title: Expression profile of maize´s stalk challenged with the corn borer Sesamia nonagrioides

city: Pontevedra

first: Victor

middle: M

last: Rodriguez

address: Apartado 28

department: Plant Genetics and Breeding

institute: Mision Biologica de Galicia (CSIC)

summary:
Stalk borers are major pests for some of the most important crops in the world, such as maize or rice. Plant defense mechanisms against these herbivores have been poorly investigated. The maize´s stalk responds to insect feeding activating defense genes including hormone biosynthetic-related or proteinase inhibitor transcripts. The most outstanding conclusion is that cells in the maize´s stalk undergo cell wall fortification after corn borer tunneling.
We performed a gene expression profiling to identify those genes differentially expressed in maize after infestation with the corn borer S. nonagrioides.

overall_design: Four genetically unrelated maize inbred lines (EP39, EP42, CM151 and PB130) were infested at VT (tasseling) developmental stage with a mass of approximately 40 eggs of S. nonagrioides laid on the sheath of the main ear. Another four biological replicates per genotype were used as control. Samples for RNA extraction were harvested fifteen days after infestation.

first: Rogelio

last: Santiago

first: Rosa

last: Malvar

first: Ana

last: Butron


title: Exploration of the sulfur metabolism in the yeast Kluyveromyces lactis

status: Public on Oct 01 2011

city: Thiverval-Grignon

first: Jean-Marie

last: Beckerich

address: Campus Agroparistech

country: France

institute: INRA

summary:
A comparison between high and low sulfur source supplies, i.e., sulfate, methionine or cystine, was carried out in order to identify key steps in the biosynthetic and catabolic pathways of the sulfur amino acids.
the transcriptomic study was carried out using Agilent 8X15k slides with a custom oligoset designed by V. Loux using the Kluyveromyces lactisORFeome extracted from genolevures database

overall_design: Two conditions experiment, high versus low sulfur conditions (sulfate, cystine or methionine with a ratio of 1 to 1000). Three biological experiments with a dye swap for each for methionine, cystine and sulfate.

first: Agnès

last: Hébert

first: Marie-Pierre

last: Forquin

first: Aurélie

last: Roux

first: Julie

last: Aubert

first: Christophe

last: Junot

first: Valentin

last: Loux

first: Jean-François

last: Heilier

first: Pascal

last: Bonnarme

first: Sophie

last: Landaud


title: Transcriptome analysis of the zebrafish embryonic host response to Edwardsiella tarda infection [experiment B]

city: Amsterdam

first: Oliver

last: Stockhammer

state: NH

address: Meibergdreef 15

department: Medical Microbiology

country: Netherlands

institute: AMC

summary: Transcriptional profiling of the zebrafish embryonic host response to infection by injection of 200 CFUs of Edwardsiella tarda (strain FL6-60)

overall_design: All infection experiments were performed using mixed egg clutches of Albino strain zebrafish. Embryos were staged at 28 hours post fertilization (hpf) by morphological criteria and approximately 200 cfu of mCherry expressing E. tarda bacteria were injected into the caudal vein close to the urogenital opening. As a control an equal volume of PBS was likewise injected. Single embryos of the infected and control group were collected 8 hours post infection (hpi).

first: J

middle: J

last: van Soest

first: O

middle: W

first: G

middle: V

last: Bloemberg

first: H

middle: P

last: Spaink

first: A

middle: H

last: Meijer


title: A broad phenotypic screen identifies novel dominant phenotypes in Huntington’s disease CAG knock-in mice

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum München GmbH

summary: Huntington’s disease (HD) is a dominantly inherited neurodegenerative disorder characterized by abnormal voluntary and involuntary movements, cognitive impairment and psychiatric disturbances. In order to identify phenotypic changes in the mouse that are most likely to be relevant to events triggered by the CAG repeat expansion in HD patients, we are interested in the earliest events that are triggered by expression of a single allele’s worth of full-length mutant huntingtin in the mouse, whether at the molecular, cellular or whole animal level. To this end, we have undertaken a broad-based, unbiased phenotypic screen in heterozygous HdhQ111/+ C57BL/6J mice.

overall_design: For expression profiling analysis, four male mice at the age of 18 weeks were analysed versus a pool of four male wildtype mice (reference) at the same age. For each single mouse, two chip hybridizations, including a dye-swap experiment, were performed per tissue. Using our genome-wide microarray platform, we performed transcriptome analysis of liver and brain.


title: Gene expression profiling of human atherosclerotic plaque: 101 peripheral plaques

city: Rahway

first: Oscar

last: Puig

state: NJ

address: 126 East Lincoln Ave

department: Molecular Profiling Research Informatics

country: USA

institute: Merck Research Laboratories

summary:
In order to identify potential new biomarkers of atherosclerotic plaque composition we performed a large scale analysis of gene expression patterns in human atherosclerotic lesions.  Whole genome expression analysis of 101 peripheral plaques identified a robust gene signature (1514 genes) dominated by inflammatory processes, and cholesterol metabolism and storage genes.  Specific pathways enriched in this signature included activation of the Toll-like receptor signaling pathway, T-cell activation, cholesterol efflux, oxidative stress response, inflammatory cytokine production, vasoconstriction and lysosomal activity.  Analysis of gene expression in plaque micro-dissected material revealed that the signature is strongly up-regulated in macrophage-rich regions and down-regulated in regions with high smooth muscle cell content.
A smaller qPCR biomarker panel and inflammatory composite score (ICS) were developed to facilitate clinical translation of discoveries from gene expression profiling.  We found that ICS correlates with histological features related to plaque vulnerability.  In addition, ICS is able to separate groups of plaques obtained from symptomatic and asymptomatic patients undergoing carotid endarerectomy.  In summary, we identified a robust mRNA biomarker panel associated with histo-pathological as well as clinical hallmarks of vulnerable atherosclerotic plaque.  This panel may be used as a diagnostic and prognostic tool in clinical setting to evaluate novel anti-atherosclerotic therapies.

overall_design: Total RNA from peripheral plaque (n=101) profiled in the Merck/Agilent 44k v1.1 against a reference pool of total RNA from 7 carotid plaques.

first: Vladimir

last: Reiser


title: Gene expression profiling of human atherosclerotic plaque: Laser capture microscopy of smooth muscle cells and macrophages

overall_design:
Laser captured smooth muscle cells and macrophages from carotid plaque sections (n=3) profiled in the Merck/Agilent 44k v1.1.
The reference sample was a pool RNA from whole sections.


title: Real-time quantitative PCR analysis of ARF-deficient macrophages

status: Public on Sep 29 2011

city: Madrid

first: Sonsoles

last: Hortelano

address: Carretera de Majadahonda-Pozuelo Km 2

country: Spain

institute: ISCIII

summary: Macrophages are a major cellular component of all inflammatory situations, generating proinflammatory cytokines such as TNF-alpha, IL-1, and IL-6 that are central to the initiation and maintenance of inflammation. To determine whether the tumor suppressor ARF plays a role in inflammatory gene expression, we used an 84-gene RT2 PCR array to examine the expression of inflammation-associated genes in WT and ARF-deficient macrophages treated with the TLR4 ligand LPS.

overall_design: Peritoneal macrophages from WT and ARF-deficient mice were obtained and treated with LPS (200ng/ml) for 4 hours. WT control (without stimulation n=4), WT LPS (n=4), ARF Control (n=4), ARF LPS (n=4)

first: Paqui

middle: G

last: Traves

first: Raquel

last: López-Fontal

first: Alfonso

last: Luque


title: A gene-expression oligo microarray for two serial passages of Ichthyophthirius multifiliis

city: Auburn

first: Eric

last: Peatman

state: AL

address: 203 Swingle Hall

department: Fisheries and Allied Aquacultures

institute: Auburn University

summary: The protozoan Ichthyophthirius multifiliis (Ich) is a eukaryotic ciliate parasite of freshwater fish.  Ich causes ichthyophthiriosis or ‘white spot disease’ characterized by white cysts covering the host skin and gills. The parasite is responsible for high mortalities and severe economic losses to farmed species as well as to ornamental species of fish.  Despite the global importance of Ich, little is known about the genetic processes underlying its infectivity. Ich has three main life-stages, an infective theront, a parasitic trophont, and a reproductive tomont. Further, Ich has been demonstrated previously to display a loss of infectivity as the number of lab-passages on a fish increase, presumably relating to senescence of the organism. To compare gene expression among two of the three Ich life-stages (the tomont and trophont life-stages) at different passages, oligonucleotide microarrays were utilized.  Gene expression was analyzed in samples taken from two of the three Ich life-stages (the tomont and trophont life-stages) at the first serial passage on channel catfish in the lab (P1), and at serial passage 100 (P100).  The results of this study will add in the understanding of protozoan global gene regulation and biology and should aid in the development of strategies aimed at the control of this important fish parasite.

overall_design: Submitted is a 12 chip oligo array design using 385 K Nimblegen arrays.  A total of 12 microarrays were used for the experiment: three replicates from two of the three Ich life-stages (tomont and trophont life-stages) at serial passage #1 (P1) and serial passage #100 (P100).  Probes were designed using 9,129 unique Ich ESTs (clustered contigs and singletons) as well as 26,273 Tetrahymena thermophila and 5,184 Plasmodium falciparum coding sequences.  The probe design strategy was to create 12 60-mer oligonucleotide probes per I. multifiliis sequence, and 10 60-mer oligonucleotide probes for both T. thermophila and P. falciparum sequences.  Total RNA was isolated in triplicate from the three life-stages of I. multifiliis and submitted to Nimblegen for labeling, hybridization, and scaning.  This microarray study is based on the GPL9449 platform built for the developmental stages of the parasite.

first: Jason

last: Abernathy

first: De-Hai

last: Xu

first: Huseyin

last: Kucuktas

first: Phillip

last: Klesius

first: Zhanjiang

last: Liu


title: Gene expression profiling of human atherosclerotic plaque: 290 peripheral plaques

summary:
In order to identify potential new biomarkers of atherosclerotic plaque composition we performed a large scale analysis of gene expression patterns in human atherosclerotic lesions. Whole genome expression analysis of 101 peripheral plaques identified a robust gene signature (1514 genes) dominated by inflammatory processes, and cholesterol metabolism and storage genes. Specific pathways enriched in this signature included activation of the Toll-like receptor signaling pathway, T-cell activation, cholesterol efflux, oxidative stress response, inflammatory cytokine production, vasoconstriction and lysosomal activity. Analysis of gene expression in plaque micro-dissected material revealed that the signature is strongly up-regulated in macrophage-rich regions and down-regulated in regions with high smooth muscle cell content.
A smaller qPCR biomarker panel and inflammatory composite score (ICS) were developed to facilitate clinical translation of discoveries from gene expression profiling. We found that ICS correlates with histological features related to plaque vulnerability. In addition, ICS is able to separate groups of plaques obtained from symptomatic and asymptomatic patients undergoing carotid endarerectomy. In summary, we identified a robust mRNA biomarker panel associated with histo-pathological as well as clinical hallmarks of vulnerable atherosclerotic plaque. This panel may be used as a diagnostic and prognostic tool in clinical setting to evaluate novel anti-atherosclerotic therapies.

overall_design: 290 human peripheral plaques were excised using the FoxHollow silverhawk catheter and stored in RNAlater. RNA was extracted, amplified and hybridized to Affymetrix/Merck custom 1.0 arrays (GPL10687).


title: Evidence of transcription in intergenic sequences in Rickettsia conorii

status: Public on Sep 27 2011

city: Marseille

first: Aurélie

last: Renvoisé

address: 27 bd Jean Moulin

institute: Urmite

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: We used a microarray covering the whole genome of R. conorii to check if intergenic sequences were found transcribed. We checked the expression signals for probes corresponding to spacers as compared to probes corresponding to Open Reading Frames (ORFs). We got total RNA from R. conorii XTC cultures; we performed cDNA synthesis and then hybridizations. The hybridizations were repeated four times, and data were compared to check the reproducibility.

overall_design:
Bacterial culture. In this study, we used R. conorii subsp. conorii, strain Malish 7. It was cultivated on XTC cells for 3 days at 28°C.
Microarray design. EArray (Agilent technologies) was used to generate a set of probes covering the whole genome of seven species of Rickettsiae (R. conorii strain Malish 7 (NC_003103), R. africae strain ESF-5 (NC_012633), R. slovaca (unpublished genome), R. massiliae (NC_009900), R. raoultii (unfinished genome), R. felis (NC_007109), R. prowazekii  strain Madrid E (NC_000963)). Only CDSs >120 nt long and spacers >60 nt long were retained to generate probes. The probes are 60 nt long, following Agilent’s recommendations, except for those corresponding to 34 short predictions (see below) of 20 nt long. The probes present the following Tm properties: mean=78.82, minimum=66.34, maximum=85.16. Preceding steps yielded a final oligonucleotide set of 14,625 probes resulting to a final coverage of 96%. Microarray design included control spots.
Expression microarrays and analysis. Using the previously obtained RNA, cDNA synthesis was performed with M-MLV reverse transcriptase (Invitrogen) following the manufacturer’s instructions. 1µg cDNA was labelled with Cy3-dCTP and Cy5-dCTP (GE Healthcare) using BioPrime DNA labelling System (Invitrogen). Labelled cDNA was purified using Minelute Reaction Cleanup kit (Qiagen). The levels of Cy3-dCTP and Cy5-dCTP incorporation were quantified by absorbance measurement at 550 nm and 650 nm, respectively, on Nanodrop (ThermoFisher). Hybridizations were performed for 17h at 62°C as previously described. Slides were scanned using Agilent scanner (Agilent Technologies, CA, USA) with a 3 µm resolution and a 20 bit format. Data were extracted by Feature Extraction TM software (10.5.1.1 version, Agilent). Data were then treated using MIDAS software (Microarray Data Analysis System) (http://www.tm4.org/midas.html) to perform a global normalization. Data were analyzed using Excel 2003 (Microsoft). A cut-off value defined as 2-standard deviation obtained for background intensities was then applied. The microarray data were analyzed after a global normalization. The hybridizations were repeated four times, and data were compared to check the reproducibility. The hybridization pattern after normalization showed a linear correlation in the relative gene expression; the correlation’s coefficients for the four repeated assays are presented in table 3A. They vary from 0.9468 to 0.9845 highlighting a good reproducibility of the experiments.

first: Svetlana

last: Shabalina

first: Khalid

last: El Karkouri

first: Gregory

last: Gimenez

first: Eugene

last: Koonin

first: Didier

last: Raoult


title: A gene-expression oligo microarray for the three developmental stages of Ichthyophthirius multifiliis

summary: The protozoan Ichthyophthirius multifiliis (Ich) is a eukaryotic ciliate parasite of freshwater fish.  Ich causes ichthyophthiriosis or ‘white spot disease’ characterized by white cysts covering the host skin and gills. The parasite is responsible for high mortalities and severe economic losses to farmed species as well as to ornamental species of fish.  Despite the global importance of Ich, little is known about the genetic processes underlying its development and infectivity. Ich has three main life-stages, an infective theront, a parasitic trophont, and a reproductive tomont.  To compare gene expression among Ich life-stages, oligonucleotide microarrays were constructed and utilized.  All publicly-available Ich ESTs (~35K) were clustered to generate 9,129 unique consensus sequences represented as probes on custom microarrays produced in coordination with Roche NimbleGen.   To facilitate comparative genomic analysis and to potentially increase gene content through cross-hybridization, gene coding sequences of related protozoans Tetrahymena thermophila and Plasmodium falciparum were also added to the microarrays.  Gene expression was analyzed in samples taken from each of the three Ich life-stages.  The results of this study will add in the understanding of protozoan global gene regulation and biology and should aid in the development of strategies aimed at the control of this important fish parasite.

overall_design: Submitted is a nine chip oligo array design using 385 K Nimblegen arrays.  A total of nine microarrays were used for the experiment: three replicates from each of the three Ich life-stages (tomont, trophont, and theront life-stages).  Probes were designed using 9,129 unique Ich ESTs (clustered contigs and singletons) as well as 26,273 Tetrahymena thermophila and 5,184 Plasmodium falciparum coding sequences.  The probe design strategy was to create 12 60-mer oligonucleotide probes per I. multifiliis sequence, and 10 60-mer oligonucleotide probes for both T. thermophila and P. falciparum sequences.  Total RNA was isolated in triplicate from the three life-stages of I. multifiliis and submitted to Nimblegen for labeling, hybridization, and scaning.


title: Comparative genomics of ten clinical Candida albicans strains

city: Shanghai

first: Feng

last: Yang

address: Guohe Road

country: China

institute: Second Military Medical University

summary: Candida albicans is the most common fungal pathogen in humans. C.albicans tolerates aneuploidy of all of its chromosomes. Genome plasticity is a hallmark of C.albicans. It is an adaptation strategy of this species. But questions like the extent of such genomic variability, which genes contribute to the divergence, and what mechanisms drive the adaptive genetic change, are not well answered yet.

overall_design: We used array-based comparative genomic hybridization (array CGH) to investigate the diversity of gene contents of 10 clinical C.albicans strains, of various anatomical origins and genotypes.  One self to self hybridization was included as a control.


title: Lymph nodes with follicular lymphoma or reactive hyperplasia

city: Bethesda

first: Yuelin

middle: Jack

last: Zhu

state: MD

address: 9000 Rockville Pike

department: Genetics Branch, Center for Cancer Research

institute: NCI

summary: Comparison of gene expression profiles of follicular lymphoma vs. reactive lymph nodes.

overall_design: 8 cases of follicular lymphoma; 5 cases of reactive lymph nodes.

first: Keith

last: Killian

first: Paul

last: Meltzer


title: Lymphomas that recur after MYC suppression continue to exhibit oncogene addiction

status: Public on Sep 24 2011

city: Stanford

first: Andrew

last: Gentles

state: CA

address: 1201 Welch Road

institute: Stanford University

summary: The suppression of oncogenic levels of MYC is sufficient to induce sustained tumor regression associated with proliferative arrest, differentiation, cellular senescence and/or apoptosis, a phenomenon known as oncogene addiction. However, after prolonged inactivation of MYC in a conditional transgenic mouse model of Em-tTA/tetO-MYC T-acute lymphomablastic lymphoma (T-ALL), some of the tumors recur, recapitulating what is frequently observed in human tumors in response to targeted therapies. Here we report that these recurring lymphomas express high levels of either transgenic or endogenous Myc suggesting that tumors continue to be addicted to oncogenic levels of MYC. Many of the recurring lymphomas (76%) harbored mutations in the tetracycline transactivator (tTA) resulting in expression of the MYC transgene even in the presence of doxycycline. Many of the remaining recurring tumors expressed high levels of endogenous Myc which was in some cases associated with a genomic rearrangement of the endogenous Myc locus or overexpression of Notch1. Gene expression profiling confirmed that the primary and recurring tumors have highly similar transcriptomes. Importantly, shRNA-mediated suppression of the high levels of MYC in recurring tumors elicited both suppression of proliferation and increased apoptosis confirming that these tumors remain oncogene addicted. These results suggest that tumors caused by MYC overexpression remain addicted to high levels of expression of this oncogene.

overall_design: 13 samples, no replicates included


title: Gene expression profiling of human atherosclerotic plaque: Carotid plaque

first: Oscar

last: Puig

summary:
In order to identify potential new biomarkers of atherosclerotic plaque composition we performed a large scale analysis of gene expression patterns in human atherosclerotic lesions.  Whole genome expression analysis of 101 peripheral plaques identified a robust gene signature (1514 genes) dominated by inflammatory processes, and cholesterol metabolism and storage genes.  Specific pathways enriched in this signature included activation of the Toll-like receptor signaling pathway, T-cell activation, cholesterol efflux, oxidative stress response, inflammatory cytokine production, vasoconstriction and lysosomal activity.  Analysis of gene expression in plaque micro-dissected material revealed that the signature is strongly up-regulated in macrophage-rich regions and down-regulated in regions with high smooth muscle cell content.
	A smaller qPCR biomarker panel and inflammatory composite score (ICS) were developed to facilitate clinical translation of discoveries from gene expression profiling.  We found that ICS correlates with histological features related to plaque vulnerability.  In addition, ICS is able to separate groups of plaques obtained from symptomatic and asymptomatic patients undergoing carotid endarerectomy.  In summary, we identified a robust mRNA biomarker panel associated with histo-pathological as well as clinical hallmarks of vulnerable atherosclerotic plaque.  This panel may be used as a diagnostic and prognostic tool in clinical setting to evaluate novel anti-atherosclerotic therapies.

overall_design: 6 human carotid plaques were sectioned in 1 mm thick slices. Alternative slices were used for gene expression profiling in Affymetrix/Merck custom 1.0 arrays (GPL10687), or  for immunohistochemistry studies (CD68, Actin)

first: Vladimir

last: Reiser


title: The vitamin D receptor and inducible nitric oxide synthase associated pathways in the development of acquired resistance to Cooperia oncophora infection in cattle

city: Beltsville

first: Robert

last: Li

address: Barc East

department: Animal & Natural Resources Institute

institute: USDA

summary: Cooperia oncophora is an economically important gastrointestinal nematode in ruminants. Acquired resistance to Cooperia oncophora infection in cattle develops rapidly as a result of prior infections. Naïve cattle, when given a primary infection of high-dose infective L3 larvae, develop a strong immunity to subsequent reinfection. Compared to primary infection, reinfection resulted in a marked reduction in worm establishment. In order to understand molecular mechanisms underlying the development of acquired resistance, we characterized the transcriptomic responses of the bovine small intestine to a primary infection and reinfection. A total of 23 pathways were significantly impacted during infection. The vitamin D receptor activation was strongly induced only during reinfection, suggesting that this pathway may play an important role in the development of acquired resistance via its potential roles in immune regulation and intestinal mucosal integrity maintenance. The expression of inducible nitric oxide synthase (NOS2) was strongly induced during reinfection but now during primary infection. As a result, several canonical pathways associated with NOS2 were impacted.  The genes involved in eicosanoid synthesis, including prostaglandin synthase 2 (PTGS2 or COX2), remained largely unchanged during infection. The rapid development of acquired resistance may help explain the lack of relative pathogenicity by Cooperia oncophora infection in cattle. Our findings will undoubtedly facilitate understanding of molecular mechanisms underlying the development of acquired resistance, which could have an important implication in vaccine design.

overall_design: The transcriptomic profiles of the bovine small intestine in response to both a primary infection and a drug-attenuated reinfection were compared. The data were analyzed using the same condition and procedure. The gene expression profiles of calves 14 days after a primary Cooperia oncophora infection and a drug-attenuated reinfection were compared to their respective age-matched controls (naive controls and drug-drenched worm-free controls)

first: Congjun

first: Louis

middle: C

last: Gasbarre


title: Transcriptome analysis of the archaeon Thermoplasma acidophilum cultured under aerobic and anaerobic conditions

city: Martinsried (Planegg)

first: István

last: Nagy

address: Am Klopferspitz 18

department: Dept. of Structural Biology

institute: Max Planck Institute of Biochemistry

summary:
Investigation of whole genome gene expression level changes in Thermoplasma acidophilum cultured under aerobic and anaerobic conditions.
The analysis are further described in Na Sun, Cuiping Pan, Stephan Nickell, Matthias Mann, Wolfgang Baumeister, and István Nagy, Quantitative proteome and transcriptome analysis of the archaeon Thermoplasma acidophilum cultured under aerobic and anaerobic conditions (submitted).

overall_design: Total RNA of T. acidophilum was isolated with the RNeasy Protect Bacteria Kit (Qiagen). The transcriptomics analysis was performed on TI273075 60mer chips of Roche NimbleGen microarrays (NimbleGen Systems of Iceland, LLC). Probes were selected for all protein sequences (1482) and labelled with Cy3. The median number of probes per sequence is 20, and each probe is replicated 5 times on the chip. The probes are randomly distributed over the surface of the array. Unused features are filled with randomly generated probes of comparable GC content. ArrayStar v2.0 software (DNASTAR, Inc.) was used for the data analysis. Three independent biological replicates were processed for aerobic and anaerobic conditions, respectively.

first: Istvan

last: Sun

first: Cuiping

last: Pan

first: Stephan

last: Nickell

first: Matthias

last: Mann

first: Wolfgang

last: Baumeister


title: Zebrafish embryo response to Diethyl maleate

city: Nagoya

first: Shin'ichi

last: Akiyama

state: Aichi

address: 65 Tsurumaicho

department: Department of Nephrology

country: Japan

institute: Nagoya University Graduate School of Medicine

summary: We have employed the Zebrafish gene expression microarray (MZH_Zebrafish_16k_v1.0) as a discovery platform to analyze the trancriptome of 108hpf (hours post fertilization) embryos exposed from the 96hpf to 108hpf to 100µM of diethylmaleate (DEM).

overall_design: Four two-color microarray studies for measuring expression levels of zebrafish embryos treated with 100µM of diethylmaleate (DEM) were performed. 8 samples were analyzed in total. Four samples were treated with 0.1% DMSO as a control; four samples were treated with 100 µM of DEM and 0.1% DMSO.

first: Hitomi

last: Nakajima

first: Yaeko

last: Nakajima-Takagi

first: Tadayuki

last: Tsujita

first: Shin-ichi

first: Takeshi

last: Wakasa

first: Katsuki

last: Mukaigasa

first: Hiroshi

last: Kaneko

first: Yutaka

last: Tamaru

first: Masayuki

last: Yamamoto

first: Makoto

last: Kobayashi


title: Budding yeast mRNA export and processing factor localization

status: Public on Sep 25 2011

city: Aurora

first: David

middle: L.

last: Bentley

state: CO

department: Biochemistry and Mol. Genetics

institute: U. Colorado School of Medicine

type: Genome binding/occupancy profiling by genome tiling array

summary:
The yeast mRNA export adaptor Yra1 binds the Pcf11 subunit of cleavage-polyadenylation factor CF1A linking export to 3'-end formation. We found a surprising consequence of this interaction is that Yra1 influences cleavage-polyadenylation. Yra1 competes with the CF1A subunit, Clp1, for binding to Pcf11, and excess Yra1 inhibits 3' processing in vitro. Release of Yra1 at the 3' ends of genes coincides with recruitment of Clp1, and depletion of Yra1 enhances Clp1 recruitment within some genes. These results suggest that CF1A is not necessarily recruited as a complete unit, but instead Clp1 can be incorporated co-transcriptionally in a process regulated by Yra1. Yra1 depletion causes widespread changes in poly(A) site choice particularly at sites where the efficiency element is divergently positioned. We propose that one way Yra1 modulates cleavage-polyadenylation is by influencing co-transcriptional assembly of the CF1A/B 3' processing factor.

Key Words: Yra1, cleavage-polyadenylation, mRNA export, Pcf11, Clp1, Sub2, alternative polyadenylation

overall_design:
Whole genome analysis of Yra1, Sub2, Pcf11, and Clp1  in WT and  Yra1-depleted cells using a GAL1-YRA1 mutant.
ChiP-ChIP using ligation-mediated PCR amplified material hybridized to Nimblegen 385K arrays 50mers median probe spacing 32 bp cat. No. C4214-00-01.

first: Hyunmin

last: Kim


title: microRNA-expression profile in a series of  Nodal marginal zone lymphoma patients [miRNA expression]

status: Public on Sep 21 2011

city: Toledo

first: Alberto

last: Arribas

state: Toledo

address: Avda Barber, 30

department: Molecular Pathology Research Unit

institute: Hospital Virgen de la Salud

summary: Nodal marginal zone lymphoma (NMZL) is a small B cell neoplasm whose molecular pathogenesis is still essentially unknown and whose differentiation from other small B cell lymphomas is hampered by the lack of specific markers. We have analyzed gene expression, miRNA profile and copy number data from 15 NMZLs. For comparison, 16 follicular lymphomas, 9 extranodal marginal zone lymphomas, 8 reactive lymph nodes and B cell subtypes were included. The results were validated by qRT-PCR in an independent paraffin-embedded series including 61 NMZLs. NMZL signature showed an enriched expression of gene sets identifying interleukins, integrins, CD40, PI3K, NFkB and TGF-Beta; and included genes expressed by normal marginal zone cells and memory B cells. The most highly overexpressed genes were SYK, TACI, CD74, CD82 and CDC42EP5. Genes linked to G2/M and germinal center were downregulated. Comparison of the gene expression profiles of NMZL and FL showed enriched expression of CHIT1 and TACI in NMZL, and BCL6, LMO2 and CD10 in FL. NMZL displayed increased expression of miR-223 and let-7f, while FL strongly expressed miR-494. Our study identifies new candidate diagnostic molecules for NMZL and reveals survival pathways activated in NMZL.

overall_design: microRNA-expression profiling was conducted in a series of 40 B-cell non-Hodgkin lymphoma patients (NMZL, and FL).  Six lymph nodes with reactive lymphoid hyperplasia (RLN) were used as controls

first: J

middle: A

first: Y

last: Campos-Martín

first: C

last: Gómez-Abad

first: P

last: Algara

first: M

last: Sánchez-Beato

middle: S

last: Rodriguez-Pinilla

first: S

last: Montes-Moreno

first: N

last: Martinez

last: Alves-Ferreira

last: Piris

last: Mollejo


title: An Extended dsRBD with a Novel Zinc-Binding Motif Mediates Nuclear Retention of Fission Yeast Dicer

status: Public on Sep 23 2011

city: Basel

first: Stephan

last: Emmerth

address: Maulbeerstrasse 66

country: Switzerland

institute: FMI

type: Expression profiling by genome tiling array

summary: Dicer proteins function in RNA interference (RNAi) pathways by generating small RNAs (sRNAs). Here we report the solution structure of the C-terminal domain of Schizosaccharomyces pombe Dicer (Dcr1). The structure reveals an unusual double-stranded RNA binding domain (dsRBD) fold embedding a novel zinc-binding motif that is conserved among dicers in yeast. Although the C-terminal domain of Dcr1 still binds nucleic acids, this property is dispensable for proper functioning of Dcr1. In contrast, disruption of zinc coordination renders Dcr1 mainly cytoplasmic and leads to remarkable changes in gene expression and loss of heterochromatin assembly. In summary, our results reveal novel insights into the mechanism of nuclear retention of Dcr1 and raise the possibility that this new class of dsRBDs might generally function in nucleo-cytoplasmic trafficking and not substrate binding. The C-terminal domain of Dcr1 constitutes a novel regulatory module that might represent a potential target for therapeutic intervention with fungal diseases.

overall_design: 12 chips representing 4 different strains. Every condition is represented by three biological replicates

first: Pierre

last: Barraud

first: Yukiko

last: Shimada

first: Hans-Rudolf

last: Hotz

first: Frédéric

last: Allain

first: Marc

last: Bühler


title: Age Dependent Decrease in Vascular Remodeling Response in LDLr-/- mice unveils a role of Quaking in Vascular Homeostasis

city: Leiden

first: Peter

last: 't Hoen

address: PO Box 9600

department: Center for Human and Clinical Genetics

institute: Leiden University Medical Center

summary:
Female C57Bl/6J LDLr -/- mice, aged 12 weeks (n=16) and 52 weeks (n=14), were put on western-type diet for 6 weeks before perivascular bilateral collar placement in the carotid artery. RNA was isolated from the carotid artery 6 weeks after collar placement. Snap frozen carotid arteries were pooled in four subgroups of three samples per age group in order to yield a sufficient amounts  of RNA. Gene expression profiles from young and old mice were compared on spotted oligonucleotide arrays containing the 22K mouse Sigma-Compugen libarary v1. A direct hybridization was used with dye swaps for each pool.
Keywords: RNA expression profiling

overall_design: Four pools of each strain were used. Direct hybridization design. Dye swap for each pair of samples. In total 8 arrays.

first: Adriaan

middle: O

last: Kraaijeveld

first: Christian

last: van der Lans

first: Eric

last: Biessen


title: Estrogenic modulation of inflammation-related genes in male rats following volume overload

city: Columbia

first: Jennifer

last: McLarty

state: SC

address: 6349 Garners Ferry Road

department: Cell Biology and Anatomy

institute: University of South Carolina-School of Medicine

summary: The purpose of this study was to determine whether estrogen had an effect on inflammation-related genes that contribute to this estrogen-mediated cardioprotection.  Volume overload on the heart was induced by aortocaval fistula in 8 week old male Sprague Dawley rats and genes of interest in shams, fistula , and  fistula +estrogen were identified using an inflammatory PCR array.

overall_design: Volume overload was induced in male rats treated with estrogen and non treated male rats to determine if inflammation-related genes contributed to estrogen-mediated cardioprotection.

middle: L


title: Propionic Acid Induces Autistic-like Gene Expression Profiles, Inhibits Neurite Outgrowth, and Promotes Neurodegeneration in Cells from Non-Autistic Individuals

status: Public on Sep 16 2011

city: Washington

first: Valerie

middle: Wailin

last: Hu

state: DC

department: Biochemistry and Molecular Medicine

institute: The George Washington University School of Medicine and Health Sciences

summary: In this study, we investigated PPA-induced changes in gene expression profiles of lymphoblastoid cell lines (LCLs) from unaffected individuals, compared with gene expression profiles of LCLs from sex-matched siblings with ASD. Global gene expression profiling analysis revealed that 96 genes in LCLs from the unaffected individuals were significantly altered after PPA exposure, exhibiting expression levels similar to those of their respective siblings with autism. Biological pathway analyses of these PPA-responsive genes suggested significant association with many neurological functions associated with autism, including synaptic transmission, neuronal cell differentiation and apoptosis. Moreover, we demonstrated that PPA also deregulated several of the responsive genes, including APOE, LIFR, NR3C1, and PTK2, in the neuroblastoma cell line SH-SY5Y. Functional analyses further showed that PPA exposure negatively impacted neurite outgrowth and promoted neurodegeneration in the human neuronal cell model. This study indicates that PPA exposure induces global changes in gene expression profiles of LCLs from non-autistic individuals that reflect expression patterns of LCLs from affected individuals.

overall_design: We conducted experiments using LCLs derived from individuals with ASD (n = 5) and their sex-matched unaffected siblings (n = 5). LCLs from non-ASD individuals were treated with 10 mM PPA, 10 mM propanol, or PBS. LCLs from individuals with ASD were treated with 10 mM propanol or PBS. At 24h after treatment, all LCLs were harvested. Gene expression profiling was conducted using TIGR 40K human cDNA microarrays. For each sample, total RNA was isolated and cDNA was synthesized, labeled with Cy-3 dye, and co-hybridized with Cy-5 labeled reference cDNA prepared from Universal human RNA (Stratagene, USA) on a TIGR 40K human cDNA microarray.

first: Tewarit

last: Sarachana

first: Xinyi

last: Zhou

first: Stephanie

last: Ramirez

first: Millie

last: Shah


title: Gene expression analysis of dendritic cells treated with small chemical compounds

status: Public on Sep 19 2011

first: Hironori

last: Matsushima

state: OH

address: 3000 Arlington Avenue Mail Stop 1021

department: Medical Microbiology and Immunology

institute: University of Toledo College of Medicine

summary: Identification of newer compounds to modulate dendritic cell functions.

overall_design: Total RNA obtained from bone marrow-derived dendritic cells treated for 6 hours with small chemical compounds or vehicle alone in the presence or absence of lipopolysaccharide (LPS).


title: Mycobacterium tuberulosis H37Rv strains: Control vs. 5-chloro-8-hydroxyquinoline

city: Changchun

first: Lu

last: Yu

address: Xi'an Road 5333

institute: Jilin university

summary: Transcriptional profiling of Mycobacterium tuberculosis H37Rv strains comparing control DMSO treated strains with 5-chloro-8-hydroxyquinoline treated strains. Goal was to determine the effects of 5-chloro-8-hydroxyquinoline against Mycobacterium tuberculosis H37Rv strains.

overall_design: Two-condition experiment,control DMSO treated strains vs. 5-chloro-8-hydroxyquinoline treated strains. Biological replicates: 2 control replicates, 2 5-chloro-8-hydroxyquinoline replicates.

last: Guo


title: Gene analysis of intracellular and extracellular Streptococcus pyogenes in human macrophages

status: Public on Sep 15 2011

city: Stockholm

first: Erika

last: Hertzén

address: Karolinska University Hospital, Huddinge, Center for Infectious Medicine, F59

country: Sweden

institute: Karolinska Institutet

summary:
The objective of this study was to investigate which genes are important for Streptococcus pyogenes during intracellular survival in human macrophages.
Streptococcus pyogenes is an important human pathogen, which has recently gained recognition as an intracellular microorganism during the course of severe invasive infections such as necrotizing fasciitis. Although the surface anchored M protein has been identified as a pivotal factor affecting phagosomal maturation and S. pyogenes survival within macrophages, the overall transcriptional profile required for the pathogen to adapt and persist intracellularly is yet unknown. To address this, gene expression profiles of S. pyogenes within human macrophages were determined and compared to those of extracellular bacteria using customized microarrays and real-time qRT-PCR. In order to model the early phase of infection involving adaptation to the intracellular compartment, samples were collected 2h post-infection and within 2 h post infection, the expression of 145 streptococcal genes was significantly altered in the intracellular environment. The majority of differentially regulated genes were associated with metabolic and energy-dependent processes. Key upregulated genes in early phase intracellular bacteria were ihk and irr, encoding a two-component gene regulatory system (TCS). We observed that an isogenic S. pyogenes mutant deficient in ihk/irr displayed significantly reduced bacterial counts as compared to wild-type bacteria following infection of macrophages. Comparison of gene expression of selected genes at 2h and 6h post-infection revealed a dramatic shift in response regulators over time with a down-regulation of ihk/irr genes concurrent with an upreguation of the well-studied covR/S two component regulator. In reinfection assays, intracellular bacteria from the 6h time point exhibited significantly greater survival within macrophages than did bacteria collected at the 2h time point. The findings illustrate how gene expression of S. pyogenes during the intracellular life cycle is fine-tuned by temporal expression of specific two-component systems.

overall_design: Five samples with three biological replicates are analysed. Each open reading frame in triplicate (three technical replicas per sample). Resulting in 6-9 data points per gene per condition. The extracellular bacteria are control samples and the internal control is the house-keeping gene gyrase.

first: Linda

last: Johansson

first: Rita

last: Kansal

first: Alexander

last: Hecht

first: Samira

last: Dahesh

first: Victor

last: Nizet

first: Malak

last: Kotb

first: Anna

last: Norrby-Teglund


title: Identification of RNAs associated with the epigenetic activator MLL1 in undifferentiated and differentiated CJ7 mouse embryonic stem cells.

city: Riverside

first: Frank

last: Sauer

state: California

address: 2202A Genomics Building

department: Biochemistry

institute: University of California Riverside

summary: The epigenetic activator “Mixed lineage leukemia 1” (Mll1) is paramount for embryonic development and hematopoiesis. We have used RNA-ChIP-on-chip assays to identify long non-coding RNAs, which associate with MLL1 in differentiating CJ7 mouse embryonic stem cells. We identified the long, non-coding RNA (lncRNA) Mistral (Mira), which originates from the spacer DNA region separating Hoxa6 and Hoxa7. Mira supports transcriptional activation of HOXA6 and HOXA7 by recruiting MLL1 to the HOXA6/HOA7 gene cassette.

overall_design:
(+RA) CJ7 mESCs [+RA, -LIF, - beta-mercaptoethanol [beta-ME]] chiped with polyclonal antibody to MLL1 vs control A: differentiating (-RA) CJ7 mESCs [-LIF, -beta-ME] chiped with antibody to MLL1; control B: undifferentiated (U) CJ7 cells chiped with antibody to MLL1; C: +RA-Control CJ7 cells [+RA, -LIF, -beta-ME] chiped with mouse antiserum; -RA-Control CJ7 cells chiped with rabbit antiserum; U-Control CJ7 cells chiped with rabbit antiserum.

The supplementary bed file contains information showing the association of MLL1 with Mira in differentiating CJ7 mouse embryonic stem cells, and was used as a figure in the manuscript.

first: Eugene

last: Bolotin

first: Stephane

last: Bertani


title: Mycobacterium tuberulosis H37Rv strains: Control vs. Osthole.

status: Public on Sep 14 2011

summary: Transcriptional profiling of Mycobacterium tuberculosis H37Rv strains comparing control DMSO treated strains with Osthole treated strains. Goal was to determine the effects of Osthole against Mycobacterium tuberculosis H37Rv strains.

overall_design: Two-condition experiment,control DMSO treated strains vs. Osthole treated strains. Biological replicates: 2 control replicates, 2 Osthole replicates.

first: Junchao

last: Liang


title: MiRNA array based, miRNA expression profiles of head and neck squamous cell carcinoma patients

first: Wei-Wen

last: Jiang

address: Room 305, Building #1,639 Zhi Zao Ju Road

institute: Department of Oral Mucosal Diseases, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine

summary: MiRNA expression profiles were successfully examined through expression profiling of a total of 656 miRNAs between 2 head and neck squamous cell carcinoma (HNSCC) tissues (C) and their paired adjacent normal mucousal tissues (AN).

overall_design: In the study presented here, 2 head and neck squamous cell carcinoma (HNSCC) tissues (C) and their paired adjacent normal mucousal tissues (AN) were examined by miRNA array


title: pBL1 impairs cellobiose metabolism in Lactococcus lactis

city: Villaviciosa

first: Beatriz

last: Martinez

address: Paseo Río Linares s/n

institute: IPLA-CSIC

summary: pBL1 is a Lactococcus lactis theta-replicating 10.9-kbp plasmid that encodes the synthetic machinery of the bacteriocin Lcn972. In this work, the transcriptomes of exponentially growing L. lactis with and without pBL1 were compared. A discrete response was observed with a total of ten genes showing significantly changed expression. Up-regulation of the lactococcal oligopeptide uptake system (opp) was observed, likely linked to a higher nitrogen demand required for Lcn972 biosynthesis. Striking, celB coding for the membrane porter IIC of the cellobiose-PTS and the upstream gene llmg0186 were down-regulated. Growth profiles for L. lactis strains MG1363, MG1363/pBL1 and MG1363ΔcelB grown in CDM-cellobiose confirmed slower growth of pBL1 and ΔcelB while no differences were scored on glucose. The presence of pBL1 shifted the fermentation products towards a mixed acid profile and promoted substantial changes in intracellular pool sizes for glycolytic intermediates in cellobiose-growing cells as determined by HPLC and NMR. Overall, these data support the genetic evidence of a constriction in cellobiose uptake. Notably, several cell wall precursors accumulated, while other UDP-activated sugars pools were lower, which could reflect rerouting of precursors towards the production of structural or storage polysaccharides. Moreover, slow cellobiose-growing cells and those lacking celB were more tolerant to Lcn972 than cellobiose adapted cells. Thus, down-regulation of celB could help to build-up a response against the antimicrobial activity of Lcn972 enhancing self-immunity of the producer cells.

platform_organism: Lactococcus cremoris subsp. cremoris MG1363

overall_design: The  transcriptomes of Lactococcus lactis MG1614 with and without the bacteriocinogenic plasmid pBL1, grown under laboratory conditions, were compared using three biological replicates.

first: B

first: Jan

last: Kok


title: Vibrio vulnificus: Wild-type vs. smcR mutant (V. vulnificus quorum sensing master regulator)

status: Public on Sep 20 2011

city: Seoul

first: Seung Min

last: Kim

address: 1 Gwanakro

country: South Korea

institute: Seoul National University

summary:
Two-condition experiment,  Wild-type vs. smcR mutant. Biological replicates: 3 control, 3 mutant strains, independently grown and harvested. One replicate per array.
A significant portion of the SmcR regulon predicted on the basis of microarray analysis results is indeed regulated by SmcR and that SmcR is a global regulator in V. vulnificus.

overall_design: For transcriptome analysis, the V. vulnificus whole genome TwinChip, manufactured and kindly provided by the 21C Frontier Microbial Genomics and Applications Center(Daejeon, South Korea), was used.

first: Seung

first: Sang

last: Choi


title: An Alternative Splicing Switch Regulates Embryonic Stem Cell Pluripotency and Reprogramming [AS microarray]

city: Cambridge

first: Xinchen

last: Wang

state: MA

address: 32 Vassar St, D514

institute: MIT

summary: Alternative splicing (AS) is a key process underlying the expansion of proteomic diversity and the regulation of gene expression. However, the contribution of AS to the control of embryonic stem cell (ESC) pluripotency is not well understood. Here, we identify an evolutionarily conserved ESC-specific AS event that changes the DNA binding preference of the forkhead family transcription factor FOXP1. We show that the ESC-specific isoform of FOXP1 stimulates the expression of transcription factor genes required for pluripotency including OCT4, NANOG, NR5A2 and GDF3, while concomitantly repressing genes required for ESC differentiation. Remarkably, this isoform also promotes the maintenance of ESC pluripotency and the efficient reprogramming of somatic cells to induced pluripotent stem cells. These results reveal an AS switch that plays a pivotal role in the regulation of pluripotency through the control of critical ESC-specific transcriptional programs.

overall_design: In order to identify AS events that potentially control stem cell pluripotency, we used microarray profiling to compare patterns of AS in undifferentiated and differentiated H9 human embryonic stem cells (hESCs).

first: Mathieu

last: Gabut

first: Payman

last: Samavarchi-Tehrani

first: Valentina

last: Slobodeniuc

first: Dave

last: O’Hanlon

first: Hoon-Ki

last: Sung

first: Manuel

last: Alvarez

first: Shaheynoor

last: Talukder

first: Qun

last: Pan

first: Knut

last: Woltjen

first: Esteban

last: Mazzoni

last: Nedelec

first: Hynek

last: Wichterle

first: Timothy

middle: R

last: Hughes

first: Peter

last: Zandstra

first: Andras

last: Nagy

first: Jeffrey

last: Wrana

first: Benjamin

last: Blencowe


title: Identification of genes associated with lens regeneration from the cornea in Xenopus laevis tadpoles

city: Dunedin

first: Caroline

last: Beck

address: 340 Great King Street

department: Zoology

country: New Zealand

institute: University of Otago

summary: Surgical removal of the lens from larval Xenopus laevis results in a rapid transdifferention of central corneal cells to form a new lens. The trigger for this process is understood to be an induction event arising from the unprecedented contact between the cornea and the vitreous humour that occurs following lens removal. The identity of this trigger is unknown. Here, we have used a functional transgenic approach to show that BMP signalling is required for lens regeneration and a microarray approach to identify genes that are upregulated specifically during this process. Analysis of the array data strongly implicates Wnt signalling and Pitx transcription factors in this process. Pluripotency genes, in contrast, are not upregulated, supporting the idea that corneal cells transdifferentiate without returning to a stem cell state. Furthermore, several genes from the array were expressed in the forming lens during embryogenesis. One of these, nipsnap1, is a known direct target of BMP signalling. We suggest that, as with tail regeneration, activation of multiple developmental signalling pathways could drive lens regeneration from the cornea.

overall_design: Three biological replicates of each of three sample types were analysed. For each replicate, lens tissue (L) was derived from 5 lenses dissected from stage 50 tadpoles. Similarly, 7-8 corneas dissected from stage 50 tadpoles from which the lens had been removed 3 days previously were pooled for each biologocal replicate (R). These samples should contain tissue that is changing from cornea to lens, to regenerate the missing lens. Finally, 7-8 corneas from eyes of tadpoles at the same stage that had the cornea lifetd but the lens left in place 3 days earlier were pooled for each biological replicate (sham operated corneas, designated S).

first: Robert

last: Day


title: Integrative nucleophosmin mutation-associated microRNA and gene expression pattern analysis identifies novel microRNA - target gene interactions in acute myeloid leukemia

status: Public on Sep 12 2011

city: Berlin

first: Lars

last: Bullinger

address: Augustenburger Platz 1

department: Hematology, Oncology and Tumorimmunology

institute: Charité

summary:
Background:
MicroRNAs are regulators of gene expression, mainly functioning by decreasing mRNA levels of their multiple targets. Deregulated microRNA expression has been shown for acute myeloid leukemia, a disease also characterized by altered gene expression associated with distinct genomic aberrations such as nucleophosmin (NPM1) mutations. To further illuminate the role of deregulated microRNA and gene expression in cytogenetically normal acute myeloid leukemia with NPM1 mutation, we performed an integrative analysis of microRNA and mRNA expression data sets.

Design and Methods:
Both microRNA and gene expression profiles were measured in a cohort of 43 adult acute myeloid leukemia patient samples (n=42 cytogenetically normal, n=1 del7q; median age 46 years [range 23-60]) of known NPM1 mutation status (n=23 mutated, n=20 wild-type) and data integratively analyzed. Putative microRNA-mRNA interactions were validated by quantitative RT-PCR, Western Blot and luciferase reporter assays. For selected microRNAs, sensitivity of microRNA-overexpressing cells to cytarabine treatment was tested by FACS viability and cell proliferation assays.

Results:
Our integrative approach of analyzing both microRNA and gene expression profiles in parallel resulted in a refined list of putative target genes affected by NPM1 mutation-associated microRNA deregulation. Of 177 putative microRNA - target mRNA interactions, we could identify and validate 77 novel candidates with known or potential implication in leukemogenesis, such as IRF2-miR-20a, KIT-miR-20a and MN1-miR-15a. Furthermore, our data showed that deregulated expression of tumor suppressor microRNAs such as miR-29a and miR-30c might contribute to the sensitivity to cytarabine, which is observed in NPM1-mutated acute myeloid leukemia.

Conclusions:
Overall, our observations highlight that integrative data analysis approaches can improve insights into leukemia biology, and lead to the identification of novel microRNA - target gene interactions of potential relevance for acute myeloid leukemia treatment.

overall_design:
MicroRNA and gene expression profiles were measured in a cohort of 43 adult (42 cytogenetically normal and 1 del7q) acute myeloid leukemia patient samples of known NPM1 mutation status (n=23 mutated, n=20 wild-type).

This submission represents the mRNA expression component of the study. The miRNA expression data will be deposited as supplementary information along with the accompanying manuscript.


title: Lactococcus lactis response to isoleucine starvation

status: Public on Sep 22 2011

city: Toulouse

first: Muriel

last: Cocaign-Bousquet

address: 135 avenue de Rangueil

department: UMR5504 INSA/CNRS - UMR792 INSA/INRA

institute: Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés

summary:
Amino acid assimilation and metabolism are crucial for bacterial growth and survival and this is particularly obvious for lactic acid bacteria (LAB) that are generally auxotroph for various amino acids. However, amino acid assimilation is poorly characterized and a complete description of the response during amino acid starvation is still lacking in LAB.
In this context, the global response of the LAB model Lactococcus lactis was characterized during isoleucine starvation in batch culture. The stress was imposed by isoleucine natural consumption in an initially rich chemically defined medium. Dynamic analyses were performed both using transcriptomic and proteomic approaches. The response was found to occur gradually and could be divided into three major parts that were firstly deduced from transcriptomic analysis and generally corroborated by proteomic results: (i) a global repression of biogenic processes (transcription, translation, and carbon metabolism and transport), (ii) a specific response related to the limiting nutrient (numerous pathways belonging to carbon or nitrogen metabolism and leading to isoleucine supply were activated) and (iii) an additional response connected to oxidative stress (induction of aerobic metabolism, electron transport, thioredoxin metabolism and pyruvate dehydrogenase). The involvement of various regulatory mechanisms such as growth rate regulation, stringent response, CodY, GlnR, and CcpA regulations, was discussed on the basis of transcriptomic data comparisons.
Above the full description of L. lactis isoleucine starvation response, this work additionally provided a complex but realistic outlook of the regulation network involved in isoleucine starvation. Such integrated and comparative approach will allow, by its implementation to other regulations and environmental conditions, the whole regulatory network of L. lactis or any other microorganism to be deciphered.

overall_design: Batch cultivation of Lactococcus lactis IL1403 were carried out on a chemically defined medium and under controlled conditions (30 °C, pH 6.6, nitrogen atmosphere). Cell samples were harvested at steady state. Total RNA was extracted from these samples and radiolabelled cDNA were prepared and hybridized on nylon arrays. 1948 amplicons specific of Lactococcus lactis IL1403 genes were spotted twice on the array. Samples corresponding to various growth rates were analyzed simultaneously and 3 independent repetitions were performed.

first: Clémentine

last: Dressaire

first: Emma

last: Redon

first: Christophe

last: Gitton

first: Pascal

last: Loubiere

first: Véronique

last: Monnet


title: Coordinated regulation of MAPK signaling pathway and microRNA in response to ionizing radiation in lung cancer cells

first: Woong Yang

last: Park

address: 28 Yongondong, Chongnogu

department: Biochemistry and Molecular Biology

summary: microRNA regulates cellular responses to ionizing radiation (IR) through the translational control of target genes. We analyzed time-series changes in microRNA expressions upon γ-irradiation in H1299 lung cancer cell lines using microarray. Significantly changed microRNAs were selected based on ANOVA analysis, target genes of which were enriched to MAPK signaling pathway. Concurrent analysis of mRNA and microRNA uncovered that the expression of miR-26b and its target ATF2 mRNA were inversely correlated in γ-irradiated H1299 cells. The overexpression of miR-26b induced the suppression of ATF2 in γ-irradiated cells. When we inhibit the MAPK signaling pathway using SP600125, JNK inhibitor, the expression of miR-26b was induced even in γ-irradiated H1299 cells. From these results, we concluded that the expression of miR-26b was coordinated regulated by MAPK signaling pathway upon ionizing radiation, and MAPK signaling pathway was regulated by miR-26b in turn.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: We analyzed the time-series miRNA profiles of radioresistant H1299 cells in response to 2 Gy of ionizing radiation (IR) by performing quadratic regression (QR) analysis to  identify genes associated with radioresistance

first: Woong-Yang


title: Microarray analysis of the Streptococcus suis serotype 2 transcriptional response to acidic conditions

status: Public on Sep 13 2011

city: Beijing

first: Ruifu

last: Yang

address: No.20, DOngdajie, Fengtai

institute: Institute of Microbiology and Epidemiology

summary: For a pathogen such as Streptococcus suis serotype 2, ecological success is determined by its ability to sense the environment and mount an appropriate adaptive transcriptional response. Thus, determining conditions for analysis of gene expression in vitro that are representative of the in vivo environment is critical for understanding the contributions of transcriptional response pathways to pathogenesis. In this study, we used analysis of the global expression profile in response to acidic pH in vitro and identified a set of regulated genes involved in diverse cellular processes. 196 (11%) genes were differentially regulated by the acid stress: 92 (47%) were down-regulated at low acid (pH 5.8) relative to the neutral condition (pH 7.2), whereas 104 (53%) were up-regulated at pH 5.8 versus pH 7.2. To confirm the microarray data, 16 genes were measured by quantitative RT-PCR. There was a strong positive correlation (r = 0.96) between the results obtained by microarray and quantitative RT-PCR. The data showed that S. suis S2 is equally capable of inducing an acid tolerance response with maximal protection provided after adaptation at pH 5.8 for survival.

overall_design: A cDNA microarray imprinted with 2156 genes representing about 98% of the Streptococcus suis serotype 2 genome was used for transcriptome analysis. For two-sample (reference vs. test) microarray hybridization, four independent bacterial cultures from each condition (pH 5.8, pH 7.2) were prepared as biological replicates for RNA isolation. Accordingly, four dual-fluorescence-labeled cDNA probes were prepared to hybridize with four slides. Pairwise comparisons were made using dye-swaps to avoid labeling bias. A ratio of mRNA levels (test/reference) was calculated for each gene. Significant changes of gene expression were identified with the SAM software. After the SAM analysis, only genes with at least 2-fold changes in expression were collected for further analysis.


title: Expression analysis of channel catfish anterior kidney at 48h post immersion vaccination with attenuated Edwardsiella ictaluri

status: Public on Sep 10 2011

city: AUBURN

first: julia

last: pridgeon

address: 990 WIRE ROAD

department: AAHRU

institute: USDA, ARS

summary:
To determine the global gene transcriptional changes in channel catfish anterior kidney after immersion vaccination with attenuated Edwardsiella ictaluri compared to sham vaccinated catfsih control.
The attenuated Edwardsiella ictaluri used for vaccination was Aquavac-ESC which was commercially available.

overall_design: A six chip study using total RNA samples including 3 control and 3 vaccinated samples. Each RNA sample used for microarray was poold fish anterior kidney samples (5 fish anterior kidney samples were pooled as one). Each chip measrues the expression level of 65,182 genes. For each sequence, 3 probes were selected. Two copies were prepared on arrays.

first: Julia

last: Pridgeon

first: Hung-Yueh

last: Yeh

first: Craig

last: Shoemaker


title: DNA copy number profiles of NSCLC tumors

city: Vancouver

first: Raj

last: Chari

state: BC

address: 675 West 10th Avenue

department: Cancer Genetics and Developmental Biology

country: Canada

institute: BC Cancer Research Centre

type: Genome variation profiling by genome tiling array

summary: Whole genome tiling path array CGH was used to measure the copy number profiles of 271 NSCLC tumors

overall_design: 271 microdissected NSCLC tumors

first: William

last: Lockwood

first: Wan

last: Lam


title: Expression data from granulocytic MDSC cultured with T cells in the absence of IFNgamma

status: Public on Sep 09 2011

city: Bethesda

first: Tim

last: Greten

address: 9000 Rockville Pike

institute: NCI

summary: Myeloid derived Suppressor cells (MDSC) are heterogenous popluation of cells consists of two major subsets namely the monocytic Gr-1dull/int. and granulocytic (Gr-1high). These distinct two subsets use different mechanism to inhibit T cell response. In addition, how the function of these subsets is regulated is not known yet. The Gr-1dull/int. MDSC are suppressing T cells through IFNg dependent nitric oxide dependent manner. However, the exact suppressive mechanism of Gr-1high MDSC is not clear. Here we studied the role of a cytokine IFNg on the suppressive function of Gr-1high MDSC by comparing the gene expression of Gr-1high cells cultured alone versus those cultured with T cells which donot produce IFNgamma.

overall_design: CD11b+Gr-1high cells were purified from the splenocyte of CT-26 colon tumor bearing mice. The purified CD11b+Gr-1high MDSCs were cultured with IFNg-/- antigen specific T cells and re- sorted after 48h and RNA was extracted and gene expression was analyzed using topic-defined PIQORTM Immunology Microarrays.

middle: F

first: Lydia

last: Haile


title: A new, highly conserved domain in Swi2/Snf2 is required for SWI/SNF remodeling

city: University Park

first: Sujana

last: Ghosh

state: PA

address: 453 North Frear

department: BMMB

institute: The Pennsylvania State University

summary: The in vivo role of a novel domain in Swi2/Snf2 required for its function was investigated using microarray analysis.

overall_design: The effect of domain deletions of Swi2/Snf2 on expression changes were studied. The ∆SnAC strain, along with Δsnf2 and wild type strains (BY4741 and Snf2-2FLAG, PSY2), were analyzed by genome-wide expression profiling with DNA microarrays. The method has been described in Chitikila et al., Mol. Cell, 10:871-882, 2002 (PMID 12419230).


title: MicroRNAs expression in 20(R)-ginsenoside Rg3-induced anti-angiogenesis

city: Hong Kong

first: Patrick

middle: YK

last: Yue

address: Waterloo Road

department: Biology

country: Hong Kong

institute: Hong Kong Baptist University

summary: The angio-suppressive effect of 20(R)-ginsenoside Rg3 (Rg3-R) has been previously demonstrated, and microRNAs (miRNAs) are a vital group of small non-coding RNAs that function as post-transcriptional modulator of gene expression. Thus, using human umbilical vein endothelial cells (HUVEC) as model, we compared the microRNA (miRNA) expression profile of vascular endothelial growth factor (VEGF)-induced cells with the profile of the cell co-treated with VEGF and Rg3-R. Among the screened 553 human miRNAs, 6 up-regulated (miR-520h, miR-487b, miR-197, miR-524*, miR-342 and miR-219) and 3 down-regulated (miR-23a, miR-489 and miR-377) miRNAs were detected in Rg3-R treated vascular endothelial growth factor (VEGF)-induced HUVECs compared to VEGF alone. Real time RT-PCR was subsequently performed to verify the miRNA microarray result.

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

overall_design: Two condition experiment: VEGF-induced HUVEC and VEGF-induced HUVEC treated with Rg3-R. Three independent microarray experiments, with triplicate per microarray.

first: Lai-Sheung

last: Chan

first: Man-Hong

last: Keung

first: Ying-Kit

first: Ngok-Shun

last: Wong


title: Screen glycosyltransferase ST6GalNAc2 KO mice and B4GalNT1/B4GalNT2 double KO mice relative to C75 Wild Type controls

status: Public on Sep 08 2011

city: La Jolla

first: Steven

last: Head

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

summary: The purpose of this experiment is to respond to the NIGMS mandate to screen Core F generated glycosyltransferase KO mice in Core E and Core C. The goal is to screen several tissues for gene expression changes in ST6GalNAc2 KO mice and B4GalNT1/B4GalNT2 double KO mice relative to C75 Wild Type controls. Tissues for Core E analysis were selected by mining public databases including the NIH GEO database for tissues that expressed the KO genes at moderate to high levels.

overall_design:
Results from Core E gene expression analysis are then used to help Core C select tissues to follow up with glycan analysis on in each of the KO mice.
For the ST6GalNAc2 KO mouse we selected: Brain, Small Intestine, Lymph Node and Thyroid for analysis. For the B4GalNT1/B4GalNT2 double KO mouse we selected: Kidney, Mammary Gland, Thymus and Testes for analysis. Wild type tissues were analyzed in parellel.

first: Bo

last: Ma

first: James

last: Paulson

first: Alex

middle: T

last: Moffit


title: Sanguinarine, putative anticancer therapeutic, interacts, modulates and transcripts in the context of chromatin

city: Bangalore

first: Tapas

middle: Kumar

last: Kundu

state: Karnataka

address: Jakkur

department: Molecular Biology and Genetics Unit

country: India

institute: Jawaharlal Nehru Centre for Advanced scientific Research

summary: DNA-binding anticancer agents cause alteration in chromatin structure and dynamics. Here, we report the dynamic interaction of the DNA intercalator and potential anticancer, plant alkaloid, sanguinarine (SGR) with chromatin. Association of SGR with different levels of chromatin structure was found to be enthalpy driven. Apart from DNA, it binds with comparable affinity to histones and induces chromatin aggregation. The dual binding property of SGR leads to inhibition of core histone modifications. Although it potently inhibits H3K9 methylation by G9a in vitro, H3K4 and H3R17 methylation are more profoundly inhibited in cells. SGR inhibits histone acetylation both in vitro and in vivo. It does not affect the in vitro transcription from DNA template but significantly represses acetylation-dependent chromatin transcription.  SGR mediated repression of epigenetic marks and the alteration of chromatin geography also result in modulation of global gene expression. These data conclusively show that the anticancer DNA-binding intercalator as a modulator of chromatin modifications and transcription in the chromatin context.

overall_design: The total RNA was isolated from control and treated cells using the TRIzol (Invitrogen) method. The Micromax direct labeling kit, MPS502 (PerkinElmer), was used to synthesize the labeled cDNA from 70 ug of total RNA and further process the hybridized cDNA on the array. All the steps were carried out according to manufacturer’s instructions (www.perkinelmer.com/lifesciences). The array slides were scanned immediately by the PerkinElmer Scan array Gx Microarray scanner. The Scan array software (PerkinElmer) was used for grid wise normalization of array images. Five arrays were used with at least two biological treatments of cells, and dye-swap experiments were included in the final analysis. The data was analysed by GeneSpring GX and Biointerpreter software from Genotypic Technology, Bangalore. The differential expression was considered if the Log 2 mean of at least -1 for the downregulated genes and +1 for the upregulated genes. We considered only the genes that were reproducible from all five replicates.

first: Kundu

last: Tapas

first: Selvi

last: B R


title: Unstable transcripts in Arabidopsis allotetraploids are associated with nonadditive gene expression in response to abiotic and biotic stresses

city: Austin

first: Z Jeffrey

middle: Jeffrey

last: Chen

state: TX

address: 2506 Speedway NMS 3.122 Stop A500

department: Molecular Biosciences

institute: The University of Texas at Austin

summary: Genome-wide analysis of gene expression has documented differential gene expression between closely related species in plants or animals and nonadditive gene expression in hybrids and allopolyploids compared to the parents. In Arabidopsis, 15-43% of genes are expressed differently between the related species, A. thaliana and A. arenosa, and the majority of them are nonadditvely expressed (differently from mid-parent value) in allotetraploids relative to the parents. The gene expression variation is associated with transcriptional and posttranscriptional mechanisms. Although transcriptional regulation by epigenetic mechanisms plays a role in nonadditive gene expression, the effects of posttranscriptional regulation on nonadditive gene expression is largely unknown. Here we reported a comprehensive genome-wide analysis of mRNA decay in Arabidopsis allotetraploids using oligo gene microarrays. Among ~26,000 annotated genes on the arrays, over 1% of genes showed a rapid decay rate with an estimated half-life of less than 60 min, and these genes are known as genes with unstable transcripts (GUTs). Interestingly, 30% of GUTs matched the nonadditively expressed genes, and their expression levels were significantly negatively correlated. These nonadditively expressed GUTs are highly enriched with a 2-8-fold increase compared to the proportion of all genes in the Gene Ontology (GO) classifications in response to stress, abiotic and biotic stimulus, signal transduction, and transcription. The data are consistent with the enrichment of nonadditvely-expressed genes in those categories in allopolyploids of Arabidopsis, wheat and cotton. Interestingly, the GUTs include some key transcription factors including circadian clock regulators, suggesting a mechanism for rapid response to light signalling and clock regulation in allotetraploids. These data collectively suggest an important role of mRNA stability in nonadditive expression of homoeologous genes in allopolyploids.

overall_design: A total of 8 slides were used for comparison (0 min vs. 120 min), including two biological and four technical replications. Each biological replication consists of two technical replications (four slides) that were hybridized with reverse-labeled probes	.

first: Jeffery

middle: Z

first: Eun-Deok

last: Kim


title: To study glycobiology-related abnormalities in retinal degeneration, an area that is relatively unexplored

summary: Retinal degeneration is the leading cause of irreversible blindness. Retinitis pigmentosa (RP) is a genetically heterogenous group of diseases.  In the United States, approximately one in 4000 individuals is affected.   RP begins with the loss of night vision due to the loss of rod photoreceptor cells.  The disease progresses slowly with the loss of peripheral vision, and eventually leads to complete debilitating and irreversible blindness. The first mutation associated with human RP was identified in the gene encoding rhodopsin, the G-protein coupled receptor of rod photoreceptor cells.  Mutations within the rhodopsin gene account for significant portion of RP cases.  Specifically, mutations of the proline at residue 347 in rhodopsin have been linked to human RP.

overall_design:
We are fortunate to have access to the P347S rhodopsin mutant mice. These mice represent an excellent transgenic mouse model of retinal degeneration. The P347S rhodopsin mutation is one of the best studied mutations, yet the mechanism by which the mutation causes degeneration is still unknown. One study has demonstrated that galectin-1 plays a role in degeneration of neuronal processes (1) and another study has shown that expression level of galectin-3 is elevated in retinas of patients with age-related macular degeneration. These studies in conjunction with the availibility of the P347S mutant mice have provided impetus to examine the pathogenesis of retinal degeneration in the context of the possible role of glycans and glycan-binding proteins. The time course of photoreceptor degeneration in the P347S mouse model has been carefully studied. In these mice, degeneration is barely detectable at 1 month of age, yet biochemical evidence suggests that the rod photoreceptor cells have already begun to die. At 4 months of age, approximately half of the rod photoreceptor cells have degenerated.
To distinguish involvement of glycogens at the various stages of retinal degeneration, we have collected retinas of wild type and the mutant mice at four time points (1, 2, 3, and 4 months of age). This will allow us to identify the genes that target early, mid- and late stages of the retinal degeneration process. Thus we request the analysis of total 24 samples as specified below: Age Group (months) Mice No of samples at each time point 1 Wild type 3 2 Wild type 3 3 Wild type 3 4 Wild type 3 1 P347S 3 2 P347S 3 3 P347S 3 4 P347S 3 Total 24.

first: Noorjahan

last: Panjwani


title: Microarray analysis of RNA of TCR transgenic CD8 T cells to assess the role of protein glycosylation in the decision between deletion vs. anergy in immune tolerance

summary: Activation of peripheral T lymphocytes in the absence of pathogen induced inflammation or costimulatory signals results in tolerance. Two different tolerance mechanisms have been described, deletion and anergy.  We recently demonstrated that an important variable which is responsible for the decision between anergy and deletion for CD8 T cells is the strength of signaling through the T cell receptor(Redmond and Sherman, Immunity 22:275,2005).  However, it is not know what the downstream signals are that result in death(deletion) vs. survival(anergy)of the activated cells.

overall_design:
Here we analysze additional conditions: 1) Wild Type mice were injected injected only once with a strain of vaccinia virus that express hemagglutinin from influenza; 2) BIM KO Clone 4 transgenic T cells were transferred into B10D2 mice then injected daily for 3 days with 1ug of KdHA peptide and sorted by flow cytometry according to their expression of CD8 and thy1.1; 3) Mice injected with 1 ug (deleted condition) of influenza hemaglutinin antigen (HA), 24 hours post injection CD8 T CL4 cells were sorted by flow cytometry (FacsARIA) and 4) WildType mice injected with 100 ug (anergic condition) of influenza hemaglutinin antigen (HA), 24 hours post injection CD8 T CL4 cells were sorted by flow cytometry (FacsARIA).
Dr. Sherman's lab aims to assess the role of protein glycosylation in the decision between deletion vs. anergy in immune tolerance, they have prepared purified TCR transgenic CD8 T cells stimulated in vivo using a strong antigenic signal (anergy conditions) or a weak antigenic signal (deletion conditions) with cognate antigen. Dr. Sherman's lab wishes to assess transcriptional differences in genes involved in protein glycosylation in these 2 cell populations. Then control population will be naïve transgenic CD8 cells. RNA preparations of mouse CD8 T cells from the B10D2 strain with three different conditions (Naïve, Deleted, and Anergic) were sent to the Microarray Core (E). The RNA was amplified, labeled, and hybridized to the GLYCOv4  microarrays.

first: Linda

last: Sherman


title: Glycan changes caused by insulin-deficient diabetes in the mouse liver

summary:
To determine the effect of insulin deficiency on global changes to expression of glycan related genes in the liver. See: Joseph R. Bishop,‡ Erin Foley,‡§ Roger Lawrence,‡ and Jeffrey D. Esko‡1 (2010) Insulin-dependent Diabetes Mellitus in Mice Does Not Alter Liver Heparan Sulfate* J Biol Chem. 2010 May 7; 285(19): 14658–14662.
We are studying the glycan changes caused by insulin-deficient diabetes in the mouse liver.  We would like to determine whether insulin-deficiency causes global changes to expression of glycan-related genes  in the liver.  Male C57BL/6 mice (4 weeks of age) were purchased from Jackson Laboratory and maintained in a temperature-controlled (25 °C) facility with a 12-h light/dark cycle. The derivation and genotyping of Ndst1f/fAlbCre+ mice have been described previously (16). Mice were fed laboratory rodent chow (Harlan-Teklad) ad libitum except when fasting blood specimens were obtained. Mice were made diabetic by administering 50 mg/kg body weight of streptozotocin (STZ; Sigma) intraperitoneally for 5 consecutive days. Because of variations in plasma triglycerides in females, only male mice were used in this study.

overall_design: Our preliminary results suggest glycosaminoglycan enzymes may be down-regulated, which may affect the turnover of lipids in the plasma.  Liver RNA samples from 3 diabetic mice will be compared to 3 wildtype samples for properly controlled analysis.

first: Jeffrey

last: Esko


title: Canine osteosarcoma cell lines and tissues

city: Minneapolis

first: Aaron

last: Sarver

state: MN

address: 425 East River Road

department: Masonic Cancer Center

institute: University of Minnesota

summary: Cell lines and tumor tissues from canine osteosarcomas with accompanying survival and breed data.

overall_design: Comparisons of gene expression between osteosarcoma-derived cell lines and osteosarcoma tissues.

first: Scott

last: Milcah


overall_design:
Marth and co-workers have previously shown that CD8 T cell apoptosis under conditions similar to those that occur during tolerance in vivo may involve a change in protein glycosylation (Van Dyken et.al., Mol.Cell.Bio.27:1096,2007).In order to assess the role of protein glycosylation in the decision between deletion vs. anergy in immune tolerance, we have prepared purified TCR transgenic CD8 T cells stimulated in vivo using a strong antigenic signal (anergy conditions) or a weak antigenic signal (deletion conditions) with cognate antigen.  We wish to assess transcriptional differences in genes involved in protein glycosylation in these 2 cell populations.  The control population will be naive trangenic CD8 cells.
Dr. Sherman's lab aims to assess the role of protein glycosylation in the decision between deletion vs. anergy in immune tolerance, they have prepared purified TCR transgenic CD8 T cells stimulated in vivo using a strong antigenic signal (anergy conditions) or a weak antigenic signal (deletion conditions) with cognate antigen. Dr. Sherman's lab wishes to assess transcriptional differences in genes involved in protein glycosylation in these 2 cell populations. Then control population will be naïve transgenic CD8 cells. RNA preparations of mouse CD8 T cells from the B10D2 strain with three different conditions (Naïve, Deleted, and Anergic) were sent to the Microarray Core (E). The RNA was amplified, labeled, and hybridized to the GLYCOv4 microarrays.


title: Salivary cytokine alterations in HIV infection part 2

city: New York

first: Minal

last: Dalvi

state: NY

address: 345 East 24th Street, Rm 917

department: Department of Basic Science

institute: New York University

summary: A 507 protein microarray was employed to provide a broad view of cytokines and chemokines in saliva and plasma in acutely HIV  infected subjects as compared to uninfected subjects. A 40 cytokine custom array derived from the initial results was refined to highlight those molecules with significant change relative to control subjects indicating the potential for biological impact.

overall_design: Systemic and local (oral mucosal) immune responses in acutely infected HIV individuals before the initiation of HAART have not been well characterized. Protein microarrays were used to analyze saliva and plasma from HIV infected and HIV uninfected subjects to identify new biomarkers for HIV disease progression and pathogenesis.

first: William

last: Abrams

first: Cheryl

last: Barber

first: Robert

last: Norman

first: Daniel

last: Malamud


title: Salivary cytokine alterations in HIV infection part 1

summary: Systemic and local (oral mucosal) immune responses in acutely infected HIV individuals before the initiation of HAART have not been well characterized. Protein microarrays were used to analyze saliva and plasma from HIV infected and HIV uninfected subjects to identify new biomarkers for HIV disease progression and pathogenesis.

overall_design: A 507 protein microarray was employed to provide a broad view of cytokines and chemokines in saliva and plasma in acutely HIV infected subjects as compared to uninfected subjects. A custom array derived from the initial results was refined to highlight those molecules with significant change relative to control subjects indicating the potential for biological impact.


title: To determine whether sialyltransferases, sulfotransferases, and/or MUC genes are expressed and if they are induced by PMA

first: Steven

last: Head

summary: We are interested in having the gene microarray done on untreated and PMA treated (10 nM x 24 hr) human and mouse epithelial cells lines including CALU-3, MLE-15, primary bronchial human airway epithelial cells.  We are especially interested in seeing whether sialyl or sulfo transferases, and MUC genes, are present and if they are induced by PMA.  We hope to use this information to optimize future experiments designed to identify Siglec lung ligands.

overall_design:
The lab is interested in studying untreated and PMA treated (10 nM x 24 hr) human and mouse epithelial cells lines including CALU-3, MLE-15, primary bronchial human airway epithelial cells.
With special interest in understanding whether sialyl or sulfo transferases, and MUC genes, are present and if they are induced by PMA.

first: Bruce

last: Bochner

first: Alex


title: ChIP-chip from Drosophila egg chambers using ORC2 antibody

status: Public on Sep 07 2011

first: Terry

last: Orr-Weaver

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: Chromatin immunoprecipitation of the Origin Recognition Complex (ORC) followed by hybridization to genome-wide tiling microarrays demonstrated that ORC does not localize to DAFC-34B after stage 10, despite a second round of replication initiation

overall_design: Comparison of ORC2 ChIP sample compared to input DNA for Drosophila egg chambers

first: Jane


title: ChIP-chip from Drosophila egg chambers using MCM2-7 antibody

summary: Chromatin immunoprecipitation of the MCM2-7 replicative helicase followed by hybridization to genome-wide tiling microarrays demonstrated that MCMs localize to the follicle cell amplicons at stages of replication initiation

overall_design: Comparison of MCM2-7 ChIP sample compared to input DNA for Drosophila egg chambers


title: Localization of Isw1-3xFLAG in wild-type yeast.

city: Kansas City

first: Michaela

last: Smolle

state: Missouri

address: 1000 E 50th Street

institute: Stowers Institute for Medical Research

summary: ChIP-chip assays to determine the localisation of 3xFLAG tagged Isw1 in wild-type yeast.

overall_design:
Two color experiment. ChIP/Input. Biological replicates=3.
Other data used in this study are provided in GEO Series GSE31015 and GSE31833.

first: Jerry

last: Workman


title: Murine lung transcripts during soluble egg antigen (SEA)-induced allergic asthma and bleomycin-induced pulmonary fibrosis in Wildtype, IL-13Ra1 and IL-13Ra2 deficient mice sensitized and challenged

city: Princeton

first: Sudhir

last: Varma

state: NJ

address: 1215 Wessex Pl

institute: HiThru Analytics

summary: Transcriptional profiling of mouse lungs by comparing PBS and saline treated lungs with SEA and bleomycin treated lungs, respectively. Mice strains used in this study include wild type (C57BL/6), IL-13Ra1 and IL-13Ra2 deficient mice.

overall_design: In mouse model of allergic asthma, mice were sensitized twice (day0 and day14) by i.p. injection of 10 µg of SEA. On days 28 and 31 mice were anesthetized with a mixture of xylazine and ketamine and given an intratracheal (I.T) airway challenge with 10 µg of SEA. Mice were sacrificed 24 h after the final airway challenge (day 32) and lungs were collected for RNA preparation. Biological replicates include 5 PBS treated and 5 SEA treated mice. In bleomycin-induced fibrosis odel, mice were anaesthetized with a xylazine and ketamine cocktail and given 0.15 U bleomycin sulfate (EMD) in saline or saline alone via the I.T. route. On day 7, mice were sacrificed and ungs were collected for RNA preparation. Biological replicates include 4 saline treated and 4 bleomycin treated mice. Goal was to determine IL-13 receptors regulated genes during SEA induced allergic asthma and bleomycin-induced fibrosis. Fluorescent cDNA targets were prepared from a 20 μg experimental RNA sample (SEA or bleomycin challenged group–dUTPCy5 – Amersham, Piscataway, NJ) and a 20 μg reference RNA sample (PBS or saline treated group–dUTPCy3- Amersham, Piscataway, NJ). Equal quantities of the above labeled cDNA (experimental and reference labeled RNA samples) were mixed and any free label present in the sample was removed by washing 3 times using a 10 kDa cutoff Vivaspin filters (Millipore). Labeled fluorescent cDNA targets were hybridized on the Whole Mouse Genome Oligo Microarray Kit (Agilent, Palo Alto, CA) containing more than 41000 gene probes.

first: Thomas

last: Wynn

first: Satish

middle: K

last: Madala


title: Ehrlichia chaffeensis Transcriptome in Mammalian and Arthropod Hosts Reveals Differential Gene Expression and Post Transcriptional Regulation

city: Galveston

first: Jeeba

last: Kuriakose

address: 301 University Blvd

department: Pathology

institute: University of Texas Medical Branch

summary:
Background
Human monocytotropic ehrlichiosis is an emerging life-threatening zoonosis caused by obligately intracellular bacterium, Ehrlichia chaffeensis. E. chaffeensis is transmitted by the lone star tick, Amblyomma americanum, and replicates in mononuclear phagocytes in mammalian hosts. Differences in the E. chaffeensis transcriptome in mammalian and arthropod hosts are unknown. Thus, we determined host-specific E. chaffeensis gene expression in human monocyte (THP-1) and in Amblyomma and Ixodes tick cell lines (AAE2 and ISE6) using a whole genome microarray.

Methodology/Principal Findings
The majority (~80%) of E. chaffeensis genes were expressed during infection in human and tick cells. There were few differences observed in E. chaffeensis gene expression between the vector Amblyomma and non-vector Ixodes tick cells, but extensive host-specific and differential gene expression profiles were detected between human and tick cells, including higher transcriptional activity in tick cells and identification of gene subsets that were differentially expressed in the two hosts. Differentially and host-specifically expressed ehrlichial genes encoded major immunoreactive tandem repeat proteins (TRP), the outer membrane protein (OMP-1) family, and hypothetical proteins that were 30–80 amino acids in length. Consistent with previous observations, high expression of p28 and OMP-1B genes was detected in human and tick cells, respectively. Notably, E. chaffeensis genes encoding TRP32 and TRP47 were highly upregulated in the human monocytes and expressed as proteins; however, although TRP transcripts were expressed in tick cells, the proteins were not detected in whole cell lysates demonstrating that TRP expression was post transcriptionally regulated.

Conclusions/Significance
Ehrlichia gene expression is highly active in tick cells, and differential gene expression among a wide variety of host-pathogen associated genes occurs. Furthermore, we demonstrate that genes associated with host-pathogen interactions are differentially expressed and regulated by post transcriptional mechanisms.

overall_design: A microarray (4-plex) study using E. chaffeensis cultivated in each cell line (THP-1, AAE2 and ISE6), three biological replicates/cell line. For each cell line, RNA was also extracted from uninfected cells (negative controls) and was processed similar to the infected cells; these samples were used for background subtraction during data analysis.

first: Jere

middle: W

last: McBride


title: Effect of Cu-Nanoparticles versus Cu-salt in Enchytraeus albidus (Oligochaeta): differential gene expression through microarray analysis

city: Aveiro

first: Susana

middle: Isabel Lopes

last: Gomes

address: Campus Universitário de Santiago, Departement of Biology, University of Aveiro

country: Portugal

institute: CESAM & University of Aveiro

summary: Despite the increased utilization of nanoparticles, the behavior and effect in the environment is largely unknown and few resources are available for health and environmental effect studies. Enchytraeids are extensively used in studies of soil ecotoxicology and recently, a cDNA microarray for Enchytraeus albidus was developed, allowing also toxicogenomic studies in this species. These organisms are ecologically relevant small worms that indirectly contribute to the regulation and degradation of organic matter. In this study we compared the gene expression profiles of E. albidus when exposed to copper-salt (CuCl2) and copper nanoparticles (Cu-NP) spiked soil. The worms were exposed for 48 hours in soil to a range of concentrations. Microarray hybridizations revealed different response patterns between copper-salt and copper nanoparticles exposed organisms, these differences are mainly related with transcripts involved in the energy metabolism of the organisms. Despite unknown gene function in the data-set there are indications that Cu-salt and Cu-NP exposure induced specific gene level responses.

overall_design: Fluorescently labelled cDNA, from enchytraeids exposed during 2 days to control soil (from Hygum site in Denmark) and to the different exposure conditions (Cy5), was synthesized for microarray analysis and hybridizations were performed. After scanning, spots were identified and ratios quantified using the QuantArray (Packard Biochip Technologies). Statistical analysis of the microarrays was performed using limmaGUI package (1.18.0) (Smyth, 2005) in the R (2.8.0) software environment (http://www.R-project.org/). After being submitted to local background subtraction, microarrays were normalized using global loess method. To statistically evaluate the differential gene expression between the different conditions, a gene-per-gene linear model (limma – linear model for microarray analysis) and empirical Bayes methods were applied. The results were then corrected for multiple testing using the Benjamini-Hochberg’s method (adjusted p<0.05 was considered significant) (Benjamini and Hochberg, 1995).

first: Sara

last: Novais

first: Janeck

last: Scott-Fordsmand

first: Wim

last: Coen

first: Amadeu

last: Soares

first: Mónica

last: Amorim


title: Effects of soil properties and time of exposure on gene expression of Enchytraeus albidus (Oligochaeta).

summary: Changes in soil properties (e.g. pH, organic matter content, granulometry) can influence chemical toxicity to organisms and act alone as stressors. Previous studies on Enchytraeus albidus showed that changes in soil properties caused effects on reproduction and avoidance behavior and also oxidative stress. In addition, results at the transcritptomic level indicated changes in gene expression profile due to soil properties changes. In this study, E. albidus was exposed to modified versions of the artificial standard OECD soil (different pH, OM and clay content) in different exposure times (2, 4 and 8 days). The gene expression profile was characterized using a class comparison statistical analysis. Results indicated that the transcriptional response was time dependent, with different genes being affected at different time points. Results also showed some genes (and biological functions) being affected in a soil specific way.

overall_design:
Fluorescently labelled cDNA, from enchytraeids exposed during 2, 4 and 8 days OECD standard soil (Cy3) and to the different exposure conditions (modified OECD soil) (Cy5), was synthesized for microarray analysis and hybridizations were performed. After scanning (Agilent Microarray Scanner from Agilent Technologies), spots were identified and ratios quantified using Quantarray (Packard Biochip Technologies).
Statistical analysis of the microarrays was performed using BRB Array Tools version 3.8.1 Stable Release (http://linus.nci.nih.gov/BRB-ArrayTools.html). After background subtraction, the replicated spots within each array were averaged, and microarrays were normalized using loess method (Smith and Speed, 2003). Statistical class comparison between groups of arrays was performed between each exposure condition and the respective “control” (exposure in OECD standard soil, for each time of exposure) using two-sample T-test and 95% of confidence level for the assessment of differentially expressed genes.


title: To examine vascular smooth muscle cells (VSMC) under  four conditions

status: Public on Sep 06 2011

first: Steven

state: CA

summary: Vascular calcification is a hallmark of atherosclerosis and end-stage renal disease (ESRD).  However, the molecular mechanism of vascular calcification is poorly understood.  Diabetes mellitus is increasingly recognized as the most important cause for atherosclerosis and ESRD.  Emerging evidence supports the concept that vascular calcification resembles the process of osteogenesis, in which the vascular smooth muscle cells (VSMC) undergo osteochondrogenic differentiation.  Recently, we have established an in vitro calcification system with primary mouse VSMC. With the use of osteogenic stimuli, we induced trans-differentiation of primary mouse VSMC into bone-like cells.  Interestingly stroptozotocin (STZ), O-GlcNAcase inhibitor and a drug that has been used to induce diabetes in mice, was able to induce calcification of VSMC and the expression of the osteogenic transcription factor Runx2, suggesting glycosylation may be involved in regulation of Runx2. We have reported an essential role of Runx2 in oxidative stress-induce VSMC calcification and have recently generated a tissue specific mouse with Runx2 ablation in smooth muscle cells.

overall_design:
Therefore, we will use STZ and other relevant reagents in the glucose synthesis/metabolism pathways as stimuli for VSMC calcification to characterize the glycogene profiles during VSMC calcification. Results from VSMC of Runx2 knockout mice will be compared with those from control mice to determine the regulation of calcification-associated glycogenes by Runx2 in response to STZ.  These studies will provide foundation for further mechanistic studies and may lead to identification of novel strategies and targets for diabetes-induced vascular calcification.
To examine vascular smooth muscle cells (VSMC)  under two conditions:  1) wild-type VSMC differentiated into bone-like cells with osteogenic media,  2) wild-type VSMC treated with STZ and osteogenic media

first: Hui

last: Wu

last: Moffit