title: PatE in transcriptional activation of acid-resistance pathways of enterohemorrhagic Escherichia coli strain EDL933

status: Public on Mar 30 2012

city: Parkville

first: Matthew

last: Wakefield

state: VIC

address: 1G Royal Parade

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute

summary: An experiment to identify the downstream targets of PatE, a prophage encoded AraC-like transcriptional regulator, in transcriptional activation of acid-resistance pathways of enterohemorrhagic Escherichia coli strain EDL933 using deletion and complementation strains (Delta3 and Delta3_1, respectively).

overall_design:
Incomplete 2 factor with dye swaps. Genotype: 3 levels (wt, detla3, delta3_1)  Bicarbonate: 2 levels (pos, neg) on wt only. 4 biological replicates, 2 in each dye orientation.
Microarrays processed at Australian Genome Research Facility.

first: Jenifer

middle: K

last: Bender

first: Marija

last: Tauschek

first: Roy

last: Robins-Browne


title: Estrogen Regulates the JNK1 Genomic Localization Program in Breast Cancer Cells to Control Gene Expression and Cell Growth

status: Public on Apr 01 2012

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

country: USA

institute: UT Southwestern Medical Center

type: Genome binding/occupancy profiling by genome tiling array

summary: JNK1 ChIP-chip and ER-alpha ChIP-chip were performed on NimbleGen genomic tiling arrays to understand the genomic binding patterns of this MAP kinase and receptor and their relationship to gene expression.

overall_design:
ChIP-chip analysis of JNK1 occupancy at promoters before and after estrogen treatment. 2 biological replicates (rep1 and rep2, rep3A and rep3B), 2 technical replicates each.
ChIP-chip analysis of ER-alpha occupancy at promoters before and after estrogen treatment. 2 biological replicates, 2 technical replicates for one of the replicates (1 and 2).

first: Miao

last: Sun

first: Gary

middle: D

last: Isaacs

first: Nasun

last: Hah

first: Nina

last: Heldring

first: Elizabeth

middle: A

last: Fogarty

first: William

middle: L


title: Colon tissue of Il10-/- mice monoassociated with Escherichia coli NC101 or Escherichia faecalis OG1RF (PAMM-073 array)

status: Public on Jul 04 2012

city: Chapel Hill

first: Janelle

middle: C

last: Arthur

state: NC

address: 111 Mason Farm Rd

institute: University of North Carolina at Chapel Hill

summary: We observed that interleukin-10 knockout (Il10-/-) mice injected with azoxymethane (AOM) and monoassociated with E. coli NC101, but not E. faecalis OG1RF, develop tumors. Histologic inflammation is not different in mice monoassociated with either bacterium. The goal of this experiment is to assess inflammatory cytokine levels in colonic tissue of these mice.

overall_design: 4 germ-free Il10-/- mice were assayed and used as controls. 4 E. coli and 4 E. faecalis monoassociated mice were experimental samples.

first: Christian

last: Jobin


title: Colon tissue of Il10-/- mice monoassociated with Escherichia coli NC101 or NC101-delta-pks

summary: We observed that deletion of polyketide synthase (pks) from E. coli NC101 reduces its ability to induce tumors in interleukin-10 knockout (Il10-/-) mice injected with azoxymethane (AOM), without altering histologic inflammation. The goal of this experiment is to assess inflammatory cytokine levels in colonic tissue of these mice.

overall_design: 2 germ-free Il10-/- mice were assayed and used as controls. 3 E. coli NC101 and 3 E. coli NC101-delta-pks monoassociated mice were experimental samples.


title: Expression analysis of Salmonella enterica serovar Typhimurium UK1 delta-iacP mutant

status: Public on Apr 30 2012

city: Seoul

first: Yong Keun

last: Park

address: Anam-dong 5Ga, Seoungbuk-Gu

department: School of Life Sciences and Biotechnology

country: South Korea

institute: Korea University

summary:
Investigation of whole genome gene expression level changes in a Salmonella enterica serovar Typhimurium UK1 delta-iacP mutant, compared to the wild-type strain. IacP is resoponsible for the secretion of virulence effector proteins via the type III secretion system, thereby contributing the virulence of S. Typhimurium.
The mutants analyzed in this study are further described in Kim et al. 2011. Role of Salmonella Pathogenicity Island 1 Protein IacP in Salmonella enterica Serovar Typhimurium Pathogenesis. Infection and Immunity 79(4):1440-1450 (PMID 21263021).

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. UK-1

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

overall_design: A chip study using total RNA recovered from two separate wild-type cultures of Salmonella enterica serovar Typhimurium UK1 and two separate cultures of a mutant strain, Salmonella enterica serovar Typhimurium UK1 delta-iacP. Each chip measures the expression level of 4,302 genes from Salmonella enterica serovar Typhimurium.

first: YongKeun

first: JeongSeon

last: Eom


title: Trancriptome analysis of honey bees (Apis mellifera) infected with Nosema ceranae

status: Public on May 23 2012

city: Notre Dame

first: Jacqueline

last: Lopez

state: Indiana

address: 019 Galvin Life Science Center

department: Biology

institute: University of Notre Dame

type: Expression profiling by genome tiling array

summary: The microsporidia Nosema ceranae are intracellular parasites that proliferate in the midgut epithelial cells of honey bees (Apis mellifera). To analyze the pathological effects of those microsporidia, we orally infected honey bee workers 7 days after their emergence. Bees were flash frozen 15 days after the infection. Then, the effects on the gut ventriculi were analyzed and compared to non-infected (control) bees.

overall_design: Comparisons of control vs Nosema ceranae bees

first: Cedric

last: Alaux

first: Jeong-Hyeon

last: Choi


title: The bovine mammary transcriptome: functional adaptation of the mammary gland during the lactation cycle

status: Public on Mar 01 2012

city: Corvallis

first: Massimo

last: Bionaz

state: OR

address: 316A Withycombe Hall

department: Animal and Rangeland Sciences

institute: Oregon State University

summary: Bovine mammary gland provide the largest amount of milk for dairy industry to date. Insight in functional adaptation of this organ is critical in order to improve efficiency of milk synthesis and milk quality. In the present experiment microarray analysis in combination with bioinformatics tools was performed in mammary tissue from 8 Holstein cows during the entire lactation cycle.

overall_design: The mammary biopsy was performed at -30, -15, 1, 15, 30, 60, 120, 240, and 300 days (d) relative to parturition. A dye-swap reference design (reference =  mixture of RNA from several bovine tissues) was used.

first: Sandra

last: Rodriguez-Zas

first: Robin

middle: E

last: Everts

first: Harris

last: Lewin

first: Walter

last: Hurley

first: Juan

middle: J

last: Loor


title: Differential expressed miRNAs in Multi-stages and Lymphoid node metastasis of Nasopharyngeal Carcinoma

city: Changsha

first: luo

last: zhaohui

state: Hunan

address: 110 Xiangya Road

country: China

institute: Cancer  Research  Institute

summary: According to the evolution of the NPC, with normal time series, we identified microRNAs (miRNAs) showing robust differential expression between nasopharyngeal carcinomas (NPCs) and normal healthy nasopharyngeal epithelial samples. This research use miRNA chip testing at different stages in 12 cases of NPC (TNM Ⅰ - II, III, IV each stage 4 cases), 4 patients matched sample and transfer lymphoma 6 samples. Analysis the difference miRNA distribution of in the NPC development, adopt modern bioinformatics methods selection differentially expressed genes.

overall_design: we study the miRNA dynamic expression profiles in different clinical stages of nasopharyngeal carcinoma and NPC lymphoid node metastasis. Samples were taken from a range of tumors of different stages. 6 cases of normal, 4 respective cases of stage I or II, III, IV and lymph node metastasis. The microdissection was performed with Methyl Green staining to separate tumor cells to non-tumor cells.

first: zhaohui

last: luo

first: zheng

last: li

first: juanjuan

last: xiang


title: Epigenetic Disruption of Cadherin-11 in human cancer metastasis

status: Public on Mar 06 2012

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

country: Spain

institute: IDIBELL

summary: The analyses of paired primary tumors-lymph node metastasis cell lines reveal the existence of metastasis-specific epigenetic events that might contribute to the progression of the disease.

overall_design: Total DNA isolated by standard procedures from primary tumor and lymph node metastasis cell lines cultured under standard conditions

first: Javier

middle: F

last: Carmona

first: Alberto

last: Villanueva

first: Clara

last: Muñoz

first: Rosa

middle: M

last: Penin

first: Montserrat

last: Goma

first: Josep

last: Piulats

first: Ricard

last: Mesia

last: Sanchez-Cespedes

last: Manos

first: Enric

last: Condom

first: Suzanne

last: Eccles


title: Differences in transcription levels among wild, domesticated, and hybrid Atlantic salmon (Salmo salar) from two environments

status: Public on Apr 23 2012

city: Halifax

first: Paul

middle: Vincent

last: Debes

state: NS

address: 1355 Oxford St

country: Canada

institute: Dalhousie University

summary: Escaped domesticated individuals can introduce disadvantageous traits into wild populations due to both adaptive differences between population ancestors and human-induced changes during domestication. In contrast to their domesticated counterparts, some endangered wild Atlantic salmon populations encounter during their marine stage large amounts of suspended sediments, which may act as a selective agent. We used microarrays to elucidate quantitative transcriptional differences between a domesticated salmon strain, a wild population and their first-generation hybrids during their marine life stage, to describe transcriptional responses to natural suspended sediments, and to test for adaptive genetic variation in plasticity relating to a history of natural exposure or nonexposure to suspended sediments. We identified 67 genes differing in transcription level among salmon groups. Among these genes, processes related to energy metabolism and ion homoeostasis were over-represented, while genes contributing to immunity and actin-/myosin-related processes were also involved in strain differentiation. Domestic–wild hybrids exhibited intermediate transcription patterns relative to their parents for two-thirds of all genes that differed between their parents; however, genes deviating from additivity tended to have similar levels to those expressed by the wild parent. Sediments induced increases in transcription levels of eight genes, some of which are known to contribute to external or intracellular damage mitigation. Although genetic variation in plasticity did not differ significantly between groups after correcting for multiple comparisons, two genes (metallothionein and glutathione reductase) tended to be more plastic in response to suspended sediments in wild and hybrid salmon, and merit further examination as candidate genes under natural selection.

platform_organism:
Oncorhynchus mykiss
Salmo salar

overall_design: Salmon of three genotypes (strains: 1. wild (Stewiacke River salmon), 2. domesticated (Saint John River salmon), and 3. first generation hybrids between the two strains, were exposed to two environments (treatment: 1. suspended sediments, 2. control: clear water), using eight biological replicates (individuals) of each of the six experimental groups, summing up to 48 individuals, each individual has two technical replicates , each technical replicate has been labelled with a different dye, each technical replicate appears on a different array, dye swaps are equilibrated for arrays that combine individuals from different genotypes and for arrays that combine individuals from the same genotype but different environments. Technical replicates of individuals always appear once on arrays that compare between environments and once on arrays that compare among genotypes. In total there are 48 arrays.

middle: V

first: Eric

last: Normandeau

first: Dylan

last: Fraser

first: Louis

last: Bernatchez

first: Jeffrey

last: Hutchings


title: Targeted transcriptome analysis of the SigB regulon in Bacillus subtilis

status: Public on Mar 14 2012

city: Greifswald

first: Leif

last: Steil

address: Friedrich-Ludwig-Jahn Str. 15A

department: Genetics and Functional Genomics

country: Germany

institute: University of Greifswald

summary: Bacillus subtilis is exposed to a wide range of transitory stress and starvation conditions. Here we investigate the expression changes observed in the B. subtilis wild type strain 168 and its isogenic sigB mutant(BSM29) with respect to each stress condition tested.

overall_design: Gene expression was queried for the stress conditions: ethanol-, butanol-, osmotic- and oxidative stress, heat shock, low temperature growth, glucose as well as oxygen limitation. For butanol-, ethanol-, osmotic-, and oxidative stress as well as heat shock : time points (0min, 5min, 10min, 15min and 20min) ; for glucose limitation and oxygen limitation : time points (0min, 15min, 30min, 45min, 60min or 90min) and for low temperature growth, samples for recording of expression values were taken during mid-exponential growth at OD540 0.9 and 1.0.

first: Priyanka

last: Nannapaneni

first: Falk

last: Hertwig

first: Maren

last: Depke

first: Michael

last: Hecker

first: Ulrike

last: Mäder

first: Uwe

last: Völker

first: Sacha

last: van Hijum


title: Examination of functional interplay between NMNAT-1 (a nuclear NAD+ synthase) and PARP-1 (a nuclear poly(ADP-ribose) polymerase)

status: Public on Feb 15 2012

first: W. Lee

last: Kraus

summary:
NMNAT-1 and PARP-1, two key enzymes in the NAD+ metabolic pathway, localize to the nucleus where integration of their enzymatic activities has the potential to control a variety of nuclear processes.  Using a variety of biochemical, molecular, cell-based, and genomic assays, we show that NMNAT-1 and PARP-1 physically and functionally interact at target gene promoters in MCF-7 cells.  Specifically, we show that PARP-1 recruits NMNAT-1 to promoters, where it produces NAD+ to support PARP-1 catalytic activity, but also enhances the enzymatic activity of PARP-1 independent of NAD+ production.  Furthermore, using two-photon excitation microscopy, we show that NMNAT-1 catalyzes the production of NAD+ in a nuclear pool that may be distinct from other cellular compartments.  In expression microarray experiments, depletion of NMNAT-1 or PARP-1 alters the expression of about 200 protein-coding genes each, with about 10% overlap between the two gene sets.  NMNAT-1 enzymatic activity is required for PARP-1-dependent PARylation at the promoters of commonly regulated target genes, as well as the expression of those target genes. Collectively, our studies link the enzymatic activities of NMNAT-1 and PARP-1 to the regulation of a set of common target genes through functional interactions at target gene promoters.
We examined the co-localization of NMNAT-1 and PARP-1 at RefSeq promoters in MCF-7 cells using ChIP-chip

overall_design: Five samples:(1) two FLAG-NMNAT-1 IP'd with FLAG antibody from MCF-7 cells ectopically expressig FLAG-NMNAT-1 and (2) three native PARP-1 IP'd from parental MCF-7 cells with PARP-1 antibody

first: W

first: Tong

last: Zhang


title: Development of gene expression profile in different tissues of zebra mussel and larvae

status: Public on Jan 27 2012

city: Barcelona

first: Anna

last: Navarro Cuenca

address: C/Jordi Girona 18-26

department: Environmental Toxicology

institute: IDAEA-CSIC

summary: To analyze the different pattern of expression among tissues in D. polymorpha it was used acustom microarray designed in our laboratory using 4057 publicly availabe DNA sequences from Dreissena and other realted genera. Transcriptome profiles were analyszed using gills, digestive gland, gonad and half a body of adult zebra mussel and larvae 24 h pf. The samples analyzed in the microarray were not treated in order to detect the normal pattern of expression in each tissue. A total of 221 transcripts changed significantly their mRNA levels in the different tissues (ANOVA p<0.01, fc ±1.5). The results showed a clear separation on transcriptome profiles between samples with the main changes in gills, larvae and half a body.

overall_design: Non treated animals were use to study different patterns of gene expression in different tissues using gills, digestive gland, gonad from both sexes, and half a body as well as larvae. It was used 2 replicate for each tissue.

last: Navarro

first: Bruno

last: Campos


title: Identification and pathway analysis of microRNAs with no previous involvement in breast cancer.

status: Public on Mar 10 2012

city: Mexico City

first: Alfredo

last: Hidalgo-Miranda

address: Periferico Sur 4124, Torre Zafiro II, piso 6

country: Mexico

institute: National Institute of Genomic Medicine

summary: microRNA expression signatures can differentiate normal and breast cancer tissues and can define specific clinico-pathological phenotypes in breast tumors. In order to further evaluate the microRNA expression profile in breast cancer, we analyzed the expression of 667 microRNAs in 29 tumors and 21 adjacent normal tissues using TaqMan Low-density arrays. 130 miRNAs showed significant differential expression (adjusted P value=0.05, Fold Change=2) in breast tumors compared to the normal adjacent tissue. Importantly, the role of 43 of these microRNAs has not been previously reported in breast cancer, including several evolutionary conserved microRNA*, showing similar expression rates to that of their corresponding leading strand.

overall_design: The procedure begins with the retro-transcription of 70ng of total RNA with stem-loop primers to obtain a cDNA template. A pre-amplification step was included in order to increase the concentration of the original material and to detect microRNAs that are expressed at low levels. The pre-amplified product was loaded into the TaqMan® Low Density Arrays and amplification signal detection was carried out using the 7900 FAST real time thermal cycler (ABI). A total of 29 tumor and 21 normal samples (two pools: one containing five samples, other containing 12 samples, plus 4 independent normal samples) were analyzed. 23 tumors and the two normal pools were processed by triplicate, representing 82% of the total samples.

first: Sandra

last: Romero-Cordoba

first: Sergio

last: Rodriguez-Cuevas

first: Rosa

last: Rebollar-Vega

first: Valeria

last: Quintanar-Jurado

first: Antonio

last: Maffuz-Aziz

first: Gerardo

last: Jimenez-Sanchez

first: Veronica

last: Bautista-Piña

first: Rocio

last: Arellano-Llamas


title: The search of genetic resources for parthenocarpic pears and comparison of gene expression between high and low parthenocarpy cultivars

status: Public on Jan 10 2012

city: Tsukuba

first: Chikako

last: Nishitani

state: Ibaraki

country: Japan

institute: National Institutes of Fruit Tree Science

summary: Parthenocarpy—the production of seedless fruits without fertilization—is very useful for fruit cultivation. Among pear cultivars (Japanese, Chinese, and European pears and their interspecific hybrids) subjected to flower emasculation and left unpollinated, only some of the European pears had a stable and high degree of fruit set and fruit enlargement. Almost all the enlarged fruits formed no seeds. Comparison of fruits produced by using emasculation without pollination or with self-pollination ruled out the possibility of stenospermocarpy in these parthenocarpic pears. The results suggested that the abovementioned characteristics were inherited maternally by the next generation and that it should be possible to introduce parthenocarpy into Japanese pears. Neither Chinese nor Japanese pears treated with emasculation and no pollination showed consistently stable fruit set or fruit enlargement. In Chinese pears, these characteristics varied greatly from year to year, and in Japanese pears they were stable but weak. Although in each cultivar highly parthenocarpic fruits weighed slightly less than cross-pollinated ones, the cortexes of the emasculated fruits were enlarged and the fruits were not greatly inferior to those of cross-pollinated ones. By using a customized pear cDNA microarray, we compared the gene expression profiles of highly and weakly parthenocarpic cultivars before flowering. Expression of several phenylpropanoid-related genes and photosystem-related genes differed significantly between the two groups. Some of these genes were contained in the chloroplast genome. These results showed the unique mechanism of genetic parthenocarpy in pome fruits as opposed to non-pome fruits.

sample_organism:
Pyrus pyrifolia
Pyrus communis
Pyrus hybrid cultivar
Pyrus communis x Pyrus pyrifolia

overall_design: The gene expression profiles between high and low parthenocarpy group before flowering were compared.

first: Fumiko

last: Hosaka

first: Shingo

last: Terakami

first: Narumi

last: Shigeta

first: Tokurou

last: Shimizu

first: Hiroshi

last: Fujii

first: Kanako

last: Yano

first: Ayako

last: Yamaguchi-Nakamura

first: Toshiya

last: Yamamoto


title: Gene expression in Drosophila Poly mutant and wild-type

status: Public on Jan 17 2012

city: Edinburgh

first: Donald

last: Dunbar

address: 47 Little France Crescent

department: Centre for Cardiovascular Science

country: United Kingdom

institute: University of Edinburgh

summary:
The Poly mutant was identified as a previously uncharacterised, but essential gene in Drosphila. Loss of Poly reults in lethality at the third larval instar stage, but only after a stage of extreme larval longevity. We aimed to assess the consequences of loss of the Poly gene on glocal gene expression by microarray analysis.
Metabolism is altered in Poly mutants and here we find altered gene expression in insulin signaling pathways. Four biological replicates each of Poly mutant and wild-type larvae were used to assess gene expression on FL002 microarrays (GPL5135) . These data reveal that Poly is a mediatior of insulin receptor/TOR signaling.

overall_design: Four biological replicates of poly mutant and wild-type Drosophila. Two arrays had wild-type in Cy5 channel and poly in Cy3 channel, the other two were reversed.

middle: R

first: Margarete

last: Heck

first: Ekin

last: Bolukbasi


title: Functional genomics resources for the North Atlantic copepod, Calanus finmarchicus: EST database and physiological microarray.

status: Public on Mar 23 2012

city: Groton

first: Ebru

last: Unal

state: CT

address: 1080 Shennecossett Road

department: Department of Marine Sciences

institute: University of Connecticut

summary: The copepod, Calanus finmarchicus is a keystone species for the North Atlantic. Because of recent changes in the geographic distribution of this species, there are questions as to how this organism responds physiologically to environmental cues. Molecular techniques allow for examination and new understanding of these physiological changes. Here, we describe the development of a microarray for high-throughput studies of the physiological ecology of C. finmarchicus. An EST database was generated for this species using a normalized cDNA library derived from adult and sub-adult individuals. Sequence data were clustered into contigs and annotated using Blastx. Target transcripts were selected, and unique, 50 base-pair, oligomer probes were generated for 995 genes. Blast2GO processing provided detailed information on gene function. The selected targets included broad representation of biological processes, cellular components, and molecular functions. The microarray was tested in two sets of comparisons: adult females maintained at different food concentrations and field-caught sub-adults showing differences in lipid storage. Up-regulated and down-regulated transcripts were identified for both comparisons. Only a small subset of the genes up-regulated in low food individuals were also up-regulated in lipid-poor animals; no overlap was seen between the genes down-regulated in the two comparisons.

overall_design:
Two comparisons were performed:
1) Lipid-rich (fat) and Lipid-poor (thin) morphotypes
2) Copepods kept under high food and low food experimental conditions

first: Petra

middle: H

last: Lenz

first: Patrick

last: Hasset

first: Christine

last: Smith

first: Ann

last: Bucklin

first: Andrew

last: Christie

first: David

middle: W

last: Towle


title: Expression analysis of Ralstonia solanacearum strain UW551 at 20°C and 28°C in rich medium (CPG) and in planta

status: Public on Jan 15 2012

city: Madison

first: Lavanya

last: Babujee

address: Department of Plant Pathology

institute: UW-Madison

summary: Investigation of whole genome gene expression level changes in the bacterial wilt pathogen Ralstonia solanacearum, strain UW551 at 20°C and 28°C in culture and in planta. The  temperatel strain UW551 can wilt and cause full-blown disease on tomato plants at 28°C as well as at 20°C.

overall_design: A 16 array study using total RNA recovered from the following: 8 separate cultures of Ralstonia solanacearum strain UW551 grown in rich medium-CPG (4 grown at 20°C and 4 grown at 28°C) 8 separate in planta samples of Ralstonia solanacearum strain UW551 harvested from diseased tomato plants cv. BonnyBest (4 recovered from plants grown at 20°C and 4 from plants grown at 28°C)  Each array (4-plex format) measures the expression level of 4318 genes from Ralstonia solanacearum strain UW551 with 2 to 6, 40-70 mer probes per gene, with two-fold technical redundancy. The arrays also contain probes for intergenic regions with no technical replicates.

first: Jonathan

last: Jacobs

first: Fanhong

last: Meng

first: Caitilyn

last: Allen


title: Temperature dependent gene expression levels at  28°C and 37°C for rhizophere Rhizosphere Originating Biocontrol Strain Pseudomonas aeruginosa M18

status: Public on Jan 01 2012

city: Shanghai

first: daqiang

last: wu

address: 800 Dongchuan Road

department: School of life science and biotechnology

institute: Shanghaijiaotong University

summary: To further understand the gene expression characteristics of originating biocontrol strain Pseudomonas aeruginosa M18, we have applied whole genome microarray expression profiling as a discovery platform to to specify the temperature dependent expression of M18 genome at rhizosphere and human body temperature. We selected 28°C as temperature representative of the rhizosphere niches and 37°C for human body. The results from the temperature dependent transcriptome analysis are consistent to our previous published data that the phzM, ptsP and lasI genes expression is upregulated at 37°C. The comparison analysis of the M18 genome expressional profiles at 28°C and 37°C indicated a total of 605 gene expressed in a temperature dependent manner over about two fold at 28°C compared that at 37°C, covering 10.6% genes in M18 whole genome.

overall_design: Cells were grown to OD600=5.0-6.0 (late exponential phase) in LB medium at 28℃ and 37℃, respectively. Three independent experiments were performed at each time.

first: Yuquan

last: Xu

first: Daqiang

last: Wu


title: miRNA profiling in the adult mouse incisor

status: Public on Dec 31 2011

city: San Francisco

last: Jheon

state: CA

address: 513 Parnassus Ave HSE1501

institute: UCSF

summary:
miRNA expression was compared in 3 distinct regions of the adult mouse incisor: the labial cervical loop, which houses ameloblast stem cells; the lingulal cervical loop, which houses stem cells but not ameloblast stem cells;
and ameloblasts. Differentially expressed miRNAs from these regions are likely involved in the renewal and differentiation of stem cells.

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

overall_design: miRNA expression in the labial and lingual cervical loops, and ameloblasts were compared from 5 specimens.

first: A

first: Chun-Ying

last: Li

first: Timothy

last: Wen

first: Frederic

last: Michon

first: Ophir

last: Klein


title: Expression analysis of Ralstonia solanacearum strain GMI1000 at 20°C and 28°C in rich medium (CPG) and in planta

summary: Investigation of whole genome gene expression level changes in the bacterial wilt pathogen Ralstonia solanacearum, strain GMI1000 at 20°C and 28°C in culture and in planta. The  tropical strain GMI1000 cannot wilt tomato plants at 20°C although it can cause full-blown disease at 28°C.

overall_design: A 16 array study using total RNA recovered from the following: 8 separate cultures of Ralstonia solanacearum strain GMI1000 grown in rich medium-CPG (4 grown at 20°C and 4 grown at 28°C) 8 separate in planta samples of Ralstonia solanacearum strain GMI1000 harvested from diseased tomato plants cv. BonnyBest (4 recovered from plants grown at 20°C and 4 from plants grown at 28°C)  Each array (4-plex format) measures the expression level of 5061 genes from Ralstonia solanacearum strain GMI1000 with 2 to 6, 40-70 mer probes per gene, with two-fold technical redundancy. The arrays also contain probes for intergenic regions with no technical replicates.


title: Metabolic switching of the PII protein GlnK in Streptomyces coelicolor

city: Tübingen

first: Kay

last: Nieselt

state: DE

address: Sand 14

department: Department for Computer Science

institute: Institute for Bioinformatics and Medical Informatics

summary: GlnK is an important nitrogen sensor protein in Streptomyces coelicolor. Deletion of glnK results in a medium-dependent failure of aerial mycelium and spore formation and loss of antibiotic production. Thus, GlnK is not only a regulator of nitrogen metabolism but also of morphological differentiation and secondary metabolite production. Through a comparative transcriptomic approach between the S. coelicolor wild-type and a S. coelicolor glnK mutant strain, 142 genes were identified that are differentially regulated in both strains. Among these are genes of the ram and rag operon, which are involved in S. coelicolor morphogenesis, as well as, genes involved in gas vesicle biosynthesis and ectoine biosynthesis. Surprisingly, no relevant nitrogen genes were found to be differentially regulated, revealing that GlnK is not an important nitrogen sensor under the tested conditions.

overall_design: 16 samples, no replicates; four hour resolution from 21-33h; one our resolution from 33-40 h; two hour resolution 40-50h

first: Eva

last: Waldvogel

first: Alexander

last: Herbig

first: Florian

last: Battke

first: Merle

last: Nentwich

first: Trond

last: Ellingsen

last: Wentzel

last: Hodgson

first: Wolfgang

last: Wohlleben

first: Yvonne

last: Mast


title: Gradient of the third maize leaf of a 14 day old plant

status: Public on Dec 21 2011

city: Duesseldorf

first: Andrea

last: Braeutigam

address: Universitaetsstrasse 1

department: Botany

institute: Heinrich Heine University Duesseldorf

summary:
To investigate the developmental gradient of the third maize leaf, the light exposed area of the leaf (corresponding to 18cm of leaf) and 2cm shaded by the sheath were sampled in ten slices. Four replicates were collected, immediately shock frozen in liquid nitrogen and subsequently cut into 2cm slices. At least 10 plants were pooled for each biological replicate.
We have systematically analyzed a developmental gradient of the third maize leaf from the point of emergence into the light to the tip in ten continuous leaf slices to study organ development and physiological and biochemical functions. Transcriptome analysis, oxygen sensitivity of photosynthesis, delta-13C values, and photosynthetic rate measurements showed that the maize leaf undergoes a sink to source transition without an intermediate phase of C3 photosynthesis or operation of a photorespiratory carbon pump. Metabolome and transcriptome analysis, chlorophyll and protein measurements, as well as dry weight determination showed continuous gradients for all analyzed items. The absence of binary on-off switches and regulons pointed to a morphogradient along the leaf as the determining factor of developmental stage. Analysis of transcription factors for differential expression along the leaf gradient defined a list of putative regulators orchestrating the sink-to-source transition and establishment of C4 photosynthesis. Finally, transcriptome and metabolome analysis, as well as enzyme activity measurements, and absolute quantification of selected metabolites revised the current model of maize C4 photosynthesis. All datasets are included within the publication to serve as a resource for maize leaf systems biology. For the transcriptional analysis, the goal of the study was to (i) identify whether the leaf contains binary switches for genes involved in photosynthesis, (ii)characterize the patterns of gene expression in the leaf, (iii) provide independent validation of maize leaf expression experiments published in Li et al. (2011) and (iv) determine transcripts co-expressed with key transcripts of C4 photosynthesis. To this end, changed transcripts were determined by ANOVA and characterized by K-means and hierachical clustering.

overall_design: Four replicates were collected for each of the ten consecutive leaf slices resulting in 40 one color arrays. Slice 1 represents the tip of the leaf, slice 10 the lowermost slice which is shaded by the sheath with all slices in between consecutively numbered.

last: Bräutigam

first: Thea

last: Pick

first: Urte

last: Schlüter

first: Uwe

last: Sonnewald

first: Andreas

middle: P

last: Weber


title: Metabolic switching in Streptomyces coelicolor wild type, time series under glutamate depletion condition

summary:
During the lifetime of a fermenter culture, the soil bacterium S. coelicolor undergoes a major metabolic switch from exponential growth to antibiotic production. We have studied gene expression patterns during this switch, using a specifically designed Affymetrix GeneChip and a high-resolution time-series of fermenter-grown samples.
This time series was conducted using medium leading to glutamate depletion and the cultivation conditions as published in Nieselt et al. BMC Genomics 2010, performed with the Streptomyces coelicolor wild type strain M145E.

overall_design: 30 samples, no replicates; one hour resolution from 20-32h and 40-42h; half our resolution from 32-40 h; two hour resolution 44-58h; sample missing for 29 and 34 h

first: David


title: Landscape of somatic allelic imbalances and copy number alterations in HER2-amplified breast cancer

status: Public on Dec 02 2011

city: Lund

first: Johan

last: Staaf

address: Medicon Village

country: Sweden

institute: SCIBLU - Swegene Centre for Integrative Biology at Lund University

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

summary: A survey of the somatic allelic imbalances and copy number alterations in HER2-amplified breast cancer.

overall_design: Genomic profiling of 26 breast tumors with amplification of HER2 using 1M and 2.5M Illumina SNP beadchips. Sample identifiers correspond to GSE21259 where sample annotations may be extracted.

first: Göran

last: Jönsson

first: Markus

last: Ringner

first: Bo

last: Baldetorp

first: Ake

last: Borg


title: Butanol Challenge of L. brevis

city: College Station

first: James

last: Winkler

address: 3122 TAMU

institute: Texas A&M University

summary: The presence of anti-microbial phenolic compounds, such as the model compound ferulic acid, in biomass hydrolysates poses significant challenges to the widespread use of biomass in conjunction with whole cell biocatalysis or fermentation. Biofuel toxicity must also be overcome to allow for efficient production of next generation biofuels such as butanol, isopropanol, and others for widespread usage. Currently, these inhibitory compounds must be removed through additional downstream processing or sufficiently diluted to create environments suitable for most industrially important microbial strains. This study explores the high ferulic acid and n-butanol tolerance in Lactobacillus brevis (L. brevis), a lactic acid bacteria often found in fermentation processes, by global transcriptional response analysis. The transcriptional profile of L. brevis under ferulic acid and butanol stress reveals that the presence of ferulic acid primarily triggers the expression of membrane proteins to counteract ferulic acid induced changes in membrane fluidity and ion leakage. In contrast to the ferulic acid stress response, butanol addition to growing cultures uniquely induced the entire fatty acid synthesis pathway in the midst of a generalized stress response. Overexpression of the rate-limiting acetyl-CoA carboxylase subunits (AccABCD) in E. coli to increase lipid synthesis had no effect on butanol tolerance, suggesting that additional engineering is necessary to produce sufficient levels of appropriate fatty acids to confer butanol tolerance. Several promising routes for understanding both phenolic acid and butanol tolerance have been identified based upon these findings. These insights may be used to guide further engineering of model industrial organisms to better tolerate both classes of inhibitors in processed biomass used for biofuel production.

overall_design: Cultures were grown to OD ~ 0.2 in MRS media (baffled flasks), T = 30 C, 100 rpm. Butanol was then added to the cultures. Samples were harvested 15, 75, and 135 min after butanol addition. Each time point has 3 biological replicates, and dye swaps were incorporated into the microarray experiments.

first: Katy

last: Kao


title: Expression data from the Arabidopsis root epidermis

status: Public on Dec 01 2011

city: Ann Arbor

first: John

last: Schiefelbein

state: Michigan

address: 830 North University Avenue

department: Molecular, Cellular, and Developmental Biology

institute: University of Michigan

summary: The root epidermis of Arabidopsis provides a simple and experimentally useful model for studying the molecular basis of cell fate and differentiation.   The goal of this study was to define the larger gene regulatory network that governs the differentiation of the root hair and non-hair cell types of the Arabidopsis root epidermis.   Transcript levels in the root epidermis of wild-type and mutant lines were assessed by purifying populations of root epidermal cells using fluorescence-based cell-sorting.  Further, the role of the plant hormones auxin and ethylene on root epidermis development was assessed by defining transcript levels in the root epidermis of plants grown on media containing IAA or ACC.  These microarray results were used to construct a comprehensive gene regulatory network that depicts the transcriptional control of root epidermal cell fate and differentiation in Arabidopsis.

overall_design: The cells of the developing root epidermis were obtained by growing plant seedlings expressing the WER::GFP transgene under sterile conditions on MS media, cutting off root tips (including all developmental stages), protoplasting the roots, and purifying cells containing GFP using FACS.   The WER::GFP transgene is expressed throughout the developing cells of the root epidermis and the lateral root cap.   Three biological replicates were analyzed for each of the 25 plant lines examined in this study.

first: Angela

last: Bruex

first: Raghu

last: Kainkaryam

first: Peter

last: Woolf


title: A Quantitative, High-Throughput Reverse Genetic Screen Reveals Novel Connections Between pre-mRNA Splicing and 5’ and 3’ end Transcript Determinants

status: Public on Dec 13 2011

city: Ithaca

first: Jeffrey

last: Pleiss

state: NY

address: 451 Biotech

department: Molecular Biology and Genetics

institute: Cornell University

type:
Expression profiling by array
Expression profiling by RT-PCR

summary: The coding portions of most eukaryotic genes are interrupted by non-coding regions termed introns that must be excised prior to their translation. The excision of introns from precursor messenger RNA (pre-mRNA), is catalyzed by the spliceosome, a large macromolecule composed of both RNA and protein components. Several studies have uncovered connections between pre-mRNA splicing and other RNA processing pathways such as the remodeling of chromatin structure, transcription and processing events which take place at the 3’ end of the transcript. To date, however, the full complement of factors which function to couple splicing to other processes in the cell remains unknown. Here, we have developed a novel screening methodology in the budding yeast, Saccharomyces cerevisiae, that allowed us to individually examine nearly all of the ~6000 genes to determine which factors functionally impact splicing. We identified mutations in components that function at either the 5' or 3' end of a gene. Most of these components have previously established roles in other aspects of gene expression, including chromatin remodeling and cleavage and polyadenylation processes, and their identification here provides the first evidence for their roles in coupling these pathways.

overall_design:
Included here are both the QPCR data generated from this high-throughput reverse genetic screen, as well as the microarray analyses of several of the candidate factors identified by the screen.

For QPCR data, *A and *B represent biological replicates. A1 and A2 are technical replicates of the same biological sample, whereas B1 and B2 are the technical replicates for the second biological replicate.


title: miRNAs expression in HepG2-HBx and HepG2-URG11

status: Public on Nov 23 2011

city: Philadelphia

first: Ke

last: Yuan

state: PA

address: 1900 N 12th Broad St

institute: Temple University

summary:
Compare microRNAs expression when HepG2 cells stably expressing HBx protein with HepG2 control cells expressing baterial chloramphenicol acetyltransferase
Compare microRNAs expression when HepG2 cells stably expressing URG11 protein with HepG2 control cells expressing baterial chloramphenicol acetyltransferase

overall_design:
microRNA expression in Cells expressing  HBx vs. Cell without HBx
microRNA expression in Cells expressing  URG11 vs. Cell without URG11


title: Transcriptome profiling during cutaneous porcine wound repair.

status: Public on Jul 30 2012

city: Dolni Dobrouc

first: Rastislav

last: Slavkovský

address: Dolni Dobrouc 401

department: R&D

country: Czech Republic

institute: Contipro Biotech

summary:
The expression profile during wound repair of cutaneous excisional wound (2x2 cm) was studied.
The tissue was sampled from the centre of the open wound (day 3/7/14) or centre of the wound scar (day 21/35/70). The microarray slide were scanned in low intensity scan and high intensity scan mode.

overall_design: Wound tissue (day 3, day 7, day 14, day 21, day 35, day 70, n = 4 per interval) vs. control - uninjured skin (day 0, n=4 ). In each interval two biological replicates of four were labeled with flip dyes.

last: Slavkovsky

first: Pavel

last: Klein

first: Vojtech

last: Pavlik

first: Jan

last: Kucera

first: Vladimir

last: Velebny


title: Screening ethnically diverse human embryonic stem cells identifies a chromosome 20 minimal amplicon conferring growth advantage

status: Public on Nov 12 2011

city: Farmington

first: Paul

last: Robson

address: 10 Discovery Way

institute: The Jackson Laboratory for Genomic Medicine

summary: The International Stem Cell Initiative analyzed 127 human embryonic stem cell lines and 11 induced pluripotent cell lines, from 39 laboratories worldwide for genetic changes occurring during culture.  Most cell lines were analyzed at an early and late passage.  Population structure analysis from SNP detection revealed that the cell lines included representatives of all major ethnic groups.  Most lines remained karyotypically normal, but there was a progressive tendency to acquire changes on prolonged culture, commonly affecting chromosomes 1, 12, 17 and 20.  DNA methylation patterns changed but haphazardly with no link to time in culture.  Structural variants (SVs), below the level of standard chromosome banding, determined from the SNP arrays, also appeared sporadically but no common variants related to culture were observed on chromosomes 1, 12 and 17.  However, overlapping SV gains acquired in the chromosome 20q11.21 region during extended culture were identified in over 20% of the cell lines.  Three genes within the minimal shared region, ID1, BCL2L1, and HM13, are expressed in human ES cells, with BCL2L1 a strong candidate for driving this culture adaptation of ES cells.

overall_design: In order to provide better insight into the frequency and types of genetic changes affecting human ES cells on prolonged passage, the ISCI has undertaken a survey by karyology and high resolution SNP array of one hundred twenty seven independent human ES cell lines, provided by thirty nine laboratories in twenty countries around the world, particularly to identify the common genetic changes that occur during prolonged culture. Here we append data from the SNP genotyping of the genomic DNA samples extracted from the human embryonic stem cells. A group of eleven human iPS cells from three laboratories was also included to provide a pilot comparison of these pluripotent cells derived by reprogramming.

last: Andrews

first: Wishva

last: Herath

first: Jieming

last: Chen

first: Astrid

last: Irwanto

first: Linda

last: Lim

first: Jameelah

middle: S

last: Mohamed


title: Expression analysis of L-rhamnose catabolism in the yeast Scheffersomyces stipitis

city: Espoo

first: Mikko

middle: Ilari

last: Arvas

address: Tietotie 2

department: Cell Factory

country: Finland

institute: VTT Technical Research Centre of Finland

summary: In Scheffersomyces stipitis and related fungal species the genes for L-rhamnose catabolism RHA1, LRA2, LRA3 and LRA4 but not LADH are clustered. We find that located next to the cluster is a transcription factor, TRC1, which is conserved among related species.Our transcriptome analysis shows that all the catabolic genes and all genes of the cluster are up-regulated on L-rhamnose. Among the genes that were also up-regulated on L-rhamnose were two transcription factors including the TRC1. In addition, in 16 out of the 32 analysed fungal species only RHA1, LRA2 and LRA3 are in a cluster. The clustering of RHA1, LRA3 and TRC1 is also conserved in species not closely related to S. stipitis. Since the LRA4 is often not part of the cluster and it has several paralogs in L-rhamnose utilising yeasts we analysed the function of one of the paralogs, RHA41 by heterologous expression and biochemical characterization. Rha41p has similar catalytic properties but the transcript was not up-regulated on L-rhamnose. The RHA1, LRA2, LRA4 and LADH genes were previously characterized in Sheffersomyces (Pichia) stipitis. We expressed the L-rhamnonate dehydratase, Rha3p, in S. cerevisiae, estimated the kinetic constants of the protein and showed that it indeed has activity with L-rhamnonate.

overall_design: A six chip study using total RNA recovered from three separate cultures of S. stipitis CBS 6054 grown glucose and respectively three separate cultures grown on rhamnose

first: Jennifer

last: Van Vleet

first: Thomas

last: Jeffries


title: R. sphaeroides delta-CryB vs. R. sphaeroides 2.4.1 microarobic conditions

status: Public on Nov 09 2011

city: Gießen

first: Gabriele

last: Klug

address: Heinrich-Buff-Ring 26-32

department: Molecular- and Microbiology

institute: Justus-Liebig University Gießen

summary: Transcriptional profiling of R. sphaeroides delta-CryB comparing to control R. sphaeroides 2.4.1 under microaerobic conditions

overall_design: Two strain experiment under microaerobic conditions. 9 Biological replicas, independetly grown and harvested at OD660=0,8; 1-3 pooled in replicate 1, 4-6 pooled in replicate 2, 7-9 pooled in replicate 3

first: Sebastian

last: Fruhwirth

last: Metz

first: Kristin

last: Teich


title: R. sphaeroides delta-cryB vs. R. sphaeroides 2.4.1 photo-oxidative stress, aerobic conditions

summary: Transcriptional profiling of R. sphaeroides delta-cryB compared to control R. sphaeroides 2.4.1 under photo-oxidative stress, aerobic conditions.

overall_design: Two-strain experiment under 20' photo-oxidative stress (singlet oxygen generated by methylene blue under high light illumination) and aerobic (180 µM) conditions


title: Identification of a methylome signature of esophageal squamous cell carcinoma

city: Bron

first: Hector

last: Hernandez-Vargas

state: Rhone

address: 36 bis Rue de la Batterie

country: France

institute: Genomics Consulting

summary:
Background & Aims: Esophageal squamous cell carcinoma (ESCC) is believed to arise from esophageal mucosa through accumulation of both genetic and epigenetic changes. DNA methylation is a critical epigenetic mechanism involved in key cellular processes and its deregulation has been linked to many human cancers, including ESCC. The aim of this study is to examine the global deregulation of methylation states in ESCC and identify potential early biomarkers.
Conclusions: This is the first study to address methylation changes in ESCC in a large panel of genes. Methylome analysis is shown as a sensitive and powerful tool to identify molecular players in ESCC. These data should prove to be the reference for future studies identifying potential biomarkers and molecular targets of ESCC.

overall_design: We performed a bead array analysis of more than 800 cancer-related genes in a series of 10 ESCC samples, 10 matched surrounding tissues, and 4 esophageal mucosa from healthy individuals. Pyrosequencing was used for validation of DNA methylation changes in up to 106 patients and 27 controls.

first: Sheila

last: Lima

first: Tatiana

last: Simao

first: Geoffroy

last: Durand

first: Cleber

last: Pinto

first: Florence

last: Le Calvez-Kelm

first: Luis

first: Zdenko

last: Herceg


title: Influence of Deoxynivalenol-contaminated diet on the liver gene expression of chicken.

status: Public on Nov 05 2011

city: Zurich

first: Bruno

last: Dietrich

address: Tannenstrasse 1

department: Department of Agricultural and Food Sciences

country: Switzerland

institute: ETH Zurich

summary: The mycotoxin deoxynivalenol (DON) is a secondary metabolite from Fusarium species and is frequently present on wheat and other cereals. The main effects of DON are a reduction of the feed intake and reduced weight gain of broilers. At the molecular level DON binds to the 60S ribosomal subunit and inhibits subsequently protein synthesis at the translational level. It has been suggested that cells and tissues with high protein turnover rate, like the liver and small intestine, are most affected by DON. However, little is known about other effects of DON e.g. at the transcriptional level. Therefore we decided to perform a microarray analysis, which allows us the investigation of thousands of transcripts in one experiment.

overall_design: The one-day old broiler chicks were separated into four groups. The diets consisted of a control diet and of three diets with moderate concentrations of 1.0, 2.5 and 5.0 mg DON/kg feed, which was attained by exchanging uncontaminated wheat with naturally DON-contaminated wheat up to the intended concentration. The chicken were held at standard conditions for 23 days and received their diet ad libitum. After slaughter the gene expression was determined in the liver of three samples per group.

first: Caspar

last: Wenk


title: Human Toll-Like Receptors Pathway Array Data

status: Public on Nov 04 2011

first: Kevin

last: Wilhelmsen

address: 513 Parnassus Ave.

department: Anesthesia

institute: University of California, San Francisco

summary: Endothelial cell (EC) Toll-like receptor 2 (TLR2) activation upregulates the expression of inflammatory mediators and of TLR2 itself, and modulates important endothelial functions, including coagulation and permeability. We defined TLR2 signaling pathways in ECs, and tested the hypothesis that TLR2 signaling differs in ECs and monocytes. We found that ERK5, heretofore unrecognized as mediating TLR2 activation in any cell type, is a central mediator of TLR2-dependent inflammatory signaling in HUVEC, primary human lung microvascular ECs and human monocytes. Additionally, we observed that whereas MEK1 negatively regulates TLR2 signaling in EC, MEK1 promotes TLR2 signaling in monocytes. We also noted that activation of TLR2 led to the upregulation of intracellularly expressed TLR2 and inflammatory mediators via NF-κB, JNK and p38-MAPK. Finally, we found that p38-MAPK, JNK, ERK5 and NF-κB promote the attachment of human neutrophils to lung microvascular EC that were pretreated with TLR2 agonists. This study newly identifies ERK5 as a key regulator of TLR2 signaling in ECs and monocytes, and indicates that there are fundamental differences in TLR signaling pathways between EC and monocytes.

overall_design: qPCR gene expression profiling.  HUVEC monolayers were grown to confluency in EGM-2 media. THP1 suspension cells were grown RPMI 1640 supplemented with 10% FBS, L-glutamine, and antibiotics. Neither cell line was treated with any agonists. RQ values were calculated using the 2-ΔΔCt method. Two biological replicates and one technical replicate were analyzed for both cell lines.

first: Kailin

last: Mesa

last: Lucero

first: Fengyun

last: Xu

first: Judith

last: Hellman


title: miRNA expression in primary human leukaemic B-cells from peripheral blood and after culture on stromal cells in the presence and absence of CD154 and IL-4

status: Public on Nov 03 2011

city: Leicester

first: Simon

middle: David

last: Wagner

address: Lancaster Road

department: CSMM

institute: University of Leicester

summary: Dynamic miRNA expression data in 377 miRNA present on Taqman low density array (TLDA) Human MicroRNA Array (A) plates (Applied Biosystems, #4398965).

overall_design: Primary human leukaemic B-cells were cultured for 24 hours on a stromal cell layer or a stromal cell layer with CD154 and IL-4 in order to find out how miRNA expression compared to that of freshly isolated leukaemic cells.

first: Shaun

last: Willimott


title: Gene expression in Citrus sinensis (L.) Osbeck following infection with the bacterial pathogen Candidatus Liberibacter asiaticus causing Huanglongbing in Florida

city: Fort Pierce

first: Ute

last: Albrecht

state: FL

address: 2001 South Rock Road

institute: USDA, ARS, US Horticultural Research Laboratory

summary:
Huanglongbing (HLB) (=citrus greening) is a destructive disease of citrus which is caused by a fastidious, phloem-inhabiting bacterium of the genus Candidatus Liberibacter.  Large-scale analysis of gene expression changes in ‘Valencia’ orange leaves were studied during the course of 19 weeks after inoculation with Ca. L. asiaticus using the Affymetrix GeneChip® citrus genome array to provide new insights into the molecular basis of citrus response to this pathogen.  Of the more than 33,000 probe sets on the microarray 21,067 were expressed in the leaves, of which 279 and 515 were differentially expressed (FDR ≤ 0.05) five to nine and 13-17 weeks after inoculation, respectively.  Results from semi-quantitative RT-PCR analysis performed on 14 selected genes were highly correlated with those observed with the microarray.  Gene expression changes involved a variety of different processes including cell defense, transport, cellular organization, photosynthesis, and carbohydrate metabolism.  Notable was the pathogen-induced accumulation of transcripts for a phloem-specific lectin PP2-like protein.  Transcriptional changes and their relation to disease symptom development are discussed.  This is the first study of transcriptional profiling in citrus in response to liberibacter infection using microarray technology.
Huanglongbing (HLB) is a destructive disease of citrus which is suspected to be caused by a phloem-inhabiting bacterium of the genus Candidatus Liberibacter.  Large-scale analysis of gene expression changes in ‘Valencia’ orange (C. sinensis) leaves were studied during the course of 19 weeks after inoculation with Ca. L. asiaticus (Las), the pathogen associated with HLB in Florida,  using the Affymetrix GeneChip® citrus genome array to provide new insights into the molecular basis of citrus response to this pathogen.

overall_design: Three year-old 'Valencia' orange (C. sinensis) scions on Cleopatra mandarin (C. reticulata Blanco) rootstocks were graft-inoculated with non-infected (control) or Las-infected tissue from greenhouse- (control) or field-grown 'Lisbon' lemon (C. limon) trees.  Fully expanded leaves were collected at 5, 9, 13, and 17 weeks after inoculation (wai).  Total RNA was extracted from two control plants and from three Las-inoculated plants per time point.  Equal amounts of RNA were combined from samples collected 5 wai and 9 wai and from samples collected 13 wai and 17 wai, resulting in two non-infected and three infected biological  replicates for both early (5-9 wai) and late (13-17 wai) time points and used for hybridization on Affymetrix citrus microarrays.

first: Kim

middle: D

last: Bowman


title: MicroRNA-145 Regulates Human Corneal Epithelial Differentiation [Agilent-016436 array data]

status: Public on Oct 10 2011

city: Hong Kong

first: Gary

last: Yam

address: 147K Argyle St, Mongkok

institute: Chinese University of Hong Kong

summary:
To investigate the microRNA expression in human limbal-peripheral corneal (LPC) epithelia containing corneal epithelial progenitor cells (CEPCs) and early transit amplifying cells, we have employed Human microRNA Microarray V2 (Agilent) as a screening platform to identify specific microRNAs.
We discovered a differential expression of 18 microRNAs against central corneal (CC) epithelia, which contains late transit amplifying cells and terminally differentiated cells. Among them, cluster miR-143/145 was expressed strongly in LPC but at low levels in CC epithelia and this was validated by real-time PCR and locked nucleic acid-based in situ hybridization.

overall_design: LPC and CC epithelia, separated by 1-mm in width, were dissected from human cornea for small RNA extraction. Total RNA was extracted by Trizol/chloroform and purified with RNeasy mini spin column. RNA samples with 28S/18S ratios in the range of 1.4 to 1.8 were used for microRNA profiling using an Agilent Human microRNA Microarray V2 platform.

first: Chi-Pui

last: Pang


title: R. sphaeroides delta-cryB vs. R. sphaeroides 2.4.1 under blue light, semiaerobic conditions

first: Gabriele

last: Klug

summary: Transcriptional profiling of R. sphaeroides delta-cryB compared to control R. sphaeroides 2.4.1 under blue light, semiaerobic conditions.

overall_design: Two-strain experiment under blue light illumination (20µmol m-2 s-1) and semiaerobic (90 µM) conditions

first: Sebastian

last: Fruhwirth

last: Metz

first: Kristin

last: Teich


title: Whole Genome Association Study on Tissue Tropism Phenotypes in Group A Streptococcus

status: Public on Oct 03 2011

city: Baltimore

first: NIKHIL

last: KUMAR

state: MD

address: 801 W. Baltimore Street

department: Institute for Genome Sciences

institute: University of Maryland, Baltimore

summary: Group A Streptococcus (GAS) has a rich evolutionary history of horizontal transfer among its core genes. Yet, despite extensive genetic mixing, GAS strains have discrete ecological phenotypes. To further our understanding of the molecular basis for ecological phenotypes, comparative genomic hybridization of a set of 97 diverse strains to a GAS pan-genome microarray was undertaken, and the association of accessory genes with emm genotypes that define tissue tropisms for infection was determined. Of the 22 non-prophage, accessory gene regions (AGRs) identified, only three AGRs account for all statistically significant linkage disequilibrium among strains having the genotypic biomarkers for throat versus skin infection specialist. Networked evolution and population structure analysis of loci representing each of the AGRs reveals that most strains with the skin specialist and generalist biomarkers form discrete clusters, whereas strains with the throat specialist biomarker are highly diverse. To identify co-inherited and co-selected accessory genes, the strength of genetic associations was determined for all possible pair wise combinations of accessory genes among the 97 GAS strains. Accessory genes showing very strong associations provide the basis for an evolutionary model, which reveals that a major transition between many throat and skin specialist haplotypes correlates with the gain or loss of genes encoding fibronectin-binding proteins. This study employs a novel synthesis of tools to help delineate the major genetic changes associated with key adaptive shifts in an extensively recombined bacterial species.

overall_design: Diverse collection of 97 GAS strains compared to Alab49 reference genome representing the majority of amplicons on the GAS pan-genome microarray. Flip dye (technical replicates) performed for all comparisons.  Ratios were determined by averaging across technical replicates.

first: Debra

last: Bessen

first: Nikhil

last: Kumar

first: Gerod

last: Hall

first: David

last: Riley

first: Feng

last: Luo

first: Sergio

last: Lizano

first: Candace

middle: N

last: Ford

first: W

last: McShan

first: Scott

last: Nguyen

first: Julie

last: Hotopp

first: Hervé

last: Tettelin


title: Tri6 is a global transcription regulator in the phytopathogen Fusarium graminearum

status: Public on Oct 01 2011

city: Ottawa

first: Linda

last: Harris

state: Ontario

address: 960 Carling Ave.

department: Eastern Cereal & Oilseed Research Centre

institute: Agriculture & Agri-Food Canada (AAFC)

summary: In F. graminearum, the transcriptional regulator TRI6 is encoded within the trichothecene gene cluster and regulates genes involved in the biosynthesis of the secondary metabolite deoxynivalenol (DON). Targeted disruption of TRI6 confirmed its role as a positive regulator of trichothecene genes and previous studies designated Tri6 as a pathway-specific transcriptional regulator. The Tri6 protein with its Cys2His2 zinc-finger may also conform to the class of broad-domain transcription regulators. This class of global transcriptional regulators mediate various environmental cues and generally responds to the demands of cellular metabolism. Expression profiling of F. graminearum grown under nitrogen-limiting conditions revealed that 49 out of 198 target genes are differentially regulated by TRI6. The identification of potential new targets together with deciphering novel binding site for Tri6, casts new light into the role of this transcriptional regulator in the overall growth and development of F. graminearum.

overall_design: Three biological replicates of Fusarium graminearum wildtype strain GZ3639 (NRRL 38155) (reference) and a tri6∆ mutant derived from GZ3639 were grown under nitrogen-limiting conditions in liquid culture for 5 hrs at 28oC

first: Charles

middle: G

last: Nasmith

first: Sean

last: Walkowiak

first: Li

last: Wang

first: Winnie

last: Leung

first: Yunchen

last: Gong

first: Anne

last: Johnston

last: Guttman

first: Rajagopal

last: Subramaniam


title: EWS siRNA knock-down in HeLa cell line

status: Public on Sep 20 2011

city: barcelona

first: BELEN

last: MINANA

state: barcelona

address: dr aiguader 88

department: GENE REGULATION, STEM CELLS AND CANCER

institute: Center for genomic regulation

summary: HeLa cell line was trasfected by a EWS siRNA oligo causing knock-down of EWS or a siRNA scrambled oligo

overall_design: Three biological replicates were labeled in direct and dye-swap microarray experiments and hybridized onto an Agilent custom splicing-sensitive microarray platform.

first: Belen

last: Minana

first: Maria

last: Paronetto

first: Juan

last: Valcarcel


title: The gene expression response of spontaneous canine sarcomas to thermoradiotherapy – response heterogeneity and combination therapeutics

status: Public on Aug 01 2011

city: Durham

first: Jen-Tsan

last: Chi

state: NC

address: 101 Science Drive, DUMC 3382

department: Molecular Genetics and Microbiology

institute: Duke University

summary: While hyperthermia has been shown to be an effective adjuvant anti-tumor treatment to radiotherapy, we still do not completely understand effects thermoradiotherapy on tumor phenotype or how these effects vary among different tumors. Here, we performed gene expression analysis in 22 spontaneous canine sarcomas before and after the first hyperthermia treatment that was administered as an adjuvant to radiotherapy. Diffusion weighted MRI (DWI) was done prior to the treatment course and at the end of therapy.  Using supervised analysis, we identified significant correlation of DWI with several genes involved in VEGF signaling, telomerase, Wnt pathways and fatty acid synthesis. When the change of gene expression caused by treatment was examined, we found that thermoradiotherapy led to the induction of well known cycle regulators p21 and mdm2 and reduced cellular proliferation in most treated tumors. We also identified two tumor subtypes with dramatic differences in the gene expression response and treatment response at the end of therapy. In the subtype with strong expression and increase in DWI, the mRNA level of hsp70, POT1 and centrosomal proteins was significantly higher. In the other subtype with modest response to hyperthermia, levels of CD31, vWF and transferrin was noted to be significantly higher. It is also possible to build a predictive model based on the pre-treatment gene expression to predict the likely treatment response of the tumors.  The differential expression between the two tumor subtypes was used to interrogate connectivity map and identify linkages to an HDAC inhibitor and geldanamycin, an HSP90 inhibitor. Both HDAC inhibitors and hsp90 inhibitor geldanamycin are shown to synergerize with thermoradiotherapy in reducing cell survival in clonogenic assays. Taken together, the gene expression studies of hyperthermia-treated spontaneous canine tumors shed mechanistic insights into the heterogeneity of thermoradiotherapy response and identified pathway-targeting compounds with synergistic potential to enhance its therapeutic benefits.  To our knowledge, this is one of the first successful attempts to link genomic and functional imaging changes together. This is the first demonstration of using such associations to understand the connection between cellular and physiologic responses to treatment.

first: Donald

last: Thrall

first: Kouros

last: Owzar

first: Chen

last: Jiang

first: Stacey

last: Snyder

first: Marlene

last: Hauck

first: Chelsea

last: Landon

first: James

last: MacFall

first: Benjamin

middle: L

last: Viglianti

first: Mark

last: Dewhirst


title: Effect of ovarian stimulation on oocyte gene expression in cow

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

institute: Université Laval

summary: The objective of the study was to analyze the impact of FSH on transcriptome changes of in vivo bovine oocytes. Oocytes were collected from naturally ovulated and superovulated animals at 2 hours pre-LH surge, 6 hours post-LH surge, and 22 hours post-LH surge.

overall_design: Six-condition experiment. Biological replicates: 1 . Technical replicate:2.

first: Thi-Kieu-Oanh

last: Chu

first: Isabelle

last: Dufort


title: A novel and divergent role of granzyme A and B in resistance to helminth infection

status: Public on Jul 29 2011

city: Hamburg

first: Thomas

last: Streichert

address: Martinistr. 52, Campus Forschung N27, 2. OG

department: Institute For Clinical Chemistry / Central Laboratories

institute: University Medical Center Hamburg-Eppendorf

summary:
Granzyme (gzm) A and B, proteases of NK cells and T killer cells, mediate cell death, but also cleave extracellular matrices, inactivate intracellular pathogens and induce cytokines. Moreover, macrophages, T helper 2 cells, regulatory T cells, mast cells and B cells can express gzms. We recently reported gzm induction in human filarial infection. Here we show that in rodent filarial infection with Litomosoides sigmodontis worm loads were significantly reduced in gzmAxB and gzmB knock out (ko) mice, but enhanced in gzmA ko compared to wildtype (wt) mice. GzmA/B deficiency was associated with a defense-promoting Th2  cytokine and antibody shift and enhanced early inflammation gene expression, whereas gzmA deficiency was linked with alternatively activated macrophages and reduced inflammation. This suggests a novel and divergent role for gzms in helminth infection with gzmA contributing to resistance and gzmB promoting susceptibility.

Keywords: knock out vs wild type

overall_design: Two different knock out mice groups (Granzyme AxB KO and Granzyme A KO) and one wild type group were compared. PLECs were isolated from 6 mice/group (gzmAxB ko, gzmA ko, wt mice) and two mice were pooled/group, yielding 9 samples.

first: Wiebke

last: Hartmann

first: Simone

last: Korten


title: Gene expression signature of c-MYC-immortalized human fibroblasts reveals loss of growth inhibitory response to TGFb

status: Public on Aug 04 2011

city: Boston

first: Julja

last: Burchard

state: MA

address: 33 Avenue Louis Pasteur

department: Computational & Systems Biology

institute: Merck & Co., Inc.

summary: Cancer cells exhibit the ability to proliferate indefinitely, but paradoxically, overexpression of cellular oncogenes in primary cells can result in a rapid and irreversible cell cycle arrest known as oncogene-induced senescence (OIS). However, we have shown that constitutive overexpression of the oncogene c-MYC in primary human foreskin fibroblasts results in a population of cells with unlimited lifespan; these immortalized cells are henceforth referred to as iMYC. Here, in order to further elucidate the mechanisms underlying the immortalization process, a gene expression signature of three independently established iMYC cell lines compared to matched early passage c-MYC overexpressing cells was derived. Network analysis of this "iMYC signature" indicated that a large fraction of the down-regulated genes were functionally connected and major nodes centered around the TGFb, IL-6 and IGF-1 signaling pathways. Here, we focused on the functional validation of the alteration of TGFb response during c-MYC-mediated immortalization. The results demonstrate loss of sensitivity of iMYC cells to activation of TGFb signaling upon ligand addition. Furthermore, we show that aberrant regulation of the p27 tumor suppressor protein in iMYC cells is a key event that contributes to loss of response to TGFb. These findings highlight the potential to reveal key pathways contributing to the self-renewal of cancer cells through functional mining of the unique gene expression signature of cells immortalized by c-MYC.  Cell Cycle. 2011 Aug 1;10(15).

overall_design:
Cell culture. Human foreskin fibroblast cell lines expressing empty vector pBABE or vector with gene sequence encoding c-MYC were previously described in PMID 17982115. Cells were cultured in Dulbecco’s modified eagle medium (DMEM) supplemented with 10% fetal bovine serum and penicillinstreptomycin. For cell growth assays, equal number of cells per cell line were plated and counted on the specified days after plating.

Microarray analysis. Total RNA was purified using an RNeasy kit (Qiagen, Valencia, CA). Genome-scale expression analysis was performed using custom microarrays (Affymetrix, Santa Clara, CA) containing oligonucleotide probes corresponding to approximately 22,000 human genes. Microarray analysis was performed as described in PMID 12925520. Data were analyzed using Rosetta Resolver(TM) software. We determined a p-value cutoff of 0.01 for genes in all three samples.

first: Myra

last: Wang

first: Ryan

last: Walsh

first: Kristin

last: Robinson

first: Steven

last: Bartz

first: Michele

last: Cleary

first: Denise

middle: A

last: Galloway

first: Carla

last: Grandori


title: Regulation of efflux pump expression and drug resistance by the transcription factors Mrr1, Upc2, and Cap1 in Candida albicans

status: Public on Jul 01 2011

city: Memphis

first: Katherine

last: Barker

state: TN

address: 881 Madison Avenue, Room 305

department: Clinical Pharmacy

institute: University of Tennessee Health Science Center

summary: Constitutive overexpression of the Mdr1 efflux pump is an important mechanism of acquired drug resistance in the yeast Candida albicans. The zinc cluster transcription factor Mrr1 is a central regulator of MDR1 expression, but other transcription factors have also been implicated in MDR1 regulation. To better understand how MDR1-mediated drug resistance is achieved in this important fungal pathogen, we studied the interdependence of Mrr1 and two other MDR1 regulators, Upc2 and Cap1, in the control of MDR1 expression. A mutated, constitutively active Mrr1 could upregulate MDR1 and confer drug resistance in the absence of Upc2 or Cap1. On the other hand, Upc2 containing a gain-of-function mutation only slightly activated the MDR1 promoter, and this activation depended on the presence of a functional MRR1 gene. In contrast, a C-terminally truncated, activated form of Cap1 could upregulate MDR1 in a partially Mrr1-independent fashion. The induction of MDR1 expression by toxic chemicals occurred independently of Upc2, but required the presence of Mrr1 and also partially depended on Cap1. Transcriptional profiling and in vivo DNA binding studies showed that a constitutively active Mrr1 binds to and upregulates most of its direct target genes in the presence or absence of Cap1. Therefore, Mrr1 and Cap1 cooperate in the environmental induction of MDR1 expression in wild-type C. albicans, but gain-of-function mutations in either of the two transcription factors can independently mediate efflux pump overexpression and drug resistance.

overall_design: We endeavored to determine how the function of a gain-of-function allele of MRR1 (shown to confer high-level azole resistance) is affected when the CAP1 gene is disrupted.

first: Sabrina

last: Schubert

first: Sadri

last: Znaidi

last: Schneider

first: Franziska

last: Dierolf

first: Nico

last: Dunkel

first: Malika

last: Aid

first: Genevieve

last: Boucher

first: P

last: Rogers

first: Martine

last: Raymond

first: Joachim

last: Morschhauser


title: miRNA expression data from low nitrate culture in leaf and root of maize

status: Public on Sep 01 2011

city: Beijing

first: Chuanxiao

last: Xie

address: Zhong-guan-cun South St. No12

department: Institute of Crop Science

institute: Chinese Academy of Agricultural Sciences

summary:
Nitrate is the major source of nitrogen available for many crop plants and is often the limiting factor for plant growth and agricultural productivity especially for maize. Many studies have been done identifying the transcriptome changes under low nitrate conditions. However, the microRNAs (miRNAs) varied under nitrate limiting conditions in maize has not been reported. MiRNAs play important roles in abiotic stress responses and nutrient deprivation.
We used the microarray systems to detect miRNAs responding to the chronic nitrate limiting conditions in maize leaves and roots.

platform_organism:
Physcomitrium patens
Populus trichocarpa
Arabidopsis thaliana
Glycine max
Medicago truncatula
Oryza sativa
Saccharum officinarum
Sorghum bicolor
Zea mays

overall_design: MicroRNAs (miRNAs) are small, endogenous RNAs that are regulators of gene expression in plants and animals. And, miRNAs have been known for years to be important for phosphate, sulphate and copper deprivation responses in plants. In Arabidopsis, small RNA deep sequencing associated with nitrate response had been analyzed. However, information about the way by which miRNA are regulated by abiotic stresses in general and by low nitrate in particular is unavailable for maize. In this study, we used SmartArrayTM microarray system to detect miRNAs responding to chronic nitrate limiting conditions in roots and leaves in maize. Leaf and root under normal and low nitrate conditions were analyzed with three biological replicates. So there are 12 samples in this study.

first: Yongmei

last: Bi

first: Shihuang

last: Zhang

middle: J

last: Rothstein

first: Zhenhua

last: Xu

first: Sihui

last: Zhong

first: Xinhai

last: Li

first: Wenxue


title: A comprehensive assessment of array-based platforms and calling algorithms for detection of copy number variants (HumanOmni2.5-Quad)

status: Public on Jun 30 2011

city: Toronto

first: Stephen

last: Scherer

address: 686 Bay Street

department: Genetics and Genomic Biology

institute: The Hospital for Sick Children

summary: Systematic evaluation of eleven array platforms commonly used for CNV detection to address parameters of quality and CNV calling.

overall_design: 14 Samples

first: Dalila

last: Pinto

first: Jeffrey

last: MacDonald


title: The Genetic Basis of Rapidly Evolving Male Genital Morphology in Drosophila.

status: Public on Jul 21 2011

city: Los Angeles

first: Justin

last: Dalton

address: 1050 Child's Way, RRI

department: Biological Sciences

institute: University of Southern California

summary: We performed genome-wide expression assays comparing gene expression in the Drosophila melanogaster third larval instar genital imaginal disc between males and females. We used microarrays to compare the relative expression levels of five independent male versus female comparisons for each of two different D. melanogaster wild-type strains, Canton-S and Berlin.

overall_design: All microarrays were dual channel direct comparisons of late third larval instar male versus female genital imaginal discs from two Drosophila melanogaster wildtype strains, Canton S and Berlin. For each strain five independent biological samples were analyzed using a dye-swap design (i.e. male samples labeled with Cy5 in three replicates were labeled with Cy3 in the other two replicates in that experimental set).

first: John

last: Masly

middle: E

first: Sudeep

last: Srivastava

first: Liang

last: Chen

first: Michelle

last: Arbeitman


title: Competition and cooperativity determine transcription factor binding and regulation

status: Public on Jun 29 2011

first: Xu

last: Zhou

address: 300 Longwood Ave

department: Pediatrics

institute: Boston Children's Hospital

summary: Binding of transcription factors to DNA is a key regulatory step in the control of gene expression.  DNA sequences with high affinity for transcription factors occur more frequently in the genome than instances of genes bound or regulated by these factors. How specific gene regulation is achieved by transcription factors remains unclear.  We used genome-wide approaches to study how trans factors shape the binding and regulatory landscape of Pho4, a budding yeast transcription factor that activates gene expression in response to phosphate limitation.  In no phosphate (0mM phosphate) medium, Pho4 is transported into the nucleus and activates transcription of a set of genes (PHO) that are necessary for cell survival in phosphate limited environment. In high phosphate (10mM phosphate) medium, Pho4 is transported outside of the nucleus and the transcription program of PHO genes are turned off.  Here we examined the transcription profiling of S. cerevisiae (W303) in various strains treated in media with 10mM or 0mM inorganic phosphate, to study the the transcription activation by Pho4 its cooperative binding factor Pho2, and its competitive binding factor Cbf1.

overall_design:
(I) To infer how much Pho4 itself, Pho2 itself, and the interaction between Pho2 and Pho4 contribute to transcriptional activation in response to Pi starvation, we applied mutant cycle analysis to compare wild type, pho2Δ, pho4Δ and pho2Δ pho4Δ strains in both 10 mM and 0 mM Pi conditions. Mutant cycle analysis is a cyclic comparison among all various mutants. For example, by comparing pho2Δ and pho2Δ pho4Δ, we can directly infer the contribution from Pho4 alone to gene activation. And by comparing wild type and pho2Δ, we can infer the contribution from Pho2 alone together with that from the interaction between Pho2 and Pho4.

(II) Compare two strains or one strain in two treatments in multiple replicates with dye-swap method.
wt no vs high Pi, to identify genes that are induced in response to Pi starvation.
cbf1Δ vs wt in high Pi, to identify the influence of Cbf1 on gene expression in high Pi condition.
cbf1Δpho4Δ vs wt in high Pi, to identify the influence of Cbf1 on gene expression that is mediated through Pho4, in high Pi condition.
rtg3Δtye7Δ vs wt in high Pi, to identify the influence of Rtg3 and Tye7 on gene expression in high Pi condition.
pho80Δ vs pho80Δpho4Δ, to identify the genes that are activated Pho4 when Pho4 is fully nuclear localized.
pho80Δcbf1Δ vs pho80Δcbf1Δpho4Δ, to identify the influence of Cbf1 on gene expression that is mediated through Pho4, when Pho4 is fully nuclear localized.

first: Erin

middle: K

last: O'Shea


title: Chromosome copy number variation in Cryptococcus neoformans influences virulence and occurs in isolates from AIDS patients: CBS7779 black and white strains

status: Public on May 31 2011

city: Vancouver

first: Guanggan

last: Hu

email: hug@msl.ubc.ca, kronstad@msl.ubc.ca

state: BC

address: 2185 East Mall

department: Michael Smith Laboratories

institute: The University of British Columbia

type: Genome variation profiling by genome tiling array

summary:
The adaptation of fungal pathogens to the host environment via large-scale genomic changes is a poorly characterized phenomenon.  We recently discovered clinical strains of Cryptococcus neoformans, the leading cause of fungal meningoencephalitis in HIV/AIDS patients, which are disomic for chromosome 13.  In the current study, we examined the relationship between disomy, expression of the virulence factor melanin and virulence in a mouse model of cryptococcosis.  We found that melanin production was correlated with monosomy at chromosome 13, and that disomic variants were less melanized and attenuated for virulence in mice.  Changes in the copy number of other chromosomes were also detected in strains showing variation in melanin formation after growth in culture and after passage through mice.
A survey of environmental and clinical isolates maintained in culture revealed few occurrences of disomic chromosomes.  However, an examination of isolates that were freshly collected from the cerebral spinal fluid of AIDS patients and minimally cultured provided evidence for mixed infections and copy number variation.  Overall, these results suggest that the genome of C. neoformans exhibits a greater degree of plasticity than previously appreciated.  Importantly, genome variation is associated with virulence factor expression and disease severity, and its occurrence in isolates from AIDS patients suggests that it may have clinical relevance.

overall_design: Genome comparison of CBS7779 black and white strains vs standard strain H99

first: Jim

last: Kronstad

first: Jaehyuk

last: Choi


title: Chromosome copy number variation in Cryptococcus neoformans influences virulence and occurs in isolates from AIDS patients: clinal and environmental strains

status: Public on Jun 01 2011

overall_design: Genome comparison of clinal and environmental strains vs standard strain H99


title: Identification of testis-relevant genes using in silico analysis from testes ESTs and cDNA microarray in the black tiger shrimp (Penaeus monodon)

status: Public on May 27 2011

city: Pathumthani

first: nitsara

last: karoonuthaisiri

state: Pathumthani

address: Paholyothin

department: Central

country: Thailand

institute: BIOTEC

summary: Comparisons of gene expression profiles between testis and ovary of juvenile and wild brooders were made through a cDNA microarray in the black tiger shrimp (Penaeus monodon).   Differentially expressed genes were identified through the microarray analysis, and the microarray results were confirmed by real-time PCR.  Selected genes were further characterized.

overall_design: A cDNA microarray was constructed from the EST libraries of P. monodon, consisting of 5,568 features. RNA samples were extracted from both testes and ovaries of pooled juveniles (4 month-old, pooled from n=114 ), individual juvenile and broodstocks from West sides of Thailand. The RNA from ovaries were labeled with Cy3 dye as a reference and those of testes were labeled with Cy5 dye.

first: Thidathip

last: Wongsurawat

first: Rungnapa

last: Leelatanawit

first: Natechanok

last: Thamniemdee

first: Umaporn

last: Uawisetwathana

first: Nitsara

last: Karoonuthaisiri

first: Piamsak

last: Menasveta

first: Sirawut

last: Klinbunga


title: Assessment of genome integrity with array CGH of cattle transgenic cell lines produced by homologous recombination and somatic cell cloning

status: Public on May 23 2011

city: Beltsville

first: George

last: Liu

address: 10300 Baltimore Ave

institute: United States Department of Agriculture

summary: Background Transgenic cattle carrying multiple genomic modifications have been produced by sequential gene targeting and serial rounds of somatic cell chromatin transfer (cloning). However, cloning efficiency tends to decline with the increase of rounds of cloning. It is possible that multiple rounds of cloning compromise the genome integrity, rendering a decline in cloning. To test this possibility, we performed 9 high density array Comparative Genomic Hybridization (CGH) experiments to test the genome integrity in 3 independent bovine transgenic cell lineages generated from serial rounds of genetic modification and cloning. Our plan included the control hybridizations (self to self) of 3 founder cell lines and 6 comparative hybridizations between these founders and their derived cell lines that are drastically different in cloning efficiency. Results We detected similar amounts of differences between the control hybridizations (8, 13 and 39 differences) and the comparative analyses of both "high" and "low" cloning efficiency cell lines (ranging from 7 to 57 with a mean of ~20). Almost 75% of the large differences (>10 kb) and about 45% of all differences shared the same type (loss or gain) and were located in nearby genomic regions across hybridizations. Therefore, it is likely that they were not true differences but caused by systematic factors associated with local genomic features (e.g. GC contents). Conclusions Our findings reveal that large copy number genomic structural variations are less likely to arise during genetic targeting and serial rounds of cloning, fortifying the notion that epigenetic errors introduced from serial cloning may be responsible for the cloning efficiency decline.

overall_design: 9 custom 2.1M high density aCGH were performed to test the genome integrity in 3 independent bovine transgenic cell lineages generated from serial rounds of genetic modification and cloning, accommodating the control hybridizations (self to self) of the 3 founder cell lines and 6 comparative hybridizations between these founders and their derived cell lines that are drastically different in cloning efficiency.

first: Yali

last: Hou

first: James

middle: M

last: Robl

first: Yoshimi

last: Kuroiwa

first: Zhongde

last: Wang


title: Corn under weed, low nitrogen, and shade stress

status: Public on May 09 2011

city: Fargo

first: David

last: Horvath

state: ND

address: 1605 Albrecht Blvd

department: Agr. Research Service

institute: US Dept. Agriculture

summary:
This study was designed to identify changes in gene expression when corn was placed under various related stresses including being grown with a competing weed (canola) to the V4 or V8 stage, or when 40% shade cloth was present to the V4 or V8  stage, or under low nitrogen (no added nitrogen fertilizer), or under weed/shade free fertilized control conditions. In all 5 treatments and the control, samples were harvested at V8.
Mechanisms underlying early season weed stress on crop growth are not well described.  Corn vegetative growth and development, yield, and gene expression response to nitrogen (N), light (40% shade), and weed stresses were compared with the response of nonstressed plants.  Vegetative parameters, including leaf area and biomass, were measured from V2 toV12 corn stages. Transcriptome (2008) or quantitative Polymerase Chain Reaction (q PCR) (2008/09) analyses examined differential gene expression in stressed versus nonstressed corn at V8. Vegetative parameters were impacted minimally by N stress although grain yield was 40% lower. Shade, present until V2, reduced biomass and leaf area > 50% at V2 and, at V12, recovering plants remained smaller than nonstressed plants.  Grain yields of shade-stressed plants were similar to nonstressed controls, unless shade remained until V8. Growth and yield reductions due to weed stress in 2008 were observed when weeds remained until V6.  In 2009, weed stress at V2 reduced vegetative growth, and weed stress until V4 or later reduced yield. Principle component analysis of differentially expressed genes indicated that shade and weed stress had more similar gene expression patterns to each other than to nonstressed or low N stressed tissues. Weed-stressed corn had 630 differentially expressed genes compared with the nonstressed control. Of these genes, 259 differed and 82 were shared with shade-stressed plants. Corn grown in N-stressed conditions shared 252 differentially expressed genes with weed-stressed plants.  Ontologies associated with light/photosynthesis, energy conversion, and signaling were down-regulated in response to all three stresses. Although shade and weed stress clustered most tightly together, only three ontologies were shared by these stresses, O-methyltransferase activity (lignification processes), Poly U binding activity (post-transcriptional gene regulation), and stomatal movement. Based on both morphologic and genomic observations, results suggest that shade, N, and weed stresses to corn are regulated by both different and overlapping mechanisms.

overall_design: three biological replicates for each treatment and the control were collected and the resulting labeled cDNA was hybridized to the 46,000-element maize microarray chip developed by the University of Arizona using their protocol (International Microarray Workshop Handbook, 2009Gardiner et al. 2005). The hybridization scheme was a dual hybridization using a rolling circle balanced dye swap design. Thus we had thre biological replicates for each growth condition amd two technical replicates for each biological sample.

first: Janet

last: Moralis

first: Stephanie

last: Hansen

last: Clay

first: Sharon


title: Transcriptional response of Atlantic salmon (Salmo salar) after primary versus secondary exposure to Infectious Salmon Anemia Virus (ISAV)

city: Moncton

first: Francis

last: LeBlanc

state: NB

address: 343 University Ave.

department: Aquatic Animal Health

institute: Fisheries & Oceans Canada

summary: Following an infection with a specific pathogen, the acquired immune system of many teleostean fish, including salmonids, is known to retain a specific memory of the infectious agent, which protects the host against subsequent infections. For example Atlantic salmon (Salmo salar), which have survived an infection with a low-virulence infectious salmon anemia virus (ISAV) isolate are less susceptible against subsequent infections with high-virulence ISAV isolates. A greater understanding of the mechanisms and immunological components involved in this acquired protection against ISAV is fundamental for the development of efficacious vaccines and treatments against this pathogen. To better understand the immunity components involved in this observed resistance, we have used an Atlantic salmon DNA microarray and RT-qPCR assays to study the global gene expression responses of preexposed Atlantic salmon (fish having survived an infection with a low-virulence ISAV isolate) during the course of a secondary infection with a high-virulence ISAV isolate

overall_design: Atlantic salmon which had survived a primary infection with a low-virulence ISAV isolate (preexposed H5R fish) were reinfected by cohabitation (H5Rc fish) or IP injection (H5Rip fish) with a high-virulence ISAV isolate and compared to preexposed H5R fish non-reinfected and naïve Atlantic salmon infected by cohabitation (Nc fish) with the high-virulence ISAV isolate using 4x44k Agilent arrays. H5Rc fish (n~6) and Nc fish (n~6) were sampled at 20d, 23d, 29d, 41d and 63d following the infection, while H5Rip fish (n~6) were sampled at 6h, 24h, 3d, 10d, 20d and 63d. Microarrays were performed using a 1-color approach

first: Jean-René

last: Arseneau

first: Steven

last: Leadbeater

first: Brian

last: Glebe

first: Mark

last: Laflamme

first: Nellie

last: Gagné


title: microRNA expression in CagA-expressing cells

status: Public on Apr 21 2011

city: Suita

first: yoshito

last: hayashi

state: Osaka

address: 2-2 Yamadaoka

department: Department of Gastroenterology and Hepatology

institute: Osaka University Graduate School of Medicine

summary: Comprehensive analysis of microRNA expression were performed with 238 rat genes of microRNA between CagA-expressing and -non-expressing cells. CagA expression was controlled by tetracycline-off system in RGM1 cells.

overall_design: In the study presented here, RGM1 cells were used to acquire expression profiles of 238 microRNA genes.

first: Yoshito

last: Hayashi

first: Masahiko

last: Tsujii


title: Gene expression profiles of human immature dendritic cells after 3h, 6h and 12h of co-cultivation with Aspergillus fumigatus

status: Public on Mar 29 2011

city: Wuerzburg

first: Susanne

middle: Elma

last: Kneitz

address: Biozentrum, Am Hubland

department: Physiologigcal Chemistry

institute: University of Wuerzburg

summary: Gene expression profiles of human immature dendritic cells after 3h, 6h, 9h and 12h of co-cultivation with Aspergillus fumigatus were compared to expression profiles from human immature dendritic cells after 3h, 6h, 9h and 12h of cultivation.

overall_design: We used microarrays to detail the gene expression of human immature dendritic cells after 3h, 6h, 9h and 12h of co-cultivation with Aspergillus fumigatus

first: Juergen

last: Loeffler

first: Oliver

last: Morton

first: Markus

last: Mezger

first: Anke

last: Hornbach


title: The nucleoid-associated protein HU controls three regulons that coordinate virulence and general physiology in Salmonella enterica serovar Typhimurium

status: Public on Mar 22 2011

city: Norwich

first: Sacha

last: Lucchini

address: Colney Lane

department: Molecular Microbiology

institute: Institute of Food Research

summary: The regulon of genes controlled by the HU nucleoid-associated proteins was examined in Salmonella enterica serovar Typhimurium (S. Typhimurium). DNA microarrays were used to detect the effect on the bacterial transcriptome of knockout mutations in the hupA, the hupB and in both the hupA and hupB genes. Distinct but overlapping patterns of gene expression were detected in the transcriptome at each time point for each of the three mutants, pointing to the existence of not one but three regulons of genes controlled by the HU proteins. Mutations in the hup genes altered the expression of regulatory and structural genes in both the SPI1 and the SPI2 pathogenicity islands. The hupA hupB double mutant was found to be defective in invasion of CACO2 and CHO epithelial cell lines and in its ability to survive in J774A.1 macrophage-like cells. The double mutant also had defective swarming activity and had a competitive fitness disadvantage compared to the wild type. In contrast, inactivation of just the hupB gene resulted in increased fitness and correlated with the up-regulation of members of the RpoS regulon in exponential phase cultures. Elimination of both the hupA and hupB genes resulted in strong down-regulation of the genes coding for the integration host factor, IHF, at all three time points.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design: The effect of hupA and hupB single-deletions and hupA and hupB double-deletion on S. Typhimurium gene expression during growth in LB was analysed at 3 different time points (1, 4 and 6 hours post-inoculation). Between two and three biological replicates, as well as technical replicates, were performed for each mutant and time point. For this study, we used Salmonella genomic DNA as the comparator which also acted as the control for spot quality.

first: Michael

last: Mangan

first: Tadhg

middle: O

last: Cróinín

first: Stephen

last: Fitzgerald

first: Jay

middle: C

last: Hinton

first: Charles

last: Dorman


title: Signature of MicroRNAs with Impact on Angiogenesis in Non-Small Cell Lung Cancer

status: Public on Mar 08 2011

city: Tromsø

first: Chris

last: Fenton

address: Thor Knutsen vg 6

department: Microarray

country: Norway

institute: UITO

summary: Angiogenesis is regarded as a hallmark in cancer development, and anti-angiogenic treatment is presently used in non-small cell lung cancer (NSCLC) patients. MicroRNAs (miRs) are small non-coding, endogenous, single stranded RNAs that regulate gene expression. As miRs are relatively stabile and measurable in both tissue and serum, they are potential prognostic and predictive markers. In this study we aimed to identify significant altered miRs related to angiogenesis in NSCLC

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Human betaherpesvirus 5
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Human gammaherpesvirus 8
Merkel cell polyomavirus
Mus musculus cytomegalovirus 2
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: From a large cohort of 335 NSCLC patients, paraffin-embedded samples from 10 patients with a short disease specific survival (DSS), 10 with a long DSS and 10 normal controls were analyzed.

first: Christopher

first: Tom

last: Donnem