribution, further promoting recombination in the naturally hypomethylated euchromatic chromosome arms, while inhibiting it in heterochromatic regions encompassing centromeric and pericentromeric hypermethylated DNA. Importantly, the total number of COs was not affected, implying that the loss of DNA methylation only led to a global redistribution of COs along chromosomes. To determine by which mechanisms altered levels of DNA methylation influenced recombination, namely whether this occurred directly in cis or indirectly in trans by changing expression of genes encoding recombination components, we analysed COs distribution in WT lines with randomly scattered and well mapped hypomethylated chromosomal segments. Results of these experiments, supported by expression profiling data, suggest that DNA methylation affects meiotic recombination in cis. As DNA methylation is subjected to significant variation even within a single species, our results implicate that it could influence evolution of plant genomes through the control of meiotic recombination.

overall_design: 2 samples: Col, epiRIL12, with 3 replicates each

first: Marie

last: Mirouze

first: Michal

last: Lieberman-Lazarovich

first: Riccardo

last: Aversano

first: Joel

last: Nicolet

first: Jon

last: Reinders

first: Jerzy

last: Paszkowski


title: Cellular and molecular characterization of the impact of laboratory setup on bovine in vitro embryo production

first: Claude

last: Robert

summary: Comparison of gene expression from expanded bovine blastocysts collected 7 days after fertilization and produced in vitro in two different laboratories using the same protocol.

overall_design: Two different laboratories with same condition, site A blastocysts vs. Site B blastocysts, Biological replicates: 3 site A, 3 site B, protocol,extract and semen shared. Dye swap.

first: Dany

last: Plourde

first: Christian

last: Vigneault

last: Laflamme

first: Patrick


title: Combining transcriptomics with functional phylogenomics elucidates the ecophysiology of sulfatases in marine bacteria

city: Marburg (Lahn)

first: Carl-Eric

last: Wegner

address: Karl von Frisch Straße 10

institute: Max Planck Institute for Terrestrial Microbiology

summary: We present a study combining gene expression analyses and bioinformatic assessment. 1120 sequences annotated as sulfatase encoding from eight Rhodopirellula strains were clustered into 173 groups of orthologous and paralogous genes. A selection of 709 sulfatase gene strains were aligned to 66 sulfatase genes of known function to check for their respective substrate specificity. Thereby, 22 major phylogenetic clusters were observed with just five being mixed clusters between Rhodopirellula and reference sequences. This indicates a huge diversity on the substrate recognition level, unexpected from conventional annotations in public databases. Exemplarily, Rhodopirellula baltica SH1T was grown on different sulfated polysaccharides. Subsequent gene expression analyses using whole genome microarrays revealed distinct sulfatase expression profiles based on substrates tested. Expression profiles strongly point towards a functional link between sulfated polysaccharides and sulfatases. Moreover, further potential functions can be deduced from the expression profiles. In silico assessment backed up in vivo findings and raised the question, whether related strains and species are even more adapted to utilizing sulfated polysaccharides present in marine environments.

overall_design: Dual channel microarrays have been used for comparing the gene expression of R. baltica SH1T under reference condition (grown on glucose) and grown on sulfated polysaccharides as substrates of interest. Substrates tested have been: Chondroitin sulfate, lambda carrageenan and fucoidan. Control: 3 Biological replicates, Substrates tested: 2-3 Biological replicates, 2-3 replicates per array

first: Tim

last: Richter-Heitmann

first: Anna

last: Klindworth

first: Christine

last: Klockow

first: Michael

last: Richter

first: Tilman

last: Achstetter

first: Jens

last: Harder

first: Frank-Oliver

last: Glöckner


title: Gene expression analysis of chickens (Gallus gallus) infected with recombinant influenza viruses

status: Public on Mar 31 2012

city: Tsukuba

first: Yuko

last: Uchida

institute: National Institute of Animal Health

summary: H5N1 subtype highly pathogenic avian influenza virus has been spreading to Asia, Eurasia and African coutries. An original or six of recombinant H5N1 subtype influenza viruses with varying survivability were infected to chickens for elucidating genes correlated with pathogenicity.

overall_design: Two chickens were infected with each 10^6EID50/ head virus intranasally, and their lung was collected from infected chicken at 24 hours after infection.

first: Takehiko

last: Saito

last: Oka


title: Effect of VEGF on expressions of C2H2 zinc finger proteins in human umbilical vein endothelial cells.

status: Public on Mar 25 2012

city: Toon-shi

first: Hidetaka

last: Ohnuki

state: Ehime

address: Shitsukawa

department: Department of Biochemistry and Molecular Genetics

institute: Ehime University

summary: Angiogenic homeostasis is maintained by a balance between vascular endothelial growth factor (VEGF) and Notch signalling in endothelial cells (ECs). We screened for molecules that might mediate the coupling of VEGF signal transduction with down-regulation of Notch signalling, and identified B-cell chronic lymphocytic leukemia/lymphoma6-associated zinc finger protein (BAZF). BAZF was induced by VEGF-A in ECs to bind to the Notch signalling factor CBF1, and to promote the degradation of CBF1 through polyubiquitination in a CBF1-cullin3 (CUL3) E3 ligase complex. BAZF disruption in vivo decreased endothelial tip cell number and filopodia protrusion, and markedly abrogated vascular plexus formation in the mouse retina, overlapping the retinal phenotype seen in response to Notch activation. Further, impaired angiogenesis and capillary remodeling were observed in skin-wounded BAZF-/- mice. We therefore propose that BAZF supports angiogenic sprouting via BAZF-CUL3-based polyubiquitination-dependent degradation of CBF1 to down-regulate Notch signalling.

overall_design: Human umbilical vein endothelial cells were stimulated with recombinant human VEGF165 for 0, 1, 2, 6, 12, 24 and 48 hours.

first: Hirofumi

last: Inoue

first: Nobuaki

last: Takemori

first: Hironao

last: Nakayama

first: Tomohisa

last: Sakaue

first: Shinji

last: Fukuda

first: Daisuke

last: Miwa

first: Eiji

last: Nishiwaki

first: Masahiko

last: Hatano

first: Takeshi

last: Tokuhisa

first: Yaeta

last: Endo

first: Masato

last: Nose

first: Shigeki

last: Higashiyama


title: Chip-chip from Mouse E11.5 distal limb tissue cells for Gabpa, Ets1, Elf1, Etv4, Etv5 antibody

status: Public on Feb 01 2012

city: Edinburgh

first: Graeme

middle: Richard

last: Grimes

address: Western General Hospital, Crewe Road

department: Human Genetics Unit

institute: University of Edinburgh, The Institute of Genetics and Cancer

summary:
Two different groups of Ets transcription factors differentially act directly at the ZRS to define the spatial expression of Shh in the limb.
Chromatin immunoprecipitation (ChIP) of Gabpa, Ets1, Etv4, Etv5 and Elf1 and by ChIP-on-chip analysis demonstrated that with the exception of Elf1 all bind  directly to the Shh limb enhancer, the ZRS.

overall_design: Array design includes 2 biological replicates for Gabpa and Elf1, and two biological replicates and one dye swap replicate for Ets1, Etv4 and Etv5 samples.

first: Iain

last: Williamson

middle: R

first: Robert

last: Hill


title: Expression analysis of murine bone marrow (BMDM) derived macrophages stimulated with C1q

status: Public on Mar 01 2012

city: South Bend

first: Manuel

last: Galvan

state: IN

address: 1234 Notre Dame Ave

institute: Indiana University School of Medicine-South Bend

summary:
Investigation of whole genome gene expression level changes in BMDM adhered for 4 or 18hrs  to Lab Tek Chamber slides pre-coated with 4ug/ml of human serum albumin (HSA) (control protein) or purified human C1q and treated with lipopolysaccharide (LPS: 20ng/ml) Mycobacterium avium 101 (M avium) or apoptotic Jurkat T cells.
BMDM were obtained from C57Bl/6 and generated as previously described in Bohlson, SS, Strasser, JA, Bower JJ, Schorey J S 2001 Role of complement in Mycobacterium avium pathogenesis: in vivo and in vitro analyses of the host response to infection in the absence of complement component C3 Infec Immun 69: 7729-7735.
Mybacterium avium 101 was obtained from Dr Jeff Schorey (University of Notre Dame).
The human Jurkat T cell line was obtained from ATCC (Manassas, VA) and induced to undergo apoptosis with dexamethasone as described in Lillis, AP, Greenlee, M C, Mikhailenko I, Pizzo, S V, Tenner, A J, Strickland, D K, Bohlson, S S 2008 Murine Low-Density Lipoprotein Receptor-Related Protein 1 (LRP) Is Required for Phagocytosis of Targets Bearing LRP Ligands but Is Not Required for C1q-triggered Enhancement of Phagocytosis J Immunol 181: 364: 373.

overall_design:
A six chip study using total RNA from 5 separate cultures of BMDM adhered to HSA  for 4 hrs, 5 separate cultures of BMDM adhered to C1q for 4 hrs, 5 separate cultures of BMDM adhered to HSA for 4 hrs and infected with M avium at a 1:500 ratio of BMDM to M avium, 5 separate cultures of BMDM adhered to C1q for 4hrs and infected with M avium at a 1:500 ratio ofBMDM to M avium, 5 separate cultures of BMDM adhered to HSA for 4 hrs and infected with M avium at a 1:1000 ratio of BMDM to M avium, 5 separate cultures of BMDM adhered to HSA  for 4 hrs and treated with 20ng/ml LPS, 5 separate cultures of BMDM adhered to C1q for 4 hrs and treated with 20ng/ml LPS, 5 separate cultures of BMDM adhered to HSA for 4 hrs and treated with 20ng/ml LPS and co-cultured with apoptotic Jurkat cells at a 1:3 ratio of BMDM to apoptotic cells, 5 separate cultures of BMDM adhered to C1q for 4 hrs and treated with 20ng/ml LPS and co-cultured with apoptotic Jurkat cells at a 1:3 ratio of BMDM to apoptotic cells, 5 separate cultures of BMDM adhered to HSA  for 18 hrs, 5 separate cultures of BMDM adhered to C1q for 18 hrs, 5 separate cultures of BMDM adhered to HSA for 18 hrs and infected with M avium at a 1:500 ratio of BMDM to M avium, 5 separate cultures of BMDM adhered to C1q for 18hrs and infected with M avium at a 1:500 ratio of BMDM to M avium, 5 separate cultures of BMDM adhered to HSA for 18 hrs and infected with M avium at a 1:1000 ratio of BMDM to M avium.  The chip utilized for these studies is a mouse whole-genome 12-plex expression microarray design by NimbleGen designed from the MM9 genome Candidate probe sequences were verified to have no cross-hybridization to human (HG19) or Mycobacterium avium (NC_008595) targets
Note: Study sample BMDM_HSA & M avium (1:500)_18hr_rep2 was not included in this submission due to quality control concerns.

first: Suzanne

last: Bohlson

first: Erliang

last: Zeng

first: John

last: Tan


title: A Comparison between In Vivo and Whole Embryo Culture using Transcriptomics:  Developmental Changes, Model Differences and Retinoic Acid Response

city: Bilthoven

first: Joshua

middle: F

last: Robinson

address: Leeuwenhoeklaan 9

department: Laboratory for Health Protection Research

institute: National Institute for Public Health and the Environment (RIVM)

summary:
The whole embryo culture (WEC) model serves as a potential replacement for classical in vivo developmental toxicity testing.  In this alternative test, cultured rat embryos are exposed during neurulation and early organogenesis and evaluated for morphological adverse outcomes.  Toxicogenomic-based approaches may improve the predictive ability of WEC by providing molecular-based markers associated with chemical exposure which can be compared across multiple parameters (e.g. time, dose, model).  Additionally, comparisons between in vitro and in vivo models may identify objective, relevant molecular responses linked with developmental toxicity endpoints in vivo.  In this study, using a transcriptomic approach, we compared all-trans-retinoic acid (RA)-exposed and non-exposed Wistar rat embryos derived using WEC (RA, 0.5µg/mL) or in vivo (RA, 50mg/kg, oral gavage) to identify overlapping and non-overlapping effects of RA on RNA expression in parallel with morphological changes. Across six time points (GD 10 + 2-48h), we observed strong similarities in RA-response at the gene (directionality, significance) and functional (e.g. embryonic development, cell differentiation) level which associated with RA-induced adverse morphological effects, including growth reduction as well as alterations of neural tube, limb, branchial, and mandible development.  Differences between models in the timing of RA-induced impacts on the expression of select genes related to embryonic development and RA-metabolism associated with specific differential morphological outcomes.  This study supports the use of WEC to examine compound-induced molecular responses relative to in vivo, and furthermore, assists in defining the applicability domain of the WEC in determining complementary windows of sensitivity for developmental toxicological investigations.
Cultured embryos mimic the morphological developmental progression of embryos (in vivo) undergoing neurulation and early organogenesis.  Using available genomics technologies, comparative molecular-based assessments between cultured embryos and in vivo models may further clarify commonalities and dissimilarities which contribute to differences between systems.  Therefore, in this study, using a transcriptomic approach, we compared cultured whole rat embryos and embryos in vivo at comparable time points in development (gestational day (GD) 10 + 2-48h, GD 0 = copulatory plug) to assess for commonalities and differences in gene expression in relation to morphology. We reveal strong parallels in time-dependent expression of genes in terms of magnitude, directionality and functionality between whole embryo culture (WEC) and in vivo (rat).  Genes changing in expression over time resemble previously hypothesized mechanisms underlying early development in mammalian systems.  Furthermore, at the gene and functional level, we identify genes which differ in expression between models, including genes related to development, oxygen transport and metabolism.  In summary, our results support the use of WEC for toxicological studies aimed at representing in vivo development during this time-window at the molecular level.  Additionally, we indicate genes which differ in expression between models, providing possible insights for improvement of culture conditions.

overall_design: 204 arrays, 8 unique embryos for each of the 24 experimental groups + 8 to 10 technical replicates

first: Aldert

middle: H

last: Piersma

first: Aart

last: Verhoef

first: Jeroen

middle: L

last: Pennings


title: Toh family 1

status: Public on Apr 17 2012

city: Singapore

first: Woei Chang

last: Liew

address: 1 Research Link, NUS

institute: Temasek Life Sciences Laboratory

summary:
Array comparative genomic hybridization was used to identify genomic differences between male and female zebrafish.
No universal sex-linked CNVR was identified.

overall_design: AB strain of zebrafish were used.The family consist of the parents and 2 male and female offspring each (total 6 samples). Dad's gDNA was used as reference sample for each family.

first: Woei

first: Richard

last: Bartfai

first: Zijie

last: Lim

first: Rajini

last: Sreenivasan

first: Kellee

last: Siegfried

first: Laszlo

last: Orban


title: Defining the Phosphodiesterase Superfamily Members in Rat Brain Microvessels

city: Little Rock

first: Li

last: Cui

state: AR

department: Neurology

institute: UAMS

summary: A filtration method followed by microarray analyses allows PDE components to be identified in brain microvessels, and confirmed that PDE4D and PDE5A are the primary forms expressed in rat brain microvessels.

overall_design: Adult male F344 rats were sacrificed and blocks of the cerebral cortex and infratentorial areas were dissected. Microvessels were isolated using a filtration method, and total RNA was extracted. Two microarrays using four sample RNAs (microvessels from the cerebral cortex vs. microvessels from the infratentorial block) were included in the present study. Microarrays demonstrated that there were 16 PDE transcripts in the PDE superfamily, exhibiting quantifiable density in the microvessels.

first: Zhen

last: He


title: MiRNA profiling during infection with H1N1 influenza A virus (A/Mexico/InDRE4487/H1N1/2009)

status: Public on Apr 10 2012

city: Vancouver

first: Victoria

last: Svinti

address: 2350 Health Sciences Mall

institute: University of British Columbia

summary: MicroRNAs (miRNAs) repress the expression levels of genes by binding to mRNA transcripts, acting as master regulators of cellular processes. Differential expression of miRNAs has been linked to viral-associated diseases involving members of the hepacivirus, herpesvirus, and retrovirus families. In contrast, limited biological and molecular information has been reported on the potential role of cellular miRNAs in the lifecycle of influenza A viruses (infA). In this study, we hypothesize that elucidating the miRNA expression signatures induced by low-pathogenic swine-origin influenza A virus (S-OIV) pandemic H1N1 (2009) and highly pathogenic avian-origin (A-OIV) H7N7 (2003) infections could reveal temporal and strain-specific miRNA fingerprints during the viral lifecycle, shedding important insights into the potential role of cellular miRNAs in host-infA interactions. Using a microfluidic microarray platform, we profiled cellular miRNA expression in human A549 cells infected with S- and A-OIVs at multiple time-points during the viral lifecycle, including global gene expression profiling during S-OIV infection. Using target prediction and pathway enrichment analyses, we identified the key cellular pathways associated with the differentially expressed miRNAs and predicted mRNA targets during infA infection, including immune system, cell proliferation, apoptosis, cell cycle, and DNA replication and repair. By identifying the specific and dynamic molecular phenotypic changes (microRNAome) triggered by S- and A-OIV infection in human cells, we provide experimental evidence demonstrating a series of temporal- and strain-specific host molecular responses involving different combinatorial contributions of multiple cellular miRNAs. Our results also identify novel potential exosomal miRNA biomarkers associated with pandemic S-OIV and deadly A-OIV-host infection.

overall_design:
Control (mock-infected) samples: 12, Infected samples: 6, for each time-point (0, 4, 8, 24, 48 and 72 hours post infection). Seven replicates for each miRNA were found on the microarray chips, for which the median has been retained. The experiment was performed in six replicates.
The H1N1 RNA in the mock-infected samples in chip 1 and the hour 4 samples in chip 2 were found to be degraded during the mRNA profiling; therefore, they were excluded from the statistical analysis.

first: Emma-Kate

last: Loveday

first: Sandra

last: Diederich

last: Pasick

first: François

last: Jean


title: Immunopurification results of cytoskeletal motor proteins in S. cerevisiae

status: Public on Jan 27 2012

city: Stanford

first: Jason

last: Casolari

state: CA

address: 279 Campus Drive

department: Dept. of Biochemistry

institute: Stanford University

summary: The accompanying dataset is the result of a systematic study to identify the RNA cargoes associated with the cytoskeletal motor proteins of Saccharomyces cerevisiae. We immunopurified, via the use of integrated, C-terminal GFP and 9Myc tags, the five actomyosin motors, Myo1, Myo2, Myo3, Myo4, and Myo5; the kinesin-like proteins Kar3, Kip1, Kip2, Kip3, and Smy1; and the dynein, Dyn1, from S. cerevisiae.  Cells were either treated with formaldehyde or with the small molecule latrunculin B.  We used formaldehyde crosslinking to stabilize associations between motors proteins and interacting RNAs before IP.   Yeast cells growing exponentially in rich medium were treated with formaldehyde, lysed and sonicated, then incubated with magnetic beads coupled to monoclonal antibodies against either 9Myc or GFP  to isolate the tagged motor proteins along with any associated RNAs.  After IP, the formaldehyde crosslinks were reversed and the enriched RNAs and RNAs purified from the corresponding total lysate were amplified and labeled respectively with Cy5 and Cy3, then jointly hybridized to custom-made, S. cerevisiae oligonucleotide microarrays (Hogan et al., PLoS Biology, 2008).  Alternatively, the addition of a low concentration of latrunculin B (2 ug/ml) to live cells to partially solubilize the actin cytoskeleton allowed for successful IP of the motor proteins and associated mRNAs without the need for a chemical crosslinker.  In both the case of latrunculin B and formaldehyde treatment, we also performed IPs in which the untagged parent yeast strains were processed for IP and microarray analysis in a manner identical to that of the tagged strains (labeled as mock).

overall_design: transcription profiling


title: BrpA-deficiency on the transcriptional profile in Streptococcus mutans during early exponential phase

status: Public on Jan 26 2012

city: New Orleans

first: Zezhang

middle: Tom

last: Wen

state: LA

address: 1100 Florida Avenue

department: Oral and Craniofacial Biology

institute: LSU Health Sciences Center

summary:
In consideration of the fact that BrpA expression is at its maximum during early-exponential phase as shown by Northern blotting and reporter gene fusion assays, we carried out a DNA microarray analysis using total RNA from early exponential phase cultures (OD600nm=0.3).  It was found that 92 genes were up-regulated and 90 down-regulated in TW14D by a factor of at least 1.5-fold (p ≤ 0.001).  At a level of P<0.01, 176 additional genes were found to be differentially expressed in TW14D, with 77 up- and 90 down-regulated.  Based on the description and putative functions of the genes identified at the significance level of P<0.001, BrpA-deficiency affects almost every aspect of the cellular physiology as well as virulence properties, including amino acid biosynthesis, carbohydrates and energy metabolism, nucleic acids and DNA metabolism, transcriptional regulation, ABC transporters, molecular chaperones and other cellular processes, and hypothetical and conserved hypothetical proteins.  The breadth of impact of BrpA-deficiency on the transcriptional profile of the deficient mutant is similar to what was observed previously with mid-exponential phase cells.  However, comparison of the two transcriptional profiles revealed that only a small number of genes were consistently up- or down-regulated in both early- and mid-exponential phase cultures, which include recA (for recombinant protein RecA), gtfD (for glucosyltransferase D), wapA (for surface-associated protein WapA), groEL (for molecular chaperone GroEL) and sod (for Mn-dependent superoxide dismutase SOD).  In addition, the magnitude of alterations in gene expression was also more dramatic in cells of the early-exponential phase, when compared to that in the mid-exponential phase cultures.
Of the genes altered as a result of BrpA-deficiency in early-exponential phase cultures, several were found to encode proteins with potential roles in peptidoglycan biosynthesis.  Among them are SMU.246 for a phospho-MurNAc-pentapeptide-transferase (RgpG), SMU.549 for an undecaprenyl-PP-MurNAc-pentapeptide-UDP-GlcNAc transferase (MurG), SMU.599 for a D-alanine-D-alanine ligase (DdlA), and SMU.1677 for a UDP-MurNAc-tripeptide synthetase (MurE). Besides, several genes encoding components of the Sec translocase were also found altered in TW14D.  These included secA, secE and secY encoding the ATP-dependent motor of the translocation machinery, SecA, and the translocon pore components, SecE and SecY, respectively. Both secA and secE were down-regulated by more than 2-fold, while secY was up-regulated by more than 2-fold.

sample_organism:
Streptococcus mutans
Streptococcus mutans UA159

overall_design: Transcriptional profiling of S. mutans was done using a spotted array (version II) obtained from TIGR (JCVI). The wild-type UA159 and its BrpA-deficient mutant (TW14D) were grown in plain BHI broth until early phase OD=0.3. Four replicates each. A common reference (mid-exponential phase wild-type UA159) was used.

first: Jacqueline

last: Abranches

first: Robert

last: Burne


title: Rap1 Competition-ChIP Galactose Induction Time Course (High Resolution)

status: Public on Mar 05 2012

city: Chapel Hill

middle: D

last: Lieb

state: NC

address: 408 Fordham Hal, CB#3280

department: Biology

institute: UNC-Chapel Hill

summary: A strain harboring two copies of RAP1 is used for a competition-ChIP experiment. One copy of RAP1 is expressed from the endogenous RAP1 promoter and a c-terminal 3X FLAG epitiope tag and the other is expressed from a weakened Galactose inducible promoter and a c-terminal 9X MYC tag. Following induction by 2% galactose Rap1-Myc and Rap1-Flag levels are determined genome wide using ChIP-chip.

overall_design: Time Course ChIP-ChIP experiment, Rap1-Flag IP and Rap1-Myc IP. 10 Time Points (0,10,20,30,40,50,60,90,120,150 Minutes) 2 Biological Replicates. Total Rap1 Occupancy at times 0 and 60 minutes in the time course; 2 Biological Replicates. mRNA expression levels at times 0 and 60 minutes in the time course; 2 biological Replicates.

first: Colin

last: Lickwar


title: Human and murine serum reactivity to specific histone posttranslational modifications in neutrophil extracellular traps

first: Chih Long

last: Liu

address: 269 Campus Drive

department: Medicine - Imm. & Rheum

summary:
Introduction:  Autoreactivity to histones is a pervasive feature of several human autoimmune disorders including systemic lupus erythematosus (SLE). Specific post-translational modifications (PTMs) of histones within neutrophil extracellular traps (NETs) may potentially drive the process by which tolerance to these chromatin-associated proteins is broken.  We hypothesized that NETs and their unique histone PTMs might be capable of inducing autoantibodies that target histones.
Methods:  We developed a novel and efficient method for the in vitro production, visualization, and broad profiling of histone-PTMs of human and murine NETs.  We also immunized Balb/c mice with murine NETs and profiled their sera on autoantigen and histone peptide microarrays for evidence of autoantibody production to their immunogen.
Results:  We confirmed specificity toward acetyl-modified histone H2B as well as to other histone PTMs in sera from patients with SLE known to have autoreactivity against histones.  We observed enrichment for distinctive histone marks of transcriptionally silent DNA during NETosis triggered by diverse stimuli.  However, NETs derived from human and murine sources did not harbor many of the PTMs toward which autoreactivity was observed in patients with SLE or in MRL/lpr mice. Further, while murine NETs were weak autoantigens in vivo, there was only partial overlap in the IgG and IgM autoantibody profiles induced by vaccination of mice with NETs and those seen in patients with SLE.
Conclusions:  Isolated in vivo exposure to NETs is insufficient to break tolerance and may involve additional factors that have yet to be identified.

sample_organism:
Homo sapiens
Mus musculus

overall_design: Serum samples from 20 systemic lupus erythematosis patients were run on the Human Epigenome Microarray Platform V1.0 (HEMP; a single-color platform), in order to profile their autoantibodies against a library of post-translationally modified histone peptides.  These 20 samples were randomly selected from a larger cohort previously profiled (data not shown) on the Utz Lab Whole Protein Autoantigen Array V2.0 (a single-color platform), where 14 were histone-reactive and 6 were histone-nonreactive.  Control sera from 9 healthy adults and a positive control comprising a mixture of autoimmune sera with defined reactivities, were also run on HEMP V1.0.  Together, these samples comprise the data appearing in Figures 1 and S1 (IgG and IgM isotype reactivity profiles, respectively), identifying IgG reactivity to 9 peptides that significantly distinguish histone-reactive from -nonreactive sera among 96 peptides profiled.    For data appearing in Figure 5, serum samples from a total of 6 Balb/c mice, consisting of two treatment groups, NETs (Neutrophil Extracellular Traps) and NETs + CRAMP (cathelicidin-related antimicrobial peptide) were collected monthly over a 3-month period, along with a zero time point.  These samples were compared with a positive control consisting of serum collected from a MLR/lpr mice exhibiting lupus-like symptoms, and a negative control with no serum.  The 0, 1 and 2 month time points were profiled on the Utz Lab Whole Protein Autoantigen Array V2.0 and are shown in Figure 5A-B, while the 1 and 3 month time points were profiled on HEMP V1.0 arrays and shown in Figure 5E.    All samples were run once with no replicates.

first: ChihLong

first: Stephanie

last: Tangsombatvisit

first: Jacob

last: Rosenberg

first: Emily

last: Gillespie

first: Ash

last: Alizadeh

first: Or

middle: P

last: Gozani

first: Paul

last: Utz


title: Murine serum reactivity to common autoantigens in response to immunization with neutrophil extracellular traps

platform_organism:
Escherichia coli
Gallus gallus
Homo sapiens
Bos taurus
Oryctolagus cuniculus
Mus musculus